gebhart/patrepeval huggingface dataset:
Equilibrium Propagation: Bridging the Gap Between Energy-Based Models\n and Backpropagation (2016)

We introduce Equilibrium Propagation, a learning framework for energy-based\nmodels. It involves only one kind of neural computation, performed in both the\nfirst phase (when the prediction is made) and the second phase of training\n(after the target or prediction error is revealed). Although this algorithm\ncomputes the gradient of an objective function just like Backpropagation, it\ndoes not need a special computation or circuit for the second phase, where\nerrors are implicitly propagated. Equilibrium Propagation shares similarities\nwith Contrastive Hebbian Learning and Contrastive Divergence while solving the\ntheoretical issues of both algorithms: our algorithm computes the gradient of a\nwell defined objective function. Because the objective function is defined in\nterms of local perturbations, the second phase of Equilibrium Propagation\ncorresponds to only nudging the prediction (fixed point, or stationary\ndistribution) towards a configuration that reduces prediction error. In the\ncase of a recurrent multi-layer supervised network, the output units are\nslightly nudged towards their target in the second phase, and the perturbation\nintroduced at the output layer propagates backward in the hidden layers. We\nshow that the signal 'back-propagated' during this second phase corresponds to\nthe propagation of error derivatives and encodes the gradient of the objective\nfunction, when the synaptic update corresponds to a standard form of\nspike-timing dependent plasticity. This work makes it more plausible that a\nmechanism similar to Backpropagation could be implemented by brains, since\nleaky integrator neural computation performs both inference and error\nback-propagation in our model. The only local difference between the two phases\nis whether synaptic changes are allowed or not.\n
The integration of optical thin film filters by hydrofluoric acid bonding (2006)

A hydrofluoric acid (HF) bonding method has been applied for the thin film filters integration. The quality of bonding was examined by the evaluation of bonding strength and the observation of bonding interface. The bonding strength depends on the applied pressure and temperature during bonding. The maximum bonding strength was more than 10 MPa. High quality bonding interface was observed by scanning electron microscope and transmission electron microscope. A color filer array of red, green and blue (RGB) was designed to separate the white light. The filters were integrated into a glass body successfully by HF bonding. Its transmittance spectra were unchanged after heating at 450<sup>o</sup>C for 20 hours. In addition, integration of filters was carried out to fabricate an optical demutiplexer for coarse wavelength division multiplexing system. It was confirmed that the integrated filter array acted as a demutiplexer.
In Vitro Antimicrobial Efficacy of Silver Lens Cases Used With a Multipurpose Disinfecting Solution (2019)

Silver-copolymerized barrel contact lens cases show promising in vitro antibacterial activity against bacterial types commonly implicated in contact lens-related corneal infections. This intervention may limit storage case contamination during use and reduce the frequency of contact lens-related microbial disease.
Inducible erythromycin resistance in staphlyococci is encoded by a member of the ATP‐binding transport super‐gene family (1990)

A Staphylococcus epidermidis plasmid conferring inducible resistance to 14-membered ring macrolides and type B streptogramins has been analysed and the DNA sequence of the gene responsible for resistance determined. A single open reading frame of 1.464 kbp, preceded by a complex control region containing a promoter and two ribosomal binding sites, was identified. The deduced sequence of the 488-amino-acid protein (MsrA) revealed the presence of two ATP-binding motifs homologous to those of a family of transport-related proteins from Gram-negative bacteria and eukaryotic cells, including the P-glycoprotein responsible for multidrug resistance. In MsrA, but not these other proteins, the two potential ATP-binding domains are separated by a Q-linker of exceptional length. Q-linkers comprise a class of flexible interdomain fusion junctions that are typically rich in glutamine and other hydrophilic amino acids and have a characteristic spacing of hydrophobic amino acids, as found in the MsrA sequence. Unlike the other transport-related proteins, which act in concert with one or more hydrophobic membrane proteins, MsrA appears to function independently when cloned in a heterologous host (Staphylococcus aureus RN4220). MsrA might, therefore, interact with and confer antibiotic specificity upon other transmembrane efflux complexes of staphylococcal cells. The active efflux of [14C]-erythromycin from cells of S. aureus RN4220 containing msrA has been demonstrated.
Throughput Maximization of Hybrid Access in Multi-Class Cognitive Radio Networks With Energy Harvesting (2021)

