GHz configurable photon pair generation from a silicon nonlinear interferometer

Low loss and high speed processing of photons is central to architectures for photonic quantum information. High speed switching enables non-deterministic photon sources and logic gates to be made deterministic, while the speed with which quantum light sources can be turned on and off impacts the clock rate of photonic computers and the data rate of quantum communication. Here we use lossy carrier depletion modulators in a silicon waveguide nonlinear interferometer to modulate photon pair generation at 1~GHz without exposing the generated photons to the phase dependent parasitic loss of the modulators. The super sensitivity of nonlinear interferometers reduces power consumption compared to modulating the driving laser. This can be a building block component for high speed programmabile, generalised nonlinear waveguide networks

Inferring late-Holocene climate in the Ecuadorian Andes using a chironomid-based temperature inference model

Presented here is the first chironomid calibration data set for tropical South America. Surface sediments were collected from 59 lakes across Bolivia (15 lakes), Peru (32 lakes), and Ecuador (12 lakes) between 2004 and 2013 over an altitudinal gradient from 150 m above sea level (a.s.l) to 4655 m a.s.l, between 0–17◦ S and 64–78◦ W. The study sites cover a mean annual temperature (MAT) gradient of 25 ◦ C. In total, 55 chironomid taxa were identified in the 59 calibration data set lakes. When used as a single explanatory variable, MAT explains 12.9% of the variance (λ1/λ2 =1.431). Two inference models were developed using weighted averaging (WA) and Bayesian methods. The best performing model using conventional statistical methods was a WA (inverse) model (R2jack= 0.890; RMSEPjack= 2.404 ◦C, RMSEP – root mean jack squared error of prediction; mean biasjack = −0.017 ◦C; max biasjack = 4.665 ◦C). The Bayesian method produced a model with R2jack = 0.909, RMSEPjack = 2.373 ◦C, mean jack biasjack = 0.598 ◦C, and max biasjack = 3.158 ◦C. Both models were used to infer past temperatures from a ca. 3000-year record from the tropical Andes of Ecuador, Laguna Pindo. Inferred temperatures fluctuated around modern-day conditions but showed significant departures at certain intervals (ca. 1600 cal yr BP; ca. 3000–2500 cal yr BP). Both methods (WA and Bayesian) showed similar patterns of temperature variability; however, the magnitude of fluctuations differed. In general the WA method was more variable and often underestimated Holocene temperatures (by ca. −7 ± 2.5 ◦C relative to the modern period). The Bayesian method provided temperature anomaly estimates for cool periods that lay within the expected range of the Holocene (ca. −3 ± 3.4 ◦C). The error associated with both reconstructions is consistent with a constant temperature of 20 ◦C for the past 3000 years. We would caution, however, against an over-interpretation at this stage. The reconstruction can only currently be deemed qualitative and requires more research before quantitative estimates can be generated with confidence. Increasing the number, and spread, of lakes in the calibration data set would enable the detection of smaller climate signals

Environmental controls on the distribution and diversity of lentic Chironomidae (Insecta: Diptera) across an altitudinal gradient in tropical South America

To predict the response of aquatic ecosystems to future global climate change, data on the ecology and distribution of keystone groups in freshwater ecosystems are needed. In contrast to mid- and high-latitude zones, such data are scarce across tropical South America (Neotropics). We present the distribution and diversity of chironomid species using surface sediments of 59 lakes from the Andes to the Amazon (0.1–17°S and 64–78°W) within the Neotropics. We assess the spatial variation in community assemblages and identify the key variables influencing the distributional patterns. The relationships between environmental variables (pH, conductivity, depth, and sediment organic content), climatic data, and chironomid assemblages were assessed using multivariate statistics (detrended correspondence analysis and canonical correspondence analysis). Climatic parameters (temperature and precipitation) were most significant in describing the variance in chironomid assemblages. Temperature and precipitation are both predicted to change under future climate change scenarios in the tropical Andes. Our findings suggest taxa of Orthocladiinae, which show a preference to cold high-elevation oligotrophic lakes, will likely see range contraction under future anthropogenic-induced climate change. Taxa abundant in areas of high precipitation, such as Micropsectra and Phaenopsectra, will likely become restricted to the inner tropical Andes, as the outer tropical Andes become drier. The sensitivity of chironomids to climate parameters makes them important bio-indicators of regional climate change in the Neotropics. Furthermore, the distribution of chironomid taxa presented here is a vital first step toward providing urgently needed autecological data for interpreting fossil chironomid records of past ecological and climate change from the tropical Andes

9~GHz measurement of squeezed light by interfacing silicon photonics and integrated electronics

