gebhart/patrepeval huggingface dataset:
Cytomegaloviral determinants of CD8 <sup>+</sup> T cell programming and RhCMV/SIV vaccine efficacy (2021)

Simian immunodeficiency virus (SIV) insert-expressing, 68-1 rhesus cytomegalovirus (RhCMV/SIV) vectors elicit major histocompatibility complex E (MHC-E)- and MHC-II-restricted, SIV-specific CD8<sup>+</sup> T cell responses, but the basis of these unconventional responses and their contribution to demonstrated vaccine efficacy against SIV challenge in the rhesus monkeys (RMs) have not been characterized. We show that these unconventional responses resulted from a chance genetic rearrangement in 68-1 RhCMV that abrogated the function of eight distinct immunomodulatory gene products encoded in two RhCMV genomic regions (<i>Rh157.5/Rh157.4</i> and <i>Rh158-161</i>), revealing three patterns of unconventional response inhibition. Differential repair of these genes with either RhCMV-derived or orthologous human CMV (HCMV)-derived sequences (<i>UL128/UL130</i>; <i>UL146/UL147</i>) leads to either of two distinct CD8<sup>+</sup> T cell response types-MHC-Ia-restricted only or a mix of MHC-II- and MHC-Ia-restricted CD8<sup>+</sup> T cells. Response magnitude and functional differentiation are similar to RhCMV 68-1, but neither alternative response type mediated protection against SIV challenge. These findings implicate MHC-E-restricted CD8<sup>+</sup> T cell responses as mediators of anti-SIV efficacy and indicate that translation of RhCMV/SIV vector efficacy to humans will likely require deletion of all genes that inhibit these responses from the HCMV/HIV vector.
Development of liquid crystal adaptive lens with circular electrodes for imaging application (2003)

This paper reports the development of the first Liquid Crystal Adaptive Lens (LCAL) with circular electrodes for imaging application. LCAL is an electro-optical device using a set of electrodes to grade the refractive index across its aperture. The principle of liquid crystal adaptive lens is briefly discussed. The special advantages and challenges in using circular electrodes are addressed. Numerical simulation is performed to predict the imaging performance. A prototype of LCAL was designed according to the requirements for application in a microscope imaging system with a diameter of 7.86 mm and a focal length adjustable from 0.2m to infinity. The structure of the LCAL with circular electrodes includes the top ITO ring electrodes and the connecting wires, insulating layer, ITO plugs, and the bottom ITO conducting wires. This prototype was fabricated on a glass substrate by using micro-fabrication process. The focusing performance of the LCAL with circular electrodes was presented. The experimental results agree well with the simulation results. The imaging experiment of LCAL is performed when LCAL focal length is 1m, 0.38m and 0.2m under incoherent source. The resolution of the images formed by LCAL combined with a fixed lens is indistinguishable from that of the image formed only by a fixed lens, while the contrast is lower.
Early user---system interaction for database selection in massive domain-specific online environments (2003)

The continued growth of very large data environments such as Westlaw and Dialog, in addition to the World Wide Web, increases the importance of effective and efficient database selection and searching. Current research focuses largely on completely autonomous and automatic selection, searching, and results merging in distributed environments. This fully automatic approach has significant deficiencies, including reliance upon thresholds below which databases with relevant documents are not searched (compromised recall). It also merges documents, often from disparate data sources that users may have discarded before their source selection task proceeded (diluted precision). We examine the impact that early user interaction can have on the process of database selection. After analyzing thousands of real user queries, we show that precision can be significantly increased when queries are categorized by the users themselves, then handled effectively by the system. Such query categorization strategies may eliminate limitations of fully automated query processing approaches. Our system harnesses the WIN search engine, a sibling to INQUERY, run against one or more authority sources when search is required. We compare our approach to one that does not recognize or utilize distinct features associated with user queries. We show that by avoiding a one-size-fits-all approach that restricts the role users can play in information discovery, database selection effectiveness can be appreciably improved.
An ion-implanted-silicon detector based probe for the intraoperative detection of beta emitters (1996)

