gebhart/patrepeval huggingface dataset:
Detailed theoretical investigation of the input power dynamic range for gain-clamped semiconductor optical amplifier gates at 10 Gb/s (1998)

A detailed theoretical investigation of the input power dynamic range for gain-clamped semiconductor optical amplifier (GC-SOA) gates at 10 Gb/s is presented. We show that although the gain is clamped, the dynamic changes of the carrier distribution in the GC-SOA causes pattern effects on a time scale given by the relaxation frequency of the GC-SOA. Combined with a higher noise figure compared to a conventional SOA, this results in a dynamic range only /spl sim/0.5 dB better than for an optimized SOA gate.
Development of the Hearing In Noise Test for the measurement of speech reception thresholds in quiet and in noise (1994)

A large set of sentence materials, chosen for their uniformity in length and representation of natural speech, has been developed for the measurement of sentence speech reception thresholds (sSRTs). The mean-squared level of each digitally recorded sentence was adjusted to equate intelligibility when presented in spectrally matched noise to normal-hearing listeners. These materials were cast into 25 phonemically balanced lists of ten sentences for adaptive measurement of sentence sSRTs. The 95% confidence interval for these measurements is +/- 2.98 dB for sSRTs in quiet and +/- 2.41 dB for sSRTs in noise, as defined by the variability of repeated measures with different lists. Average sSRTs in quiet were 23.91 dB(A). Average sSRTs in 72 dB(A) noise were 69.08 dB(A), or -2.92 dB signal/noise ratio. Low-pass filtering increased sSRTs slightly in quiet and noise as the 4- and 8-kHz octave bands were eliminated. Much larger increases in SRT occurred when the 2-kHz octave band was eliminated, and bandwidth dropped below 2.5 kHz. Reliability was not degraded substantially until bandwidth dropped below 2.5 kHz. The statistical reliability and efficiency of the test suit it to practical applications in which measures of speech intelligibility are required.
Type II regulatory subunits of cAMP-dependent protein kinase and their binding proteins in the nervous system of Aplysia californica. (1994)

Two type 11 regulatory (R) subunits of CAMP-dependent protein kinase (PKA) of 50 and 47 kDa have been identified in Aplyeia neurons by several criteria which include phosphorylation by the catalytic subunit of PKA and nanomolar affinity for a peptide fragment of the human thyroid protein Ht 31, properties that in mammals distinguish type 11 from type I R subunits.The neuronal type I1 R subunits are differentially localized within cells.For example, the SO-kDa polypeptide is enriched in taxol-stabilized microtubules.In addition, at least seven high molecular mass neuronal RII-binding proteins ranging in mass from 110 to 420 kDa have been demonstrated by a blot overlay technique, which uses SPP-labeled bovine RIIa as a probe.The RII-binding proteins also exhibit discrete patterns of subcellular localization.For example, the 420 kDa species is enriched in taxol-stabilized microtubules and therefore may serve to anchor the SO-kDa RII subunit.The localization of PKA through the association of RII subunits with the binding proteins may anchor the multifunctional kinase close to key substrates and thereby contribute to the spatial organization required to mediate the orderly phosphorylation events that underly neuronal modulation.Neuronal modulation (1) is the basis of diverse physiological processes including changes in the behavior of organisms.One important component of neuronal modulation, in both invertebrates and vertebrates, is the activation of intracellular signal transduction pathways in target neurons upon binding of neuromodulatory transmitters (2, 3).In the marine invertebrate Aplysia californica, presynaptic facilitation at sensorimotor synapses contributes to sensitization of the defensive gill-and tail-withdrawal reflexes, simple forms of learning and memory.cAMP-dependent protein kinase (PKA)' plays crucial roles in NS26760 (To H. B.) and GM 48231 (to J. D. S.).
High-throughput sequencing of the T-cell receptor repertoire: pitfalls and opportunities (2016)

