gebhart/patrepeval huggingface dataset:
Enhancement of the lateral resolution of Raman microscopy by use of structured illumination (2015)

Recent developments in optical microscopy especially fluorescence microscopy have pushed the limits of spatial resolution below the diffraction limit, to as low as several nanometers. Most of these super-resolution techniques, however, cannot be adapted to Raman microscopy because their working principle is based on manipulating the fluorescence emission properties of the sample. On the other hand, structured illumination microscopy (SIM) utilizes the Moire effect (interference of the structured light pattern with the sample structure) to double the spatial resolution [1] and therefore does not impose particular optical properties on the sample, making it a feasible technique for Raman microscopy.
Structure‐Based Discovery and Experimental Verification of Novel AI‐2 Quorum Sensing Inhibitors against <i>Vibrio harveyi</i> (2008)

Quorum sensing has been implicated in the control of pathologically relevant bacterial behavior such as secretion of virulence factors, biofilm formation, sporulation, and swarming motility. The AI-2 quorum sensing pathway is found in both gram-positive and gram-negative bacteria. Therefore, antagonizing AI-2 quorum sensing is a possible approach to modifying bacterial behaviour. However, efforts in developing inhibitors of AI-2-mediated quorum sensing are especially lacking. High-throughput virtual screening using the V. harveyi LuxP crystal structure identified two compounds that were found to antagonize AI-2-mediated quorum sensing in V. harveyi without cytotoxicity. The sulfone functionality of these inhibitors was identified as critical to their ability to mimic the natural ligand in their interactions with Arg 215 and Arg 310 of the active site.
Dynamic synapse: A new concept of neural representation and computation (1996)

Presynaptic mechanisms influencing the probability of neurotransmitter release from an axon terminal, such as facilitation, augmentation, and presynaptic feedback inhibition, are fundamental features of biological neurons and are cardinal physiological properties of synaptic connections in the hippocampus. The consequence of these presynaptic mechanisms is that the probability of release becomes a function of the temporal pattern of action potential occurrence, and hence, the strength of a given synapse varies upon the arrival of each action potential invading the terminal region. From the perspective of neural information processing, the capability of dynamically tuning the synaptic strength as a function of the level of neuronal activation gives rise to a significant representational and processing power of temporal spike patterns at the synaptic level. Furthermore, there is an exponential growth in such computational power when the specific dynamics of presynaptic mechanisms varies quantitatively across axon terminals of a single neuron, a recently established characteristic of hippocampal synapses. During learning, alterations in the presynaptic mechanisms lead to different pattern transformation functions, whereas changes in the postsynaptic mechanisms determine how the synaptic signals are to be combined. We demonstrate the computational capability of dynamic synapses by performing speech recognition from unprocessed, noisy raw waveforms of words spoken by multiple speakers with a simple neural network consisting of a small number of neurons connected with synapses incorporating dynamically determined probability of release. The dynamics included in the model are consistent with available experimental data on hippocampal neurons in that parameter values were chosen so as to be consistent with time constants of facilitative and inhibitory processes governing the dynamics of hippocampal synaptic transmission studied using nonlinear systems analytic procedures. © 1997 Wiley-Liss, Inc.
Enzyme-Responsive Amphiphilic PEG-Dendron Hybrids and Their Assembly into Smart Micellar Nanocarriers (2014)

Enzyme-responsive micelles have great potential as drug delivery platforms due to the high selectivity of the activating enzymes. Here we report a highly modular design for the efficient and simple synthesis of amphiphilic block copolymers based on a linear hydrophilic polyethyleneglycol (PEG) and an enzyme-responsive hydrophobic dendron. These amphiphilic hybrids self-assemble in water into micellar nanocontainers that can disassemble and release encapsulated molecular cargo upon enzymatic activation. The utilization of monodisperse dendrons as the stimuli-responsive block enabled a detailed kinetic study of the molecular mechanism of the enzymatically triggered disassembly. The modularity of these PEG-dendron hybrids allows control over the disassembly rate of the formed micelles by simply tuning the PEG length. Such smart amphiphilic hybrids could potentially be applied for the fabrication of nanocarriers with adjustable release rates for delivery applications.
Particle trajectories in a drifting resonance field separation device (1998)

