gebhart/patrepeval huggingface dataset:
Severe acute respiratory syndrome (SARS) related coronavirus in bats (2021)

Three major human coronavirus disease outbreaks, severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS) and 2019 coronavirus disease (COVID-19), occurred in the twenty-first century and were caused by different coronaviruses (CoVs). All these viruses are considered to have originated from bats and transmitted to humans through intermediate hosts. SARS-CoV-1 and SARS-CoV-2, disease agent of COVID-19, shared around 80% genomic similarity, and thus belong to SARS-related CoVs. As a natural reservoir of viruses, bats harbor numerous other SARS-related CoVs that could potentially infect humans around the world, causing SARS or COVID-19 like outbreaks in the future. In this review, we summarized the current knowledge of CoVs on geographical distribution, genetic diversity, cross-species transmission potential and possible pathogenesis in humans, aiming for a better understanding of bat SARS-related CoVs in the context of prevention and control.
Imidazole- and imidazolium-containing polymers for biology and material science applications (2010)

The imidazole ring is ubiquitous in nature and imidazole functionality plays a critical role in many structures within the human body, notably as histamine and histadine. Imidazoles offer many biophysical interactions including their ability to hydrogen bond with drugs and proteins. In contrast, imidazolium salts have lost their strong hydrogen-bonding ability through alkylation of both nitrogens, but they are able to aggregate electrostatically. Imidazolium salts are used to extract metal ions from aqueous solutions, dissolve carbohydrates, create polyelectrolyte brushes on surfaces, coat metal nanoparticles, provide antimicrobial action, and create oriented liquid crystals. Bioactive applications include imidazolium hydrogels, antiarrhythmics, and anti-metastic agents. This review will describe the synthesis and design of imidazole derivatives and imidazolium-containing polymers as bioactive materials. Imidazole-based polymers readily associate with biological molecules through hydrogen-bonding, and imidazolium analogs offer electrostatic interactions, aggregation, and self-assembly. Design of novel imidazole- and imidazolium-based macromolecules remains as an exciting and emerging field.
DNA-Dependent ATPase from HeLa Cells Is Related to Human Ku Autoantigen (1994)

A 150-kDa DNA-dependent ATPase composed of 83/68-kDa subunits was previously reported to cofractionate with a 21S complex of enzymes for DNA synthesis from HeLa cells (Vishwanatha, J. K., & Baril, E. F. (1990) Biochemistry 29, 8753-8759). The DNA-dependent ATPase was purified to electrophoretic homogeneity from a HeLa cell homogenate by a modified procedure that involves subcellular fractionation, poly(ethylene-glycol) precipitation of the combined nuclear extract/cytosol, and chromatography on Q-Sepharose and native and denatured DNA/celluloses followed by Mono-S fast protein liquid chromatography. The purified enzyme showed equimolar amounts of 83- and 68-kDa polypeptides following polyacrylamide gel electrophoresis under denaturing conditions. Sequence analysis of peptide fragments derived from the separated 83- and 68-kDa polypeptides showed 90-100% homology with the corresponding 80- and 70-kDa subunits of human Ku protein. Immunoblot analysis of the ATPase during the course of its purification and immunoprecipitation with antibodies to the 80- and 70-kDa subunits of human Ku protein confirmed the relationship of the 83- and 68-kDa polypeptides of the human DNA-dependent ATPase to the subunits of human Ku protein. Both the 83- and 68-kDa polypeptides are phosphorylated by a DNA-dependent protein kinase that cofractionates with the ATPase. The DNA-dependent ATPase activity is up regulated by phosphorylation.
Manuscripts (2010)

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Preclinical profile of cabazitaxel (2014)

