gebhart/patrepeval huggingface dataset:
Molecular Cloning, Expression, and Characterization of a Novel Mouse Liver SULT1B1 Sulfotransferase (1998)

A mouse liver homogenate was shown to contain enzymatic activities catalyzing the sulfation of 3,4-dihydroxyphenylalanine (Dopa) and tyrosine isomers with a pH optimum of 8.25. Western blot analysis revealed a 34 kDa protein exhibiting immunologic cross-reactivity to antiserum against rat liver SULT1B1 sulfotransferase. By employing the reverse transcriptase-polymerase chain reaction (RT-PCR) technique, a 910-base pair product encoding the putative mouse liver SULT1B1 sulfotransferase was obtained. Using this PCR product as a probe, a cDNA containing the entire open reading frame of the mouse liver SULT1B1 sulfotransferase was cloned from a mouse liver Lambda ZAP cDNA library. The nucleotide sequence indicated it is a new enzyme. The deduced amino acid sequence exhibited 87.6, 72.3, 55.9, 54.2, 52.8, 51.1, and 49.4% identity to the amino acid sequences of the rat liver SULT1B1 sulfotransferase, human thyroid hormone sulfotransferase, mouse phenol sulfotransferase, rat liver phenol sulfotransferase, rat liver hydroxyarylamine sulfotransferase, mouse estrogen sulfotransferase, and rat estrogen sulfotransferase. Upon transfection of COS-7 cells with an expression vector (pcDNA3) harboring the cDNA encoding this new enzyme, a 34 kDa protein exhibiting immunologic cross-reactivity to antiserum against the rat liver SULT1B1 sulfotransferase was expressed. The recombinant sulfotransferase exhibited enzymatic activities toward Dopa and tyrosine isomers, as well as dopamine and 3,3',5-triiodo-L-thyronine. Northern blot analyses indicated the SULT1B1 sulfotransferase was predominantly expressed in liver, but not in the other ten mouse organs examined. Furthermore, the enzyme was found to be expressed in a developmental stage-dependent manner, being at a very low level in liver samples from 1-day-old mice and then gradually increasing to the maximum level in liver samples from 4-week-old mice.
A trinocular stereo system for highway obstacle detection (2003)

Presents a trinocular stereo algorithm that we have developed as part of an obstacle detection system that detects small obstacles at long range on the highway. We describe the stages of the stereo algorithm itself and the reasons behind the design decisions that were made. This is followed by a description of the obstacle detection system that we have built. Finally, we show results from our system for a variety of different obstacles.
The Value of Lowering Cholesterol after Myocardial Infarction (1990)

CURRENT recommendations for lowering the cholesterol level to prevent coronary heart disease have focused largely on primary prevention and have paid less attention to the issue of lowering cholesterol in patients who already have coronary disease.1 2 3 4 5 6 It remains a common conception that in survivors of infarction the extent of myocardial damage is the prime determinant of outcome and serum cholesterol is not a major risk factor.7 The opposing view is that the modifiable risk factors after a myocardial infarction are the same as those before and merit treatment.8 , 9 In current practice, it appears that most patients with coronary disease do . . .
Leveraging user-session data to support Web application testing (2005)

Web applications are vital components of the global information infrastructure, and it is important to ensure their dependability. Many techniques and tools for validating Web applications have been created, but few of these have addressed the need to test Web application functionality and none have attempted to leverage data gathered in the operation of Web applications to assist with testing. In this paper, we present several techniques for using user session data gathered as users operate Web applications to help test those applications from a functional standpoint. We report results of an experiment comparing these new techniques to existing white-box techniques for creating test cases for Web applications, assessing both the adequacy of the generated test cases and their ability to detect faults on a point-of-sale Web application. Our results show that user session data can be used to produce test suites more effective overall than those produced by the white-box techniques considered; however, the faults detected by the two classes of techniques differ, suggesting that the techniques are complementary.
Prevention of transmission of HIV by organ and tissue transplantation (1993)

