gebhart/patrepeval huggingface dataset:
A Vesicular Stomatitis Virus Replicon-Based Bioassay for the Rapid and Sensitive Determination of Multi-Species Type I Interferon (2011)

Type I interferons (IFN) comprise a family of cytokines that signal through a common cellular receptor to induce a plethora of genes with antiviral and other activities. Recombinant IFNs are used for the treatment of hepatitis C virus infection, multiple sclerosis, and certain malignancies. The capability of type I IFN to suppress virus replication and resultant cytopathic effects is frequently used to measure their bioactivity. However, these assays are time-consuming and require appropriate biosafety containment. In this study, an improved IFN assay is presented which is based on a recombinant vesicular stomatitis virus (VSV) replicon encoding two reporter proteins, firefly luciferase and green fluorescent protein. The vector lacks the essential envelope glycoprotein (G) gene of VSV and is propagated on a G protein-expressing transgenic cell line. Several mammalian and avian cells turned out to be susceptible to infection with the complemented replicon particles. Infected cells readily expressed the reporter proteins at high levels five hours post infection. When human fibroblasts were treated with serial dilutions of human IFN-β prior to infection, reporter expression was accordingly suppressed. This method was more sensitive and faster than a classical IFN bioassay based on VSV cytopathic effects. In addition, the antiviral activity of human IFN-λ (interleukin-29), a type III IFN, was determined on Calu-3 cells. Both IFN-β and IFN-λ were acid-stable, but only IFN-β was resistant to alkaline treatment. The antiviral activities of canine, porcine, and avian type I IFN were analysed with cell lines derived from the corresponding species. This safe bioassay will be useful for the rapid and sensitive quantification of multi-species type I IFN and potentially other antiviral cytokines.
Angiopoietin-2 Stimulates Blood Flow Recovery After Femoral Artery Occlusion by Inducing Inflammation and Arteriogenesis (2008)

These results suggest that Ang2 induced in ischemic tissue plays a critical role in blood flow recovery by stimulating inflammation and arteriogenesis.
Boosting magnetic resonance imaging signal-to-noise ratio using magnetic metamaterials (2019)

Magnetic resonance imaging (MRI) represents a mainstay among the diagnostic imaging tools in modern healthcare. Signal-to-noise ratio (SNR) represents a fundamental performance metric of MRI, the improvement of which may be translated into increased image resolution or decreased scan time. Recently, efforts towards the application of metamaterials in MRI have reported improvements in SNR through their capacity to interact with electromagnetic radiation. While promising, the reported applications of metamaterials to MRI remain impractical and fail to realize the full potential of these unique materials. Here, we report the development of a magnetic metamaterial enabling a marked boost in radio frequency field strength, ultimately yielding a dramatic increase in the SNR (~ 4.2X) of MRI. The application of the reported magnetic metamaterials in MRI has the potential for rapid clinical translation, offering marked enhancements in SNR, image resolution, and scan efficiency, thereby leading to an evolution of this diagnostic tool.
Learning Equations for Extrapolation and Control (2018)

We present an approach to identify concise equations from data using a shallow neural network approach. In contrast to ordinary black-box regression, this approach allows understanding functional relations and generalizing them from observed data to unseen parts of the parameter space. We show how to extend the class of learnable equations for a recently proposed equation learning network to include divisions, and we improve the learning and model selection strategy to be useful for challenging real-world data. For systems governed by analytical expressions, our method can in many cases identify the true underlying equation and extrapolate to unseen domains. We demonstrate its effectiveness by experiments on a cart-pendulum system, where only 2 random rollouts are required to learn the forward dynamics and successfully achieve the swing-up task.
Phototransposition chemistry of 1-phenylpyrazole. Experimental and computational studies (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhototransposition chemistry of 1-phenylpyrazole. Experimental and computational studiesJames W. Pavlik, Robert E. Connors, Douglas S. Burns, and Edyth M. KurzweilCite this: J. Am. Chem. Soc. 1993, 115, 17, 7645–7652Publication Date (Print):August 1, 1993Publication History Published online1 May 2002Published inissue 1 August 1993https://pubs.acs.org/doi/10.1021/ja00070a008https://doi.org/10.1021/ja00070a008research-articleACS PublicationsRequest reuse permissionsArticle Views712Altmetric-Citations33LEARN 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-Alertsclose Get e-Alerts
Control of Viscous Fingering Patterns in a Radial Hele-Shaw Cell (2009)

