gebhart/patrepeval huggingface dataset:
Crystal Structure of Norwalk Virus Polymerase Reveals the Carboxyl Terminus in the Active Site Cleft (2004)

Norwalk virus is a major cause of acute gastroenteritis for which effective treatments are sorely lacking. To provide a basis for the rational design of novel antiviral agents, the main replication enzyme in Norwalk virus, the virally encoded RNA-dependent RNA polymerase (RdRP), has been expressed in an enzymatically active form, and its structure has been crystallographically determined both in the presence and absence of divalent metal cations. Although the overall fold of the enzyme is similar to that seen previously in the RdRP from rabbit hemorrhagic disease virus, the carboxyl terminus, surprisingly, is located in the active site cleft in five independent copies of the protein in three distinct crystal forms. The location of this carboxyl-terminal segment appears to interfere with the binding of double-stranded RNA in the active site cleft and may play a role in the initiation of RNA synthesis or mediate interactions with accessory replication proteins.
6H to 3C Polytype Transformation in Silicon Carbide (1999)

The conditions for the polytype transformation from 6H-SiC to 3C-SiC and the physical properties of the transformed crystals have been studied. When 6H-SiC crystals are annealed in vacuum for 1 hour at 2180 K or 4 hours at 2080 K, the crystals are completely transformed into 3C-SiC. Shorter annealing times at these temperatures result in partial transformation. No transformation occurs below 2080 K or above 2270 K. Physical properties of the transformed crystals have been studied using X-ray diffraction, photoluminescence, and optical absorption. The optical bandgap of the transformed 3C-SiC crystal is 2.34±0.02 eV and has much lower carrier concentration ((1–5)×10 15 cm -3 ) than the initial 6H-SiC crystal (10 18 –10 19 cm -3 ). The transformation takes place in solid phase with an activation energy of 140±15 kcal/mol.
Robust control for the improvement of loudspeaker low-frequency response (2002)

The low-frequency response of an electodynamic loudspeaker is improved through the use of robust control techniques. The problem of shaping the low-frequency response of the loudspeaker is reformulated as the problem of tracking a desired speaker cone trajectory. A desired speaker trajectory is described, and a robust controller is formulated which provides the desired speaker cone position tracking, and thereby improves the overall low-frequency response of the loudspeaker. Simulation results are used to validate the performance of the controller.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Access List Based VLAN Map Architecture and Modified 802.1q Frame Scheme for Addressing VTP Issues (2010)

Cisco's VLAN Trunk Protocol reduces administration in a switched network. Not much research has been pursued in addressing in-depth complexities of VTP. VTP encounters intricate situations first, when we try to insert a VTP client or server with higher config revision number and second, when we insert a switch with different VTP domain name. Solutions to both of these issues involve considerable manual re-configuration which transcends from manually changing VTP modes, domain names to manually adding missing or deleting un-wanted VLANs. Amount of manual configuration cited as obvious solution to these VTP problems increases exponentially for a mid-size scalable switched network and moreover this might also add to network downtime and subsequently to network management cost. This paper explores different options of eliminating manual configuration by comprehensively automating the applicability of proposed innovative solutions when VTP encounters above specified issues. An access list based VLAN map architecture is proposed for addressing the first issue. Modification in 802.1q frame is proposed to address the second concern of inserting switch with different VTP domain. Comprehensive analysis of simulated network is pursued to demonstrate the repercussions of VTP issues and finally, applicability of proposed architectures are introspected as viable way-out.
Atomic constraint in hydrogenated ‘‘diamond-like’’ carbon (1991)

Carbon bonding environments (measured by nuclear magnetic resonance spectroscopy) and compressive stress in plasma-deposited hydrogenated diamond-like carbon (DLC) films have been examined systematically as a function of substrate bias voltage. These results are related in terms of random network theory to show that hard DLC formed in an intermediate voltage range (100–400 V) consists of small graphitic clusters linked in a random network which is stiffened by a high density of quaternary carbon.
Text joins for data cleansing and integration in an RDBMS (2004)

An organization's data records are often noisy because of transcription errors, incomplete information, lack of standard formats for textual data or combinations thereof. A fundamental task in a data cleaning system is matching textual attributes that refer to the same entity (e.g., organization name or address). This matching is effectively performed via the cosine similarity metric from the information retrieval field. For robustness and scalability, these "text joins" are best done inside an RDBMS, which is where the data is likely to reside. Unfortunately, computing an exact answer to a text join can be expensive. We propose an approximate, sampling-based text join execution strategy that can be robustly executed in a standard, unmodified RDBMS.
Rational Structure-Based Rescaffolding Approach to De Novo Design of Interleukin 10 (IL-10) Receptor-1 Mimetics (2016)

