gebhart/patrepeval huggingface dataset:
Probing the Binding Pocket of the Broadly Tuned Human Bitter Taste Receptor TAS2R14 by Chemical Modification of Cognate Agonists (2016)

Sensing potentially harmful bitter substances in the oral cavity is achieved by a group of (˜) 25 receptors, named TAS2Rs, which are expressed in specialized sensory cells and recognize individual but overlapping sets of bitter compounds. The receptors differ in their tuning breadths ranging from narrowly to broadly tuned receptors. One of the most broadly tuned human bitter taste receptors is the TAS2R14 recognizing an enormous variety of chemically diverse synthetic and natural bitter compounds, including numerous medicinal drugs. This suggests that this receptor possesses a large readily accessible ligand binding pocket. To allow probing the accessibility and size of the ligand binding pocket, we chemically modified cognate agonists and tested receptor responses in functional assays. The addition of large functional groups to agonists was usually possible without abolishing agonistic activity. The newly synthesized agonist derivatives were modeled in the binding site of the receptor, providing comparison to the mother substances and rationalization of the in vitro activities of this series of compounds.
Progress in the development of lightweight nickel electrode for aerospace applications (1992)

The NASA Lewis Research Center is currently developing nickel electrodes for nickel-hydrogen (Ni-H2) cells and batteries. These electrodes are lighter in weight and have higher specific energy than the heavy sintered state of the art nickel electrodes. In the present approach, lightweight materials or plaques are used as conductive supports for the nickel hydroxide active material. These plaques (fiber, felt, and nickel plated plastic) are fabricated into nickel electrodes by electrochemically impregnating them with active material. Initial performance tests include capacity measurements at five discharge levels, C/2, 1.0C, 1.37C, 2.0C, and 2.74C. The electrodes that pass the initial tests are life cycle tested at 40 and 80 percent depths of discharge (DOD). Different formulations of nickel fiber materials obtained from several manufacturers are currently being tested as possible candidates for nickel electrodes. Over 7,000 cycles of life cycle testing have been accumulated at 40 percent DOD, using the lightweight fiber electrode in a boiler plate Ni-H2 cell with stable voltage.
A widely tunable side-polished fiber filter based on dispersive evanescent wave tunneling (2004)

Wideband tunable fiber short-pass filters are demonstrated using standard side polished fibers (SPFs) with dispersive polymer. The tuning range can be as wide as 400 nm within 15/spl deg/C. The insertion loss for passband is negligible and the rejection efficiency for stopband is higher than 50 dB.
Flowroute (2010)

The reconvergence of routing protocols in response to changes in network topology can impact application performance. While improvements in protocol specification and implementation have significantly reduced reconvergence times, increasingly performance-sensitive applications continue to raise the bar for these protocols. As such, monitoring the performance of routing protocols remains a critical activity for network operators. We design tool{}, a tool based on passive data plane measurements that we use in conjunction with control plane monitors for offline debugging and analysis of forwarding table dynamics. We discuss practical constraints that affect tool{}, and show how they can be addressed in real deployment scenarios. As an application of tool{}, we study forwarding table updates by backbone routers at a tier-1 ISP. We detect interesting behavior such as delayed forwarding table updates and routing loops due to buggy routers -- confirmed by network operators -- that are not detectable using traditional control plane monitors.
A Fourier transform microscope for x-ray imaging (1992)

This is a progress report on development of a new x-ray imaging system, called a Fourier transform microscope, intended for use with x-ray emitting targets in laser fusion experiments. It is being built by Naval Research Laboratory and Lawrence Livermore National Laboratory. The system works at energies from 3 to 7 keV. We describe the development of the design, which utilizes fine etched grids to extract Fourier amplitudes for the source brightness distribution at selected spatial frequencies. The finest grids in the prototype system will have rib dimensions of 2 μm. The prototype system is expected to achieve position resolution of 4 μm in 3–7 keV. Simulations of the expected imaging performance are presented.
Mining Quantified Temporal Rules: Formalism, Algorithms, and Evaluation (2009)