We study numerically and experimentally the dynamics and control of viscous fingering patterns in a circular Hele-Shaw cell. The nonlocality and nonlinearity of the system, especially interactions among developing fingers, make the emergent pattern difficult to predict and control. By controlling the injection rate of the less viscous fluid, we can precisely suppress the evolving interfacial instabilities. There exist denumerable attractive, self-similarly evolving symmetric, universal shapes. Experiments confirm the feasibility of the control strategy, which is summarized in a morphology diagram.
Destruction mechanism and destruction detection technique for multilayer ceramic actuators (2002)

The destruction process of piezoelectric actuators under bipolar driving was studied using acoustic emission (AE) monitoring and induced-displacement measurement. The effect of floating electrode over the internal electrode's end was also investigated. Floating electrodes can suppress the field concentration and cracking in the actuator.
Stabilization of ion selectivity filter by pore loop ion pairs in an inwardly rectifying potassium channel (1997)

Ion selectivity is critical for the biological functions of voltage-dependent cation channels and is achieved by specific ion binding to a pore region called the selectivity filter. In voltage-gated K+, Na+ and Ca2+ channels, the selectivity filter is formed by a short polypeptide loop (called the H5 or P region) between the fifth and sixth transmembrane segments, donated by each of the four subunits or internal homologous domains forming the channel. While mutagenesis studies on voltage-gated K+ channels have begun to shed light on the structural organization of this pore region, little is known about the physical and chemical interactions that maintain the structural stability of the selectivity filter. Here we show that in an inwardly rectifying K+ (IRK) channel, IRK1, short range interactions of an ion pair in the H5 pore loop are crucial for pore structure and ion permeation. The two residues, a glutamate and an arginine, appear to form exposed salt bridges in the tetrameric channel. Alteration or disruption of such ion pair interactions dramatically alters ion selectivity and permeation. Since this ion pair is conserved in all IRK channels, it may constitute a general mechanism for maintaining the stability of the pore structure in this channel superfamily.
Probing Heterotrimeric G Protein Activation: Applications to Biased Ligands (2012)

Cell surface G protein-coupled receptors (GPCRs) drive numerous signaling pathways involved in the regulation of a broad range of physiologic processes. Today, they represent the largest target for modern drugs development with potential application in all clinical fields. Recently, the concept of “ligand-directed trafficking” has led to a conceptual revolution in pharmacological theory, thus opening new avenues for drug discovery. Accordingly, GPCRs do not function as simple on-off switch but rather as filters capable of selecting the activation of specific signals and thus generating texture responses to ligands, a phenomenon often referred to as ligand-biased signaling. Also, one challenging task today remains optimization of pharmacological assays with increased sensitivity so to better appreciate the inherent texture of ligands. However, considering that a single receptor has pleiotropic signaling properties and that each signal can crosstalk at different levels, biased activity remains thus difficult to evaluate. One strategy to overcome these limitations would be examining the initial steps following receptor activation. Even, if some G protein independent functions have been recently described, heterotrimeric G protein activation remains a general hallmark for all GPCRs families and the first cellular event subsequent to agonist binding to the receptor. Herein, we review the different methodologies classically used or recently developed to monitor G protein activation and discussed them in the context of G protein biased-ligands Keywords: GPCRs, G protein, biased agonist, ligand-directed trafficking, ligand efficacy, G protein sensors, signaling pathways, protein activation, pleiotropic signaling properties, calcium concentrations
Tunable twin‐guide (TTG) laser diodes with metal‐clad ridge‐waveguide (MCRW) structure for coherent optical communications (1992)

Abstract Tunable twin‐guide (TTG) laser diodes with metal‐clad ridge‐waveguide (MCRW) structure were developed for advanced coherent optical communication systems at 1.55 μm wavelength. The essential advantage of these lasers over previous devices is the simplified handling due to the inherent continuous tuning behaviour enabling the unambiguous wavelength control by only one tuning current. With 400 μm long devices, threshold currents around 50 mA, optical output power levels above 10 mW and tuning ranges around 1.2 nm (150 GHz) are achieved by maintaining the linewidth below 4 MHz. With an optimized design a maximum continuous tuning range of 2 nm has been obtained.
Effect of Cations and Anions on the Formation of Polypseudorotaxanes (2002)

Aqueous solutions of alpha-, beta-, or gamma-cyclodextrin form stable and crystallizable inclusion complexes (polypseudorotaxanes) when added to long chain polymers such as PEG, PPG, and alkanols. This process consists of the threading of several cyclodextrin molecules around a single chain, with a kinetic profile that depends on temperature and solvent nature. We have studied the effect of salts on this threading process for a polypropylene glycol derivative with,beta-cyclodextrin at 25 degreesC. What emerges is that changes in the threading time are strongly dependent on the nature of both cations and anions. The formation of a polypseudorotaxane is then a process where hydrophobic forces clearly play a dominant role, and in this paper, we show that the diversity of salt effects is related to the microscopic frequency dependent dielectric properties of the ion pair, that account for the dispersion potential experienced by the different ions in solution.
A transportable high-resolution gamma-ray spectrometer and analysis system applicable to mobile, autonomous or unattended applications (1995)

