Photonic neuromorphic information processing and reservoir computing

Photonic neuromorphic computing is attracting tremendous research interest now, catalyzed in no small part by the rise of deep learning in many applications. In this paper, we will review some of the exciting work that has been going in this area and then focus on one particular technology, namely, photonic reservoir computing

Protein sequestration generates a flexible ultrasensitive response in a genetic network

Ultrasensitive responses are crucial for cellular regulation. Protein sequestration, where an active protein is bound in an inactive complex by an inhibitor, can potentially generate ultrasensitivity. Here, in a synthetic genetic circuit in budding yeast, we show that sequestration of a basic leucine zipper transcription factor by a dominant-negative inhibitor converts a graded transcriptional response into a sharply ultrasensitive response, with apparent Hill coefficients up to 12. A simple quantitative model for this genetic network shows that both the threshold and the degree of ultrasensitivity depend upon the abundance of the inhibitor, exactly as we observed experimentally. The abundance of the inhibitor can be altered by simple mutation; thus, ultrasensitive responses mediated by protein sequestration are easily tuneable. Gene duplication of regulatory homodimers and loss-of-function mutations can create dominant negatives that sequester and inactivate the original regulator. The generation of flexible ultrasensitive responses is an unappreciated adaptive advantage that could explain the frequent evolutionary emergence of dominant negatives

Robustness in Glyoxylate Bypass Regulation

The glyoxylate bypass allows Escherichia coli to grow on carbon sources with only two carbons by bypassing the loss of carbons as CO2 in the tricarboxylic acid cycle. The flux toward this bypass is regulated by the phosphorylation of the enzyme isocitrate dehydrogenase (IDH) by a bifunctional kinase–phosphatase called IDHKP. In this system, IDH activity has been found to be remarkably robust with respect to wide variations in the total IDH protein concentration. Here, we examine possible mechanisms to explain this robustness. Explanations in which IDHKP works simultaneously as a first-order kinase and as a zero-order phosphatase with a single IDH binding site are found to be inconsistent with robustness. Instead, we suggest a robust mechanism where both substrates bind the bifunctional enzyme to form a ternary complex

Environment of the submillimeter-bright massive starburst HFLS3 at z∼z\sim6.34

We describe the search for Lyman-break galaxies (LBGs) near the sub-millimeter bright starburst galaxy HFLS3 at $z$$=$6.34 and a study on the environment of this massive galaxy during the end of reionization.We performed two independent selections of LBGs on images obtained with the \textit{Gran Telescopio Canarias} (GTC) and the \textit{Hubble Space Telescope} (HST) by combining non-detections in bands blueward of the Lyman-break and color selection. A total of 10 objects fulfilling the LBG selection criteria at $z$$>$5.5 were selected over the 4.54 and 55.5 arcmin$^2$ covered by our HST and GTC images, respectively. The photometric redshift, UV luminosity, and the star-formation rate of these sources were estimated with models of their spectral energy distribution. These $z$$\sim$6 candidates have physical properties and number densities in agreement with previous results. The UV luminosity function at $z$$\sim$6 and a Voronoi tessellation analysis of this field shows no strong evidence for an overdensity of relatively bright objects (m$_{F105W}$$<$25.9) associated with \textit{HFLS3}. However, the over-density parameter deduced from this field and the surface density of objects can not excluded definitively the LBG over-density hypothesis. Moreover we identified three faint objects at less than three arcseconds from \textit{HFLS3} with color consistent with those expected for $z$$\sim$6 galaxies. Deeper data are needed to confirm their redshifts and to study their association with \textit{HFLS3} and the galaxy merger that may be responsible for the massive starburst.Comment: 14 pages, 12 figures, accepted for publication in Ap

The inositol phosphatase MTMR4 is a novel target of the ubiquitin ligase Nedd4

The inositol phosphatase, MTMR4 (myotubularin-related protein 4), was identified as a novel interactor of the ubiquitin ligase Nedd4 (neural-precursor-cell-expressed developmentally down-regulated 4). hMTMR4 (human MTMR4) and Nedd4 co-immunoprecipitated and co-localized to late endosomes. The PY (Pro-Tyr) motif of hMTMR4 binds to WW (Trp-Trp) domains of hNedd4. MTMR4 expression was decreased in atrophying muscle, whereas Nedd4 expression was increased and hMTMR4 was ubiquitinated by hNedd4, suggesting that this novel interaction may underlie the biological process of muscle breakdown

Defective Membrane Remodeling in Neuromuscular Diseases: Insights from Animal Models

