gebhart/patrepeval huggingface dataset:
Cellular and Cytokine Correlates of Mucosal Protection in Murine Model of Oral Candidiasis (2000)

Host protection against Candida albicans infection in a model of oral candidiasis involving infection-prone [DBA/2 (H-2(d))] and less infection-prone [BALB/c (H-2(d))] mouse strains was analyzed in terms of antibody and cellular responses, and in terms of cytokine patterns from regional lymph node cells. There was a selective expansion of gamma/delta(+) T-cell receptor cells, which correlated with the patterns of colonization in both mouse strains, with higher numbers of gamma/delta T cells detected in BALB/c mice. Antigen-induced T-cell proliferation was significantly higher in BALB/c mice than in DBA/2 mice. Higher levels of serum immunoglobulin G (IgG) and salivary IgA antibodies were detected in BALB/c mice than in DBA/2 mice, but only after the infection was cleared. The cervical lymph node cells from infected mice were assessed for interleukin-4 (IL-4), IL-12, and gamma interferon (IFN-gamma) mRNA gene expression by reverse transcription-PCR and protein production in the culture supernatants following restimulation in vitro. In BALB/c mice, an early increase in levels of IL-4, IFN-gamma, and IL-12 correlated with rapid elimination of C. albicans. In DBA/2 mice, where resolution of infection was delayed, IL-4 message expression was delayed and the IL-4 secretion level was lower. Neutralization of IL-4 by multiple injections of an anti-IL-4 monoclonal antibody in BALB/c mice resulted in increased carriage rate and delayed clearance of the yeasts. Collectively, the data suggest that the T-cell response to C. albicans in the regional lymph nodes which correlates best with rapid oral clearance of C. albicans is a balanced Th0 cytokine response involving early secretion of both IFN-gamma and IL-4.
ADAPTIVE BASEBANDNF PREDISTORTER FOR POWER AMPLIFIERS CHARACTERIZATION USING DIGITAL RECEIVERS THROUGH INSTANTANEOUS AM-AM AND AM-PM (2000)

This paper presents a powerful adaptive basedband/RF predistorter, which uses advantageously the concept of digital receiver technology into power amplifier (PA) linearization area. The linearizer performs an instantaneous characterization of the PA using two digital receivers to supply its AM-AM and AM-PM transfer functions. W-CDMA signals applying different stress level on PA are used to evaluate the performance of the predistorter. The entire system is validated using DSPmF CO-simulation for a typical class AB power amplifier. Results from different cases of standards signals reveal a significant reduction in effective output power back off (OBO).
Polyurethanes Based on Fluorinated Diols (1996)

Two types of fluorinated polyurethanes were prepared, and their thermal and surface properties were evaluated. Polyurethanes containing fluorinated segments in the backbone were synthesized based on ethylene-fluoroalkyl-ethylene diols and 1,6-hexamethylene diisocyanate (HDI). Polyurethanes containing fluorinated side chains were prepared from a polyfluorooxetane prepolymer, methylene bis(phenylene isocyanate) (MDI) or isophorone diisocyanate (IPDI), and using benzene dimethanol (BDM) as the chain extender. Both types of polyurethanes show low glass transition temperatures and low surface energies (i.e. high advancing contact angles of water.)
Time-Steered Array with a Chirped Grating Beamformer (1997)

Optical techniques for time-steered control of phased array antennas have been under intense study in recent years [1].
Responsive Polymer Coatings for Smart Applications in Chromatography, Drug Delivery Systems, and Cell Sheet Engineering (2012)

This chapter contains sections titled: Introduction Temperature-Responsive Chromatography Temperature-Responsive Polymer Micelles Temperature-Responsive Culture Surfaces Cell Sheet Engineering Conclusions References
Airborne radioactive contamination monitoring (1996)

