gebhart/patrepeval huggingface dataset:
Molecular Structure, Conformational Analysis, and Structure−Activity Studies of Dendrotoxin and Its Homologues Using Molecular Mechanics and Molecular Dynamics Techniques (1996)

Three-dimensional structures of Dendrotoxin (DtX), Toxin-I (DpI), and Toxin-K (DpK) were determined using molecular mechanics and molecular dynamics techniques. The overall molecular conformation and protein folding of the three dendrotoxins are very similar to the published crystal structures of bovine pancreatic trypsin inhibitor (BPTI) and alpha-DtX. Major secondary structural regions of the dendrotoxins are stable without much fluctuation during the dynamics simulation; the regions corresponding to the turns and bends (rich in lysines and arginines) exhibit more fluctuations. The conformational angles and the C alpha...C alpha' distances of the three disulfides (in each of the dendrotoxins) are different from each other. Comparative model building studies, involving the dendrotoxins and the proteinases, reveal that the key interactions (observed in BPTI-trypsin complex) needed for anti-protease activity are absent due to structural differences between the dendrotoxins and BPTI at the anti-protease loop; this explains the inability of the dendrotoxins to inhibit proteinases. The model also suggests that the solvent-exposed beta-turn region, rich in lysines (residues 26-28), might bind directly to the extracellular anionic sites of the receptors (K+ channels) by ionic interactions. The strikingly homologous cysteine distribution (Cys-x-x-x-Cys) in DtX, DpI, and DpK, at the C-terminus, induces the occurrence of a characteristic conformational motif, consisting of an alpha-helix (in an amphiphilic environment) stabilized by two disulfides, one involving a cysteine at the beta-strand, and the other at the N-terminus. This amphiphilic secondary structural element seems to provide the rigid frame work needed for exposing the proposed active site region of the dendrotoxins to the anionic sites of the K+ channel receptors.
Mode Selective Filtering by a Coupling Mechanism Between Glass Fiber and Thin-Film Slab Waveguide (1974)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text C. A. Goben, D. L. Begley, and M. Davarpanah, "Mode Selective Filtering by a Coupling Mechanism Between Glass Fiber and Thin-Film Slab Waveguide," Appl. Opt. 13, 2757-2758 (1974) Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Activation of toll‐like receptors 2 and 4 by gram‐negative periodontal bacteria (2007)

Gram-negative periodontal bacteria predominantly stimulated TLR2, which may be of importance for the Th1/Th2 cell orientation of the immune response in periodontitis.
Using superconducting qubit circuits to engineer exotic lattice systems (2010)

We propose an architecture based on superconducting qubits and resonators for the implementation of a variety of exotic lattice systems, such as spin and Hubbard models in higher or fractal dimensions and higher-genus topologies. Spin systems are realized naturally using qubits, while superconducting resonators can be used for the realization of Bose-Hubbard models. Fundamental requirements for these designs, such as controllable interactions between arbitrary qubit pairs, have recently been implemented in the laboratory, rendering our proposals feasible with current technology.
Universal Basic Income in Developing Countries: Issues, Options, and Illustration for India (2018)

This paper discusses two common arguments for the adoption of a UBI; that it can be a more effective way of supporting low-income households when existing safety net programs are inefficient, and that it can generate broad support for structural reforms. Using India as an illustration, the paper discusses the trade-offs that need to be recognized in adopting a UBI in these contexts. It shows that replacing the 2011 Public Distribution System (PDS) with a UBI results in losses for many low-income households, although much of this can be reduced by recycling the “out-of-system” PDS losses and the fiscal savings from excluding the highest-income groups as higher UBI transfers. In contrast, replacing inefficient energy subsidies—raising energy prices to efficient levels to internalize the negative environmental externalities of energy consumption—could simultaneously deliver unambiguous distributional gains, help address fiscal pressures, and improve energy efficiency with associated environmental and health gains. Implementing such reforms would, of course, require careful communication and implementation to address political barriers to reform.
Cycle-Time Key Factor Identification and Prediction in Semiconductor Manufacturing Using Machine Learning and Data Mining (2011)