Human immunodeficiency virus (HIV) can be transmitted by solid organ and some forms of tissue transplantation. Although routine screening of organ and tissue donors for anti-HIV antibodies was implemented in most Western European countries and North America in 1985, several recent case reports indicate that a definite, albeit very small, risk of HIV transmission still remains. The screening tests that are currently used cannot rule out a false-negative test result occurring during the window period. Moreover, massive transfusion of the donor during the donor procedure may result in an undetectable anti-HIV antibody titer (by dilution of donor blood) that consequently leads to a false-negative test result. These risks of HIV transmission via transplantation and important issues in HIV testing are discussed in detail. Furthermore, several recommendations for the prevention of transmission and a protocol for HIV testing for both organ and tissue donation are presented. These may serve as intermediary guidelines until official ones, such as already exist for blood donation, are defined by the transplantation communities. The exclusion of donors whose behavior may place potential recipients at risk for HIV infection is essential. A thorough heteroanamnesis of the donor's next of kin during the donor procedure should provide sufficient information about donor history to enable a decision to be made in this respect. Special attention is given to the question of whether the existing donor selection criteria for blood donation should be applied in a similar way to organ donation since the strict application of selection criteria may limit the number of available donor organs.(ABSTRACT TRUNCATED AT 250 WORDS)
Microbial production of 2-keto-L-gulonic acid from L-sorbose and D-sorbitol by Gluconobacter melanogenus. (1990)

The strain SPO1 producing 13 g of 2-keto-L-gulonic acid (2KGA) per liter was isolated as a spontaneous mutant of Gluconobacter melanogenus IFO 3293. For the enhancement of 2KGA productivity, we did further strain improvement studies of the mutant. As a result, the mutant U13, producing about 60 g of 2KGA per liter from 100 g of L-sorbose per liter, was obtained. In addition, the mutant Z84, producing about 60 g of 2KGA per liter from 100 g of o-sorbitol per liter, was also obtained. During the fermentation from L-sorbose and D-sorbitoI, 5 to 10 g of L-idonic acid per liter was produced as a by-product, but L-idonic acid was converted to 2KGA before the end of fermentation.
Looking Under the Hood: Deep Neural Network Visualization to Interpret Whole-Slide Image Analysis Outcomes for Colorectal Polyps (2017)

Histopathological characterization of colorectal polyps is an important principle for determining the risk of colorectal cancer and future rates of surveillance for patients. The process of characterization is time-intensive and requires years of specialized medical training. In this work, we propose a deep-learning-based image analysis approach that not only can accurately classify different types of polyps in whole-slide images, but also generates major regions and features on the slide through a model visualization approach. We argue that this visualization approach will make sense of the underlying reasons for the classification outcomes, significantly reduce the cognitive burden on clinicians, and improve the diagnostic accuracy for whole-slide image characterization tasks. Our results show the efficacy of this network visualization approach in recovering decisive regions and features for different types of polyps on whole-slide images according to the domain expert pathologists.
PREDICTION OF "S" CHARACTERISTICS OF A PUMP-TURBINE WITH SMALL OPENING BASED ON V2F MODEL (2012)

The characteristic of a pump-turbine during the whole starting or stopping period couldn't be calculated accurately by CFD method and most of turbulence models were found inaccurate in the calculation of small opening condition, so a proper turbulence model was needed for the further study of pump-turbine. V2F model which was valid to the solid wall and SST k-ω model were used to calculate the pump-turbine with two openings that one was a small opening and the other was large opening. Results showed that V2F model can be used to simulate characteristics of pump-turbine in the whole opening range and the SST k-ω model can be used only for large openings. Results of V2F model are accuracy and it realizes the real flow in the near wall region. Results of V2F model can obtain small vortexes and some complex flow phenomenon and they are much different from results of SST k-ω model. The V2F model might be used to simulate the starting or stopping period of a pump-turbine.
Molecular characterization and applications of recombinant scFv antibodies to CD152 co‐stimulatory molecule (2000)