First-generation taxanes have changed the treatment paradigm for a wide variety of cancers, but innate or acquired resistance frequently limits their use. Cabazitaxel is a novel second-generation taxane developed to overcome such resistance. In vitro, cabazitaxel showed similar antiproliferative activity to docetaxel in taxane-sensitive cell lines and markedly greater activity in cell lines resistant to taxanes. In vivo, cabazitaxel demonstrated excellent antitumor activity in a broad spectrum of docetaxel-sensitive tumor xenografts, including a castration-resistant prostate tumor xenograft, HID28, where cabazitaxel exhibited greater efficacy than docetaxel. Importantly, cabazitaxel was also active against tumors with innate or acquired resistance to docetaxel, suggesting therapeutic potential for patients progressing following taxane treatment and those with docetaxel-refractory tumors. In patients with tumors of the central nervous system (CNS), and in patients with pediatric tumors, therapeutic success with first-generation taxanes has been limited. Cabazitaxel demonstrated greater antitumor activity than docetaxel in xenograft models of CNS disease and pediatric tumors, suggesting potential clinical utility in these special patient populations. Based on therapeutic synergism observed in an in vivo tumor model, cabazitaxel is also being investigated clinically in combination with cisplatin. Nonclinical evaluation of the safety of cabazitaxel in a range of animal species showed largely reversible changes in the bone marrow, lymphoid system, gastrointestinal tract, and male reproductive system. Preclinical safety signals of cabazitaxel were consistent with the previously reported safety profiles of paclitaxel and docetaxel. Clinical observations with cabazitaxel were consistent with preclinical results, and cabazitaxel is indicated, in combination with prednisone, for the treatment of patients with hormone-refractory metastatic prostate cancer previously treated with docetaxel. In conclusion, the demonstrated activity of cabazitaxel in tumors with innate or acquired resistance to docetaxel, CNS tumors, and pediatric tumors made this agent a candidate for further clinical evaluation in a broader range of patient populations compared with first-generation taxanes.
Current-Induced Nanomagnet Dynamics for Magnetic Fields Perpendicular to the Sample Plane (2004)

We present electrical measurements of high-frequency magnetic dynamics excited by spin-polarized currents in Co/Cu/Ni(80)Fe20 nanopillar devices, with a magnetic field applied perpendicular to the sample layers. As a function of current and magnetic field, the dynamical phase diagram contains several distinguishable precessional modes and also static magnetic states. Using detailed comparisons with numerical simulations, we provide rigorous tests of the theory of spin-transfer torques.
Identification, purification, and subcellular localization of prostate-specific membrane antigen PSM' protein in the LNCaP prostatic carcinoma cell line. (1998)

An alternatively spliced variant of prostate-specific membrane antigen (PSMA) designated PSM' was originally described following identification of its mRNA in normal prostate. We have purified the PSM' protein from LNCaP cells using two immunoaffinity columns in tandem. The first column contained a monoclonal antibody (7E11) that was reactive with the NH2 terminus of PSMA, which specifically depleted the LNCaP lysate of full-length PSMA. The nonbinding fraction was then passed over a second column composed of a monoclonal antibody (PEQ226.5), the epitope of which was located within the 134-437 domain of PSMA and shared with PSM'. The protein eluted from the second immunoaffinity column produced a Mr 95,000 band on SDS-PAGE, which was slightly lower than the full-length PSMA at Mr 100,000. The band was NH2-terminally sequenced through 15 residues, and the assigned sequence coincided with the predicted sequence for PSM' protein minus the first two NH2 terminus amino acids. The PSM' protein, therefore, began with residue 60 of PSMA (alanine). LNCaP cells were fractionated, and PSM' was localized to the cytoplasm.
Cyclopropanation of Olefins with Diazoalkanes, Catalyzed by CoII(porphyrin) Complexes − A Synthetic and Mechanistic Investigation and the Molecular Structure of CoIII(TPP)(CH2CO2Et) (TPP = Dianion of meso‐Tetraphenylporphyrin) (2003)

Abstract Cobalt( II ) porphyrin complexes catalyze reactions between ethyl diazoacetate (EDA) and styrenes to give the corresponding cyclopropanes with trans selectivity. The reactions of other diazoalkanes and other olefins have also been carried out, and the mechanism of the reaction has been investigated. Kinetic data and stoichiometric reactions support the formation of a diazoalkane cobalt‐porphyrin complex that reacts with the olefins to generate the cyclopropane. Diethyl maleate and fumarate are not formed in the presence of an excess of olefin . On treatment of EDA with Co II (TPP) (TPP = dianion of meso ‐tetraphenylporphyrin) in the absence of the olefin, an alkyl cobalt( III ) complex Co III (TPP)(CH 2 CO 2 Et) was isolated, and its structure has been solved by X‐ray diffraction. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2003)
Interpretation of DFA Color Gradients in Oil Columns Using the Flory-Huggins Solubility Model (2010)