Current technologies for the detection of airborne radioactive contamination do not provide real-time capability. Most of these techniques are based on the capture of particulate matter in air onto filters which are then processed in the laboratory; thus, the turnaround time for detection of contamination can be many days. To address this shortcoming, an effort is underway to adapt LRAD (Long-Range-Alpha-Detection) technology for real-time monitoring of airborne releases of alpa-emitting radionuclides. Alpha decays in air create ionization that can be subsequently collected on electrodes, producing a current that is proportional to the amount of radioactive material present. Using external fans on a pipe containing LRAD detectors, controlled samples of ambient air can be continuously tested for the presence of radioactive contamination. Current prototypes include a two-chamber model. Sampled air is drawn through a particulate filter and then through the first chamber, which uses an electrostatic filter at its entrance to remove ambient ionization. At its exit, ionization that occurred due to the presence of radon is collected and recorded. The air then passes through a length of pipe to allow some decay of short-lived radon species. A second chamber identical to the first monitors the remaining activity. Further development is necessary on air samples without the use of particulate filtering, both to distinguish ionization that can pass through the initial electrostatic filter on otherwise inert particulate matter from that produced through the decay of radioactive material and to separate both of these from the radon contribution. The end product could provide a sensitive, cost-effective, real-time method of determining the presence of airborne radioactive contamination.
Abstract IA13: Recurrent SPOP mutations define a distinct molecular subclass of prostate cancer (2012)

Abstract Prostate cancer is a clinically heterogeneous disease with marked variability in outcomes. To identify somatic mutations that may drive prostate cancer and aid in molecular characterization, we sequenced the exomes of 112 tumor/normal pairs obtained from men with localized disease. SPOP (Speckled Type POZ) was the most frequently mutated gene, with mutations involving the SPOP substrate binding cleft in 6-15% of tumors from multiple independent cohorts. SPOP-mutant prostate cancers lacked ETS rearrangements and exhibited a distinct pattern of genomic alterations. Thus, SPOP mutations may define a new molecular subtype of prostate cancer. Citation Format: Christopher E. Barbieri, Sylvan C. Baca, Michael S. Lawrence, Gad Getz, Mark A. Rubin, Levi A. Garraway, On the behalf of the Broad Institute and Weill Cornell Medical College Prostate Cancer Sequencing Group. Recurrent SPOP mutations define a distinct molecular subclass of prostate cancer [abstract]. In: Proceedings of the AACR Special Conference on Advances in Prostate Cancer Research; 2012 Feb 6-9; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2012;72(4 Suppl):Abstract nr IA13.
No-reference Harmony-Guided Quality Assessment (2013)

Color harmony of simple color patterns has been widely studied for color design. Rules defined then by psychological experiments have been applied to derive image aesthetic scores, or to re-colorize pictures. But what is harmonious or not in an image? What can the human eye perceive disharmonious? Extensive research has been done in the context of quality assessment to define what is visible or not in images and videos. Techniques based on human visual system models use signal masking to define visibility thresholds. Based on results in both fields, we present a harmony quality assessment method to assess what is harmonious or not in an image. Color rules are used to detect what part of images are disharmonious, and visual masking is applied to estimate to what extent an image area can be perceived disharmonious. The output perceptual harmony quality map and scores can be used in a photo editing framework to guide the user getting the best artistic effects. Results show that the harmony maps reflect what a user perceives and that the score is correlated to the artistic intent.
VisNIR integrated multi-sensing penetrometer for in situ high-resolution vertical soil sensing (2020)

An in situ penetrometer system that can measure profile soil properties rapidly, cost-effectively, and at high vertical resolution would benefit the soil science and agriculture communities. A visible and near infrared (VisNIR) integrated multi-sensing penetrometer system was developed to automatically measure in situ soil VisNIR reflectance spectra, penetration resistance, and insertion depth along a soil profile. The system was tested in 11 agricultural fields in Nebraska, Illinois, Iowa, and South Dakota of the U.S. An independent soil VisNIR spectral library was used to build calibration models for soil property prediction. External Parameter Orthogonalization (EPO) was used to correct for the field intactness of in situ VisNIR spectra. The results showed that EPO was effective in correcting for the spectral disparity between in situ and dry-ground VisNIR spectra. The EPO correction showed an improvement of prediction accuracy of soil total carbon (R2 and RMSE improved from 0.29 and 3.06 % to 0.5 and 0.79 %, respectively) and total nitrogen (R2 and RMSE improved from 0.51 and 0.36 % to 0.62 and 0.06 %, respectively). The system also predicted soil bulk density with an RMSE of 0.12 g cm−3 and R2 of 0.80. It is concluded that the VisNIR multi-sensing penetrometer, along with the use of external soil spectral libraries and the spectral correction algorithm EPO, can lead to a rapid, robust and cost-effective system for in situ high resolution vertical soil sensing.
Thermal and fluid characteristics during cryogen spray cooling (2001)