Recombinant human monoclonal antibodies against CD152 have been generated by selecting a synthetic phage scFv library with purified CD152-Ig fusion protein. Sixteen scFv fragments were isolated which specifically react with CD152 by enzyme-linked immunoabsorbent assay (ELISA) and Western blot resulting in their clustering into two groups recognizing different antigenic determinants. One group of scFvs (#3, #13, #40, #44, #47, #51, #57, #80 #83) recognized an epitope on CD152 dimer whereas another group (#15, #18, #31, #35, #54, #72, #81) recognized an epitope on both dimeric and monomeric CD152 molecule suggesting their possible use in understanding the subunit structure of CD152 which is still controversial. Sequencing of the VH genes revealed that all the scFvs belonged to the VH3 gene family but they were different in CDR3 length and composition. It was possible to correlate specific CDR3 sequences with reactivity of the two groups of scFvs. Four scFvs, #3, #40, #81 and #83, each representative of one specific CDR3, were selected for further analysis. Competition ELISA experiments showed that they recognize CD152 in its native configuration and bound to different epitopes from the CD80/CD86 interaction site. The scFvs were able to stain human T lymphocytes stimulated either with anti-CD3 and CD28 antibodies or PHA, PMA and ionomycin by cytofluorimetry suggesting that they can be useful reagents for monitoring the kinetics of surface-bound and intracellular CD152.
Expression of myc‐family genes in established human multiple myeloma cell lines: L‐myc but not c‐myc gene expression in the U‐266 myeloma cell line (1992)

Deregulated c-myc expression, as a consequence of translocation of the c-myc gene to one of the immunoglobulin loci, appears to play an important role in the pathogenesis of several B-cell tumors, including Burkitt's lymphoma, mouse plasmacytoma and rat immunocytoma. This study investigated the expression of c-myc and 2 other members of the myc gene family, L- and N-myc, at the mRNA and protein level, and analyzed for possible rearrangements of these genes in the human counterpart to the mouse plasmacytoma--multiple myeloma (MM). Nine well-characterized MM cell lines were examined by using Northern- and Southern-blot analysis and immunoprecipitation. The c-myc gene was found to be highly expressed in most MM cell lines. The level of expression was comparable to that observed in the COLO 320 and HL-60 cell lines, carrying amplified c-myc genes, and to that of B-cell lines with a higher proliferative activity than the MM cell lines. In the U-266 MM cell line, L-myc, but no c-myc mRNA or protein, was found. The L-myc gene was expressed in both early- and late-passage U-266 cells, suggesting that the L-myc expression was not the result of the in vitro cultivation. N-myc was not expressed in any of the MM cell lines. No rearrangements of c-myc or L-myc genes were found. We thus conclude that (a) in contrast to the corresponding mouse and rat B-cell tumors, c-myc is not frequently rearranged in MM; (b) c-myc is highly expressed in most MM lines; and (c) L-myc but not c-myc is expressed in the U-266 MM cell line.
Human Ex Vivo Wound Healing Model (2013)

Wound healing is a spatially and temporally regulated process that progresses through sequential, yet overlapping phases and aims to restore barrier breach. To study this complex process scientists use various in vivo and in vitro models. Here we provide step-by-step instructions on how to perform and employ an ex vivo wound healing model to assess epithelization during wound healing in human skin.
Stoichiometry and compartmentation of NADH metabolism inSaccharomyces cerevisiae (2001)

In Saccharomyces cerevisiae, reduction of NAD(+) to NADH occurs in dissimilatory as well as in assimilatory reactions. This review discusses mechanisms for reoxidation of NADH in this yeast, with special emphasis on the metabolic compartmentation that occurs as a consequence of the impermeability of the mitochondrial inner membrane for NADH and NAD(+). At least five mechanisms of NADH reoxidation exist in S. cerevisiae. These are: (1) alcoholic fermentation; (2) glycerol production; (3) respiration of cytosolic NADH via external mitochondrial NADH dehydrogenases; (4) respiration of cytosolic NADH via the glycerol-3-phosphate shuttle; and (5) oxidation of intramitochondrial NADH via a mitochondrial 'internal' NADH dehydrogenase. Furthermore, in vivo evidence indicates that NADH redox equivalents can be shuttled across the mitochondrial inner membrane by an ethanol-acetaldehyde shuttle. Several other redox-shuttle mechanisms might occur in S. cerevisiae, including a malate-oxaloacetate shuttle, a malate-aspartate shuttle and a malate-pyruvate shuttle. Although key enzymes and transporters for these shuttles are present, there is as yet no consistent evidence for their in vivo activity. Activity of several other shuttles, including the malate-citrate and fatty acid shuttles, can be ruled out based on the absence of key enzymes or transporters. Quantitative physiological analysis of defined mutants has been important in identifying several parallel pathways for reoxidation of cytosolic and intramitochondrial NADH. The major challenge that lies ahead is to elucidate the physiological function of parallel pathways for NADH oxidation in wild-type cells, both under steady-state and transient-state conditions. This requires the development of techniques for accurate measurement of intracellular metabolite concentrations in separate metabolic compartments.
2-Alkyl-5,5-dimethyl-1,3,2-dioxaphosphorinan-2-ones α-lithiated carbanions. Synthesis, stability, and conformation (1990)

