gebhart/patrepeval huggingface dataset:
MSET modeling of Crystal River-3 venturi flow meters. (1998)

The analysis of archived Crystal River-3 feedwater flow data reveals a slow and steady degradation of the flow meter measurements during the 1992/1993 operating cycle. MSET can reliably estimate the true flow rate and quantify the degree of departure between the indicated signal and the true flow rate with high accuracy. The MSET computed flow rate could, in principle, be used to provide an improved estimate of the reactor power and hence avoid the revenue loss associated with derating the reactor based on a faulty feedwater flow rate indication.
Biosynthesis of a Natural Polyketide-Isoprenoid Hybrid Compound, Furaquinocin A: Identification and Heterologous Expression of the Gene Cluster (2006)

Furaquinocin (FQ) A, produced by Streptomyces sp. strain KO-3988, is a natural polyketide-isoprenoid hybrid compound that exhibits a potent antitumor activity. As a first step toward understanding the biosynthetic machinery of this unique and pharmaceutically useful compound, we have cloned an FQ A biosynthetic gene cluster by taking advantage of the fact that an isoprenoid biosynthetic gene cluster generally exists in flanking regions of the mevalonate (MV) pathway gene cluster in actinomycetes. Interestingly, Streptomyces sp. strain KO-3988 was the first example of a microorganism equipped with two distinct mevalonate pathway gene clusters. We were able to localize a 25-kb DNA region that harbored FQ A biosynthetic genes (fur genes) in both the upstream and downstream regions of one of the MV pathway gene clusters (MV2) by using heterologous expression in Streptomyces lividans TK23. This was the first example of a gene cluster responsible for the biosynthesis of a polyketide-isoprenoid hybrid compound. We have also confirmed that four genes responsible for viguiepinol [3-hydroxypimara-9(11),15-diene] biosynthesis exist in the upstream region of the other MV pathway gene cluster (MV1), which had previously been cloned from strain KO-3988. This was the first example of prokaryotic enzymes with these biosynthetic functions. By phylogenetic analysis, these two MV pathway clusters were identified as probably being independently distributed in strain KO-3988 (orthologs), rather than one cluster being generated by the duplication of the other cluster (paralogs).
Lightness perception in high dynamic range images: Local and remote luminance effects (2012)

We measured the perceived lightness of target patches embedded in high dynamic range checkerboards. We independently varied the luminance of checks immediately surrounding the test and those remote from it. The data establish context transfer functions (CTFs) that characterize perceptual matches across checkerboard contexts. Several features of the CTFs are broadly consistent with previous research: Matched luminance decreases when overall context luminance decreases; matched luminance increases when overall context luminance increases; manipulating context locations near the target has a greater effect than manipulating locations far from the target patch. The measured CTFs are not well described, however, by changes with context in multiplicative gain alone or by changes in both multiplicative and subtractive adaptation parameters. We were able to fit the data with a three-parameter model of adaptation. This allowed us to characterize the CTFs by specifying the luminances that appeared white, black, and gray (white point, black point, and gray point, respectively). The white and black points depended additively on the local and remote contrasts, but accounting for the gray point required an interaction term. Analysis of this effect suggests that the target patch itself must be included in a description of the visual context.
An Efficient Palladium N‐Heterocyclic Carbene Catalyst Allowing the Suzuki–Miyaura Cross‐Coupling of Aryl Chlorides and Arylboronic Acids at Room Temperature in Aqueous Solution (2014)

Abstract The application of a highly active Pd‐NHC catalyst for the Suzuki–Miyaura cross‐coupling of a broad variety of electronically activated and deactivated aryl chlorides with different arylboronic acids in excellent yields is described. This catalyst can be handled under aerobic conditions, is active with low catalyst loadings at room temperature and in an aqueous reaction medium and allows the application of cheap potassium carbonate as the base. magnified image
The mouse Wnt-1 gene can act via a paracrine mechanism in transformation of mammary epithelial cells. (1992)

