Si/Ge phototransistor with responsivity >1000A/W on a silicon photonics platform.

In this article, we report a Si/Ge waveguide phototransistor with high responsivity and low dark current under low bias voltages, due to an engineered electric field distribution. The photodetector consists of n-i-p-i-n doping regions and shows a responsivity of 606 A/W at 1 V bias, and 1032 A/W at 2.8V bias with an input optical power of -50 dBm, and dark current of 4 µA and 42 µA respectively. This is achieved by placing two p+-doped regions in the silicon slab region beneath the Ge epitaxial layer. A measured small signal -3 dB bandwidth of 1.5 GHz with a -80 dBc/Hz phase noise response at 1 KHz frequency offset were demonstrated experimentally.

Reconfigurable integrated photonic filters for optical signal processing using a silicon photonic platform.

We present a systematic photonic filter design approach by deploying pole-zero optimization. The filter transfer function is derived from its specifications by formulating closed-form optimization objective functions and subsequently translating them into optical design parameters. Two distinct filter examples, namely Chebyshev and elliptic filters, are considered for the design and validation. A compact reconfigurable three-pole photonic filter is fabricated on a silicon photonic platform to illustrate the proposed design technique including transmission tunability. Integrated thermal phase shifters coupled with micro-ring resonators are used to reconfigure filter responses. A well-matched experimental demonstration is presented to validate the proposed tuning method. We achieved a sharp out-of-band edge rejection of at least 20 and 40 dB for the elliptic and Chebyshev filter, respectively.

Souporcell: robust clustering of single-cell RNA-seq data by genotype without reference genotypes.

Methods to deconvolve single-cell RNA-sequencing (scRNA-seq) data are necessary for samples containing a mixture of genotypes, whether they are natural or experimentally combined. Multiplexing across donors is a popular experimental design that can avoid batch effects, reduce costs and improve doublet detection. By using variants detected in scRNA-seq reads, it is possible to assign cells to their donor of origin and identify cross-genotype doublets that may have highly similar transcriptional profiles, precluding detection by transcriptional profile. More subtle cross-genotype variant contamination can be used to estimate the amount of ambient RNA. Ambient RNA is caused by cell lysis before droplet partitioning and is an important confounder of scRNA-seq analysis. Here we develop souporcell, a method to cluster cells using the genetic variants detected within the scRNA-seq reads. We show that it achieves high accuracy on genotype clustering, doublet detection and ambient RNA estimation, as demonstrated across a range of challenging scenarios.

Silicon-thulium hybrid microdisk lasers with low threshold and wide emission wavelength range.

We demonstrate low-threshold and wide emission wavelength range hybrid-integrated silicon-thulium microdisk lasers based on a pulley-coupled design. The resonators are fabricated on a silicon-on-insulator platform using a standard foundry process and the gain medium is deposited using a straightforward, low-temperature post-processing step. We show lasing in 40- and 60-µm diameter microdisks with up to 2.6 mW double-sided output power and bidirectional slope efficiencies of up to 13.4% with respect to 1620 nm pump power launched to the bus waveguides. We observe thresholds less than 1 mW versus on-chip pump power and both single-mode and multimode laser emission spanning across wavelengths from 1825 to 1939nm. These low threshold lasers with emissions over a > 100 nm range open the door to monolithic silicon photonic integrated circuits with broadband optical gain and highly compact and efficient light sources in the emerging ∼1.8-2.0 µm wavelength band.

Application of the TDFA window in true optical time delay systems.

Recent advances in silicon photonic components operating in the thulium-doped fiber amplifier (TDFA) wavelength regime around 2-µm have shown that these wavelengths hold great promise for on-chip photonic systems. Here we present our work on characterizing a Mach-Zehnder interferometer coupled silicon photonic ring resonator operating in the TDFA window for optical time delay applications. We describe the optical transmission and variable time delay properties of the resonator, including a detailed characterization and comparison of the directional coupler and Mach-Zehnder interferometer base components at both 1930 and 1550 nm wavelengths. The results show tuning of a ring from a 190-ps peak time delay at a resonant extinction ratio of 5.1-dB to a 560-ps peak time delay at an extinction ratio of 11.0-dB, in good agreement with optical models of the device. These results demonstrate significant promise towards the future application of TDFA band devices in optical time delay systems.

Thulium-doped tellurium oxide waveguide amplifier with 7.6 dB net gain on a silicon nitride chip: publisher's note.

This publisher's note contains corrections to Opt. Lett.44, 5788 (2019)OPLEDP0146-959210.1364/OL.44.005788.