Cryogen spray cooling (CSC) is a technique to protect the epidermis from non-specific thermal injury during laser treatment of various dermatoses. Successful application of CSC in conjunction with laser treatment of heavily pigmented individuals, and high radiant exposures which may be required for effective therapeutic outcomes, requires enhancement of heat removal. We have investigated the thermal mechanisms, and effects of droplet size, density and velocity on heat removal during CSC. Our results suggest that although the inherent thermal diffusivity of skin may be a limiting factor in heat removal, parameters such as droplet size, density, and velocity are important, and should be optimized for maximum heat removal.
Recent Development in Synthetic Strategies for Oseltamivir Phosphate (2011)

Abstract Recent developments in synthetic strategies toward an important anti‐influenza drug, oseltamivir phosphate, are discussed. The importance of the drug further increased after the influenza A (H1N1) pandemic in 2009 and the emergence of the highly virulent avian influenza H5N1, which might eventually acquire the ability to spread between humans. Currently, the drug is produced in an industrial process of 11 chemical steps starting from (–)‐shikimic acid, whose availability is limited due to the massive demand of the drug. Thus, many chemists have been working to develop alternative synthetic processes to produce this important drug starting from readily available materials using environmentally benign, operationally safe, and cost‐effective methods. Synthetic efforts made by each group of chemists are described in this review article. The development of novel synthetic methodologies and novel reactions has had a great impact on the efficient syntheses of functional molecules, such as drugs like oseltamivir phosphate.
A Novel Efficient Method for Conflicts Set Generation for Model-Based Diagnosis (2009)

In this paper we present a new efficient algorithmic method for generating the conflicts set for model based diagnosis. Our new method combines the strength of the two different approaches proposed in the literature, that is, the fault detection and isolation (FDI), which is based on automatic control theory and statistical decision theory, and the other one, known as DX, which is based on artificial intelligence techniques. The first building block in our method is a new efficient algorithm for generation of the complete set of analytical redundancy relations (ARRs) for the system in an implicit form. For the diagnosis, our method first performs (similar to DX approaches) a system simulation to calculate the expected values of the measurements. Any discrepancy, i.e., the difference between expected and actual value of measurement, would trigger our diagnosis process. To this end, only those ARRs which involve the measurement with discrepancy are checked for consistency which lead a to a significant reduction in the number of consistency checks usually performed by DX approaches. We demonstrate the efficiency of our new method by its application to several synthetic systems and compare it with that of GDE.
Stat6-Dependent and -Independent Pathways for IL-4 Production (1999)

Stat6 has been shown to have a crucial role in the IL-4-dependent differentiation of Th2 cells. In this report, we explore whether in vitro Th2 differentiation driven by altered costimulatory signals or Ag dose is Stat6 dependent. We find that blocking B7-1 signaling in vitro promotes the differentiation of IL-4-secreting Th2 cells in wild-type but not Stat6-deficient T cell cultures. Additionally, stimulation with peptide Ag doses that normally result in the production of Th2 cells in vitro fails to do so in cultures of Stat6-deficient cells. We also demonstrate that Stat6 is required for the in vitro differentiation of CD8+ T cells into IL-4-secreting cytotoxic T cell type 2 cells. However, IL-4 expression is not absolutely dependent on Stat6. We demonstrate that populations of T cells that do not require IL-4 for their development, such as NK T cells, are still competent to secrete IL-4 in the absence of Stat6. These results demonstrate that Stat6 is required for the differentiation program leading to the generation of Th2 and cytotoxic T cell type 2 cells but not for IL-4 expression in cells that do not undergo differentiation in response to IL-4.
Beam forming method and apparatus therefor in ultrasonic imaging system (1994)

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IFN for Treatment of Severe Idiopathic Sudden Sensorineural Hearing Loss. IFN Therapy without Steroids. (1995)

