gebhart/patrepeval huggingface dataset:
Effect of Overexpression of a Soluble Pyridine Nucleotide Transhydrogenase (UdhA) on the Production of Poly(3-hydroxybutyrate) in Escherichia coli (2006)

A soluble pyridine nucleotide transhydrogenase (UdhA) has been used to increase the productivity and yield of PHB in vivo. By inducing a high level of UdhA, which can transfer reducing equivalents between NAD and NADP, we have increased NADPH availability, resulting in high yield and productivity of PHB in Escherichia coli. Coexpression of the phb operon from Alcaligenes eutrophus H16 and the native udhA from E. coli from high copy plasmids resulted in an increase in PHB yield from 49 to 66% g of PHB per gram of total cell dry weight and an increase in final concentration from 3.52 to 6.42 g/L; the PHB concentration of the udhA carrying strain is almost twice that of the control strain expressing only the phb operon. The results of this study demonstrate the effectiveness of cofactor manipulation and its application as a tool in metabolic engineering.
Interactive Local Color Transfer Between Images (2007)

Altering image’s color is one of the most common tasks in image processing. However, most of existing methods are aimed to perform global color transfer. This usually means that the whole image is affected. But in many cases colors of only a part of an image needs changing, so it is important that the rest of the image remains unmodified. In this article we offer a fast and simple interactive algorithm based on local color statistics that allows altering color of only a part of an image, preserving image’s details and natural look.
Microdroplet identification and size measurement in sprays with lasing images (2002)

Two-dimensional fluorescence and lasing images of a Rhodamine-6G doped water spray are observed with color photography. The orange-red lasing microdroplets are identified by their two reciprocal lasing spots. The microdroplet sizes are measured using the digitized images. The obtained microdroplet size distribution compares favorably with the normal Gaussian size distribution.
Influence of Brownian Rotations and Energy Transfer upon the Measurements of Fluorescence Lifetime (1970)

The depolarization of the fluorescence of solutions by either Brownian rotations or intermolecular energy transfer may be simply described by a system of first-order linear differential equations containing as only parameters the rate of fluorescence emission and the rate of transport of the excitation from one orthogonal component of the emission to another. The steady-state solution has the form of Perrin's equation describing the depolarization by Brownian rotations, and the time-dependent depolarization following a unit light impulse is that originally described by Jablonski. The solution for sinusoidal excitation is novel in that: 1. It shows the difference in lifetime between the polarized components of the emission to be a sensitive function of the ratio of the modulation frequency ω to the emission rate λ. For ω/λ &amp;gt; 1 the difference between the polarized lifetimes may become many times greater than that observed after a unit light impulse. 2. It permits the determination of both the rate of transport of the excitation and the limiting polarization of the fluorescence from observations at one fixed temperature and viscosity. 3. It allows the definition of conditions under which the true or exponential decay of the fluorescence may be measured. Experimental tests of the theory by phase fluorometry are described: These include observations upon dilute solutions in media of limited viscosity where Brownian motion is the only cause of depolarization and observations upon concentrated frozen solutions where depolarization is due to energy transfer alone.
Cytochrome P450 Family Member CYP704B2 Catalyzes the ω -Hydroxylation of Fatty Acids and Is Required for Anther Cutin Biosynthesis and Pollen Exine Formation in Rice (2010)

Abstract The anther cuticle and microspore exine act as protective barriers for the male gametophyte and pollen grain, but relatively little is known about the mechanisms underlying the biosynthesis of the monomers of which they are composed. We report here the isolation and characterization of a rice (Oryza sativa) male sterile mutant, cyp704B2, which exhibits a swollen sporophytic tapetal layer, aborted pollen grains without detectable exine, and undeveloped anther cuticle. In addition, chemical composition analysis indicated that cutin monomers were hardly detectable in the cyp704B2 anthers. These defects are caused by a mutation in a cytochrome P450 family gene, CYP704B2. The CYP704B2 transcript is specifically detected in the tapetum and the microspore from stage 8 of anther development to stage 10. Heterologous expression of CYP704B2 in yeast demonstrated that CYP704B2 catalyzes the production of ω -hydroxylated fatty acids with 16 and 18 carbon chains. Our results provide insights into the biosynthesis of the two biopolymers sporopollenin and cutin. Specifically, our study indicates that the ω -hydroxylation pathway of fatty acids relying on this ancient CYP704B family, conserved from moss to angiosperms, is essential for the formation of both cuticle and exine during plant male reproductive and spore development.
An Isoleucine-based Allosteric Switch Controls Affinity and Shape Shifting in Integrin CD11b A-domain (2000)

