gebhart/patrepeval huggingface dataset:
Substrate Specificity of the RND-Type Multidrug Efflux Pumps AcrB and AcrD of Escherichia coli Is Determined Predominately by Two Large Periplasmic Loops (2002)

AcrAB-TolC is a constitutively expressed, tripartite efflux transporter complex that functions as the primary resistance mechanism to lipophilic drugs, dyes, detergents, and bile acids in Escherichia coli. TolC is an outer membrane channel, and AcrA is an elongated lipoprotein that is hypothesized to span the periplasm and coordinate efflux of such substrates by AcrB and TolC. AcrD is an efflux transporter of E. coli that provides resistance to aminoglycosides as well as to a limited range of amphiphilic agents, such as bile acids, novobiocin, and fusidic acid. AcrB and AcrD belong to the resistance nodulation division superfamily and share a similar topology, which includes a pair of large periplasmic loops containing more than 300 amino acid residues each. We used this knowledge to test several plasmid-encoded chimeric constructs of acrD and acrB for substrate specificity in a marR1 DeltaacrB DeltaacrD host. AcrD chimeras were constructed in which the large, periplasmic loops between transmembrane domains 1 and 2 and 7 and 8 were replaced with the corresponding loops of AcrB. Such constructs provided resistance to AcrB substrates at levels similar to native AcrB. Conversely, AcrB chimeras containing both loops of AcrD conferred resistance only to the typical substrates of AcrD. These results cannot be explained by simply assuming that AcrD, not hitherto known to interact with AcrA, acquired this ability by the introduction of the loop regions of AcrB, because (i) both AcrD and AcrA were found, in this study, to be required for the efflux of amphiphilic substrates, and (ii) chemical cross-linking in intact cells efficiently produced complexes between AcrD and AcrA. Since AcrD can already interact with AcrA, the alterations in substrate range accompanying the exchange of loop regions can only mean that substrate recognition (and presumably binding) is determined largely by the two periplasmic loops.
Vesicle-associated Membrane Protein 2 Is Essential for cAMP-regulated Exocytosis in Rat Parotid Acinar Cells (1996)

Amylase exocytosis of the parotid gland is mediated by intracellular cAMP. To investigate whether cAMP-dependent secretion has a mechanism similar to that of regulated neuroexocytosis, we examined the expression of synaptosome-associated proteins. In rat parotid acinar cells, we found 25 (p25) and 18 kDa (p18) proteins reacted with antibodies against Rab3A and vesicle-associated membrane protein 2 (VAMP-2), respectively. On the other hand, syntaxin 1 and SNAP-25, which interact with VAMP-2 at synapses, were undetectable. Rab3A-like p25 and VAMP-2-like p18 were also expressed in other exocrine acinar cells. The latter was localized at secretory granule membranes, and the former was detected in secretory granule and cytosolic fractions. The antibody against VAMP-2 used in this study did not react with cellubrevin, and p18 was cleaved with botulinum neurotoxin B. Thus, we identified p18 as VAMP-2. Botulinum neurotoxin B inhibited the cAMP-induced amylase release from streptolysin O-permeabilized acinar cells. Therefore, VAMP-2 is required for cAMP-regulated amylase release in rat parotid acinar cells. This is the first report that VAMP-2 is involved in regulated exocytosis that is independent of Ca2+. Amylase exocytosis of the parotid gland is mediated by intracellular cAMP. To investigate whether cAMP-dependent secretion has a mechanism similar to that of regulated neuroexocytosis, we examined the expression of synaptosome-associated proteins. In rat parotid acinar cells, we found 25 (p25) and 18 kDa (p18) proteins reacted with antibodies against Rab3A and vesicle-associated membrane protein 2 (VAMP-2), respectively. On the other hand, syntaxin 1 and SNAP-25, which interact with VAMP-2 at synapses, were undetectable. Rab3A-like p25 and VAMP-2-like p18 were also expressed in other exocrine acinar cells. The latter was localized at secretory granule membranes, and the former was detected in secretory granule and cytosolic fractions. The antibody against VAMP-2 used in this study did not react with cellubrevin, and p18 was cleaved with botulinum neurotoxin B. Thus, we identified p18 as VAMP-2. Botulinum neurotoxin B inhibited the cAMP-induced amylase release from streptolysin O-permeabilized acinar cells. Therefore, VAMP-2 is required for cAMP-regulated amylase release in rat parotid acinar cells. This is the first report that VAMP-2 is involved in regulated exocytosis that is independent of Ca2+.
AUTOMATIC ASSESSMENT OF SECOND LANGUAGE LEARNERS' FLUENCY (1999)

