Bridging scales in cancer progression: Mapping genotype to phenotype using neural networks

In this review we summarize our recent efforts in trying to understand the role of heterogeneity in cancer progression by using neural networks to characterise different aspects of the mapping from a cancer cells genotype and environment to its phenotype. Our central premise is that cancer is an evolving system subject to mutation and selection, and the primary conduit for these processes to occur is the cancer cell whose behaviour is regulated on multiple biological scales. The selection pressure is mainly driven by the microenvironment that the tumour is growing in and this acts directly upon the cell phenotype. In turn, the phenotype is driven by the intracellular pathways that are regulated by the genotype. Integrating all of these processes is a massive undertaking and requires bridging many biological scales (i.e. genotype, pathway, phenotype and environment) that we will only scratch the surface of in this review. We will focus on models that use neural networks as a means of connecting these different biological scales, since they allow us to easily create heterogeneity for selection to act upon and importantly this heterogeneity can be implemented at different biological scales. More specifically, we consider three different neural networks that bridge different aspects of these scales and the dialogue with the micro-environment, (i) the impact of the micro-environment on evolutionary dynamics, (ii) the mapping from genotype to phenotype under drug-induced perturbations and (iii) pathway activity in both normal and cancer cells under different micro-environmental conditions

The Study of a Laboratory Screw Press Washer as a Means of Deinking Offset Newsprint at High Consistencies

The objective of this thesis is to study a laboratory horizontal screw press washer as an effective, yet economical, means of deinking offset newsprint wastes at high consistencies. The theoretical advantages of utilizing a high consistency deinking process include minimal water consumption, reduced and more concentrated filtrate volumes, low effluent solids and fiber loss, and minimal space requirements. The disadvantages include a relatively high unit power consumption, high capital cost, sometimes an inefficient amount of fillers and fines removed, and ink particles may get trapped at consistencies greater than 18%. Results proved many of these theoretical advantages and disadvantages. Also, the screw press did prove to be an effective piece of equipment for removing offset ink at high consistencies. However, further work concerning the screw press is recommended as results were not able to be duplicated due to limiting time factors and mechanical failures of the equipment

Superconductivity from purely repulsive interactions in the strong coupling approach : Application of the SU(2) slave-rotor theory to the Hubbard model

We propose a mechanism of superconductivity from purely repulsive interactions in the strong coupling regime, where the BCS (Bardeen-Cooper-Schrieffer) mechanism such as the spin-fluctuation approach is difficult to apply. Based on the SU(2) slave-rotor representation of the Hubbard model, we find that the single energy scale for the amplitude formation of Cooper pairs and their phase coherence is separated into two energy scales, allowing the so called pseudogap state where such Cooper pairs are coherent locally but not globally, interpreted as realization of the density-phase uncertainty principle. This superconducting state shows the temperature-linear decreasing ratio of superfluid weight, resulting from strong phase fluctuations

Removal of Confined Ionic Liquid from a Metal Organic Framework by Extraction with Molecular Solvents

This work was supported in part by NSF Grant No. CHE-1223988 and by EPSRC Grant No. EP/K00090X/1.Peer reviewedPostprin

Role of spatial coherence in polarization tomography

We analyze an experimental setup in which a quasi-monochromatic spatially coherent beam of light is used to probe a paraxial optical scatterer. We discuss the effect of the spatial coherence of the probe beam on the Mueller matrix representing the scatterer. We show that according to the degree of spatial coherence of the beam, the \emph{same} scattering system can be represented by \emph{different} Mueller matrices. This result should serve as a warning for experimentalists.Comment: 3 pages, 1 figur

Consular Discretion in the Immigrant Visa-Issuing Process

This study examines the exercise of discretion by consular officers in deciding whether to issue or refuse immigrant visas in an effort to determine if these decisions are arbitrary or unlawful. The study begins by examining the procedures and factors mandated by the Immigration and Nationality Act for use in determining eligibility to immigrate. The study then discusses and compares the typical procedures and eligibility factors utilized by consular offices in the field. Next the study does an evaluation of extra-statutory factors affecting the consular officer\u27s determination including personal background, the effect of intermediaries, lack of time, the promotion system, and attitudes towards applicants and the immigration policy. The study concludes by making recommendations for limiting the discretion of consular officers in deciding whether to issue or refuse immigrant visas

Effects of morphology on phonons of nanoscopic silver grains

The morphology of nanoscopic Ag grains significantly affects the phonons. Atomistic simulations show that realistic nanograin models display complex vibrational properties. (1) Single-crystalline grains. Nearly-pure torsional and radial phonons appear at low frequencies. For low-energy, faceted models, the breathing mode and acoustic gap (lowest frequency) are about 10% lower than predicted by elasticity theory (ET) for a continuum sphere of the same volume. The sharp edges and the atomic lattice split the ET-acoustic-gap quintet into a doublet and triplet. The surface protrusions associated with nearly spherical, high-energy models produce a smaller acoustic gap and a higher vibrational density of states (DOS) at frequencies \nu<2 THz. (2) Twined icosahedra. In contrast to the single-crystal case, the inherent strain produce a larger acoustic gap, while the core atoms yield a DOS tail extending beyond the highest frequency of single-crystalline grains. (3) Mark's decahedra, in contrast to (1) and (2), do not have a breathing mode; although twined and strained, do not exhibit a high-frequency tail in the DOS. (4) Irregular nanograins. Grain boundaries and surface disorder yield non-degenerate phonon frequencies, and significantly smaller acoustic gap. Only these nanograins exhibit a low-frequency \nu^2 DOS in the interval 1-2 THz.Comment: Version published in Phys. Rev.

A Fractional Fokker-Planck Model for Anomalous Diffusion

In this paper we present a study of anomalous diffusion using a Fokker-Planck description with fractional velocity derivatives. The distribution functions are found using numerical means for varying degree of fractionality observing the transition from a Gaussian distribution to a L\'evy distribution. The statistical properties of the distribution functions are assessed by a generalized expectation measure and entropy in terms of Tsallis statistical mechanics. We find that the ratio of the generalized entropy and expectation is increasing with decreasing fractionality towards the well known so-called sub-diffusive domain, indicating a self-organising behavior.Comment: 22 pages, 14 figure

Multi--hump soliton--like structures in interactions of lasers and Bose--Einstein condensates

An investigation is made of multi-hump and periodic solutions of the semi-classical coupled equations describing laser radiation copropagating with a Bose-Einstein condensate. Solutions reminiscent of optical vector solitons have been found and have been used to gain understanding of the dynamics observed in the numerical simulations, in particular to shed light on the phenomenon of jet emission from a condensate interacting with a laser.Comment: 6 pages, 4 figures; submitted to European Physics Letter