In response to cell activation signals, integrins switch from a low to a high affinity state. Physiologic ligands bind to integrins through a von Willebrand Factor A-type domain. Crystallographic studies revealed two conformations of this domain, "closed" and "open." The latter crystallizes in complex with a pseudoligand or ligand, suggesting that it represents the high affinity state; data linking structure and activity are lacking however. In this communication, we expressed stable low and high affinity forms of integrin CD11b A-domain and determined their binding isotherms and crystal structures. The low affinity form, generated by deleting an N-terminal extension extrinsic to the domain, did not bind to physiologic ligands, and crystallized in the closed conformation. The high affinity form was generated by either deleting or substituting an invariable C-terminal Ile(316), wedged into a hydrophobic socket in the closed form, but displaced from it in the open structure. Both mutants crystallized in the open conformation, and the Ile(316) --> Gly-modified integrin displayed high affinity. Structural differences between the low and high affinity forms were detected in solution. These data establish the structure-function correlates for the CD11b A-domain, and define a ligand-independent isoleucine-based allosteric switch intrinsic to this domain that controls its conformation and affinity.
Nonsteroidal Anti-Inflammatory Drugs Can Lower Amyloidogenic Aß 42 by Inhibiting Rho (2003)

A subset of nonsteroidal anti-inflammatory drugs (NSAIDs) has been shown to preferentially reduce the secretion of the highly amyloidogenic, 42-residue amyloid-beta peptide Abeta42. We found that Rho and its effector, Rho-associated kinase, preferentially regulated the amount of Abeta42 produced in vitro and that only those NSAIDs effective as Rho inhibitors lowered Abeta42. Administration of Y-27632, a selective Rock inhibitor, also preferentially lowered brain levels of Abeta42 in a transgenic mouse model of Alzheimer's disease. Thus, the Rho-Rock pathway may regulate amyloid precursor protein processing, and a subset of NSAIDs can reduce Abeta42 through inhibition of Rho activity.
Engineering a high-affinity methyl-CpG-binding protein (2006)

Core members of the MBD protein family (MeCP2, MBD1, MBD2 and MBD4) share a methyl-CpG-binding domain that has a specific affinity for methylated CpG sites in double-stranded DNA. By multimerizing the MDB domain of Mbd1, we engineered a poly-MBD protein that displays methyl-CpG-specific binding in vitro with a dissociation constant that is >50-fold higher than that of a monomeric MBD. Poly-MBD proteins also localize to methylated foci in cells and can deliver a functional domain to reporter constructs in vivo. We propose that poly-MBD proteins are sensitive reagents for the detection of DNA methylation levels in isolated native DNA and for cytological detection of chromosomal CpG methylation.
New therapies for the rheumatic diseases. (1989)

The investigational therapies of the rheumatic diseases reviewed in this issue are at various stages of clinical development. Methotrexate and sulfasalazine represent examples of chemotherapies in which the short-term efficacy and toxicities, at least in rheumatoid arthritis, have been carefully documented by controlled trials. The limited information available on cyclosporin A, combination chemotherapy, and radiotherapy is encouraging and appears to warrant additional, more extensive studies. In particular, randomized trials to determine the effects of these interventions on relevant long-term outcomes such as functional disability, organ failure, and life expectancy are necessary. Careful attention to the adverse consequences associated with these interventions, a limiting factor in many currently available therapies, will be mandatory. Disease modification by biologic agents holds the promise of ushering in an entirely new, more selective approach to therapy. A number of these biologic agents are currently at the threshold of clinical evaluation. In all likelihood, the scientific knowledge of pathogenic mechanisms operative in the rheumatic diseases gained through the use of these agents will be of equal importance to the therapeutic benefits.
The Cardiac-specific Nuclear δB Isoform of Ca2+/Calmodulin-dependent Protein Kinase II Induces Hypertrophy and Dilated Cardiomyopathy Associated with Increased Protein Phosphatase 2A Activity (2002)

