gebhart/patrepeval huggingface dataset:
The RecD Subunit of the RecBCD Enzyme from Escherichia coli Is a Single-stranded DNA-dependent ATPase (1997)

We have expressed the RecD subunit of the RecBCD enzyme from Escherichia coli as a fusion protein with a 31-amino acid NH2-terminal extension including 6 consecutive histidine residues (HisRecD). The overexpressed fusion protein can be purified in urea-denatured form by metal chelate affinity chromatography. The mixture of renatured HisRecD protein and the RecB and RecC proteins has a high level of ATP-dependent nuclease activity with either single- or double-stranded DNA, enhanced DNA unwinding activity, enhanced ATP hydrolysis activity in the presence of a small DNA oligomer cosubstrate, and chi-cutting activity. These are all characteristics of the RecBCD holoenzyme. The HisRecD protein by itself hydrolyzes ATP in the presence of high concentrations of single-stranded DNA (polydeoxythymidine). The activity is unstable at 37 degrees C, but is measurable at room temperature (about 23 degrees C). The HisRecD has very little ATPase activity in the presence of a much shorter single-stranded DNA (oligodeoxy(thymidine)12). HisRecD hydrolyzes ATP more efficiently than GTP and UTP, and has very little activity with CTP. We also purified a fusion protein containing a Lys to Gln mutation in the putative ATP-binding site of RecD. This mutant protein has no ATPase activity, indicating that the observed ATP hydrolysis activity is intrinsic to the RecD protein itself.
Analysis of cis- and trans- Acting Factors Involved in Regulation of the Streptococcus mutans Fructanase Gene ( fruA ) (2002)

There are two primary levels of control of the expression of the fructanase gene (fruA) of Streptococcus mutans: induction by levan, inulin, or sucrose and repression in the presence of glucose and other readily metabolized sugars. The goals of this study were to assess the functionality of putative cis-acting regulatory elements and to begin to identify the trans-acting factors involved in induction and catabolite repression of fruA. The fruA promoter and its derivatives generated by deletions and/or site-directed mutagenesis were fused to a promoterless chloramphenicol acetyltransferase (CAT) gene as a reporter, and strains carrying the transcriptional fusions were then analyzed for CAT activities in response to growth on various carbon sources. A dyadic sequence, ATGACA(TC)TGTCAT, located at -72 to -59 relative to the transcription initiation site was shown to be essential for expression of fruA. Inactivation of the genes that encode fructose-specific enzymes II resulted in elevated expression from the fruA promoter, suggesting negative regulation of fruA expression by the fructose phosphotransferase system. Mutagenesis of a terminator-like structure located in the 165-base 5' untranslated region of the fruA mRNA or insertional inactivation of antiterminator genes revealed that antitermination was not a mechanism controlling induction or repression of fruA, although the untranslated leader mRNA may play a role in optimal expression of fructanase. Deletion or mutation of a consensus catabolite response element alleviated glucose repression of fruA, but interestingly, inactivation of the ccpA gene had no discernible effect on catabolite repression of fruA. Accumulating data suggest that expression of fruA is regulated by a mechanism that has several unique features that distinguish it from archetypical polysaccharide catabolic operons of other gram-positive bacteria.
Promoter and nucleotide sequences of the Zymomonas mobilis pyruvate decarboxylase (1987)

DNA sequence analysis showed that pyruvate decarboxylase (one of the most abundant proteins in Zymomonas mobilis) contains 559 amino acids. The promoter for the gene encoding pyruvate decarboxylase was not recognized by Escherichia coli, although the cloned gene was expressed at relatively high levels under the control of alternative promoters. The promoter region did not contain sequences which could be identified as being homologous to the generalized promoter structure for E. coli. Hydropathy plots for the amino acid sequence indicated that pyruvate decarboxylase contains a large number of hydrophobic domains which may contribute to the thermal stability of this enzyme.
Color and texture features for person recognition (2005)