In this paper, the hybrid interweave/underlay channel access mode is studied for an energy harvesting (EH) cognitive radio network with multi-class secondary users (SUs). The hybrid channel access mode combines the benefits of interweave transmission (opportunistic access with high throughput) and that of the underlay transmission (any time transmission with controlled power). EH upgrades the SUs' devices to be self sustainable. Additionally, classifying the SUs helps to meet their different quality of service (QoS) requirements. The system is modelled as a mixed observable Markov decision process (MOMDP) to handle the uncertainty in the primary user (PU) activity and consider future rewards. The MOMDP model is solved to maximize the SUs' throughput using two algorithms, namely, the point-based value iteration and the heuristic search value iteration (HSVI). Moreover, skipping the schedule of some SUs is proved to increase the channel utilization. The HSVI is proved to be efficient and reduces the time complexity significantly. Compared to related work in literature, the proposed model is proved to be superior in terms of throughput, tunable to meet the different QoS requirements of SU classes, and can accommodate any number of SU classes. Finally, the effect of some system parameters on the proposed system performance is studied and some insights are derived about the structure of the optimal policy and the system parameters values.
Far field of gratings with rough strips (2008)

In this work, we analyze the far-field pattern produced by a grating made of strips with two different random roughness levels. The efficiency and shape of the diffraction orders is obtained, which are shown to depend on the statistical properties of roughness. We assume for the calculations that the grating can be used in a mobile mechanical system. A preliminary experimental approach which partially corroborates the theoretical results is also performed.
Improved Bst DNA Polymerase Variants Derived <i>via</i> a Machine Learning Approach (2021)

The DNA polymerase I from <i>Geobacillus stearothermophilus</i> (also known as <i>Bst</i> DNAP) is widely used in isothermal amplification reactions, where its strand displacement ability is prized. More robust versions of this enzyme should be enabled for diagnostic applications, especially for carrying out higher temperature reactions that might proceed more quickly. To this end, we appended a short fusion domain from the actin-binding protein villin that improved both stability and purification of the enzyme. In parallel, we have developed a machine learning algorithm that assesses the relative fit of individual amino acids to their chemical microenvironments at any position in a protein and applied this algorithm to predict sequence substitutions in <i>Bst</i> DNAP. The top predicted variants had greatly improved thermotolerance (heating prior to assay), and upon combination, the mutations showed additive thermostability, with denaturation temperatures up to 2.5 °C higher than the parental enzyme. The increased thermostability of the enzyme allowed faster loop-mediated isothermal amplification assays to be carried out at 73 °C, where both <i>Bst</i> DNAP and its improved commercial counterpart Bst 2.0 are inactivated. Overall, this is one of the first examples of the application of machine learning approaches to the thermostabilization of an enzyme.
Cool, or simple and cheap? Why not both? (2012)

A graphical abstract is available for this content
Measurement and modeling of high-frequency acoustic channels for a moving source in shallow water. (2009)

Acoustic systems used in underwater communications are sensitive to both scattering and Doppler shifts. In order to assess these sensitivities, an experiment (KAM08) was conducted during summer 2008 under variable environmental conditions. During the experiment, high-frequency (&amp;lt;10 kHz) acoustic signals were emitted from a towed source and measured by multiple hydrophone arrays moored in 100-m depth. Environmental parameters including wind, surface waves, and water-column temperature were collected concurrently with acoustic transmissions, which took place under variable sea states. Linear frequency modulated (LFM) signals and coherent m-sequence transmissions in the frequency band of 13–19 kHz were used to determine detailed channel characteristics for multiple source-receiver geometries. Both parabolic equation and ray-based models were run with moving source and simulated sea surface configurations in order to accurately reproduce experimental conditions. [Work supported by ONR 321OA].
Quantum Mechanical and Experimental Validation that Cyclobis(paraquat‐<i>p</i>‐phenylene) Forms a 1:1 Inclusion Complex with Tetrathiafulvalene (2016)

