gebhart/patrepeval huggingface dataset:
Monoclonal antibodies define a domain on herpes simplex virus glycoprotein B involved in virus penetration (1988)

In an earlier report (S.D. Marlin, S.L. Highlander, T.C. Holland, M. Levine, and J.C. Glorioso, J. Virol. 59: 142-153), we described the production and use of complement-dependent virus-neutralizing monoclonal antibodies (MAbs) and MAb-resistant (mar) mutants to identify five antigenic sites (I to V) on herpes simplex virus type 1 glycoprotein B (gB). In the present study, the mechanism of virus neutralization was determined for a MAb specific for site III (B4), the only site recognized by MAbs which exhibited complement-independent virus-neutralizing ability. This antibody had no detectable effect on virus attachment but neutralized viruses after adsorption to cell monolayers. These findings implied that the mechanism of B4 neutralization involved blocking of virus penetration. The remaining antibodies, which recognized sites I, II, and IV, required active complement for effective neutralization. These were further studied for their ability to impede virus infectivity in the absence of complement. Antibodies to sites I (B1 and B3) and IV (B6) slowed the rate at which viruses penetrated cell surfaces, supporting the conclusion that antibody binding to gB can inhibit penetration by a virus. The data suggest that MAbs can interfere with penetration by a virus by binding to a domain within gB which is involved in this process. In another assay of virus infection, MAb B6 significantly reduced plaque development, indicating that antibody binding to gB expressed on infected-cell surfaces can also interfere with the ability of a virus to spread from cell to cell. In contrast to these results, antibodies to site II (B2 and B5) had no effect on virus infectivity; this suggests that they recognized structures which do not play a direct role in the infectious process. To localize regions of gB involved in these phenomena, antibody-binding sites were operationally mapped by radioimmunoprecipitation of a panel of truncated gB molecules produced in transient-expression assays. Residues critical to recognition by antibodies which affect penetration by a virus (sites I, III, and IV) mapped to a region of the molecule (amino acid residues 241 to 441) which is centrally located within the external domain. Antibodies which had no effect on penetration (site II) recognized sequences distal to this region (residues 596 to 737) near the transmembrane domain. The data suggest that these gB-specific MAbs recognize two major antigenic sites which reside in physically distinct components of the external domain of gB.(ABSTRACT TRUNCATED AT 400 WORDS)
Continuous Monitoring of Salivary Flow Rate and pH at the Surface of the Dentition following Consumption of Acidic Beverages (1997)

Use of a splint-mounted flexible pH electrode has allowed reliable continuous monitoring of pH at the surface of the dentition whilst still enabling subjects to drink normally. pH was monitored at the palatal upper left central incisor and upper right first permanent molar sites after drinking 1% (w/v) citric acid. A maximal decrease in pH to values of 2-3 was observed after 1 min followed by a slower recovery which was above pH 5.5 within 2 min at the former site and in 4-5 min at the latter site. A sharp rise in parotid saliva flow rate was seen at 1 min after drinking the same concentration of citric acid by glass, straw or feeder cup, which returned to resting levels within 6 min although the fall-off of flow rate was slower with the feeder cup. Thus, after dietary acid intake the pH at the surface of the dentition is below the critical pH for enamel dissolution for shorter periods than previously suggested, which is probably a reflection of salivary neutralisation and washing.
An 11-GHz GaAs frequency divider using source-coupled FET Logic (1986)

A GaAs one-fourth frequency divider is fabricated to evaluate the ultrahigh-speed performance of source-coupled FET logic (SCFL) having normally-on FET's with small negative V th values. High-transconductance (240 ms/mm) 1/2-µm gate-length FET's and an air-bridge interconnection line technology are successfully developed. A maximum toggle frequency F <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">max</inf> of 11 GHz is achieved with a power dissipation of 149 mW. Furthermore, 9.7-GHz F <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">max</inf> with low power dissipation of 52 mW was also obtained.
ac and dc properties of Josephson-junction arrays with long-range interaction (1993)

