gebhart/patrepeval huggingface dataset:
Immunization with an Interferon‐γ–gp120 Fusion Protein Induces Enhanced Immune Responses to Human Immunodeficiency Virus gp120 (2001)

Cytokines, including interferon (IFN)-gamma, can be effective immunologic adjuvants but often lack the potency of other, more reactogenic compounds. On the basis of the observation that attachment of IFN-gamma to antigen could further enhance its adjuvanticity, a chimeric protein involving IFN-gamma and gp120 of human immunodeficiency virus was produced, using varying lengths of amino acid linkers between the two moieties. All resultant fusion proteins appeared to be dimerized, but full IFN-gamma biological activity was present only with the longest, 34-aa linker. Immunization with the fusion protein gave rise to enhanced primary antibody responses to gp120, particularly of the IgG2a subclass. In addition, both T cell proliferation and IFN-gamma production in response to antigen were strongly enhanced by primary immunization with the fusion protein. IFN-gamma fused to antigen is a more potent adjuvant for Th1-like responses than is IFN-gamma mixed with antigen.
On the Role of Metal Contaminants in Catalyses with FeCl<sub>3</sub> (2009)

Warning: Catalyzed N-, O-, and C-arylation reactions ascribed to FeCl3 can instead result from catalysis by trace quantities of copper salts.
VALVES FOR CONTROLLING HIGH-TEMPERATURE FLUIDS (1957)

A valve for high-temperature liquid (sodium) with a selfsealing leak- proof gland of (a plurality of) O-ring seals arranged as an insert over the spindle on a sleeve-like extension of the valve body. The extension and the spindle are of such length that combined with fins around the extension, a temperature drop is caused between the valve seat and the gland which results in liquid sodium passing through the valve becoming solid at the gland. (auth)
Real-time identification of operating room state from video (2007)

Managers of operating rooms (ORs) and of units upstream (e.g., ambulatory surgery) and downstream (e.g., intensive care and post-anesthesia care) of the OR require real-time in-formation about OR occupancy. Which ORs are in use, and when will each ongoing operation end? This information is used to make decisions about how to assign staff, when to prepare patients for the OR, when to schedule add-on cases, when to move cases, and how to prioritize room cleanups (Dexter et al. 2004). It is typically gathered by OR managers manually, by walking to each OR and estimating the time to case completion. This paper presents a system for deter-mining the state of an ongoing operation automatically from video. Support vector machines are trained to identify rele-vant image features, and hiddenMarkov models are trained to use these features to compute a sequence of OR states from the video. The system was tested on video captured over a 24 hour period in one of the 19 operating rooms in Baltimore’s R. Adams Crowley Shock Trauma Center. It was found to be more accurate and have less delay while providing more fine-grained state information than the current state-of-the-art system based on patient vital signs used by the Shock Trauma Center.
Development of a Method To Analyze Single Cell Activity by Using Dielectrophoretic Levitation (2005)

In cell fusion and genetic recombination, although the activity of single cells is extremely important, there is no method to analyze single cell activity. Development of a quick analyzing method for single cell activity is desired in various fields. Dielectrophoresis (DEP) refers to the force exerted on the induced dipole moment of an uncharged dielectric and/or conductive particle by a nonuniform electric field. By applying DEP, we obtained experimentally a relationship between the cell activity and the dielectric property, Re[K(omega)], and examined how to evaluate the single cell activity by measuring Re[K(omega)] of a single cell. A cone and plate electrode geometry was adapted in order to achieve the feedback-controlled DEP levitation. The single cell is exposed to a nonuniform field induced by the cone and plate electrode, and a more polarizable cell is moved to the direction of the cone electrode by the DEP force. The cell settles in the position where the DEP force and gravity are balanced by controlling applied voltage. This settled position, measured on the center axis of the cone electrode, depended on the dielectric constant of the cell. From these results, the relationship between the specific growth rates in cell growth phase and the dielectric properties Re[K(omega)] was obtained. Furthermore, the effect on the cell activity of various stresses, such as concentration of carbon dioxide, temperature, etc., was examined.
Stability of an RNA secondary structure affects in vitro transcription pausing in the trp operon leader region. (1984)

