Landau functions for non-interacting bosons

We discuss the statistics of Bose-Einstein condensation (BEC) in a canonical ensemble of N non-interacting bosons in terms of a Landau function L_N^{BEC} (q) defined by the logarithm of the probability distribution of the order parameter q for BEC. We also discuss the corresponding Landau function for spontaneous symmetry breaking (SSB), which for finite N should be distinguished from L_N^{BEC}. Only for intinite N BEC and SSB can be described by the same Landau function which depends on the dimensionality and on the form of the external potential in a surprisingly complex manner. For bosons confined by a three-dimensional harmonic trap the Landau function exhibits the usual behavior expected for continuous phase transitions.Comment: 4 pages, 4 figures; final version to appear as a rapid communication in Physical Review A. Abstract modified and typos correcte

Native structure-based modeling and simulation of biomolecular systems per mouse click

Background Molecular dynamics (MD) simulations provide valuable insight into biomolecular systems at the atomic level. Notwithstanding the ever-increasing power of high performance computers current MD simulations face several challenges: the fastest atomic movements require time steps of a few femtoseconds which are small compared to biomolecular relevant timescales of milliseconds or even seconds for large conformational motions. At the same time, scalability to a large number of cores is limited mostly due to long-range interactions. An appealing alternative to atomic-level simulations is coarse-graining the resolution of the system or reducing the complexity of the Hamiltonian to improve sampling while decreasing computational costs. Native structure-based models, also called Gō-type models, are based on energy landscape theory and the principle of minimal frustration. They have been tremendously successful in explaining fundamental questions of, e.g., protein folding, RNA folding or protein function. At the same time, they are computationally sufficiently inexpensive to run complex simulations on smaller computing systems or even commodity hardware. Still, their setup and evaluation is quite complex even though sophisticated software packages support their realization. Results Here, we establish an efficient infrastructure for native structure-based models to support the community and enable high-throughput simulations on remote computing resources via GridBeans and UNICORE middleware. This infrastructure organizes the setup of such simulations resulting in increased comparability of simulation results. At the same time, complete workflows for advanced simulation protocols can be established and managed on remote resources by a graphical interface which increases reusability of protocols and additionally lowers the entry barrier into such simulations for, e.g., experimental scientists who want to compare their results against simulations. We demonstrate the power of this approach by illustrating it for protein folding simulations for a range of proteins. Conclusions We present software enhancing the entire workflow for native structure-based simulations including exception-handling and evaluations. Extending the capability and improving the accessibility of existing simulation packages the software goes beyond the state of the art in the domain of biomolecular simulations. Thus we expect that it will stimulate more individuals from the community to employ more confidently modeling in their research

Impact of the Affordable Care Act on Colorectal Cancer Screening, Incidence, and Survival in Kentucky

Background Kentucky ranks first in the US in cancer incidence and mortality. Compounded by high poverty levels and a high rate of medically uninsured, cancer rates are even worse in Appalachian Kentucky. Being one of the first states to adopt the Affordable Care Act (ACA) Medicaid expansion, insurance coverage markedly increased for Kentucky residents. The purpose of our study was to determine the impact of Medicaid expansion on colorectal cancer (CRC) screening, diagnosis, and survival in Kentucky. Study Design The Kentucky Cabinet for Health and Family Services and the Kentucky Cancer Registry were queried for individuals (≥20 years) undergoing CRC screening (per US Preventative Services Task-Force) or diagnosed with primary invasive CRC from January 1, 2011 to December 31, 2016. CRC screening rates, incidence, and survival were compared before (2011-2013) and after (2014-2016) ACA implementation. Results Colorectal cancer screening was performed in 930,176 individuals, and 11,441 new CRCs were diagnosed from 2011 to 2016. Screening for CRC increased substantially for Medicaid patients after ACA implementation (+230%, p \u3c 0.001), with a higher increase in screening among the Appalachian (+44%) compared with the non-Appalachian (+22%, p \u3c 0.01) population. The incidence of CRC increased after ACA implementation in individuals with Medicaid coverage (+6.7%, p \u3c 0.001). Additionally, the proportion of early stage CRC (stage I/II) increased by 9.3% for Appalachians (p = 0.09), while there was little change for non-Appalachians (−1.5%, p = 0.60). Colorectal cancer survival was improved after ACA implementation (hazard ratio 0.73, p \u3c 0.01), particularly in the Appalachian population with Medicaid coverage. Conclusions Implementation of Medicaid expansion led to a significant increase in CRC screening, CRC diagnoses, and overall survival in CRC patients with Medicaid, with an even more profound impact in the Appalachian population