The promiscuous encapsulation of π-electron-rich guests by the π-electron-deficient host, cyclobis(paraquat-p-phenylene) (CBPQT(4+)), involves the formation of 1:1 inclusion complexes. One of the most intensely investigated charge-transfer (CT) bands, assumed to result from inclusion of a guest molecule inside the cavity of CBPQT(4+), is an emerald-green band associated with the complexation of tetrathiafulvalene (TTF) and its derivatives. This interpretation was called into question recently in this journal based on theoretical gas-phase calculations that reinterpreted this CT band in terms of an intermolecular side-on interaction of TTF with one of the bipyridinium (BIPY(2+)) units of CBPQT(4+), rather than the encapsulation of TTF inside the cavity of CBPQT(4+). We carried out DFT calculations, including solvation, that reveal conclusively that the CT band emerging upon mixing TTF with CBPQT(4+) arises from the formation of a 1:1 inclusion complex. In support of this conclusion, we have performed additional experiments on a [2]rotaxane in which a TTF unit, located in the middle of its short dumbbell, is prevented sterically from interacting with either one of the two BIPY(2+) units of a CBPQT(4+) ring residing on a separate [2]rotaxane in a side-on fashion. This [2]rotaxane has similar UV/Vis and (1)H NMR spectroscopic properties with those of 1:1 inclusion complexes of TTF and its derivatives with CBPQT(4+). The [2]rotaxane exists as an equimolar mixture of cis- and trans-isomers associated with the disubstituted TTF unit in its dumbbell component. Solid-state structures were obtained for both isomers, validating the conclusion that the TTF unit, which gives rise to the CT band, resides inside CBPQT(4+).
Photoionized plasmas in laboratory: a connection to astrophysics and planetary sciences (2015)

In this work photoionized plasmas were created by irradiation of atomic and molecular gases by soft X-ray and extreme ultraviolet intense radiation pulses. Two different laser-produced plasma sources, employing a low energy Nd:YAG laser system (NL 129) and a high energy iodine laser system (PALS), were used for creation of photoionized plasmas. In both cases the SXR/EUV beam irradiated the gas stream, injected into a vacuum chamber synchronously with the radiation pulse. Radiation spectra, measured for photoionized plasmas produced in Ne and Ar gases, are dominated by L-shell emission lines except the Ne plasma produced using the high energy system where K-shell emission dominates. Additionally electron density measurements were performed by laser interferometry employing a femtosecond laser system synchronized with the irradiating system. Maximum electron density for Ne plasma, induced using the high energy system, reached 2·10<sup>18</sup>cm<sup>-3</sup>. In case of employing the low energy system a detection limit was too high for interferometric measurements, thus only an upper estimation for electron density could be made.
Expression of human NDRG2 by myeloid dendritic cells inhibits down-regulation of activated leukocyte cell adhesion molecule (ALCAM) and contributes to maintenance of T cell stimulatory activity (2007)

We reported previously that N-myc downstream-regulated gene 2 (NDRG2), a member of a new family of differentiation-related genes, is expressed specifically in dendritic cells (DC) differentiated from monocytes, CD34(+) progenitor cells, and the myelomonocytic leukemic cell line. In this study, we demonstrate that NDRG2 protein expression is detected, not only in in vitro-differentiated DC but also in primary DC from lymph nodes, thymus, and skin when anti-NDRG2 antibodies are used. As predicted from previous studies investigating the mRNA expression pattern of several types of cell lines, progenitor cells, and DC, NDRG2 protein was expressed strongly in DC. Its expression was detected at significant levels after differentiation from progenitor cells. RNA interference of NDRG2 demonstrated that activated leukocyte cell adhesion molecule (ALCAM) expression is down-regulated specifically in DC differentiated from NDRG2 small interfering RNA (siRNA)-transfected monocytes. This was consistent with our observation that U937 cells transfected with NDRG2 became resistant to the GM-CSF/IL-4-induced ALCAM reduction. Furthermore, DC, which had differentiated from NDRG2 siRNA-transfected monocytes, showed a reduced ability to induce T cell proliferation. Taken together, our results indicate that NDRG2 is able to preserve ALCAM expression during DC differentiation from monocytes under cytokine culture conditions and that its expression helps DC maintain costimulatory signals necessary for T cell stimulation.
Influence du nombre de cellules élémentaires sur le comportement des Surfaces Haute Impédance (2011)

