gebhart/patrepeval huggingface dataset:
Partial Inhibition of Vesicular Stomatitis Virus by the Interferon-Induced Human 9-27 Protein (1996)

To determine whether the interferon-induced 9-27 protein of human cells contributes to the antiviral state, we expressed the 9-27 cDNA under the control of a constitutive promoter and assayed transfected cells for enhanced virus resistance. The intracellular distribution of 9-27 resembled that of cytoskeleton-associated proteins. Analysis at the single-cell level by indirect immunofluorescence revealed that mouse cells expressing 9-27 were less permissive for vesicular stomatitis virus than control cells not expressing 9-27. No significant inhibition of influenza virus was observed. When tested in parallel, 9-27 was found to have less powerful antiviral activity toward vesicular stomatitis virus than the interferon-induced MxA protein. Thus, 9-27 joins the family of interferon-induced proteins with intrinsic antiviral activity.
An ultra low-cost 32-element 28 GHz phased-array transceiver with 41 dBm EIRP and 1.0–1.6 Gbps 16-QAM link at 300 meters (2017)

This paper presents a 32-element phased-array architecture suitable for fifth-generation (5G) communication links. A 28-32 GHz silicon core chip is designed with 4 transmit/receive elements each with 14 dB gain control, 6-bit phase control, 4.6 dB measured noise figure (NF) in the RX mode and 10 dBm output 1 dB compression point (OP1dB) in the TX mode. Eight of these chips are flipped on a low-cost printed circuit board (PCB) with integrated antennas and Wilkinson combiners. The 32-element array has a measured EIRP of 41 dBm at P1dB, can scan to ±20° and ±50° in E- and H-planes, and comsumes 4.2 W and 6.4 W in RX and TX modes, respectively. The array is used in a 300 meter wireless link and achieves a data rate of 1.0-1.6 Gbps at 16-QAM for all scan angles with <;12% EVM. To our knowledge, this represents state-of-the art in 28 GHz phased-arrays in terms of chip performance and integration level.
Encapsulation of Hemoglobin in Non-Phospholipid Vesicles (1994)

The efficiency of encapsulating hemoglobin in non-phospholipid liposomes by rapidly mixing hemoglobin with lipids heated above their solid-liquid phase transition temperature was examined. Human hemoglobin was mixed at 55-60 degrees C with a lipid solution containing polyoxyethylene-2 cetyl ether and cholesterol (molar ratio, 3:1) at 60-65 degrees C. Repeated mixing was carried out through a high-shear orifice, followed by rapid cooling and additional mixing. Lipid vesicles were heterogeneous in size, with diameters from approximately 300 nm to 10 microns. The non-encapsulated aqueous phase was removed by centrifugation, and total hemoglobin was determined spectrophotometrically. Encapsulation efficiency was calculated as the percentage of hemoglobin associated with the liposome phase (i.e., encapsulated) as a function of hemoglobin concentration and the aqueous:lipid hydration ratio. Hemoglobin concentrations were varied from 1 to 10 nM (in heme). Aqueous:lipid ratios of 8:1 and 4:1 were tested. Percent encapsulation varied from 13-30%, with the greatest efficiency, i.e., 30%, at a 4:1 hydration ratio of hemoglobin:lipid at 5.6 mM hemoglobin.
Determination of Absolute Phosphate Metabolite Concentrations in RIF‐1 Tumors in Vivo by <sup>31</sup>P‐<sup>1</sup>H‐<sup>2</sup>H NMR Spectroscopy Using Water as an Internal Intensity Reference (1992)