The mouse Wnt-1 gene plays an essential role in fetal brain development and can contribute to tumorigenesis when activated aberrantly in the mammary gland. The gene encodes secretory glycoproteins associated with the extracellular or pericellular matrix, and it has been proposed that Wnt-1, as well as its Drosophila homolog wingless, may function in intercellular signalling. We show here that fibroblasts expressing Wnt-1 protein, although not transformed themselves, are able to elicit morphological transformation of neighboring C57MG mammary epithelial cells in coculture experiments. Heparin inhibits this effect, possibly by displacing Wnt-1 protein from its normal site of action. Our results indicate that the Wnt-1 gene can act via a paracrine mechanism in cell culture and strongly support the notion that in vivo the gene may function in cell-to-cell communication.
Recombinant Chicken IFN-gamma Expressed in Escherichia coli: Analysis of C-Terminal Truncation and Effect on Biologic Activity (1999)

Interferon-gamma (IFN-gamma) possesses potent immunostimulatory properties, and it has recently been shown to have potential therapeutic properties. Recombinant protein technology is frequently used for commercial production of therapeutics, such as IFN. Biologically active recombinant chicken IFN-gamma (rChIFN-gamma) constructs bearing an N-terminal poly-His tag were expressed in Escherichia coli. Preparations of rChIFN-gamma contained varying ratios of a full-length and a truncated protein species (18 and 16 kDa, respectively). Amino acid sequence analysis of the full-length protein corroborated the sequence previously predicted from the cDNA sequence. Full-length rChIFN-gamma contains two cysteine residues at the C-terminus, and these were labeled by reduction and subsequent specific alkylation with fluorescent tag (5-I-AEDANS) to distinguish between full-length and C-terminally truncated forms of rChIFN-gamma. Comparative peptide mapping, amino acid sequencing, and mass spectrometry revealed that the 16 kDa protein was truncated at Lys133. It was also observed that the 18 kDa rChIFN-gamma protein was infrequently contaminated with small quantities of protein truncated at Arg141. A truncated recombinant construct (His1-Lys133) was also expressed in E. coli and had biologic activity comparable with that of the full-length construct. The 3-D structure of rChIFN-gamma was deduced by comparative modeling with bovine and human IFN-gamma crystallographic structures. Analysis of sequences and comparison of structures have revealed that the 3-D structure of rChIFN-gamma is similar to those of bovine and human molecules despite an overall amino acid identity of only 32%.
Association of FcγRIIa (CD32a) with Lipid Rafts Regulates Ligand Binding Activity (2009)

Binding of Igs to myeloid cells via FcR is a key event in the control of innate and acquired immunity. FcgammaRIIa (CD32a) is a receptor for multivalent IgG expressed predominantly by myeloid cells, and its association with microdomains rich in cholesterol and sphingolipids, termed as lipid rafts, has been reported to be essential for efficient signaling. However, for many myeloid cell types, ligand binding to CD32a is suppressed by as yet undefined mechanisms. In this study, we have examined the role of CD32a-lipid raft interactions in the regulation of IgG binding to CD32a. Disruption of lipid raft structure following depletion or sequestration of membrane cholesterol greatly inhibited CD32a-mediated IgG binding. Furthermore, specific CD32a mutants, which show reduced association with lipid rafts (A224S and C241A), displayed decreased levels of IgG binding compared with wild-type CD32a. In contrast, constitutively lipid raft-associated CD32a (GPI-anchored CD32a) exhibited increased capacity for IgG binding compared with the full-length transmembrane CD32a. Our findings clearly suggest a major role for lipid rafts in the regulation of IgG binding and, more specifically, that suppression of CD32a-mediated IgG binding in myeloid cells is achieved by receptor exclusion from lipid raft membrane microdomains.
Multistation multiparameter flow cytometry: Some influences of instrumental factors on system performance (1983)