The severe type of idiopathic sudden sensor-ineural hearing loss (ISSHL) was treated with recombinant interferon alpha-2a (IFN-α) (3MU/day for 10 days) without steroids. Complete recovery was observed in nine out of eleven patients with severe ISSHL, and the hearing of the remaining two patients recovered ≥30dB.Ototoxicity, including sensorineural hearing loss has been reported to be induced by IFN. Our results with IFN in ISSHL suggest that, although IFN can be ototoxic at high doses, low dose IFN may be effective in the treatment of ISSHL caused by inner ear damage.Thus, IFN may actually be an effective substitute for steroids in ISSHL therapy.
Organocatalytic Aziridine Synthesis Using F<sup>+</sup> Salts (2009)

This paper describes a unique application of the fluoronium cation (F+) as an organocatalyst for mediating the reaction between N-substituted imines and ethyl diazoacetate affording excellent yields of N-substituted aziridines.
<title>Sensor web: a new instrument concept</title> (2001)

The confluence of the rapidly expanding sensor, computation, and telecommunication industries has allowed for a new instrument concept: the Sensor Web. A Sensor Web consists of intra-communicating, spatially-distributed sensor pods that are deployed to monitor and explore environments. It is capable of automated reasoning for it can perform intelligent autonomous operations in uncertain environments, respond to changing environmental conditions, and carry out automated diagnosis and recovery. Sensor Webs could have as much an impact on the uses of sensors as the Internet did on the uses of computers. Sensor Webs are often confused with distributed sensors or sensor networks. The unique feature of the Sensor Web is that information gathered by one pod is shared and used by other pods. In contrast, sensor networks merely gather data and information gathered by a particular pod on such a network does not influence the behavior of another pod. Thus, sensor networks collect data while Sensor Webs can react and modify their behavior on the basis of the collected data. This paper will outline the potential of the Sensor Web concept and describe the Jet Propulsion Laboratory Sensor Webs Project. In particular, a prototype Sensor Web deployed at the Huntington Botanical Gardens will be discussed.
Flexibility Reserve in Power Systems: Definition and Stochastic Multi-Fidelity Optimization (2019)

This paper defines flexibility reserve trajectory as a single reserve product that not only supplies the energy imbalance in real-time operation but also the resulting ramping requirements by embedding the flexible ramping trajectories as time derivative of the reserve trajectories. Further, a stochastic optimization model is proposed for multi-fidelity co-optimization of energy and flexibility reserve in day-ahead power systems operation. The proposed model integrates operation decisions with different levels of modeling fidelity in a single stochastic optimization problem. More specifically, day-ahead energy trajectories, day-ahead flexibility reserve capacity trajectories, and real-time flexibility reserve deployment trajectories are modeled by Bernstein polynomials with different degrees as required to match the load and renewable generation with different levels of variability in day-ahead and real-time operations. The proposed model is implemented on the IEEE reliability test system using load and solar generation data of California ISO, where the numerical results demonstrate that the proposed model schedules a reserve capacity that more accurately matches the real-time energy imbalance and ramping requirements of net-load, while reducing the total operation cost of the system.
A peptidomimetic with a chiral switch is an inhibitor of epidermal growth factor receptor heterodimerization (2017)

// Shanthi P. Kanthala 1 , Yong-Yu Liu 1 , Sitanshu Singh 1 , Rushikesh Sable 1 , Sandeep Pallerla 1 and Seetharama D. Jois 1 1 Basic Pharmaceutical Sciences, School of Pharmacy, University of Louisiana at Monroe, Monroe LA 71201, USA Correspondence to: Seetharama D. Jois, email: jois@ulm.edu Keywords: HER2, protein-protein interaction, breast cancer, peptidomimetic, dual inhibitor Received: February 15, 2017      Accepted: June 16, 2017      Published: July 05, 2017 ABSTRACT Among different types of EGFR dimers, EGFR-HER2 and HER2-HER3 are well known in different types of cancers. Targeting dimerization of EGFR will have a significant impact on cancer therapies. A symmetric peptidomimetic was designed to inhibit the protein-protein interaction of EGFR. The peptidomimetic (Cyclo(1,10)PpR ( R ) Anapa-FDDF-( R )-Anapa)R, compound 18) was shown to exhibit antiproliferative activity with an IC 50 of 194 nM in HER2-expressing breast cancer cell lines and 18 nM in lung cancer cell lines. The peptidomimetic has a Pro-Pro sequence in the structure to stabilize the β-turn and a β-amino acid, amino napthyl propionic acid. To investigate the effect of the chirality of β-amino acid on the structure of the peptide and its antiproliferative activity, diastereoisomers of compound 18 were designed and synthesized. Structure-activity relationships of these compounds indicated that there is a chiral switch at β-amino acid in the designed compound. The peptidomimetic with R configuration at β-amino acid and with a L-Pro-D-Pro sequence was the most active compound (18). Using enzyme complement fragmentation assay and proximity ligation assay, we show that compound 18 inhibits HER2:HER3 and EGFR:HER2 dimerization. Surface plasmon resonance studies suggested that compound 18 binds to the HER2 extracellular domain and in particular to domain IV. The anticancer activity of compound 18 was evaluated using a xenograft model of breast cancer in mice; compound 18 suppressed the tumor growth in mice compared to control. Compound 18 was also shown to have a synergistic effect with erlotinib on EGFR mutated lung cancer cell lines.
Butterfly Structure for Viterbi Decoders of All Rates k/n (2007)