The need for automatic visual surveillance is increasing and the research on person recognition systems is more and more supported. As many biometric recognition methods, e.g. face recognition, are based on quite high camera resolutions which are not available in many situations, we examine features as well as classifier techniques for full body recognition. We present our experiments with color and texture features in the application of full body person recognition. On a database of 53 individuals we tested approved features for object recognition as well as MPEG7 color and texture descriptors on a person recognition task. For comparison, we used an RBF network classifier as well as a nearest-neighbor classifier. Our experiments showed that color as well as texture information is important for a person recognition system. Additionally, a combination of these two kind of features results in a performance improvement.
WDM systems with unequally spaced channels (1995)

Crosstalk due to four-wave mixing (FWM) is the dominant nonlinear effect in long-haul multichannel optical communication systems employing dispersion-shifted fiber. A method is discussed to find non-uniform channel separations for which no four-wave mixing product is superimposed on any of the transmitted channels, therefore suppressing FWM crosstalk. The residual crosstalk, due to channel power depletion only, is analytically evaluated for intensity-modulated repeaterless wavelength-division-multiplexed (WDM) systems and compared to experimental results. The theory includes the effect of the channel depletion on the amplitude of each phase-matched FWM wave. The probability of error is evaluated including the statistics of the pattern dependent channel depletion. The BER curve computed for an 8-channel WDM system is found to be in good agreement with experimental results. In the experiment, repeaterless transmission of eight 10 Gb/s WDM channels over 137 km (11 Tb/s-km) of dispersion-shifted fiber was demonstrated and error-free operation was achieved over a wide range of input powers using unequally spaced channels. The same system with equally spaced channels could not achieve a probability of error lower than 10/sup -6/. The use of unequal channel spacing allowed fiber input power to be increased by as much as 7 dB, which could be translated into a fivefold increase of the bit rate per channel (and therefore of the system capacity), or to an increase in the system length of about 30 km.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
T cell-mediated eradication of murine metastatic melanoma induced by targeted interleukin 2 therapy. (1996)

Induction of a T-cell mediated antitumor response is the ultimate goal for tumor immunotherapy. We demonstrate here that antibody-targeted IL2 therapy is effective against established pulmonary and hepatic melanoma metastases in a syngeneic murine tumor model. The effector mechanisms involved in this tumor eradication are not dependent on NK cells, since the therapeutic effect of antibody-IL2 fusion protein was not altered in NK cell-deficient mice. In contrast, T cells are essential for the observed antitumor effect, since therapy with antibody IL2 fusion proteins is unable to induce tumor eradication in T cell-deficient SCID mice. In vivo depletion studies characterized the essential effector cell population further as CD8 + T cells. Such CD8 + T cells, isolated from tumor bearing mice after antibody-directed IL2 therapy, exerted a MHC class I-restricted cytotoxicity against the same tumor in vitro. These data demonstrate the ability of antibody-targeted IL2 delivery to induce a T cell-dependent host immune response that is capable of eradicating established melanoma metastases in clinically relevant organs.
Peripheral white blood cell alterations in early labor. (1981)

The peripheral blood counts of 101 pregnant women in very early labor and 41 nonpregnant controls were compared through automated total and differential blood count techniques. There were profound quantitative changes in the peripheral bloods of the pregnant women. These included, in association with pregnancy, increases in the absolute number (per ml) of total white cell counts (p less than 0.0005), segmented neutrophils (p less than 0.0005), band neutrophils (p less than 0.0005), and monocytes (p less than 0.0005). In contrast, there was a significant decrease in the absolute number (per ml) of peripheral lymphocytes in pregnancy (p less than 0.05) and a significantly larger proportion of bloods from pregnant women had less than 10(6) lymphocytes per ml (p less than 0.0005). The percentage of segmented neutrophils increased significantly during pregnancy (p less than 0.0005) as did band neutrophils (p less than 0.0005). We also noted a significant decrease in the percentages of peripheral lymphocytes (p less than 0.0005). In contrast, there were no significant differences in the percentages of monocytes between pregnant women and nonpregnant controls. The increase in the absolute number of monocytes and the decrease in the absolute number of lymphocytes led to a significant decrease in lymphocyte-monocyte ratio (p less than 0.0005) during pregnancy. It is concluded that the maternal peripheral blood changes in late pregnancy may reflect immune changes required for the immune adaption between fetus and mother-host.
Pharmacokinetics and antitumor activity of a bivalent disulfide-stabilized Fv immunotoxin with improved antigen binding to erbB2. (1999)

