gebhart/patrepeval huggingface dataset:
Trans-activation of the JC virus late promoter by the tat protein of type 1 human immunodeficiency virus in glial cells. (1990)

Progressive multifocal leukoencephalopathy (PML) is a demyelinating disease of the central nervous system caused by the JC virus (JCV), a human papovavirus. PML is a relatively rare disease seen predominantly in immunocompromised individuals and is a frequent complication observed in AIDS patients. The significantly higher incidence of PML in AIDS patients than in other immunosuppressive disorders has suggested that the presence of human immunodeficiency virus type 1 (HIV-1) in the brain may directly or indirectly contribute to the pathogenesis of this disease. In the present study we have examined the expression of the JCV genome in both glial and non-glial cells in the presence of HIV-1 regulatory proteins. We find that the HIV-1-encoded trans-regulatory protein tat increases the basal activity of the JCV late promoter, JCVL, in glial cells. In a reciprocal experiment, the JCV early protein, the large tumor antigen, stimulates expression from JCVL and HIV-1 long terminal repeat promoter in both glial and non-glial cells. This trans-activation occurs at the level of RNA synthesis, as measured by the rate of transcription, stability of the message, and translation. We conclude that the presence of the HIV-1-encoded tat protein may positively affect the JCV lytic cycle in glial cells by stimulating JCV gene expression. Our results suggest a mechanism for the relatively high incidence of PML in AIDS patients than in other immunosuppressive disorders. Furthermore, our findings indicate that the HIV-1 regulatory protein tat may stimulate other viral and perhaps cellular promoters, in addition to its own.
A comparison of select trigger algorithms for automated global seismic phase and event detection (1998)

Abstract Digital algorithms for robust detection of phase arrivals in the presence of stationary and nonstationary noise have a long history in seismology and have been exploited primarily to reduce the amount of data recorded by data logging systems to manageable levels. In the present era of inexpensive digital storage, however, such algorithms are increasingly being used to flag signal segments in continuously recorded digital data streams for subsequent processing by automatic and/or expert interpretation systems. In the course of our development of an automated, near-real-time, waveform correlation event-detection and location system (WCEDS), we have surveyed the abilities of such algorithms to enhance seismic phase arrivals in teleseismic data streams. Specifically, we have considered envelopes generated by energy transient (STA/LTA), Z-statistic, frequency transient, and polarization algorithms. The WCEDS system requires a set of input data streams that have a smooth, low-amplitude response to background noise and seismic coda and that contain peaks at times corresponding to phase arrivals. The algorithm used to generate these input streams from raw seismograms must perform well under a wide range of source, path, receiver, and noise scenarios. Present computational capabilities allow the application of considerably more robust algorithms than have been historically used in real time. However, highly complex calculations can still be computationally prohibitive for current workstations when the number of data streams become large. While no algorithm was clearly optimal under all source, receiver, path, and noise conditions tested, an STA/LTA algorithm incorporating adaptive window lengths controlled by nonstationary seismogram spectral characteristics was found to provide an output that best met the requirements of a global correlation-based event-detection and location system.
Enhancement of macrophage immune and nonimmune receptor-mediated phagocytosis by a low molecular weight soluble factor from resident thymocytes. (1984)

Macrophage phagocytic activity is regulated in part by products of activated T lymphocytes. We previously reported that a heat-stable soluble factor derived from resident (nonactivated) thymocytes increases murine peritoneal macrophage Fc-dependent phagocytosis. In the present study, we further investigate the effect of the thymocyte factor on immune and nonimmune receptor-mediated phagocytosis, Fc receptor expression, and its approximate m.w. After 4 days of incubation, cellfree thymocyte supernatant produced a mean (three experiments) 2.10-, 2.08-, and 1.97-fold increase in macrophage phagocytosis of C3-, IgG-, and tannic acid-treated erythrocytes, respectively. Macrophage IL 1 production was not enhanced by a similar concentration of thymocyte supernatant. The thymocyte factor(s) increased the number of IgG2a Fc receptors (FcRI) from 2.4 x 10(5) to 3.8 x 10(5) receptor sites per macrophage. The number of Fc receptors that bind IgG1 and IgG2b (FcRII) was not altered. The soluble factor(s) that increased Fc-mediated phagocytosis passed through both 6000- to 8000-dalton and 2000-dalton cutoff dialysis membranes and eluted from a Sephadex G-25 Fine column over a m.w. range of 200 to 1000 daltons, with a peak activity at 450 daltons. These data suggest that resident thymocytes enhance macrophage phagocytosis of opsonized and nonopsonized particles through the elaboration of a low m.w. substance(s).
Porous LiFePO<sub>4</sub>/C Microspheres as High-Power Cathode Materials for Lithium Ion Batteries (2013)