The use of electron and positron-sensitive surgical probes intended for the detection and localization of tumor-avid radiopharmaceuticals has gained increased attention. Much of this interest is due to the success in targeting of positron-emitting radiopharmaceuticals, such as 2-[Fluorine-18]-Fluoro-2-Deoxy-D-Glucose (FDG), to many types of human cancers. The background flux of annihilation photons produced by positron annihilation, however, complicates the detection of the positrons. To overcome this problem the use of a substance with a low photon cross section, plastic scintillator for example, is often employed. We have investigated the use of a substance with a low photon cross section, plastic scintillator for example, is often employed. We have investigated the use of an ion-implanted-silicon detector (IISD) to replace plastic scintillator as the basis for an intraoperative beta-sensitive probe. IISDs are very sensitive to beta particles (given a sufficient depletion depth) and, due to the very thin nature of the devices, have low photon detection cross sections. The excellent energy resolution of these detectors facilitates the efficient use of energy discrimination to reject many of the photons which are detected. At an energy threshold of 13.6 keV, a positron-to-annihiliation photon ratio of 15:1 was measured in tests with Fluorine-18. At this energymore » threshold, positron detection sensitivity is 3740 cps/{mu}Ci (101 cps/kBq), which is comparable to the best plastic scintillation probes. Resolution of the 8 mm diameter probe was measured in an environment simulating annihilation photon fluxes present in the thorax of a patient injected with 10 mCi (370 MBq) of FDG 1 hour after injection. A modest 7% reduction in spatial resolution was observed. Finally, this prototype probe potentially can detect small amounts of residual tumor in a surgical field.« less
Electrically tunable semiconductor Fabry-Perot filter (1994)

A key component of Wavelength Division Multiplexed (WDM) networks is a tunable broadband wavelength demultiplexer, with good selectivity and high tuning speed. In this communication we report low waveguide loss InGaAsP Fabry-Perot filters, grown by Metal Organic Vapor Phase Epitaxy, with tuning ranges up to 3.07 nm (380 GHz). These filters have waveguides with bandgap wavelengths between 1.3 and 1.48 μm so that they are transparent at zero bias and at low tuning currents (<2 mA) for 1.55 μm light. Their performance is independent of light level and they should be capable of high speed operation.
Ranking, Boosting, and Model Adaptation (2008)

We present a new ranking algorithm that combines the strengths of two previous methods: boosted tree classification, and LambdaR ank, which has been shown to be empirically optimal for a widely used information retrieval measure. The algorithm is based on boosted regression trees, although the ideas apply to any weak learners, and it is significantly fast er in both train and test phases than the state of the art, for comparable accuracy. We also show how to find the optimal linear combination for any two ran kers, and we use this method to solve the line search problem exactly during boosting. In addition, we show that starting with a previously tra ined model, and boosting using its residuals, furnishes an effective techn ique for model adaptation, and we give results for a particularly pressing prob lem in Web Search - training rankers for markets for which only small amounts of labeled data are available, given a ranker trained on much more data from a larger market.
<title>Electro-optic effect and second-order optical nonlinearity in poled silica fibers</title> (1996)

A simple fabrication technique, readily extensible to volume manufacturing, is presented to produce an electro-optically active fiber segment hat can be simply integrated into optoelectronic devices. The fabrication technique offers a dielectric isolation structure surrounding the fiber to a low high field poling, a pair of electrodes used both for poling and for inducing an electro-optic effect, and needs of the fiber unaffected by the fabrication and available for splicing to additional fiber sections. An electro-optic coefficient, including overlap between the nonlinearity and the fiber mode, as high as 0.4 pm.V was obtained by combined temperature/electric field poling. The related device applications are discussed.
Implicit Slicing for Functionally Tailored Additive Manufacturing (2016)