We have generated a stable bivalent Fv molecule [(dsFv)2] of the anti-erbB2 monoclonal antibody e23 in which the V(H) and V(L) domains of the Fv are linked to each other by a disulfide bond and the two Fvs are connected by a 15-amino acid linker (T. K. Bera et al., J. Mol. Biol., 281: 475-483, 1998). The e23 (dsFv)2 molecule is linked to a truncated form of Pseudomonas exotoxin (PE38) to generate a bivalent disulfide-stabilized immunotoxin e23 (dsFv)2-PE38. Compared to the monovalent immunotoxin, the (dsFv)2 immunotoxin showed greatly increased cytotoxicity to four cancer cell lines expressing low levels of erbB2 but not to four other cell lines with high erbB2 expression. e23 (dsFv)2-PE38 was administered i.v. to mice, and its half-life was determined. The t(1/2)alpha and t(1/2)beta were 20 and 325 min, respectively, whereas the corresponding values for the monovalent dsFv immunotoxin were shorter, 6 and 52 min. The antitumor activities of the monovalent and bivalent immunotoxin were compared using mice bearing A431 tumors. Despite the fact that e23 (dsFv)2-PE38 was 13-fold more active than e23 dsFv-PE38 on A431 cells in cell culture, its antitumor activity in mice was <2-fold that of the monovalent immunotoxin. These data show that a large increase in avidity does not always lead to an increase in cytotoxic activity. Furthermore, in one of the cases in which cytotoxic activity in vitro was greatly enhanced, there was only a small increase in antitumor activity.
The Mechanism of Joint Capsule Thermal Modification in an In Vitro Sheep Model (2000)

The purpose of this study was to understand the mechanism responsible for joint capsule shrinkage after nonablative laser application in an in-vitro sheep model. Femoropatellar joint capsular tissue specimens harvested from 20 adult sheep were treated with one of three power settings of a holmium:yttrium-aluminum-garnet laser or served as a control. Laser treatment significantly shortened the tissue and decreased tissue stiffness in all three laser groups, whereas failure strength was not altered significantly by laser treatment. Transmission electron microscopic examination showed swollen collagen fibrils and loss of membrane integrity of fibroblasts. A thermometric study revealed nonablative laser energy caused tissue temperature to rise in the range of 64 degrees C to 100 degrees C. Electrophoresis after trypsin digestion of the tissue revealed significant loss of distinct alpha bands of Type I collagen in laser treated samples, whereas alpha bands were present in laser treated tissue without trypsin digestion. The results of this study support the concept that the primary mechanism responsible for the effect of nonablative laser energy is thermal denaturation of collagen in joint capsular tissue associated with unwinding of the triple helical structure of the collagen molecule.
Determination of the photoluminescence quantum yield of dilute dye solutions (IUPAC Technical Report) (2013)

Procedures for the determination of photoluminescence quantum yields with optical methods are addressed, and challenges associated with these measurements are discussed. Special emphasis is dedicated to relative measurements of fluorescent (i.e., short excited-state lifetime), transparent, dilute dye solutions in conventional cuvettes in a 0&amp;deg;/90&amp;deg; measurement geometry. Recommendations on the selection of suitable quantum yield standards are presented, and requirements for the documentation of photoluminescence quantum yields are derived.
Theoretical modeling of nonequilibrium optical phonons and electron energy relaxation in GaN (1999)

The decay of the zone-center longitudinal optical (LO) phonon in GaN into a transverse optical (TO) phonon and a longitudinal acoustic (LA) phonon is theoretically investigated. Its decay into two LA phonons is forbidden. A theoretical model is presented to study the effect of nonequilibrium LO and TO phonons on the electron energy relaxation rate. The electron energy relaxation time is calculated, and its value is shown to strongly depend on the finite lifetimes of both LO and TO phonons. The individual contributions of A1 mode and E1 mode optical phonons in the overall electron energy relaxation processes are also discussed.
Handheld micromanipulation with vision-based virtual fixtures (2011)