The absolute metabolite quantification method of Thulborn and Ackerman [J. Magn. Reson. 55, 357 (1983)] in which the tissue water proton signal is used as an internal intensity standard and its more recent variation in which NMR peak intensities are referenced to that of the natural abundance deuterium signal of water [Li et al., SMRM Abstr. 2, 825 (1988); Song et al., Magn. Reson. Med. 25, 45 (1992) have been implemented to obtain absolute phosphate metabolite concentrations in subcutaneous RIF-1 tumors during untreated growth and following treatment with 5-fluorouracil. The equivalence of these two hydrogen isotopes as intensity standards and the validity of their use in the determination of absolute metabolite concentrations in vivo by NMR has been demonstrated. On matched in vivo and extract tumor samples (n = 5), excellent agreement has been obtained between nucleoside triphosphate concentrations determined by NMR and those derived by HPLC analysis for the control tumors. Following 3 days of untreated growth, absolute concentrations of phosphate metabolites in RIF-1 tumors (n = 10) decreased significantly, except for the Pi concentration which did not vary. For the treated tumors (n = 10) there were no changes in metabolite concentrations except for a decrease in the PCr and, possibly, Pi concentrations. The PCr/Pi ratio in the latter tumors did not change. These observations suggest that changes in absolute metabolite concentrations may be more sensitive indices of response to therapy than changes in metabolite peak amplitude ratios, a parameter commonly used to express in vivo NMR data.
Test Directive Generation for Functional Coverage Closure Using Inductive Logic Programming (2006)

Functional verification is a complex and time-consuming task in the design process. Recently, various approaches have been developed to improve verification efficiency, including advanced coverage analysis techniques, coverage-driven verification methodologies and coverage-directed stimulus generation techniques. One remaining challenge is to fully automate functional coverage closure. This paper presents a novel approach for coverage-directed stimulus generation based on inductive learning from examples. Test sequences and their related coverage are examined to induce general rules which describe the characteristics of these tests. Coverage closure can be automated by applying the rule learning to clusters similar to the target coverage hole and combining the resulting rules to obtain directives for test generation. The validity of the approach is demonstrated on a pilot case study
Analysis of Nonexponential Transient Response Due to a Constant‐Phase Element (1994)

To characterize electrical losses of fuel cells or batteries, impedance spectroscopy (IS) or current interruption (CI) can be used. Analysis and parameter determination of impedance data is widely used. The system under study is usually represented by an equivalent circuit from which the system parameters can be determined. However, the analysis of current‐interruption data is often carried out with too simple circuits, e.g., using pure exponential behavior, because analysis in the time domain (CI) is often much more awkward than analysis in the frequency domain (IS). A comparative study has been carried out on the analysis of a relatively ideal electrical circuit, containing a pure capacitor, and a more realistic circuit where the capacitor is replaced by a constant‐phase element. Equations describing the response in the frequency and time domain are presented. Emphasis is put upon the analysis of circuits containing a constant‐phase element because impedance measurements clearly indicate the presence of such an element in many types of experiments, and because there is only limited literature available describing the behavior in the time domain.
Optimising the synthesis of shaped beam antenna patterns (1985)

A technique is introduced which uses the conventional polynomial representation of the antenna pattern produced by an equispaced linear array. Certain roots are displaced from the unit circle radially, to fill a portion of the pattern, which before this displayed lobes interspersed by deep nulls. The angular and radial positions of all the roots are simultaneously adjusted so that the amplitude of each ripple in the shaped region and the height of each sidelobe in the nonshaped region are individually controlled. Applications to a cosec2Θ × cos Θ pattern and to a flat-topped beam are presented. Experimental validation is also offered.
A Fully Integrated Dual-Channel On-Coil CMOS Receiver for Array Coils in 1.5–10.5 T MRI (2017)

Magnetic resonance imaging (MRI) is among the most important medical imaging modalities. Coil arrays and receivers with high channel counts (16 and more) have to be deployed to obtain the image quality and acquisition speed required by modern clinical protocols. In this paper, we report the theoretical analysis, the system-level design, and the circuit implementation of the first receiver IC (RXIC) for clinical MRI fully integrated in a modern CMOS technology. The dual-channel RXIC sits directly on the sensor coil, thus eliminating any RF cable otherwise required to transport the information out of the magnetic field. The first stage LNA was implemented using a noise-canceling architecture providing a highly reflective input used to decouple the individual channels of the array. Digitization is performed directly on-chip at base-band by means of a delta-sigma modulator, allowing the subsequent optical transmission of data. The presented receiver, implemented in a CMOS technology, is compatible with MRI scanners up to . It reaches sub- noise figure for MRI units and features a dynamic range up to at a power consumption below per channel, with an area occupation of . Mounted on a small-sized printed circuit board (PCB), the receiver IC has been employed in a commercial MRI scanner to acquire in-vivo images matching the quality of traditional systems, demonstrating the first step toward multichannel wearable MRI array coils.
[Effect of modified mahuang fuzi xixin decoction extract on atrioventricular block induced by ischemia/reperfusion in New Zealand rabbits]. (2008)