We present an experimental investigation of arrays with long-range interaction, together with a model to explain observed deviations from the predictions of earlier theoretical work. These arrays consist of N horizontal and N vertical superconducting filaments arranged in two parallel planes separated by an oxide layer, so that every wire is Josephson coupled to every other wire in the array as nearest- or next-nearest neighbors. We have performed ac-susceptibility and dc-transport measurements on both ordered and disordered arrays. Our ac measurements show a strong feature at a temperature ${\mathit{T}}_{\mathit{c}}$, which we interpret as a transition to the macroscopically phase-coherent state. We find that this feature is field dependent in ordered arrays, but not in disordered arrays. dc-transport measurements reveal that these arrays have unexpectedly low critical currents and show voltage steps in their I-V curves; moreover, they are hysteretic despite the fact that they consist of nonhysteretic junctions. Our analysis of these results shows that the finite ratio of the wire inductance to the Josephson inductance cannot be ignored since it limits the effective number of Josephson junctions along a wire to ${\mathit{N}}_{\mathit{e}\mathit{f}\mathit{f}}$\ensuremath{\ll}N.
Masking release for low- and high-pass-filtered speech in the presence of noise and single-talker interference (2009)

Speech intelligibility was measured for sentences presented in spectrally matched steady noise, single-talker interference, or speech-modulated noise. The stimuli were unfiltered or were low-pass (LP) (1200 Hz cutoff) or high-pass (HP) (1500 Hz cutoff) filtered. The cutoff frequencies were selected to produce equal performance in both LP and HP conditions in steady noise and to limit access to the temporal fine structure of resolved harmonics in the HP conditions. Masking release, or the improvement in performance between the steady noise and single-talker interference, was substantial with no filtering. Under LP and HP filtering, masking release was roughly equal but was much less than in unfiltered conditions. When the average F0 of the interferer was shifted lower than that of the target, similar increases in masking release were observed under LP and HP filtering. Similar LP and HP results were also obtained for the speech-modulated-noise masker. The findings are not consistent with the idea that pitch conveyed by the temporal fine structure of low-order harmonics plays a crucial role in masking release. Instead, any reduction in speech redundancy, or manipulation that increases the target-to-masker ratio necessary for intelligibility to beyond around 0 dB, may result in reduced masking release.
Network Coding Theory: Single Sources (2005)

Store-and-forward had been the predominant technique for transmitting information through a network until its optimality was refuted by network coding theory. Network coding offers a new paradigm for network communications and has generated abundant research interest in information and coding theory, networking, switching, wireless communications, cryptography, computer science, operations research, and matrix theory.
Japanese Alzheimer’s Disease and Other Complex Disorders Diagnosis Based on Mitochondrial SNP Haplogroups (2012)

This paper first explains how the relations between Japanese Alzheimer's disease (AD) patients and their mitochondrial SNP frequencies at individual mtDNA positions examined using the radial basis function (RBF) network and a method based on RBF network predictions and that Japanese AD patients are associated with the haplogroups G2a and N9b1. It then describes a method for the initial diagnosis of Alzheimer's disease that is based on the mtSNP haplogroups of the AD patients. The method examines the relations between someone's mtDNA mutations and the mtSNPs of AD patients. As the mtSNP haplogroups thus obtained indicate which nucleotides of mtDNA loci are changed in the Alzheimer's patients, a person's probability of becoming an AD patient can be predicted by comparing those mtDNA mutations with that person's mtDNA mutations. The proposed method can also be used to diagnose diseases such as Parkinson's disease and type 2 diabetes and to identify people likely to become centenarians.
C-reactive protein and vein graft disease: evidence for a direct effect on smooth muscle cell phenotype via modulation of PDGF receptor-β (2008)