One crucial component of the additive manufacturing software toolchain is a class of geometric algorithms known as “slicers.” The purpose of the slicer is to compute a parametric toolpath defined at the mesoscale and associated g-code commands, which direct an additive manufacturing system to produce a physical realization of a three-dimensional input model. Existing slicing algorithms operate by application of geometric transformations upon the input geometry in order to produce the toolpath. In this paper we introduce an implicit slicing algorithm that computes mesoscale toolpaths from the level sets of heuristics-based or physics-based fields defined over the input geometry. This enables computationally efficient slicing of arbitrarily complex geometries in a straight forward fashion. The calculation of component “infill” is explored, as a process control parameter, due to its strong influence on the produced component’s functional performance. Several examples of the application of the proposed implicit slicer are presented. It is demonstrated — via proper experimentation — that the implicit slicer can produce a mesoscale structure leading to objects of superior functional performance such as greatly increased stiffness and ultimate strength without an increase of mass. We conclude with remarks regarding the strengths of the implicit approach relative to existing explicit approaches, and discuss future work required in order to extend the methodology.
<i>Helicobacter pylori</i> overcomes natural immunity in repeated infections (2016)

Repeated experimental reinfection of two subjects indicates that <i>Helicobacter pylori</i> infection does not promote an immune response protective against future reinfection. Our results highlight the importance of preventing reinfection after eradication, through public health initiatives, and possibly treatment of family members. They indicate difficulties for vaccine development, especially therapeutic vaccines.
Automated UV-C Mutagenesis of Kluyveromyces marxianus NRRL Y-1109 and Selection for Microaerophilic Growth and Ethanol Production at Elevated Temperature on Biomass Sugars (2013)

The yeast Kluyveromyces marxianus is a potential microbial catalyst for fuel ethanol production from a wide range of biomass substrates. To improve its growth and ethanol yield at elevated temperature under microaerophilic conditions, K. marxianus NRRL Y-1109 was irradiated with UV-C using automated protocols on a robotic platform for picking and spreading irradiated cultures and for processing the resulting plates. The plates were incubated under anaerobic conditions on xylose or glucose for 5 mo at 46 °C. Two K. marxianus mutant strains (designated 7-1 and 8-1) survived and were isolated from the glucose plates. Both mutant strains, but not wild type, grew aerobically on glucose at 47 °C. All strains grew anaerobically at 46 °C on glucose, galactose, galacturonic acid, and pectin; however, only 7-1 grew anaerobically on xylose at 46 °C. Saccharomyces cerevisiae NRRL Y-2403 did not grow at 46 °C on any of these substrates. With glucose as a carbon source, ethanol yield after 3 d at 46 °C was higher for 8-1 than for wild type (0.51 and 0.43 g ethanol/g glucose, respectively). With galacturonic acid as a carbon source, the ethanol yield after 7 d at 46 °C was higher for 7-1 than for wild type (0.48 and 0.34 g ethanol/g galacturonic acid, respectively). These mutant strains have potential application in fuel ethanol production at elevated temperature from sugar constituents of starch, sucrose, pectin, and cellulosic biomass.
An Aggregation-Specific Enzyme-Linked Immunosorbent Assay: Detection of Conformational Differences between Recombinant PrP Protein Dimers and PrP <sup>Sc</sup> Aggregates (2005)

The conversion of the normal cellular prion protein, PrP(C), into the protease-resistant, scrapie PrP(Sc) aggregate is the cause of prion diseases. We developed a novel enzyme-linked immunosorbent assay (ELISA) that is specific for PrP aggregate by screening 30 anti-PrP monoclonal antibodies (MAbs) for their ability to react with recombinant mouse, ovine, bovine, or human PrP dimers. One MAb that reacts with all four recombinant PrP dimers also reacts with PrP(Sc) aggregates in ME7-, 139A-, or 22L-infected mouse brains. The PrP(Sc) aggregate is proteinase K resistant, has a mass of 2,000 kDa or more, and is present at a time when no protease-resistant PrP is detectable. This simple and sensitive assay provides the basis for the development of a diagnostic test for prion diseases in other species. Finally, the principle of the aggregate-specific ELISA we have developed may be applicable to other diseases caused by abnormal protein aggregation, such as Alzheimer's disease or Parkinson's disease.
Canagliflozin primes antitumor immunity by triggering PD-L1 degradation in endocytic recycling (2023)