Within the complex and competitive semiconductor manufacturing industry, lot cycle time (CT) remains one of the key performance indicators. Its reduction is of strategic importance as it contributes to cost decreasing, time-to-market shortening, faster fault detection, achieving throughput targets, and improving production-resource scheduling. To reduce CT, we suggest and investigate a data-driven approach that identifies key factors and predicts their impact on CT. In our novel approach, we first identify the most influential factors using conditional mutual information maximization, and then apply the selective naive Bayesian classifier (SNBC) for further selection of a minimal, most discriminative key-factor set for CT prediction. Applied to a data set representing a simulated fab, our SNBC-based approach improves the accuracy of CT prediction in nearly 40% while narrowing the list of factors from 182 to 20. It shows comparable accuracy to those of other machine learning and statistical models, such as a decision tree, a neural network, and multinomial logistic regression. Compared to them, our approach also demonstrates simplicity and interpretability, as well as speedy and efficient model training. This approach could be implemented relatively easily in the fab promoting new insights to the process of wafer fabrication.
Relationships between the Prefrontal Cortex and the Basal Ganglia in the Rat: Physiology of the Cortico-Nigral Circuits (1999)

The prelimbic/medial orbital areas (PL/MO) of the rat prefrontal cortex are connected to substantia nigra pars reticulata (SNR) through three main circuits: a direct nucleus accumbens (NAcc)-SNR pathway, an indirect NAcc-SNR pathway involving the ventral pallidum (VP) and the subthalamic nucleus (STN), and a disynaptic cortico-STN-SNR pathway. The present study was undertaken to characterize the effect of PL/MO stimulation on SNR cells and to determine the contribution of these different pathways. The major pattern of responses observed in the SNR was an inhibition preceded by an early excitation and followed or not by a late excitation. The inhibition resulted from the activation of the direct NAcc-SNR pathway because it disappeared after acute blockade of the glutamatergic cortico-striatal transmission by CNQX application into the NAcc. The late excitation resulted from the activation of the indirect NAcc-VP-STN-SNR pathway via a disinhibition of the STN because it disappeared after either CNQX application into the NAcc or blockade of the GABAergic striato-pallidal transmission by bicuculline application into the VP. The early excitation, which was markedly decreased after blockade of the cortico-STN transmission by CNQX application into the STN, resulted from the activation of the disynaptic cortico-STN-SNR pathway. Finally, the blockade of the cortico-STN-VP circuit by CNQX application into STN or VP modified the influence of the trans-striatal circuits on SNR cells. This study suggests that, in the prefrontal cortex-basal ganglia circuits, the trans-subthalamic pathways, by their excitatory effects, participate in the shaping of the inhibitory influence of the direct striato-nigral pathway on SNR neurons.
35-kV GaAs subnanosecond photoconductive switches (1990)

High-voltage, fast-pulse generation using GaAs photoconductive switches is investigated. It is possible to generate 35-kV pulses with risetimes as short as 135 ps using 5-mm gap switches, and electric field hold-off of greater than 100 kV/cm is achieved. An approximately 500-ps FWHM on/off electrical pulse is generated with an amplitude of approximately 3 kV using neutron-irradiated GaAs having short carrier lifetimes. Experimental results are described, and fabrication of switches and the diagnostics used to measure these fast signals are discussed. Experience with the nonlinear lock-on and avalanche modes of operation observed in GaAs is also described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Microwave Kinetic Inductance Detectors: The First Decade (2009)

Microwave Kinetic Inductance Detectors, or MKIDs, are non‐equilibrium superconducting detectors made out of high quality factor superconducting microwave resonant circuits. Their primary advantage over other low temperature detector technologies is their built‐in frequency domain multiplexing at GHz frequencies, allowing thousands of detectors to be read out through a single transmission line. MKIDs are now celebrating their tenth birthday, so this review aims to sum up what has been learned over the first decade and explore the diversity of current MKID projects.
Preparation of fluorescent Au–SiO<sub>2</sub>core–shell nanoparticles and nanorods with tunable silica shell thickness and surface modification for immunotargeting (2016)