Abstract In an effort aimed at design of a flow cytometer/sorter system in which light scattering, fluorescence, and extinction measurements could be made in as many as five spatially separated illuminating beams, the performance of different mechanical components, light sources, illumination and collection optics, and flow chambers was compared by changing individual components while maintaining the same basic instrument configuration. A protocol was developed, and is here described, allowing rapid setup of a flow cytometer using a mercury arc lamp and two laser beams for illumination. When two or more illuminating beams are derived from a single laser, it is generally necessary to incorporate automatic gain control in the detector electronics to compensate for source intensity fluctuations and so to achieve acceptable measurement precision. It is, however, possible to use a single laser beam as a source for several flow cytometers without the need for such compensation. Mercury arc lamps provide adequate excitation in the near ultraviolet (uv) for DNA fluorochromes, such as Hoechst 33342, and may be preferable to ion lasers for this purpose. Reported differences in precision and sensitivity between stream‐in‐air and enclosed flow systems appear owing more to differences in the illumination and collection optics used in different instruments; five flow chamber designs gave equivalent performance when tested in the same instrument. Relatively inexpensive achromatic microscope objectives of numerical aperture (NA) approximately 0.5 may offer the best combination of depth of focus and light gathering power when used as fluorescence collection lenses for flow cytometers; image plane apertures improve system performance in fluorescence measurement.
Evidence for Enhanced Adipogenesis in the Orbits of Patients with Graves’ Ophthalmopathy (2004)

The signs and symptoms of Graves' ophthalmopathy (GO) result from increased volume of the orbital contents, including adipose, connective, and extraocular muscle tissues. We wanted to determine whether the expanded adipose tissue volume might be in part attributable to de novo adipogenesis. We measured levels of mRNA encoding leptin, adiponectin, peroxisome proliferator-activated receptor gamma (PPAR gamma), preadipocyte factor-1, and TSH receptor (TSHr) genes in orbital adipose tissues from GO patients (n = 22) and normal individuals (n = 18) and in orbital preadipocyte cultures derived from GO patients (n = 6) and normal subjects (n = 3) using quantitative real-time RT PCR. We found increased leptin, adiponectin, PPAR gamma, and TSHr expression in GO compared with normal orbital tissue samples, with positive correlations in the GO tissues between TSHr and leptin, adiponectin and PPAR gamma. In vitro differentiation of GO and normal preadipocytes resulted in enhanced adiponectin, leptin, and TSHr expression, with greater expression of the latter two genes in the GO cultures. These results suggest that de novo adipogenesis within orbital tissues with parallel enhanced expression of TSHr may be important in the pathogenesis of GO, and that potential therapies for GO might include inhibition of the adipogenic pathway.
Proteasome Function Is Regulated by Cyclic AMP-dependent Protein Kinase through Phosphorylation of Rpt6 (2007)

Dysregulation of the proteasome has been documented in a variety of human diseases such as Alzheimer, muscle atrophy, cataracts etc. Proteolytic activity of 26 S proteasome is ATP- and ubiquitin-dependent. O-GlcNAcylation of Rpt2, one of the AAA ATPases in the 19 S regulatory cap, shuts off the proteasome through the inhibition of ATPase activity. Thus, through control of the flux of glucose into O-GlcNAc, the function of the proteasome is coupled to glucose metabolism. In the present study we found another metabolic control of the proteasome via cAMP-dependent protein kinase (PKA). Contrary to O-Glc-NAcylation, PKA activated proteasomes both in vitro and in vivo in association with the phosphorylation at Ser(120) of another AAA ATPase subunit, Rpt6. Mutation of Ser(120) to Ala blocked proteasome function. The stimulatory effect of PKA and the phosphorylation of Rpt6 were reversible by protein phosphatase 1 gamma. Thus, hormones using the PKA system can also regulate proteasomes often in concert with glucose metabolism. This finding might lead to novel strategies for the treatment of proteasome-related diseases.
Flexible time management in data stream systems (2004)

Continuous queries in a Data Stream Management System (DSMS) rely on time as a basis for windows on streams and for defining a consistent semantics for multiple streams and updatable relations. The system clock in a centralized DSMS provides a convenient and well-behaved notion of time, but often it is more appropriate for a DSMS application to define its own notion of time---its own clock(s), sequence numbers, or other forms of ordering and times-tamping. Flexible application-defined time poses challenges to the DSMS, since streams may be out of order and uncoordinated with each other, they may incur latency reaching the DSMS, and they may pause or stop. We formalize these challenges and specify how to generate heartbeats so that queries can be evaluated correctly and continuously in an application-defined time domain. Our heartbeat generation algorithm is based on parameters capturing skew between streams, unordering within streams, and latency in streams reaching the DSMS. We also describe how to estimate these parameters at run-time, and we discuss how heartbeats can be used for processing continuous queries.
Dual microcolumn immunoaffinity liquid chromatography: an analytical application to human plasma proteins (1993)