The preparation and a conformational study of lithiated 2-alkyl-5,5-dimethyl-1,3,2-dioxaphosphorinan-2-ones (2) in THF–hexane are described. These anions are present as two rapidly interconverting species with the PO bond either axial (2a) or equatorial (2e). They are thermally unstable, but can be stabilised by the presence of one equivalent of LiBr or of lithium di-isopropylamide. A 31P NMR study of the self condensation of the carbanions (2) showed that the phosphorus atom in the axial conformation (2a) is more electrophilic than in the equatorial one (2e). An X-ray structural study of 2,5,5-trimethyl-1,3,2-dioxaphosphorinan-2-one is described.
Association of Chronic Lyme Arthritis with HLA-DR4 and HLA-DR2 Alleles (1990)

Particular Class II major histocompatibility genes determine a host immune response to B. burgdorferi that results in chronic arthritis and lack of response to antibiotic therapy.
Cloning of a Mouse β1,3N-Acetylglucosaminyltransferase GlcNAc(β1,3)Gal(β1,4)Glc-ceramide Synthase Gene Encoding the Key Regulator of Lacto-series Glycolipid Biosynthesis (2001)

The distinction between the different classes of glycolipids is conditioned by the action of specific core transferases. The entry point for lacto-series glycolipids is catalyzed by the beta1,3 N-acetylglucosaminyltransferase GlcNAc(beta1,3)Gal(beta1,4)Glc-ceramide (Lc3) synthase enzyme. The Lc3 synthase activity has been shown to be regulated during development, especially during brain morphogenesis. Here, we report the molecular cloning of a mouse gene encoding an Lc3 synthase enzyme. The mouse cDNA included an open reading frame of 1131 base pairs encoding a protein of 376 amino acids. The Lc3 synthase protein shared several structural motifs previously identified in the members of the beta1,3 glycosyltransferase superfamily. The Lc3 synthase enzyme efficiently utilized the lactosyl ceramide glycolipid acceptor. The identity of the reaction products of Lc3 synthase-transfected CHOP2/1 cells was confirmed by thin-layer chromatography immunostaining using antibodies TE-8 and 1B2 that recognize Lc3 and Gal(beta1,4)GlcNAc(beta1,3)Gal(beta1,4)Glc-ceramide (nLc4) structures, respectively. In addition to the initiating activity for lacto-chain synthesis, the Lc3 synthase could extend the terminal N-acetyllactosamine unit of nLc4 and also had a broad specificity for gangliosides GA1, GM1, and GD1b to generate neolacto-ganglio hybrid structures. The mouse Lc3 synthase gene was mainly expressed during embryonic development. In situ hybridization analysis revealed that that the Lc3 synthase was expressed in most tissues at embryonic day 11 with elevated expression in the developing central nervous system. Postnatally, the expression was restricted to splenic B-cells, the placenta, and cerebellar Purkinje cells where it colocalized with HNK-1 reactivity. These data support a key role for the Lc3 synthase in regulating neolacto-series glycolipid synthesis during embryonic development.
Biological activity of some naturally occurring resins, gums and pigments against in vitro LDL oxidation (2003)

Abstract Naturally occurring gums and resins with beneﬁcial pharmaceutical and nutraceutical properties were tested for their possible protective effect against copper‐induced LDL oxidation in vitro . Chios mastic gum (CMG) ( Pistacia lentiscus var. Chia resin) was the most effective in protecting human LDL from oxidation. The minimum and maximum doses for the saturation phenomena of inhibition of LDL oxidation were 2.5 mg and 50 mg CMG (75.3% and 99.9%, respectively). The methanol/water extract of CMG was the most effective compared with other solvent combinations. CMG when fractionated in order to determine a structure–activity relationship showed that the total mastic essential oil, collofonium‐like residue and acidic fractions of CMG exhibited a high protective activity ranging from 65.0% to 77.8%. The other natural gums and resins (CMG resin ‘liquid collection’, P. terebinthus var. Chia resin, dammar resin, acacia gum, tragacanth gum, storax gum) also tested as above, showed 27.0%–78.8% of the maximum LDL protection. The other naturally occurring substances, i.e. triterpenes (amyrin, oleanolic acid, ursolic acid, lupeol, 18‐a‐glycyrrhetinic acid) and hydroxynaphthoquinones (naphthazarin, shikonin and alkannin) showed 53.5%–78.8% and 27.0%–64.1% LDL protective activity, respectively. The combination effects (68.7%–76.2% LDL protection) of ursolic‐, oleanolic‐ and ursodeoxycholic‐ acids were almost equal to the effect (75.3%) of the CMG extract in comparable doses. Copyright © 2003 John Wiley &amp; Sons, Ltd.
Facet‐Free Selective Silicon Epitaxy by Reduced‐Pressure Chemical Vapor Deposition Process Evaluation and Impact on Shallow Trench Isolation (1999)