Tackling protein interfaces with small molecules capable of modulating protein-protein interactions remains a challenge in structure-based ligand design. Particularly arduous are cases in which the epitopes involved in molecular recognition have a non-structured and discontinuous nature. Here, the basic strategy of translating continuous binding epitopes into mimetic scaffolds cannot be applied, and other innovative approaches are therefore required. We present a structure-based rational approach involving the use of a regular expression syntax inspired in the well established PROSITE to define minimal descriptors of geometric and functional constraints signifying relevant functionalities for recognition in protein interfaces of non-continuous and unstructured nature. These descriptors feed a search engine that explores the currently available three-dimensional chemical space of the Protein Data Bank (PDB) in order to identify in a straightforward manner regular architectures containing the desired functionalities, which could be used as templates to guide the rational design of small natural-like scaffolds mimicking the targeted recognition site. The application of this rescaffolding strategy to the discovery of natural scaffolds incorporating a selection of functionalities of interleukin-10 receptor-1 (IL-10R1), which are relevant for its interaction with interleukin-10 (IL-10) has resulted in the de novo design of a new class of potent IL-10 peptidomimetic ligands.
X-ray microscopy (1995)

The subject of X-ray microscopy (high-resolution X-ray imaging of general nonperiodic structures), an area in which much progress has been made in recent years, is reviewed. The main techniques are briefly described. Achievable performance levels, which for many years were highly speculative, can now be understood with fair accuracy in terms of basic X-ray and specimen properties, and techniques have progressed to the point where actual results are nearing those levels. In terms of specimen size and imaging resolution, X-ray microscopies lie between electron and light microscopy, and are thus suited to imaging extremely large and complex structures; in addition, they demand little or no specimen preparation, and can be used to observe local composition and chemical state as well as structure. Thus X-rays, which have played the leading role in imaging crystallizable materials, may also prove to be highly valuable in the imaging of very large non-crystalline structures. Throughout the treatment, attention is paid to the relationships connecting the subject with X-ray crystallography.
Lifespan-regulating genes in C. elegans (2016)

The molecular mechanisms underlying the aging process have garnered much attention in recent decades because aging is the most significant risk factor for many chronic diseases such as type 2 diabetes and cancer. Until recently, the aging process was not considered to be an actively regulated process; therefore, discovering that the insulin/insulin-like growth factor-1 signaling pathway is a lifespan-regulating genetic pathway in <i>Caenorhabditis elegans</i> was a major breakthrough that changed our understanding of the aging process. Currently, it is thought that animal lifespans are influenced by genetic and environmental factors. The genes involved in lifespan regulation are often associated with major signaling pathways that link the rate of aging to environmental factors. Although many of the major mechanisms governing the aging process have been identified from studies in short-lived model organisms such as yeasts, worms and flies, the same mechanisms are frequently observed in mammals, indicating that the genes and signaling pathways that regulate lifespan are highly conserved among different species. This review summarizes the lifespan-regulating genes, with a specific focus on studies in <i>C. elegans</i>.
Consistency management of product line requirements (2002)

Contemporary software engineering utilizes product lines for reducing time to market and development cost of a single product variant, for improving quality of the products, and for creating better estimations of the development process. Most product line development processes rely on performing a domain analysis to find out commonalities among proposed family members and to estimate how they will vary. On the other hand, most requirements engineering methods focus on the specification of a single system. Despite active research efforts to close this, gap there is still no effective method that allows product specifications in arbitrary levels of detail for a hierarchical product family. In particular, it is not possible to combine different specification mechanisms to produce a complete family specification. The authors approach these problems by presenting a method that allows system specifications both in the product line variant as well as the product family level. This exposes many problems in managing consistency between different methods to specify families of systems. To achieve this, our method offers derivation of consistency management support between different specification levels and among family variants.
Optimal Task Allocation in Vehicular Fog Networks Requiring URLLC: An Energy-Aware Perspective (2019)

In order to make intelligent transportation systems (ITSs) come true, execution of a large amount of data needs to be migrated from the cloud centers to the edge nodes, especially in the scenarios requiring ultra reliable low latency communications (URLLC). In this article, we propose to study the energy-aware task allocation problem in the vehicular fog networks considering URLLC. Specifically, a requester who has some bursty computation tasks which cannot be finished within a required time by itself, needs to decide whether the nearby computation nodes can meet the latency and reliability requirements, and which nodes should be chosen. Given the required latency and reliability, the maximum computation capacity of each fog node is first calculated based on the martingale-theory-derived delay bound. Then, if the available fog nodes can accommodate the computation tasks, two different optimization problems concerning the energy efficiency maximization and the energy consumption minimization are constructed further. The corresponding solutions are also provided. Specifically, the optimal solution in maximizing the energy efficiency is not unique, while the optimal solution in minimizing the energy consumption is unique. Moreover, the latter solution is provided as a truncated-channel-inversion like policy. At last, numerical results are illustrated to demonstrate effectiveness of the proposed optimal task allocation schemes from the perspectives of the energy efficiency and the energy consumption.
Induction of quinone reductase NQO1 by resveratrol involves antioxidant response element ARE and is accompanied by nuclear translocation of transcription factor Nrf2 (2006)

