RNA degradation compromises the reliability of microRNA expression profiling

Background: MicroRNAs are small non-coding RNAs that post-transcriptionally regulate gene expression and their expression is frequently altered in human diseases, including cancer. To correlate clinically relevant parameters with microRNA expression, total RNA is frequently prepared from samples that were archived for various time periods in frozen tissue banks but, unfortunately, RNA integrity is not always preserved in these frozen tissues. Here, we investigate whether experimentally induced RNA degradation affects microRNA expression profiles. Results: Tissue samples were maintained on ice for defined time periods prior to total RNA extraction, which resulted in different degrees of RNA degradation. MicroRNA expression was then analyzed by microarray analysis (miCHIP) or microRNA-specific real-time quantitative PCR (miQPCR). Our results demonstrate that the loss of RNA integrity leads to in unpredictability of microRNA expression profiles for both, array-based and miQPCR assays. Conclusion: MicroRNA expression cannot be reliably profiled in degraded total RNA. For the profiling of microRNAs we recommend use of RNA samples with a RNA integrity number equal to or above seven

Polymorphism in cyclohexanol

The crystal structures and phase behaviour of phase II and the metastable phases III0 and III of cyclohexanol, C6H11OH, have been determined using high-resolution neutron powder, synchrotron X-ray powder and single-crystal X-ray diffraction techniques. Cyclohexanol-II is formed by a transition from the plastic phase I cubic structure at 265 K and crystallizes in a tetragonal structure, space group P�4421c (Z0 = 1), in which the molecules are arranged in a hydrogen-bonded tetrameric ring motif. The structures of phases III0 and III are monoclinic, space groups P21/c (Z0 = 3) and Pc (Z0 = 2), respectively, and are characterized by the formation of hydrogen-bonded molecular chains with a threefold-helical and wave-like nature, respectively. Phase III crystallizes at 195 K from a sample of phase I that is supercooled to ca 100 K. Alternatively, phase III may be grown via phase III0, the latter transforming from supercooled phase I at ca 200 K. Phase III0 is particularly unstable and is metastable with respect to both I and II. Its growth is realised only under very restricted conditions, thus making its characterization especially challenging. The cyclohexanol molecules adopt a chair conformation in all three phases with the hydroxyl groups in an equatorial orientation. No evidence was found indicating hydroxyl groups adopting an axial orientation, contrary to the majority of spectroscopic literature on solid-state cyclohexanol; however, the H atom of the equatorial OH groups is found to adopt both in-plane and out-of-plane orientations

Electric-field tuning of the valley splitting in silicon corner dots

We perform an excited state spectroscopy analysis of a silicon corner dot in a nanowire field-effect transistor to assess the electric field tunability of the valley splitting. First, we demonstrate a back-gate-controlled transition between a single quantum dot and a double quantum dot in parallel that allows tuning the device in to corner dot formation. We find a linear dependence of the valley splitting on back-gate voltage, from $880~\mu \text{eV}$ to $610~\mu \text{eV}$ with a slope of $-45\pm 3~\mu \text{eV/V}$ (or equivalently a slope of $-48\pm 3~\mu \text{eV/(MV/m)}$ with respect to the effective field). The experimental results are backed up by tight-binding simulations that include the effect of surface roughness, remote charges in the gate stack and discrete dopants in the channel. Our results demonstrate a way to electrically tune the valley splitting in silicon-on-insulator-based quantum dots, a requirement to achieve all-electrical manipulation of silicon spin qubits.Comment: 5 pages, 3 figures. In this version: Discussion of model expanded; Fig. 3 updated; Refs. added (15, 22, 32, 34, 35, 36, 37

Low-temperature tunable radio-frequency resonator for sensitive dispersive readout of nanoelectronic devices

We present a sensitive, tunable radio-frequency resonator designed to detect reactive changes in nanoelectronic devices down to dilution refrigerator temperatures. The resonator incorporates GaAs varicap diodes to allow electrical tuning of the resonant frequency and the coupling to the input line. We find a resonant frequency tuning range of 8.4 MHz at 55 mK that increases to 29 MHz at 1.5 K. To assess the impact on performance of different tuning conditions, we connect a quantum dot in a silicon nanowire field-effect transistor to the resonator, and measure changes in the device capacitance caused by cyclic electron tunneling. At 250 mK, we obtain an equivalent charge sensitivity of $43~\mu e / \sqrt{\text{Hz}}$ when the resonator and the line are impedance-matched and show that this sensitivity can be further improved to $31~\mu e / \sqrt{\text{Hz}}$ by re-tuning the resonator. We understand this improvement by using an equivalent circuit model and demonstrate that for maximum sensitivity to capacitance changes, in addition to impedance matching, a high-quality resonator with low parasitic capacitance is desired.Comment: Includes supplementary informatio