Abstract Downhole fluid analysis (DFA) has been successfully used to delineate reservoir attributes such as vertical and lateral connectivity and properties of the produced fluids. The new-generation DFA tools not only measure bulk fluid properties such as gas/oil ratio (GOR), density, and light-end compositions of CO2, C1, C2, C3–C5, and C6+ more accurately but also color (optical density) that is related to the heavy ends (asphaltenes and resins) in real time at downhole conditions. In addition, the color measurement is one of the most robust measurements in DFA. Therefore, color gradient analysis in oil columns becomes vital to discern reservoir complexities by means of integrating advanced asphaltene science with DFA Fluid Profiling. In this paper, a thermodynamic asphaltene grading model was developed to describe equilibrium distributions of heavy ends in oil columns using the multicomponent Flory-Huggins regular solution model combined with a gravitational contribution. The variations of oil properties such as molar volume, molar mass, solubility parameter, and density with depth were calculated by the equation of state (EOS). A three-parameter Gamma distribution function was employed to characterize asphaltene components. The primary factors governing asphaltene distribution in reservoirs are the gravitational term, which is determined in part by the size of the asphaltene molecular or colloidal particle, and the solubility term, which is determined in large part by the GOR. Consequently, it is critical to accurately measure both the fluid coloration and the GOR to understand the asphaltene distribution. The two field case studies showed that colored resins (asphaltene-like heavy resins) were molecularly dissolved in condensate oil columns whereas asphaltenes were dispersed as nanoaggregates in crude oils. The heavy ends (resins or asphaltenes) have a preference of going to the bottom of the oil column both because of gravity and the variation of the liquid-phase (live oil mixture) solubility parameter. The results obtained in this work were in accord with the observations in recent advances in asphaltene science. The asphaltene distributions were consistent with an equilibrium distribution implying reservoir connectivity. In both cases, the subsequent production data proved the reservoir connectivity and the methods developed herein were validated. This methodology establishes a new powerful approach for conducting DFA color and GOR gradient analyses by coupling advanced asphaltene science with DFA Fluid Profiling to address reservoir connectivity.
Critical issues regarding HPS, a high performance microarchitecture (1985)

HPS is a new model for a high performance microarchitecture which is targeted for implementing very dissimilar ISP architectures. It derives its performance from executing the operations within a restricted window of a program out-of-order, asynchronously, and concurrently whenever possible. Before the model can be reduced to an effective working implementation of a particular target architecture, several issues need to be resolved. This paper discusses these issues, both in general and in the context of architectures with specific characteristics.
Teaching for understanding: what it is and how to do it (2001)

Something to think with OverviewNot everything has to be, or can be, carried in the head.Often, it is possible to give learners something which behaves a little like a memo or notepad.This chapter looks at some examples.In addition, analogies can be powerful devices for supporting productive thought.Thinking with the help of analogies is a natural process that even young children can handle, given certain conditions.In spite of this, many teachers ignore or neglect them.For this reason, analogies receive particular attention in this chapter.Various kinds of analogy and their uses are described.Although they are valuable possessions, their limitations must also be recognized.
Embryonic stem cells develop into functional dopaminergic neurons after transplantation in a Parkinson rat model (2002)

Although implantation of fetal dopamine (DA) neurons can reduce parkinsonism in patients, current methods are rudimentary, and a reliable donor cell source is lacking. We show that transplanting low doses of undifferentiated mouse embryonic stem (ES) cells into the rat striatum results in a proliferation of ES cells into fully differentiated DA neurons. ES cell-derived DA neurons caused gradual and sustained behavioral restoration of DA-mediated motor asymmetry. Behavioral recovery paralleled in vivo positron emission tomography and functional magnetic resonance imaging data demonstrating DA-mediated hemodynamic changes in the striatum and associated brain circuitry. These results demonstrate that transplanted ES cells can develop spontaneously into DA neurons. Such DA neurons can restore cerebral function and behavior in an animal model of Parkinson's disease.
CMOS micromechanical bandpass filter design using a hierarchical MEMS circuit library (2002)