MFXDE could improve the ischemia/reperfusion induced A-V conductive function.
The Biomechanical and Histologic Effects of Platelet-Rich Plasma on Rat Rotator Cuff Repairs (2012)

The decreased tendon tissue stiffness acutely and failure to enhance tendon-to-bone healing of repairs should be considered before augmenting rotator cuff repairs with PRP. Further studies will be necessary to determine the role of PRP in clinical practice.
Action Potential-Dependent Regulation of Gene Expression: Temporal Specificity in Ca<sup>2+</sup>, cAMP-Responsive Element Binding Proteins, and Mitogen-Activated Protein Kinase Signaling (1997)

Specific patterns of neural impulses regulate genes controlling nervous system development and plasticity, but it is not known how intracellular signaling cascades and transcriptional activation mechanisms can regulate specific genes in response to specific patterns of action potentials. Studies using electrical stimulation of mouse dorsal root ganglion neurons in culture show that the temporal dynamics of intracellular signaling pathways are an important factor. Expression of c-fos varied inversely with the interval between repeated bursts of action potentials. Transcription was not dependent on a large or sustained increase in intracellular Ca2+, and high Ca2+ levels separated by long interburst intervals (5 min) produced minimal increases in c-fos expression. Levels of the transcription factor cAMP-responsive element binding protein (CREB), phosphorylated at Ser-133, increased rapidly in response to brief action potential stimulation but remained at high levels several minutes after an action potential burst. These kinetics limited the fidelity with which P-CREB could follow different patterns of action potentials, and P-CREB levels were not well correlated with c-fos expression. The extracellular-regulated kinase (ERK) mitogen-activated protein kinases (MAPK) also were stimulated by action potentials of appropriate temporal patterns. Bursts of action potentials separated by long intervals (5 min) did not activate MAPK effectively, but they did increase CREB phosphorylation. This was a consequence of the more rapid dephosphorylation of MAPK in comparison to CREB. High expression of c-fos was dependent on the combined activation of the MAPK pathway and phosphorylation of CREB. These observations show that temporal features of action potentials (and associated Ca2+ transients) regulate expression of neuronal genes by activating specific intracellular signaling pathways with appropriate temporal dynamics.
Privatisation and appalling transport decisions (2014)

Proposed changes to Sydney's public transport will complicate travel arrangements for passengers, and some commuters who travel by train for part of their journey will pay more for doing so.
Learning the pattern of epistasis linking genotype and phenotype in a protein (2019)

Understanding the pattern of epistasis-the non-independence of mutations-is critical for relating genotype and phenotype. However, the combinatorial complexity of potential epistatic interactions has severely limited the analysis of this problem. Using new mutational approaches, we report a comprehensive experimental study of all 2<sup>13</sup> mutants that link two phenotypically distinct variants of the Entacmaea quadricolor fluorescent protein-an opportunity to examine epistasis up to the 13<sup>th</sup> order. The data show the existence of many high-order epistatic interactions between mutations, but also reveal extraordinary sparsity, enabling novel experimental and computational strategies for learning the relevant epistasis. We demonstrate that such information, in turn, can be used to accurately predict phenotypes in practical situations where the number of measurements is limited. Finally, we show how the observed epistasis shapes the solution space of single-mutation trajectories between the parental fluorescent proteins, informative about the protein's evolutionary potential. This work provides conceptual and experimental strategies to profoundly characterize epistasis in a protein, relevant to both natural and laboratory evolution.
A group communication protocol for CORBA (2003)

Group communication protocols are used in fault-tolerant systems to maintain strong replica consistency. The Fault-Tolerant Multicast Protocol (FTMP) described here is a group communication protocol specifically designed for the common object request broker architecture (CORBA). FTMP operates over IP Multicast, and consists of the reliable Multicast protocol (RMP) that provides reliable source-ordered message delivery, the reliable ordered Multicast protocol (ROMP) that provides reliable totally-ordered message delivery, and the processor group membership protocol (PGMP) that provides processor group membership services.
Cost-effectiveness of ibrutinib as first-line therapy for chronic lymphocytic leukemia in older adults without deletion 17p (2018)

