gebhart/patrepeval huggingface dataset:
General Acid/Base Catalysis in the Active Site of <i>Escherichia coli</i> Thioredoxin (1997)

Enzymic catalysts of thiol:disulfide oxidoreduction contain two cysteine residues in their active sites. Another common residue is an aspartate (or glutamate), the role of which has been unclear. Escherichia coli thioredoxin (Trx) is the best characterized thiol:disulfide oxidoreductase, and in Trx these three active-site residues are Cys32, Cys35, and Asp26. Structural analyses had indicated that the carboxylate of Asp26 is positioned properly for the deprotonation of the thiol of Cys35, which would facilitate its attack on Cys32 in enzyme-substrate mixed disulfides. Here, Asp26 of Trx was replaced with isologous asparagine and leucine residues. D26N Trx and D26L Trx are reduced and oxidized more slowly than is wild-type Trx during catalysis by E.coli thioredoxin reductase. Stopped-flow spectroscopy demonstrated that the cleavage of the mixed disulfide between Trx and a substrate is slower in the D26N and D26L enzymes. Buffers increase the rate of mixed disulfide cleavage in these variants but not in wild-type Trx. These results indicate that Asp26 serves as an acid/base in the oxidation/reduction reactions catalyzed by Trx. Specifically, Asp26 protonates (during substrate oxidation) or deprotonates (during substrate reduction) the thiol of Cys35. A similar role is likely filled by the analogous aspartate (or glutamate) residue in protein disulfide isomerase, DsbA, and other thiol:disulfide oxidoreductases. Moreover, these results provide the first evidence for general acid/base catalysis in a thiol:disulfide interchange reaction.
A Coarse-Grained Model of Unstructured Single-Stranded DNA Derived from Atomistic Simulation and Single-Molecule Experiment (2014)

A simple coarse-grained model of single-stranded DNA (ssDNA) was developed, featuring only two sites per nucleotide that represent the centers of mass of the backbone and sugar/base groups. In the model, the interactions between sites are described using tabulated bonded potentials optimized to reproduce the solution structure of DNA observed in atomistic molecular dynamics simulations. Isotropic potentials describe nonbonded interactions, implicitly taking into account the solvent conditions to match the experimentally determined radius of gyration of ssDNA. The model reproduces experimentally measured force-extension dependence of an unstructured DNA strand across 2 orders of magnitude of the applied force. The accuracy of the model was confirmed by measuring the end-to-end distance of a dT<sub>14</sub> fragment via FRET while stretching the molecules using optical tweezers. The model offers straightforward generalization to systems containing double-stranded DNA and DNA binding proteins.
Critical Review of Data, Models and Performance Metrics for Wind and Solar Power Forecast (2021)

Global climatic changes and increased carbon footprints provided the main impetus for the decrease in the use of fossil fuels for electricity generation and transportation. Matured manufacturing technologies of solar PV panels and on-shore and off-shore windmills have brought down the cost of generation of electricity using solar energy on par with conventional fossil fuel. Initially, solar and wind power generation was envisioned for microgrids, serving small local communities. However, advancements in power electronics have now facilitated large solar and wind farms to be integrated with main power grids. In this context, hosting capacity, which is the amount of distributed energy resources a grid can accommodate, without significant infrastructure up-gradation, has gained importance. In determining the hosting capacity at a particular location, the uncertainties of wind and solar power generation play a role. Effective forecasting models using time-series weather data can be built to predict wind and solar power generation. This forecast is essential to ensure proper grid operation and control when renewable energy sources are already installed. The forecast is also useful in the planning stages for investment decisions and distribution system planning. While long-term forecasts are rarely needed for the operation of integrated grids, accurate short-term predictive models are necessary for scheduling. This paper presents an extensive review of various forecast models available in the literature. The study mainly focuses on the short-term forecast, providing a critical review of the duration of data used in each model and a synoptic comparison of their performance indices.
Multicomponent Olivine Cathode for Lithium Rechargeable Batteries: A First-Principles Study (2009)