Drifting resonance field (DRF), a new method for the separation of particle/fluid suspensions is introduced. Unlike particle filters using ultrasound-induced coagulation, the DRF method only utilizes the primary acoustic radiation force to achieve the separation effect. This is done by cyclically switching the driving frequency of the DRF resonator between consecutive resonances, causing a directed motion of the particles and thus concentrating the particles in a certain region of the separation volume. Trajectories of polystyrene spheres (approximately 12 microns in diameter) suspended in distilled water have been measured in a prototype DRF resonator, varying the number of the utilized resonance frequencies and the acoustic power input. The measured particle trajectories are compared to computer simulations based on the same process parameters as used in the experimental setup, showing a high correspondence between experimental and simulated data. Both experiments and simulations prove the high potential of the DRF method for separation technology. A promising field of application is the up-scaling of acoustic cell retention systems recently introduced in animal cell culture, potentially yielding higher flow-through rates. The presented results are a valuable basis for design and process parameter optimization of future DRF separation devices.
Realtime query completion via deep language models (2018)

Search engine users nowadays heavily depend on query completion and correction to shape their queries. Typically, the completion is done by database lookup which does not understand the context and cannot generalize to prefixes not in the database. In the paper, we propose to use unsupervised deep language models to complete and correct the queries given an arbitrary prefix. We show how to address two main challenges that renders this method practical for large-scale deployment: 1) we propose a method for integrating error correction into the language model completion via a edit-distance potential and a variant of beam search that can exploit these potential functions; and 2) we show how to efficiently perform CPU-based computation to complete the queries, with error correction, in real time (generating top 10 completions within 16 ms). Experiments show that the method substantially increases hit rate over standard approaches, and is capable of handling tail queries.
Optical Soliton Generator Based on a Single Mach-Zehnder Modulator (1994)

The use of Erbium-doped fiber amplifiers in optical communication systems has eliminated loss as a limitation, thereby, allowing transmission over trans-oceanic distances without regeneration. The capacity of these long systems are now limited by fiber dispersion, fiber non-linearities and amplifier noise. Systems in which the information propagates in the form of solitons balance the effects of fiber dispersion and non-linearity to ameliorate these limitations. However, these soliton systems require a source of nearly transform-limited sech2 optical pulses to form solitons in the transmission fiber. Here we report on an optical pulse source that should prove ideal as a practical optical soliton generator.
Piezoelectric lead zirconate titanate coatings on metallic wires (1989)

Acoustic measurements of thin piezoelectric lead zirconate titanate (PZT) films coated on metallic wires are presented. These experiments have demonstrated that PZT coatings fabricated by a sol-gel process can be not only coated on curved metal substrates for high-frequency focused ultrasonic transducer applications, but also on metallic wires with a long coating length for low-frequency acoustic vibrators.
Protection of Relational Databases by Means of Watermarking: Recent Advances and Challenges (2017)

Databases represent today great economical and strategic concerns for both enterprises and public institutions. In that context, where data leaks, robbery as well as innocent or even hostile data degradation represent a real danger, and watermarking appears as an interesting tool. Watermarking is based on the imperceptible embedding of a message or watermark into a database in order, for instance, to determine its origin as well as to detect if it has been modified. A major advantage of watermarking in relation to other digital content protection mechanisms is that it leaves access to the data while keeping them protected by means of a watermark, independent of the data format storage. Nevertheless, it is necessary to ensure that the introduced distortion does not perturb the exploitation of the database. In this chapter, we give a general overview of the latest database watermarking methods, focusing on those dealing with distortion control. In particular, we present a recent technique based on an ontological modeling of the database semantics that represent the relationships in between attributes—relationships that should be preserved in order to avoid the appearance of incoherent and unlikely records.
Practical Locally Private Heavy Hitters (2017)