The delta isoform of Ca(2+)/calmodulin-dependent protein kinase II (CaMKII) predominates in the heart. To investigate the role of CaMKII in cardiac function, we made transgenic (TG) mice that express the nuclear delta(B) isoform of CaMKII. The expressed CaMKIIdelta(B) transgene was restricted to the myocardium and highly concentrated in the nucleus. Cardiac hypertrophy was evidenced by an increased left ventricle to body weight ratio and up-regulation of embryonic and contractile protein genes including atrial natriuretic factor, beta-myosin heavy chain, and alpha-skeletal actin. Echocardiography revealed ventricular dilation and decreased cardiac function, which was also observed in hemodynamic measurements from CaMKIIdelta(B) TG mice. Surprisingly, phosphorylation of phospholamban at both Thr(17) and Ser(16) was significantly decreased in the basal state as well as upon adrenergic stimulation. This was associated with diminished sarcoplasmic reticulum Ca(2+) uptake in vitro and altered relaxation properties in vivo. The activity and expression of protein phosphatase 2A were both found to be increased in CaMKII TG mice, and immunoprecipitation studies indicated that protein phosphatase 2A directly associates with CaMKII. Our findings are the first to demonstrate that CaMKII can induce hypertrophy and dilation in vivo and indicate that compensatory increases in phosphatase activity contribute to the resultant phenotype.
Aqueduct: Online Data Migration with Performance Guarantees (2002)

Modern computer systems are expected to be up continuously: even planned downtime to accomplish system reconfiguration is becoming unacceptable, so more and more changes are having to be made to live systems that are running production workloads. One of those changes is data migration: moving data from one storage device to another for load balancing, system expansion, failure recovery, or a myriad of other reasons. Traditional methods for achieving this either require application down-time, or severely impact the performance of foreground applications - neither a good outcome when performance predictability is almost as important as raw speed. Our solution to this problem, Aqueduct, uses a control-theoretical approach to statistically guarantee a bound on the amount of impact on foreground work during a data migration, while still accomplishing the data migration in as short a time as possible. The result is better quality of service for the end users, less stress for the system administrators, and systems that can be adapted more readily to meet changing demands.
Effects of substitution on polyglycerol phosphate-specific antibody binding to lipoteichoic acids (1983)

The influence of D-alanine and carbohydrate substitution of lipoteichoic acids (LTAs) on the binding of antibody directed to the polyglycerol phosphate (PGP) portion was found to be at least partially dependent upon the mode of presentation of the antigen. There were greater differences in binding of anti-PGP immunoglobulins to substituted and unsubstituted LTAs in solution (micellar presentation) than when the same LTAs were adsorbed to the erythrocyte surface, which suggests that there is greater hindrance of access to the PGP chain, possibly as a result of closer packing, in a vesicle or micelle than when LTA is bound to a membrane surface. Although the difference in binding of anti-PGP immunoglobulins was nearly 20-fold between unsubstituted and highly substituted LTAs, rocket heights by rocket immunoelectrophoresis were only 4-fold different for the most highly substituted LTA and unsubstituted LTA. However, unsubstituted LTA clearly bound more immunoglobulin molecules than was reflected in the rocket height alone, since the resulting immunoprecipitates were much more prominent or intense, both before and after staining, than those of highly substituted LTAs. Differences between lightly and moderately substituted LTAs were less than twofold, indicating that under most circumstances estimates of LTA concentrations in samples where the composition is unknown will be within approximately twofold of the estimate.
TREM2-Transduced Myeloid Precursors Mediate Nervous Tissue Debris Clearance and Facilitate Recovery in an Animal Model of Multiple Sclerosis (2007)

Intravenously applied bone marrow-derived and TREM2-tranduced myeloid precursor cells limit tissue destruction and facilitate repair within the murine CNS by clearance of cellular debris during EAE. TREM2 is a new attractive target for promotion of repair and resolution of inflammation in multiple sclerosis and other neuroinflammatory diseases.
Inducing and modulating anisotropic DNA bends by pseudocomplementary peptide nucleic acids (2004)