The in-depth study of the multicomponent effect on the structural and electrochemical properties of olivine cathodes is conducted using state-of-the-art first-principles calculations. The distribution of multiple transition metals in olivine structure alters local crystal structure and electronic structure, affecting its kinetic and thermodynamic properties. We find that local structure change, such as the reduced Jahn−Teller effect of Mn, significantly enhances both Li mobility and electron (polaron) conductivity when the redox Mn element neighbors Fe or Co. The unexpected one-phase Li insertion/extraction reaction of the multicomponent olivine cathode is explained with respect to the multiple interactions of M/Li or M/vacancy (M = transition metals). The redox potential of each transition metal also could shift as a result of charge redistribution and the relative energy change from the multiple M/Li interactions. Implications of multicomponent olivine as a useful strategy for tailoring the electrochemical properties of olivine compounds are discussed for designing better-performing Li rechargeable batteries.
Head Injuries in Children (1972)

Two-hundred children with head injury admitted consecutively to paediatric wards in the two main hospitals in Newcastle upon Tyne have been studied. Eight children required neurosurgical operation. There were two deaths. Details of the cause and consequences of the accidents have been analysed and an attempt has been made to identify psychological or physical factors that may predispose to injury. There was a slightly higher proportion of children with what are regarded as adverse personality factors among the head injuries than in a control group and there were more left-handed children than would be expected in the general population. The results suggest that the modern "high-rise" bicycle may carry a special risk of head injury.
An SDN-based framework for elastic resource sharing in integrated FDD/TDD LTE-A HetNets (2014)

Spectrum and infrastructure sharing among multiple mobile network operators have recently drawn significant attention from the industry and the academia sectors. Recent advances in the area of Software Defined Networking (SDN) launch the design of innovative SDN-based solutions for resource sharing in multi-tier networks of macrocell and small-sized base stations, a.k.a. HetNet. In this paper, we present a novel SDN-based framework that enables efficient and elastic spectrum utilization among multiple operators in 3GPP LTE-A HetNet scenario. Assuming a multi-operator environment of Frequency Division Duplex (FDD) macrocells complemented by multi-tenant Time Division Duplex (TDD) pico cells, we present a SDN-based architecture that allows efficient resource sharing among the TDD and FDD systems in a dynamic way. A TDD frame re-configuration mechanism is also employed, to optimize the ratio of uplink and downlink slots in the TDD frame of picocells. System-level simulation results demonstrate that the combination of these two functional enhancements in the LTE-A HetNet, significantly reduces the application layer delay for both the FDD macrocell and TDD picocell systems, leading to highly efficient and dynamic spectrum sharing among multiple network operators.
Compound optical-fiber-based resonators (1988)

The relative merits of three designs of compound optical-fiber-based resonators for application to line narrowing in fiber lasers and demultiplexing in optical-communications systems are discussed. The three resonator designs are a set of concatenated rings, a three-reflector resonator with loop mirrors, and a fiber Fox–Smith interferometer.
Unbiased Selection of Peptide–Peptoid Hybrids Specific for Lung Cancer Compared to Normal Lung Epithelial Cells (2015)

To develop widely applicable diagnostic and potentially therapeutic approaches overcoming protein heterogeneity in human cancer, we have developed a technology to unbiasedly select high specificity compound(s) that bind any biomolecule (e.g., proteins, lipids, carbohydrates) presented on the cancer cell surface but not on normal cells. We utilized a peptidomimetic based on-bead two-color (OBTC) combinatorial cell screen that can detect differences between two cell surfaces at high accuracy by looking for beads (where each bead in the library had one peptide-peptoid hybrid on the surface) that only bound cancer but not normal cells. We screened a library of 393 216 compounds targeting HCC4017 lung adenocarcinoma cells (labeled in red) in the presence of HBEC30KT normal bronchial epithelial cells (labeled in green) derived from the same tissue of the same patient. This screen identified a peptide-peptoid hybrid called PPS1 which displayed high specific binding for HCC4017 cancer cells over HBEC30KT cells. Specificity was validated through on-bead, ELISA-like and magnetic bead pulldown studies, while a scrambled version of PPS1 did not show any binding. Of interest, the simple dimeric version (PPS1D1) displayed cytotoxic activity on HCC4017 cells, but not on normal HBEC30KT cells. PPS1D1 also strongly accumulated in HCC4017 lung cancer xenografts in mice over control constructs. We conclude that such combinatorial screens using tumor and normal cells from the same patient have significant potential to develop new reagents for cancer biology, diagnosis, and potentially therapy.
Plasma ionization enhancement by laser line radiation (1970)

