Browsing by Type "Journal Articles"
Now showing 1 - 13 of 13
Results Per Page
Sort Options
Item ALL-OPTICAL NONLINEAR ACTIVATION FUNCTION FOR PHOTONIC NEURAL NETWORKS(Optica, 2018) Miscuglio, Mario; Mehrabian, Armin; Hu, Zibo; Azzam, Shaimaa I.; George, Jonathan; Kildishev, Alexander V.; Pelton, Matthew; Sorger, Volker J.With the recent successes of neural networks (NN) to perform machine-learning tasks, photonic-based NN designs may enable high throughput and low power neuromorphic compute paradigms since they bypass the parasitic charging of capacitive wires. Thus, engineering data-information processors capable of executing NN algorithms with high efficiency is of major importance for applications ranging from pattern recognition to classification. Our hypothesis is therefore, that if the time-limiting electro-optic conversion of current photonic NN designs could be postponed until the very end of the network, then the execution time of the photonic algorithm is simple the delay of the time-of-flight of photons through the NN, which is on the order of picoseconds for integrated photonics. Exploring such all-optical NN, in this work we discuss two independent approaches of implementing the optical perceptron’s nonlinear activation function based on nanophotonic structures exhibiting i) induced transparency and ii) reverse saturated absorption. Our results show that the all-optical nonlinearity provides about 3 and 7 dB extinction ratio for the two systems considered, respectively, and classification accuracies of an exemplary MNIST task of 97% and near 100% are found, which rivals that of software based trained NNs, yet with ignored noise in the network. Together with a developed concept for an all-optical perceptron, these findings point to the possibility of realizing pure photonic NNs with potentially unmatched throughput and even energy consumption for next generation information processing hardware.Item Analyzing Visible Light Communication Through Air–Water Interface(IEEE, 2019-08-30) ISLAM, MD SHAFIQUL; YOUNIS, MOHAMED F.In underwater wireless networks (UWNs), conventionally there is no direct communication between an underwater node and a remote command center. A floating base-station is often used to serve as an interface to a UWN; such a base-station would typically have both acoustic and radio modems to communicate with underwater nodes and off-shore centers, respectively. Although employing an airborne base-station would avoid the logistically-complicated surface nodes deployment, communication across the air-water interface becomes the main challenge since it involves two mediums. This paper promotes a novel way to interconnect UWNs to airborne base-stations through visible light communication (VLC) links. The paper analyzes the viability of VLC across the air-water interface by determining the coverage area and intensity inside the water for a light transmitter placed in the air. We show that enough intensity can be achieved for VLC communication even in the presence of a wavy water surface. We then provide guidelines for using single and multiple light sources to establish robust VLC links under rough environmental conditions like high water current and turbidity. Our approach is validated using simulation and a lab experiment is done to validate the simulation result for flat water surfaces.Item Assigning NMR spectra of RNA, peptides and small organic molecules using molecular network visualization software(Springer Netherlands, 2019-07-19) Marchant, Jan; Summers, Michael F.; Johnson, Bruce A.NMR assignment typically involves analysis of peaks across multiple NMR spectra. Chemical shifts of peaks are measured before being assigned to atoms using a variety of methods. These approaches quickly become complicated by overlap, ambiguity, and the complexity of correlating assignments among multiple spectra. Here we propose an alternative approach in which a network of linked peak-boxes is generated at the predicted positions of peaks across all spectra. These peak-boxes correlate known relationships and can be matched to the observed spectra. The method is illustrated with RNA, but a variety of molecular types should be readily tractable with this approach.Item A comparison of Lyse-It to other cellular sample preparation, bacterial lysing, and DNA fragmentation technologies(PLOS, 2019-07-23) Santaus, Tonya M.; Li, Shan; Saha, Lahari; Chen, Wilbur H.; Bhagat, Siya; Stine, O. Colin; Geddes, Chris D.The ability for safe and rapid pathogenic sample transportation and subsequent detection is an increasing challenge throughout the world. Herein, we describe and use bead-beating, vortex, sonication, 903 protein saver cards, and Lyse-It methods, aiming to inactivate Grampositive and -negative bacteria with subsequent genome DNA (quantitative Polymerase Chain Reaction) qPCR detection. The basic concepts behind the four chosen