This paper describes an experiment aimed at determining whether speech. automatic assessment of second language learners’ fluency in This experiment produced interesting results in two respects, spontaneous speech is feasible a nd whether it differs from a. fluency assessment by expert raters and b . the relationship a utomatic fluency assessment in read speech. Spontaneous speech between expert f luency ratings and automatically obtained objective of 60 learners of Dutch was scored for fluency by five raters and f luency measures. With regard to a., the results showed that expert was analyzed b y means of a c ontinuous s peech recognizer to r atings of fluency in read speech are reliable (Cronbachs’ varies ca lculate seven quantitative m easures of speech quality known to be between .90 and .96). With respect t o b ., very high correlations related to p erceived fluency. The results s how that automatic were found b etween the expert fluency ratings and the automatic assessm ent of second language learners’ fluency in spontaneous m easures of fluency: five automatic measures showed correlations s peech is feasible, although not all variables suitable for measuring with the fluency scores whose magnitude varied between .77 and fluency in read speech are as effective in spontaneous speech. In . 91. The highest correlations were found f or rate of speech (between particular, m easures that express the rate a t which sounds are .86 and .91). Further analyses revealed that t wo factors are produced w ithout t aking pauses into account appear to b e important f or perceived fluency in read speech: the rate at which unsuitable f or measuring fluency in spontaneous speech. s peakers articulate the sounds and the number of pauses they make. Furthermore, the correlations between machine scores and human Rate of speech appears to be such a good predictor of perceived r atings are lower for spontaneous speech. Possible explanations are f luency because it incorporates these two aspects. discussed. Since automatic assessment of fluency in read speech turned
Neurotoxicity Induced by Antiepileptic Drugs in Cultured Hippocampal Neurons: A Comparative Study between Carbamazepine, Oxcarbazepine, and Two New Putative Antiepileptic Drugs, BIA 2‐024 and BIA 2‐093 (2004)

In all parameters assayed, OXC was more toxic than the other AEDs used. Because the new putative AEDs have previously been shown to have an efficacy in preventing seizures similar to that of CBZ and OXC, and are less toxic to neuronal cells, they may be considered as alternatives to the current available therapies for the treatment of epilepsy.
Postoperative patient‐controlled analgesia with sufentanil: analgesic efficacy and minimum effective concentrations (1991)

Sufentanil has so far seldom been used for intravenous postoperative patient-controlled analgesia (PCA), and the resulting serum concentrations have not yet been determined. Forty ASA I-III patients recovering from major gynecological operations were investigated to evaluate analgesic efficacy, side effects, patient acceptance and threshold concentrations of sufentanil in serum during the early postoperative period, using the On-Demand Analgesia Computer (ODAC). Following an individualized intravenous loading dose of 19.1 +/- 35.7 micrograms (mean +/- 1 s.d.), sufentanil demand doses were 6 micrograms with a concurrent infusion of 1.15 micrograms/h and a maximum hourly dose of 40 micrograms/h; the lockout time was set to 1 min. The duration of PCA was 17.3 +/- 2.1 h. During this time 16 +/- 11 demands per patient were recorded, resulting in an average sufentanil consumption of 131.1 +/- 69.4 micrograms or 7.5 +/- 3.7 micrograms/h (including loading dose). analgesia was mostly judged good. Side effects were only of minor intensity. Sufentanil proved to be about 2.2 to 3.8 times as potent an analgesic as fentanyl when both analgesic effect and duration were considered. Minimum effective sufentanil serum concentration (MEC) as determined by radioimmunoassay varied greatly and could be best described by a log-normal distribution (range less than 0.01-0.56 ng/ml, median 0.024 ng/ml). Intraindividual MEC variability was slightly lower than intersubject variability (76.0 vs. 84.8%). It is concluded that sufentanil is suitable for postoperative PCA. To get into the therapeutic window for analgesia, a serum sufentanil concentration of more than 0.03 ng/ml seems to be necessary.
Characterization of Maize Chlorotic Mottle Virus (1991)