Transcription of the tryptophan (trp) operon of Escherichia coli and other bacterial species is regulated by the formation of alternative secondary structures in the leader segment of the transcript. During in vitro transcription of the trp leader region RNA polymerase pauses at base pair 92 after synthesis of an RNA hairpin secondary structure. We studied the dependence of pausing on hairpin stability by examining mutant trp templates containing base pair substitutions in the region corresponding to the hairpin secondary structure. Base changes that lower the stability of the hairpin were found to reduce both the frequency and half-life of RNA polymerase pausing while base changes that do not affect hairpin stability had little effect on pausing. Pausing was enhanced by the nusA protein; this enhancement was greatly reduced on mutant templates specifying less stable hairpins. The frequency of pausing on some mutant templates was correlated with the extent of read-through transcription beyond the trp attenuator, suggesting a possible role for pausing in the coupling of transcription and translation during transcription of the leader region of the operon.
Stable and unbiased flow turbulence estimation from pulse echo ultrasound (1999)

A new method for stable and unbiased flow turbulence estimation has been developed for medical ultrasonic color flow imaging. Conventional turbulence estimates from a finite number of transmitted pulses could be biased, unreliable, and erroneous. We found that a conventional method cannot provide quantitative estimates of variance of flow velocity. We propose a new approach for flow turbulence estimation that is based on analysis of the flow velocity vectors. The new method estimates the variance of the flow velocity and provides reliable estimates for flow turbulence. Numerical examples, computer simulations, and experiments using a flow phantom demonstrate that the new method can estimate variance of flow velocity accurately and without bias. This work also reports a complete derivation in the time domain for both unbiased velocity and turbulence estimations. The results include two velocity estimation equations agreeing with the 1-D and 2-D autocorrelation methods derived from the frequency domain. The results indicate that the new method for flow turbulence is particularly useful when the 2-D autocorrelation method is used for color flow imaging. The new method also appears to be able to detect low turbulence; therefore, it may be useful for diagnosing abnormalities such as minor stenoses and valvular jets.
Sketching stencils (2007)

Performance of stencil computations can be significantly improved through smart implementations that improve memory locality, computation reuse, or parallelize the computation. Unfortunately, efficient implementations are hard to obtain because they often involve non-traditional transformations, which means that they cannot be produced by optimizing the reference stencil with a compiler. In fact, many stencils are produced by code generators that were tediously handcrafted.
Modulating the activity of oligonucleotides by carbohydrate conjugation: solid phase synthesis of sucrose-oligonucleotide hybrids (2004)

In order to expand the repertoire of available oligosaccharide-oligonucleotide hybrids, the on-line solid phase synthesis of oligonucleotides conjugated at the 3'-and/or 5'-end with a preformed disaccharide unit has been performed. The key compound in the synthetic scheme described here is an appropriate phosphoramidite derivative of fully protected sucrose, used in association with a solid support functionalized with DMT-protected sucrose. The sucrose units at both ends of selected oligonucleotide sequences were shown to increase their chemical and enzymatic stability, while not interfering with duplex formation and with the ability of G-rich sequences to adopt a quadruplex structure.
Isolated Chromaffin Cells from Adrenal Medulla Contain Primarily Monoamine Oxidase B (1984)

Cultured chromaffin cells from bovine adrenal medulla were found to contain primarily the B form of monoamine oxidase. This monoamine oxidase B enzyme was somewhat distinct from B enzymes from other sources, in that noradrenaline was a much poorer substrate than serotonin. Nonetheless, studies with selective inhibitors of the A form (clorgyline) and the B form [(-)-deprenyl] confirmed that chromaffin cell monoamine oxidase was the B form. The observation that chromaffin cell monoamine oxidase has poor affinity for catecholamines is consistent with physiological needs that require the cell to synthesize and store large amounts of catecholamines.
Laser densification of optical films (1992)