Non-perturbative renormalization-group approach to zero-temperature Bose systems

We use a non-perturbative renormalization-group technique to study interacting bosons at zero temperature. Our approach reveals the instability of the Bogoliubov fixed point when $d\leq 3$ and yields the exact infrared behavior in all dimensions $d>1$ within a rather simple theoretical framework. It also enables to compute the low-energy properties in terms of the parameters of a microscopic model. In one-dimension and for not too strong interactions, it yields a good picture of the Luttinger-liquid behavior of the superfluid phase.Comment: v1) 6 pages, 8 figures; v2) added references; v3) corrected typo

Pcdh18a regulates endocytosis of E-cadherin during axial mesoderm development in zebrafish

The notochord defines the axial structure of all vertebrates during development. Notogenesis is a result of major cell reorganization in the mesoderm, the convergence and the extension of the axial cells. However, it is currently not fully understood how these processes act together in a coordinated way during notochord formation. The prechordal plate is an actively migrating cell population in the central mesoderm anterior to the trailing notochordal plate cells. We show that prechordal plate cells express Protocadherin 18a (Pcdh18a), a member of the cadherin superfamily. We find that Pcdh18a-mediated recycling of E-cadherin adhesion complexes transforms prechordal plate cells into a cohesive and fast migrating cell group. In turn, the prechordal plate cells subsequently instruct the trailing mesoderm. We simulated cell migration during early mesoderm formation using a lattice-based mathematical framework and predicted that the requirement for an anterior, local motile cell cluster could guide the intercalation and extension of the posterior, axial cells. Indeed, a grafting experiment validated the prediction and local Pcdh18a expression induced an ectopic prechordal plate-like cell group migrating towards the animal pole. Our findings indicate that the Pcdh18a is important for prechordal plate formation, which influences the trailing mesodermal cell sheet by orchestrating the morphogenesis of the notochord

Diagnostic pitfalls in fine needle aspiration of solitary pulmonary nodules: two cases with radio-cyto-histological correlation

BACKGROUND: Fine needle aspiration is an important tool for diagnosis and preoperative evaluation of solitary nodules of the lung. It provides a definitive diagnosis in most patients at low cost with minimal trauma. However, because of the nature of the study and the presentation of the cells in a more distorted and incomplete tissue structure than a histological slide, false positive results can occur. Prior detailed clinical knowledge about the patient, procedures and methods of radiology in obtaining the aspirate specimen is extremely useful in the accurate interpretation of fine needle cytological specimens. CASE PRESENTATION: We report two cases of solitary pulmonary nodules in two elderly females, which were initially diagnosed as malignant by fine needle aspiration biopsy. Both cases subsequently underwent pulmonary lobectomy in which, one turned out to be a pulmonary hamartoma and the other appeared to be a middle lobe syndrome of the right lung with liver tissue contamination at the time of fine needle aspiration of the lung. CONCLUSIONS: We are now strong believers that much care must be taken in the interpretation of fine needle aspiration of solitary nodules of the lung. Complete study of the entire specimen, including the cell block, is warranted, since what one interprets as malignant, could have different features in another part of the sample. Last but not the least, prior knowledge of the complete clinical history of the patient together with the salient radiological findings would greatly facilitate the cytopathologist to reach an accurate diagnosis