Maize chlorotic mottle virus (MCMV) is an icosahedral plant virus 30 nm in diameter, composed of a single 25-kDa capsid protein subunit and a 4.4-kb single-stranded, positive-sense genomic RNA. The genomic RNA is capped at the 5'terminus with m 7 GpppA, and no genome-linked protein was detected. MCMV infection produces two discrete double-stranded RNA species in infected maize plants, corresponding to single-stranded RNAs of 4.4 and 1.1 kb (...)
Sterol Specificity of Pancreatic Cholesterol Esterase. (1954)

Pancreatic cholesterol esterase catalyzes the esterincation and hydrolysis of a number of different sterols and sterol esters. The order of activity observed in the esterifying system with oleic acid was as follows: dihydrocholesterol cholesterol β-sitosterol sitosterol stigmasterol ergosterol. Of these sterols, only dihydrocholesterol and cholesterol were esterified with butyric acid. In the hydrolytic system all of the sterol butyrates tested were split very rapidly, with the exception of ergosterol butyrate. the order of splitting of the oleates in the first 4 hours was: cholesterol oleate sitosterol oleate stigmasterol oleate ergosterol oleate. The relation of enzyme activity to sterol structure is discussed.
Differential effects of PCSK9 loss of function variants on serum lipid and PCSK9 levels in Caucasian and African Canadian populations (2013)

We showed that the L10A53V and I474V PCSK9 variants were significantly associated with lower LDLC levels in Caucasian Canadians but differed in their effect on serum PCSK9 concentrations, illuminating differences in their mechanism of inaction and indicating that that PCSK9 measurement alone may not always be a good indicator of PCSK9 function.Full exonic sequencing of PCSK9 pointed to factors that may contribute to L10Ins PCSK9 variant loss of function in Canadians of Caucasian but not those of African descent. These included; (1) its tight linkage with the A53V variant in Caucasians and/or (2) for both the L10 and I474V, the combined (and negating) effect of multiple, differing phenotypic PCSK9 variants within individuals of African ancestry for which combinations of PCSK9 variations and their overall frequency was higher. No population studies, to our knowledge, have addressed or accessed the effect of multiple PCSK9 variants on cholesterol profiles. Our results indicate that this should be considered.
Bub1: Escapades in a Cellular World (2007)

The spindle assembly checkpoint is an important surveillance mechanism that ensures high fidelity mitotic chromosome segregation. This is accomplished by monitoring whether sister chromatids lack tension or attachment to spindle microtubules. It is mediated by checkpoint complexes or individual proteins that inhibit the ubiquitin ligase activity of the anaphase-promoting complex/cyclosome (APC/C) via targeting of the Cdc20 regulatory subunit. The Bub1 kinase is a key spindle checkpoint regulatory protein. Bub1 also plays more pleiotropic roles. Thus, Bub1 is required for assembly of a functional inner centromere, sister chromatid cohesion via targeting of the Shugoshin protein, and metaphase congression. Evidence based on Bub1 mutations in colorectal cancers suggests it might be a driving force in tumorigenesis via generation of chromosomal instability (CIN) and aneuploidy. Recently we reported a surveillance mechanism linking loss of Bub1 to activation of the p53 pathway, specifically premature cell senescence in normal human fibroblasts. Interestingly, SV40 large T antigen (LT) targets Bub1 and this is correlated with oncogenic transformation and compromise of the spindle checkpoint. Future studies on Bub1 combining genetic approaches with analysis of LT perturbations are likely to yield further insight.
Carbohydrate-deficient glycoprotein syndrome type Ib. Phosphomannose isomerase deficiency and mannose therapy. (1998)

Phosphomannose isomerase (PMI) deficiency is the cause of a new type of carbohydrate-deficient glycoprotein syndrome (CDGS). The disorder is caused by mutations in the PMI1 gene. The clinical phenotype is characterized by protein-losing enteropathy, while neurological manifestations prevailing in other types of CDGS are absent. Using standard diagnostic procedures, the disorder is indistinguishable from CDGS type Ia (phosphomannomutase deficiency). Daily oral mannose administration is a successful therapy for this new type of CDG syndrome classified as CDGS type Ib.
Method for the Quantification of Diamorphine and its Metabolites in Pediatric Plasma Samples by Liquid Chromatography-Tandem Mass Spectrometry (2010)

