gebhart/patrepeval huggingface dataset:
Fully-automated in vivo single cell electrophysiology (2013)

In this work, we report progress in developing a device that allows fully autonomous sequential patch clamp experimentation. The machine works by integrating a storage magazine of pre-filled pipettes that can be accessed, and swapped, by the headstage at the conclusion of each experiment. In operation, following each neuron measurement, the program enters “swap” state where a set of programmed actuator movements take place. First, the headstage translates towards the pipette storage assembly and deposits its used pipette. The storage assembly rotates to index a fresh pipette, its is grasped, and finally, the headstage returns to its previously designated home position in preparation of subsequent experiments.
Multipeak fat‐corrected complex R2* relaxometry: Theory, optimization, and clinical validation (2013)

The use of complex fitting and fat-correction improves the robustness, noise performance, and accuracy of R2* measurements, and are necessary to establish R2* as quantitative imaging biomarker in the liver.
New technique for calibrating hydrocarbon gas flowmeters (1984)

A technique for measuring calibration correction factors for hydrocarbon mass flowmeters is described. It is based on the Nernst theorem for matching the partial pressure of oxygen in the combustion products of the test hydrocarbon, burned in oxygen-enriched air, with that in normal air. It is applied to a widely used type of commercial thermal mass flowmeter for a number of hydrocarbons. The calibration correction factors measured using this technique are in good agreement with the values obtained by other independent procedures. The technique is successfully applied to the measurement of differences as low as one percent of the effective hydrocarbon content of the natural gas test samples.
CC Chemokine Receptor 5-Mediated Signaling and HIV-1 Co-receptor Activity Share Common Structural Determinants (1997)

There is a close correspondence between the ability of RANTES and macrophage inflammatory proteins 1alpha and 1beta to activate CC chemokine receptor 5 (CCR5) and the ability to inhibit CCR5-dependent membrane fusion mediated by the envelope glycoprotein of human immunodeficiency virus (HIV), type 1. This finding suggests that some of the structural determinants for CC chemokine/CCR5 interactions and CCR5 HIV-1 fusion co-receptor activity may be shared. Recent studies using human CCR5/CCR2B chimeras have suggested that the determinants of CCR5 co-receptor activity are complex and may involve multiple extracellular receptor domains and that viral co-receptor activity is dissociable from ligand-dependent signaling responses. However, conclusive evidence demonstrating an important role for the second and third extracellular regions of human CCR5 is lacking. Furthermore, to determine whether the determinants for CCR5 co-receptor activity overlap with those required for agonist activity, studies that compare the chemokine specificity for inhibition of envelope-mediated cell fusion and the agonist profile of chimeric receptors are necessary. In the present report, using a series of CCR5/CCR2B chimeras we ascribe an important role for the second and third extracellular loop of CCR5 in supporting the co-receptor activity of CCR5. We also provide evidence that the intracytoplasmic tail of CCR5 does not play an important role in supporting HIV-1 entry. The hypothesis that the structural determinants for CC chemokine/CCR5 interactions and CCR5 HIV-1 fusion co-receptor activity may be shared was confirmed by two novel observations: first, the fusion activity supported by two hybrid receptors could be inhibited by both RANTES and monocyte chemoattractant protein-1, chemokines specific to CCR5 and CCR2B, respectively; and second, the chemokine specificity for inhibition of envelope-mediated cell fusion matched the agonist profile of these hybrid receptors. These data shed new light on the structural determinants involved in these distinct activities of CCR5 and may have important implications for the development of CCR5-targeted anti-viral compounds.
Benchtop Electrochemical Liquid–Liquid–Solid Growth of Nanostructured Crystalline Germanium (2011)