The Safeguards Technology Program at the Lawrence Livermore National Laboratory is developing systems based on a compact electro-mechanically cooled high-purity germanium (HPGe) detector. This detector system broadens the practicality of performing high- resolution gamma-ray spectrometry in the field. Utilizing portable computers, multi-channel analyzers and software these systems greatly improve the ease of performing mobile high-resolution gamma-ray spectrometry. Using industrial computers, we can construct systems that will run autonomously for extended periods of time without operator input or maintenance. These systems can start or make decisions based on sensor inputs rather than operator interactions. Such systems can provide greater capability for wider domain of safeguards, treaty verification application, and other unattended, autonomous or in-situ applications.
Effect of cigarette smoking on pentane excretion in alveolar breath (1996)

The concentrations of acetone, isoprene, and pentane in alveolar breath were examined in 50 smokers and 50 nonsmokers by gas chromatography. The baseline pentane in smokers was 0.17 +/- 0.03 nmol/L (mean +/- SE), which was not different from pentane in nonsmokers (0.23 +/- 0.03 nmol/L). There were also no differences between smokers and nonsmokers in the concentrations of acetone and isoprene. Serial breath samples were obtained from 15 smokers before smoking and at 5, 15, and 60 min after smoking. Although acetone was not altered by smoking, isoprene increased by 86% +/- 26% 5 min after smoking (P <0.001) and returned to baseline 10 min later. Pentane increased by 456% +/- 156% 5 min after smoking (P <0.001) and remained increased 10 min later (204% +/- 73% of baseline, P <0.05). Isoprene concentrations in mainstream cigarette smoke were >5000 times greater than breath concentrations, whereas pentane could not be detected in mainstream smoke. Because pentane is produced from the peroxidation of n-6 polyunsaturated fatty acids, the results provide evidence that cigarette smoking causes an immediate increase in lipid peroxidation.
Structural and Functional Variation within the Alanine-Rich Repetitive Domain of Streptococcal Antigen I/II (2002)

ABSTRACT Members of the antigen I/II family of cell surface proteins are highly conserved, multifunctional adhesins that mediate interactions of oral streptococci with other oral bacteria, with cell matrix proteins (e.g., type I collagen), and with salivary glycoproteins, e.g., gp340. The interaction of gp340 (formerly designated salivary agglutinin) with Streptococcus mutans requires an alanine-rich repetitive domain (A region) of antigen I/II that is highly conserved in all members of this family of proteins. In this report, we show that the A regions from the two Streptococcus gordonii M5 antigen I/II proteins (SspA and SspB) interact differently with the salivary gp340 glycoprotein and appear to be structurally distinct. Recombinant polypeptides encompassing the A region of SspA or from a highly related S. mutans antigen I/II protein (SpaP) competitively inhibited the interaction of gp340 with intact S. gordonii and S. mutans cells, respectively. In contrast, an A region polypeptide from SspB was inactive, and furthermore, it did not bind to purified gp340 in vitro. Circular dichroism spectra suggested that all three polypeptides were highly α-helical and may form coiled-coil structures. However, the A region of SspB underwent a conformational change and exhibited reduced α-helical structure at pH 8.5, whereas the A region polypeptides from SspA and SpaP were relatively stable under these conditions. Melt curves also indicated that at physiological pH, the A region of SspB lost α-helical structure more rapidly than that of SspA or SpaP when the temperature was increased from 10 to 40°C. Furthermore, the SspB A region polypeptide denatured completely at a temperature that was 7 to 9°C lower than that required for the A region polypeptide of SspA or SpaP. The full-length SspB protein and the three A region peptides migrated in native gel electrophoresis and column chromatography with apparent molecular masses that were approximately 2- to 2.5-fold greater than their predicted molecular masses. However, sedimentation equilibrium ultracentrifugation data showed that the A region peptides sedimented as monomers, suggesting that the peptides may form nonglobular intramolecular coiled-coil structures under the experimental conditions used. Taken together, our results suggest that the A region of SspB is less stable than the corresponding A regions of SspA and SpaP and that this structural difference may explain, at least in part, the functional variation observed in their interactions with salivary gp340.
Oral signs of intravenous chemotherapy with 5-Fluorouracil and Leucovorin calcium in colon cancer treatment. (2009)