Libraries usually impose constraints on how clients should use them. Often these constraints are not well-documented. In this paper, we address the problem of recovering such constraints automatically, a problem referred to as specification mining. Given some client programs that use a given library, we identify constraints on the library usage that are (almost) satisfied by the given set of clients.The class of rules we target for mining combines simple binary temporal operators with state predicates (involving equality constraints) and quantification. This is a simple yet expressive subclass of temporal properties that allows us to capture many common API usage rules. We focus on recovering rules from execution traces and apply classical data mining concepts to be robust against bugs (API usage rule violations) in clients. We present new algorithms for mining rules from execution traces. We show how a propositional rule mining algorithm can be generalized to treat quantification and state predicates in a unified way. Our approach enables the miner to be complete - mine all rules within the targeted class that are satisfied by the given traces - while avoiding an exponential blowup.We have implemented these algorithms and used them to mine API usage rules for several Windows APIs. Our experiments show the efficiency and effectiveness of our approach.
Synthesis and Properties of Metallic Glasses That Contain Aluminum (1988)

The synthesis and properties of a class of metallic glasses containing up to 90 atomic percent aluminum are reported. The unusual formability of the glasses and their structural features are pointed out. Mechanical properties including tensile fracture strength and Young's modulus are reported along with crystallization temperatures. The unusually high strengths of the aluminum glasses can be of significant importance in obtaining high-strength low-density materials.
Antibody neutralization of an influenza virus that uses neuraminidase for receptor binding (2020)

Abstract Influenza virus infection elicits antibodies against the receptor-binding protein hemagglutinin (HA) and the receptor-cleaving protein neuraminidase (NA). Because HA is essential for viral entry, antibodies targeting HA often potently neutralize the virus in single-cycle infection assays. But antibodies against NA are not potently neutralizing in such assays, since NA is dispensable for single-cycle infection. Here we show that a modified influenza virus that depends on NA for receptor binding is much more sensitive than a virus with receptor-binding HA to neutralization by some anti-NA antibodies. Specifically, virus with a receptor-binding G147R N1 NA and a binding-deficient HA is completely neutralized in single-cycle infections by an antibody that binds near the NA active site. Infection is also substantially inhibited by antibodies that bind NA epitopes distant from the active site. Finally, we demonstrate that this modified virus can be used to efficiently select mutations in NA that escape antibody binding, a task that can be laborious with typical influenza viruses that are not well-neutralized by anti-NA antibodies. Thus, viruses dependent on NA for receptor binding allow for sensitive in vitro detection of antibodies binding near the catalytic site of NA and enable selection of viral escape mutants.
Efficient implementation of parallel decision feedback decoders for broadband applications (2003)

Parallel Decision-Feedback Decoders (PDFD) use a joint equalization and channel decoding scheme that performs decision-feedback equalization based on each survivor path in the channel decoder. In this paper, we propose novel efficient computation methods to implement the PDFD. We show that, contrary to the belief that PDFD is too complex to implement, standard Viterbi decoders can be modified to implement the PDFD and achieve very high bit-rates.
Syntheses and Structure−Activity Relationships of Novel Nor-seco Taxoids (1998)

A series of novel nor-seco taxoids (4a−b, 5a−d, 6), including either a C-13 ester linkage or a C-13 amide linkage, was synthesized by means of the β-lactam synthon method using the coupling of (3R,4S)-1-acyl-β-lactams with properly protected nor-seco baccatin III derivatives (1, 2, 3) as the key step. Nor-seco baccatin III derivatives were prepared through oxidative cleavage of the A ring of 14β-hydroxy-10-deacetylbaccatin III followed by reduction, amination using Mitsunobu conditions, or reductive amination. Nor-seco taxoids with a C-13 ester linkage (4a−b) or a C-13 N-Me amide linkage (6) show reduced cytotoxicity against human cancer cell lines as compared with paclitaxel, but still retain a certain level of activity despite the destruction of the taxane A ring. However, none of the analogues with a C-13 N-H amide linkage (5a−d) exhibit appreciable activity (IC50 > 1.0 μM). A restrained molecular dynamics study reveals the inability of 5a−d to attain the proposed bioactive conformation, which accounts for the loss of activity.
Nontapered fused-fiber couplers (1985)