An electrochemical liquid-liquid-solid (ec-LLS) process that produces large amounts of crystalline semiconductors with tunable nanostructured shapes without any physical or chemical templating agent is presented. Electrodeposition of Ge from GeO(2)(aq) solutions followed by dissolution into a liquid Hg electrode, saturation of the liquid alloy, and precipitation can yield polycrystalline Ge(s) under ambient conditions. A unique advantage of ec-LLS is that it involves precipitation under electrochemical control, where the applied bias precisely defines the flux of Ge into the liquid electrode. Fidelity of the saturation and precipitation of Ge from liquid electrodes affords a variety of material morphologies, including dense films of oriented nanostructured filaments with large aspect ratios (>10(3)). Electrodeposition involving a liquid electrolyte, a liquid electrode, and a solid deposit under ambient conditions represents a conceptually unexplored direct wet-chemical route for the preparation of bulk quantities of crystalline group-IV semiconductors without the time- and energy-intensive processing steps required in traditional preparations of semiconductor materials.
Using dynamic contrast‐enhanced MRI to quantitatively characterize maternal vascular organization in the primate placenta (2014)

The dynamic contrast-enhanced magnetic resonance imaging analysis described here provides quantitative estimates of the number of maternal perfusion domains in a primate placenta and estimates flow within each domain. Anticipated extensions of this technique are to the study placental function in non-human primate models of obstetric complications.
A rapid pneumococcal serotyping system based on monoclonal antibodies and PCR (2008)

Streptococcus pneumoniae expresses at least 91 different polysaccharide (PS) capsules and the currently available serotyping methods are tedious to perform. We have been developing a rapid pneumococcal serotyping assay (named the 'multibead assay') based on the capacity of pneumococcal lysates to inhibit the ability of 24 different anti-capsule antibodies to bind to latex beads coated with 24 different PSs (serotypes 1, 3, 4, 5, 6A, 6B, 7F, 9N, 9V, 14, 18C, 19A, 19F, 23F, 2, 8, 10A, 11A, 12F, 15B, 17F, 20, 22F and 33F). Because the polyclonal antibodies used for 10 serotypes (2, 8, 10A, 11A, 12F, 15B, 17F, 20, 22F and 33F) had limited serotype specificity, we replaced them with monoclonal antibodies for the 10 serotypes. To extend the serotype coverage beyond the 24 serotypes, we have adapted multiplexed PCR for five additional serotypes (15A, 15C, 16F, 35B and 38) to be useful with the pneumococcal lysates prepared for the multibead assay. We then validated the combined assay with 157 clinical isolates from the Centers for Disease Control and Prevention and found that the new combined assay produced results that are concordant with the quellung reaction. The combined assay is robust and could be used to rapidly identify the serotypes of the majority of pneumococci ( approximately 90 %). In addition, the assay validation study suggests the presence of serological subtypes within serotype 11A.
Inexpensive photonic crystal spectrometer for colorimetric sensing applications (2013)

Photonic crystal spectrometers possess significant size and cost advantages over traditional grating-based spectrometers. In a previous work [Pervez, et al, Opt. Express 18, 8277 (2010)] we demonstrated a proof of this concept by implementing a 9-element array photonic crystal spectrometer with a resolution of 20 nm. Here we demonstrate a photonic crystal spectrometer with improved performance. The dependence of the spectral recovery resolution on the number of photonic crystal arrays and the width of the response function from each photonic crystal is investigated. A mathematical treatment, regularization based on known information of the spectrum, is utilized in order to stabilize the spectral estimation inverse problem and achieve improved spectral recovery. Colorimetry applications, the measurement of CIE 1931 chromaticities and the color rendering index, are demonstrated with the improved spectrometer.
Induction of immune responses to functional determinants of a cell surface streptococcal antigen. (1996)

Antibodies directed against the cell surface adhesin, termed streptococcal antigen I/II of Streptococcus mutans can protect against dental caries. Streptococcal antigen I/II (SA I/II) interacts with salivary glycoproteins and promotes adhesion to the tooth surface. Topical application of monoclonal antibodies which recognize a domain within residues 816-1213 (fragment 3) prevents colonization by S. mutans in primates. In this study the immunogenicity and antigenicity of fragment 3 was investigated in five strains of mice. Fragment 3 induced an immune response following immunization with whole cells of S. mutans in all strains of mice. Immunization with recombinant fragment 3 also induced T-cell proliferative and antibody responses both to fragment 3 and to the SA I/II. Antibody responses to the previously defined adhesion determinants (residues 1005-1044) were weak or undetectable. Immunization of three representative strains of mice with a recombinant polypeptide (residues 975-1044) comprising this adhesion epitope and an adjacent T-cell epitope (residues 975-1004) elicited both T- and B-cell responses to the polypeptide and to native SA I/II. The B-cell epitopes overlapped with the adhesion determinant. These findings provide a means of directing immune responses to functional determinants of SA I/II.
An iterative channel estimator for fast-varying channels using successive OFDM symbols (2009)