Large Anisotropic Thermal Expansion Anomaly near the Superconducting Transition Temperature in MgB2

An anisotropic lattice anomaly near the superconducting transition temperature, Tc, was observed in MgB2 by high-resolution neutron powder diffraction. The a-axis thermal expansion becomes negative near Tc, while the c-axis thermal expansion is unaffected. This is qualitatively consistent with a depletion of the boron-boron s-band as the superconducting gap opens, resulting in weaker bonding. However, the observed anomaly is much larger than predicted by the Ehrenfest relation, strongly suggesting that the phonon thermal expansion also changes sign, as commonly observed in hexagonal layered crystals. These two effects may be connected through subtle changes in the phonon spectrum at Tc.Comment: 11 pages, 4 figure

The genome of the jellyfish Aurelia and the evolution of animal complexity

We present the genome of the moon jellyfish Aurelia, a genome from a cnidarian with a medusa life stage. Our analyses suggest that gene gain and loss in Aurelia is comparable to what has been found in its morphologically simpler relatives—the anthozoan corals and sea anemones. RNA sequencing analysis does not support the hypothesis that taxonomically restricted (orphan) genes play an oversized role in the development of the medusa stage. Instead, genes broadly conserved across animals and eukaryotes play comparable roles throughout the life cycle. All life stages of Aurelia are significantly enriched in the expression of genes that are hypothesized to interact in protein networks found in bilaterian animals. Collectively, our results suggest that increased life cycle complexity in Aurelia does not correlate with an increased number of genes. This leads to two possible evolutionary scenarios: either medusozoans evolved their complex medusa life stage (with concomitant shifts into new ecological niches) primarily by re-working genetic pathways already present in the last common ancestor of cnidarians, or the earliest cnidarians had a medusa life stage, which was subsequently lost in the anthozoans. While we favour the earlier hypothesis, the latter is consistent with growing evidence that many of the earliest animals were more physically complex than previously hypothesized

Large dispersive interaction between a CMOS double quantum dot and microwave photons

We report a large coupling rate, $g_0/(2\pi)=183$ MHz, between the charge state of a double quantum dot in a CMOS split-gate silicon nanowire transistor and microwave photons in a lumped-element resonator formed by hybrid integration with a superconducting inductor. We enhance the coupling by exploiting the large interdot lever arm of an asymmetric split-gate device, $\alpha=0.72$, and by inductively coupling to the resonator to increase its impedance, $Z_\text{r}=560$ $\Omega$. In the dispersive regime, the large coupling strength at the DQD hybridisation point produces a frequency shift comparable to the resonator linewidth, the optimal setting for maximum state visibility. We exploit this regime to demonstrate rapid gate-based readout of the charge degree of freedom, with an SNR of 3.3 in 50 ns. In the resonant regime, the fast charge decoherence rate precludes reaching the strong coupling regime, but we show a clear route to spin-photon circuit quantum electrodynamics using hybrid CMOS systems.Comment: 9 pages, 7 figure

Extended Time, Elevated Expectations: the Unappreciated Downsides of Pausing the Tenure Clock

In 1971, Stanford became the first university to introduce tenure clock extensions in academia for new mothers. The American Association of University Professors (AAUP) began recommending such policies a few years later, and in 2001, modified their recommendation to include primary or coequal caregivers, following either the birth or adoption of a child (1). By 2004, 43% of 255 surveyed institutions had formal clock-stop policies..

Multi-module microwave assembly for fast read-out and charge noise characterization of silicon quantum dots

Fast measurements of quantum devices is important in areas such as quantum sensing, quantum computing and nanodevice quality analysis. Here, we develop a superconductor-semiconductor multi-module microwave assembly to demonstrate charge state readout at the state-of-the-art. The assembly consist of a superconducting readout resonator interfaced to a silicon-on-insulator (SOI) chiplet containing quantum dots (QDs) in a high-$\kappa$ nanowire transistor. The superconducting chiplet contains resonant and coupling elements as well as $LC$ filters that, when interfaced with the silicon chip, result in a resonant frequency $f=2.12$~GHz, a loaded quality factor $Q=680$, and a resonator impedance $Z=470$~$\Omega$. Combined with the large gate lever arms of SOI technology, we achieve a minimum integration time for single and double QD transitions of 2.77~ns and 13.5~ns, respectively. We utilize the assembly to measure charge noise over 9 decades of frequency up to 500~kHz and find a 1/$f$ dependence across the whole frequency spectrum as well as a charge noise level of 4~$\mu$eV/$\sqrt{\text{Hz}}$ at 1~Hz. The modular microwave circuitry presented here can be directly utilized in conjunction with other quantum device to improve the readout performance as well as enable large bandwidth noise spectroscopy, all without the complexity of superconductor-semiconductor monolithic fabrication.Comment: Main: 7 pages, 4 figures. Supplementary: 6 pages, 5 figure