BgeeDB, an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests.

BgeeDB is a collection of functions to import into R re-annotated, quality-controlled and re-processed expression data available in the Bgee database. This includes data from thousands of wild-type healthy samples of multiple animal species, generated with different gene expression technologies (RNA-seq, Affymetrix microarrays, expressed sequence tags, and in situ hybridizations). BgeeDB facilitates downstream analyses, such as gene expression analyses with other Bioconductor packages. Moreover, BgeeDB includes a new gene set enrichment test for preferred localization of expression of genes in anatomical structures ("TopAnat"). Along with the classical Gene Ontology enrichment test, this test provides a complementary way to interpret gene lists. Availability: https://www.bioconductor.org/packages/BgeeDB/

The Extinction and Distance of Maffei 1

We have obtained low- and high-resolution spectra of the core of the highly-reddened elliptical galaxy Maffei 1. From these data, we have obtained the first measurement of the Mg2 index, and have measured the velocity dispersion and radial velocity with improved accuracy. To evaluate the extinction, a correlation between the Mg2 index and effective V-I colour has been established for elliptical galaxies. Using a new method for correcting for effective wavelength shifts, we find A_V = 4.67 +/- 0.19 mag, which is lower by 0.4 mag than previously thought. To establish the distance, the Fundamental Plane for elliptical galaxies has been constructed in I. The velocity dispersion of Maffei 1, measured to be 186.8 +/- 7.4 km/s, in combination with modern wide-field photometry in I, leads to a distance of 2.92 +/- 0.37 Mpc. The Dn-sigma relation, which is independently calibrated, gives 3.08 +/- 0.85 Mpc and 3.23 +/- 0.67 Mpc from photometry in B and K`, respectively. The weighted mean of the three estimates is 3.01 +/- 0.30 Mpc. The distance and luminosity make Maffei 1 the nearest giant elliptical galaxy. The radial velocity of Maffei 1 is +66.4 +/- 5.0 km/s, significantly higher than the accepted value of -10 km/s. The Hubble distance corresponding to the mean velocity of Maffei 1, Maffei 2 and IC342 is 3.5 Mpc. Thus, it is unlikely that Maffei 1 has had any influence on Local Group dynamics

An Integrated-Photonics Optical-Frequency Synthesizer

Integrated-photonics microchips now enable a range of advanced functionalities for high-coherence applications such as data transmission, highly optimized physical sensors, and harnessing quantum states, but with cost, efficiency, and portability much beyond tabletop experiments. Through high-volume semiconductor processing built around advanced materials there exists an opportunity for integrated devices to impact applications cutting across disciplines of basic science and technology. Here we show how to synthesize the absolute frequency of a lightwave signal, using integrated photonics to implement lasers, system interconnects, and nonlinear frequency comb generation. The laser frequency output of our synthesizer is programmed by a microwave clock across 4 THz near 1550 nm with 1 Hz resolution and traceability to the SI second. This is accomplished with a heterogeneously integrated III/V-Si tunable laser, which is guided by dual dissipative-Kerr-soliton frequency combs fabricated on silicon chips. Through out-of-loop measurements of the phase-coherent, microwave-to-optical link, we verify that the fractional-frequency instability of the integrated photonics synthesizer matches the $7.0*10^{-13}$ reference-clock instability for a 1 second acquisition, and constrain any synthesis error to $7.7*10^{-15}$ while stepping the synthesizer across the telecommunication C band. Any application of an optical frequency source would be enabled by the precision optical synthesis presented here. Building on the ubiquitous capability in the microwave domain, our results demonstrate a first path to synthesis with integrated photonics, leveraging low-cost, low-power, and compact features that will be critical for its widespread use.Comment: 10 pages, 6 figure

Integrated frequency comb laser with narrow intrinsic optical linewidth based on a dielectric waveguide feedback circuit

We present an integrated hybrid semiconductor-dielectric (InP-Si$_3$N$_4$) waveguide laser that generates frequency combs at a wavelength around 1.5 $\mu$m with a record-low intrinsic optical linewidth of 34 kHz. This is achieved by extending the cavity photon lifetime using a low-loss dielectric waveguide circuit. In our experimental demonstration, the on-chip, effective optical path length of the laser cavity is extended to 6 cm. The resulting linewidth narrowing shows the high potential of on-chip, highly coherent frequency combs with direct electrical pumping, based on hybrid and heterogeneous integrated circuits making use of low-loss dielectric waveguides

Academics' perceptions of students' motivation for learning and their own motivation for teaching in a marketized higher education context

Background. The marketisation of higher education (HE), which positions students as consumers and academics as service providers, may adversely affect students’ motivation for learning and academics’ motivation for teaching. According to self-determination theory (SDT), high-quality forms of motivation are achieved when individuals experience fulfilment of three psychological needs: competence, autonomy, and relatedness. Aims. This study applied SDT to examine academics’ perceptions of whether the marketized HE context in England, UK, supported or undermined these three psychological needs for their students and for themselves. It also examined their perceptions of the impact that this context had on their teaching. Sample. Participants were 10 academics teaching at five post-1992 higher education institutions in England, UK. Method. Semi-structured interviews were conducted and subsequently analyzed using thematic analysis. Results. Academics observed that students identifying as consumers seemed to display lower levels of competence, autonomy, and relatedness. This contributed to an HE environment that diminished the academics’ own psychological needs. Although some felt able to improve student motivation through their teaching, others felt demotivated and disempowered by top-down pressure from managers and bottom-up pressure from students. Conclusions. The marketized HE context may undermine high-quality motivation for students’ learning and academics’ teaching. Academics should be supported to teach in ways that facilitate competence, autonomy, and relatedness in their students and themselves

Bridging ultrahigh-Q devices and photonic circuits

Optical microresonators are essential to a broad range of technologies and scientific disciplines. However, many of their applications rely on discrete devices to attain challenging combinations of ultra-low-loss performance (ultrahigh Q) and resonator design requirements. This prevents access to scalable fabrication methods for photonic integration and lithographic feature control. Indeed, finding a microfabrication bridge that connects ultrahigh-Q device functions with photonic circuits is a priority of the microcavity field. Here, an integrated resonator having a record Q factor over 200 million is presented. Its ultra-low-loss and flexible cavity design brings performance to integrated systems that has been the exclusive domain of discrete silica and crystalline microcavity devices. Two distinctly different devices are demonstrated: soliton sources with electronic repetition rates and high-coherence/low-threshold Brillouin lasers. This multi-device capability and performance from a single integrated cavity platform represents a critical advance for future photonic circuits and systems

Integrated Photonics for NASA Applications

No abstract availabl