Revisiting the displacement operator for quantum systems with position-dependent mass

Recently R. N. Costa Filho et al. (PRA 84, 050102(R) (2011)) have introduced a position dependent infinitesimal translation operator which corresponds to a position dependent linear momentum and consequently to a position dependent effective mass quantum particle. Although there is no doubt in novelty of the idea and the formalism, we believe that some aspects of the quantum mechanics could be complemented in their original work. Here in this letter first we address those points and then an alternative will be introduced. Finally we apply the formalism for a quantum particle under a null potential confined in a square well and the results will be compared with those in the paper mentioned above.Comment: 4 pages, 3 figures. Final version to appear in Phys. Rev.

Bacterial chromosome organization II: few special cross-links, cell confinement, and molecular crowders play the pivotal roles

Using a bead-spring model of bacterial DNA polymers of {\em C. crescentus} and {\em E. coli} we show that just $33$ and $38$ effective cross-links at special positions along the chain contour of the DNA can lead to the large-scale organization of the DNA polymer, where confinement effects of the cell walls play a key role in the organization. The positions of the $33$ cross-links along the chain contour are chosen from the contact map data of {\em C. crescentus}. We represent $1000$ base pairs as a coarse-grained monomer in our bead-spring flexible ring polymer model of the DNA. Thus a $4017$ beads on a flexible ring polymer represents the {\em C. crescentus} DNA with $4017$ kilo-base pairs. Choosing suitable parameters from our preceding study, we also incorporate the role of molecular crowders and the ability of the chain to release topological constraints. We validate our prediction of the organization of the {\em C. crescentus} with available experimental contact map data and also give a prediction of the approximate positions of different segments within the cell in 3D. For the {\em E. coli} chromosome with $4.6$ million base pairs, we need around $38$ effective cross-links with cylindrical confinement to organize the chromosome. We also predict the 3D organization of the {\em E. coli} chromosome segments within the cylinder which represents the cell wall.Comment: 13 pages, 11 figure

Origin of spatial organization of DNA-polymer in bacterial chromosomes

In-vivo DNA organization at large length scales ($\sim 100nm$) is highly debated and polymer models have proved useful to understand the principle of DNA-organization. Here, we show that $<2$% cross-links at specific points in a ring polymer can lead to a distinct spatial organization of the polymer. The specific pairs of cross-linked monomers were extracted from contact maps of bacterial DNA. We are able to predict the structure of 2 DNAs using Monte Carlo simulations of the bead-spring polymer with cross-links at these special positions. Simulations with cross-links at random positions along the chain show that the organization of the polymer is different in nature from the previous case.Comment: arXiv admin note: text overlap with arXiv:1701.0506

Gene Expression Profile Changes After Short-activating RNA-mediated Induction of Endogenous Pluripotency Factors in Human Mesenchymal Stem Cells

It is now recognized that small noncoding RNA sequences have the ability to mediate transcriptional activation of specific target genes in human cells. Using bioinformatics analysis and functional screening, we screened short-activating RNA (saRNA) oligonucleotides designed to target the promoter regions of the pluripotency reprogramming factors, Kruppel-like factor 4 (KLF4) and c-MYC. We identified KLF4 and c-MYC promoter-targeted saRNA sequences that consistently induced increases in their respective levels of nascent mRNA and protein expression in a time- and dose-dependent manner, as compared with scrambled sequence control oligonucleotides. The functional consequences of saRNA-induced activation of each targeted reprogramming factor were then characterized by comprehensively profiling changes in gene expression by microarray analysis, which revealed significant increases in mRNA levels of their respective downstream pathway genes. Notably, the microarray profile after saRNA-mediated induction of endogenous KLF4 and c-MYC showed similar gene expression patterns for stem cell- and cell cycle-related genes as compared with lentiviral vector-mediated overexpression of exogenous KLF4 and c-MYC transgenes, while divergent gene expression patterns common to viral vector-mediated transgene delivery were also noted. The use of promoter-targeted saRNAs for the activation of pluripotency reprogramming factors could have broad implications for stem cell research

Higher dimensional thin-shell wormholes in Einstein-Yang-Mills-Gauss-Bonnet gravity

We present thin-shell wormhole solutions in Einstein-Yang-Mills-Gauss-Bonnet (EYMGB) theory in higher dimensions d\geq5. Exact black hole solutions are employed for this purpose where the radius of thin-shell lies outside the event horizon. For some reasons the cases d=5 and d>5 are treated separately. The surface energy-momentum of the thin-shell creates surface pressures to resist against collapse and rendering stable wormholes possible. We test the stability of the wormholes against spherical perturbations through a linear energy-pressure relation and plot stability regions. Apart from this restricted stability we investigate the possibility of normal (i.e. non-exotic) matter which satisfies the energy conditions. For negative values of the Gauss-Bonnet (GB) parameter we obtain such physical wormholes.Comment: 9 pages, 6 figures. Dedicated to the memory of Rev. Ibrahim Eken (1927-2010) of Turke

Equality and Value-holism

In this paper, I consider a recent challenge to egalitarianism raised by Michael Huemer. Huemer?s challenge takes the form of a dilemma: egalitarians can either be atomists or holists about equality?s value. If they are atomists, then they must accept that equality in fact does not have intrinsic value; if they are holists, then their view will be inconsistent with an intuitively very plausible form of consequentialism. I show that this dilemma should not trouble egalitarians. Egalitarians can be holists about value and still embrace consequentialism

Technical Development of a New Semispherical Radiofrequency Bipolar Device (RONJA): Ex Vivo and In Vivo Studies

The aim of this study is to inform about the development of a new semispherical surgical instrument for the bipolar multielectrode radiofrequency liver ablation. Present tools are universal; however they have several disadvantages such as ablation of healthy tissue, numerous needle punctures, and, therefore, longer operating procedure. Our newly designed and tested semispherical surgical tool can solve some of these disadvantages. By conducting an in vivo study on a set of 12 pigs, randomly divided into two groups, we have compared efficiency of the newly developed instrument with the commonly used device. Statistical analysis showed that there were no significant differences between the groups. On average, the tested instrument RONJA had shorter ablation time in both liver lobes and reduced the total operating time. The depth of the thermal alteration was on average 4 mm larger using the newly tested instrument. The new radiofrequency method described in this study could be used in open liver surgery for the treatment of small liver malignancies (up to 2 cm) in a single application with the aim of saving healthy liver parenchyma. Further experimental studies are needed to confirm these results before clinical application of the method in the treatment of human liver malignancies