gebhart/patrepeval huggingface dataset:
Carbon Nanotubes Based Nanoelectrode Arrays: Fabrication, Evaluation, and Sensing Applications (2004)

In humans, immunity to Plasmodium sp. generally takes the form of protection from symptomatic malaria (i.e., 'clinical immunity') rather than infection ('sterilizing immunity'). In contrast, mice infected with Plasmodium develop sterilizing immunity, hindering progress in understanding the mechanistic basis of clinical immunity. Here we present a novel model in which mice persistently infected with P. chabaudi exhibit limited clinical symptoms despite sustaining patent parasite burdens for many months. Characterization of immune responses in persistently infected mice revealed development of CD4+ T cell exhaustion, increased production of IL-10, and expansion of B cells with an atypical surface phenotype. Additionally, persistently infected mice displayed a dramatic increase in circulating nonclassical monocytes, a phenomenon that we also observed in humans with both chronic Plasmodium exposure and asymptomatic infection. Following pharmacological clearance of infection, previously persistently infected mice could not control a secondary challenge, indicating that persistent infection disrupts the sterilizing immunity that typically develops in mouse models of acute infection. This study establishes an animal model of asymptomatic, persistent Plasmodium infection that recapitulates several central aspects of the immune response in chronically exposed humans. As such, it provides a novel tool for dissection of immune responses that may prevent development of sterilizing immunity and limit pathology during infection.
Improving INS/GPS Navigation Accuracy through Compensation of Kalman Filter Errors (2006)

The Kalman filter is often used to integrate satellite navigation systems with inertial navigation systems. Such integrated systems are especially useful for navigation of vehicles in urban environments where satellite signals are frequently blocked by tall buildings. The filter weights the measurements of both navigation systems to provide an overall optimal solution. Unfortunately, an optimal solution is only achieved when the filter has been supplied with ideal a priori information such as proper measurement noise characteristics and system dynamics. If such parameters are not perfect they can be detected and compensated for using an intelligent navigation scheme which is adaptable to different sensors. As dynamics are encountered, satellite signal blockages are simulated to test the optimality of the filter. A neural network is then trained to learn any residual deterministic errors which are then removed from future system drifts during signal blockages.
Cloud thermodynamic phase detection using an all-sky imaging polarimeter (2017)

At any given time, clouds cover approximately 60% of the Earth’s surface and they strongly influence weather and climate; however, they are one of the largest sources of uncertainty in climate models and predictions of atmospheric effects on remote sensing measurements. Knowing the cloud thermodynamic phase – whether a cloud is composed of ice crystals or liquid particles – is critical in these applications. Knobelspiesse et al. (Atmos. Meas. Tech., 8, 1537–1554, 2015) showed theoretically that the sign of the S1 Stokes parameter can be used to detect cloud thermodynamic phase when observed with a ground-based passive polarimeter and demonstrated this principle with a zenith-viewing polarimeter. In this theory, a positive S<sub>1</sub> value indicates a liquid cloud, while a negative S<sub>1</sub> value indicates an ice cloud. In this paper, we report the use of our all-sky polarimeter, operating at 450 nm (10 nm band) to detect ice, liquid, and multi-layered clouds. The cloud thermodynamic phase was independently verified with a dual-polarization lidar pointed at the zenith.
Design, Synthesis, and Antiviral Evaluation of Some Polyhalogenated Indole <i>C</i>-nucleosides (2005)

2,5, 6-Trichloro-1-(beta-D-ribofuranosyl)benzimidazole (TCRB), 2-bromo-5, 6-dichloro-1-(beta-D-ribofuranosyl)benzimidazole (BDCRB) and 2-benzylthio-5,6-dichloro-1-(beta-D-ribofuranosyl)benzimidazole (BTDCRB) are benzimidazole nucleosides that exhibit strong and selective anti-HCMV activity. Polyhalogenated indole C-nucleosides were prepared as 1-deaza analogs of the benzimidazole nucleosides TCRB and BDCRB. A mild Knoevenagel coupling reaction between an indol-2-thione and a ribofuranose derivative was developed for the synthesis of 2-benzylthio-5, 6-dichloro-3-(beta-D-ribofuranosyl)indole (12). 3-(beta-D-ribofuranosyl)-2,5,6-trichloroindole (16) was prepared from 12 in 4 steps. A Lewis acid-mediated glycosylation method was then developed to prepare the targeted 2-haloindole C-nucleoside 16 stereoselectively in four steps from the corresponding 2-haloindole aglycons. Only 12 was active against HCMV but it also was somewhat cytotoxic.
Hydrophobic moments of protein structures: Spatially profiling the distribution (2001)