T-cell specificity is determined by the T-cell receptor, a heterodimeric protein coded for by an extremely diverse set of genes produced by imprecise somatic gene recombination. Massively parallel high-throughput sequencing allows millions of different T-cell receptor genes to be characterized from a single sample of blood or tissue. However, the extraordinary heterogeneity of the immune repertoire poses significant challenges for subsequent analysis of the data. We outline the major steps in processing of repertoire data, considering low-level processing of raw sequence files and high-level algorithms, which seek to extract biological or pathological information. The latest generation of bioinformatics tools allows millions of DNA sequences to be accurately and rapidly assigned to their respective variable V and J gene segments, and to reconstruct an almost error-free representation of the non-templated additions and deletions that occur. High-level processing can measure the diversity of the repertoire in different samples, quantify V and J usage and identify private and public T-cell receptors. Finally, we discuss the major challenge of linking T-cell receptor sequence to function, and specifically to antigen recognition. Sophisticated machine learning algorithms are being developed that can combine the paradoxical degeneracy and cross-reactivity of individual T-cell receptors with the specificity of the overall T-cell immune response. Computational analysis will provide the key to unlock the potential of the T-cell receptor repertoire to give insight into the fundamental biology of the adaptive immune system and to provide powerful biomarkers of disease.
Simultaneous transdermal extraction of glucose and lactate from human subjects by reverse iontophoresis (2008)

This study investigated the possibility of simultaneously extracting glucose and lactate from human subjects, at the same skin location, using transdermal reverse iontophoresis. Transdermal monitoring using iontophoresis is made possible by the skin's permeability to small molecules and the nanoporous and microporous nature of the structure of skin. The study was intended to provide information which could be used to develop a full, biosensor-based, monitoring system for multiple parameters from transdermal extraction. As a precursor to the human study, in vitro reverse iontophoresis experiments were performed in an artificial skin system to establish the optimum current waveforms to be applied during iontophoresis. In the human study, a bipolar DC current waveform (with reversal of the electrode current direction every 15 minutes) was applied to ten healthy volunteers via skin electrodes and utilized for simultaneous glucose and lactate transdermal extraction at an applied current density of 300 microA/cm2. Glucose and lactate were successfully extracted through each subject's skin into the conducting gel that formed part of each iontophoresis electrode. The results suggest that it will be possible to noninvasively and simultaneously monitor glucose and lactate levels in patients using this approach and this could have future applications in diagnostic monitoring for a variety of medical conditions.
Immortalized porcine liver sinusoidal endothelial cells: an in vitro model of xenotransplantation‐induced thrombocytopenia (2012)

Immortalized porcine LSEC retain a phagocytic phenotype, making them a good model for the study of xenotransplantation-induced thrombocytopenia and may provide further insight into the phagocytic role of LSEC.
Molded porous poly (L-lactide) membranes for guided bone regeneration with enhanced effects by controlled growth factor release (2001)

The aim of this study was to develop platelet-derived growth factor (PDGF-BB) loaded moldable porous poly (L-lactide) (PLLA)-tricalcium phosphate (TCP) membranes for guided bone regeneration (GBR) therapy. The membranes were designed to fit various types of bone defect sites. PDGF-BB-dissolved PLLA-TCP in methylene chloride-ethyl acetate solution was cast on a dome shaped metallic mold to fabricate a model membrane. The release rate of PDGF-BB, the osteoblast attachment test, and guided bone regeneration potential were evaluated with PDGF-BB-loaded PLLA-TCP membranes. Regular pores were generated throughout the membrane mainly due to phase inversion of PLLA-methylene chloride-ethyl acetate solution. A therapeutic amount of PDGF-BB was released from the membrane. The release rate could be controlled by varying the initial loading content of PDGF-BB. A significant amount of cells attached onto the PDGF-BB-loaded membrane rather than onto the unloaded membrane. Dome shaped bone formation was achieved in rabbit calvaria at 4 weeks. This indicated that restoration of bone defects to the bone's original shape can be made possible by using molded membranes, which guide bone regeneration along with providing sufficient spaces. Bone forming efficiency was increased remarkably due to PDGF-BB release from PLLA-TCP membranes. These results suggested that the PDGF-BB releasing molded PLLA-TCP membrane may potentially improve GBR efficiency in various types of bone defects.
EIGRP--A Fast Routing Protocol based on Distance Vectors (1994)