A 550 kHz CMOS micromechanical bandpass filter, is designed using a parameterized cell library, "NODAS", for schematic representation and behavioral HDL simulation. The filler employs a unique resonator and coupling spring structure implemented in a CMOS-MEMS technology. As an alternative design method, an equivalent SPICE model is derived for the filter. Frequency response around the filter passband from SPICE simulation matches that from NODAS simulation to within 2%. Compared to an equivalent SPICE model methodology: the NODAS methodology enables convenient composition and simulation of complicated MEMS. The experimental result of the fabricated device shows that the center frequency and bandwidth match NODAS simulation to within 3%, which provides component level validation of the NODAS-based MEMS design methodology. Nonideal effects such as manufacturing variations are also simulated and discussed.
The addition of tramadol to morphine via patient‐controlled analgesia does not lead to better post‐operative pain relief after total knee arthroplasty (2006)

Our study does not support the combination of tramadol and morphine via PCA for post-operative pain relief after primary TKA. In addition, our study indicates that morphine via PCA as the sole means of post-operative analgesia does not provide sufficient pain relief after TKA. Thus, other means of post-operative analgesia should be used following TKA.
Stratal slicing; Part 1, Realistic 3-D seismic model (1998)

Abstract Two-dimensional, fenced 2-D, and 3-D isosurface displays of some realistic 3-D seismic models built in the lower Miocene Powderhorn Field, Calhoun County, Texas, demonstrate that a seismic event does not necessarily follow an impedance boundary defined by a geological time surface. Instead, the position of a filtered impedance boundary relative to the geological time surface may vary with seismic frequency because of inadequate resolution of seismic data and to the en echelon or ramp arrangement of impedance anomalies of sandstone. Except for some relatively time-parallel seismic events, the correlation error of event picking is large enough to distort or even miss the majority of the target zone on stratal slices. In some cases, reflections from sandstone bodies in different depositional units interfere to form a single event and, in one instance, an event tying as many as six depositional units (interbedded sandy and shaly layers) over 50 m was observed. Frequency independence is a necessary condition for selecting time-parallel reference events. Instead of event picking, phantom mapping between such reference events is a better technique for picking stratal slices, making it possible to map detailed depositional facies within reservoir sequences routinely and reliably from 3-D seismic data.
HLA GENE AND HAPLOTYPE FREQUENCIES IN THE NORTH AMERICAN POPULATION (1997)

These data represent an important resource for investigators in the fields of transplantation and population genetics. The gene and haplotype frequencies can be used to aid clinicians in advising patients about the probability of finding a match within a specific ethnic group, or to determine donor recruitment goals and strategies. The information is also a valuable resource for individuals who are interested in population genetics, selection and evolution of polymorphic human genes, and HLA-disease association.
Ago2 Immunoprecipitation Identifies Predicted MicroRNAs in Human Embryonic Stem Cells and Neural Precursors (2009)

Extending the classic definition of microRNAs, this large number of new microRNA genes, the majority of which are less conserved than their canonical counterparts, likely represent evolutionarily recent regulators of early differentiation. The enrichment in Ago2 containing complexes, the presence of chromatin marks indicative of regulated gene expression, and differential expression over development all support the identification of 146 new microRNAs active during early hESC differentiation.
Effects of Bouvardin (NSC 259968), a cyclic hexapeptide from Bouvardia ternifolia, on the progression capacity of cultured Chinese hamster. (1978)