Gold-silica (Au-SiO<sub>2</sub>) core-shell nanoparticles (NPs) enable multifunctional properties for in vivo biomedical applications. However, scalable synthesis methods are lacking for the preparation of Au-SiO<sub>2</sub> core-shell NPs less than 30 nm in overall diameter with a tunable silica shell less than 10 nm in thickness. Therefore, we prepared monodispersed Au-SiO<sub>2</sub> core-shell NPs less than 30 nm in overall diameter with a uniform, tunable silica shell ∼1 to 14 nm in thickness using either citrate reduction followed by a modified Stöber method or oleylamine reduction followed by a reverse microemulsion method. Oleylamine reduction enabled up to 80-fold greater concentration yield compared to the citrate reduction method currently used for synthesizing Au core NPs. The formation of a tunable silica shell less than 10 nm in thickness was facilitated by controlling the molecular weight of the priming polymer (modified Stöber) or surfactant (reverse microemulsion) in addition to the concentration of the silane precursor, and was robust for encapsulating non-spherical morphologies such as Au nanorods. The reverse microemulsion method enabled several distinct advantages over the modified Stöber method, including greater control over the silica shell thickness, ∼16-fold greater yield in core-shell NP concentrations for scalable synthesis, and the ability to encapsulate controlled concentrations of a molecular payload (e.g., fluorophores with four different emission profiles) in the silica shell. Au-SiO<sub>2</sub> core-shell NPs were also bioconjugated with immunoglobulin-G (IgG) as a model antibody to demonstrate immunotargeting. Bioactivity of Au-SiO<sub>2</sub>-IgG core-shell NPs was confirmed by agglomeration in the presence of protein A. The presence and proper orientation of IgG on NP surfaces was verified by direct observation in electron microscopy after negative staining. Therefore, the methods in this study for preparing and modifying Au-SiO<sub>2</sub> core-shell NPs provide a platform for engineering core-shell NPs with size-dependent functional properties for multispectral/multimodal imaging, drug delivery, and combined theranostics.
Infrequent p53 gene mutation but UV gradient‐like p53 protein positivity in keloids (2012)

Keloids are characterized by extreme fibroblastic overgrowth of unknown pathogenesis after skin injury. Previous studies, mostly in non-Caucasian populations, suggest that p53 mutations may be involved. To substantiate this, we performed DNA sequence analysis of exons 4-8 of the p53 gene and immunohistochemical staining of p53 protein in archived keloidal tissue samples from 23 Caucasian patients. In contrast to previous reports, we found mutated p53 in keloidal tissue in a minority of cases (2/23; 12%). The G allele frequency and C allele frequency at the p53 polymorphic codon 72 were 0.72 (33/46) and 0.28 (13/46), respectively, in our study, a finding that was similar to the 0.77 (184/240) vs. 0.23 (56/240) (P = 0.4580; chi-squared test) observed in the Hap Map data of a European population but statistically significantly different from the 0.43 (547/1258) vs. 0.57 (711/1258) (P = 0.0002; chi-squared test) observed in the 1000 Genome project [Database of Single Nucleotide Polymorphisms (dbSNP). Bethesda (MD): National Center for Biotechnology Information, National Library of Medicine. dbSNP accession:rs1042522, (dbSNP Build ID: 132). Available from: (http://www.ncbi.nlm.nih.gov/SNP/] a difference most likely due to the different genetic background of the populations enrolled. However, one-third of the keloidal samples showed lesional nuclear p53 staining with a UV penetration gradient-like positivity (P ≤ 0.0084). Staining with an anti-cyclobutane pyrimidine dimer antibody revealed the total absence of short-term photoproducts in the epidermis as well as keloidal tissue. Furthermore, all fibroblasts expressing p53 stained negative for Ki-67, indicating that these cells were in a quiescent stage and p53 upregulation did not contribute to keloidal proliferation. We conclude that p53 plays no major role in the pathogenesis of keloids in the Caucasian population.
CacheScouts: Fine-Grain Monitoring of Shared Caches in CMP Platforms (2007)

As multi-core architectures flourish in the marketplace, multi-application workload scenarios (such as server consolidation) are growing rapidly. When running multiple applications simultaneously on a platform, it has been shown that contention for shared platform resources such as last-level cache can severely degrade performance and quality of service (QoS). But today's platforms do not have the capability to monitor shared cache usage accurately and disambiguate its effects on the performance behavior of each individual application. In this paper, we investigate low-overhead mechanisms for fine-grain monitoring of the use of shared cache resources along three vectors: (a) occupancy - how much space is being used and by whom, (b) interference - how much contention is present and who is being affected and (c) sharing - how are threads cooperating. We propose the CacheScouts monitoring architecture consisting of novel tagging (software-guided monitoring IDs), and sampling mechanisms (set sampling) to achieve shared cache monitoring on per application basis at low overhead (<0.1%) and with very little loss of accuracy (<5%). We also present case studies to show how CacheScouts can be used by operating systems (OS) and virtual machine monitors (VMMs) for (a) characterizing execution profiles, (b) optimizing scheduling for performance management, (c) providing QoS and (d) metering for chargeback.
An Overlay Gateway for the Integration of IP Multimedia Subsystem and Mobile Sink Based - Wireless Sensor Networks (2010)