It is generally accepted that globular proteins fold with a hydrophobic core and a hydrophilic exterior. Might the spatial distribution of amino acid hydrophobicity exhibit common features? The hydrophobic profile detailing this distribution from the protein interior to exterior has been examined for 30 relatively diverse structures obtained from the Protein Data Bank, for 3 proteins of the 30S ribosomal subunit, and for a simple set of 14 decoys. A second-order hydrophobic moment has provided a simple measure of the spatial variation. Shapes of the calculated spatial profiles of all native structures have been found to be comparable. Consequently, profile shapes as well as particular profile features should assist in validating predicted protein structures and in discriminating between different protein-folding pathways. The spatial profiles of the 14 decoys are clearly distinguished from the profiles of their native structures.
Tailored Gires–Tournois etalons as tunable dispersion slope compensators (2004)

We present a novel concept of a tailored Gires-Tournois etalon structure and show that such a device is useful for the fabrication of a dispersion-slope compensator with an almost arbitrary dispersion profile and also with tunability in the dispersion slope.
Protective Immune Responses Elicited by Fusion Protein Containing PsaA and PspA Fragments (2015)

Streptococcus pneumoniae is an important pathogen accounting for a large number of deaths worldwide. Due to drawbacks of the current polysaccharide-based vaccine, the most promising way to generate an improved vaccine may be to utilize protection-eliciting pneumococcal proteins. Pneumococcal surface adhesin A (PsaA) and pneumococcal surface protein A (PspA) are two vaccine candidates which have been evaluated against S. pneumoniae infection in animal models or human clinical trials with encouraging results. In this study, the efficacy of the fusion protein PsaA-PspA, which includes PsaA part and PspA part, in inducing immunoprotective effects against fatal pneumococcal challenge was evaluated in an animal model. PspA part of PsaA-PspA fusion protein contains both family1 N-terminal region and family 2 N-terminal clade-defining region of PspA. Immunization with the PsaA-PspA fusion protein induced high levels of antibodies against both PsaA and PspA, which could bind to intact S. pneumoniae strains bearing different PspAs. Ex vivo stimulation of splenocytes from mice immunized with PsaA-PspA induced IL-17A secretion. Mice immunized with PsaA-PspA showed reduced S. pneumoniae levels in the blood and lungs compared with the PBS group after intranasal infection. Finally, mice immunized with PsaA-PspA fusion proteins were protected against fatal challenge with pneumococcal strains expressing different PspAs regardless of the challenge route. These results support the PsaA-PspA fusion protein as a promising vaccine strategy, as demonstrated by its ability to enhance the immune response and stimulate production of high titer antibodies against S. pneumoniae strains bearing heterologous PspAs, as well as confer protection against fatal challenge with PspA family 1 and family 2 strains.
Amplification by injection locking of a Josephson oscillator (1974)

Josephson oscillations near 9 GHz, produced by a point-contact junction mounted in a coaxial resonator and biased onto the cavity-induced step in its V-I curve, have been pulled in frequency and phase locked by a weak injected signal at a nearby frequency. The resulting output was at the signal frequency and had the narrow bandwidth and frequency stability of the input but the power level of the Josephson oscillations. Maximum gain of 51 dB was achieved for an input of 10−16 W.
New algorithms for QT dispersion analysis (2002)

New algorithms for QT dispersion analysis on standard 12-lead ECG are described. A singular-value-decomposition (SVD)-based filter was designed to smooth T wave and a pattern recognition method was developed to find different T wave patterns and their peaks. Then a least-square curve fitting method was used to locate the T end. A fuzzy thresholding approach was adopted to decide the final T peak and T end. Subsequently, Q to T end dispersion and Q to T peak dispersion of all 12 leads and 6 precordial leads were computed We also studied a SVD-based template matching for QT dispersion. We have tested the new QT dispersion algorithms on ECGs from normals, acute myocardial infarction patients, and serial ECGs for reproducibility. Results show that the new method is effective and consistent in differentiating normal subjects from the abnormal group. The QT dispersion difference for reproducibility is within 1 to 2 sample points.
Artificial Intelligence Assisted Infrastructure Assessment using Mixed Reality Systems (2019)