Sol-gel derived SiO<SUB>2</SUB>-TiO<SUB>2</SUB> and WO<SUB>3</SUB> films were densified with a CO<SUB>2</SUB> laser. Laser fired SiO<SUB>2</SUB>-TiO<SUB>2</SUB> films had higher optical loss (6 dB/cm) than similar films fired in a furnace (< 1 dB/cm). For coating shrinkages up to about 40% the increase in refractive index during firing was similar for both laser and furnace fired SiO<SUB>2</SUB>-TiO<SUB>2</SUB> coatings. At higher shrinkages both anatase and rutile were observed in the laser fired coatings. Loss measurements of laser fired samples in this and, likely, in previous studies were made in crystalline coatings. It is proposed that this, at least in part, is the cause of the high optical losses typically measured in laser densified silica-titania waveguides. The electrochromic coloring behavior of the WO<SUB>3</SUB> films was examined using proton insertion. The coloring characteristics (< 20 s for 90% coloring) and bleaching characteristics (< 3 s for 90% bleaching) of laser fired WO<SUB>3</SUB> films were comparable to the coloring and bleaching characteristics of high-quality sol-gel derived films fired in a furnace. Optimal coloring was obtained using moderate laser energy densities (approximately 50 - 100 J/cm<SUP>2</SUP>). This optimum occurred with less shrinkage than for furnace fired electrochromic films with similar coloring behavior.
How and why phosphotyrosine-containing peptides bind to the SH2 and PTB domains (1998)

The binding energies of phosphotyrosine-containing complexes can be effectively predicted using the procedure developed here. It was also possible to predict the bound conformations of flexible short peptides correctly from random starting conformations.
Automated Foucault test for focus sensing (1983)

A chopper wheel, a bicell photodetector, and an electronic phase detector are used in a mechanization of the Foucault optical test to obtain a linear focus error voltage for an isolated point image. Geometrical and diffraction analyses of the technique are included which show the sensitivity of the technique to aberrations of higher order than focus.
Review: Cardiovascular & Renal Recent developments in hypocholesterolaemic agents (1995)

Hypercholesterolaemia is a major risk factor in the development of atherosclerosis. The recent marketing of several HMG-CoA reductase inhibitors (i.e. lovastatin, simvastatin, pravastatin and fluvas-tatin) has demonstrated a huge market for hypocholesterolaemic agents. Several companies are involved in developing other cholesterol biosynthesis inhibitors in addition to agents which decrease dietary cholesterol absorption. This review presents some of the recent trends in hypocholesterolaemic research as indicated by the activity in the patent literature over the past 3 years.
Determination of the chiral status of different novel psychoactive substance classes by capillary electrophoresis and β‐cyclodextrin derivatives (2020)

Besides the abuse of well-known illicit drugs, consumers discovered new synthetic compounds with similar effects but minor alterations in their chemical structure. Originally, these so-called novel psychoactive substances (NPS) have been created to circumvent law of prosecution because of illicit drug abuse. During the past decade, such compounds came up in generations, the most popular compound was a synthetic cathinone derivative named mephedrone. Cathinones are structurally related to amphetamines; to date, more than 120 completely new derivatives have been synthesized and are traded via the Internet. Cathinones possess a chiral center; however, only little is known about the pharmacology of their enantiomers. However, NPS comprise further chiral compound classes such as amphetamine derivatives, ketamines, 2-(aminopropyl)benzofurans, and phenidines. In continuation of our project, a cheap and easy-to-perform chiral capillary zone electrophoresis method for enantioseparation of cathinones presented previously was extended to the aforementioned compound classes. Enantioresolution was achieved by simply adding native β-cyclodextrin, acetyl-β-cyclodextrin, 2-hydroxypropyl-β-cyclodextrin, or carboxymethyl-β-cyclodextrin as chiral selector additives to the background electrolyte. Fifty-one chiral NPS served as analytes mainly purchased from online vendors via the Internet. Using 10 mM of the aforementioned β-cyclodextrins in a 10 mM sodium phosphate buffer (pH 2.5), overall, 50 of 51 NPS were resolved. However, chiral separation ability of the selectors differed depending on the analyte. Additionally, simultaneous enantioseparations, the determination of enantiomeric migration orders of selected analytes, and a repeatability study were performed successfully. It was proven that all separated NPS were traded as racemic mixtures.
The Unique Transmembrane Hairpin of Flavivirus Fusion Protein E Is Essential for Membrane Fusion (2011)