Plasma C-reactive protein (CRP) concentration is a biomarker of systemic atherosclerosis and may also be associated with vein graft disease. It remains unclear whether CRP is also an important modulator of biological events in the vessel wall. We hypothesized that CRP influences vein graft healing by stimulating smooth muscle cells (SMCs) to undergo a phenotypic switch. Distribution of CRP was examined by immunohistochemistry in prebypass human saphenous veins (HSVs, n = 21) and failing vein grafts (n = 18, 25-4,400 days postoperatively). Quiescent HSV SMCs were stimulated with human CRP (5-50 microg/ml). SMC migration was assessed in modified Boyden chambers with platelet-derived growth factor (PDGF)-BB (5-10 ng/ml) as the chemoattractant. SMC viability and proliferation were assessed by trypan blue exclusion and reduction of Alamar Blue substrate, respectively. Expression of PDGF ligand and receptor (PDGFR) genes was examined at RNA and protein levels after 24-72 h of CRP exposure. CRP staining was present in 13 of 18 diseased vein grafts, where it localized to the deep media and adventitia, but it was minimally detectable in most prebypass veins. SMCs pretreated with CRP demonstrated a dose-dependent increase in migration to PDGF-BB (P = 0.02), which was inhibited by a PDGF-neutralizing antibody. SMCs treated with CRP showed a dose-dependent increase in PDGFRbeta expression and phosphorylation after 24-48 h. Exogenous CRP had no effect on SMC viability or proliferation. These data suggest that CRP is detectable within the wall of most diseased vein grafts, where it may exert local effects. Clinically relevant levels of CRP can stimulate SMC migration by a mechanism that may involve upregulation and activation of PDGFRbeta.
InP 2D photonic crystal microlasers on siliconwafer:room temperature operation at 1.55 µm (2001)

Room temperature pulsed laser operation of 2D photonic crystal microcavities around 1.55 µm is reported. Such devices are based on thin III/V heterostructures transferred onto silicon and include an InGaAs/InP multiquantum well (MQW) active layer.
Hepatocyte growth factor induces colonic cancer cell invasiveness via enhanced motility and protease overproduction. Evidence for PI3 kinase and PKC involvement (2001)

Tumour progression to the metastatic phenotype is mainly dependent on tumour cell invasiveness. Cell migration is a crucial step in this process. Here we investigate the effect of hepatocyte growth factor (HGF) on the induction of in vitro invasiveness of poorly aggressive Caco-2 colonic cancer epithelial cells. Invasion assays through a Matrigel barrier were performed. Proteases were assessed by zymography, reverse transcription-polymerase chain reaction and immunoblotting. Caco-2 cells were found to express HGF receptor but not HGF and to secrete several proteases, namely matrix metalloproteinase-1 (MMP-1), MMP-2, possibly MMP-9 and urokinase plasminogen activator (uPA). Exogenous HGF promoted invasiveness of Caco-2 cells through an artificial basement membrane matrix and enhanced their production of proteases. In addition, analyses of media at the end of invasion assays indicated that anti-HGF antibody inhibited protease production in parallel with cell invasion. The involvement of proteases in the HGF-induced invasion process was further investigated using either a synthetic general MMP inhibitor or neutralizing antibodies against MMPs or uPA. All components significantly inhibited HGF-promoted cell invasion. Moreover, specific inhibitors of PKCalpha/beta1 and PI3 kinase also decreased both HGF-promoted cell invasion and protease expression in invasion assay media. Thus, our findings provide evidence that the process of HGF-activated invasiveness of Caco-2 cells involves PI3 kinase and PKC and results from close association of two events, stimulation of cell motile activity and concomitant overproduction of proteases, which permits cell migration through a degraded extracellular matrix.
Rapid Roughening in Thin Film Growth of an Organic Semiconductor (Diindenoperylene) (2003)

The scaling exponents alpha, beta, and 1/z in thin films of the organic molecule diindenoperylene deposited on SiO2 under UHV conditions are determined. Atomic-force microscopy, x-ray reflectivity, and diffuse x-ray scattering were employed. The surface width displays power law scaling over more than 2 orders of magnitude in film thickness. We obtained alpha = 0.684+/-0.06, beta = 0.748+/-0.05, and 1/zeta = 0.92+/-0.20. The derived exponents point to an unusually rapid growth of vertical roughness and lateral correlations. We suggest that they could be related to lateral inhomogeneities arising from the formation of grain boundaries between tilt domains in the early stages of growth.
Hormones and the hippocampus (2001)