DNA bending is significant for various DNA functions in the cell. Here, we demonstrate that pseudocomplementary peptide nucleic acids (pcPNAs) represent a class of versatile, sequence-specific DNA-bending agents. The occurrence of anisotropic DNA bends induced by pcPNAs is shown by gel electrophoretic phasing analysis. The magnitude of DNA bending is determined by circular permutation assay and by electron microscopy, with good agreement of calculated mean values between both methods. Binding of a pair of 10-meric pcPNAs to its target DNA sequence results in moderate DNA bending with a mean value of 40-45 degrees, while binding of one self-pc 8-mer PNA to target DNA yields a somewhat larger average value of the induced DNA bend. Both bends are found to be in phase when the pcPNA target sites are separated by distances of half-integer numbers of helical turns of regular duplex DNA, resulting in an enhanced DNA bend with an average value in the range of 80-90 degrees. The occurrence of such a sharp bend within the DNA double helix is confirmed and exploited through efficient formation of 170-bp-long DNA minicircles by means of dimerization of two bent DNA fragments. The pcPNAs offer two main advantages over previously designed classes of nonnatural DNA-bending agents: they have very mild sequence limitations while targeting duplex DNA and they can easily be designed for a chosen target sequence, because their binding obeys the principle of complementarity. We conclude that pcPNAs are promising tools for inducing bends in DNA at virtually any chosen site.
Purification of Bacillus circulans F-2 amylase and its general properties. (1983)

An extracellular amylase produced by Bacillus circulans F-2 was purified to show a single band on SDS polyacrylamide gel electrophoresis. The purified enzyme has a molecular weight of 93, 000, an optimum pH of 6.0-6.5 and an optimum temperature of 60°C. On isoelectric focusing, the enzyme exhibited 2 bands with isoelectric points of 4.88 and 4.93. When acting on amylaceous polysaccharides, the enzyme removed maltohexaose from their non-reducing ends but the produced maltohexaose was then split into maltotetraose and maltose. Although it digested corn starch granules at approximately the same rate as porcine pancreatic and Streptococcus bovis amylases, it digested potato starch granules far faster than those amylases.
PHASE UNWRAPPING, POSSIBILITIES AND LIMITATIONS* (1982)

A bstract An unwrapped phase curve from the principal values of the phase can be computed in a simple way. The validity of the unwrapping procedure is tested by exploiting the phase information in the signal's first moment. The significance of the unwrapped answer around notches in the amplitude spectrum is seriously degraded by noise. The proposed method and the validity test are illustrated with examples.
Highly Efficient Phase Boundary Biocatalysis with Enzymogel Nanoparticles (2013)

The enzymogel nanoparticle made of a magnetic core and polymer brush shell demonstrates a novel type of remote controlled phase-boundary biocatalysis that involves remotely directed binding to and engulfing insoluble substrates, high mobility, and stability of the catalytic centers. The mobile enzymes reside in the polymer brush scaffold and shuttle between the enzymogel interior and surface of the engulfed substrate in the bioconversion process. Biocatalytic activity of the mobile enzymes is preserved in the enzymogel while the brush-like architecture favors the efficient interfacial interaction when the enzymogel spreads over the substrate and extends substantially the reaction area as compared with rigid particles.
[Ilizarov's method. Histological and radiological aspects]. (1991)

The Ilizarov method is an original technique of surgical lengthening of long bones. The constraints in compression and distraction obtained with this method favor the bony healing. The straining of extension induces stimulating consequences on the bone. The healing process is different from that of the fractures because the bony regeneration is accomplished by a membranous bony mechanism without intermediate fibrous or cartilaginous medium. The maturation occurs when the lamellated bone is present, at the end of the 4th month.
Novel Fast Lithium Ion Conduction in Garnet‐Type Li 5 La 3 M 2 O 12 (M = Nb, Ta) (2003)