Porous LiFePO4/C microspheres were synthesized by a novel hydrothermal reaction combined with high-temperature calcinations. The morphology of the prepared material was investigated by field-emission scanning electron microscopy. Porous microspheres with diameters around 1-3 microm were obtained, which consisting of primary LiFePO4 nanoparticles. The electrochemical performances of the as-prepared LiFePO4 microspheres were evaluated by cyclic voltammetry, electrochemical impedance spectroscopy and galvanostatic charge-discharge cycling. The carbon coated LiFePO4 microspheres showed lower polarization, higher rate capability, and better cycling stability than that of pristine LiFePO4 microspheres, indicating the potential application as the cathode material for high-power lithium ion batteries.
Dispersive liquid–liquid microextraction using extraction solvent lighter than water (2009)

For the first time a dispersive liquid-liquid microextraction method on the basis of an extraction solvent lighter than water was presented in this study. Three organophosphorus pesticides (OPPs) were selected as model compounds and the proposed method was carried out for their preconcentration from water samples. In this extraction method, a mixture of cyclohexane (extraction solvent) and acetone (disperser) is rapidly injected into the aqueous sample in a special vessel (see experimental section) by syringe. Thereby, a cloudy solution is formed. In this step, the OPPs are extracted into the fine droplets of cyclohexane dispersed into aqueous phase. After centrifuging the fine droplets of cyclohexane are collected on the upper of the extraction vessel. The upper phase (0.40 microL) is injected into the gas chromatograph (GC) for separation. Analytes were detected by a flame ionization detector (FID) (for high concentrations) or MS (for low concentrations). Some important parameters, such as the kind of extraction and dispersive solvents and volume of them, extraction time, temperature, and salt amount were investigated. Under the optimum conditions, the enrichment factors (EFs) ranged from 100 to 150 and extraction recoveries varied between 68 and 105%, both of which are relatively high over those of published methods. The linear ranges were wide (10-100 000 microg/L for GC-FID and 0.01-1 microg/L for GC-MS) and LODs were low (3-4 microg/L for GC-FID and 0.003 microg/L for GC-MS). The RSDs for 100.0 microg/L of each OPP in water were in the range of 5.3-7.8% (n = 5).
Stable and Selective Recognition of Three Base Pairs in the Parallel Triple‐Helical DNA Binding Motif (2004)

Die Modifikation von Basen in parallele Tripelhelices bildenden Oligonucleotiden mit einem 2′-O-Aminoethyl-Rückgrat machte einen erweiterten Code zur DNA-Tripelhelix-Erkennung zugänglich, der bei der Steuerung der Genexpression genutzt werden kann. Entfernen des Sauerstoffatoms am Thymin-C4 überführt die Donor/Acceptorbase in eine doppelte Acceptorbase und bewirkt statt der A-T- eine starke und hoch selektive C-G-Erkennung (siehe Schema).
Semiconducting Polymers and Block Copolymers Prepared by Chain-Growth Living Polymerization (2011)

