gebhart/patrepeval huggingface dataset:
Myasthenogenicity of the main immunogenic region and endogenous muscle nicotinic acetylcholine receptors (2011)

In myasthenia gravis (MG) and experimental autoimmune MG (EAMG), many pathologically significant autoantibodies are directed at the main immunogenic region (MIR), a conformation-dependent region at the extracellular tip of α1 subunits of muscle nicotinic acetylcholine receptors (AChRs). Human muscle AChR α1 MIR sequences were integrated into Aplysia ACh-binding protein (AChBP). The chimera was potent in inducing both acute and chronic EAMG, though less potent than Torpedo electric organ AChR. Wild-type AChBP also induced EAMG but was less potent, and weakness developed slowly without an acute phase. AChBP is more closely related in sequence to neuronal α7 AChRs that are also homomeric; however, autoimmune responses were induced to muscle AChR, but not to neuronal AChR subtypes. The greater accessibility of muscle AChRs to antibodies, compared to neuronal AChRs, may allow muscle AChRs to induce self-sustaining autoimmune responses. The human α1 subunit MIR is a potent immunogen for producing pathologically significant autoantibodies. Additional epitopes in this region or other parts of the AChR extracellular domain contribute significantly to myasthenogenicity. We show that an AChR-related protein can induce EAMG. Thus, in principle, an AChR-related protein could induce MG. AChBP is a water-soluble protein resembling the extracellular domain of AChRs, yet rats that developed EAMG had autoantibodies to AChR cytoplasmic domains. We propose that an initial autoimmune response, directed at the MIR on the extracellular surface of muscle AChRs, leads to an autoimmune response sustained by muscle AChRs. Autoimmune stimulation sustained by endogenous muscle AChR may be a target for specific immunosuppression.
Mixed-Backbone Oligonucleotides Containing Segments of Deoxynucleosides Phosphorothioate and 2'-O-Methylribonucleosides Methylphosphonate: Synthesis and Properties (1999)

Abstract Synthesis of mixed-backbone oligonucleotides containing segments of deoxynucleoside. phosphorothioate and 2'-O-methylribonucleoside methylphosphonate have been achieved by using N-Pent-4-enoyl (PNT) heterocyclic base-protected 2'-O-methylribonucleoside methylphosphonamidites. Use of PNT for heterocyclic base-protection allows the deprotection to be carried out under milder conditions without affecting base labile methylphosphonate internucleotide linkages. New MBOs have reduced phosphorothioate internucleotide linkages while maintaining affinity with target RNA and are stable towards nucleases. Keywords:: Phosphorothioatemethylphosphonatemethylphosphonamiditephosphoramiditeoligonucleotideantisense
Expansins in growing tomato leaves (1995)

An expansin-like protein from growing tomato leaves was identified by its ability to restore the 'acid-growth' response to heat-inactivated tomato walls and by its similarity to expansins from cucumber hypocotyls. Native walls from growing tomato leaves exhibit an endogenous acid-induced extension (creep) that resembles in various biochemical characteristics the acid-growth activity of cucumber hypocotyls. For example, the acid-growth activity is lost when the walls of tomato leaves are briefly heated and is largely restored by addition of a crude protein extract from the walls of growing leaves. Wall proteins from growing leaves enhance the stress relaxation spectrum of tomato walls in a fashion characteristic of cucumber expansins. HPLC fractionation of the crude wall protein from tomato leaves yielded an active fraction containing a major 27 kDa protein that cross-reacts with an antibody raised against cucumber expansin. The results show that tomato leafwalls possess at least one expansin that is responsible for the acid-growth property of leaves and indicate that cell wall extension in leaves shares an underlying protein mechanism common to cell wall expansion in stems.
Whole-animal imaging of bacterial infection using endoscopic excitation of β-lactamase (BlaC)-specific fluorogenic probe (2016)

Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), remains one of the most frequent causes of death worldwide. The slow growth rate of Mtb limits progress toward understanding tuberculosis including diagnosis of infections and evaluating therapeutic efficacy. Development of near-infrared (NIR) β-lactamase (BlaC)-specific fluorogenic substrate has made a significant breakthrough in the whole-animal imaging to detect Mtb infection. The reporter enzyme fluorescence (REF) system using a BlaC-specific fluorogenic substrate has improved the detection sensitivity in whole-animal optical imaging down to ~10<sup>4</sup> colony forming units (CFU) of bacteria, about 100-fold improvement over recombinant strains. However, improvement of detection sensitivity is strongly needed for clinical diagnosis of early stage infection at greater tissue depth. In order to improve detection sensitivity, we have integrated a fiber-based microendoscpe into a whole-animal imaging system to transmit the excitation light from the fiber bundle to the fluorescent target directly and measure fluorescent level using BlaC-specific REF substrate in the mouse lung. REF substrate, CNIR800, was delivered via aerosol route to the pulmonary infected mice with <i>M. bovis </i>BCG strain at 24 hours post-infection and groups of mice were imaged at 1–4 hours post-administration of the substrate using the integrated imaging system. In this study we evaluated the kinetics of CNIR800 substrate using REF technology using the integrated imaging system. Integration of these technologies has great promise for improved detection sensitivity allowing pre-clinical imaging for evaluation of new therapeutic agents.
The development and application of 2-phase switched reluctance drives (1997)

When selecting or designing a switched reluctance (SR) system for a particular application, one of the first decisions that has to be made is that of the phase number to be used. It is well-known that SR systems can use any phase number from 1 upwards, though systems with more than 7 phases are rare. For high-power and/or industrial applications, 3-phase systems predominate, though 4-phase drives are well documented. Higher phase numbers have been advocated for some specialised applications. For low-power drives requiring only a modest performance level, 1-phase systems are often selected. This is particularly the case for domestic appliance drives, where cost sensitivity is extreme. By contrast, 2-phase systems have been virtually neglected. Though some authors report on the use of a 2-phase machine in their investigations of a particular phenomenon, there is very little work published on the design or application of 2-phase systems per se. This paper reports on the application of 2-phase SR Drives(R) in an industrial application at much higher power levels.
Flexible active-matrix organic light-emitting diode display enabled by MoS <sub>2</sub> thin-film transistor (2018)

Atomically thin molybdenum disulfide (MoS<sub>2</sub>) has been extensively investigated in semiconductor electronics but has not been applied in a backplane circuitry of organic light-emitting diode (OLED) display. Its applicability as an active drive element is hampered by the large contact resistance at the metal/MoS<sub>2</sub> interface, which hinders the transport of carriers at the dielectric surface, which in turn considerably deteriorates the mobility. Modified switching device architecture is proposed for efficiently exploiting the high-<i>k</i> dielectric Al<sub>2</sub>O<sub>3</sub> layer, which, when integrated in an active matrix, can drive the ultrathin OLED display even in dynamic folding states. The proposed architecture exhibits 28 times increase in mobility compared to a normal back-gated thin-film transistor, and its potential as a wearable display attached to a human wrist is demonstrated.
Quantized Multi-Rank Beamforming for MIMO-OFDM Systems (2008)

We consider the sum-rate maximization via linear preceding in downlink MIMO-OFDM systems with quantized feedback. We address the preceding codebook design based on the capacity measure by introducing a new distance metric. We propose a codebook structure and its associated design algorithm that allows for significant reduction in the memory requirement and computational complexity in real-time system implementation. We then provide a system design approach comprising of four main ingredients: (i) a multi-rank beamforming (MRBF) scheme, (ii) an efficient CQI-based precoder selection algorithm, (iii) reduced feedback strategies, and (iv) novel channel quality indicator (CQI) combining. Our simulation results show that the proposed MRBF scheme can approach the precoding upper bounds with relatively few feedback bits. Moreover, with the same number of bits, the proposed scheme simultaneously achieves higher throughput and lower computational complexity in comparison to the other existing precoding schemes.
2′Fluoro Modification Differentially Modulates the Ability of RNAs to Activate Pattern Recognition Receptors (2016)