Imaging-guided chest biopsies: techniques and clinical results

Background This article aims to comprehensively describe indications, contraindications, technical aspects, diagnostic accuracy and complications of percutaneous lung biopsy. Methods Imaging-guided biopsy currently represents one of the predominant methods for obtaining tissue specimens in patients with lung nodules; in many cases treatment protocols are based on histological information; thus, biopsy is frequently performed, when technically feasible, or in case other techniques (such as bronchoscopy with lavage) are inconclusive. Results Although a coaxial system is suitable in any case, two categories of needles can be used: fine-needle aspiration biopsy (FNAB) and core-needle biopsy (CNB), with the latter demonstrated to have a slightly higher overall sensitivity, specificity and accuracy. Conclusion Percutaneous lung biopsy is a safe procedure even though a few complications are possible: pneumothorax, pulmonary haemorrhage and haemoptysis are common complications, while air embolism and seeding are rare, but potentially fatal complications

Damping of phase fluctuations in superfluid Bose gases

Using Popov's hydrodynamic approach we derive an effective Euclidean action for the long-wavelength phase fluctuations of superfluid Bose gases in D dimensions. We then use this action to calculate the damping of phase fluctuations at zero temperature as a function of D. For D >1 and wavevectors | k | << 2 mc (where m is the mass of the bosons and c is the sound velocity) we find that the damping in units of the phonon energy E_k = c | k | is to leading order gamma_k / E_k = A_D (k_0^D / 2 pi rho) (| k | / k_0)^{2 D -2}, where rho is the boson density and k_0 =2 mc is the inverse healing length. For D -> 1 the numerical coefficient A_D vanishes and the damping is proportional to an additional power of |k | /k_0; a self-consistent calculation yields in this case gamma_k / E_k = 1.32 (k_0 / 2 pi rho)^{1/2} |k | / k_0. In one dimension, we also calculate the entire spectral function of phase fluctuations.Comment: 6 pages, 4 figures, published versio

Infrared behavior of interacting bosons at zero temperature

We review the infrared behavior of interacting bosons at zero temperature. After a brief discussion of the Bogoliubov approximation and the breakdown of perturbation theory due to infrared divergences, we present two approaches that are free of infrared divergences -- Popov's hydrodynamic theory and the non-perturbative renormalization group -- and allow us to obtain the exact infrared behavior of the correlation functions. We also point out the connection between the infrared behavior in the superfluid phase and the critical behavior at the superfluid--Mott-insulator transition in the Bose-Hubbard model.Comment: 8 pages, 4 figures. Proceedings of the 19th International Laser Physics Workshop, LPHYS'10 (Foz do Iguacu, Brazil, July 5-9, 2010

Modeling of Wnt-mediated tissue patterning in vertebrate embryogenesis

This is the final version. Available on open access from Public Library of Science via the DOI in this recordData Availability: All relevant data are within the manuscript and its Supporting Information files.During embryogenesis, morphogens form a concentration gradient in responsive tissue, which is then translated into a spatial cellular pattern. The mechanisms by which morphogens spread through a tissue to establish such a morphogenetic field remain elusive. Here, we investigate by mutually complementary simulations and in vivo experiments how Wnt morphogen transport by cytonemes differs from typically assumed diffusion-based transport for patterning of highly dynamic tissue such as the neural plate in zebrafish. Stochasticity strongly influences fate acquisition at the single cell level and results in fluctuating boundaries between pattern regions. Stable patterning can be achieved by sorting through concentration dependent cell migration and apoptosis, independent of the morphogen transport mechanism. We show that Wnt transport by cytonemes achieves distinct Wnt thresholds for the brain primordia earlier compared with diffusion-based transport. We conclude that a cytoneme-mediated morphogen transport together with directed cell sorting is a potentially favored mechanism to establish morphogen gradients in rapidly expanding developmental systems.Biotechnology & Biological Sciences Research Council (BBSRC)Wellcome TrustChinese Scholarship Council (CSC)Medical Research Council (MRC