Organic semiconducting polymers are the unique materials that considered a basis for the next generation of electronic and optoelectronic applications. However, high device performance of semiconducting polymers strongly depends on their molecular structure and nanoscale organization. Therefore, it is an essential task to develop robust and versatile synthetic approaches to build such well-defined semiconducting polymer materials. This Ph.D. study aimed at design of state-of-the-art synthetic approaches towards organic semiconducting polymers via chain-growth living polymerization as well as development of polymer architectures which can self-organize into supramolecular nanoassemblies or allow external control of the polymer’s properties. First, we prepared a series of temperature-responsive water-soluble poly(N-isopropylacrylamide)-functionalized polythiophenes, and showed that their supramolecular organization and temperature control of their conformation and conjugation length was strongly dependent on the extent of regioregularity of the polythiophene backbone. In order to improve the regioregularity, we developed a general approach to highly efficient external catalytic initiators for the synthesis of various semiconducting polymers. Extensive studies allowed better understanding of the unusual catalytic systems, and their behavior in chain-growth living polymerization reactions. Using this approach, we synthesized a variety of amphiphilic polythiophene block copolymers incorporating a low energy gap perylenedicarboximide (PDCI) unit to demonstrate the possibility to control supramolecular organization and photophysical properties of such systems by using external stimuli (such as solvent and temperature). As part of our general studies towards design of near-infrared (NIR) fluorescent conjugated polymers, we developed a synthetic approach to a novel class of such materials which are based on cyanine dyes as monomeric repeating units. The obtained polymers showed a variety of properties (thermal stability, solubility, absorption and fluorescence in the NIR range) that may make them a useful class of NIR fluorescent conjugated polymers.
The Physics and Chemistry behind the Bubbling Properties of Champagne and Sparkling Wines:  A State-of-the-Art Review (2005)

In this review, the latest results about the chemical physics behind the bubbling properties of Champagne and sparkling wines are collected and fully illustrated. The chemistry of carbon dioxide molecules dissolved into the liquid matrix (section 2) is presented, as are the three main steps of a fleeting bubble's life, that is, the bubble nucleation on tiny particles stuck on the glass wall (section 3), the bubble ascent and growth through the liquid matrix (section 4), and the bursting of bubbles at the liquid surface (section 5), which constitutes the most intriguing, functional, and visually appealing step.
Nitroxide-Mediated Polymerization of Methyl Methacrylate and Styrene with New Alkoxyamines from 4-Nitrophenyl 2-Methylpropionat-2-yl Radicals (2010)

The N-phenylalkoxyamine N-(1-methyl-(1-(4-nitrophenoxy)carbonyl)ethoxy)-N-(1-methyl-(1-(4-nitrophenoxy)carbonyl)ethyl)benzenamine (1) was prepared by the addition of 4-nitrophenyl 2-methylpropionat-2-yl radicals across the double bond of nitrosobenzene and evaluated as an initiator for nitroxide-mediated polymerization (NMP). N-Phenylalkoxyamines have not been extensively studied in NMP, though they have shown promise in controlling methyl methacrylate (MMA) polymerization to moderate conversions. It is thought that delocalization of the nitroxide radical through the N-phenyl substituent may minimize cross-disproportionation of the nitroxide with the chain end that has made NMP of MMA difficult. Here, we show that alkoxyamine 1 is capable of controlling the NMP of MMA to 50% conversion while maintaining narrow molecular weight distributions (Mw/Mn = 1.12−1.30). Additionally, chain extension from the resulting PMMA macroinitiators with MMA or styrene allows the formation of diblock copolymers. The corresponding N-tert-butylalkoxyamine, 2,2-dimethyl-3-(1-methyl-(1-(4-nitrophenoxy)carbonyl)ethoxy)-4-methyl-(4-(4-nitrophenoxy)carbonyl)ethyl-3-azapentane (2), was synthesized by the addition of 4-nitrophenyl 2-methylpropionat-2-yl radicals across the double bond of 2-methyl-2-nitrosopropane. Polymerization of MMA with alkoxyamine 2 was uncontrolled, which suggests the paramount importance of the N-phenyl group for MMA polymerizations.
Constraint-driven communication synthesis (2002)