technologies is their versatility, cost, and ease of use in developed and underdeveloped countries. The four methods target the testing of bacterial resilience, cellular extraction from general and complex media and subsequent DNA extraction for qPCR detection and amplification. These results demonstrate that conventional high temperature heating, 903 protein saver cards, and Lyse-It are all viable options for inactivating bacterial growth for safe shipping. Additionally, Lyse-It was found to be particularly useful as this technology can inactivate bacteria, extract cells from 903 protein saver cards, lyse bacterial cells, and additionally keep genomic DNA viable for qPCR detection.Item Escherichia Coli FeoC Binds a Redox-Active, Rapidly Oxygen-Sensitive [4Fe-4S] Cluster(2019-02-07) Smith, Aaron T.; Linkous, Richard O.; Max, Nathan J.; Sestok, Alexandrea E.; Szalai, Veronika A.; Chacón, Kelly N.The acquisition of iron is essential to establishing virulence among most pathogens. Under acidic and/or anaerobic conditions, most bacteria utilize the widely-distributed ferrous iron (Fe²⁺) uptake (Feo) system to import metabolically-required iron. The Feo system is inadequately understood at the atomic, molecular, and mechanistic levels, but we do know it is comprised of a main membrane component (FeoB) essential for iron translocation, as well as two small, cytosolic proteins (FeoA and FeoC) hypothesized to function as accessories to this process. FeoC has many hypothetical functions, including that of an iron-responsive transcriptional regulator. Here, we demonstrate for the first time that Escherichia coli FeoC (EcFeoC) binds an [Fe-S] cluster. Using electronic absorption, X-ray absorption, and electron paramagnetic resonance spectroscopies, we extensively characterize the nature of this cluster. Under strictly anaerobic conditions after chemical reconstitution, we demonstrate that EcFeoC binds a redox-active [4Fe-4S]²⁺ᐟ⁺ cluster that is rapidly oxygen-sensitive (t₁/₂ ≈ 20 s), similar to the [Fe-S] cluster in the fumarate and nitrate reductase (FNR) transcriptional regulator. In a manner similar to FNR, we further probed the nature of the oxygen-induced cluster decay products and report conversion of a [4Fe-4S]²⁺ cluster to a [2Fe-2S]²⁺ cluster. In contrast to FNR, we show that [4Fe-4S]²⁺ cluster binding to EcFeoC is associated with modest conformational changes of the polypeptide, but not protein dimerization. Finally, we posit a working hypothesis in which the cluster-binding FeoCs may function as oxygen-sensitive iron sensors that fine-tune pathogenic ferrous iron acquisition.Item Family planning demand generation in Rwanda: Government efforts at the national and community level impact interpersonal communication and family norms(PLOS One, 2022-04-07) Corey, Julia; Schwandt, Hilary; Boulware, Angel; Herrera, Ana; Linus, Jessica; et alBetween 2005 and 2020, total contraceptive use among married women in Rwanda increased from 17% to 64%. The aim of this study is to better understand how the Rwandan government’s mobilization and demand generation efforts have impacted community norms and interpersonal discourse surrounding family planning. Eight focus group discussions with family planning providers and 32 in-depth interviews with experienced modern contraceptive users were conducted in 2018 in the two Rwandan districts with the highest and the lowest contraceptive prevalence rates. Results suggest that outspoken government support, mass media, and community meetings were valuable sources of information about family planning. Information received through these channels generated interpersonal dialogue about contraceptives through both conversation and observation; however, rumors and misinformation remained a significant barrier to use. A once taboo subject is now normative among married couples. Continuing to address common fears and misinformation through communication channels such as mass media and community meetings may help to further increase contraceptive uptake in Rwanda.Item Gamma-ray emission in radio galaxies under the VLBI scope(EDP Sciences, 2019-06-19) Angioni, R.; Ros, E.; Kadler, M.; Ojha, R.; Müller, C.; Edwards, P. G.; Burd, P. R.; Carpenter, B.; Dutka, M. S.; Gulyaev, S.; Hase, H.; Horiuchi, S.; Krauß, F.; Lovell, J. E. J.; Natusch, T.; Phillips, C.; Plötz, C.; Quick, J. F. H.; Rösch, F.; Schulz, R.; Stevens, J.; Tzioumis, A. K.; Weston, S.; Wilms, J; Zensus, J. A.Aims. In the framework of the multi-wavelength and very long baseline interferometry (VLBI) monitoring program TANAMI (Tracking Active Nuclei with Austral Milliarcsecond Interferometry), we study the evolution of the parsec-scale radio emission in radio galaxies in the southern hemisphere and their relationship to the γ-ray properties of the sources. Our study investigates systematically, for the first time, the relationship between the two energy regimes in