Dual-column microcolumn immunoaffinity chromatography was accomplished by coupling immunoaffinity (IAC) and reversed-phase high-performance liquid chromatography (RP-HPLC) analysis columns. The IAC support was prepared by hydrophobically adsorbing the appropriate antibody onto an octyl silica-based stationary phase contained in a 250-microns-l.d. fused-silica microcolumn. Once the antigen was captured, the antigen-subtracted human plasma could be sent to the RP-HPLC microcolumn for plasma profiling. The antigen was quantitated by desorbing it from the IAC column and transferring it to the RP-HPLC system. Human plasma profiles were generated after removal of albumin, and transferrin and alpha 1-antitrypsin were quantitated with nanogram sensitivity. All analyses were accomplished with less than 1 microL of human plasma.
Comparison of Three Analgesics for Extracorporeal Shock Wave Lithotripsy (2002)

Diclofenac sodium and tramadol were found to be safe and effective analgesics with lower side-effects than fentanyl.
Chemical Modifications of the Toxic Lectins Abrin and Ricin (1978)

Abrin, ricin and their isolated A and B chains were subjected to various chemical treatments and the effect on their toxicity in mice, their ability to inhibit protein synthesis in a cell-free system and to induce indirect hemagglutination were studied. Reductive methylation reduced slightly the toxicity of abrin in mice and its ability to induce indirect agglutination, while its ability to inhibit protein synthesis in a cell-free system was unimpaired, indicating reduced ability of the B chain to bind to cell-surface receptors. The effect on ricin was slighter. Both periodate oxidation of methylated abrin and succinylation of abrin reduced strongly its toxicity to mice and its hemagglutinating ability, while its ability to inhibit protein synthesis in a cell-free system was much less reduced. Such treatments of ricin had little effect on its biological properties. Acetylation of tyrosyl groups with N-acetyl-imidazole strongly reduced the toxicity of abrin and ricin as well as their ability to induce hemagglutination. The change could be fully reversed by removing the acetyl groups introduced, indicating that tyrosyl groups are important for the binding sites of the toxin B chains. There was no change in the ability of the toxins to inhibit cell-free protein synthesis. Attempts to modify tryptophan groups in abrin and ricin by treatment with N-bromosuccinimide resulted in strongly reduced toxicity and in most cases the proteins showed changes in immunological and electrophoretic properties. In contrast, the toxins were much less affected by treatment with 2-hydroxy-5-nitrobenzyl bromide. Only when the treatment was carried out at low pH was the toxicity reduced. The results demonstrate that abrin and ricin may be chemically modified to inactivate primarily the B chain, responsible for binding of the toxins to animal cells, without affecting appreciably the activity of the A chain which is responsible for the toxic action of the proteins.
Hydrogen-Bonded Aggregates of Oligoaramide−Poly(ethylene glycol) Block Copolymers (2010)

Rod−coil copolymers with an oligomeric rod aggregate on a nanometer length scale, which is important for many applications like e.g. organic photovoltaics. However, this aggregation behavior and the driving forces such as hydrogen bonding and π−π interactions, as well as the role of side groups, are not yet fully understood. Here, we investigated these noncovalent interactions in oligo(p-benzamide)−poly(ethylene glycol) (OPBA−PEG) copolymers using solid-state NMR supported by wide-angle X-ray scattering (WAXS), differential scanning calorimetry (DSC), and polarization optical microscopy (POM). It was found that longer OPBAs form layered β-sheet-like aggregates and that these are stabilized by amide hydrogen bonds in both unsubstituted OPBAs and OPBA−PEG rod−coil copolymers. The binding of the PEG also introduces a liquid crystalline phase. As a consequence, the local structural order is improved in the copolymer. Thus, by combining different methods of structural investigation, we were able to develop a model of local aggregation and packing in both the liquid crystalline and the solid state.
A new approach for treatment of deep skin infections by an ethosomal antibiotic preparation: an in vivo study (2005)