Hippocampal lesions produce memory deficits, but the exact function of the hippocampus remains obscure. Evidence is presented that its role in memory may be ancillary to physiological regulation. Molecular studies demonstrate that the hippocampus is a primary target for ligands that reflect body physiology, including ion balance and blood pressure, immunity, pain, reproductive status, satiety and stress. Hippocampal receptors are functional, probably accessible to their ligands, and mediate physiological and cognitive changes. This argues that an early role of the hippocampus may have been in sensing soluble molecules (termed here 'enteroception') in blood and cerebrospinal fluid, perhaps reflecting a common evolutionary origin with the olfactory system ('exteroception'). Functionally, hippocampal enteroception may reflect feedback control; evidence is reviewed that the hippocampus modulates body physiology, including the activity of the hypothalamus-pituitary-adrenal axis, blood pressure, immunity, and reproductive function. It is suggested that the hippocampus operates, in parallel with the amygdala, to modulate body physiology in response to cognitive stimuli. Hippocampal outputs are predominantly inhibitory on downstream neuroendocrine activity; increased synaptic efficacy in the hippocampus (e.g. long-term potentiation) could facilitate throughput inhibition. This may have implications for the role of the hippocampus and long-term potentiation in memory.
Modeling non-uniform airflow distribution in large grain silos using Fluent. (2006)

Computational fluid dynamics software (Fluent) was used to successfully model non-uniform airflow through large grain storage silos using Ergun’s equation, which can account for material properties of a grain mass such as porosity and fines concentration. Three example applications were investigated: a peaked grain mass, a grain mass with a high fines concentration core, and a grain mass aerated from a ring duct around the bottom of the silo wall. The velocity magnitude through a peaked grain mass decreased from 0.0163 m/s at the air inlet to less than 0.008 m/s at 1.0 m below the peak of the grain mass. The velocity magnitude in a core of high fine material concentration decreased from 0.0142 m/s at the air inlet to 0.008 m/s, which resulted in a 40 % lower effective airflow rate through the grain core versus the rest of the grain mass. This non-uniform airflow behavior confirmed the observation by practitioners that moving a cooling front through peaked grain or a core with high fines concentration takes substantially longer than through a leveled and/ or cored grain mass. Aerating grain from a ring along the bottom of the silo wall in order to target, for example, chilled air through warmer grain near the silo wall resulted in the spreading of the airflow throughout the grain mass. The airflow became more and more uniform as it moved upwards and no targeted cooling effect would be expected beyond about 1/10 of the grain depth.
Studies on Differentiation-Inducers from Arctium Fructus. (1993)

In the course of studying differentiation-inducers from plants, their isolation was performed from the methanolic extract of Arctium Fructus (the fruits of Arctium lappa L., Compositae), and then their phagocytic activity on differentiated mouse myeloid leukemia cells (M1) was monitered. Thirteen compounds, including five new ones, were isolated as differentiation-inducers toward M1 cells. These consisted of two lignans, eight sesquilignans and three dilignans. Arctigenin (2) was the most effective compound of all those isolated, and it induced differentiation of M1 cells at a concentration 0.5 μM. Sesquilignans were less effective than lignans and dilignans showed even weaker activity. These lignoids were inactive towards a human acute promyelocytic leukemia cell line (HL-60).
Online learning in autonomic multi-hop wireless networks for transmitting mission-critical applications (2010)

In this paper, we study how to optimize the transmission decisions of nodes aimed at supporting mission-critical applications, such as surveillance, security monitoring, and military operations, etc. We focus on a network scenario where multiple source nodes transmit simultaneously mission-critical data through relay nodes to one or multiple destinations in multi-hop wireless Mission-Critical Networks (MCN). In such a network, the wireless nodes can be modeled as agents that can acquire local information from their neighbors and, based on this available information, can make timely transmission decisions to minimize the end-to-end delays of the mission-critical applications. Importantly, the MCN needs to cope in practice with the time-varying network dynamics. Hence, the agents need to make transmission decisions by considering not only the current network status, but also how the network status evolves over time, and how this is influenced by the actions taken by the nodes. We formulate the agents' autonomic decision making problem as a Markov decision process (MDP) and construct a distributed MDP framework, which takes into consideration the informationally-decentralized nature of the multi-hop MCN. We further propose an online model-based reinforcement learning approach for agents to solve the distributed MDP at runtime, by modeling the network dynamics using priority queuing. We compare the proposed model-based reinforcement learning approach with other model-free reinforcement learning approaches in the MCN. The results show that the proposed model-based reinforcement learning approach for mission-critical applications not only outperforms myopic approaches without learning capability, but also outperforms conventional model-free reinforcement learning approaches.
Characterization of special fibers and fiber devices (1989)

