gebhart/patrepeval huggingface dataset:
Clustering of Large Hydrophobes in the Hydrophobic Core of Two-stranded α-Helical Coiled-Coils Controls Protein Folding and Stability (2003)

The de novo design and biophysical characterization of two 60-residue peptides that dimerize to fold as parallel coiled-coils with different hydrophobic core clustering is described. Our goal was to investigate whether designing coiled-coils with identical hydrophobicity but with different hydrophobic clustering of non-polar core residues (each contained 6 Leu, 3 Ile, and 7 Ala residues in the hydrophobic core) would affect helical content and protein stability. The disulfide-bridged P3 and P2 differed dramatically in alpha-helical structure in benign conditions. P3 with three hydrophobic clusters was 98% alpha-helical, whereas P2 was only 65% alpha-helical. The stability profiles of these two analogs were compared, and the enthalpy and heat capacity changes upon denaturation were determined by measuring the temperature dependence by circular dichroism spectroscopy and confirmed by differential scanning calorimetry. The results showed that P3 assembled into a stable alpha-helical two-stranded coiled-coil and exhibited a native protein-like cooperative two-state transition in thermal melting, chemical denaturation, and calorimetry experiments. Although both peptides have identical inherent hydrophobicity (the hydrophobic burial of identical non-polar residues in equivalent heptad coiled-coil positions), we found that the context dependence of an additional hydrophobic cluster dramatically increased stability of P3 (Delta Tm approximately equal to 18 degrees C and Delta[urea](1/2) approximately equal to 1.5 M) as compared with P2. These results suggested that hydrophobic clustering significantly stabilized the coiled-coil structure and may explain how long fibrous proteins like tropomyosin maintain chain integrity while accommodating polar or charged residues in regions of the protein hydrophobic core.
Treatment of Autoimmune Arthritis Using RNA Interference-Modulated Dendritic Cells (2010)

Dendritic cells (DCs) have a dual ability to either stimulate or suppress immunity, which is primarily associated with the expression of costimulatory molecules. Ag-loaded DCs have shown encouraging clinical results for treating cancer and infectious diseases; however, the use of these cells as a means of suppressing immune responses is only recently being explored. Here, we describe the induction of RNA interference through administering short interfering RNA (siRNA) as a means of specifically generating tolerogenic DCs. Knockdown of CD40, CD80, and CD86, prior to loading DCs with the arthritogenic Ag collagen II, led to a population of cells that could effectively suppress onset of collagen-induced arthritis. Maximum benefits were observed when all three genes were concurrently silenced. Disease suppression was associated with inhibition of collagen II-specific Ab production and suppression of T cell recall responses. Downregulation of IL-2, IFN-gamma, TNF-alpha, and IL-17 and increased FoxP3(+) cells with regulatory activity were observed in collagen-induced arthritis mice treated with siRNA-transfected DCs. Collectively, these data support the use of ex vivo gene manipulation in DCs using siRNA to generate tailor-made tolerogenic vaccines for treating autoimmunity.
Knowledge Graph Embedding Based Question Answering (2019)

Question answering over knowledge graph (QA-KG) aims to use facts in the knowledge graph (KG) to answer natural language questions. It helps end users more efficiently and more easily access the substantial and valuable knowledge in the KG, without knowing its data structures. QA-KG is a nontrivial problem since capturing the semantic meaning of natural language is difficult for a machine. Meanwhile, many knowledge graph embedding methods have been proposed. The key idea is to represent each predicate/entity as a low-dimensional vector, such that the relation information in the KG could be preserved. The learned vectors could benefit various applications such as KG completion and recommender systems. In this paper, we explore to use them to handle the QA-KG problem. However, this remains a challenging task since a predicate could be expressed in different ways in natural language questions. Also, the ambiguity of entity names and partial names makes the number of possible answers large. To bridge the gap, we propose an effective Knowledge Embedding based Question Answering (KEQA) framework. We focus on answering the most common types of questions, i.e., simple questions, in which each question could be answered by the machine straightforwardly if its single head entity and single predicate are correctly identified. To answer a simple question, instead of inferring its head entity and predicate directly, KEQA targets at jointly recovering the question's head entity, predicate, and tail entity representations in the KG embedding spaces. Based on a carefully-designed joint distance metric, the three learned vectors' closest fact in the KG is returned as the answer. Experiments on a widely-adopted benchmark demonstrate that the proposed KEQA outperforms the state-of-the-art QA-KG methods.
Uniform, Dense Arrays of Vertically Aligned, Large-Diameter Single-Walled Carbon Nanotubes (2012)