The phytochemical resveratrol has been reported to induce NQO1, an enzyme involved in detoxification reactions, by as yet undetermined mechanisms. Using K562 cells as a model, we showed that 25‐50 μM resveratrol caused an optimal increase in NQO1 that peaked at 48 h. A 2.5‐fold induction in NQO1 protein expression was accompanied by a 1.8‐fold elevation in mRNA levels and a greater than 5‐fold increase in NQO1 enzymatic activity. Real‐time PCR analysis showed that resveratrol caused a maximum increase in NQO1 mRNA copy number at 24 h. Using fluorescent microscopy in combination with transfection experiments with plasmids harboring different promoter elements of NQO1 linked to a luciferase reporter gene, we demonstrated that modulation of NQO1 gene expression by resveratrol involved the ARE, concomitant with or accompanied by a change in the cellular localization of the transcription factor Nrf2. The results indicate that resveratrol disrupts the Nrf2‐Keap1 complex and facilitates the translocation of Nrf2 into the nucleus where it locates ARE, leading to activation of transcription of NQO1.
Learning Hidden Unit Contributions for Unsupervised Acoustic Model Adaptation (2016)

This work presents a broad study on the adaptation of neural network acoustic models by means of learning hidden unit contributions (LHUC) - a method that linearly re-combines hidden units in a speaker- or environment-dependent manner using small amounts of unsupervised adaptation data. We also extend LHUC to a speaker adaptive training (SAT) framework that leads to a more adaptable DNN acoustic model, working both in a speaker-dependent and a speaker-independent manner, without the requirements to maintain auxiliary speaker-dependent feature extractors or to introduce significant speaker-dependent changes to the DNN structure. Through a series of experiments on four different speech recognition benchmarks (TED talks, Switchboard, AMI meetings, and Aurora4) comprising 270 test speakers, we show that LHUC in both its test-only and SAT variants results in consistent word error rate reductions ranging from 5% to 23% relative depending on the task and the degree of mismatch between training and test data. In addition, we have investigated the effect of the amount of adaptation data per speaker, the quality of unsupervised adaptation targets, the complementarity to other adaptation techniques, one-shot adaptation, and an extension to adapting DNNs trained in a sequence discriminative manner.
An Optimized Blockwise Non Local Means Denoising Filter for 3D Magnetic Resonance Images (2007)

A critical issue in image restoration is the problem of noise removal while keeping the integrity of relevant image information. Denoising is a crucial step to increase image quality and to improve the performance of all the tasks needed for quantitative imaging analysis. The method proposed in this paper is based on a 3-D optimized blockwise version of the nonlocal (NL)-means filter (Buades, , 2005). The NL-means filter uses the redundancy of information in the image under study to remove the noise. The performance of the NL-means filter has been already demonstrated for 2-D images, but reducing the computational burden is a critical aspect to extend the method to 3-D images. To overcome this problem, we propose improvements to reduce the computational complexity. These different improvements allow to drastically divide the computational time while preserving the performances of the NL-means filter. A fully automated and optimized version of the NL-means filter is then presented. Our contributions to the NL-means filter are: 1) an automatic tuning of the smoothing parameter; 2) a selection of the most relevant voxels; 3) a blockwise implementation; and 4) a parallelized computation. Quantitative validation was carried out on synthetic datasets generated with BrainWeb (Collins, , 1998). The results show that our optimized NL-means filter outperforms the classical implementation of the NL-means filter, as well as two other classical denoising methods [anisotropic diffusion (Perona and Malik, 1990)] and total variation minimization process (Rudin, , 1992) in terms of accuracy (measured by the peak signal-to-noise ratio) with low computation time. Finally, qualitative results on real data are presented.
A Low-ppm Digitally Controlled Crystal Oscillator Compensated by a New 0.19-mm<sup>2</sup> Time-Domain Temperature Sensor (2016)