radio galaxies. In this first paper, we focus on Fermi-LAT-detected sources. Methods. The TANAMI program monitors a large sample of radio-loud AGN at 8.4 GHz and 22.3 GHz with the Australian long baseline array (LBA) and associated telescopes in Antarctica, Chile, New Zealand and South Africa. We performed a kinematic analysis for five γ-ray detected radio galaxies using multi-epoch 8.4 GHz VLBI images, deriving limits on intrinsic jet parameters such as speed and viewing angle. We analyzed 103 months of Fermi-LAT data in order to study possible connections between the γ-ray properties and the pc-scale jets of Fermi-LAT-detected radio galaxies, both in terms of variability and average properties. We discuss the individual source results and draw preliminary conclusions on sample properties including published VLBI results from the MOJAVE (Monitoring Of Jets in Active galactic nuclei with VLBA Experiments) survey, with a total of fifteen sources. Results. We find that the first γ-ray detection of Pictor A might be associated with the passage of a new VLBI component through the radio core, which appears to be a defining feature of high-energy emitting Fanaroff-Riley type II radio galaxies. We detect subluminal parsec-scale jet motions in the peculiar AGN PKS 0521−36, and we confirm the presence of fast γ-ray variability in the source down to timescales of six hours, which is not accompanied by variations in the VLBI jet. We robustly confirm the presence of significant superluminal motion, up to βapp ∼ 3, in the jet of the TeV radio galaxy PKS 0625−35. Our VLBI results constrain the jet viewing angle to be θ < 53◦ , allowing for the possibility of a closely aligned jet. Finally, by analyzing the first pc-scale multi-epoch images of the prototypical compact symmetric object (CSO) PKS 1718−649, we place an upper limit on the separation speed between the two mini-lobes. This in turn allows us to derive a lower limit on the age of the source. Conclusions. We can draw some preliminary conclusions on the relationship between pc-scale jets and γ-ray emission in radio galaxies, based on Fermi-LAT-detected sources with available multi-epoch VLBI measurements. We find that the VLBI core flux density correlates with the γ-ray flux, as seen in blazars. On the other hand, the γ-ray luminosity does not show any dependence on the core brightness temperature and core dominance, which are two common indicators of jet Doppler boosting. This seems to indicate that γ-ray emission in radio galaxies is not driven by orientation-dependent effects, as in blazars, in accordance with the unified model of jetted AGN.Item GENPass: A Multi-Source Deep Learning Model For Password Guessing(IEEE, 2019-09-11) Xia, Zhiyang; Yi, Ping; Liu, Yunyu; Jiang, Bo; Wang, Wei; Zhu, TingThe password has become today’s dominant method of authentication. While brute-force attack methods such as HashCat and John the Ripper have proven unpractical, the research then switches to password guessing. State-of-the-art approaches such as the Markov Model and probabilistic contextfree grammar (PCFG) are all based on statistical probability. These approaches require a large amount of calculation, which is time-consuming. Neural networks have proven more accurate and practical in password guessing than traditional methods. However, a raw neural network model is not qualified for crosssite attacks because each dataset has its own features. Our work aims to generalize those leaked passwords and improves the performance in cross-site attacks. In this paper, we propose GENPass, a multi-source deep learning model for generating “general” password. GENPass learns from several datasets and ensures the output wordlist can maintain high accuracy for different datasets using adversarial generation. The password generator of GENPass is PCFG+LSTM (PL). We are the first to combine a neural network with PCFG. Compared with Long short-term memory (LSTM), PL increases the matching rate by 16%-30% in cross-site tests when learning from a single dataset. GENPass uses several PL models to learn datasets and generate passwords. The results demonstrate that the matching rate of GENPass is 20% higher than by simply mixing datasets in the cross-site test. Furthermore, we propose GENPass with probability (GENPass-pro), the updated version of GENPass, which can further increase the matching rate of GENPass.Item A Non-Linear Model of an All-Elastomer, in-Plane, Capacitive, Tactile Sensor Under the Application of Normal Forces(MDPI, 2018-10-24) Kalayeh, Kourosh M.; Charalambides, Panos G.In this work, a large deformation, non-linear semi-analytical model for an all-elastomer, capacitive tactile unit-sensor is developed. The model is capable of predicting the response of such sensors over their entire sensing range under the application of normal forces. In doing so the finite flat punch indentation model developed earlier