Although the use of RNAs has enormous therapeutic potential, these RNA-based therapies can trigger unwanted inflammatory responses by the activation of pattern recognition receptors (PRRs) and cause harmful side effects. In contrast, the immune activation by therapeutic RNAs can be advantageous for treating cancers. Thus, the immunogenicity of therapeutic RNAs should be deliberately controlled depending on the therapeutic applications of RNAs. In this study, we demonstrated that RNAs containing 2'fluoro (2'F) pyrimidines differentially controlled the activation of PRRs. The activity of RNAs that stimulate toll-like receptors 3 and 7 was abrogated by the incorporation of 2'F pyrimidine. By contrast, incorporation of 2'F pyrimidines enhanced the activity of retinoic acid-inducible gene 1-stimulating RNAs. Furthermore, we found that transfection with RNAs containing 2'F pyrimidine and 5' triphosphate (5'ppp) increased cell death and interferon-β expression in human cancer cells compared with transfection with 2'hydroxyl 5'ppp RNAs, whereas RNAs containing 2'O-methyl pyrimidine and 5'ppp completely abolished the induction of cell death and cytokine expression in the cells. Our findings suggest that incorporation of 2'F and 2'O-methyl nucleosides is a facile approach to differentially control the ability of therapeutic RNAs to activate or limit immune and inflammatory responses depending on therapeutic applications.
<i>In Vitro</i> Activity of the Novel Antimicrobial Peptide Dendrimer G3KL against Multidrug-Resistant Acinetobacter baumannii and Pseudomonas aeruginosa (2015)

The in vitro activity of the novel antimicrobial peptide dendrimer G3KL was evaluated against 32 Acinetobacter baumannii (including 10 OXA-23, 7 OXA-24, and 11 OXA-58 carbapenemase producers) and 35 Pseudomonas aeruginosa (including 18 VIM and 3 IMP carbapenemase producers) strains and compared to the activities of standard antibiotics. Overall, both species collections showed MIC50/90 values of 8/8 μg/ml and minimum bactericidal concentrations at which 50% or 90% of strains tested are killed (MBC50/90) of 8/8 μg/ml. G3KL is a promising molecule with antibacterial activity against multidrug-resistant and extensively drug-resistant A. baumannii and P. aeruginosa isolates.
LY3298176, a novel dual GIP and GLP-1 receptor agonist for the treatment of type 2 diabetes mellitus: From discovery to clinical proof of concept (2018)

Based on these results, the pharmacology of LY3298176 translates from preclinical to clinical studies. LY3298176 has the potential to deliver clinically meaningful improvement in glycaemic control and body weight. The data warrant further clinical evaluation of LY3298176 for the treatment of T2DM and potentially obesity.
Intermetallic reinforced Cr alloys for high-temperature use (1999)

AbstractA new family of Cr(Ta)-Cr2Ta intermetallic alloys based on Cr-(6-10)Ta (at%) is currently under development for structural use in oxidizing environments in the 1,000–1,300°C temperature range. These alloys show excellent strength and creep resistance and good oxidation resistance at high temperatures in air. Oxidation resistance comparable to commercial reactive element doped chromia-forming alloys and creep resistance comparable to single-crystal superalloys have been demonstrated. To date, only modest room-temperature fracture toughness (in the 11–12 MPa m½ range) has been achieved. Preliminary results of a promising approach to improve room-temperature fracture toughness via ductilization of Cr with MgO additions are discussed.Keywords: Intermetallic reinforced Cr alloysCroxidationLaves phasemechanical propertiesMgO
Supervised Multi-View Canonical Correlation Analysis (sMVCCA): Integrating Histologic and Proteomic Features for Predicting Recurrent Prostate Cancer (2014)