The IP Multimedia Subsystem (IMS) aims to provide cellular access to all the services that the Internet offers; it is an overlay control layer on top of an IP layer. Wireless Sensor Networks (WSN) with mobile sinks are useful in a wide range of scenarios since they can improve the overall network lifetime and increase data capacity. Combining the capabilities of IMS with the rich set of contextual information captured by mobile sink WSNs will open the door to a wide range of novel multimedia services. This paper proposes an overlay architecture for the integration of IMS with mobile sink-based WSN. The Presence service is used as entry point to the IMS world. The gateway which is the heart of our architecture is an overlay built on top of the very same mobile phones that act as mobile sinks, presence publishers / watchers, and end-user devices. A prototype is built using JXME, an extension of JXTA with P2P middleware.
A Generative Approach to the Modeling of Isomorphic Hidden-Figure Items (1991)

A generative approach to psychometric model ing consists of encoding information about the cognitive processes and structures that underlie test performance into an item-generation algorithm in such a way that the generated items have known psychometric parameters. An important by-product of the approach is that the knowledge about the response process is tested every time a test is ad ministered. Validation thus becomes an ongoing process rather than an occasional event. This ap proach is illustrated through an analysis of hidden- figure items, and is shown to be feasible.
Signal processing in a nonperiodically time-varying magnetoelastic medium (1968)

Wave propagation in a nonperiodically time-varying medium provides a means for realizing in simple physical structures a variety of signal-processing operations, such as frequency translation and coding, variable delay recall, gating, time-scale stretching or shrinking, and time reversal. The use of low-velocity modes, such as acoustic, spin, or magnetoelastic waves in solids, reduces the length of the propagation structure required to less than an inch. A general review is given of the principles of wave propagation in a spatially uniform medium with nonperiodic time variation. Both abrupt and gradual time variations are discussed. Illustrations are given for the cases of spin-wave and magnetoelastic-wave propagation and signal processing operations in these media are explained. Consideration is given to the problem of spin-wave propagation in a time-and space-varying magnetic field of the form encountered in experiments; and it is shown that a simple separated variable solution exists. For the more difficult problem of magnetoelastic propagation with both space and time variations, an approximate space-time ray theory is described. Experimental results for pulsed-field processing of spin and magnetoelastic waves are given and related to the theory.
Nucleic‐Acid Analogues with Constraint Conformational Flexibility in the Sugar‐Phosphate Backbone (‘Bicyclo‐DNA’). Part 1. Preparation of (3<i>S</i>,5′<i>R</i>)‐2′‐Deoxy‐3′,5′‐ethano‐αβ‐<scp>D</scp>‐ribonucleosides (‘Bicyclonucleosides’) (1993)

Abstract We describe the synthesis of 2′‐deoxy‐3′,5′‐ethano‐ D ‐ribonucleosides 1 – 8 (= (5′,8′‐dihydroxy‐2′‐oxabicyclo‐[3.3.0]oct‐3′‐yl)purines or ‐pyrimidines) of the nucleobases adenine, thymine, cytosine, and guanine. They differ from natural 2′‐deoxyribonucleosides only by an additional ethylene bridge between the centers C(3′) and C(5′). The configuration at these centers (3 S ,5′ R ) was chosen as to match the geometry of a repeating nucleoside unit in duplex DNA as close as possible. These nucleosides were designed to confer, as constituents of an oligonucleotide chain, a higher degree of preorganization of a single strand for duplex formation with respect to natural DNA, thus leading to an entropic advantage for the pairing process. The synthesis of these ‘bicyclonucleosides’ was achieved by construction of an enantiomerically pure carbohydrate precursor 18 / 19 ( Schemes 1 ), which was then converted to the corresponding nucleosides by known methods in nucleoside synthesis ( Schemes 2 and 3 ). In all cases, both anomeric forms of the nucleosides were obtained in pure crystalline form, the relative configuration of which was established by 1 H‐NMR‐NOE spectroscopy. A conformational analysis of the nucleosides with β‐configuration at the anomeric center by means of X‐ray and 1 H‐NMR (including NOE) spectroscopy show the furanose part of the molecules to adopt uniformly a 1′ exo ‐conformation with the base substituents preferentially in the anti ‐range in the pyrimidine nucleosides ( anti / syn ca. 2:1) distribution in the purine nucleosides (in solution).
A dual-base triggered SCR with very low leakage current and adjustable trigger voltage (2008)