Conventional methods for visual assessment of civil infrastructures have certain limitations, such as subjectivity of the collected data, long inspection time, and high cost of labor. Although some new technologies (i.e., robotic techniques) that are currently in practice can collect objective, quantified data, the inspector’s own expertise is still critical in many instances because these technologies are not designed to work interactively with a human inspector. This study aims to create a smart, human-centered method that offers significant contributions to infrastructure inspection, maintenance, management practice, and safety for the bridge owners. By developing a smart mixed reality (MR) framework, which can be integrated into a wearable holographic headset device, a bridge inspector, for example, can automatically analyze a certain defect such as a crack that he or she sees on an element, and display its dimension information in real-time along with the condition state. Such systems can potentially decrease the time and cost of infrastructure inspections by accelerating essential tasks of the inspector such as defect measurement, condition assessment, and data processing to management systems. The human-centered artificial intelligence (AI) will help the inspector collect more quantified and objective data while incorporating the inspector’s professional judgment. This study explains in detail the described system and related methodologies of implementing attention guided semisupervised deep learning into MR technology, which interacts with the human inspector during assessment. Thereby, the inspector and the AI will collaborate/communicate for improved visual inspection.
Effect of 2-Fluorohistidine Labeling of the Anthrax Protective Antigen on Stability, Pore Formation, and Translocation (2007)

The action of anthrax toxin relies in part upon the ability of the protective antigen (PA) moiety to form a heptameric pore in the endosomal membrane, providing a portal for entry of the enzymic moieties of the toxin into the cytosol. Pore formation is dependent on a conformational change in the heptameric prepore that occurs in the neutral to mildly acidic pH range, and it has been hypothesized that protonation of one or more histidine residues triggers this transition. To test this hypothesis, we used biosynthetic methods to incorporate the unnatural amino acid analogue 2-fluorohistidine (2-FHis) into PA. 2-FHis is isosteric with histidine but resists protonation at physiological pH values due to a dramatically reduced side-chain pKa ( approximately 1). We found that 2-FHis-labeled PA was biologically inactive, as judged by its inability to deliver a model intracellular effector, LFN-DTA, to the cytosol of CHO-K1 cells. However, whereas 2-FHis blocked a conformational transition in the full-length PA83 protein in the pH 5-6 range, the pH dependence of prepore-to-pore conversion of (PA63)7 was unchanged from the wild-type protein, implying that this conversion is not dependent on His protonation. Consistent with this result, the labeled, trypsin-activated PA was able to permeabilize liposomes to K+ and retained pore-forming activity in planar phospholipid bilayers. The pores in planar bilayers were incapable, however, of translocating a model ligand in response to a transmembrane pH gradient or elevated voltage. The results indicate that protonation of residues other than His, presumably Glu and/or Asp side chains, triggers pore formation in vitro, but His residues are nonetheless important for PA functioning in vivo.
An Analysis of Flash Page Reuse With WOM Codes (2018)

Flash memory is prevalent in modern servers and devices. Coupled with the scaling down of flash technology, the popularity of flash memory motivates the search for methods to increase flash reliability and lifetime. Erasures are the dominant cause of flash cell wear, but reducing them is challenging because flash is a write-once medium— memory cells must be erased prior to writing. An approach that has recently received considerable attention relies on write-once memory (WOM) codes, designed to accommodate additional writes on write-once media. However, the techniques proposed for reusing flash pages with WOM codes are limited in their scope. Many focus on the coding theory alone, whereas others suggest FTL designs that are application specific, or not applicable due to their complexity, overheads, or specific constraints of multilevel cell (MLC) flash. This work is the first that addresses all aspects of page reuse within an end-to-end analysis of a general-purpose FTL on MLC flash. We use a hardware evaluation setup to directly measure the short- and long-term effects of page reuse on SSD durability and energy consumption, and show that FTL design must explicitly take them into account. We then provide a detailed analytical model for deriving the optimal garbage collection policy for such FTL designs, and for predicting the benefit from reuse on realistic hardware and workload characteristics.
Motion Artifact Suppression Technique (MAST) for MR Imaging (1987)