Early routing protocols were based on distance vectors; they were very simple and easy to implement but had the severe drawbacks of counting to in nity and routing loops.These problems were reduced using such techniques as split horizon and hold-downs; however, for these techniques to work in practice, long convergence times are introduced.Routing protocols based on link states have been implemented to address the problem of slow convergence in distance-vector protocols, but they add complexity i n con guration and troubleshooting.We present a new distance-vector protocol that converges as quickly as current link-state protocols, while maintaining loop freedom at every instant.The protocol is based on three main elements: a transport algorithm that supports the reliable exchange of messages among routers, the di using update algorithm, which computes shortest paths distributedly, and modules that permit the operation of the new routing protocol in a multiprotocol environment.
Plant intron sequences: evidence for distinct groups of introns (1988)

In vivo and in vitro RNA splicing experiments have demonstrated that the intron splicing machineries are not interchangeable in all organisms. These differences have prevented the efficient in vivo expression of monocot genes containing introns in dicot plants and the in vitro excision of some plant introns in HeLa cell in vitro splicing extracts. We have analyzed plant introns for sequence differences which potentially account for the functional splicing differences. Three classes of plant introns can be differentiated by the purine or pyrimidine-richness of sequences upstream from the 3' splice site. The frequency of these three types of introns in monocots and dicots varies significantly. The degree of variability in the 5' and 3' intron boundaries is evaluated for each of these classes in monocots and dicots. The 5' splice site consensus sequences developed for the monocot and dicot introns differ in their ability to base pair with conserved nucleotides present at the 5' end of many U1 snRNAs.
Reliable chemical exchange saturation transfer imaging of human lumbar intervertebral discs using reduced‐field‐of‐view turbo spin echo at 3.0 T (2013)

The reduced field-of-view (rFOV) turbo-spin-echo (TSE) technique, which effectively suppresses bowel movement artifacts, is developed for the purpose of chemical exchange saturation transfer (CEST) imaging of the intervertebral disc (IVD) in vivo. Attempts to quantify IVD CEST signals in a clinical setting require high reliability and accuracy, which is often compromised in the conventionally used technique. The proposed rFOV TSE CEST method demonstrated significantly superior reproducibility when compared with the conventional technique on healthy volunteers, implying it is a more reliable measurement. Phantom study revealed a linear relation between CEST signal and glycosaminoglycan (GAG) concentration. The feasibility of detecting IVD degeneration was demonstrated on a healthy volunteer, indicating that the proposed method is a promising tool to quantify disc degeneration.
A depropargylation-triggered spontaneous cyclization based fluorescent “turn-on” chemodosimeter for the detection of palladium ions and its application in live-cell imaging (2016)

A novel depropargylation-triggered spontaneous cyclization reaction based fluorescent turn-on chemodosimeter for the detection of palladium ions has been rationally designed and developed.
Preparation of Y-Ba-Cu Oxides with Superconducting Transition above Liquid-Nitrogen Temperature (1987)

Details of sample preparation of Y-Ba-Cu oxides with superconducting transition temperatures well above the boiling point of liquid nitrogen are reported. The mid-point of the resistive transition is at 92.6 K , and the zero-resistance state is maintained up to 83.3 K. The ac susceptibility and the infrared spectra of superconductive Y-Ba-Cu oxides are also presented.
Characterization of a polyhistidine‐tagged form of human myristoyl‐CoA:protein N‐myristoyltransferase produced in Escherichia coli (1994)

The enzyme myristoyl-CoA:protein N-myristoyltransferase is responsible for the attachment of a myristoyl group to the N-terminal glycine of a number of cell, viral and fungal proteins. In order to overcome the difficulties of purification of this enzyme from tissue sources, we have produced an N-terminally polyhistidine-tagged version of the enzyme and expressed this in Escherichia coli. The resulting enzyme has a molecular mass of 53 kDa and is fully active showing the expected specificity for myristic acid and causing the N-terminal myristoylation of both synthetic peptide and protein substrates in vitro. The enzyme exhibits a broad pH optimum peaking at a pH of 8.0 and has a Km for myristoyl-CoA of 7.6 microM. The two synthetic peptide substrates based on the N-terminal sequence of the catalytic subunit of protein kinase A (GNAAAARR) and of p60src (GSSKSKPKDPSQRRRY) have different kinetic parameters with Km values of 115.2 microM and 44.2 microM and Vmax values of 95 and 120 nmol.min-1.mg-1, respectively. The expressed enzyme is partially inhibited (50%) by iodoacetamide at 5 mM and fully inhibited by diethylpyrocarbonate at 10 mM. This latter inhibition can be prevented by including histidine in the incubation of the enzyme and inhibitor. Antisera raised to synthetic peptides based on sequences derived from the N- and C- terminus of the human enzyme reacted with the expressed protein on Western blots, but only the N-terminal sequence reacted with the native protein suggesting that the C-terminus may be not be accessible. The enzyme can catalyse the removal of a myristoyl group from myristoylated peptides but does so only in the presence of added coenzyme A.
An indirect-drive non-cryogenic double-shell path to 1ω Nd-laser hybrid inertial fusion–fission energy (2010)