is integrated with a capacitance model to predict the change-in-capacitance as a function of applied normal forces. The empirical change-in-capacitance expression, based on the parallel plate capacitance model, is developed to account for the fringe field and saturation effects. The elastomeric layer used as a substrate in these sensors is modeled as an incompressible, non-linear, hyperelastic material. More specifically, the two term Mooney-Rivlin strain energy function is used as a constitutive response to relate the stresses and strains. The developed model assumes both geometrical as well as material non-linearity. Based on the related experimental work presented elsewhere, the inverse analysis, combining finite element (FE) modeling and non-linear optimization, is used to obtain the Mooney-Rivlin material parameters. Finally, to validate the model developed herein the model predictions are compared to the experimental results obtained elsewhere for four different tactile sensors. Great agreements are found to exist between the two which shows the model capabilities in capturing the response of these sensors. The model and methodologies developed in this work, may also help advancing bio-material studies in the determination of biological tissue properties.Item Quantitative high-throughput screening assays for the discovery and development of SIRPα-CD47 interaction inhibitors(PLOS, 2019-07-05) Miller, Thomas W.; Amason, Joshua D.; Garcin, Elsa D.; Lamy, Laurence; Dranchak, Patricia K.; Macarthur, Ryan; Braisted, John; Rubin, Jeffrey S.; Burgess, Teresa L.; Farrell, Catherine L.; Roberts, David D.; Inglese, JamesCD47 is an immune checkpoint molecule that downregulates key aspects of both the innate and adaptive anti-tumor immune response via its counter receptor SIRPα, and it is expressed at high levels in a wide variety of tumor types. This has led to the development of biologics that inhibit SIRPα engagement including humanized CD47 antibodies and a soluble SIRPα decoy receptor that are currently undergoing clinical trials. Unfortunately, toxicological issues, including anemia related to on-target mechanisms, are barriers to their clinical advancement. Another potential issue with large biologics that bind CD47 is perturbation of CD47 signaling through its high-affinity interaction with the matricellular protein thrombospondin-1 (TSP1). One approach to avoid these shortcomings is to identify and develop small molecule molecular probes and pretherapeutic agents that would (1) selectively target SIRPα or TSP1 interactions with CD47, (2) provide a route to optimize pharmacokinetics, reduce on-target toxicity and maximize tissue penetration, and (3) allow more flexible routes of administration. As the first step toward this goal, we report the development of an automated quantitative high-throughput screening (qHTS) assay platform capable of screening large diverse drug-like chemical libraries to discover novel small molecules that inhibit CD47-SIRPα interaction. Using time-resolved Fo¨rster resonance energy transfer (TR-FRET) and bead-based luminescent oxygen channeling assay formats (AlphaScreen), we developed biochemical assays, optimized their performance, and individually tested them in small-molecule library screening. Based on performance and low false positive rate, the LANCE TR-FRET assay was employed in a ~90,000 compound library qHTS, while the AlphaScreen oxygen channeling assay served as a cross-validation orthogonal assay for follow-up characterization. With this multi-assay strategy, we successfully eliminated compounds that interfered with the assays and identified five compounds that inhibit the CD47- SIRPα interaction; these compounds will be further characterized and later disclosed. Importantly, our results validate the large library qHTS for antagonists of CD47-SIRPα interaction and suggest broad applicability of this approach to screen chemical libraries for other protein-protein interaction modulators.Item Soft and hard X-ray dips in the light curves of γ Cassiopeiae(Oxford University Press, 2019-07-26) Smith, M. A.; Oliveira, R. Lopes deThe available six archival XMM–Newton observations of the anomalous X-ray emitter γ Cas (B0.5 IVe) have been surveyed for the presence of soft X-ray ‘dips’ in X-ray light curves. In addition to discovering such events in the soft band (≤2 keV), we show that sometimes they are accompanied by minor, nearly simultaneous dips in the hard X-ray band. Herein, we investigate how these occurrences can be understood in the ‘magnetic star–disc interaction’ hypothesis proposed in the literature to explain the hard, variable X-ray emission of this Be star. In this scenario, the soft X-ray dips are interpreted as transits by comparatively dense, soft X-ray-absorbing blobs that move across the lines of sight to the surface of the Be star. We find that these blobs have similar properties