High-speed performance of a TDFA-band micro-ring resonator modulator and detector.

We demonstrate a silicon-on-insulator micro-ring resonator (MRR) modulator and defect-mediated (DM) detector operating at a wavelength near 2 µm for use in the thulium doped fiber amplifier wavelength band. The MRR modulator was critically coupled with an unbiased notch-depth of 20 dB and Q-factor of 4700. The resonance shift under reverse bias was 23 pm/V with a calculated VπLπ of 2.2 to 2.6 V·cm from -1 to -8 V, respectively. Simulations are in good agreement with the measured data. The experimental modulation bandwidth was 12.5 GHz, limited by the response of the commercial external detector used for this measurement. The DM detector was operated in avalanche mode, had 1.97 µm wavelength responsivities of 0.04 and 0.14 A/W, and had bandwidths greater than 16 and 7.5 GHz at -15 and -30 V biases, respectively. Large-signal measurement demonstrated open eye-diagrams at 5, 10, and 12.5 Gbps for the DM detector and also for an optical link consisting of the modulator and detector integrated on the same silicon chip.

Subwavelength grating metamaterial waveguides functionalized with tellurium oxide cladding.

We report on the design, fabrication and characterization of subwavelength grating metamaterial waveguides coated with tellurium oxide. The structures are first fabricated using a standard CMOS compatible process on a silicon-on-insulator platform. Amorphous tellurium oxide top cladding material is then deposited via post-process RF magnetron sputtering. The photonic bandstructure is controlled by adjustment of the device geometry, opening a wide range of operating regimes, including subwavelength propagation, slow light and the photonic bandgap, for various wavelength bands within the 1550 nm telecommunications window. Propagation loss of 1.0 ± 0.1 dB/mm is reported for the tellurium oxide-cladded device, compared to 1.5 ± 0.1 dB/mm propagation loss reported for the silicon dioxide-cladded reference structure. This is the first time that a high-index (n > 2) oxide cladding has been demonstrated for subwavelength grating metamaterial waveguides, thus introducing a new material platform for on-chip integrated optics.

Correction to: Niacin-mediated rejuvenation of macrophage/microglia enhances remyelination of the aging central nervous system.

The article Niacin­mediated rejuvenation of macrophage/microglia enhances remyelination of the aging central nervous system, written by Khalil S. Rawji, Adam M.H. Young, Tanay Ghosh, Nathan J. Michaels, Reza Mirzaei, Janson Kappen, Kathleen L. Kolehmainen, Nima Alaeiilkhchi, Brian Lozinski, Manoj K. Mishra, Annie Pu, Weiwen Tang, Salma Zein, Deepak K. Kaushik, Michael B. Keough, Jason R. Plemel, Fiona Calvert, Andrew J. Knights, Daniel J. Gaffney, Wolfram Tetzlaff, Robin J. M. Franklin and V. Wee Yong, was originally published electronically on the publisher's internet.

Niacin-mediated rejuvenation of macrophage/microglia enhances remyelination of the aging central nervous system.

Remyelination following CNS demyelination restores rapid signal propagation and protects axons; however, its efficiency declines with increasing age. Both intrinsic changes in the oligodendrocyte progenitor cell population and extrinsic factors in the lesion microenvironment of older subjects contribute to this decline. Microglia and monocyte-derived macrophages are critical for successful remyelination, releasing growth factors and clearing inhibitory myelin debris. Several studies have implicated delayed recruitment of macrophages/microglia into lesions as a key contributor to the decline in remyelination observed in older subjects. Here we show that the decreased expression of the scavenger receptor CD36 of aging mouse microglia and human microglia in culture underlies their reduced phagocytic activity. Overexpression of CD36 in cultured microglia rescues the deficit in phagocytosis of myelin debris. By screening for clinically approved agents that stimulate macrophages/microglia, we have found that niacin (vitamin B3) upregulates CD36 expression and enhances myelin phagocytosis by microglia in culture. This increase in myelin phagocytosis is mediated through the niacin receptor (hydroxycarboxylic acid receptor 2). Genetic fate mapping and multiphoton live imaging show that systemic treatment of 9-12-month-old demyelinated mice with therapeutically relevant doses of niacin promotes myelin debris clearance in lesions by both peripherally derived macrophages and microglia. This is accompanied by enhancement of oligodendrocyte progenitor cell numbers and by improved remyelination in the treated mice. Niacin represents a safe and translationally amenable regenerative therapy for chronic demyelinating diseases such as multiple sclerosis.