The possibility of increasing the degree of ionization in a plasma, by use of incident laser wavelengths matched to specific atomic transitions, is theoretically investigated. Such electron production occurs via a multistep process involving laser excitation of neutral atoms to electronic levels near the continuum and subsequent ionization of these atoms through collisions with thermalized plasma electrons. Detailed calculations for atomic oxygen, nitrogen, carbon, and cesium indicate that present state-of-the-art pulsed lasers are capable of raising 10 to 10 cm~ electron densities by a factor of two. Use of laser-diode and lasershock tube combinations for diagnostic studies of recombination processes is discussed briefly.
Conserved Residues Asp16 and Pro24 of TnaC-tRNA <sup>Pro</sup> Participate in Tryptophan Induction of <i>tna</i> Operon Expression (2008)

In Escherichia coli, interactions between the nascent TnaC-tRNA(Pro) peptidyl-tRNA and the translating ribosome create a tryptophan binding site in the ribosome where bound tryptophan inhibits TnaC-tRNA(Pro) cleavage. This inhibition delays ribosome release, thereby inhibiting Rho factor binding and action, resulting in increased tna operon transcription. Replacing Trp12 of TnaC with any other amino acid residue was previously shown to prevent tryptophan binding and induction of tna operon expression. Genome-wide comparisons of TnaC amino acid sequences identify Asp16 and Pro24, as well as Trp12, as highly conserved TnaC residues. Replacing these residues with other residues was previously shown to influence tryptophan induction of tna operon expression. In this study, in vitro analyses were performed to examine the potential roles of Asp16 and Pro24 in tna operon induction. Replacing Asp16 or Pro24 of TnaC of E. coli with other amino acids established that these residues are essential for free tryptophan binding and inhibition of TnaC-tRNA(Pro) cleavage at the peptidyl transferase center. Asp16 and Pro24 are in fact located in spatial positions corresponding to critical residues of AAP, another ribosome regulatory peptide. Sparsomycin-methylation protection studies further suggested that segments of 23S RNA were arranged differently in ribosomes bearing TnaCs with either the Asp16Ala or the Pro24Ala change. Thus, features of the amino acid sequence of TnaC of the nascent TnaC-tRNA(Pro) peptidyl-tRNA, in addition to the presence of Trp12, are necessary for the nascent peptide to create a tryptophan binding/inhibition site in the translating ribosome.
The In Vitro Effects of Instrumentation on Multilevel Cervical Strut-Graft Mechanics (1999)

Multilevel cervical instrumentation effectively increases stiffness after corpectomy. However, anterior or posterior plating alone excessively loads the graft with small degrees of motion, which may promote pistoning and failure of multilevel constructs.
Oxygen Diffusion and Solubility Studies in Ag and Pt Using AC Impedance Spectroscopy (1986)

The ac impedance spectroscopy technique is used to study the oxygen solubility and diffusivity in solid platinum and silver. The results are compared with previous results and are discussed in relation to the use of these metals as electrodes for solid oxide electrolytes. Bulk diffusion is the rate limiting step for silver, whereas surface diffusion is the oxygen rate limiting mechanism for Pt; Pt is essentially impermeable to oxygen, even at elevated temperatures.
Internetwork Protocol Approaches (1980)

The motivation for interconnecting networks is to provide one or more consistent services to the set of users of the interconnected networks. To provide these services either new end-to-end service protocols must be defined or the service protocols of the individual networks must be made to interwork. In either case the issues of addressing, routing, buffering, flow control, error control, and security must be considered. Two examples of interconnection strategy are examined: the interconnection of X.25 networks, and the interconnection of ARPA research networks. The models for interconnection of networks and the role of internetwork protocols are discussed.
Detection of enteroviruses by spot hybridization (1984)