This paper deals with pilot-based channel estimation for fast varying channels in Orthogonal Frequency Division Multiplexing (OFDM) systems. Due to the variation of the channel during one OFDM symbol, one-tap channel estimation and the corresponding equalization is no longer the optimum solution and such a variation results in inter-carrier interference (ICI). One of the possible approaches to predict this interfering effect is to use basis expansion model (BEM) with which the variation of the channel can be approximated successfully. However, as the pure BEM does not solve completely the problem, we investigate the estimation problem using decision feedback to enhance the performance. In particular, we propose a simple algorithm based on using two successive OFDM symbols to filter channel coefficients and improve not only the convergence of pure decision feedback based estimation but also the system performance. Simulation results based on Jake's channel model with a high Doppler spread and a practical high data rate system sustain our claims.
Magnetic circuit for planar diaphragm type loudspeaker (1983)

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Mitigation of low-frequency underwater sound using large encapsulated bubbles and freely-rising bubble clouds (2012)

Low-frequency anthropogenic noise may affect marine life, motivating the need to minimize its potential impact. Bubbles cause significant dispersion and attenuation of underwater sound at frequencies near the individual bubble resonance and can potentially be used to abate this noise. Such effects have been reported for large encapsulated bubbles with resonance frequencies below 100 Hz, and significant attenuation due to bubble resonance phenomena and acoustic impedance mismatch was observed in a tank experiment [J. Acoust. Soc. Am.
HIGH CAPACITY SUBSTRATES AS A PLATFORM FOR A DNA PROBE ARRAY GENOTYPING ASSAY (2001)

Colloidal silica particles were deposited on a glass substrate to produce high-capacity porous supports for high-density DNA probe arrays. Porous surfaces were used to increase the addressable surface area and number of probes available for hybridization. Surfaces derived from 70-100 nm size particles deposited in films from 0.15 to 2 microns thick exhibited excellent performance in light-directed oligonucleotide synthesis. Evaluation of these substrates in a genotyping assay is reported.
Tensil Film Clamps And Mounting Block For Viscoelastometers (1989)

Set of clamps and mounting block developed for use in determining tensile moduli and damping properties of films in manually operated or automated commercial viscoelastometer. These clamps and block provide uniformity of sample gripping and alignment in instrument. Dependence on operator and variability of data greatly reduced.
3′-End Formation of Baculovirus Late RNAs (2000)

Baculovirus late RNAs are transcribed by a four-subunit RNA polymerase that is virus encoded. The late viral mRNAs are capped and polyadenylated, and we have previously shown that capping is mediated by the LEF-4 subunit of baculovirus RNA polymerase. Here we report studies undertaken to determine the mechanism of 3'-end formation. A globin cleavage/polyadenylation signal, which was previously shown to direct 3'-end formation of viral RNAs in vivo, was cloned into a baculovirus transcription template. In vitro assays with purified baculovirus RNA polymerase revealed that 3' ends were formed not by a cleavage mechanism but rather by termination after transcription of a T-rich region of the globin sequence. Terminated RNAs were released from ternary complexes and were subsequently polyadenylated. Mutational analyses indicated that the T-rich sequence was essential for termination and polyadenylation, but the poly(A) signal and the GT-rich region of the globin polyadenylation/cleavage signal were not required. Termination was not dependent on ATP hydrolysis, indicating a slippage mechanism.
Tripartite Hemolysin BL from Bacillus cereus (1997)