Understanding the regulatory mechanisms of PD-L1 expression in tumors provides key clues for improving immune checkpoint blockade efficacy or developing novel oncoimmunotherapy. Here, we showed that the FDA-approved sodium-glucose cotransporter-2 (SGLT2) inhibitor canagliflozin dramatically suppressed PD-L1 expression and enhanced T cell-mediated cytotoxicity. Mechanistic study revealed that SGLT2 colocalized with PD-L1 at the plasma membrane and recycling endosomes and thereby prevented PD-L1 from proteasome-mediated degradation. Canagliflozin disturbed the physical interaction between SGLT2 and PD-L1 and subsequently allowed the recognition of PD-L1 by Cullin3SPOP E3 ligase, which triggered the ubiquitination and proteasome-mediated degradation of PD-L1. In mouse models and humanized immune-transformation models, either canagliflozin treatment or SGLT2 silencing significantly reduced PD-L1 expression and limited tumor progression - to a level equal to the PD-1 mAb - which was correlated with an increase in the activity of antitumor cytotoxic T cells. Notably, prolonged progression-free survival and overall survival curves were observed in the group of PD-1 mAb-treated patients with non-small cell lung cancer with high expression of SGLT2. Therefore, our study identifies a regulator of cell surface PD-L1, provides a ready-to-use small-molecule drug for PD-L1 degradation, and highlights a potential therapeutic target to overcome immune evasion by tumor cells.
Control Strategies for a Linear MR-Brake With Serpentine Flux Path for Haptics (2012)

In haptics applications actuators with compact volume and high force output are desired for stable and stiff interfaces. Magnetorheological (MR) brakes are viable options since they have large force-to-volume ratios. However, linear MR-brakes available on the market have limited stroke due to the piston-cylinder design and show viscous damping behavior where the force output highly depends on the velocity of the actuator resulting in a high off-state friction force. Another problem is the inherent magnetic hysteresis, which requires complex control systems. In this research, we focused on the development and control of a linear MR-brake with infinite stroke and minimal off-state friction. The common piston-cylinder arrangement was removed from the design to address the limited stroke and high off-state-friction issues. The serpentine flux path methodology was followed to achieve compact geometry. Three control strategies namely, open-loop control, force feedback control, and current feedback with Preisach model, were implemented on the developed prototype. The results using Preisach model showed that the hysteresis could be reduced significantly without the need for an expensive force sensor in the control loop. Our new device has a 3% ratio of the off-state friction force to the maximum force output in comparison to more than 10% for most MR-damper devices in the literature. At the same time, our prototype is about half the size of a commercially available product.
A Novel Multi-Point Scan Architecture for a High Frame Rate Multi-Spectral Confocal Microendoscope (2009)

A new architecture for a confocal microscope is presented. The approach is a hybrid multi-point scanning system that allows real-time grayscale and multi-spectral imaging and is being developed for confocal microendoscopy.
Feasibility study of high spatial resolution multimodality fluorescence tomography in ex vivo biological tissue (2017)

Previously, we demonstrated that temperature-modulated fluorescence tomography (TM-FT) could provide fluorescence images with high quantitative accuracy and the spatial resolution of focused ultrasound. TM-FT is based on scanning the focused ultrasound across the medium to activate temperature-reversible fluorescent nanoprobes (ThermoDots). This technique can resolve small fluorescent targets located several centimeters deep in turbid media with millimeter resolution. Our past studies with this multimodality technique used agar phantoms, which could not represent the true heterogeneous nature of the acoustic and optical properties of biological tissue. In this work, we report the results of the first TM-FT study performed on ex vivo chicken breast tissue. In order to improve the spatial resolution of this technique, diffuse optical tomography is also used to better estimate the optical property maps of the tissue, which is utilized as functional a priori for the TM-FT reconstruction algorithm. These ex vivo results show that TM-FT can accurately recover the concentration and position of a 1.5 mm×5 mm inclusion filled with ThermoDots. Since the inclusion is embedded 2 cm deep in the chicken breast sample, these results demonstrate the great potential of TM-FT for future in vivo small animal imaging.
Highly emissive organic solids with remarkably broad color tunability based on N,C-chelate, four-coordinate organoborons (2015)