Therapy with ethosomal erythromycin applied to the skin of S. aureus-infected mice was as effective as systemically administered erythromycin, suggesting a new possibility to treat deep dermal infections by local application of antibiotic in ethosomal carrier.
Molecular cloning of a mammalian hyaluronidase reveals identity with hemopexin, a serum heme-binding protein. (1994)

Hyaluronan is the most abundant glycosaminoglycan of the extracellular matrix and is a critical substrate for cellular attachment and locomotion. Little is known about the class of enzymes, termed hyaluronidases, that are responsible for hyaluronan catabolism in mammals. We have determined a partial amino acid sequence from a purified preparation of porcine liver hyaluronidase and have used this information as the basis for cloning complementary DNA that encodes the corresponding protein. When expressed in a recombinant baculovirus system, the protein exhibited hyaluronidase activity in a substrate-gel assay. The deduced sequence of this mammalian hyaluronidase is that of a 459-amino-acid polypeptide bearing four potential N-glycosylation sites as well as a copy of a proposed hyaluronan binding motif. Remarkably, amino acid sequence comparisons and immunologic cross-reactivities strongly suggest that the cloned protein is identical to hemopexin, an abundant, heme-binding serum protein. Although hemopexin has not previously been reported to possess any enzymatic activity, it includes a conserved domain found in collagenases, stromelysins, and other enzymes that metabolize the extracellular matrix. We conclude that hemopexin is the predominant hyaluronidase expressed in mammalian liver.
Opportunistic packet scheduling algorithm for load balancing in a multi-hop relay-enhanced cellular OFDMA-TDD System (2008)

In this paper, we consider a multi-hop relay-enhanced cellular OFDMA-TDD system with the full frequency-reuse capability, in which a TDD frame can be asymmetrically divided into two different intervals, one for access link to mobile stations and the other for relay link to base station (BS)-relay station (RS) communication, while the same radio resource is fully reused by every RS in the cell. Since a single common boundary between access and relay links is employed for the system, some access link associated with an individual RS can be either overloaded or under-loaded when traffic load is non-uniformly distributed, which causes an inefficient resource allocation. This paper proposes a load-balancing opportunistic (LoBO) scheduling algorithm that improves the overall system throughput in a weighted proportional fairness manner while balancing the traffic load over the access link to be shared by all RSpsilas. The proposed algorithm dynamically determines the common access-to-relay interval boundary as a part of packet scheduling, which has been shown to outperform the conventional system in which the boundary selection and packet scheduling are implemented as the separate processes.
Transient State Kinetics of Transcription Elongation by T7 RNA Polymerase (2006)

The single subunit DNA-dependent RNA polymerase (RNAP) from bacteriophage T7 catalyzes both promoter-dependent transcription initiation and promoter-independent elongation. Using a promoter-free substrate, we have dissected the kinetic pathway of single nucleotide incorporation during elongation. We show that T7 RNAP undergoes a slow conformational change (0.01-0.03 s(-1)) to form an elongation competent complex with the promoter-free substrate (dissociation constant (Kd) of 96 nM). The complex binds to a correct NTP (Kd of 80 microM) and incorporates the nucleoside monophosphate (NMP) into RNA primer very efficiently (220 s(-1) at 25 degrees C). An overall free energy change (-5.5 kcal/mol) and internal free energy change (-3.7 kcal/mol) of single NMP incorporation was calculated from the measured equilibrium constants. In the presence of inorganic pyrophosphate (PPi), the elongation complex catalyzes the reverse pyrophosphorolysis reaction at a maximum rate of 0.8 s(-1) with PPi Kd of 1.2 mM. Several experiments were designed to investigate the rate-limiting step in the pathway of single nucleotide addition. Acid-quench and pulse-chase kinetics indicated that an isomerization step before chemistry is rate-limiting. The very similar rate constants of sequential incorporation of two nucleotides indicated that the steps after chemistry are fast. Based on available data, we propose that the preinsertion to insertion isomerization of NTP observed in the crystallographic studies of T7 RNAP is a likely candidate for the rate-limiting step. The studies here provide a kinetic framework to investigate structure-function and fidelity of RNA synthesis and to further explore the role of the conformational change in nucleotide selection during RNA synthesis.