A high-yield, room temperature, double-shell target design using a Nd : glass laser driver at the fundamental frequency 1ω is developed for hybrid inertial fusion–fission energy generation (Moses et al 2009 Fusion Sci. Technol. 56 547). The associated 4–10× fission energy gain relaxes the gain requirements of the fusion driver, enabling the prospect of a volume-ignition target with high thermonuclear burn fraction, simplified (1ω) laser operations from a quasi-impulsive power history, room temperature fielding, minimal shock-timing requirements and reduced risk of plasma-mediated laser backscatter with a vacuum hohlraum.
PBK/TOPK mediates promyelocyte proliferation via Nrf2-regulated cell cycle progression and apoptosis (2015)

Acute myeloid leukemia (AML) is a disorder involving hematopoietic stem cells, characterized by blockage of hematopoietic cell differentiation and an increase in clonal neoplastic proliferation. AML is associated with poor patient outcome. PBK/TOPK is a protein kinase derived from PDZ-binding kinase (PBK)/T-lymphokine-activated killer (T-LAK) cell-originated protein kinase (TOPK). Previous studies have shown that PBK/TOPK is expressed in hematologic tumors. In the present study, we aimed to investigate the role of PBK/TOPK in promyelocyte proliferation and to clarify the molecular mechanism. PBK/TOPK knockdown (KD) significantly decreased cell proliferation and viability in the NB4 and HL-60 promyelocytes. PBK/TOPK KD resulted in G2/M cell cycle arrest that attributed to a decrease in cdc2 and cyclin B expression. In addition, PBK/TOPK KD caused apoptosis, as evidenced by activation of the mitochondrial apoptotic pathway and an increase in TUNEL-positive cells. PBK/TOPK KD induced mitochondrial dysfunction and ROS generation, and inhibition of mitochondrial dysfunction and ROS production suppressed PBK/TOPK KD-induced cell cycle arrest and apoptosis. Moreover, PBK/TOPK KD decreased Nrf2 expression and ARE-binding activity. Overexpression of Nrf2 inhibited the PBK/TOPK KD-induced decrease in cdc2 and cyclin B expression and cell cycle arrest, and blocked ROS production and apoptosis. Based on literature and our results, it was demonstrated that Nrf2 may be a crucial regulator that mediates PBK/TOPK-exerted promotion of cell proliferation. PBK/TOPK stabilizes Nrf2, strictly regulates the ROS level, promotes cell cycle progression and inhibits apoptosis, contributing to the proliferation of promyelocytes. Our results provide new insights into the molecular mechanism of PBK/TOPK-mediated promyelocyte proliferation and shed light on the pathogenesis of AML.
Robotic ultrasound systems in medicine (2013)

Robots ultrasound (RUS) can be defined as the combination of ultrasound imaging with a robotic system in medical interventions. With their potential for high precision, dexterity, and repeatability, robots are often uniquely suited for ultrasound integration. Although the field is relatively young, it has already generated a multitude of robotic systems for application in dozens of medical procedures. This paper reviews the robotic ultrasound systems that have been developed over the past two decades and describes their potential impact on modern medicine. The RUS projects reviewed include extracorporeal devices, needle guidance systems, and intraoperative systems.
Thermodynamics of Solutions with Liquid Crystal Solvents. IV. GLC Determination of the Degree of Order in a Nematic Mesophase (1971)