as the ‘cloudlets’ responsible for migrating subfeatures in UV and optical spectral lines and therefore may be part of a common distribution of co-rotating occulters. The frequencies, amplitudes, and longevities of these dips vary widely. Additionally, the most recent spectra from 2014 July suggest that the ‘warm’ (kT ≈ 0.6–4 keV) plasma sources responsible for some of the soft flux are much more widely spread over the Be star’s surface than the hot plasma sites that dominate the flux at all X-ray energies. We finally call attention to a sudden drop in all X-ray energies of the 2014 light curve of γ Cas and a similar sudden drop in a light curve of the ‘analog’ HD 110432. We speculate that these could be related to appearances of particularly strong soft X-ray dips several hours earlier.Item Spatial Dynamic Functional Connectivity Analysis Identifies Distinctive Biomarkers in Schizophrenia(Frontiers in Neuroscience, 2019-09-24) Bhinge, Suchita; Long, Qunfang; Calhoun, Vince D; Adali, TulayDynamic functional network connectivity (dFNC) analysis is a widely-used to study associations between dynamic functional correlations and cognitive abilities. Traditional methods analyze time-varying association of different spatial networks while assuming that the spatial network itself is stationary. However, there has been very little work focused on voxelwise spatial variability. Exploiting the variability across both the temporal and spatial domains provide a more promising direction to obtain reliable dynamic functional patterns. However, methods for extracting time-varying spatio-temporal patterns from large-scale functional magnetic resonance imaging (fMRI) data present some challenges, such as degradation in performance with respect to increase in size of the data, estimation of the number of dynamic components, and the potential sensitivity of the resulting dFNCs to selection of the networks. In this work, we implement subsequent extraction of exemplars and dynamics using a constrained independent vector analysis, a data-driven method that efficiently estimates spatial and temporal dynamics from large-scale resting-state fMRI data. We explore the benefits of analyzing spatial dFNC (sdFNC) patterns over temporal dFNC (tdFNC) patterns in the context of differentiating healthy controls and patients with schizophrenia. Our results indicate that for resting-state fMRI data, sdFNC patterns were able to better classify patients and controls, and yield more distinguishing features compared with tdFNC patterns. We also estimate structured patterns of connectivity/states using sdFNC patterns, an area that has not been studied so far, and observe that sdFNC was able to successfully capture distinct information from healthy controls and patients with schizophrenia. In addition, sdFNC patterns were also able to identify functional patterns that associate with signs of paranoia and abnormalities in the patients group. We also observe that patients with schizophrenia tend to switch to or stay in a state corresponding to a hyperconnected brain network.Item Systemic coordination and the problem of seasonal harmful algal blooms in Lake Erie(2019) Berardo, Ramiro; Turner, V. Kelly; Rice, StianThe management of natural resources may potentially be improved when governance structures in social-ecological systems enable coordination among multiple actors who may operate on the same or different geographic and/or governmental scales. In this article, we analyze the network of formal coordination ties that link governmental and nongovernmental actors in the Maumee River watershed, which is the largest source of phosphorus loading into Lake Erie, one of the five Laurentian Great Lakes of North America. Since the 1990s, Lake Erie has seen a return of the seasonal harmful algal blooms (HAB) that were common in the 1960s and 1970s, and considerable research suggests that they might be triggered by excessive amounts of phosphorus produced by agriculture. Analyzing an assortment of documents that collectively detail how stakeholders relate to each other on the topic of nutrient management in the watershed, we examine who are the actors that are more likely to fulfill coordination roles, and the scales at which coordination takes place (vertically vs horizontally). Results suggest that coordination has been formalized vertically, with actors who operate at higher governmental levels being more likely to coordinate the activities of actors at lower levels. In addition, we see evidence of horizontal coordination but only in the confines of the individual state jurisdictions that share the watershed. We see this as a potentially important obstacle to solving the HABs problem in Lake Erie, given that the management of interjurisdictional watersheds is likely to be ineffective in the absence of proper coordination across the different jurisdictions that share the watershed.