Photonic quantum technology can be enhanced by monolithic fabrication of both the underpinning quantum hardware and the corresponding electronics for classical readout and control. Together, this enables miniaturisation and mass-manufacture of small quantum devices---such as quantum communication nodes, quantum sensors and sources of randomness---and promises the precision and scale of fabrication required to assemble useful quantum computers. Here we combine CMOS compatible silicon and germanium-on-silicon nano-photonics with silicon-germanium integrated amplification electronics to improve performance of on-chip homodyne detection of quantum light. We observe a 3 dB bandwidth of 1.7 GHz, shot-noise limited performance beyond 9 GHz and minaturise the required footprint to 0.84 mm. We use the device to observe quantum squeezed light, from 100 MHz to 9 GHz, generated in a lithium niobate waveguide. This demonstrates that an all-integrated approach yields faster homodyne detectors for quantum technology than has been achieved to-date and opens the way to full-stack integration of photonic quantum devices.Comment: Nat. Photonics (2020

Forests protect aquatic communities from detrimental impact by volcanic deposits in the tropical Andes (Ecuador)

Volcanic activity impacts ecosystems sometimes with multiple, complex and long-lasting consequences, including volcanic tephra (airborne material) causing widespread disruptions. We study the effects of tephra deposition around two tropical lakes of Ecuador using a multi-proxy analysis of lake sediment archives spanning the last 2000 years. We present the dynamics of terrestrial vegetation (pollen), aquatic macroinvertebrate fauna (chironomids) and organic matter (stable isotopes) in: (i) a high elevation, stream-connected, open alpine grassland (Andean páramo) and (ii) a mid-elevation, stream-isolated, pre-montane forest. Páramo vegetation showed a slight increase in herbs and quick recovery after the tephra deposition; however, the aquatic community suffered a regime shift not reversed today c. 1500 years after the event. In the pre-montane location, the canopy opened up following tephra deposition, and it took c. 150 years to return to pre-impact levels. At the forested site, no major changes in the aquatic fauna were observed related to the tephra deposition. We hypothesise that the forest acted as a protective barrier preventing a large fallout of ash into the aquatic system. Forest not only acted as a buffer for ash falling into the water from the air, but also prevented landslides of tephra by enhancing soil stability, contrary to what was observed in the open system. We demonstrate the protective ecosystem service that forests play in sustaining ecological resilience and water quality facing natural (volcanic) disturbance. The ongoing deforestation of tropical regions therefore might increase the vulnerability of aquatic ecosystems, threatening the water quality for ecosystems and human populations

BUMPER v1.0: a Bayesian user-friendly model for palaeo-environmental reconstruction

We describe the Bayesian user-friendly model for palaeo-environmental reconstruction (BUMPER), a Bayesian transfer function for inferring past climate and other environmental variables from microfossil assemblages. BUMPER is fully self-calibrating, straightforward to apply, and computationally fast, requiring ~2 s to build a 100-taxon model from a 100-site training set on a standard personal computer. We apply the model’s probabilistic framework to generate thousands of artificial training sets under ideal assumptions.We then use these to demonstrate the sensitivity of reconstructions to the characteristics of the training set, considering assemblage richness, taxon tolerances, and the number of training sites. We find that a useful guideline for the size of a training set is to provide, on average, at least 10 samples of each taxon. We demonstrate general applicability to real data, considering three different organism types (chironomids, diatoms, pollen) and different reconstructed variables. An identically configured model is used in each application, the only change being the input files that provide the training-set environment and taxon-count data. The performance of BUMPER is shown to be comparable with weighted average partial least squares (WAPLS) in each case. Additional artificial datasets are constructed with similar characteristics to the real data, and these are used to explore the reasons for the differing performances of the different training sets

Aquatic community response to volcanic eruptions on the Ecuadorian Andean flank: evidence from the palaeoecological record