A low-ppm digitally controlled crystal oscillator (DCXO) in a Pierce readout topology with a new 0.19-mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> CMOS time-domain temperature sensor (TDTS) circuit for temperature compensation is designed and fabricated in this paper. The Pierce readout circuit is designed to output a 16-MHz oscillating signal as an important base clock for mobile devices. To cope with inevitable imprecision caused by environmental temperature variation, the readout should be compensated based on crystal's frequency-temperature curve via a temperature sensor. To this end, a new low-power, small-sized, CMOS on-chip temperature sensor circuit is successfully synthesized by 20-stages of newly designed delay cells. Each delay cell is compensated by a CMOS-process-compatible varactor, enabling a TDTS consisting of only a low number of delay cells to generate long enough delay that is proportional to temperature and in required precisions. In addition to Pierce and TDTS circuits, the DCXO consists of the logics to compute capacitance correction, a switchedcapacitor array to adjust Pierce capacitances, and regulators for DCXO and TDTS. The proposed circuits are fabricated by TSMC 0.18-μm CMOS process, where the active area is 0.516 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> for the whole chip, while 0.19 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> for the TDTS. With temperature compensation enabled, the best measured frequency deviations of a calibrated TCXO is within ±0.2 ppm from -40 °C to 85 °C. The temperature resolution of the developed TDTS is successfully designed to reach 0.18 °C/LSB with an accuracy of ±1 °C validated by one of the tape-out chips.
Kinetic characterization of guanine-nucleotide-induced exocytosis from permeabilized rat mast cells (1993)

We have measured the time course of secretion of hexosaminidase from rat mast cells permeabilized (in simple buffered NaCl solutions) in response to guanine nucleotides [GTP or guanosine 5'-[gamma-thio]triphosphate (GTP[S])] and Ca2+. In these experiments, ATP was excluded from the system (and the cells were pretreated with metabolic inhibitors). For cells permeabilized in the absence of Mg2+ but in the presence of Ca2+, secretion commences promptly in response to addition of GTP; when Mg2+ (2 mM) is provided, secretion commences after an extended delay, much higher concentrations of GTP are required, and the final extent of secretion is decreased. Ongoing secretion due to GTP and Ca2+ is abruptly terminated by addition of Mg2+ to cells initially stimulated in its absence. In contrast, although Mg2+ has no effect on the sensitivity to the non-hydrolysable analogue GTP[S], its absence does nevertheless cause delays in the onset of secretion triggered by the addition of GTP[S] to cells initially permeabilized in the presence of Ca2+ (micromolar range, again in the absence of ATP). However, exocytosis from cells triggered with Ca2+ after permeabilization in the presence of high concentrations of GTP[S] is instantaneous. The delays due to triggering by GTP[S] have GTP[S]-concentration-dependent and -independent components. The guanine-nucleotide-concentration-dependent component is expressed as an extended duration of delay as the concentration of GTP[S] is decreased, and may reflect the binding of GTP[S] to GE. The concentration-independent component is manifested as a limiting delay which cannot be further diminished by increasing the guanine nucleotide concentration. The duration of the limiting delay is sensitive to the identity of the stimulating nucleotide (GTP < GTP[S] < p[NH]ppG) and may reflect the time taken for an activating conformational change to occur after binding. Since both components of the delays are abolished by the presence of Mg2+, both the binding of guanine nucleotide and the activation of GE appear to be Mg(2+)-dependent. We therefore conclude that nucleotide binding, activation and the GTPase activity of GE are strongly dependent on Mg2+, in common with the same three processes in Gs and Gi.
Short-wavelength InGaAlP visible laser diodes (1991)

Results achieved on the operation of short-wavelength InGaAlP visible-light laser diodes are described. It is found that there is a strong correlation between operation temperature and oscillation wavelength. The deterioration of favorable temperature characteristics in the short-wavelength region is attributed to an increase in the leakage current, which originates in a small conduction-band discontinuity inherent in the InGaAlP material system. The introduction of a highly doped p-cladding layer improves these temperature characteristics. Short-wavelength oscillation at 630-nm-band wavelength was achieved for transverse-mode stabilized InGaAlP lasers.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Protection Against Oxidative Damage to CNS by α-Phenyl-tert-butyl Nitrone and Other Spin-Trapping Agents: A Novel Series of Nonlipid Free Radical Scavengers (1992)

Observations have been made in the last few years clearly indicating that ROS (reactive oxygen species which include oxygen free radicals, singlet oxygen, lipid hydroperoxides, and hydrogen peroxide) are etiologic agents in the mechanism of development of several pathologic conditions. Thus, recent research efforts have implicated ROS in the following: ischemia/reperfusion injury, arthritis, aging, carcinogenesis, hyperbaric oxygen toxicity, ionizing irradiation injury, ozone damage, damage caused by some xenobiotics, and the mechanism of action of some antitumor agents, etc. Progress has been made possible by new methodologies that more accurately quantitate the in vivo flux of oxygen free radicals. Two of these newer methodologies include salicylate trapping of hydroxyl free radical flux in vivo and the use of spin-trapping compounds to quantitate and characterize the free radicals being produced in vivo. Our laboratories have been active in the development and use of these new methodologies, and in the course of this work we have made the fascinating observation that certain spin-trapping agents are very effective in protecting brain from oxidative damage.