Non-Central Potentials and Spherical Harmonics Using Supersymmetry and Shape Invariance

It is shown that the operator methods of supersymmetric quantum mechanics and the concept of shape invariance can profitably be used to derive properties of spherical harmonics in a simple way. The same operator techniques can also be applied to several problems with non-central vector and scalar potentials. As examples, we analyze the bound state spectra of an electron in a Coulomb plus an Aharonov-Bohm field and/or in the magnetic field of a Dirac monopole.Comment: Latex, 12 pages. To appear in American Journal of Physic

Confinement induced three-dimensional trajectories of microswimmers in rectangular channels

We study the trajectories of a model microorganism inside three-dimensional channels with square and rectangular cross-sections. Using (i) numerical simulations based on lattice-Boltzmann method, and (ii) analytical expressions using far-field hydrodynamic approximations and method of images we systematically investigate the role of the strength and finite-size of the squirmer, confinement dimensions, and initial conditions in determining the three dimensional trajectories of microswimmers. Our results indicate that the hydrodynamic interactions with the confining walls of the channel significantly affect the swimming speed and trajectory of the model microswimmer. Specifically, pullers always display sliding motion inside the channel: weak pullers slide through the channel centerline, while strong pullers slide through a path close to any of the walls. Pushers generally follow helical motion in a square channel. Unlike pullers and pushers, the trajectories of neutral swimmers are not easy to generalize, and are sensitive to the initial conditions. Despite this diversity in the trajectories, the far-field expressions capture the essential features of channel-confined swimmers. Finally, we propose a method based on the principle of superposition to understand the origin of the three-dimensional trajectories of channel confined swimmers. Such construction allows us to predict and justify the origin of apparently complex 3D trajectories generated by different types of swimmers in channels with square and rectangular cross sections

Semiclassical Approach to Quantum-mechanical Problems with Broken Supersymmetry

The semiclassical WKB approximation method is reexamined in the context of nonrelativistic quantum-mechanical bound-state problems with broken supersymmetry (SUSY). This gives rise to an alternative quantization condition (denoted by BSWKB) which is different from the standard WKB formula and also different from the previously studied supersymmetric (SWKB) formula for unbroken SUSY. It is shown that to leading order in ħ, the BSWKB condition yields exact energy eigenvalues for shape-invariant potentials with broken SUSY (harmonic oscillator, Pöschl-Teller I and II) which are known to be analytically solvable. Further, we show explicitly that the higher-order corrections to these energy eigenvalues, up to sixth order in ħ, vanish identically. We also consider a number of examples of potentials with broken supersymmetry that are not analytically solvable. In particular, for the broken SUSY superpotential W=Ax2d [A\u3e0, d=(integer)], we evaluate contributions up to the sixth order and show that these results are in excellent agreement with numerical solutions of the Schrödinger equation. While the numerical BSWKB results in lowest order are not always better than the corresponding WKB results, they are still a considerable improvement because they guarantee equality of the corresponding energy eigenvalues for the supersymmetric partner potentials V+ and V-. This is of special importance in those situations where these partner potentials are not related by parity

Electrohydrodynamics within electrical double layer in a pressure-driven flow in presence of finite temperature gradients

A wide spectrum of electrokinetic studies is modelled as isothermal ones to expedite analysis even when such conditions may be extremely difficult to realize in practice. As a clear and novel departure from this trend, we address the case of flow-induced electrohydrodynamics, commonly referred to as streaming potential, in a situation where finite temperature gradients do indeed exist. By way of analysing a model problem of flow through a narrow parallel plate channel, we show that the temperature gradients have a significant effect on the streaming potential, and, consequently, on the flow itself. We incorporate thermoelectric effects in our model by a full-fledged coupling among the electric potential, the ionic species distribution, the fluid velocity and the local fluid temperature fields without resorting to ad hoc simplifications. We expect this expository study to contribute towards more sophisticated future inquiries into practical micro-/nano-fluidic applications coupling thermal field focusing with electrokinetic effects.Comment: 13 pages, 5 figure

Breed and adaptive response modulate bovine peripheral blood cells’ transcriptome