Ibrutinib is a novel oral therapy that has shown significant efficacy as initial treatment of chronic lymphocytic leukemia (CLL). It is a high-cost continuous therapy differing from other regimens that are given for much shorter courses. Our objective was to evaluate the cost-effectiveness of ibrutinib for first-line treatment of CLL in patients older than age 65 years without a 17p deletion. We developed a semi-Markov model to analyze the cost-effectiveness of ibrutinib vs a comparator therapy from a US Medicare perspective. No direct comparison between ibrutinib and the best available treatment alternative, obinutuzumab plus chlorambucil (chemoimmunotherapy), exists. Therefore, we compared ibrutinib to a theoretical treatment alternative, which was modeled to confer the effectiveness of an inferior treatment (chlorambucil alone) and the costs and adverse events of chemoimmunotherapy, which would provide ibrutinib with the best chance of being cost-effective. Even so, the incremental cost-effectiveness ratio of ibrutinib vs the modeled comparator was $189 000 per quality-adjusted life-year (QALY) gained. To reach a willingness-to-pay threshold (WTP) of $150 000 per QALY, the monthly cost of ibrutinib would have to be at most $6800, $1700 less than the modeled cost of $8500 per month (a reduction of $20 400 per year). When the comparator efficacy is increased to more closely match that seen in trials evaluating chemoimmunotherapy, ibrutinib costs more than $262 000 per QALY gained, and the monthly cost of ibrutinib would need to be lowered to less than $5000 per month to be cost-effective. Ibrutinib is not cost-effective as initial therapy at a WTP threshold of $150 000 per QALY gained.
Microglial Cells: The Main HIV-1 Reservoir in the Brain (2019)

Despite efficient combination of the antiretroviral therapy (cART), which significantly decreased mortality and morbidity of HIV-1 infection, a definitive HIV cure has not been achieved. Hidden HIV-1 in cellular and anatomic reservoirs is the major hurdle toward a functional cure. Microglial cells, the Central Nervous system (CNS) resident macrophages, are one of the major cellular reservoirs of latent HIV-1. These cells are believed to be involved in the emergence of drugs resistance and reseeding peripheral tissues. Moreover, these long-life reservoirs are also involved in the development of HIV-1-associated neurocognitive diseases (HAND). Clearing these infected cells from the brain is therefore crucial to achieve a cure. However, many characteristics of microglial cells and the CNS hinder the eradication of these brain reservoirs. Better understandings of the specific molecular mechanisms of HIV-1 latency in microglial cells should help to design new molecules and new strategies preventing HAND and achieving HIV cure. Moreover, new strategies are needed to circumvent the limitations associated to anatomical sanctuaries with barriers such as the blood brain barrier (BBB) that reduce the access of drugs.
Very low resistivity ohmic contact to <i>p</i> -type GaAs using In <sub>x</sub> Ga <sub>1−x</sub> As interlayer (1990)

A very low resistivity ohmic contact to 5 × 1017 at/cm3 beryllium doped GaAs was obtained by interposing a small bandgap p+InxGa1−xAs layer, grown by molecular beam epitaxy, between the p-GaAs and the metallisation. The thickness of the interlayer was less than 2000 Å. Specific contact resistance as low as 6.4 × 10−8Ωcm2 was achieved. These contacts exhibit excellent adhesion, have smooth surfaces and are easy to fabricate.
Using fluorine-containing amphiphilic random copolymers to manipulate the quantum yields of aggregation-induced emission fluorophores in aqueous solutions and the use of these polymers for fluorescent bioimaging (2012)