Constraint-driven Communication Synthesis enables the automatic design of the communication architecture of a complex system from a library of pre-defined Intellectual Property (IP) components. The key communication parameters that govern all the point-to-point interactions among system modules are captured as a set of arc constraints in the communication constraint graph. Similarly, the communication features offered by each of the components available in the IP communication library are captured as a set of feature resources together with its cost figures. Then, every communication architecture that can be built using the available components while satisfying all constraints is implicitly considered (as an implementation graph matching the constraint graph) to derive the optimum design solution with respect to the desired cost figure. The corresponding constrained optimization problem is efficiently solved by a novel algorithm that is presented here together with its rigorous theoretical foundations.
Analysis of Potential Conversion Efficiency of a Solar Hybrid System With High-Temperature Stage (2005)

The analysis is given of hybrid system of solar energy conversion having a stage operating at high temperature. The system contains a radiation concentrator, a photovoltaic solar cell, and a thermal generator, which could be thermoelectric one or a heat engine. Two options are discussed, one (a) with concentration of the whole solar radiation on the PV cell working at high temperature and coupled to the high-temperature stage, and another (b) with a special PV cell construction, which allows the use of the part of solar spectrum not absorbed in the semiconductor material of the cell (“thermal energy”) to drive the high-temperature stage while the cell is working at ambient temperature. The possibilities of using different semiconductor materials are analyzed. It is shown that the demands to the cell material are different in the two cases examined: in system (a) with high temperature of cell operation, the materials providing minimum temperature dependence of the conversion efficiency are necessary, for another system (b) the materials with the larger band gap are profitable. The efficiency of thermal generator is assumed to be proportional to that of the Carnot engine. The optical and thermal energy losses are taken into account, including the losses by convection and radiation in the high-temperature stage. The radiation losses impose restrictions upon the working temperature of the thermal generator in the system (b), thus defining the highest possible concentration ratio. The calculations made show that the hybrid system proposed could be both efficient and practical, promising the total conversion efficiency around 25-30% for system (a), and 30-40% for system (b).
Transcription Factors Controlling Muscle-Specific Gene Expression (1993)

Understanding the mechanisms responsible for activation of cell-type-specific gene expression during development is a fundamental problem in molecular biology. Skeletal muscle has provided an important system for investigating this problem because differentiation of skeletal myoblasts is accompanied by the coordinate induction of a battery of genetically unlinked muscle-specific genes whose products are required for the specialized functions of the mature muscle fiber. Analysis of the events associated with muscle differentiation has also been facilitated by the availability of established muscle cell lines that differentiate rapidly and synchronously and whose differentiation can be negatively regulated by individual peptide growth factors or activated oncogenes encoding proteins which transduce growth factor signals from the cell membrane to the nucleus.
Phase I trial of dolastatin-10 (NSC 376128) in patients with advanced solid tumors. (1999)

Dolastatin-10 (dola-10) is a potent antimitotic peptide, isolated from the marine mollusk Dolabela auricularia, that inhibits tubulin polymerization. Preclinical studies of dola-10 have demonstrated activity against a variety of murine and human tumors in cell cultures and mice models. The purpose of this Phase I clinical trial was to characterize the maximum tolerated dose, pharmacokinetics, and biological effects of dola-10 in patients with advanced solid tumors. Escalating doses of dola-10 were administered as an i.v. bolus every 21 days, using a modified Fibonacci dose escalation schema. Pharmacokinetic studies were performed with the first treatment cycle. Neurological testing was performed on each patient prior to treatment with dola-10, at 6 weeks and at study termination. Thirty eligible patients received a total of 94 cycles (median, 2 cycles; maximum, 14 cycles) of dola-10 at doses ranging from 65 to 455 microg/m2. Dose-limiting toxicity of granulocytopenia was seen at 455 microg/m2 for minimally pretreated patients (two or fewer prior chemotherapy regimens) and 325 microg/m2 for heavily pretreated patients (more than two prior chemotherapy regimens). Nonhematological toxicity was generally mild. Local irritation at the drug injection site was mild and not dose dependent. Nine patients developed new or increased symptoms of mild peripheral sensory neuropathy that was not dose limiting. This toxicity was more frequent in patients with preexisting peripheral neuropathies. Pharmacokinetic studies demonstrated a rapid drug distribution with a prolonged plasma elimination phase (t 1/2z = 320 min). The area under the concentration-time curve increased in proportion to administered dose, whereas the clearance remained constant over the doses studied. Correlation analysis demonstrated a strong relationship between dola-10 area under the concentration-time curve values and decrease from baseline for leukocyte counts. In conclusion, dola-10 administered every 3 weeks as a peripheral i.v. bolus is well tolerated with dose-limiting toxicity of granulocytopenia. The maximum tolerated dose (and recommended Phase II starting dose) is 400 microg/m2 for patients with minimal prior treatment (two or fewer prior chemotherapy regimens) and 325 microg/m2 for patients who are heavily pretreated (more than two prior chemotherapy regimens).
A black phosphorus based synergistic antibacterial platform against drug resistant bacteria (2018)