Precisely controlled reactive chemical vapor synthesis of highly uniform, dense arrays of vertically aligned single-walled carbon nanotubes (SWCNTs) using tailored trilayered Fe/Al(2)O(3)/SiO(2) catalyst is demonstrated. More than 90% population of thick nanotubes (>3 nm in diameter) can be produced by tailoring the thickness and microstructure of the secondary catalyst supporting SiO(2) layer, which is commonly overlooked. The proposed model based on the atomic force microanalysis suggests that this tailoring leads to uniform and dense arrays of relatively large Fe catalyst nanoparticles on which the thick SWCNTs nucleate, while small nanotubes and amorphous carbon are effectively etched away. Our results resolve a persistent issue of selective (while avoiding multiwalled nanotubes and other carbon nanostructures) synthesis of thick vertically aligned SWCNTs whose easily switchable thickness-dependent electronic properties enable advanced applications in nanoelectronic, energy, drug delivery, and membrane technologies.
Molecular epidemiology and prevention of cancer. (1995)

Preventable environmental causes of cancer, including tobacco smoke and other carcinogens in the diet, workplace, and ambient environment are responsible for the vast majority of human cancers. This paper reviews recent molecular epidemiologic studies that have focused on environmental carcinogenesis and environment-host interactions. Biomarkers such as carcinogen-DNA and carcinogen-protein adducts, mutations in reporter or target genes (e.g., HPRT, GPA, ras, p53), or genetic or acquired susceptibility factors (e.g., polymorphisms in the P450 or glutathione-S-transferase genes and serum levels of antioxidants) have shown significant potential in prevention. They should be useful in early identification of at risk individuals and in designing and monitoring interventions (smoking cessation, exposure reduction, and chemoprevention).
Two 4K static 5-V RAM's (1976)

This paper describes two 4096-bit, static, TTL compatible, 5 V only, MOS RAM's with worst case access times down to 200 ns and worst case power dissipations down to 370 mW. One is organized as 1K/spl times/4 and the other as 4K/spl times/1. Both devices are obtained from the same 192- by 197-mil die by a metal mask option and both are assembled in 22-pin dual-in-line packages. A novel memory status output signal is provided to allow the system designer to utilize actual memory performance rather than worst case data sheet specifications. This allows improved system benchmarks in addition to simplified timing.
Antioxidant protection by haemopexin of haem-stimulated lipid peroxidation (1988)

Haem (ferrous protoporphyrin IX) is a reactive low-molecular-mass form of iron able to participate in oxygen-radical reactions that can lead to the degradation of proteins, lipids, carbohydrates and DNA. Oxygen-radical reactions are likely to occur upon tissue damage. Extracellular fluids rely on antioxidant mechanisms different from those found inside the cell, and circulating proteins limit radical reactions by converting pro-oxidant forms of iron into less-reactive forms. Of the compounds tested, only apohaemopexin and the chain-breaking antioxidant butylated hydroxytoluene inhibited (by more than 90%) haemin-stimulated peroxidation as measured by formation of conjugated dienes, thiobarbituric acid-reactive material from linolenic acid or peroxidation-induced phospholipid fluorescence. Haptoglobin, the haemoglobin-binding serum protein, was ineffective. Conversely, only haptoglobin significantly inhibited haemoglobin-stimulated lipid peroxidation. Iron-salt-induced lipid peroxidation was inhibited only by apotransferrin and the iron-chelator desferrioxamine. All lipid peroxidations were inhibited by the radical scavengers butylated hydroxytoluene and propyl gallate. These findings support the concept that transport and conservation of body iron stores are closely linked to antioxidant protection.
A novel plant-based synergist for pyrethrum and pyrethroids against urban public health pests. (2008)

Natural pyrethrum and its synthetic analogues are among the most widely used insecticides in medical, veterinary and agricultural use. Low application rates, rapid knock-down and kill, range of duration of activity and good mammalian safety profile make them an active of choice in most domestic applications. The threat to continued use of these compounds is that of resistance in target organisms. To overcome resistance it is common to add a synergist, such as piperonyl butoxide. In this study we report the potential synergistic effects of a botanical substance derived from dill seed oil (Anethum sowa), which has been proven to enhance the biocidal activity of pyrethrins and overcome kdr-type resistance in malaria vector mosquitoes. With an optimal ratio of 1:3.6 pyrethrum to dill seed oil, and an enhanced biocidal activity against medically important urban pest species including Periplaneta americana (L.), Musca domestica (L.) and a pyrethroid-resistant strain of the Asian urban malaria vector Anopheles stephensi (Liston), we consider this combination may be suitable in a wide range of pest control situations.
Wearable Shell Antenna for 2.4 GHz Hearing Instruments (2016)