The fusion of enveloped viruses with cellular membranes is mediated by proteins that are anchored in the lipid bilayer of the virus and capable of triggered conformational changes necessary for driving fusion. The flavivirus envelope protein E is the only known viral fusion protein with a double membrane anchor, consisting of two antiparallel transmembrane helices (TM1 and TM2). TM1 functions as a stop-transfer sequence and TM2 as an internal signal sequence for the first nonstructural protein during polyprotein processing. The possible role of this peculiar C-terminal helical hairpin in membrane fusion has not been investigated so far. We addressed this question by studying TM mutants of tick-borne encephalitis virus (TBEV) recombinant subviral particles (RSPs), an established model system for flavivirus membrane fusion. The engineered mutations included the deletion of TM2, the replacement of both TM domains (TMDs) by those of the related Japanese encephalitis virus (JEV), and the use of chimeric TBEV-JEV membrane anchors. Using these mutant RSPs, we provide evidence that TM2 is not just a remnant of polyprotein processing but, together with TM1, plays an active role in fusion. None of the TM mutations, including the deletion of TM2, affected early steps of the fusion process, but TM interactions apparently contribute to the stability of the postfusion E trimer and the completion of the merger of the membranes. Our data provide evidence for both intratrimer and intertrimer interactions mediated by the TMDs of E and thus extend the existing models of flavivirus membrane fusion.
Factor VII-Activating Protease Is Activated in Multiple Trauma Patients and Generates Anaphylatoxin C5a (2012)

Severe tissue injury results in early activation of serine protease systems including the coagulation and complement cascade. In this context, little is known about factor VII-activating protease (FSAP), which is activated by substances released from damaged cells such as histones and nucleosomes. Therefore, we have measured FSAP activation in trauma patients and have identified novel FSAP substrates in human plasma. Mass spectrometry-based methods were used to identify FSAP binding proteins in plasma. Anaphylatoxin generation was measured by ELISA, Western blotting, protein sequencing, and chemotaxis assays. Plasma samples from trauma patients were analyzed for FSAP Ag and activity, nucleosomes, C5a, and C3a. Among others, we found complement components C3 and C5 in FSAP coimmunoprecipitates. C3 and C5 were cleaved by FSAP in a dose- and time-dependent manner generating functional C3a and C5a anaphylatoxins. Activation of endogenous FSAP in plasma led to increased C5a generation, but this was not the case in plasma of a homozygous carrier of Marburg I single nucleotide polymorphism with lower FSAP activity. In multiple trauma patients there was a large increase in circulating FSAP activity and nucleosomes immediately after the injury. A high correlation between FSAP activity and C5a was found. These data suggest that activation of FSAP by tissue injury triggers anaphylatoxin generation and thereby modulates the posttraumatic inflammatory response in vivo. A strong link between C5a, nucleosomes, and FSAP activity indicates that this new principle might be important in the regulation of inflammation.
Synthesis of fluorescent probe – carbohydrate conjugates (1981)

A new type of luminescent label has been synthesized and a range of carbohydrates has been derivatized with various fluorescent probes. Amine-containing labels were readily transformed with chloroacetylchloride into the corresponding fluorescent chloroacetamide reagents 1–4. Suitably blocked monosaccharides containing either a free thio 9, hydroxyl 11, or carboxyl 17 functionality have been conjugated with (a) 4-chloroacetamido labels 1 and 2, (b) with 4-aminobenzophenone 5, and (c) with 1-dimethyl-1-aminonaphthalene-5-sulfonylchloride 21, to form the fluorescent carbohydrate conjugates 10, 16, 18, and 20. Direct derivatization of the unblocked disaccharides 22 and 23 was achieved by reductive amination with amines 5 and 7 and sodium cyanoborohydride affording the 1-deoxyglycit-1-yl derivatives 24–26, which were characterized by 13 C nmr spectroscopy. The synthesis of fluorescent polysaccharides is exemplified by the condensation of 9-anthraldehyde with chitosan either via Schiff 's base formation to afford 32, or via reductive alkylation to form 33.
Theoretical considerations for mapping activation in human cardiac fibrillation (2013)