A facet‐free, selective epitaxy process has been identified using the chemistry in single‐wafer reduced‐pressure chemical vapor deposition. The process window has been explored with respect to shallow trench isolation, simultaneous polycrystalline silicon (polysilicon) deposition, facet formation, and electrical parameters of polysilicon sheet resistance and junction leakage current. The isolation structure can be severely degraded by aggressive pre‐epitaxy bakes through volatile SiO formation; however, the impact is minimized when the prebake is limited to 900°C, 60 s. Concurrent deposition of polysilicon and silicon epitaxy can result in significantly different deposition rates. Low process pressures result in greater relative epitaxy growth rates and high pressures result in lower relative epitaxy deposition rates. The facet‐free process depends heavily on both the gate sidewall structure and the process conditions, where the combination of an undercut into the pad oxide and the nitride sidewall with the process pressure yield a reliably facet‐free process. Electrical results demonstrate that standard Ti or Co self‐aligned silicidation can be extended into a 0.1 μm gate length regime. © 1999 The Electrochemical Society. All rights reserved.
Rapid Evolution of Reversible Denaturation and Elevated Melting Temperature in a Microbial Haloalkane Dehalogenase (2001)

Haloalkane dehalogenases have the potential for use in high-value biocatalytic processes to convert haloalkanes into epoxides via intermediate haloalcohols. Initial bioreactor studies probing the hydrolysis of 1,2,3-trichloropropane by immobilized wild-type dehalogenase isolated from Rhodococcus rhodochrous demonstrated, however, that productivity was too low to realize a commercially viable process. A strategy to increase enzyme performance was undertaken to increase the reaction temperature, however it was determined that the wild-type enzyme was not stable for long periods of time at elevated temperatures. The accelerated laboratory evolution technique of Gene Site Saturation Mutagenesis (GSSM TM) was used to create a clonal enzyme library comprising all single site sequence variants of the Rhodococcus enzyme. Using high throughput screening techniques and rapid kinetics assays, this library was probed for improvements in thermostability and for the ability of the enzyme to undergo a fully reversible cycle of thermal denaturation-renaturation. Eight single site mutants were discovered that had considerable effects on these aspects of the dehalogenase phenotype. Compared to the parental dehalogenase (t1/2 = 11 minutes at 55 °C) single site variants have half-lives ranging from 300 minutes to 2700 minutes. Combinations of these mutations dramatically improved the half-life demonstrating the enhancing effects of mutational additivity. Combining five of the mutations into a single protein (Dhla5) improved the half-life to 29,000 min and a combination of all eight single-site mutations (Dhla8) increased the half-life by another factor of ten. Thus, the final Dhla8 protein was 30,000 times more stable than the parent molecule as measured by its ability to refold after denaturation at high temperature. Kinetic analysis showed that the improvement in thermal stability associated with Dhla5 did not negatively affect the rate of catalysis at ambient temperature, and allowed a significant increase in rate with no deactivation at 55 °C. Differential scanning calorimetry demonstrated that mutational combinations in both Dhla5 and Dhla8 led to an 8 °C increase in Tm and substantiated that partial reversibility (Dhla5) and full reversibility of Dhla8. Thermal denaturation of Dhla8 was fully reversible upon scanning up to 90 °C. Bioreactor studies showed that improved thermal stability of Dhla5 and Dhla8 correlated qualitatively with increased productivity when haloalkane hydrolysis was conducted using immobilized forms of these evolved enzymes under high temperature conditions.