A cloned partial cDNA copy of the coxsackievirus B3 genome was used for detecting enteroviruses in infected cells by employing a nucleic acid hybridization procedure. Cells infected with coxsackieviruses A and B, echovirus, and poliovirus gave positive hybridization signals, whereas cells infected with nonrelated viruses did not.
The Effect of Rigid Cervical Collars on Internal Jugular Vein Dimensions (2009)

Internal jugular vein cross-sectional area increases after application of a rigid cervical collar. This supports the hypothesis that venous obstruction in the neck may contribute to the increase in ICP seen after rigid collar application.
Closed-loop operation of actuator arrays (2002)

An actuator array performs distributed manipulation where an object being transported and manipulated rests on a large number of stationary supporting actuators. The authors have developed a macroscopic actuator array consisting of many motorized wheels. As opposed to a MEMS array, the analysis requires the explicit modeling of the discreteness in the system, including the set of supports, distribution of weight, and generation of traction forces. Using an open-loop wheel velocity field, discreteness causes undesirable behavior such as unstable rotational equilibria, suggesting the use of object feedback. Discrete distributed control algorithms are derived by inverting the dynamics of manipulation. These algorithms reduce the many-input-three-output control problem to a three-input-three-output control problem.
Synthesis of Certain Acyclic Nucleoside Analogs of 1,2,4-Triazolo[3,4-<i>f</i>][1,2,4]triazine and Pyrimido[5,4-<i>d</i>]pyrimidine (1995)

Abstract Synthesis of 2-penten-1-yl (8a) and ganciclovir analog (8b) of 1,2,4-triazolo[3,4-f][1,2,4]triazine was accomplished by the ring annulation of the corresponding hydrazides (6a and 6b), which in turn was obtained by the dehydrative coupling of 4 with 5a or 5b. Base catalysed ring expansion of N9-alkylpurine-6-carbonitriles (10a 10c 10e) provided the acyclic analogs of 4-aminopyrimido-[5,4-d]pyrimidines (13a 13d 13e). Debenzylation of 13e afforded the ganciclovir analog (13f) of 4-amino-8-(β-D-ribofuranosylamino)-pyrimido[5,4-d]pyrimidine. However, compound 10b did not undergo the expected rearrangement but resulted in the formation of the methyl formimidate derivative (12).
KaitoroBase: Visual Exploration of Software Architecture Documents (2009)

This paper describes a software architecture documentation tool (KaitoroBase) built within the Thinkbase Visual Wiki to provide support for non-linear navigation and visualization of Software Architecture Documents (SADs) produced using the Attribute-Driven Design (ADD) method. This involves constructing the meta-model for the SAD in Freebase which provides the foundation for the graph-based interactive visualization enabled by Thinkbase. The resulting tool displays a graphical, high-level structure of SAD, allows for exploratory search, non-linear navigation, and at the same time connects to low-level details of SADs in a wiki.
Blood Culture Contamination: Persisting Problems and Partial Progress (2003)

Although it has been widely appreciated for many years among physicians and microbiologists that blood cultures are among the most important laboratory tests performed in the diagnosis of serious infections (35), it has become equally apparent in more recent years that contaminated blood cultures are common (25, 42), enormously costly (3, 29), and frequently confusing for clinicians (1, 12, 14, 26). Clinical studies of bloodstream infections over 3 decades have provided guidelines for differentiating true pathogens from contaminants or organisms of unknown significance (14, 18, 41, 42); however, a true “gold standard” for differentiating pathogens from contaminants does not exist (4, 25). Moreover, the most common blood culture contaminants, coagulase-negative staphylococci (CoNS), which were almost always such several decades ago (18, 41), now are pathogens more frequently (19, 25, 26, 42), and judging the clinical significance of this group of microorganisms in blood has proven to be especially problematic (1, 11, 22, 24, 26, 42; S. J. Peacock, I. C. Bowler, and D. W. Crook., Letter, Lancet 346:191-192, 1995). This review focuses on how pathogen-contaminant decisions are made, the phenomenon of increasing contamination of blood cultures, potential methods for addressing high contamination rates, and practical laboratory approaches to the workup of likely contaminants.
Transgenic Mouse Models of Alzheimer's Disease (2000)