Defining mechanisms for cardiac fibrillation is challenging because, in contrast to other arrhythmias, fibrillation exhibits complex non-repeatability in spatiotemporal activation but paradoxically exhibits conserved spatial gradients in rate, dominant frequency, and electrical propagation. Unlike animal models, in which fibrillation can be mapped at high spatial and temporal resolution using optical dyes or arrays of contact electrodes, mapping of cardiac fibrillation in patients is constrained practically to lower resolutions or smaller fields-of-view. In many animal models, atrial fibrillation is maintained by localized electrical rotors and focal sources. However, until recently, few studies had revealed localized sources in human fibrillation, so that the impact of mapping constraints on the ability to identify rotors or focal sources in humans was not described. Here, we determine the minimum spatial and temporal resolutions theoretically required to detect rigidly rotating spiral waves and focal sources, then extend these requirements for spiral waves in computer simulations. Finally, we apply our results to clinical data acquired during human atrial fibrillation using a novel technique termed focal impulse and rotor mapping (FIRM). Our results provide theoretical justification and clinical demonstration that FIRM meets the spatio-temporal resolution requirements to reliably identify rotors and focal sources for human atrial fibrillation.
ATP Site-Directed Inhibitors of Protein Kinase CK2: An Update (2011)

CK2 denotes a pleiotropic, constitutively active protein kinase whose abnormally high level in many cancer cells is held as an example of "non oncogene addiction". A wide spectrum of cell permeable, fairly specific ATP site-directed CK2 inhibitors are currently available which are proving useful to dissect its biological functions and which share the property of inducing apoptosis of cancer cells with no comparable effect on their "normal" counterparts. One of these, CX-4945, has recently entered clinical trials for the treatment of advanced solid tumors, Castelman's disease and multiple myeloma. The solution of a wide range of 3D structures of inhibitors bound to the catalytic subunits of CK2 reveals that their efficacy substantially relies on hydrophobic interactions within a cavity which is smaller than in other protein kinases. Accordingly the potency of tetra-halogenated benzimidazoles increases upon replacement of chlorine by bromine and, even more, by iodine, and decreases if two unique bulky side chains on CK2 (Val66 and Ile174) are mutated to alanines. Many CK2 inhibitors have been tested on a panel of more than 60 kinases providing Promiscuity Scores useful to evaluate their selectivity, the lowest value (9.47), denoting highest selectivity, being displayed by quinalizarin. The observation that CK2 inhibitors with medium/high promiscuity scores share the ability to inhibit a group of protein kinases as effectively as CK2 discloses the possibility of using their scaffolds for the rational development of selective inhibitors of these kinases, with special reference to PIMs, DYRKs, HIPK2, PKD and ERK8.
Versatile Regulation of Cytosolic Ca2+ by Vanilloid Receptor I in Rat Dorsal Root Ganglion Neurons (2003)

Analysis of small dorsal root ganglion (DRG) neurons revealed novel functions for vanilloid receptor 1 (VR1) in the regulation of cytosolic Ca(2+). The VR1 agonist capsaicin induced Ca(2+) mobilization from intracellular stores in the absence of extracellular Ca(2+), and this release was inhibited by the VR1 antagonist capsazepine but was unaffected by the phospholipase C inhibitor xestospongins, indicating that Ca(2+) mobilization was dependent on capsaicin receptor binding and was not due to intracellular inositol-1,4,5-trisphosphate generation. Confocal microscopy revealed extensive expression of VR1 on endoplasmic reticulum, consistent with VR1 operating as a Ca(2+) release receptor. The main part of the capsaicin-releasable Ca(2+) store was insensitive to thapsigargin, a selective endoplasmic reticulum Ca(2+)-ATPase inhibitor, suggesting that VR1 might be predominantly localized to a thapsigargin-insensitive endoplasmic reticulum Ca(2+) store. In addition, VR1 was observed to behave as a store-operated Ca(2+) influx channel. In DRG neurons, capsazepine attenuated Ca(2+) influx following thapsigargin-induced Ca(2+) store depletion and inhibited thapsigargin-induced inward currents. Conversely, transfected HEK-293 cells expressing VR1 showed enhanced Ca(2+) influx and inward currents following Ca(2+) store depletion. Combined data support topographical and functional diversity for VR1 in the regulation of cytosolic Ca(2+) with the plasma membrane-associated form behaving as a store-operated Ca(2+) influx channel and endoplasmic reticulum-associated VR1 possibly functioning as a Ca(2+) release receptor in sensory neurons.