Proteins involved in membrane remodeling play an essential role in a plethora of cell functions including endocytosis and intracellular transport. Defects in several of them lead to human diseases. Myotubularins, amphiphysins, and dynamins are all proteins implicated in membrane trafficking and/or remodeling. Mutations in myotubularin, amphiphysin 2 (BIN1), and dynamin 2 lead to different forms of centronuclear myopathy, while mutations in myotubularin-related proteins cause Charcot-Marie-Tooth neuropathies. In addition to centronuclear myopathy, dynamin 2 is also mutated in a dominant form of Charcot-Marie-Tooth neuropathy. While several proteins from these different families are implicated in similar diseases, mutations in close homologues or in the same protein in the case of dynamin 2 lead to diseases affecting different tissues. This suggests (1) a common molecular pathway underlying these different neuromuscular diseases, and (2) tissue-specific regulation of these proteins. This review discusses the pathophysiology of the related neuromuscular diseases on the basis of animal models developed for proteins of the myotubularin, amphiphysin, and dynamin families. A better understanding of the common mechanisms between these neuromuscular disorders will lead to more specific health care and therapeutic approaches

The Effect of Testing on the Retention of Coherent and Incoherent Text Material

Research has shown that testing during learning can enhance the long-term retention of text material. In two experiments, we investigated the testing effect with a fill-in-the-blank test on the retention of text material. In Experiment 1, using a coherent text, we found no retention benefit of testing compared to a restudy (control) condition. In Experiment 2, text coherence was disrupted by scrambling the order of the sentences from the text. The material was subsequently presented as a list of facts as opposed to connected discourse. For the incoherent version of the text, testing slowed down the rate of forgetting compared to a restudy (control) condition. The results suggest that the connectedness of materials can play an important role in determining the magnitude of testing benefits for long-term retention. Testing with a completion test seems most beneficial for unconnected materials and less so for highly structured materials

Mapping and monitoring carbon stocks with satellite observations: a comparison of methods

Mapping and monitoring carbon stocks in forested regions of the world, particularly the tropics, has attracted a great deal of attention in recent years as deforestation and forest degradation account for up to 30% of anthropogenic carbon emissions, and are now included in climate change negotiations. We review the potential for satellites to measure carbon stocks, specifically aboveground biomass (AGB), and provide an overview of a range of approaches that have been developed and used to map AGB across a diverse set of conditions and geographic areas. We provide a summary of types of remote sensing measurements relevant to mapping AGB, and assess the relative merits and limitations of each. We then provide an overview of traditional techniques of mapping AGB based on ascribing field measurements to vegetation or land cover type classes, and describe the merits and limitations of those relative to recent data mining algorithms used in the context of an approach based on direct utilization of remote sensing measurements, whether optical or lidar reflectance, or radar backscatter. We conclude that while satellite remote sensing has often been discounted as inadequate for the task, attempts to map AGB without satellite imagery are insufficient. Moreover, the direct remote sensing approach provided more coherent maps of AGB relative to traditional approaches. We demonstrate this with a case study focused on continental Africa and discuss the work in the context of reducing uncertainty for carbon monitoring and markets

IL-13 expression by blood T cells and not eosinophils is increased in asthma compared to non-asthmatic eosinophilic bronchitis

<p>Abstract</p> <p>Background</p> <p>In asthma interleukin (IL)-13 is increased in the airway compared with non-asthmatic eosinophilic bronchitis. Whether this differential expression is specific to the airway or is more generalised is uncertain.</p> <p>Methods</p> <p>We sought to examine IL-13 expression in peripheral blood T-cells and eosinophils in asthma and non-asthmatic eosinophilic bronchitis. Peripheral blood CD3+ cell and eosinophil intracellular IL-13 expression from subjects with asthma, non-asthmatic eosinophilic bronchitis and healthy controls was assessed. The effect of priming by asthmatic serum on the release of IL-13 by peripheral blood mononuclear cells from healthy subjects was examined and the serum from these subjects was analysed for a range of chemokines and cytokines.</p> <p>Results</p> <p>The median (IQR)% intracellular IL-13 expression by CD3+ cells was increased in asthma [5.3 (2.7–9.8)%; n = 12] compared to non-asthmatic eosinophilic bronchitis [1.1 (0.5–3)%; n = 7] and healthy controls [1.7 (0.2–3%); n = 9] (p = 0.02), but was not significantly different in eosinophils across the groups. IL-13 released from healthy peripheral blood mononuclear cells (n = 10) was increased by asthmatic serum [117 (47.8–198)pg/ml] compared to control [78.5 (42.6–128)pg/ml; p = 0.02), but was not affected by non-asthmatic serum.</p> <p>Conclusion</p> <p>Our findings support the view that IL-13 expression is increased in peripheral blood-derived T cells in asthma and that asthmatic serum up-regulates IL-13 release from healthy peripheral blood mononuclear cells.</p