Methods for characterizing birefringent fibers (both those with high circular or linear birefringence and those with negligible intrinsic birefringence) are presented, and their relative merits are discussed. Fibers with high nonlinear coefficients exhibit interesting optical phenomena, and methods are developed to determine second harmonic, Pockels and Kerr effects, parametric phenomena, and the Verdet constant of silica and higher-loss, nonsilica fibers. Fibers containing rare-earth ions are of interest both as active (laser and amplifiers) and passive systems. Techniques are developed to characterize these devices, and conventional methods are modified to quantify dopant parameters within the fiber. Techniques for the measurement of the diverse properties of all these different fibers are presented with results, and, where appropriate, the problems with their characterization are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
CHEMICAL AND ENZYMATIC SYNTHESIS OF 4′-THIO-β-D-ARABINOFURANOSYLCYTOSINE MONOPHOSPHATE AND TRIPHOSPHATE (2005)

N4-Acetyl-1-(2, 3-di-O-acetyl-4-thio-beta-D-arabinofuranosyl) cytosine (2) was synthesized in three steps from 1-(4-thio-beta-D-arabinofuranosyl) cytosine (1). The reaction of this partially blocked 4'-thio-ara-C derivative 2 with 2-chloro-4H-1,3,2-benzodioxaphosphorin-4-one gave the 5-phosphitylate derivative 3, which on reaction with pyrophosphate gave the 5'-nucleosidylcyclotriphosphite 4. Product 4 was then oxidized with iodine/pyridine/water and deblocked with concentrated ammonium hydroxide to provide the desired 4'-thio-ara-C-5'-triphosphate 5. This triphosphate 5 was converted to 4'-thio-ara-C -5'-monophosphate 6 by treatment with snake venom phosphodiesterase I. The details of the synthesis, purification, and characterization of both nucleotides are described.
Fundamental Aspects of H<sub>2</sub>S Adsorption on CPO-27-Ni (2013)

Adsorption of H2S on the Ni2(dhtp)(H2O)2·8H2O metal–organic framework (known as CPO-27-Ni or MOF-74-Ni) is characterized by in situ powder X-ray diffraction (PXRD), Fourier transform infrared (FTIR), Raman, and UV–visible spectroscopy) and by first-principles periodic boundary conditions calculations. PXRD results show very high stability of CPO-27-Ni framework in the presence of H2S. Nevertheless, as evidenced by change in color of the sample from pale yellow to dark green, the adsorption of H2S strongly affects the coordination of Ni sites. FTIR results show the reversible molecular adsorption of H2S. Experimental and computed energies of interaction reveal good agreement. Quantitative data considering energetic aspects (calorimetric measurements) are also included. This work highlights the fundamentals of H2S adsorption onto the CPO-27-Ni framework.
Fabrication of a bunch of sub-30-nm nanofibers inside microchannels using photopolymerization via a long exposure technique (2006)

Experimental studies on the fabrication of sub-30-nm nanofibers using two-photon initiated photopolymerization (TPP) have been carried out. To generate nanofibers at the interior region of microstructures, a photopolymerization method involving a long laser-exposure technique (LET) is proposed. A multitude of nanofibers with a notably high resolution (about 22nm) in TPP were produced using the LET. Furthermore, it is also demonstrated that thin interconnecting networks were created regularly in a weakly polymerized region existing around the boundary of a densely polymerized voxel, allowing for the creation of various embossing patterns. By controlling the distance between adjacent voxels or lines, a selective generation of nanofibers in a local area is possible, which leads to the fabrication of high-functional filters and mixers. Embossing patterns and microchannels including nanofibers inside were fabricated by the LET so as to demonstrate the practical feasibility of this approach. These sub-30-nm nanofibers may find meaningful applications such as biofilters, mixers, and photon emitters in diverse research fields.
Encryption (1997)

We begin with a brief discussion of the need for information security. This is followed by a short introduction to cryptography, with emphasis on the need to provide confidentiality and authentication. The difference between symmetric and asymmetric (public key) systems is explained, and the importance of digital signatures and key management is emphasised. The paper ends with a discussion of how GSM uses symmetric cryptography to provide authentication and confidentiality.