Experimental quantification of the free-carrier effect in silicon waveguides at extended wavelengths.

We examine the electro-optic effect at wavelengths ranging from 1.31 to 2.02 µm for: (1) an Electronic Variable Optical Attenuator (EVOA); and (2) a Micro-Ring Resonator (MRR). For the EVOA, simulations were performed to ascertain the relationship between free-carrier concentration and optical attenuation, and are in agreement with our observation of an increase in attenuation with increasing wavelength. MRRs were fabricated for use around wavelengths of 2 µm to explore the sensitivity of operation to bus-to-ring coupling gap and p-n junction offset. Trends observed in the experiment are replicated by simulation, calibrated using the observations of the EVOA operation. The previously proposed efficiency increase of operation around 2 µm compared to more traditional wavelengths is demonstrated. Future development of devices for these wavelengths, supported by amplification using Thulium Doped Fiber Amplifier (TDFA) technology, is a promising route to aid in the alleviation of increasing demands on communication networks.

Low-loss TeO2-coated Si3N4 waveguides for application in photonic integrated circuits.

We report on high-quality tellurium oxide waveguides integrated on a low-loss silicon nitride wafer-scale platform. The waveguides consist of silicon nitride strip features, which are fabricated using a standard foundry process and a tellurium oxide coating layer that is deposited in a single post-processing step. We show that by adjusting the Si3N4 strip height and width and TeO2 layer thickness, a small mode area, small bend radius and high optical intensity overlap with the TeO2 can be obtained. We investigate transmission at 635, 980, 1310, 1550 and 2000 nm wavelengths in paperclip waveguide structures and obtain low propagation losses down to 0.6 dB/cm at 2000 nm. These results illustrate the potential for compact linear, nonlinear and active tellurite glass devices in silicon nitride photonic integrated circuits operating from the visible to mid-infrared.

Thulium-doped tellurium oxide waveguide amplifier with 7.6 dB net gain on a silicon nitride chip.

We report on thulium-doped waveguide amplifiers integrated on a low-loss silicon nitride platform. The amplifier structure consists of a thulium-doped tellurium oxide thin film coated on a silicon nitride strip waveguide on silicon. We determine a waveguide background loss of 0.7 dB/cm at 1479 nm based on the quality factor measured in microring resonators. Gain measurements were carried out in straight and 6.7-cm-long s-bend waveguides realized on a 2.2-cm-long chip. We measure internal net gain over the wavelength range 1860-2000 nm under 1620 nm pumping and up to 7.6 dB total gain at 1870 nm, corresponding to 1.1 dB/cm. These results are promising for the realization of highly compact thulium-doped amplifiers in the emerging 2 µm band for silicon-based photonic microsystems.

Differential phase-shift-keying demodulation by coherent perfect absorption in silicon photonics.

We demonstrate a novel differential phase-shift-keying (DPSK) demodulator based on coherent perfect absorption (CPA). Our DPSK demodulator chip device, which incorporates a silicon ring resonator, two bus waveguide inputs, and monolithically integrated detectors, operates passively at a bit rate of 10 Gbps at telecommunication wavelengths, and fits within a mm-scale footprint. Critical coupling is used to achieve efficient CPA by tuning the gap between the ring and bus waveguides. The device has a vertical eye opening of 12.47 mV and a quality factor exceeding 3×104. The fundamental principle behind this photonic circuit can be extended to other formats of integrated demodulators.

Resonance control of a silicon micro-ring resonator modulator under high-speed operation using the intrinsic defect-mediated photocurrent.

A method to stabilize the resonance wavelength of a depletion-type silicon micro-ring resonator modulator during high-speed operation is described. The method utilizes the intrinsic defect-mediated photo-absorption of a silicon waveguide and results in a modulator chip fabrication process that is free of heterogeneous integration (for example using germanium), thus significantly reducing the complexity and cost of manufacture. Residual defects, present after p-n junction formation, are found to produce an adequate photocurrent for use as a feedback signal, while an integrated heater is used to compensate for thermal drift via closed-loop control. The photocurrent is measured by a source-meter, which simultaneously provides a DC bias to the integrated heater during high-speed operation. A drop-port or an integrated extrinsic detector is not needed. This feedback control method is experimentally demonstrated via a computer-aided proportional-integral-differential loop. The resonance locking is validated for 12.5 Gb/s intensity modulation in a back-to-back bit-error-rate measurement. The stabilization method described is not limited to a specific modulator design and is compatible with speeds greatly in excess of 12.5 Gb/s, in contrast to the bandwidth limitation of other stabilization methods that rely on intrinsic photo-carrier generation through non-linear processes such as two-photon-absorption. Further, the use of intrinsic defects present after standard fabrication insures that no excess loss is associated with this stabilization method.