We present new practical local differentially private heavy hitters algorithms achieving optimal or near-optimal worst-case error and running time -- TreeHist and Bitstogram. In both algorithms, server running time is $\tilde O(n)$ and user running time is $\tilde O(1)$, hence improving on the prior state-of-the-art result of Bassily and Smith [STOC 2015] requiring $O(n^{5/2})$ server time and $O(n^{3/2})$ user time. With a typically large number of participants in local algorithms ($n$ in the millions), this reduction in time complexity, in particular at the user side, is crucial for making locally private heavy hitters algorithms usable in practice. We implemented Algorithm TreeHist to verify our theoretical analysis and compared its performance with the performance of Google's RAPPOR code.
Sparsity-Enforced Slice-Selective MRI RF Excitation Pulse Design (2008)

We introduce a novel algorithm for the design of fast slice-selective spatially-tailored magnetic resonance imaging (MRI) excitation pulses. This method, based on sparse approximation theory, uses a second-order cone optimization to place and modulate a small number of slice-selective sinc-like radio-frequency (RF) pulse segments ("spokes") in excitation k-space, enforcing sparsity on the number of spokes allowed while simultaneously encouraging those that remain to be placed and modulated in a way that best forms a user-defined in-plane target magnetization. Pulses are designed to mitigate B(1) inhomogeneity in a water phantom at 7 T and to produce highly-structured excitations in an oil phantom on an eight-channel parallel excitation system at 3 T. In each experiment, pulses generated by the sparsity-enforced method outperform those created via conventional Fourier-based techniques, e.g., when attempting to produce a uniform magnetization in the presence of severe B(1) inhomogeneity, a 5.7-ms 15-spoke pulse generated by the sparsity-enforced method produces an excitation with 1.28 times lower root mean square error than conventionally-designed 15-spoke pulses. To achieve this same level of uniformity, the conventional methods need to use 29-spoke pulses that are 7.8 ms long.
Superconducting and structural properties of in-plane aligned <i>a</i>-axis oriented YBa2Cu3O7−<i>x</i> thin films (1995)

We report the superconducting and structural properties of a-axis oriented YBa2Cu3O7−x (YBCO) films as a function of deposition temperature of PrBa2Cu3O7−x (PBCO) template layers. X-ray diffraction (XRD) analysis revealed the orientation relationship in which the b axis of the PBCO template layers and the a axis of the YBCO films were normal to the LaSrGaO4 (100) substrate surface. In-plane aligned a-axis oriented YBCO films having a zero resistance temperature of 88 K and an anisotropy ratio of resistivity of 11.5 at 275 K were obtained on PBCO template layers deposited at 630 °C among the deposition temperatures ranging from 600 to 650 °C at intervals of 10 °C. The degree of in-plane alignment of the a-axis oriented YBCO films which was estimated by the ratio of relative intensity at 90° and 180° in the XRD φ scan of the (102) YBCO peak was 0.5, 0.045, and 0.053 for the films on PBCO templates deposited at 620, 630, and 640 °C, respectively. In conclusion, the deposition temperature of PBCO template layers is critical to fabricate the in-plane aligned a-axis oriented YBCO films on LaSrGaO4 (100) substrates.
A Noninvasive Thin Film Sensor for Monitoring Oxygen Tension during in Vitro Cell Culture (2009)

Oxygen tension in mammalian cell culture can profoundly affect cellular differentiation, viability, and proliferation. However, precise measurement of dissolved oxygen in real time remains difficult. We report a new noninvasive sensor that can accurately measure oxygen concentration during cell culture while being compatible with live-cell imaging techniques such as fluorescence and phase contrast microscopy. The sensor is prepared by integrating the porphyrin dye, Pt(II) meso-tetrakis(pentafluorophenyl)porphine (PtTFPP) into polydimethylsiloxane (PDMS) thin films. Response of the sensor in the presence of oxygen can be characterized by the linear Stern-Volmer relationship with high sensitivity (K(SV) = 584 +/- 71 atm(-1)). A multilayer sensor design, created by sandwiching the PtTFPP-PDMS with a layer of Teflon AF followed by a second PDMS layer, effectively mitigates against dye cytotoxicity while providing a substrate for cell attachment. Using this sensor, changes in oxygen tension could be monitored in real-time as attached cells proliferated. The oxygen tension was found to decrease due to oxygen consumption by the cells, and the data could be analyzed using Fick's law to obtain the per-cell oxygen consumption rate. This sensor is likely to enable new studies on the effects of dissolved oxygen on cellular behavior.
High energy resolution with transparent ceramic garnet scintillators (2014)