A technique has been developed that significantly improves the image resolution and reduces motion artifacts in conventional two-dimensional Fourier transform and three-dimensional Fourier transform magnetic resonance imaging sequences. Modifications on the gradient waveforms completely refocus the transverse magnetization at the echo time, regardless of the motion occurring between the time of the 90 degrees radiofrequency excitation and the echo time (within-view). This accomplishes suppression of motion artifacts and regains the signal from flowing blood and CSF. Images of the head, abdomen, chest, and spine are reproduced which show the increase in signal and anatomical detail that would otherwise be degraded and lost in artifact noise. This technique has reduced the practical difficulty of obtaining clinically diagnostic T2-weighted abdominal images. It also has allowed diagnostic quality T1- and T2-weighted images to be obtained with one acquisition per view, thus reducing the total scan time.
Ultrasound interstitial thermal therapy (USITT) for the treatment of uterine myomas (2007)

Uterine myomas (fibroids) are the most common pelvic tumors occurring in women, and are the leading cause of hysterectomy. Symptoms can be severe, and traditional treatments involve either surgical removal of the uterus (hysterectomy), or the fibroids (myomectomy). Interstitial ultrasound technologies have demonstrated potential for hyperthermia and high temperature thermal therapy in the treatment of benign and malignant tumors. These ultrasound devices offer favorable energy penetration allowing large volumes of tissue to be treated in short periods of time, as well as axial and angular control of heating to conform thermal treatment to a targeted tissue, while protecting surrounding tissues from thermal damage. The goal of this project is to evaluate interstitial ultrasound for controlled thermal coagulation of fibroids. Multi-element applicators were fabricated using tubular transducers, some of which were sectored to produce 180° directional heating patterns, and integrated with water cooling. Human uterine fibroids were obtained after routine myomectomies, and instrumented with thermocouples spaced at 0.5, 1.0, 1.5, 2.0, 2.5 and 3.0 cm from the applicator. Power levels ranging from 8-15 W per element were applied for up to 15 minute heating periods. Results demonstrated that therapeutic temperatures >50° C and cytotoxic thermal doses (<i>t</i><sub>43</sub>) extended beyond 2 cm radially from the applicator (>4 cm diameter). It is anticipated that this system will make a significant contribution toward the treatment of uterine fibroids.
Single-longitudinal-mode ring diamond Raman laser (2017)

Summary form only given. Continuous-wave single-longitudinal-mode (SLM) lasers are an important tool for applications exploiting light-matter interactions. However, mature laser technologies using inversion gain media cover only a limited part of the optical spectrum. Therefore, nonlinear frequency conversion is necessary to reach wavelengths outside this range. Conversion using stimulated Raman scattering can be a simple and robust approach [1], and an SLM diamond Raman laser using a 40 W pump laser has been recently reported [2].Here we present efficient Raman conversion of a SLM Ti:sapphire laser (SolsTiS, M Squared Lasers) outputting 5 W at 790 nm. The pump field was cavity-enhanced in a ring cavity with a 1% transmissive input mirror, which also contained a 5 mm long Brewster-cut diamond crystal (Element Six). Raman lasing within the enhancement cavity occurred for pump powers above 1 W, generating a Stokes field at 893 nm. Stokes output was emitted though the input mirror that had 1% transmission at the Stokes wavelength.
Characterization of Rat Cytochrome P-450MC Synthesized in Saccharomyces cerevisiae1 (1985)