Precise movement during micromanipulation becomes difficult in submillimeter workspaces, largely due to the destabilizing influence of tremor. Robotic aid combined with filtering techniques that suppress tremor frequency bands increases performance; however, if knowledge of the operator's goals is available, virtual fixtures have been shown to greatly improve micromanipulator precision. In this paper, we derive a control law for position-based virtual fixtures within the framework of an active handheld micromanipulator, where the fixtures are generated in real-time from microscope video. Additionally, we develop motion scaling behavior centered on virtual fixtures as a simple and direct extension to our formulation. We demonstrate that hard and soft (motion-scaled) virtual fixtures outperform state-of-the-art tremor cancellation performance on a set of artificial but medically relevant tasks: holding, move-and-hold, curve tracing, and volume restriction.
Optimized conditions for chelation of yttrium-90-DOTA immunoconjugates. (1998)

The optimization of 90Y-DOTA chelation conditions represents an important advance in 90Y RIT because it facilitates the dependable and cost-effective preparation of 90Y-DOTA pharmaceuticals.
<title>Using correlated CT images in compensation for attenuation in PET (positron emission tomography) image reconstruction</title> (1991)

Applying structural information from x-ray computed tomograghy (CT) to image reconstruction in positron emission tomography (PET) for compensation of the effect of photon attenuation can provide improved quality of the reconstructed PET images. CT and PET scans can be registered precisely using a surface-matching technique. Anatomical maps are then obtained by reslicing the CT images along the PET image planes. Attenuation coefficient maps for the corresponding PET images can be derived from the anatomical maps by considering the difference in photon energies observed in CT and in PET. These attenuation coefficient maps are reprojected to produce a set of attenuation correction factors for each projection profile. PET images reconstructed using these attenuation correction factors exhibit significant reduction in noise. 1.
White-Light Emission from Magic-Sized Cadmium Selenide Nanocrystals (2005)

Magic-sized cadmium selenide (CdSe) nanocrystals have been pyrolytically synthesized. These ultra-small nanocrystals exhibit broadband emission (420-710 nm) that covers most of the visible spectrum while not suffering from self absorption. This behavior is a direct result of the extremely narrow size distribution and unusually large Stokes shift (40-50 nm). The intrinsic properties of these ultra-small nanocrystals make them an ideal material for applications in solid state lighting and also the perfect platform to study the molecule-to-nanocrystal transition.
[Several infection factors of Pseudoperonospora cubensis]. (2005)

The study on the effects of temperature and humidity on the pathogenicity of Pseudoperonospora cubensis showed that the optimum temperature for the occurrence of cucumber downy mildew was 25-35 degrees C. An alternation of 15/35 degrees C was the most propitious to the infection of Pseudoperonospora cubensis, while the high temperature above 35 degrees C could kill the pathogens. 2 hours humid was enough for infection. Pseudoperonospora cubensis stored at -20 degrees C for 10 months and dried for 7 days could still infect cucumber. The infected cucumber leaves could continuously produce sporangium, with its quantity gradually decreased with time. The quantity of sporangium produced in vivo was more than that in vitro.
Definition of drug resistant epilepsy: Consensus proposal by the ad hoc Task Force of the ILAE Commission on Therapeutic Strategies (2009)

To improve patient care and facilitate clinical research, the International League Against Epilepsy (ILAE) appointed a Task Force to formulate a consensus definition of drug resistant epilepsy. The overall framework of the definition has two "hierarchical" levels: Level 1 provides a general scheme to categorize response to each therapeutic intervention, including a minimum dataset of knowledge about the intervention that would be needed; Level 2 provides a core definition of drug resistant epilepsy using a set of essential criteria based on the categorization of response (from Level 1) to trials of antiepileptic drugs. It is proposed as a testable hypothesis that drug resistant epilepsy is defined as failure of adequate trials of two tolerated, appropriately chosen and used antiepileptic drug schedules (whether as monotherapies or in combination) to achieve sustained seizure freedom. This definition can be further refined when new evidence emerges. The rationale behind the definition and the principles governing its proper use are discussed, and examples to illustrate its application in clinical practice are provided.
Tax protein of HTLV-1 interacts with the Rel homology domain of NF-kappa B p65 and c-Rel proteins bound to the NF-kappa B binding site and activates transcription. (1994)