Abstract Owing to thermal motion, molecular orientation is never entirely complete in a nematic mesophase. The commonly used methods of obtaining a measure of the extent of parallelism in this mesophase are ESR and NMR. Proposed here is a gas-liquid chromatography (GLC) approach for determining the degree of order, S. Our working model regards the nematic phase as composed of a fraction of completely aligned molecules and a fraction of completely isotropie molecules. Further, solute molecules dissolved in the nematic state are assumed to distribute themselves between these two arrangements. Based on the assumptions of this “two phase” model and on exact thermodynamic arguments, a set of simultaneous equations is derived for evaluating S from GLC-determined solute infinite dilution activity coefficients and partial molar excess enthalpies. From meassurements on two nematogenic substances, P-azoxyanisole and 4, 4′-dihexoxyazoxybenzene, S values are obtained which are independent of the nature of the solute probe. The advantages and limitations of this method and the reason for the minor discrepanies between our S values and those determined from resonance experiments (ours are slightly lower) are discussed. The thermodynamic quantities corresponding to solution in completely aligned solvent are determined and discussed. The potential utility of this approach (e.g., studying order within the cholesteric mesophase) is also described.
Potent Inhibition of HIV-1 Infectivity in Macrophages and Lymphocytes by a Novel CCR5 Antagonist (1997)

The chemokine receptors CXCR4 and CCR5 have recently been shown to act as coreceptors, in concert with CD4, for human immunodeficiency virus-type 1 (HIV-1) infection. RANTES and other chemokines that interact with CCR5 and block infection of peripheral blood mononuclear cell cultures inhibit infection of primary macrophages inefficiently at best. If used to treat HIV-1-infected individuals, these chemokines could fail to influence HIV replication in nonlymphocyte compartments while promoting unwanted inflammatory side effects. A derivative of RANTES that was created by chemical modification of the amino terminus, aminooxypentane (AOP)-RANTES, did not induce chemotaxis and was a subnanomolar antagonist of CCR5 function in monocytes. It potently inhibited infection of diverse cell types (including macrophages and lymphocytes) by nonsyncytium-inducing, macrophage-tropic HIV-1 strains. Thus, activation of cells by chemokines is not a prerequisite for the inhibition of viral uptake and replication. Chemokine receptor antagonists like AOP-RANTES that achieve full receptor occupancy at nanomolar concentrations are strong candidates for the therapy of HIV-1-infected individuals.
Regulation of immediate early gene expression and AP-1 binding in the rat nucleus accumbens by chronic cocaine. (1992)

Chronic treatment of rats with cocaine leads to long-term biochemical changes in the nucleus accumbens (NAc), a brain region implicated in mediating the reinforcing effects of cocaine and other drugs of abuse. Immediate early genes (IEGs) and their protein products appear to play an important role in transducing extracellular stimuli into altered patterns of cellular gene expression and, therefore, into long-term changes in cellular functioning. We therefore examined changes in the mRNA levels for the IEGs c-fos, c-jun, fosB, junB, and zif268 in the NAc of rats treated acutely and chronically with cocaine. A single cocaine injection increased the mRNA levels of all of the IEGs examined. Following chronic cocaine treatment, however, IEG expression had returned to control levels and was not significantly increased following a further acute challenge with cocaine, suggesting desensitization in the ability of cocaine to induce these IEGs. Similarly, levels of Fos-like immunoreactivity, which are increased in the NAc by acute cocaine, were reduced to control levels in chronic cocaine-treated rats. Fos, Jun, and a number of related proteins activate or repress transcription of genes by binding to DNA response elements called AP-1 sites. As would be expected from the RNA data and immunohistochemistry, acute cocaine administration increased AP-1 binding activity in the NAc, an effect that reverted completely to control levels within 8-12 hr. In contrast, AP-1 binding activity in the NAc of animals treated chronically with cocaine remained elevated at acute levels 18 hr after the last chronic injection, a time at which c-fos and c-jun mRNA levels and Fos-like immunoreactivity had returned to control values. An additional acute cocaine challenge did not further increase AP-1 binding. The data suggest that chronic cocaine treatment leads to a persistent increase in AP-1 binding activity, which may be involved in some of the physiological and behavioral aspects of cocaine addiction.