A new dual-base triggered SCR is presented. By adjusting the device sizings in the trigger circuit, the designer sets the trigger voltage to an application appropriate-value. The turn on time is comparable to that of DTSCRs fabricated in the same technology node, but the leakage is orders of magnitude lower.
Single-Nucleotide Changes in the HIV Rev-Response Element Mediate Resistance to Compounds That Inhibit Rev Function (2011)

Previously we described the identification of two compounds (3-amino-5-ethyl-4,6-dimethylthieno[2,3-b]pyridine-2-carboxamide [103833] and 4-amino-6-methoxy-2-(trifluoromethyl)-3-quinolinecarbonitrile [104366]) that interfered with HIV replication through the inhibition of Rev function. We now describe resistant viral variants that arose after drug selection, using virus derived from two different HIV proviral clones, NL4-3 and R7/3. With HIV(NL4-3), each compound selected a different single point mutation in the Rev response element (RRE) at the bottom of stem-loop IIC. Either mutation led to the lengthening of the stem-loop IIC stem by an additional base pair, creating an RRE that was more responsive to lower concentrations of Rev than the wild type. Surprisingly, wild-type HIV(R7/3) was also found to be inhibited when tested with these compounds, in spite of the fact this virus already has an RNA stem-loop IIC similar to the one in the resistant NL4-3 variant. When drug resistance was selected in HIV(R7/3), a virus arose with two nucleotide changes that mapped to the envelope region outside the RRE. One of these nucleotide changes was synonymous with respect to env, and one was not. The combination of both nucleotide changes appeared to be necessary for the resistance phenotype as the individual point mutations by themselves did not convey resistance. Thus, although drug-resistant variants can be generated with both viral strains, the underlying mechanism is clearly different. These results highlight that minor nucleotide changes in HIV RNA, outside the primary Rev binding site, can significantly alter the efficiency of the Rev/RRE pathway.
Amyloid β-Protein:  Monomer Structure and Early Aggregation States of Aβ42 and Its Pro<sup>19</sup>Alloform (2005)

The amyloid beta-protein (Abeta) is a seminal neuropathic agent in Alzheimer's disease (AD). Recent evidence points to soluble Abeta oligomers as the probable neurotoxic species. Among the naturally occurring Abeta peptides, the 42-residue form Abeta42 is linked particularly strongly with AD, even though it is produced at approximately 10% of the levels of the more abundant 40-residue form Abeta40. Here, we apply mass spectrometry and ion mobility to the study of Abeta42 and its Pro19 alloform. The Phe19 --> Pro19 substitution blocks fibril formation by [Pro19]Abeta42. Evidence indicates that solution-like structures of Abeta monomers are electrosprayed and characterized. Unfiltered solutions of Abeta42 produce only monomers and large oligomers, whereas [Pro19]Abeta42 solutions produce abundant monomers, dimers, trimers, and tetramers but no large oligomers. When passed through a 10,000 amu filter and immediately sampled, Abeta42 solutions produce monomers, dimers, tetramers, hexamers, and an aggregate of two hexamers that may be the first step in protofibril formation. These results are consistent with recently published photochemical cross-linking data and lend support to recent aggregation mechanisms proposed by Bitan, Teplow, and co-workers [J. Biol. Chem. 2003, 278, 34882-34889].
SARS-CoV-2 escape <i>in vitro</i> from a highly neutralizing COVID-19 convalescent plasma (2020)

Three mutations allowed SARS-CoV-2 to evade the polyclonal antibody response of a highly neutralizing COVID-19 convalescent plasma.