A novel concept for an electrically small on-body antenna targeted for 2.4 GHz ISM band custom in-the-ear (ITE) hearing instrument (HI) applications is introduced. The antenna is based upon a cavity-backed design in order to take advantage of the maximum volume available ITE while providing isolation from the user's body, and it occupies only 40% of the volume of the sphere with radius a = 12 mm. The antenna is implemented on a realistic three-dimensional (3-D)-printed lossy substrate and exhibits high efficiency of 70% and 22%, and a 6-dB impedance bandwidth of 108 and 149 MHz, when the antenna is measured in free space (FS) and ITE, respectively. A measurement campaign conducted in FS and on a specific anthropomorphic mannequin (SAM) head with ears shows that the radiation pattern is optimal for HI applications. Furthermore, the antenna is primarily polarized normal to the surface of the head to ensure the best on-body path gain (PG). This is substantiated by the study of the ear-to-ear (E2E) PG, which is measured and compared to analytic and numerical results.
User-driven narrative variation in large story domains using monte carlo tree search (2014)

Planning-based techniques are powerful tools for automated narrative generation, however, as the planning domain grows in the number of possible actions traditional planning techniques suffer from a combinatorial explosion. In this work, we apply Monte Carlo Tree Search to goal-driven narrative generation. We demonstrate our approach to have an order of magnitude improvement in performance over traditional search techniques when planning over large story domains. Additionally, we propose a Bayesian story evaluation method to guide the planning towards believable narratives which achieve user-defined goals. Finally, we present an interactive user interface which enables users of our framework to modify the believability of different actions, resulting in greater narrative variety.
A resource-aware and time-critical IoT framework (2017)

Internet of Things (IoT) systems produce great amount of data, but usually have insufficient resources to process them in the edge. Several time-critical IoT scenarios have emerged and created a challenge of supporting low latency applications. At the same time cloud computing became a success in delivering computing as a service at affordable price with great scalability and high reliability. We propose an intelligent resource allocation system that optimally selects the important IoT data streams to transfer to the cloud for processing. The optimization runs on utility functions computed by predictor algorithms that forecast future events with some probabilistic confidence based on a dynamically recalculated data model. We investigate ways of reducing specifically the upload bandwidth of IoT video streams and propose techniques to compute the corresponding utility functions. We built a prototype for a smart squash court and simulated multiple courts to measure the efficiency of dynamic allocation of network and cloud resources for event detection during squash games. By continuously adapting to the observed system state and maximizing the expected quality of detection within the resource constraints our system can save up to 70% of the resources compared to the naive solution.
Mechanism of plutonium metal dissolution in HNO/sub 3/-HF-N/sub 2/H/sub 4/ solution (1985)

An oxidation-reduction balance of the products of the dissolution of plutonium metal and alloys in HNO/sub 3/-HF-N/sub 2/H/sub 4/ solution shows that the major reactions during dissolution are the reduction of nitrate to NH/sub 3/, N/sub 2/ and N/sub 2/O by the metal, and the oxidation of H free radicals to NH/sub 3/ by N/sub 2/H/sub 4/. Reactions between HNO/sub 3/ and N/sub 2/H/sub 4/ produce varying amounts of HN/sub 3/. The reaction rate is greater for delta-Pu than alpha-Pu, and is increased by higher concentrations of HF and HNO/sub 3/. The low yield of reduced nitrogen species indicates that nitrate is reduced on the metal surface without producing a significant concentration of species that react with N/sub 2/H/sub 4/. It is conjectured that intermediate Pu valences and electron transfer within the metal are involved. 7 refs., 3 tabs.
Production data based optimal etch time control design for a reactive ion etching process (1999)

This paper addresses the issue of end point detection and etch time control for a reactive ion etch process. Our approach involves the use of neural networks to model the functional relationship between an end point detection signal, as well as various in situ measurements, and the resulting film thickness remaining. An optimization algorithm is then employed to determine the optimal etch time based on the neural network model in order to achieve the desired level of film thickness remaining. This circumvents the need for monitoring and operating on noisy end point detection signals typically associated with conventional detection schemes. Simulation studies based on production data are presented to further demonstrate the associated design procedures and the feasibility of the algorithm. Tested on data from 89 randomly selected wafers, our controller yields a film thickness distribution with the standard deviation of 6.42 /spl Aring/, a 50% improvement over the scheme currently implemented in production.
A cloud-assisted design for autonomous driving (2012)

This paper presents Carcel, a cloud-assisted system for autonomous driving. Carcel enables the cloud to have access to sensor data from autonomous vehicles as well as the roadside infrastructure. The cloud assists autonomous vehicles that use this system to avoid obstacles such as pedestrians and other vehicles that may not be directly detected by sensors on the vehicle. Further, Carcel enables vehicles to plan efficient paths that account for unexpected events such as road-work or accidents.
End-to-end security in the presence of intelligent data adapting proxies: the case of authenticating transcoded streaming media (2005)