This paper proposes a butterfly structure for Viterbi decoders, which works for convolutional codes of all rates k/n. The proposed butterfly structure can exploit the inherent symmetry of trellis branches, so that only some branch metrics need to be computed, while the others can be derived from the computed branches. Consequently, the computational complexity of the Viterbi decoder can be significantly reduced without any error performance loss. The applicability of the butterfly structure is validated by the best codes of rates 1/2, 2/3, and 3/4. Most of the best codes can apply the butterfly structure to reduce their branch metric computation complexity by a factor of 2 or 4. This study also reports a number of new codes with high branch symmetry under the symmetry consideration. Their branch metric computation can be reduced by a factor of 4, 8 or 16 with the similar performance to the best codes.
Selectively etched undercut apertures in AlAsSb-based VCSELs (2001)

Apertures were formed in single-growth, AsSb-based, long-wavelength (1.55 μm) vertical-cavity surface-emitting lasers by laterally etching the active region. The materials contrast between the AlAsSb-based mirrors and the AlInGaAs-based active region leads to a high selectivity for the etch, allowing long apertures to be formed with minimal etching of the mirrors. Lasers showing reduced threshold currents and increased efficiencies were demonstrated using these apertures.
Coat–protein–mediated resistance to tobacco mosaic virus: discovery mechanisms and exploitation (1999)

In 1986 we reported that transgenic plants which accumulate the coat protein of tobacco mosaic virus (TMV) are protected from infection by TMV, and by closely related tobamoviruses. The phenomenon is referred to as coat-protein-mediated resistance (CP-MR), and bears certain similarities to cross protection, a phenomenon described by plant pathologists early in this century. Our studies of CP-MR against TMV have demonstrated that transgenically expressed CP interferes with disassembly of TMV particles in the inoculated transgenic cell. However, there is little resistance to local, cell-to-cell spread of infection. CP-MR involves interaction between the transgenic CP and the CP of the challenge virus, and resistance to TMV is greater than to tobamo viruses that have CP genes more distantly related to the transgene. Using the known coordinates of the three-dimensional structure of TMV we developed mutant forms of CP that have stronger inter-subunit interactions, and confer increased levels of CP-MR compared with wild-type CP. Similarly, it is predicted that understanding the cellular and structural basis of CP-MR will lead to the development of variant CP transgenes that each can confer high levels of resistance against a range of tobamoviruses.
AutoISES: automatically inferring security specifications and detecting violations (2008)

The importance of software security cannot be overstated. In the past, researchers have applied program analysis techniques to automatically detect security vulnerabilities and verify security properties. However, such techniques have limited success in reality because they require manually provided code-level security specifications. Manually writing and generating these code-level security specifications are tedious and error-prone. Additionally, they seldom exist in production software.

In this paper, we propose a novel method and tool, called AutoISES, which Automatically Infers Security Specifications by statically analyzing source code, and then directly use these specifications to automatically detect security violations. Our experiments with the Linux kernel and Xen demonstrated the effectiveness of this approach - AutoISES automatically generated 84 security specifications and detected 8 vulnerabilities in the Linux kernel and Xen, 7 of which have already been confirmed by the corresponding developers.