Abstract Bouvardin (NSC 259968) was examined for effects on survival and cell cycle progression capacity in exponentially growing populations of line CHO Chinese hamster cells. Cells were slowed in their ability to traverse the cell cycle by concentrations of Bouvardin as low as 0.2 µg/ml, with complete inhibition observed at concentrations in excess of 1.0 µg/ml. Flow cytometric analysis indicated that there was very little rearrangement of cells around the cell cycle in treated cultures, suggesting that Bouvardin arrested cell progression uniformly throughout the entire cell cycle. Cells treated for prolonged periods of time with levels of Bouvardin inducing a total inhibition of cell division were highly resistant to drug-specific cytotoxicity (i.e., 58% of the cells continuously exposed to Bouvardin (2.0 µg/ml) for 62 hr were capable of forming colonies). Cells entering mitosis either in the presence of the drug or following drug removal were free of chromosome aberrations. Asynchronous cells exposed to Bouvardin exhibited a terminal point of inhibition of traverse capacity situated 20 min prior to prophase. Concentrations of Bouvardin that affected cell cycle traverse capacity drastically reduced the incorporation of labeled leucine into acid-precipitable material, both in whole cells and in a cell-free, protein-synthesizing system. Consideration of both the incorporation data and the cell kinetic response and terminal point of action measurements led to the conclusion that Bouvardin was acting as a protein synthesis inhibitor. In view of these kinetic and cytotoxic properties, questions are raised concerning the value of Bouvardin as a chemotherapeutic agent.
Expression and activity of C/EBPβ and δ are upregulated by dexamethasone in skeletal muscle (2005)

The influence of glucocorticoids on the expression and activity of the transcription factors CCAAT/enhancer binding protein (C/EBP)beta and delta in skeletal muscle was examined by treating rats or cultured L6 myotubes with dexamethasone. Treatment of rats with 10 mg/kg of dexamethasone resulted in increased C/EBPbeta and delta DNA binding activity in the extensor digitorum longus muscle as determined by electrophoretic mobility shift assay (EMSA) and supershift analysis. A similar response was noticed in dexamethasone-treated myotubes. In other experiments, myocytes were transfected with a plasmid containing a promoter construct consisting of multiple C/EBP binding elements upstream of a luciferase reporter gene. Treatment of these cells with dexamethasone resulted in a fourfold increase in luciferase activity, suggesting that glucocorticoids increase C/EBP-dependent gene activation in muscle cells. In addition, dexamethasone upregulated the protein and gene expression of C/EBPbeta and delta in the myotubes in a time- and dose-dependent fashion as determined by Western blotting and real-time PCR, respectively. The results suggest that glucocorticoids increase C/EBPbeta and delta activity and expression through a direct effect in skeletal muscle.
Functionally associated targets in mantle cell lymphoma as defined by DNA microarrays and RNA interference (2007)

Mantle cell lymphoma (MCL) is a non-Hodgkin lymphoma with poor prognosis. Its hallmark is the translocation t(11:14)q (13;32), leading to overexpression of cyclin D1, a positive regulator of the cell cycle. As cyclin D1 up-regulation is not sufficient for inducing malignant transformation, we combined DNA microarray and RNA interference (RNAi) approaches to identify novel deregulated genes involved in the progression of MCL. DNA microarray analysis identified 46 genes specifically up-regulated in MCL compared with normal B cells; 20 of these were chosen for further studies based on their cellular functions, such as growth and proliferation. The Granta 519 cell line was selected as an MCL in vitro model, to set up the RNAi protocol. To confirm the functionality of overexpression of the 20 disease-associated genes, they were knocked down using small interfering RNAs (siRNAs). In particular, knockdown of 3 genes, encoding the hepatoma-derived growth factor related protein 3 (HDGFRP3), the frizzled homolog 2 (FZD2), and the dual specificity phosphatase 5 (DUSP5), induced proliferative arrest in Granta 519 MCL cells. These genes emerged as functionally associated in MCL, in relation to growth and survival, and interfering with their function would increase insight into lymphoma growth regulation, potentially leading to novel clinical intervention modalities.
Greater occipital nerve block using local anaesthetics alone or with triamcinolone for transformed migraine: a randomised comparative study (2007)

Adding triamcinolone to local anaesthetics when performing GONB and TPIs was not associated with improved outcome in this sample of patients with TM.
Fabrication of diffractive–reflective optical interconnects for infrared operation based on total internal reflection (1989)

Diffractive-reflective optical interconnects (DROIs) for optical chip-to-chip interconnection were introduced in a 1988 paper. In this paper we demonstrate the use of total internal reflection for guiding the light. inside the glass plate. The required holographic grating couplers were produced by expoiting the wavelength change from blue light recording to red light reconstruction. Several types of fan-out DROI have been made in dichromated gelatin.