Lithium metal oxides with the nominal composition Li 5 La 3 M 2 O 12 (M = Nb, Ta), possessing a garnetlike structure, have been investigated with regard to their electrical properties. These compounds form a new class of solid‐state lithium ion conductors with a different crystal structure compared with all those known so far. The materials are prepared by solid‐state reaction and characterized by powder XRD and ac impedance to determine their lithium ionic conductivity. Both the niobium and tantalum members exhibit the same order of magnitude of bulk conductivity (∼10 −6 S/cm at 25°C). The activation energies for ionic conductivity (&lt;300°C) are 0.43 and 0.56 eV for Li 5 La 3 Nb 2 O 12 and Li 5 La 3 Ta 2 O 12 , respectively, which are comparable to those of other solid lithium conductors, such as Lisicon, Li 14 ZnGe 4 O 16 . Among the investigated materials, the tantalum compound Li 5 La 3 Ta 2 O 12 is stable against reaction with molten lithium. Further tailoring of the compositions by appropriate chemical substitutions and improved synthesizing methods, especially with regard to minimizing grain‐boundary resistance, are important issues in view of the potential use of the new class of compounds as electrolytes in practical lithium ion batteries.
Growth of Trypanosoma cruzi in a cloned macrophage cell line and in a variant defective in oxygen metabolism (1983)

A continuous cloned murine macrophage-like cell line, clone 16 derived from J774, has been found upon appropriate stimulation to be capable of oxidizing glucose by the hexose monophosphate shunt and producing O2- and H2O2. A variant in oxidative metabolism, clone C3C, was selected from this cell line which under similar conditions is unable to produce significant amounts of O2- and H2O2. When cells of the parental clone 16 were infected with epimastigotes of Trypanosoma cruzi, there was significant killing or growth inhibition of the parasites at 3 to 4 days after infection. In contrast, the parasites grew in the oxidative variant, clone C3C. Trypomastigote forms of T. cruzi were found to be only partially killed in the parental clone 16 but grew abundantly in the oxidative variant. Infection of the parental clone, but not the variant, was sufficient to stimulate oxygen metabolism as demonstrated by the increased reduction of nitro blue tetrazolium. Studies on the killing of T. cruzi epimastigotes in cell-free suspension by xanthine-xanthine oxidase indicated that 90% of the killing was catalase sensitive and due to H2O2, with at most 7 to 8% killing which could be inhibited by scavengers of . OH and singlet oxygen (1O2). In the in vitro experiment with H2O2 produced by glucose and glucose oxidase, the 50% lethal doses of epimastigotes and trypomastigotes were 6.0 and 8.7 nmol of H2O2 per min per ml, respectively, indicating that trypomastigotes were more resistant to killing by H2O2 than epimastigotes were. A reconstitution experiment of trypanocidal activity in clone C3C by ingestion of zymosan particles coupled with glucose oxidase showed that H2O2 was essential for this cytocidal process in the macrophage cell line. These results provide clear evidence for killing of an intracellular parasite by a continuous macrophage-like cell line and suggest the importance of the oxidative cytocidal mechanism in this process.
Clinical efficacy of abatacept, tocilizumab, and etanercept in Japanese rheumatoid arthritis patients with inadequate response to anti-TNF monoclonal antibodies (2014)

The aim of this study was to compare the efficacy and retention rates of three biologics (abatacept, tocilizumab, and etanercept) after switching from first-course anti-TNF monoclonal antibody therapy. We performed a retrospective multicenter study of 89 patients who underwent second-course biologic therapy for 52 weeks after switching from first-course anti-TNF monoclonal antibody therapy. Patients at baseline had a mean age of 58.7 years, mean disease duration of 9.8 years, and mean clinical disease activity index (CDAI) of 22.4. There was no significant difference between the three drugs, except in rheumatoid factor positivity. Retention rates for abatacept, tocilizumab, and etanercept treatment at 52 weeks were 72.0, 89.5 and 84.6 %, respectively. The evaluation of CDAI indicated no significant difference at 52 weeks among the three drugs. Discontinuation due to all unfavorable causes did not significantly differ among the three drugs in hazard ratio-based evaluations. Our results show that patients treated with abatacept, tocilizumab, and etanercept achieved a high response rate with no significant differences in drug retention rates and clinical efficacy. These drugs represent good therapeutic options for patients with RA who are refractory to anti-TNF monoclonal antibody therapy.