Breakthrough energy resolution, R(662keV) < 4%, has been achieved with an oxide scintillator, Cerium-doped Gadolinium Yttrium Gallium Aluminum Garnet, or GYGAG(Ce). Transparent ceramic GYGAG(Ce), has a peak emission wavelength of 550 nm that is better matched to Silicon photodetectors than to standard PMTs. We are therefore developing a spectrometer based on pixelated GYGAG(Ce) on a Silicon photodiode array that can provide R(662 keV) = 3.6%. In comparison, with large 1-2 in<sup>3</sup> size GYGAG(Ce) ceramics we obtain R(662 keV) = 4.6% with PMT readout. We find that ceramic GYGAG(Ce) of a given stoichiometric chemical composition can exhibit very different scintillation properties, depending on sintering conditions and post-anneal treatments. Among the characteristics of transparent ceramic garnet scintillators that can be controlled by fabrication conditions are: scintillation decay components and their amplitudes, intensity and duration of afterglow, thermoluminescence glow curve peak positions and amplitudes, integrated light yield, light yield non-proportionality - as measured in the Scintillator Light Yield Non-Proportionality Characterization Instrument (SLYNCI), and energy resolution for gamma spectroscopy. Garnet samples exhibiting a significant fraction of Cerium dopant in the tetravalent valence also exhibit: faster overall scintillation decay, very low afterglow, high light yield, but poor light yield proportionality and degraded energy resolution.
Spatially-resolved electroluminescence of operating organic light-emitting diodes using conductive atomic force microscopy (2004)

A conductive atomic force microscopy (cAFM) technique has been developed that concurrently monitors topography, charge transport, and electroluminescence. This cAFM approach is particularly well suited for probing the electroluminescent response characteristics of operating organic light-emitting diodes (OLEDs) over short length scales. In a typical experiment, charge is injected into individual OLED structures with the cAFM tip, and the resulting electroluminescence and current are measured with collecting optics and a variable gain photomultiplier tube. As a proof of principle, the real-time spatial and temporal current–voltage and electroluminescence–voltage properties of 8μm×8μm OLED pixels are simultaneously imaged.
Context Aware Service Policy Orchestration (2007)

While service oriented computing is gaining popularity and design methodology for functional features is becoming mature, design of non-functional features and governance capabilities is increasingly important. WS-policy has been touted as a standard way to specify service policy for these features and map service policy to upper layers of SOA policy model for SOA governance. This paper introduces a novel model-driven method to orchestrate service policy within system context in design time. By applying top-down SOA design methodology, firstly the logical service policy model is created to describe relation among service policy in logical level, and then it is transformed to physical service policy model with more factors of real system topology considered. Finally, service policy deployment model is generated to describe the relation among policy related artifacts and policy repositories, and guide and automate the deployment of policies in runtime environment as well. Leveraging system topology and behavior information, service policies are orchestrated vertically and horizontally according to service policy dependency, business policy, service level agreement (SLA), and domain specific constraints. Meta-policy based service policy conflict detection and resolution is highlighted. We demonstrate how this approach significantly enhances the capability to ensure the correctness and consistency of service policy within service oriented computing environment.
New Method for Contact Patterning of High-Efficiency Solar Cells using a Mechanical Scriber (2002)

A new method for patterning the rear contacts on the passivation layers of solar cells using a mechanical scriber has been developed and successfully adapted to fabricate high-efficiency passivated emitter and rear cell (PERC). Three types of rear contact patterns, dot patterns by photolithography, solid line and dashed line patterns using a mechanical scriber have been processed in order to optimize the rear contact structure. An efficiency of 19.42% has been achieved on the mechanically scribed (MS)-PERC solar cell on 0.5 Ωcm, p-type floating-zone silicon (FZ-Si) wafer and is comparable to that of conventional PERC solar cells fabricated by photolithography.
Isolation of Campylobacter jejuni from retail mushrooms (1986)