Molecular fluorophores based on N,C-chelate, four-coordinate organoborons exhibit tunable solid-state emission colors that cover the whole visible region from blue to red. The emission color can be tuned through the substituents on either quinolines or the boron center.
RETRACTED ARTICLE: Evaluating polymicrobial immune responses in patients suffering from tick-borne diseases (2018)

There is insufficient evidence to support screening of various tick-borne diseases (TBD) related microbes alongside Borrelia in patients suffering from TBD. To evaluate the involvement of multiple microbial immune responses in patients experiencing TBD we utilized enzyme-linked immunosorbent assay. Four hundred and thirty-two human serum samples organized into seven categories followed Centers for Disease Control and Prevention two-tier Lyme disease (LD) diagnosis guidelines and Infectious Disease Society of America guidelines for post-treatment Lyme disease syndrome. All patient categories were tested for their immunoglobulin M (IgM) and G (IgG) responses against 20 microbes associated with TBD. Our findings recognize that microbial infections in patients suffering from TBDs do not follow the one microbe, one disease Germ Theory as 65% of the TBD patients produce immune responses to various microbes. We have established a causal association between TBD patients and TBD associated co-infections and essential opportunistic microbes following Bradford Hill's criteria. This study indicated an 85% probability that a randomly selected TBD patient will respond to Borrelia and other related TBD microbes rather than to Borrelia alone. A paradigm shift is required in current healthcare policies to diagnose TBD so that patients can get tested and treated even for opportunistic infections.
Syntheses of 2′,3′-Dideoxykanamycin A, 2′,3′-Dideoxyamikacin and Related Substances (1987)

Abstract 2′,3′-Dideoxykanamycin A has been prepared via two ways. 2″-O-Acetyl-4″,6″-O-benzylidene-6′-N,4′-O-carbonyl-1,3,3″-tri-N-tosylkanamycin A was converted to a 2′,3′-unsaturated compound by a modified Tipson and Cohen method. Hydrogenation followed by deblocking gave 2′,3′-dideoxykanamycin A (12). Another route for 12 was through 2′,3′-anhydro-4′,2″,4″,6″-tetra-O-benzoyl-2′-epi-1,3,6′,3″-tetrakis(N-ethoxycarbonyl)kanamycin A (16). Epoxide-ring opening of 16 with hydrogen iodide gave the 3′,2′-iodohydrin, which, after 2′-O-mesylation, led to the 2′,3′-unsaturated compound (19). Deblocking and hydrogenation of 19 gave 12. 2′,3′-Dideoxykanamycin A thus synthesized was led to 2′,3′-dideoxyamikacin and other related compounds by amino protection of 12 other than the 1-amino group by zinc acetate–ethyl trifluoroacetate method followed by 1-N-acyl or 1-urethane formation with appropriate reagents. Their antibacterial activities were described.
TUNICAMYCIN, A NEW ANTIBIOTIC. I (1971)

Tunicamycin is a new antiviral antibiotic produced by Streptomyces lysosuperificus, nov. sp. The active substance in culture broth is purified by solvent extraction followed by chromatography on silicic acid. It has a mole- cular weight of about 870. The antibiotic is active against animal and plant viruses, Gram-positive bacteria, yeast and fungi. Tunicamycin is similar in some properties to a few known antibiotics but differs from them in certain special characteristics.
The demonstration of low-cost and logic process fully-compatible OTP memory on advanced HKMG CMOS with a newly found dielectric fuse breakdown (2015)

For the first time, the dielectric fuse breakdown has been observed in HKMG and poly-Si CMOS devices. It was found that, different from the conventional anti-fuse dielectric breakdown, such as the hard and soft breakdowns, this new fuse-breakdown behavior exhibits a typical property of an open gate and can be operated in much lower programming current (<; 50μA), fast speed (~20μsec), and excellent data retention, in comparison to the other fuse mechanisms. Based on this new mechanism, we have designed a smallest memory cell array which can be easily integrated into state-of-the-art advanced CMOS technology to realize highly reliable, secure, and dense OTP functionality with very low cost to meet the requirements of memory applications in the IoT era.