Oct-2 forms a complex with Oct-1 on the iNOS promoter and represses transcription by interfering with recruitment of RNA PolII by Oct-1.

Oct-1 (POU2f1) and Oct-2 (POU2f2) are members of the POU family of transcription factors. They recognize the same DNA sequence but fulfil distinct functions: Oct-1 is ubiquitous and regulates a variety of genes while Oct-2 is restricted to B-cells and neurones. Here we examine the interplay and regulatory mechanisms of these factors to control the inducible nitric oxide synthase (iNOS, NOS2). Using two breast cancer cell lines as a comparative model, we found that MCF-7 express iNOS upon cytokine stimulation while MDA-MB-231 do not. Oct-1 is present in both cell lines but MDA-MB-231 also express high levels of Oct-2. Manipulation of Oct-2 expression in these cell lines demonstrates that it is directly responsible for the repression of iNOS in MDA-MB-231. In MCF-7 cells Oct-1 binds the iNOS promoter, recruits RNA PolII and triggers initiation of transcription. In MDA-MB-231 cells, both Oct-1 and Oct-2 bind the iNOS promoter, forming a higher-order complex which fails to recruit RNA PolII, and as a consequence iNOS transcription does not proceed. Unravelling the mechanisms of transcription factor activity is paramount to the understanding of gene expression patterns that determine cell behaviour.

Experimental demonstration of coherent perfect absorption in a silicon photonic racetrack resonator.

We present the first experimental demonstration of coherent perfect absorption (CPA) in an integrated device using a silicon racetrack resonator at telecommunication wavelengths. Absorption in the racetrack is achieved by Si+-ion-implantation, allowing for phase controllable amplitude modulation at the resonant wavelength. The device is measured to have an extinction of 24.5 dB and a quality-factor exceeding 3000. Our results will enable integrated CPA devices for data modulation and detection.

Extent, causes, and consequences of small RNA expression variation in human adipose tissue.

Small RNAs are functional molecules that modulate mRNA transcripts and have been implicated in the aetiology of several common diseases. However, little is known about the extent of their variability within the human population. Here, we characterise the extent, causes, and effects of naturally occurring variation in expression and sequence of small RNAs from adipose tissue in relation to genotype, gene expression, and metabolic traits in the MuTHER reference cohort. We profiled the expression of 15 to 30 base pair RNA molecules in subcutaneous adipose tissue from 131 individuals using high-throughput sequencing, and quantified levels of 591 microRNAs and small nucleolar RNAs. We identified three genetic variants and three RNA editing events. Highly expressed small RNAs are more conserved within mammals than average, as are those with highly variable expression. We identified 14 genetic loci significantly associated with nearby small RNA expression levels, seven of which also regulate an mRNA transcript level in the same region. In addition, these loci are enriched for variants significant in genome-wide association studies for body mass index. Contrary to expectation, we found no evidence for negative correlation between expression level of a microRNA and its target mRNAs. Trunk fat mass, body mass index, and fasting insulin were associated with more than twenty small RNA expression levels each, while fasting glucose had no significant associations. This study highlights the similar genetic complexity and shared genetic control of small RNA and mRNA transcripts, and gives a quantitative picture of small RNA expression variation in the human population.

Monolithic silicon waveguide photodiode utilizing surface-state absorption and operating at 10 Gb/s.

We have fabricated a waveguide integrated monolithic silicon infrared detector. The photodiode consists of a p-i-n junction across a silicon-on-insulator (SOI) rib waveguide. Absorption is due to surface-states at the silicon/air interface of the waveguide. A 2 mm long detector shows a response of 0.045 A/W (calculated as a function of coupled light) and is capable of operation at 10 Gb/s at a reverse bias voltage of 2 V.

Silicon-on-insulator sensors using integrated resonance-enhanced defect-mediated photodetectors.

A resonance-enhanced, defect-mediated, ring resonator photodetector has been implemented as a single unit biosensor on a silicon-on-insulator platform, providing a cost effective means of integrating ring resonator sensors with photodetectors for lab-on-chip applications. This method overcomes the challenge of integrating hybrid photodetectors on the chip. The demonstrated responsivity of the photodetector-sensor was 90 mA/W. Devices were characterized using refractive index modified solutions and showed sensitivities of 30 nm/RIU.