Campylobacter jejuni was isolated from 3 (1.5%) of 200 retail, polyvinyl chloride film-wrapped, fresh mushrooms. These results indicate that fresh mushrooms may indeed be a source of C. jejuni and support previously reported epidemiological data (Seattle-King County Department of Public Health, Surveillance of the Flow of Salmonella and Campylobacter in a Community, 1984) which revealed an an elevated relative risk of developing campylobacter enteritis in individuals who consume mushrooms.
Peripheral Angiography Digital Image Acquisition Using Rapid Continuous Sweeps of a Moving Gantry (1989)

We are investigating the technical feasibility of a novel acquisition scheme for peripheral angiography that consists of taking images from a gantry that continuously sweeps back-and-forth while the contrast is flowing. The clinical advantage of such a multiple-pass system is that images at each position are spread over a longer time interval, increasing the chance of imaging contrast filled arteries and thus decreasing the need for retakes. Image acquisition during rapid sweeping is technically feasible. The duration of x-ray pulses is short enough to reduce the extent of motion blurring to less than one pixel, using mA and kV parameters available on our angiography system. Contrast and mask image pair superpositioning is excellent, permitting DSA processing.
Ultrasonic echograph for measuring high velocities of blood flows (1995)

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Inhibitors of cellular signalling are cytotoxic or block the budded-to-hyphal transition in the pathogenic yeast Candida albicans (2009)

The pathogenic yeast Candida albicans can grow in multiple morphological states including budded, pseudohyphal and true hyphal forms. The ability to interconvert between budded and hyphal forms, herein termed the budded-to-hyphal transition (BHT), is important for C. albicans virulence, and is regulated by multiple environmental and cellular signals. To identify small-molecule inhibitors of known cellular processes that can also block the BHT, a microplate-based morphological assay was used to screen the BIOMOL-Institute of Chemistry and Cell Biology (ICCB) Known Bioactives collection from the ICCB-Longwood Screening Facility (Harvard Medical School, Boston, MA, USA). Of 480 molecules tested, 53 were cytotoxic to C. albicans and 16 were able to block the BHT without inhibiting budded growth. These 16 BHT inhibitors affected protein kinases, protein phosphatases, Ras signalling pathways, G protein-coupled receptors, calcium homeostasis, nitric oxide and guanylate cyclase signalling, and apoptosis in mammalian cells. Several of these molecules were also able to inhibit filamentous growth in other Candida species, as well as the pathogenic filamentous fungus Aspergillus fumigatus, suggesting a broad fungal host range for these inhibitory molecules. Results from secondary assays, including hyphal-specific transcription and septin localization analysis, were consistent with the inhibitors affecting known BHT signalling pathways in C. albicans. Therefore, these molecules will not only be invaluable in deciphering the signalling pathways regulating the BHT, but also may serve as starting points for potential new antifungal therapeutics.
Precise bit error probability analysis of DCT OFDM in the presence of carrier frequency offset on AWGN channels (2005)

A precise method for calculating the bit error probability of a discrete cosine transform (DCT)-based orthogonal frequency-division multiplexing (OFDM) system on AWGN channels in the presence of frequency offset is derived. These accurate results are used to examine and compare the bit error probability performances of a DCT-OFDM system and the conventional discrete Fourier transform (DFT)-based OFDM system. Several signaling formats, such as binary phase shift keying (BPSK), quaternary phase shift keying (QPSK), and 16-ary quadrature amplitude modulation (16-QAM) are considered. Analysis and simulation results show that the DCT-OFDM system outperforms the DFT-OFDM system in the presence of carrier frequency offset.
Synthesis and isolation of a stable, axially-chiral seven-membered N-heterocyclic carbene (2009)

A chiral seven-membered N-heterocyclic carbene (NHC) has been synthesized from its phenol adduct (NHC-HOPh) by a novel base-induced alpha-elimination method, and its donor strength has been determined from the IR stretching frequencies of the NHC-Rh(CO)(2)Cl complex.