In the fight against pathogenic bacteria, traditional antibiotic therapy is challenged by low efficiency and drug resistance. These drawbacks motivate the development of synergistic antibacterial therapy, but there is a lack of efficient synergistic platforms. Herein, with methicillin-resistant Staphylococcus aureus (MRSA) as a pathogenic bacterial model, we explored the potential of black phosphorus (BP) as a synergistic therapeutic platform for drug resistant bacterial infection. Acting as a substrate, reductant and stabilizer, BP nanosheets were decorated with Ag nanoparticles (NP) through an in situ growth strategy. The photothermal effect of the BP nanosheets allows Ag@BP nanohybrids to rapidly disrupt a bacterial membrane under near infrared (NIR) light irradiation. Moreover, the slowly released Ag<sup>+</sup> elevates oxidative stress and sustainably suppresses bacterial proliferation for a long time. The combination of these two aspects endows the Ag@BP nanohybrids with synergistically enhanced antibacterial performance. Different from traditional antibiotics, the antibacterial effects of the Ag@BP nanohybrids are independent of the bacterial structure, which bypasses the issue of drug resistance. The in vivo studies show that the Ag@BP nanohybrids efficiently decrease the MRSA bacterial burden in mice and minimize infection associated tissue lesions. Besides, the excellent biocompatibility of the Ag@BP nanohybrids guarantees their biosafety for future clinical applications. Accordingly, this work demonstrates the potential of the BP nanosheets in the synergistic antibacterial therapy against drug resistant bacteria, and paves the way for developing 2D semiconductor based synergistic antibacterial nanodrugs.
Restoration of a discrete-time signal segment by interpolation based on the left-sided and right-sided autoregressive parameters (1996)

This paper presents an algorithm for the interpolation of a missing signal segment on the assumption that the signal can be modeled as an autoregressive (AR) process. Unlike previous algorithms, the presented algorithm does not model the signal of the missing segment and the neighboring signal portions by a single AR-parameter vector. Instead, two separate vectors are used so that stationarity need no longer be assumed to extend beyond both sides of the missing segment. The relaxation of this stationarity assumption is essential when the duration of the missing segment is on the order of the short-time stationarity duration of the signal. The algorithm provides the optimal solution to the problem of interpolating a missing segment based on the left-sided and right-sided AR-parameter vectors. The solution is optimal in the sense of a least-squares residual. The algorithm is applied to speech and music signals and is compared with other restoration techniques.
Determination of monoamine oxidase. (1985)

A robust, sensitive and reliable radiochemical assay for monoamine oxidase is described, and the procedures necessary to ensure the validity of the results obtained are discussed. Methods for determining the activities of the two forms of monoamine oxidase, A and B, separately, are outlined and some alternative assay methods are considered.
Bidirectional activity of the rat insulin II 5'-flanking region in transgenic mice. (1987)

We have identified a new transcription initiation site in the 5'-flanking regulatory region of the rat insulin II gene. This site is located on the opposite strand with respect to the insulin gene promoter, upstream of the insulin gene transcriptional enhancer. The cell-specific activity of this reverse promoter element is demonstrated in two lineages of transgenic mice, in which it directs expression of simian virus 40 T antigen specifically to the beta cells of the endocrine pancreas, resulting in development of pancreatic tumors. Analysis of RNA from the tumor cells demonstrates bidirectional transcription from the insulin regulatory region of the transgene. These data raise the possibility that bidirectional activity is a quality of the regulatory region of the insulin gene in its natural genomic context.