Aquatic ecosystems in the tropical Andes are under increasing pressure from human modification of the landscape (deforestation and dams) and climatic change (increase of extreme events and 1.5 °C on average temperatures are projected for AD 2100). However, the resilience of these ecosystems to perturbations is poorly understood. Here we use a multi-proxy palaeoecological approach to assess the response of aquatic ecosystems to a major mechanism for natural disturbance, volcanic ash deposition. Specifically, we present data from two Neotropical lakes located on the eastern Andean flank of Ecuador. Laguna Pindo (1°27.132′S–78°04.847′W) is a tectonically formed closed basin surrounded by a dense mid-elevation forest, whereas Laguna Baños (0°19.328′S–78°09.175′W) is a glacially formed lake with an inflow and outflow in high Andean Páramo grasslands. In each lake we examined the dynamics of chironomids and other aquatic and semi-aquatic organisms to explore the effect of thick (> 5 cm) volcanic deposits on the aquatic communities in these two systems with different catchment features. In both lakes past volcanic ash deposition was evident from four large tephras dated to c.850 cal year BP (Pindo), and 4600, 3600 and 1500 cal year BP (Baños). Examination of the chironomid and aquatic assemblages before and after the ash depositions revealed no shift in composition at Pindo, but a major change at Baños occurred after the last event around 1500 cal year BP. Chironomids at Baños changed from an assemblage dominated by Pseudochironomus and Polypedilum nubifer-type to Cricotopus/Paratrichocladius type-II, and such a dominance lasted for approximately 380 years. We suggest that, despite potential changes in the water chemistry, the major effect on the chironomid community resulted from the thickness of the tephra being deposited, which acted to shallow the water body beyond a depth threshold. Changes in the aquatic flora and fauna at the base of the trophic chain can promote cascade effects that may deteriorate the ecosystem, especially when already influenced by human activities, such as deforestation and dams, which is frequent in the high Andes

Recovery of Barotrauma Injuries in Chinook Salmon, Oncorhynchus tshawytscha from Exposure to Pile Driving Sound

Juvenile Chinook salmon, Oncorhynchus tshawytscha, were exposed to simulated high intensity pile driving signals to evaluate their ability to recover from barotrauma injuries. Fish were exposed to one of two cumulative sound exposure levels for 960 pile strikes (217 or 210 dB re 1 µPa2·s SELcum; single strike sound exposure levels of 187 or 180 dB re 1 µPa2⋅s SELss respectively). This was followed by an immediate assessment of injuries, or assessment 2, 5, or 10 days post-exposure. There were no observed mortalities from the pile driving sound exposure. Fish exposed to 217 dB re 1 µPa2·s SELcum displayed evidence of healing from injuries as post-exposure time increased. Fish exposed to 210 dB re 1 µPa2·s SELcum sustained minimal injuries that were not significantly different from control fish at days 0, 2, and 10. The exposure to 210 dB re 1 µPa2·s SELcum replicated the findings in a previous study that defined this level as the threshold for onset of injury. Furthermore, these data support the hypothesis that one or two Mild injuries resulting from pile driving exposure are unlikely to affect the survival of the exposed animals, at least in a laboratory environment

Reactome: a database of reactions, pathways and biological processes

Reactome (http://www.reactome.org) is a collaboration among groups at the Ontario Institute for Cancer Research, Cold Spring Harbor Laboratory, New York University School of Medicine and The European Bioinformatics Institute, to develop an open source curated bioinformatics database of human pathways and reactions. Recently, we developed a new web site with improved tools for pathway browsing and data analysis. The Pathway Browser is an Systems Biology Graphical Notation (SBGN)-based visualization system that supports zooming, scrolling and event highlighting. It exploits PSIQUIC web services to overlay our curated pathways with molecular interaction data from the Reactome Functional Interaction Network and external interaction databases such as IntAct, BioGRID, ChEMBL, iRefIndex, MINT and STRING. Our Pathway and Expression Analysis tools enable ID mapping, pathway assignment and overrepresentation analysis of user-supplied data sets. To support pathway annotation and analysis in other species, we continue to make orthology-based inferences of pathways in non-human species, applying Ensembl Compara to identify orthologs of curated human proteins in each of 20 other species. The resulting inferred pathway sets can be browsed and analyzed with our Species Comparison tool. Collaborations are also underway to create manually curated data sets on the Reactome framework for chicken, Drosophila and rice

The Evolution of the DLK1-DIO3 Imprinted Domain in Mammals

A comprehensive, domain-wide comparative analysis of genomic imprinting between mammals that imprint and those that do not can provide valuable information about how and why imprinting evolved. The imprinting status, DNA methylation, and genomic landscape of the Dlk1-Dio3 cluster were determined in eutherian, metatherian, and prototherian mammals including tammar wallaby and platypus. Imprinting across the whole domain evolved after the divergence of eutherian from marsupial mammals and in eutherians is under strong purifying selection. The marsupial locus at 1.6 megabases, is double that of eutherians due to the accumulation of LINE repeats. Comparative sequence analysis of the domain in seven vertebrates determined evolutionary conserved regions common to particular sub-groups and to all vertebrates. The emergence of Dlk1-Dio3 imprinting in eutherians has occurred on the maternally inherited chromosome and is associated with region-specific resistance to expansion by repetitive elements and the local introduction of noncoding transcripts including microRNAs and C/D small nucleolar RNAs. A recent mammal-specific retrotransposition event led to the formation of a completely new gene only in the eutherian domain, which may have driven imprinting at the cluster