Hemolysin BL (HBL) is a unique membrane-lytic toxin from Bacillus cereus composed of three distinct proteins, designated B, L1, and L2. HBL produces a paradoxical zone phenomenon in gel diffusion assays in sheep blood agar. Lysis does not begin immediately adjacent to the source of diffusion; rather, it begins several millimeters away. Cells near the source and at intersections of lysis zones remain intact longer. Here, we developed a spectrophotometric hemolysis assay system that measures the activities of the individual HBL components and used it to analyze the mechanisms of hemolysis and the paradoxical zone phenomenon. The B component was rate-limiting, and erythrocytes were slowly primed by B at an optimal concentration of about 1.3 nM to rapid lytic action by the combination of the L components (L(1+2)). All of the individual components bound to cells independently, and membrane-associated HBL components were neutralized by specific antibodies, suggesting that lysis was caused by formation of a membrane attack complex on the cell surface. Osmotic protection experiments indicate a colloid osmotic lysis mechanism. Concentrations of the B component above 1.3 nM caused inhibition of L1-mediated lysis, and L1 inhibited the priming reaction of B over a similar concentration range. From analyses of spectrophotometric and diffusion assays we constructed a basic model for the interactions between HBL components and for the paradoxical zone phenomenon in blood agar. In the latter, areas of slow lysis near diffusion sources are caused primarily by the accumulation of inhibitory levels of L1 reached before cells are primed by B.
Silicon Liquid Crystal Light Valve for Flight Simulation Applications. (1981)

The basic objective of this program has been to develop a silicon photoconductor liquid crystal light valve (Si LCLV) for application in wide-field-of-view simulators. The Si LCLV is expected to offer several advantages over the cadmium sulfide (CdS) photoconductor LCLV, including higher sensitivity, a significantly better switching ratio, higher resolution, and (most importantly) a fast response time to allow higher 60-Hz operation. The main thrust of this program was to upgrade the device in the following areas: (1) Scale up to a 2-inch aperture device (from a 1 cm x 1 cm active area). (2) Implement the silicon/silicon dioxide (Si/SiO2) dielectric mirror and improve the light blocking layer. (3) Upgrade device resolution by optimizing the focusing grid. (4) Increase the contrast ratio by improving silicon processing. (5) Implement the dc-biased guard ring to prevent edge breakdown. (6) Optimize liquid crystal operation to reduce the reponse time. Significant improvements were achieved in all areas.
Abstract 14016: Adenoviral Gene Delivery Reprograms Cardiac Fibroblasts into Cardiomyocyte-like Cells with in vitro Contractile Activity: Implications for Clinical Cardiac Regeneration (2014)

Background: A newly demonstrated capability to directly convert fibroblasts into cardiomyocyte-like cells (induced cardiomyocytes [iCMs]) has great potential for the in situ regeneration of functional myocardial tissue from cardiac scar tissue and treatment of cardiovascular disease. Whereas such transdifferentiation has previously been demonstrated using retrovirus and lentivirus vectors, the clinical utility of this cardiac regeneration strategy would be facilitated by the use of a non-integrating, short-term expression viral vector such as adenovirus. In the present study, we sought to determine whether rat cardiac fibroblasts could be converted to iCMs by adenoviral expression of Gata4 (G), Mef2c (M), and Tbx5 (T) and compare the efficiencies of two viral reprogramming strategies. Methods and Results: Human adenovirus serotype 5 (Ad5) or lentivirus expressing rat GMT or corresponding null viruses were transduced into cultures of rat primary cardiac fibroblasts. After 48 hours viruses were removed and the cells were allowed to transdifferentiate under normal culture conditions. Transdifferentiation was determined 2 weeks post-transduction by FACS and immunofluorescence (IF) analysis for the activation of endogenous cardiac troponin T (cTnT) and other cardiac markers, as well as detection of in vitro contractile activity. Consistent with IF expression patterns, FACS analysis demonstrated that the Ad encoding for GMT induced 7% of adult cardiac fibroblasts to express cTnT, compared with 6% cells treated with lentivirus encoding GMT, and 0.3% of cells treated with a null virus. Importantly, only AdGMT-treated cells demonstrated in vitro contractile activity, occurring 14 days after GMT administration. Conclusion: Adenoviral vectors encoding GMT effectively reprogram cardiac fibroblasts into cardiomyocyte-like cells possessing in vitro contractile activity. These findings represent an important milestone in the utilization of a clinically relevant, short-term expression (adenovirus) vector to generate induced cardiomyocytes.
Online State Estimation for Systems with Asynchronous Sensors. (2020)