In this work, we present a new methodology to facilitate prediction of recurrent prostate cancer (CaP) following radical prostatectomy (RP) via the integration of quantitative image features and protein expression in the excised prostate. Creating a fused predictor from high-dimensional data streams is challenging because the classifier must 1) account for the "curse of dimensionality" problem, which hinders classifier performance when the number of features exceeds the number of patient studies and 2) balance potential mismatches in the number of features across different channels to avoid classifier bias towards channels with more features. Our new data integration methodology, supervised Multi-view Canonical Correlation Analysis (sMVCCA), aims to integrate infinite views of highdimensional data to provide more amenable data representations for disease classification. Additionally, we demonstrate sMVCCA using Spearman's rank correlation which, unlike Pearson's correlation, can account for nonlinear correlations and outliers. Forty CaP patients with pathological Gleason scores 6-8 were considered for this study. 21 of these men revealed biochemical recurrence (BCR) following RP, while 19 did not. For each patient, 189 quantitative histomorphometric attributes and 650 protein expression levels were extracted from the primary tumor nodule. The fused histomorphometric/proteomic representation via sMVCCA combined with a random forest classifier predicted BCR with a mean AUC of 0.74 and a maximum AUC of 0.9286. We found sMVCCA to perform statistically significantly (p < 0.05) better than comparative state-of-the-art data fusion strategies for predicting BCR. Furthermore, Kaplan-Meier analysis demonstrated improved BCR-free survival prediction for the sMVCCA-fused classifier as compared to histology or proteomic features alone.
EFFECT OF MICRITE CONTENT ON CALCITE CEMENTATION IN AN UPPER JURASSIC CARBONATE RESERVOIR, EASTERN SAUDI ARABIA (2018)

Cementation is a primary factor reducing the porosity of carbonate rocks. It is a challenge to accurately model cementation for reservoir quality prediction because cementation is often a syndepositional process. In addition, cementation requires fluid flow to transport chemical species for precipitation within the pore spaces in a sediment. The development of fully‐coupled depositional‐hydrogeochemical models for cementation prediction is desirable, but the parameters which control the extent of cementation need to be identified and evaluated. This study uses petrographic data from 583 carbonate samples from 15 wells in an Upper Jurassic (Kimmeridgian) reservoir at a giant oilfield in eastern Saudi Arabia to investigate the controlling effects of micrite content on cementation in carbonate rocks. The results indicate that the amount of cement decreases with increasing micrite content in the carbonate rocks analysed. In addition, a modified Houseknecht method has been developed to assess the relative fractions of porosity reduction in carbonate sediments due to compaction and cementation. The method highlights variations in depositional porosity for different rock textures and distinguishes microporosity from interparticle porosity. In the studied samples, the total porosity loss due to compaction and cementation is generally less than 45%, and samples lose more porosity due to compaction than cementation. The relative importance of compaction and cementation in reducing porosity is different for different rock textures: wackestones and mudstones lose porosity mostly as a result of compaction, while grainstones, mud‐lean packstones and packstones lose porosity due to both compaction and cementation.
A quantum key distribution system for optical fiber networks (2005)

A novel, user-friendly quantum key distribution (QKD) system operating at a wavelength of 1550nm and at a clock rate of 10MHz was constructed to explore the compatibility of this emerging technology with the optical fiber network environment. Custom circuit boards providing the low-level control and sensing functions for both the transmitter and receiver were developed, allowing software-based system reconfiguration via USB interface to personal computers. The computer control allowed the user to change operating parameters such as detector bias voltages and pulse delays and also allowed for self-tuning of the system. Epitaxx avalanche photodiodes, operated in Geiger mode, were used to detect the single photons. A complete QKD protocol stack incorporating the sifting, reconciliation, privacy amplification, authentication and key confirmation functions was implemented in software. The system was tested over twenty five kilometers of dark underground fiber, producing 18.6 million sifted bits, with a sifted bit error rate of 4.9% at an average number of photons per pulse of 0.2, during a continuous 12-hour period of self-sustaining operation: a small portion of the secret bits distilled from each session's sifted bits were used to authenticate the next session. A total of 6.8 million shared secret bits were produced.
Thermal Calibration of Silicon MEMS Gyroscopes (2012)

We report our progress on the development of thermal calibration and stabilization for silicon MEMS gyroscopes with high quality (Q) factors. The temperature-induced drifts of most MEMS limit their potential applications in realworld missions. To address this limitation, we investigated a long-term bias drift compensation algorithm using the silicon MEMS quadruple mass gyroscope (QMG) with signal-tonoise ratio enhanced by 1.2 million Q-factor. The thermal calibration using an external temperature sensor removed a 99% temperature correlation between the temperature and the gyroscope output. The calibration stabilized the QMG output subject to temperature variations during a 24 hr run, resulting in Allan deviation bias instability improvement from 0.6 °/hr to 0.35 °/hr. Most importantly, this method removed a temperature ramp and resolved a 1 °/hr/ p hr rate
On optimal call admission control in cellular networks (2002)