Two new series of aggregation-induced emission (AIE) fluorophore-containing amphiphilic copolymers possessing the segments of a monomeric AIE fluorophore, N-(2-hydroxypropyl)methacrylamide (HPMA), [2-(methacryloyloxy)ethyl]trimethylammonium chloride (MATMA), and/or 2,2,2-trifluoroethyl methacrylate (TFEMA) were synthesized. Photophysical properties were investigated using UV-Vis absorbance and fluorescence spectrofluorometry. The increases of molar fractions of the hydrophobic AIE fluorophores and/or the trifluoroethyl moieties result in the higher quantum yields of the AIE fluorophores in the polymers. Using 1-mol% of AIE fluorophores with the tuning of molar fractions of TFEMA, 40% quantum yield was achieved, whereas only less than 10% quantum yield was obtained for the polymers without the TFEMA segments. The quantum yield difference indicates the importance of the fluorine segments for getting high quantum yields of the AIE fluorophores. These polymers were explored for fluorescent bioimaging using human brain glioblastoma U87MG and human esophagus premalignant CP-A cell lines. All the polymers are cell permeable and located in the cellular cytoplasma area. Cellular uptake was demonstrated to be through endocytosis, which is time and energy dependent. The polymers are non-cytotoxic to the two cell lines. Because the polymers contain (19)F segments, we studied the spin-lattice relaxation time (T1) and spin-spin relaxation time (T2) of these polymers. T1 and T2 are the two important parameters for the evaluations of the capacity of these polymers for further applications in (19)F magnetic resonance imaging ((19)F MRI). Structure influence on T1 and T2, especially for T2, was observed. These new multifunctional materials are the first series of fluorinated polymers with AIE fluorophores for bioapplications.
Variable binding affinities of listeriolysin O peptides for the H‐2K<sup>d</sup> class I molecule (1993)

Previously we used the peptide-binding motif for the murine class I major histocompatibility complex molecule H-2Kd to identify a nonamer peptide of the Listeria monocytogenes listeriolysin (LLO) protein that was recognized by cytotoxic T lymphocytes (CTL) in association with H-2Kd. Eleven nonamer peptides contained in the LLO sequence were synthesized and one, LLO 91-99, proved to be a CTL target. Using peptide binding competition assays with H-2Kd-restricted CTL, we show that 3 out of the 11 LLO peptides, including the CTL epitope, have a high binding affinity for H-2Kd; 2 of 11 peptides have approximately 10-fold lower affinity, while the remaining 6 peptides have no or very low affinity for H-2Kd. Single residue changes were made in the LLO 91-99 peptide and two other LLO peptides to identify non-anchor amino acids that might interfere with peptide binding. In addition, we used the LLO peptides which bound well to H-2Kd to attempt to restimulate a secondary CTL response from L. monocytogenes-primed spleen cells. Only LLO 91-99 was able to induce such a response. Thus only a fraction of nonamer peptides which fit the original binding motif have a high affinity for the H-2Kd class I molecule, and only a fraction of these serve as CTL epitopes.
B-domain deleted factor VIII is aggregated and degraded through proteasomal and lysosomal pathways (2005)

Factor VIII (FVIII) processing within mammalian cells is demonstrated to be much less efficient than proteins of similar size. The deletion of the B-domain from FVIII improves the level of production, due partly to the increase in mRNA synthesis. We aimed to characterise the cellular fate and the intracellular processing of the FVIII molecule devoid of B-domain. A B-domain deleted factor VIII (BDD-FVIII) possessing a furin consensus cleavage site in the connecting segment between the heavy and the light chain, was produced in CHO cell line. In such cells, FVIII was retained as two single chain products from which a majority was aggregated. The two species were located in Triton X-100 soluble (for 60-80%) and insoluble fractions (for 20-40%). The incubation of the expressing cells with tunicamycin (5 mug/ml) and the treatment of the intracellular species with a mixture of Neuraminidase and N-glycosidase-F revealed that both intracellular species were N-glycosylated. Furin over-expression neither diminished the intracellular FVIII contents nor improved its extracellular production. Intracellular FVIII was degraded through both lysosomal and proteasomal pathways as evidenced by inhibitor treatments (e.g. NH(4)Cl, leupeptin, clasto-Lactacystin beta-lactone and MG-132), pulse-chase analysis and confocal observations. This study demonstrates that a BDD-FVIII expressed in CHO cells is inefficiently processed consecutively to intracellular aggregation, proteasomal degradation, and routage to lysosomes.