Several methods of fabricating fused-fiber couplers have been reported.1–5 The coupler which appears to be generating the most interest is that which uses the biconical taper technique.2 The tapered region in these couplers is drawn to a small diameter and is typically suspended in air, since direct contact with a potting compound can degrade performance. This air suspension can complicate package design for high mechanical reliability, hermeticity, and/or high-pressure applications. Other coupler fabrication techniques generally require precision cleaving and tapering for fusion between matched fiber endfaces.3–5
Co-expression network analysis reveals immune response pathways important for pathogenesis of <i>Chlamydial</i> pelvic inflammatory disease (PID). (HUM8P.329) (2014)

Abstract Processes driving development of immune pathology after Chlamydia trachomatis infection are poorly understood. To provide insight into the pathways that may be underappreciated by individual gene analysis, weighted gene co-expression network analysis was performed to identify network modules using blood transcriptional profiles of women with chlamydial PID (N=15) and asymptomatically infected women (N=84). Modules, defined as centrally connected genes, that were significantly associated with chlamydial PID were further accessed via Ingenuity Pathway analysis. Type I and type II interferon (IFN) signaling pathways were significantly up regulated in women with chlamydial PID. Up regulation of both of these pathways has been detected in the transcriptomes of patients with active tuberculosis, suggesting a parallel role in PID. Up regulation of aryl hydrocarbon receptor, agranulocyte/granulocyte adhesion and diapedesis pathways was also noted, while EIF2/EIF4, mTOR and ILK signaling, granzyme A/B signaling, cross talk between dendritic cells and natural killer cells, signaling in T helper cells and T cell receptor pathways were down-regulated. Pathways likely to contribute to immunopathogenesis, including migration of leukocytes and inflammation were activated in chlamydial PID, while those involved in cell growth/proliferation and clearance of infected cells were decreased. Bioinformatics provides a new avenue to improve understanding of chlamydial disease mechanisms.
Feature sets for nonstationary signals derived from moments of the singular value decomposition of Cohen-Posch (positive time-frequency) distributions (2000)

This article presents a new method for determining the principal features of a nonstationary time series process based on the singular value decomposition (SVD) of the Cohen-Posch (1985) positive time-frequency distribution. This new method uses density functions derived from the SVD singular vectors to generate moments that are associated with the principal features of the nonstationary process. Since the SVD singular vectors are orthonormal, the vectors whose elements are composed of the squared elements of the SVD vectors are discrete density functions. Moments generated from these density functions are the principal features of the nonstationary time series process. The main reason for determining features of a time series process is to characterize it by a few simple descriptors.
Practical Network-Wide Compression of IP Routing Tables (2012)

The memory Internet routers use to store paths to destinations is expensive, and must be continually upgraded in the face of steadily increasing routing table size. Unfortunately, routing protocols are not designed to gracefully handle cases where memory becomes full, which arises increasingly often due to misconfigurations and routing table growth. Hence router memory must typically be heavily overprovisioned by network operators, inflating operating costs and administrative effort. The research community has primarily focused on clean-slate solutions that cannot interoperate with the deployed base of protocols. This paper presents an incrementally-deployable Memory Management System (MMS) that reduces associated router state by up to 70%. The MMS coalesces prefixes to reduce memory consumption and can be deployed locally on each router or centrally on a route server. The system can operate transparently, without requiring changes in other ASes. Our memory manager can extend router lifetimes up to seven years, given current prefix growth trends.
Reclaiming silver from silver zeolite (1991)