Rat cytochrome P-450MC cDNA was expressed in Saccharomyces cerevisiae AH22, SHY3 and NA87-11A cells under the control of the yeast ADH1 promoter and terminator. Although the three yeast strains transformed with the constructed expression plasmid, pAMC1, contained approximately three copies of the plasmid, the levels of both P-450MC mRNA and the corresponding protein in the AH22 cells carrying plasmid pAMC1 were 1.4- to 1.7-fold and 2-fold higher than in the other two strains, respectively. The P-450MC protein was purified from the microsomal fraction of AH22 cells carrying pAMC1 by a rapid purification method. The apparent molecular weight, chromatographic behavior, spectral properties, substrate specificity and immunochemical properties of the purified P-450MC protein were indistinguishable from those of rat liver P-450MC-I and P-450MC-II (Sasaki, T., et al. (1984) J. Biochem. 96, 117-126). The NH2-terminal amino acid sequence of the purified protein up to 10 residues was the same as those of P-450MC-I and P-450MC-II. In addition, HPLC analysis of the microsomal fraction of AH22 cells containing pAMC1 indicated that the synthesized P-450MC protein corresponds to P-450MC-II, but not P-450MC-I. With another purification method, we obtained the cleaved P-450MC protein which lacked the NH2-terminal 30 amino acids of intact P-450MC. The spectral properties and monooxygenase activities towards benzo(a)pyrene and 7-ethoxycoumarin of the cleaved P-450MC were nearly the same as those of intact P-450MC.
An Evaluation of an Automatic Gear-shifting System for Manual Wheelchairs (2012)

Frontiers Abstracts An Evaluation of an Automatic Gear-shifting System for Manual Wheelchairs Scott C. Daigle, Scott C. Daigle Department of Mechanical Science and Engineering,University of Illinois at Urbana-Champaign Search for other works by this author on: This Site PubMed Google Scholar Jacob J. Sosnoff, Jacob J. Sosnoff Department of Kinesiology and Community Health,University of Illinois at Urbana-Champaign Search for other works by this author on: This Site PubMed Google Scholar Elizabeth T. Hsiao-Wecksler Elizabeth T. Hsiao-Wecksler Department of Mechanical Science and Engineering,University of Illinois at Urbana-Champaign Search for other works by this author on: This Site PubMed Google Scholar Author and Article Information Scott C. Daigle Department of Mechanical Science and Engineering,University of Illinois at Urbana-Champaign Jacob J. Sosnoff Department of Kinesiology and Community Health,University of Illinois at Urbana-Champaign Elizabeth T. Hsiao-Wecksler Department of Mechanical Science and Engineering,University of Illinois at Urbana-Champaign J. Med. Devices. Mar 2012, 6(1): 017563 (1 pages) https://doi.org/10.1115/1.4026741 Published Online: March 12, 2012 Article history Received: May 27, 2011 Revision Received: November 7, 2011
A monoclonal antibody against murine PlGF blocks primary tumor growth in syngeneic mouse tumor models (2005)

Gene targeting studies in mice have elucidated a functional role of placental growth factor PlGF, a homologue of VEGF, in pathological angiogenesis. Loss of PlGF, while not causing any vascular defects during embryonic development, reproduction or normal adult life, impaired angiogenesis in pathological conditions, such as cancer. We generated a neutralizing anti- mPlGF monoclonal antibody which inhibits PlGF binding to its receptor Flt1. Here we report the effect of this anti-mPlGF mAb on tumor angiogenesis and growth in syngeneic, subcutaneous B16 melanoma, CT26 colon and orthotopic Panc02 pancreatic tumor models. Treatment was initiated when tumors reached a size of 60mm³ or at 3 days after orthotopic tumor cell inoculation. Compared to a control antibody, intraperitoneal administration of anti-mPlGF mAb every other day significantly suppressed the growth of primary B16 melanoma tumors (end-stage tumor volume: 1,470±81mm³ after anti-PlGF vs. 2,660±81mm³ after control; p=0.001), colon CT26 tumors (729±73mm³ vs. 1,533±113mm³; p=0.001) and pancreatic Panc02 tumors (1,230±220mm³ vs. 2,313±290mm³; p=0.007). Histological examination on CD31-stained tumor sections revealed that the vessel density in anti-mPlGF mAb treated tumors was reduced. Moreover, unlike VEGF inhibitors, the anti- mPlGF mAb failed to affect pregnancy or skin wound healing, did not induce hypertension or pruning of quiescent vessels in the trachea and thyroid gland, and failed to elevate plasma levels of PAI–1, a marker of thrombotic risk. These findings may offer novel therapeutic opportunities for the treatment of cancer.