Two important quality-of-service (QoS) measures for current cellular networks are the fractions of new and handoff "calls" that are blocked due to unavailability of "channels" (radio and/or computing resources). Based on these QoS measures, we derive optimal admission control policies for three problems: minimizing a linear objective function of the new and handoff call blocking probabilities (MINOBJ), minimizing the new call blocking probability with a hard constraint on the handoff call blocking probability (MINBLOCK) and minimizing the number of channels with hard constraints on both of the blocking probabilities (MINC). We show that the well-known guard channel policy is optimal for the MLNOBJ problem, while a new fractional guard channel policy is optimal for the MINBLOCK and MINC problems. The guard channel policy reserves a set of channels for handoff calls while the fractional guard channel policy effectively reserves a non-integral number of guard channels for handoff calls by rejecting new calls with a probability that depends on the current channel occupancy. It is also shown that the fractional policy results in significant savings (20-50%) in the new call blocking probability for the MINBLOCK problem and provides some, though small, gains over the integral guard channel policy for the MINC problem. Further, we also develop computationally inexpensive algorithms for the determination of the parameters for the optimal policies.
60-GHz LTCC Patch Antenna Array With an Integrated EBG Structure for Gain Enhancement (2016)

This letter presents a 60-GHz 2 × 2 low temperature co-fired ceramic (LTCC) aperture-coupled patch antenna array with an integrated Sievenpiper electromagnetic band-gap (EBG) structure used to suppress TM-mode surface waves. The merit of this EBG structure is to yield a predicted 4-dB enhancement in broadside directivity and gain, and an 8-dB improvement in sidelobe level. The novelty of this antenna lies in the combination of a relatively new LTCC material system (DuPont Greentape 9K7) along with laser ablation processing for fine line and fine slot definition (50-μm gaps with +/ - 6 μm tolerance) allowing the first successful integration of a Sievenpiper EBG structure with a millimeter-wave LTCC patch array. A measured broadside gain/directivity of 11.5/14 dBi at 60 GHz is achieved with an aperture footprint of only 350 × 410 mil <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> (1.78λ × 2.08λ) including the EBG structure. This thin (27 mil) LTCC array is well suited for chip-scale package applications.
Cloning and functional expression of a cDNA encoding a pheromone gland-specific acyl-CoA Δ <sup>11</sup> -desaturase of the cabbage looper moth, <i>Trichoplusia ni</i> (1998)

Desaturation of coenzyme-A esters of saturated fatty acids is a common feature of sex pheromone biosynthetic pathways in the Lepidoptera. The enzymes that catalyze this step share several biochemical properties with the ubiquitous acyl-CoA Delta9-desaturases of animals and fungi, suggesting a common ancestral origin. Unlike metabolic acyl-CoA Delta9-desaturases, pheromone desaturases have evolved unusual regio- and stereoselective activities that contribute to the remarkable diversity of chemical structures used as pheromones in this large taxonomic group. In this report, we describe the isolation of a cDNA encoding a pheromone gland desaturase from the cabbage looper moth, Trichoplusia ni, a species in which all unsaturated pheromone products are produced via a Delta11Z-desaturation mechanism. The largest ORF of the approximately 1,250-bp cDNA encodes a 349-aa apoprotein (PDesat-Tn Delta11Z) with a predicted molecular mass of 40,240 Da. Its hydrophobicity profile is similar overall to those of rat and yeast Delta9-desaturases, suggesting conserved transmembrane topology. A 182-aa core domain delimited by conserved histidine-rich motifs implicated in iron-binding and catalysis has 72 and 58% similarity (including conservative substitutions) to acyl-CoA Delta9Z-desaturases of rat and yeast, respectively. Northern blot analysis revealed an approximately 1,250-nt PDesat-Tn Delta11Z mRNA that is consistent with the spatial and temporal distribution of Delta11-desaturase enzyme activity. Genetic transformation of a desaturase-deficient strain of the yeast Saccharomyces cerevisiae with an expression plasmid encoding PDesat-Tn Delta11Z resulted in complementation of the strain's fatty acid auxotrophy and the production of Delta11Z-unsaturated fatty acids.