The paper investigates the problem of estimating the state of a network from heterogeneous sensors with different sampling and reporting rates. In lieu of a batch linear least-squares (LS) approach, well-suited for static networks, where a sufficient number of measurements could be collected to obtain a full-rank design matrix, the paper proposes an online algorithm to estimate the possibly time-varying network state by processing measurements as and when available. The design of the algorithm hinges on a generalized LS cost augmented with a proximal-point-type regularization. With the solution of the regularized LS problem available in closed-form, the online algorithm is written as a linear dynamical system where the state is updated based on the previous estimate and based on the new available measurements. Conditions under which the algorithmic steps are in fact a contractive mapping are shown, and bounds on the estimation error are derived for different noise models. Numerical simulations, including a power system case, are provided to corroborate the analytical findings.
Tryptophan Hydroxylase-2 Controls Brain Serotonin Synthesis (2004)

Dysregulation of brain serotonin contributes to many psychiatric disorders. Tryptophan hydroxylase-2 (Tph2), rather than Tph1, is preferentially expressed in the brain. We report a functional (C1473G) single-nucleotide polymorphism in mouse Tph2 that results in the substitution of Pro447 with Arg447 and leads to decreased serotonin levels in PC12 cells. Moreover, in BALB/cJ and DBA/2 mice that are homozygous for the 1473G allele, brain serotonin tissue content and synthesis are reduced in comparison to C57Bl/6 and 129X1/SvJ mice that are homozygous for the 1473C allele. Our data provide direct evidence for a fundamental role of Tph2 in brain serotonin synthesis.
A new, soft-switched boost converter with isolated active snubber (1999)

A boost power converter which employs an isolated active snubber to reduce the losses caused by the reverse-recovery characteristic of the boost rectifier and the turn-on discharge loss of the output capacitance of the boost switch is described. The proposed isolated active snubber consists of a coupled inductor, clamp capacitor and ground-referenced n-type MOSFET. The performance of the proposed power converter is evaluated on a 1 kW, universal-line-range, boost input-current shaper.
Targeting hypoxic cancer stem cells (CSCs) with Doxycycline: Implications for optimizing anti-angiogenic therapy (2017)

Here, we report new mechanistic insight into how chronic hypoxia increases 'stemness' in cancer cells. Using chemical inhibitors, we provide direct experimental evidence that ROS production and mitochondrial biogenesis are both required for the hypoxia-induced propagation of CSCs. More specifically, we show that hypoxic CSCs can be effectively targeted with i) simple mitochondrial anti-oxidants (Mito-TEMPO) and/or ii) inhibitors of mitochondrial biogenesis (Doxycycline). In this context, we discuss the idea that mitochondrial biogenesis itself may be a primary driver of "stemness" in hypoxic cancer cells, with metabolic links to fatty acid oxidation (FAO). As Doxycycline is an FDA-approved drug, we propose that it could be re-purposed to target hypoxic CSCs, either alone or in combination with chemotherapy, i.e., Paclitaxel. For example, we demonstrate that Doxycycline effectively targets the sub-population of hypoxia-induced CSCs that are Paclitaxel-resistant, overcoming hypoxia-induced drug-resistance. Finally, anti-angiogenic therapy often induces tumor hypoxia, allowing CSCs to survive and propagate, ultimately driving tumor progression. Therefore, we suggest that Doxycycline could be used in combination with anti-angiogenic agents, to actively prevent or minimize hypoxia-induced treatment failure. In direct support of this assertion, Paclitaxel is already known to behave as an angiogenesis inhibitor.
Nuclear magnetic resonance gyroscope: Developing a primary rotation sensor (2018)

Information on the Nuclear Magnetic Resonance Gyro (NMRG) under development by Northrop Grumman Systems Corporation in collaboration with Freedom Photonics is presented. The basics principles of Operation are summarized and the current state of development is discussed. Many details have been left out for the sake of brevity, but the principles are still complete. Recently encountered fabrication and performance challenges are also discussed.