National audience
Measurement-induced entanglement and teleportation on a noisy quantum processor (2023)

Measurement has a special role in quantum theory: by collapsing the wavefunction it can enable phenomena such as teleportation and thereby alter the "arrow of time" that constrains unitary evolution. When integrated in many-body dynamics, measurements can lead to emergent patterns of quantum information in space-time that go beyond established paradigms for characterizing phases, either in or out of equilibrium. On present-day NISQ processors, the experimental realization of this physics is challenging due to noise, hardware limitations, and the stochastic nature of quantum measurement. Here we address each of these experimental challenges and investigate measurement-induced quantum information phases on up to 70 superconducting qubits. By leveraging the interchangeability of space and time, we use a duality mapping, to avoid mid-circuit measurement and access different manifestations of the underlying phases -- from entanglement scaling to measurement-induced teleportation -- in a unified way. We obtain finite-size signatures of a phase transition with a decoding protocol that correlates the experimental measurement record with classical simulation data. The phases display sharply different sensitivity to noise, which we exploit to turn an inherent hardware limitation into a useful diagnostic. Our work demonstrates an approach to realize measurement-induced physics at scales that are at the limits of current NISQ processors.
EXPERIMENTAL STUDY OF IMPULSIVE SYNCHRONIZATION OF CHAOTIC AND HYPERCHAOTIC CIRCUITS (1999)

In this paper, experimental results on impulsive synchronization of two kinds of chaotic circuits; namely, Chua's oscillator and a hyperchaotic circuit, are presented. To impulsively synchronize two Chua's oscillators, synchronization impulses sampled from one state variable of the driving circuit are transmitted to the driven circuit. To impulsively synchronize two hyperchaotic circuits, synchronizing impulses sampled from two signals of the driving circuit are sent to the driven circuit. Our experimental results show that the accuracy of impulsive synchronization depends on both the period and the width of the impulse. The ratio between the impulse width and impulse period for "almost-identical" synchronization increases as the impulse period increases. The robustness of impulsive synchronization to additive noise is also experimentally studied. For sufficiently short impulse periods, no significant differences are observed between impulsive and continuous synchronizations. The performance of chaotic spread spectrum communication systems based on impulsive synchronization is also studied experimentally.
Evaluation of Sucrose Laurate as an Intestinal Permeation Enhancer for Macromolecules: Ex Vivo and In Vivo Studies (2019)

Oral delivery of macromolecules requires permeation enhancers (PEs) adaptable to formulation. Sucrose laurate (SL) (D1216), a food grade surfactant, was assessed in Caco-2 monolayers, isolated rat intestinal tissue mucosae, and rat intestinal instillations. Accordingly, 1 mM SL increased the apparent permeability coefficient (<i>P</i><sub>app</sub>) of [<sup>14</sup>C]-mannitol and reduced transepithelial electrical resistance (TEER) across monolayers. It altered expression of the tight junction protein, ZO-1, increased plasma membrane potential, and decreased mitochondrial membrane potential in Caco-2 cells. The concentrations that increased flux were of the same order as those that induced cytotoxicity. In rat colonic tissue mucosae, the same patterns emerged in respect to the concentration-dependent increases in paracellular marker fluxes and TEER reductions with 5 mM being the key concentration. While the histology revealed some perturbation, ion transport capacity was retained. In rat jejunal and colonic instillations, 50 and 100 mM SL co-administered with insulin induced blood glucose reductions and achieved relative bioavailability values of 2.4% and 8.9%, respectively, on a par with the gold standard PE, sodium caprate (C<sub>10</sub>). The histology of the intestinal loops revealed little damage. In conclusion, SL is a candidate PE with high potential for emulsion-based systems. The primary action is plasma membrane perturbation, leading to tight junction openings and a predominant paracellular flux.
A Distributed Delay Method for Event-Triggered Control of T–S Fuzzy Networked Systems With Transmission Delay (2019)