This treatment caused functional salivary gland disorders as evidenced by basal and stimulated hyposialia, and acidification of stimulated saliva pH during the intermediate phase. Increase in basal urea may be due to proteic catabolism arising from plasma or glands. Variation in Na+ and K+ of basal saliva concentrates might be assumed as a possible duct disorder. Recovery of bleeding and Löe and Silness rates may point to a transient inflammatory effect associated to a decrease in salivary flow. Increase in the depth rates of the periodontal vestibular sulcus could be correlated with a higher risk of periodontal disease.
Endocrine Therapy–Induced Alopecia in Patients With Breast Cancer (2018)

Endocrine therapies are associated with a pattern alopecia similar to androgenetic-type, consistent with the mechanism of action of causal agents. A significant negative impact on QoL was reported by patients, despite mostly mild alopecia severity.
Active damping based on decoupled collocated control (2002)

Abstract—Robust stability of controlled mechanical systems is often obtained using collocated actuator-sensor-pairs. Collocation enables the implementation of a passive control law, which is ro-bustly stable, irrespective of structural modeling errors. Within the context of vibration control, this knowledge is used to obtain robust active damping. However, collocated control is inherently in terms of “local ” coordinates, whereas vibration analysis is usu-ally in terms of “modal ” coordinates. Therefore, modal decoupling of the collocated control loops is required. It is shown that, under mild conditions, transformation of the control problem from local into modal coordinates yields control loops that again enable the implementation of passive and thus robustly stable control laws. The presented theory is illustrated by means of experiments on the six-degrees-of-freedom (DOF) actively controlled lens suspension within a micro-lithography machine. Index Terms—Active damping, decoupled control, integral force feedback, micro-lithography, modal control, multiple-input–mul-tiple-output (MIMO) collocated control, vibration control. I.
Reproducibility of Dynamic Chest Radiography with a Flat-panel Detector -Respiratory Changes in Pixel Value- (2009)

Dynamic chest radiography using a flat panel detector (FPD) with a large field of view is expected to be a useful pulmonary functional evaluation method based on the respiratory changes in pixel value. For clinical use as a follow-up and therapeutic evaluation tool, the system must have a high degree of reproducibility in measurements of pixel values. The present study was performed to investigate the reproducibility of respiratory changes in pixel values. Dynamic chest radiographs of five normal subjects and one patient were obtained. Imaging was performed twice in each subject. The slope (X-ray translucency variation) was then calculated from the changes in pixel value from distance lung apex-diaphragm, and the slopes of two sequences were compared. The results showed there were no significant differences in changes in pixel value between the two sequences in all normal subject (5 males, p>0.05). The results indicated that the present method has reproducibility for measuring pulmonary function and also has potential as a tool for follow-up and therapeutic evaluation.
Distribution of the Time Through a Directed, Acyclic Network (1965)

Let there be associated with each arc of a directed, acyclic network a random variable, conveniently referred to as the arc passage time. It is assumed that the arc passage times are independent and have a finite range. A method is presented for the efficient computation of the density function of the passage time from source to sink of this network, under the restriction that the arc density functions are polynomials. In particular, an algorithm is described that reduces a series-parallel network to a single arc whose density function is that of the time through the original network. The specialization of this algorithm to the class of polynomial density functions leads to a detailed examination of the convolution operation for polynomials. Finally, a method is presented whereby any directed, acyclic network can be transformed to series-parallel form, permitting application of a modified version of the series-parallel algorithm. These techniques are used to find the probability that an arc is on the critical path and a numerical example is presented.
CMOS triode transconductor for continuous-time active integrated filters (1985)

A ‘triode transconductor’ fully differential transconductance element for use in continuous-time CMOS integrated filters is proposed. It is based on a common-source pair of triodemode MOS transistors. Preliminary experimental results from breadboarded transconductors and complete filters show good distortion performance. Several practical advantages are claimed over previous approaches.
Ultrasensitive and label-free biosensor for the detection of Plasmodium falciparum histidine-rich protein II in saliva (2019)

Malaria elimination is a global public health priority. To fulfil the demands of elimination diagnostics, we have developed an interdigitated electrode sensor platform targeting the Plasmodium falciparum Histidine Rich Protein 2 (PfHRP2) protein in saliva samples. A protocol for frequency-specific PfHRP2 detection in phosphate buffered saline was developed, yielding a sensitivity of 2.5 pg/mL based on change in impedance magnitude of the sensor. This protocol was adapted and optimized for use in saliva with a sensitivity of 25 pg/mL based on change in resistance. Further validation demonstrated detection in saliva spiked with PfHRP2 from clinical isolates in 8 of 11 samples. With a turnaround time of ~2 hours, the label-free platform based on impedance sensors has the potential for miniaturization into a point-of-care diagnostic device for malaria elimination.