Tax protein of human T cell leukemia virus type 1 (HTLV-1) enhances transcription of several cellular genes through activation of a specific enhancer, the NF-kappa B binding site. We found previously that Tax binds to NF-kappa B p50, which is a member of the Rel/NF-kappa B family proteins, and associates with the DNA sequence of the NF-kappa B binding site. In the present study, we tested other NF-kappa B family proteins and found that NF-kappa B p65 and c-Rel proteins also bind to Tax and that their complexes with Tax bind to the DNA sequence of the NF-kappa B binding site. The Tax binding site on NF-kappa B p50 is the Rel homology domain, which is conserved in the Rel/NF-kappa B family proteins. The formations of these complexes by Tax mutants were well correlated with their transactivating capacities. In F9 embryonic carcinoma cells, Tax enhanced transcription synergistically with NF-kappa B p65 or c-Rel. Thus Tax interacts with the Rel homology domain of Rel/NF-kappa B family proteins which bind to the NF-kappa B binding site and activates transcription.
The Genomic Organization, Complete mRNA Sequence, Cloning, and Expression of a Novel Human Intracellular Membrane-associated Calcium-independent Phospholipase A2 (2000)

During the sequencing of the long arm of chromosome 7 in the Human Genome Project, a predicted protein product of 40 kDa was identified, which contained two approximately 10-amino acid segments homologous to the ATP and lipase consensus sequences present in the founding members of a family of calcium-independent phospholipases A(2). Detailed inspection of the identified sequence (residues 79, 671-109,912 GenBank accession no. AC005058) demonstrated that it represented only a partial sequence of a larger undefined polypeptide product. Accordingly, we identified the complete genomic organization of this putative phospholipase A(2) through analyses of previously published expressed sequence tags, PCR of human heart cDNA, and 5'-rapid amplification of cDNA ends. Polymerase chain reaction and Northern blotting demonstrated a 3.4-kilobase message, which encoded a polypeptide with a maximum calculated molecular weight of 88476.9. This 3.4-kilobase message was present in multiple human parenchymal tissues including heart, skeletal muscle, placenta, brain, liver, and pancreas. Cloning and expression of the protein encoded by this message in Sf9 cells resulted in the production of two proteins of apparent molecular masses of 77 and 63 kDa as assessed by Western analyses utilizing immunoaffinity-purified antibody. Membranes from Sf9 cells expressing recombinant protein released fatty acid from sn-2-radiolabeled phosphatidylcholine and plasmenylcholine up to 10-fold more rapidly than controls. The initial rate of fatty acid release from the membrane fraction was 0. 3 nmol/mg.min. The recombinant protein was entirely calcium-independent, had a pH optimum of 8.0, was inhibited by (E)-6-(bromomethylene)-3-(1-naphthalenyl)-2H-tetrahydropyran-2-one (IC(50) = 3 microM), and was predominantly present in the membrane-associated fraction. Collectively, these results describe the genomic organization, complete mRNA sequence, and sn-2-lipase activity of a novel intracellular calcium-independent membrane-associated phospholipase A(2).
The investigation of degradation reaction of various saccharides in high temperature and high pressure water (2008)

Recently, conversions of polysaccharides included in biomass resources have been studied in order to recover valuable chemicals. Degradation of polysaccharides has been attracted by many researchers, whereas by-products from secondary reactions of the materials have not been studied very well. For the purpose of understanding reaction behavior of various monosaccharides in high-temperature and high-pressure water regions, we investigated reaction pathway and kinetics through reaction experiments of degradation of saccharides in subcritical water. The experiment was conducted by using continuous flow-type micro-reactors. Glucose was used as the starting material. From the experimental results, the conversion of glucose increased with increasing the residence time. The yields of fructose and 1, 6-anhydro-β-D-glucose decreased with increasing the residence time. The yields of organic acids and some aldehydes increased with increasing the residence time.
The Path of Carbon in Photosynthesis – XXVIII – Response of Plants to Polyalkylglucopyranose and Polyacylglucopyranose (2012)

The Path of Carbon in Photosynthesis – XXVIII – Response of Plants to Polyalkylglucopyranose and Polyacylglucopyranose