BBMS + + – basic bioinformatics meta-searcher

In this paper we present a Basic Bioinformatics Meta-searcher (BBMS), a web-based service aiming to simplify and integrate biological data searching through selected biological databases. BBMS facilitates biological data searching enabling multiple sources transparently, increasing research productivity as it avoids time consuming learning and parameterization of different search engines. As a complementary service, BBMS provides insight and links to common online bioinformatics tools. Users’ feedback when evaluating BBMS in terms of usability, usefulness and efficiency was very positive

Microfluidic and Nanofluidic Cavities for Quantum Fluids Experiments

The union of quantum fluids research with nanoscience is rich with opportunities for new physics. The relevant length scales in quantum fluids, 3He in particular, are comparable to those possible using microfluidic and nanofluidic devices. In this article, we will briefly review how the physics of quantum fluids depends strongly on confinement on the microscale and nanoscale. Then we present devices fabricated specifically for quantum fluids research, with cavity sizes ranging from 30 nm to 11 microns deep, and the characterization of these devices for low temperature quantum fluids experiments.Comment: 12 pages, 3 figures, Accepted to Journal of Low Temperature Physic

Propagator of a Charged Particle with a Spin in Uniform Magnetic and Perpendicular Electric Fields

We construct an explicit solution of the Cauchy initial value problem for the time-dependent Schroedinger equation for a charged particle with a spin moving in a uniform magnetic field and a perpendicular electric field varying with time. The corresponding Green function (propagator) is given in terms of elementary functions and certain integrals of the fields with a characteristic function, which should be found as an analytic or numerical solution of the equation of motion for the classical oscillator with a time-dependent frequency. We discuss a particular solution of a related nonlinear Schroedinger equation and some special and limiting cases are outlined.Comment: 17 pages, no figure

Breast feeding in Australia: A comparative study of Aboriginal and non Aboriginal women

The superiority of breast feeding over bottle feeding is universally acknowledged, and its crucial contribution to infant health is accepted by health authorities. Australia in recognition of the importance of breast feeding to infant health, aims to increase the prevalence of breast feeding. Breast feeding provides benefits for all children, however the health advantage that is gained by breast feeding in comparison to artificial feeding is more apparent among disadvantaged groups. Aboriginal Australians are identified as one such disadvantaged group. This study compares the available literature regarding the prevalence of breast feeding in Aboriginal and non Aboriginal women. It is apparent that breast feeding prevalence differs, between population groups within Australia. Aboriginal children are less likely to have been breast fed than non Aboriginal children. The comparison, indicates that there are deficiencies in the research regarding breast feeding prevalence in both population groups. Many factors affect a woman's decision to breast feed, and the duration of her breast feeding. These factors include, socioeconomic status, age, marital status, educational attainment, occupation and smoking status. These factors are clearly associated with breast feeding in non Aboriginal women. For Aboriginal women, the factors influencing breast feeding are more complex. It is recommended therefore, that it is essential for future research to examine the attitudinal and socialdeterminants of infant feeding practices in Aboriginal women. This is necessary, if educational or interventional strategies are to be effective for this population

Metastability Driven by Soft Quantum Fluctuation Modes

The semiclassical Euclidean path integral method is applied to compute the low temperature quantum decay rate for a particle placed in the metastable minimum of a cubic potential in a {\it finite} time theory. The classical path, which makes a saddle for the action, is derived in terms of Jacobian elliptic functions whose periodicity establishes the one-to-one correspondence between energy of the classical motion and temperature (inverse imaginary time) of the system. The quantum fluctuation contribution has been computed through the theory of the functional determinants for periodic boundary conditions. The decay rate shows a peculiar temperature dependence mainly due to the softening of the low lying quantum fluctuation eigenvalues. The latter are determined by solving the Lam\`{e} equation which governs the fluctuation spectrum around the time dependent classical bounce.Comment: Journal of Low Temperature Physics (2008) Publisher: Springer Netherland

A deep learning system accurately classifies primary and metastatic cancers using passenger mutation patterns.

In cancer, the primary tumour's organ of origin and histopathology are the strongest determinants of its clinical behaviour, but in 3% of cases a patient presents with a metastatic tumour and no obvious primary. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, we train a deep learning classifier to predict cancer type based on patterns of somatic passenger mutations detected in whole genome sequencing (WGS) of 2606 tumours representing 24 common cancer types produced by the PCAWG Consortium. Our classifier achieves an accuracy of 91% on held-out tumor samples and 88% and 83% respectively on independent primary and metastatic samples, roughly double the accuracy of trained pathologists when presented with a metastatic tumour without knowledge of the primary. Surprisingly, adding information on driver mutations reduced accuracy. Our results have clinical applicability, underscore how patterns of somatic passenger mutations encode the state of the cell of origin, and can inform future strategies to detect the source of circulating tumour DNA

SPIN-DEPENDENT NUCLEAR STRUCTURE FUNCTIONS: GENERAL APPROACH WITH APPLICATION TO THE DEUTERON

We study deep-inelastic scattering from polarized nuclei within a covariant framework. A clear connection is established between relativistic and non-relativistic limits, which enables a rigorous derivation of convolution formulae for the spin-dependent nuclear structure functions g_1^A and g_2^A in terms of off-mass-shell extrapolations of polarized nucleon structure functions, g_1^N and g_2^N. Approximate expressions for g_{1,2}^A are obtained by expanding the off-shell g_{1,2}^N about their on-shell limits. As an application of the formalism we consider nuclear effects in the deuteron, knowledge of which is necessary to obtain accurate information on the spin-dependent structure functions of the neutron.Comment: 26 pages RevTeX, 9 figures available upon reques

scRNA-seq in medulloblastoma shows cellular heterogeneity and lineage expansion support resistance to SHH inhibitor therapy

Targeting oncogenic pathways holds promise for brain tumor treatment, but inhibition of Sonic Hedgehog (SHH) signaling has failed in SHH-driven medulloblastoma. Cellular diversity within tumors and reduced lineage commitment can undermine targeted therapy by increasing the probability of treatment-resistant populations. Using single-cell RNA-seq and lineage tracing, we analyzed cellular diversity in medulloblastomas in transgenic, medulloblastoma-prone mice, and responses to the SHH-pathway inhibitor vismodegib. In untreated tumors, we find expected stromal cells and tumor-derived cells showing either a spectrum of neural progenitor-differentiation states or glial and stem cell markers. Vismodegib reduces the proliferative population and increases differentiation. However, specific cell types in vismodegib-treated tumors remain proliferative, showing either persistent SHH-pathway activation or stem cell characteristics. Our data show that even in tumors with a single pathway-activating mutation, diverse mechanisms drive tumor growth. This diversity confers early resistance to targeted inhibitor therapy, demonstrating the need to target multiple pathways simultaneously