Modeling association between DNA copy number and gene expression with constrained piecewise linear regression splines

DNA copy number and mRNA expression are widely used data types in cancer studies, which combined provide more insight than separately. Whereas in existing literature the form of the relationship between these two types of markers is fixed a priori, in this paper we model their association. We employ piecewise linear regression splines (PLRS), which combine good interpretation with sufficient flexibility to identify any plausible type of relationship. The specification of the model leads to estimation and model selection in a constrained, nonstandard setting. We provide methodology for testing the effect of DNA on mRNA and choosing the appropriate model. Furthermore, we present a novel approach to obtain reliable confidence bands for constrained PLRS, which incorporates model uncertainty. The procedures are applied to colorectal and breast cancer data. Common assumptions are found to be potentially misleading for biologically relevant genes. More flexible models may bring more insight in the interaction between the two markers.Comment: Published in at http://dx.doi.org/10.1214/12-AOAS605 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Charge transport in nanoscale vertical organic semiconductor pillar devices

We report charge transport measurements in nanoscale vertical pillar structures incorporating ultrathin layers of the organic semiconductor poly(3-hexylthiophene)(P3HT). P3HT layers with thickness down to 5 nm are gently top-contacted using wedging transfer, yielding highly reproducible, robust nanoscale junctions carrying high current densities (up to $10^6$ A/m$^2$). Current-voltage data modeling demonstrates excellent hole injection. This work opens up the pathway towards nanoscale, ultrashort-channel organic transistors for high-frequency and high-current-density operation.Comment: 30 pages, 8 figures, 1 tabl

The Kondo Effect in the Unitary Limit

We observe a strong Kondo effect in a semiconductor quantum dot when a small magnetic field is applied. The Coulomb blockade for electron tunneling is overcome completely by the Kondo effect and the conductance reaches the unitary-limit value. We compare the experimental Kondo temperature with the theoretical predictions for the spin-1/2 Anderson impurity model. Excellent agreement is found throughout the Kondo regime. Phase coherence is preserved when a Kondo quantum dot is included in one of the arms of an Aharonov-Bohm ring structure and the phase behavior differs from previous results on a non-Kondo dot.Comment: 10 page

Gate-tunable band structure of the LaAlO3_3-SrTiO3_3 interface

The 2-dimensional electron system at the interface between LaAlO$_{3}$ and SrTiO$_{3}$ has several unique properties that can be tuned by an externally applied gate voltage. In this work, we show that this gate-tunability extends to the effective band structure of the system. We combine a magnetotransport study on top-gated Hall bars with self-consistent Schr\"odinger-Poisson calculations and observe a Lifshitz transition at a density of $2.9\times10^{13}$ cm$^{-2}$. Above the transition, the carrier density of one of the conducting bands decreases with increasing gate voltage. This surprising decrease is accurately reproduced in the calculations if electronic correlations are included. These results provide a clear, intuitive picture of the physics governing the electronic structure at complex oxide interfaces.Comment: 14 pages, 4 figure

Electronic transport through a parallel--coupled triple quantum dot molecule: Fano resonances and bound states in the continuum

The electronic transport through a triple quantum dot molecule attached in parallel to leads in presence of a magnetic flux is studied. Analytical expressions of the linear conductance and density of states for the molecule in equilibrium at zero temperature are obtained. As a consequence of quantum interference, the conductance exhibits in general a Breit--Wigner and two Fano resonances, the positions and widths of which are controlled by the magnetic field. Every two flux quanta, there is an inversion of roles of the bonding and antibonding states. For particular values of the magnetic flux and dot-lead couplings, one or even both Fano resonances collapse and bound states in the continuum (BIC's) are formed. The line broadenings of the molecular states are examined as a function of the Aharonov--Bohm phase around the condition for the formation of BIC's, finding resonances extremely narrow and robust against variations of the magnetic field.Comment: 15 pages, 7 figure

From Living Apart to Living Together:Do Children Born before the Current Partnership Matter?

This study examines the association between having children born before the current partnership and women’s and men’s likelihood of transitioning from living apart together (LAT) to co-residing. LAT partnerships are common among individuals with pre-partnership children, but have so far been under-researched. Our study not only focuses on those in LAT relations, but also takes the different pathways to becoming a single parent into account. Event-history analysis was performed using waves 1-4 from the Netherlands Kinship Panel Study. The results indicate that separated and widowed mothers were less likely to transition to co-residence with their LAT partner than childless women who had previously been in a co-residential union. Mothers who had previous out-of-union children were found to be even less likely to enter co-residence. Results were mostly similar for men and women. The only exception was the effect of being widowed with children; for men this resulted in higher chances of transitioning to co-residence with a new partner whereas for women the chances were lower. The findings suggest that individuals’ parenthood and union histories are associated with the development of their later partnerships, and that these patterns vary by gender. Given contemporary and future patterns of partnership separation, our study provides insights for better understanding how LAT relations develop for different sub-populations

Covalent coupling of nanoparticles with low-density functional ligands to surfaces via click chemistry

We demonstrate the application of the 1,3-dipolar cycloaddition (“click” reaction) to couple gold nanoparticles (Au NPs) functionalized with low densities of functional ligands. The ligand coverage on the citrate-stabilized Au NPs was adjusted by the ligand:Au surface atom ratio, while maintaining the colloidal stability of the Au NPs in aqueous solution. A procedure was developed to determine the driving forces governing the selectivity and reactivity of citrate-stabilized and ligand-functionalized Au NPs on patterned self-assembled monolayers. We observed selective and remarkably stable chemical bonding of the Au NPs to the complimentarily functionalized substrate areas, even when estimating that only 1–2 chemical bonds are formed between the particles and the substrate