Silver zeolite is used to capture radioiodines from air cleaning systems in some nuclear facilities at the Idaho National Engineering Laboratory. It may become radioactively contaminated and/or poisoned by hydrocarbon vapors, which diminishes its capacity for iodine. Silver zeolite contains up to 38 wt% silver. A pyrometallurgical process was developed to reclaim the silver before disposing of the unserviceable zeolite as a radioactive waste. A flux was formulated to convert the refractory aluminosilicate zeolite structure into a low-melting fluid slag, with Na{sub 2}O added as NAOH instead of Na{sub 2}CO{sub 3} to avoid severe foaming due to CO{sub 2} evolution. A propane-fired furnace was built to smelt 45 kg charges at 1300C in a carbon-bonded silicon carbide crucible. A total of 218 kg (7000 tr oz) of silver was reclaimed from 1050 kg of unserviceable zeolite. Silver recoveries of 97% were achieved, and the radioisotopes were fixed as stable silicates in a vitreous slag that was disposed of as a low level waste. Recovered silver was refined using oxygen and cast into 100 tr oz bars assaying 99.8+% silver and showing no radioactive contamination.
Using Semantic Web Technologies to Enable Cancer Genomics Discovery at Petabyte Scale (2018)

Increased efforts in cancer genomics research and bioinformatics are producing tremendous amounts of data. These data are diverse in origin, format, and content. As the amount of available sequencing data increase, technologies that make them discoverable and usable are critically needed. In response, we have developed a Semantic Web-based Data Browser, a tool allowing users to visually build and execute ontology-driven queries. This approach simplifies access to available data and improves the process of using them in analyses on the Seven Bridges Cancer Genomics Cloud (CGC; www.cancergenomicscloud.org). The Data Browser makes large data sets easily explorable and simplifies the retrieval of specific data of interest. Although initially implemented on top of The Cancer Genome Atlas (TCGA) data set, the Data Browser's architecture allows for seamless integration of other data sets. By deploying it on the CGC, we have enabled remote researchers to access data and perform collaborative investigations.
Investigations into Ruthenium Metathesis Catalysts with Six-Membered Chelating NHC Ligands: Relationship between Catalyst Structure and Stereoselectivity (2013)

A series of ruthenium catalysts bearing five-membered chelating NHC architectures that exhibit very high <i>Z</i>-selectivity in a variety of metathesis reactions have recently been reported. It was envisioned that catalysts possessing sixmembered chelates could similarly exhibit high <i>Z</i>-selectivity and address limitations of this methodology. We thus prepared a number of new catalysts and systematically investigated the impact of the NHC and anionic ligand on their stereoselectivity. In standard metathesis assays, only catalysts containing six-membered chelated NHC structures and η<sup>2</sup>-bound anionic ligands favored the <i>Z</i>-olefin products compared to traditional ruthenium catalysts. In addition, substitution with bulkier <i>N</i>-aryl groups led to improved <i>Z</i>-selectivity. The effect of ligand structure on stereoselectivity discovered in this study will be useful in the future design of highly active and <i>Z</i>-selective ruthenium catalysts.
Cure of Mice Infected with <i>Trypanosoma rhodesiense</i> by <i>cis</i> -Diamminedichloroplatinum (ii) and Disulfiram Rescue (1982)

Mice infected with Trypanosoma rhodesiense were treatment concurrently with cis-diamminedichloroplatinum (II) (DDP), disulfiram, and hydration. Most of the mice (92.5 percent) were cured; inoculation of blood or suspensions of brain or heart from these animals did not produce disease in recipient mice. The dose of DDP needed to eliminate the trypanosomes, 3 milligrams per kilogram of body weight per day for 7 days, was lethally toxic unless the animals received disulfiram orally and subcutaneous injections of physiologic saline, which reduced the acute renal necrosis caused by DDP alone. Some mild to moderate reversible renal damage was noted upon pathologic examination of the treated mice.
A polymorphism within a conserved β<sub>1</sub>-adrenergic receptor motif alters cardiac function and β-blocker response in human heart failure (2006)