Background: Adaptive response includes a variety of physiological modifications to face changes in external or internal conditions and adapt to a new situation. The acute phase proteins (APPs) are reactants synthesized against environmental stimuli like stress, infection, inflammation. Methods: To delineate the differences in molecular constituents of adaptive response to the environment we performed the whole-blood transcriptome analysis in Italian Holstein (IH) and Italian Simmental (IS) breeds. For this, 663 IH and IS cows from six commercial farms were clustered according to the blood level of APPs. Ten extreme individuals (five APP+ and APP- variants) from each farm were selected for the RNA-seq using the Illumina sequencing technology. Differentially expressed (DE) genes were analyzed using dynamic impact approach (DIA) and DAVID annotation clustering. Milk production data were statistically elaborated to assess the association of APP+ and APP- gene expression patterns with variations in milk parameters. Results: The overall de novo assembly of cDNA sequence data generated 13,665 genes expressed in bovine blood cells. Comparative genomic analysis revealed 1,152 DE genes in the comparison of all APP+ vs. all APP- variants; 531 and 217 DE genes specific for IH and IS comparison respectively. In all comparisons overexpressed genes were more represented than underexpressed ones. DAVID analysis revealed 369 DE genes across breeds, 173 and 73 DE genes in IH and IS comparison respectively. Among the most impacted pathways for both breeds were vitamin B6 metabolism, folate biosynthesis, nitrogen metabolism and linoleic acid metabolism. Conclusions: Both DIA and DAVID approaches produced a high number of significantly impacted genes and pathways with a narrow connection to adaptive response in cows with high level of blood APPs. A similar variation in gene expression and impacted pathways between APP+ and APP- variants was found between two studied breeds. Such similarity was also confirmed by annotation clustering of the DE genes. However, IH breed showed higher and more differentiated impacts compared to IS breed and such particular features in the IH adaptive response could be explained by its higher metabolic activity. Variations of milk production data were significantly associated with APP+ and APP- gene expression patterns

Comprehensive molecular characterization of gastric adenocarcinoma

Gastric cancer is a leading cause of cancer deaths, but analysis of its molecular and clinical characteristics has been complicated by histological and aetiological heterogeneity. Here we describe a comprehensive molecular evaluation of 295 primary gastric adenocarcinomas as part of The Cancer Genome Atlas (TCGA) project. We propose a molecular classification dividing gastric cancer into four subtypes: tumours positive for Epstein–Barr virus, which display recurrent PIK3CA mutations, extreme DNA hypermethylation, and amplification of JAK2, CD274 (also known as PD-L1) and PDCD1LG2 (also knownasPD-L2); microsatellite unstable tumours, which show elevated mutation rates, including mutations of genes encoding targetable oncogenic signalling proteins; genomically stable tumours, which are enriched for the diffuse histological variant and mutations of RHOA or fusions involving RHO-family GTPase-activating proteins; and tumours with chromosomal instability, which show marked aneuploidy and focal amplification of receptor tyrosine kinases. Identification of these subtypes provides a roadmap for patient stratification and trials of targeted therapies

Comprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma

SummaryWe describe a comprehensive genomic characterization of adrenocortical carcinoma (ACC). Using this dataset, we expand the catalogue of known ACC driver genes to include PRKAR1A, RPL22, TERF2, CCNE1, and NF1. Genome wide DNA copy-number analysis revealed frequent occurrence of massive DNA loss followed by whole-genome doubling (WGD), which was associated with aggressive clinical course, suggesting WGD is a hallmark of disease progression. Corroborating this hypothesis were increased TERT expression, decreased telomere length, and activation of cell-cycle programs. Integrated subtype analysis identified three ACC subtypes with distinct clinical outcome and molecular alterations which could be captured by a 68-CpG probe DNA-methylation signature, proposing a strategy for clinical stratification of patients based on molecular markers

The Somatic Genomic Landscape of Chromophobe Renal Cell Carcinoma

We describe the landscape of somatic genomic alterations of 66 chromophobe renal cell carcinomas (ChRCCs) based on multidimensional and comprehensive characterization, including mitochondrial DNA (mtDNA) and whole genome sequencing. The result is consistent that ChRCC originates from the distal nephron compared to other kidney cancers with more proximal origins. Combined mtDNA and gene expression analysis implicates changes in mitochondrial function as a component of the disease biology, while suggesting alternative roles for mtDNA mutations in cancers relying on oxidative phosphorylation. Genomic rearrangements lead to recurrent structural breakpoints within TERT promoter region, which correlates with highly elevated TERT expression and manifestation of kataegis, representing a mechanism of TERT up-regulation in cancer distinct from previously-observed amplifications and point mutations

Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin

Recent genomic analyses of pathologically-defined tumor types identify “within-a-tissue” disease subtypes. However, the extent to which genomic signatures are shared across tissues is still unclear. We performed an integrative analysis using five genome-wide platforms and one proteomic platform on 3,527 specimens from 12 cancer types, revealing a unified classification into 11 major subtypes. Five subtypes were nearly identical to their tissue-of-origin counterparts, but several distinct cancer types were found to converge into common subtypes. Lung squamous, head & neck, and a subset of bladder cancers coalesced into one subtype typified by TP53 alterations, TP63 amplifications, and high expression of immune and proliferation pathway genes. Of note, bladder cancers split into three pan-cancer subtypes. The multi-platform classification, while correlated with tissue-of-origin, provides independent information for predicting clinical outcomes. All datasets are available for data-mining from a unified resource to support further biological discoveries and insights into novel therapeutic strategies