We consider the problem of maintaining end-to-end security in the presence of intelligent proxies that may adaptively modify data being transmitted across a network. The video coding community considers this problem in the context of transcoding media streams, but their approaches either fail to address authentication or fail to provide meaningful security guarantees. We present two provably-secure schemes, LISSA and TRESSA, that allow an intelligent network intermediary to intercept a stream signed by a content provider, and adapt it dynamically, while preserving the ultimate receiver's ability to securely verify the content provider's signature (and, hence, authenticity and integrity of the data received). Our schemes allow the intermediary to selectively remove portions of the stream and, thus, permit common media transcoding techniques such as scalable compression and multiple file switching. Moreover, a content provider only has to encode and sign its entire data stream once, as opposed to nondynamically encoding and signing different versions for each anticipated combination of device, network configuration, and channel condition. Our implementation results demonstrate efficiency.
Analysis and Compensation of the AM-AM and AM-PM Distortion for CMOS Cascode Class-E Power Amplifier (2009)

Analysis and compensation methodology of the AM-AM and AM-PM distortion of cascode class-E power amplifiers are presented. A physical-based model is proposed to illustrate that the nonlinear capacitance and transconductance cause the AM-AM and AM-PM distortion when modulating the supply voltage of the PA. A novel methodology that can reduce the distortion is also proposed. By degenerating common-gate transistor into a resistor, the constant equivalent impedance is obtained so that the AM-AM and AM-PM distortion is compensated. An experimental prototype of 2.6 GHz cascode class-E power amplifier with the AM-AM and AM-PM compensation has been integrated in a 0.18 <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mi>μ</mml:mi></mml:math>m CMOS technology, occupies a total die area of 1.6 <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:msup><mml:mrow><mml:mtext>mm</mml:mtext></mml:mrow><mml:mn>2</mml:mn></mml:msup></mml:mrow></mml:math>. It achieves a drain efficiency of 17.8% and a power-added efficiency of 16.6% while delivering 12 dBm of linear output power and drawing 31 mA from a 1.8 V supply. Finally, a co-simulation result demonstrated that, when the distortion of the PA has been compensated, the EVM is improved from −17 dB to −19 dB with an IEEE802.11a-like signal source.
Assessment of soil surface BRDF using an imaging spectrometer (2010)

Ground reference data are important for understanding and characterizing angular effects on the images acquired by satellite sensors with off-nadir capability. However, very few studies have considered image-based soil reference data for that purpose. Compared to non-imaging instruments, imaging spectrometers can provide detailed information to investigate the influence of spatial components on the bidirectional reflectance distribution function (BRDF) of a mixed target. This research reported in this paper investigated soil spectral reflectance changes as a function of surface roughness, scene components and viewing geometries, as well as wavelength. Soil spectral reflectance is of particular interest because it is an essential factor in interpreting the angular effects on images of vegetation canopies. BRDF data of both rough and smooth soil surfaces were acquired in the laboratory at 30° illumination angle using a Specim V10E imaging spectrometer mounted on the University of Lethbridge Goniometer System version 2.5 (ULGS-2.5). The BRDF results showed that the BRDF of the smooth soil surface was dominated by illuminated pixels, whereas the shaded pixels were a larger component of the BRDF of the rough surface. In the blue, green, red, and near-infrared (NIR), greater BRDF variation was observed for the rough than for the smooth soil surface. For both soil surface roughness categories, the BRDF exhibited a greater range of values in the NIR than in the blue, green, or red. The imaging approach allows the characterization of the impact of spatial components on soil BRDF and leads to an improved understanding of soil reflectance compared to non-imaging BRDF approaches. The imaging spectrometer is an important sensor for BRDF investigations where the effects of individual spatial components need to be identified.
Performance evaluation of an efficient multiple copy update algorithm (2002)

The authors study the response-time behavior of a symmetric distributed update-synchronization algorithm where nodes need to obtain permission from only O( square root N) (N being the number of database copies) other nodes before performing an update (as opposed to N/2+1 nodes in the well-known Thomas majority consensus algorithm). The algorithm used is an adaptation of M. Maekawa's O( square root N) distributed mutual exclusion algorithm (1985) to multiple-copy update-synchronization. This increase in the efficiency of the update-synchronization algorithm enhances performance in two ways. First, the reduction in transaction service time reduces the response time. Second, the decrease in response time reduces the number of waiting transactions in the system. This reduces the probability of conflict between transactions. To capture the interaction between the probability of conflict and the transaction response time, the authors define a new measure called the conflict response-time product. They show that optimizing this measure yields a different and more appropriate choice of system parameters than simply minimizing the mean transaction response time.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>