Heterogeneity of heart failure (HF) phenotypes indicates contributions from underlying common polymorphisms. We considered polymorphisms in the beta(1)-adrenergic receptor (beta(1)AR), a beta-blocker target, as candidate pharmacogenomic loci. Transfected cells, genotyped human nonfailing and failing ventricles, and a clinical trial were used to ascertain phenotype and mechanism. In nonfailing and failing isolated ventricles, beta(1)-Arg-389 had respective 2.8 +/- 0.3- and 4.3 +/- 2.1-fold greater agonist-promoted contractility vs. beta(1)-Gly-389, defining enhanced physiologic coupling under relevant conditions of endogenous expression and HF. The beta-blocker bucindolol was an inverse agonist in failing Arg, but not Gly, ventricles, without partial agonist activity at either receptor; carvedilol was a genotype-independent neutral antagonist. In transfected cells, bucindolol antagonized agonist-stimulated cAMP, with a greater absolute decrease observed for Arg-389 (435 +/- 80 vs. 115 +/- 23 fmol per well). Potential pathophysiologic correlates were assessed in a placebo-controlled trial of bucindolol in 1,040 HF patients. No outcome was associated with genotype in the placebo group, indicating little impact on the natural course of HF. However, the Arg-389 homozygotes treated with bucindolol had an age-, sex-, and race-adjusted 38% reduction in mortality (P = 0.03) and 34% reduction in mortality or hospitalization (P = 0.004) vs. placebo. In contrast, Gly-389 carriers had no clinical response to bucindolol compared with placebo. Those with Arg-389 and high baseline norepinephrine levels trended toward improved survival, but no advantage with this allele and exaggerated sympatholysis was identified. We conclude that beta(1)AR-389 variation alters signaling in multiple models and affects the beta-blocker therapeutic response in HF and, thus, might be used to individualize treatment of the syndrome.
Auto-detection of cervical collagen and elastin in Mueller matrix polarimetry microscopic images using K-NN and semantic segmentation classification (2021)

We propose an approach for discriminating fibrillar collagen fibers from elastic fibers in the mouse cervix in Mueller matrix microscopy using convolutional neural networks (CNN) and K-nearest neighbor (K-NN) for classification. Second harmonic generation (SHG), two-photon excitation fluorescence (TPEF), and Mueller matrix polarimetry images of the mice cervix were collected with a self-validating Mueller matrix micro-mesoscope (SAMMM) system. The components and decompositions of each Mueller matrix were arranged as individual channels of information, forming one 3-D voxel per cervical slice. The classification algorithms analyzed each voxel and determined the amount of collagen and elastin, pixel by pixel, on each slice. SHG and TPEF were used as ground truths. To assess the accuracy of the results, mean-square error (MSE), peak signal-to-noise ratio (PSNR), and structural similarity (SSIM) were used. Although the training and testing is limited to 11 and 5 cervical slices, respectively, MSE accuracy was above 85%, SNR was greater than 40 dB, and SSIM was larger than 90%.
Design of a Self-Actuating, Traction Drive Speed Reducer (2000)

Abstract Traction drive speed reducers offer certain advantages over geared speed reducers. In particular, they generally run quieter than geared units, and they provide an opportunity for higher efficiency by eliminating sliding motion between contacting elements. In order to generate a sufficiently high output torque, some means must be provided to create a normal force between the rolling elements. This normal force, along with the friction coefficient, enables the device to transmit torque from one rolling member to the next. The speed reducer proposed here is designed so that the configuration of the rolling elements creates the needed normal force in response to the torque exerted back on the system by the downstream loading. Thus the device is self-actuating. Since the normal force is only present when needed, the rolling elements of the device can readily be disengaged. This eliminates the need for a separate clutch in the drive system. This feature can be exploited to design a transmission with several distinct speed ratios which can be engaged and disengaged in response to changing speed requirements.
Design considerations for charge equalization of an electric vehicle battery system (1995)

Charge equalization for series connected battery strings has important ramifications on battery life. It enhances the uniformity of the battery cells and hence improves the life of the battery as a whole. A new charge equalization technique for a series string of battery cells has been recently proposed by the authors. The basic technique utilizes a simple isolated DC-to-DC power converter with a capacitive output filter along with a multi-winding transformer. The possibility of integrating the trickle charge function with the charge equalization function is potentially very attractive, as it can lead to an efficient and low cost implementation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>