This paper presents the event-triggered control for Takagi-Sugeno (T-S) fuzzy networked systems with transmission delay. An integral-based model is proposed for designing a new event-triggered scheme, which relies on the mean of the system state and the last triggered state. To handle the asynchronous premises of the fuzzy system and fuzzy controller, a novel triggering condition is added into the event-triggered mechanism. Then, the closed-loop T-S fuzzy event-triggered control system is established as a distributed delay system. With the help of the Legendre polynomials and their properties, the co-design conditions of triggering parameters and controller gains are given in linear matrix inequalities to ensure the asymptotic stability of the resulting closed-loop system. Finally, an experiment via a practical wireless network is implemented to illustrate the effectiveness of the proposed approach.
Spontaneous Dissection of the Vertebral Artery (1989)

Spontaneous (nontraumatic) dissection of the carotid and vertebral arteries, once thought to be rare, is being recognized and reported more frequently. We report one case of spontaneous dissection of the vertebral artery initially diagnosed by magnetic resonance imaging and subsequently confirmed by angiography.
Sex-specific transcriptomic and epitranscriptomic signatures of PTSD-like fear acquisition (2021)

Abstract Our understanding of the molecular pathology of posttraumatic stress disorder (PTSD) is rapidly evolving and is being driven by advances in sequencing techniques. Conventional short-read RNA sequencing (RNA-seq) is a central tool in transcriptomics research that enables unbiased gene expression profiling. With the recent emergence of Oxford Nanopore direct RNA-seq (dRNA-seq), it is now also possible to interrogate diverse RNA modifications, collectively known as the ‘epitranscriptome’. Here, we present our analyses of the male and female mouse amygdala transcriptome and epitranscriptome, obtained using parallel Illumina RNA-seq and Oxford Nanopore dRNA-seq, associated with the acquisition of PTSD-like fear induced by Pavlovian cued-fear conditioning. We report significant sex-specific differences in the amygdala transcriptional response during fear acquisition, and a range of shared and dimorphic epitranscriptomic signatures. Differential RNA modifications are enriched among mRNA transcripts associated with neurotransmitter regulation and mitochondrial function, many of which have been previously implicated in PTSD. Very few differentially modified transcripts are also differentially expressed, suggesting an influential, expression-independent role for epitranscriptional regulation in PTSD-like fear-acquisition. Overall, our application of conventional and newly developed methods provides a platform for future work that will lead to new insights into and therapeutics for PTSD.
AM1 calculations of reaction field effects on the tautomeric equilibria of nucleic acid pyrimidine and purine bases and their 1-methyl analogs (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAM1 calculations of reaction field effects on the tautomeric equilibria of nucleic acid pyrimidine and purine bases and their 1-methyl analogsAlan R. Katritzky and Mati KarelsonCite this: J. Am. Chem. Soc. 1991, 113, 5, 1561–1566Publication Date (Print):February 1, 1991Publication History Published online1 May 2002Published inissue 1 February 1991https://pubs.acs.org/doi/10.1021/ja00005a017https://doi.org/10.1021/ja00005a017research-articleACS PublicationsRequest reuse permissionsArticle Views199Altmetric-Citations135LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Catheter-based plasmid-mediated transfer of genes into ischemic myocardium using the pCOR plasmid (2000)

With a catheter-based approach, the pCOR plasmid was successfully used to deliver genes into designated myocardial regions, and provides sustained expression of protein for at least 7 days, of roughly similar magnitudes in ischemic and nonischemic myocardium.