Alzheimer's disease (AD) pathology is characterized by A beta peptide-containing plaques, neurofibrillary tangles consisting of hyperphosphorylated tau, extensive neuritic degeneration, and distinct neuron loss. We generated several transgenic mouse lines expressing the human amyloid precursor protein (APP751) containing the AD-linked KM670/671NL double mutation (Swedish mutation) under the control of a neuron-specific Thy-1 promoter fragment. In the best APP-expressing line (APP23), compact A beta deposits can be detected at 6 months of age. These plaques dramatically increase with age, are mostly Congo Red positive, and accumulate typical plaque-associated proteins such as heparansulfate proteoglycan and apolipoprotein E. Activated astrocytes and microglia indicative of inflammatory processes reminiscent of AD accumulate around the deposits. Furthermore, plaques are surrounded by enlarged dystrophic neurites as visualized by neurofilament or Holmes-Luxol staining. Strong staining for acetylcholinesterase activity is found throughout the plaques and is accompanied by local distortion of the cholinergic fiber network. All congophilic plaques contain hyperphosphorylated tau reminiscent of early tau pathology. Modern stereologic methods demonstrate a significant loss of neurons in the hippocampal CA1 region, correlating with an increasing A beta plaque load. Interestingly, APP23 mice develop cerebral amyloid angiopathy in addition to amyloid plaques even though the APP transgene is only expressed in neurons. Crossbreeding of APP23 mice with transgenic mice carrying AD-linked presenilin mutations but not wild-type presenilin resulted in enhanced formation of pathology. In conclusion, our APP transgenic mice present many pathologic features, similar to those observed in AD and therefore offer excellent tools for studying the contribution of A beta to AD pathogenesis.
The Zone Diet: An Anti-Inflammatory, Low Glycemic-Load Diet (2004)

The Zone Diet was developed on the concept that the hormonal responses of macronutrients could be orchestrated to maintain key hormones within therapeutic zones to control inflammatory responses. In particular, the two hormonal systems that are directly affected by dietary macronutrients are (1) the insulin/glucagon axis and (2) eicosanoids. Each of these hormonal systems can have a significant impact on the inflammatory process. This hormonal approach to optimizing an anti-inflammatory diet has significant ramifications in treatment of those chronic diseases (obesity, type 2 diabetes, and cardiovascular disease) that are known to produce inflammatory responses. On the other hand, an inappropriate balance of macronutrients (especially high glycemic- load carbohydrates) can lead to increased inflammation. A primary example of this is the promotion of the United States Department of Agriculture's Food Guide Pyramid. Since its adoption, the prevalence of obesity and type 2 diabetes has risen substantially. Both conditions also demonstrate a significant increase in inflammatory markers. The purpose of this article is to review the historical factors that led to the development of the Zone Diet, to understand how the Zone Diet can alter inflammatory responses, and to review the published literature on its ability to affect hormonal and metabolic responses.
Intent Generation for Goal-Oriented Dialogue Systems based on Schema.org Annotations (2018)

Goal-oriented dialogue systems typically communicate with a backend (e.g. database, Web API) to complete certain tasks to reach a goal. The intents that a dialogue system can recognize are mostly included to the system by the developer statically. For an open dialogue system that can work on more than a small set of well curated data and APIs, this manual intent creation will not scalable. In this paper, we introduce a straightforward methodology for intent creation based on semantic annotation of data and services on the web. With this method, the Natural Language Understanding (NLU) module of a goal-oriented dialogue system can adapt to newly introduced APIs without requiring heavy developer involvement. We were able to extract intents and necessary slots to be filled from schema.org annotations. We were also able to create a set of initial training sentences for classifying user utterances into the generated intents. We demonstrate our approach on the NLU module of a state-of-the art dialogue system development framework.
A wide range dB-linear variable gain CMOS amplifier (1997)

A 10 MHz 6-stage CMOS amplifier with variable gain from 0 dB up to 80 dB is presented. Differential inputs and outputs provide a high PSRR. The gain is controlled by a dB-linear differential voltage. At a single power supply voltage of 5 V the maximum linear input and output swing is 600 mV. The amplifier has been fabricated in a 1.6µm CMOS process and covers a chip area of 0.72 mm2. Measurements of a fully integrated automatic gain control are presented.