In recent years, intranasal diamorphine (DIM) has been recommended as an alternative to intravenous administration for the treatment of acute-to-severe pain in children. This provides a rapid and less painful route of administration without decreasing the effectiveness of the analgesic properties. A sensitive technique for the detection and quantitation of DIM and its metabolites is essential because of the low concentrations of DIM and metabolites in children's plasma, which are a result of the low dose of DIM given and the limited sample volume obtained from children (0.25 mL or less). DIM can be easily hydrolyzed to 6-monoacetylmorphine (6-MAM) during sample preparation and extraction, so this must be considered when developing a solid-phase extraction (SPE) method to prevent the hydrolysis of DIM. This work was aimed at validating and developing a liquid chromatography-tandem mass spectrometry (LC-MS-MS) method with electrospray ionization for the identification and quantification of DIM and its metabolites, namely 6-MAM, MOR, M3G, M6G, and NMOR in plasma samples obtained from children who are under treatment for acute-to-severe pain. Following the addition of deuterated internal standards, analytes were extracted by SPE with Bond Elut C(18) cartridges followed by LC-MS-MS analysis. Intraday and interday precision for all analytes were determined at five concentration (1, 5, 25, 50, and 200 ng/mL), and these were found to be 2.5-13.4% and 1.8-15%, respectively. Recoveries of analytes of interest were between 81 and 109%. Calibration curves were linear for all analytes over the concentration range 0.1-50 ng/mL, and correlation coefficients were better than 0.999. Limits of detection and quantitation were 0.08-0.37 ng/mL and 0.28-1.22 ng/mL, respectively. DIM and metabolites were detected in all case samples with the exception of NMOR, which tested negative in all cases. The pharmacokinetics of DIM and its metabolites following INDIM and IVDIM administration in children have been compared for the first time in this study, which confirmed that INDIM can achieve therapeutic plasma concentrations of DIM and its active metabolites, although these are lower than those obtained with IVDIM and occur at later times after administration.
Gastric and oesophageal emptying in insulin‐dependent diabetes mellitus (1986)

Abstract Gastric emptying of a digestible solid and liquid meal and oesophageal emptying of a solid bolus were measured with scintigraphic techniques in 45 randomly selected insulin‐dependent diabetics and in 22 control subjects. In the diabetics, the relationships between oesophageal emptying, gastric emptying, age, duration of diabetes mellitus, upper gastrointestinal symptoms, glycaemic control and the complications, autonomic neuropathy, peripheral neuropathy and retinopathy were examined. The lag period before solid food left the stomach was not significantly different in diabetics compared with control subjects, but the percentage retention of solid food at 100 min was greater ( P &lt; 0.001) in the diabetic subjects. Both the early phase (percentage retention at 10 min) and the 50% emptying time for liquid gastric emptying were delayed ( P &lt; 0.001) in the diabetic subjects. Of the diabetics, 58% had delayed gastric emptying of either the solid and/or the liquid meal; oesophageal emptying was delayed in 42%. Upper gastrointestinal symptoms correlated poorly with both gastric and oesophageal emptying. Oesophageal emptying, solid gastric emptying and the liquid 50% emptying time correlated with the severity of autonomic nerve dysfunction ( P &lt; 0.05). The early phase of liquid emptying (retention at 10 min) was significantly slower ( P &lt; 0.05) in patients with mean plasma glucose concentrations of &gt; 15 mmol/l during the gastric emptying test and the lag period for solid emptying correlated with both the glycosylated haemoglobin and mean plasma glucose concentrations.
Buffer free direct growth of GaN on 6H–SiC by metalorganic vapor phase epitaxy (2000)

The growth of GaN on 6H–SiC is three dimensional (3D) and results in the formation of large islands presenting hexagonal truncated shape with {1–101} lateral facets and a top {0001} facet. In this work, we present a three steps growth process that enables us to grow high quality mirrorlike GaN layers without using AlN buffer layers. During a first step, a thin 3D GaN layer is deposited at high temperature. This layer is smoothed under ammonia flow for several minutes when the growth is interrupted. The subsequent growth of GaN is two dimensional. 600 nm thick GaN films were grown. They were analyzed by high resolution x-ray diffraction, reflectivity, and photoluminescence. All the layers are under strong tensile biaxial strain. The correlation between residual tensile strain in GaN layers and their optical properties is reported for biaxial deformations εxx ranging up to 0.37%.
A new fuzzy clustering validity criterion and its application to color image segmentation (2002)

A new strategy for the determination of the degree of validity of a fuzzy partition is introduced. The strategy is mathematically justified via its relation to hard partition validity measures. The relationship between this fuzzy validity function and the most general, and well defined, hard clustering validity function (the separation index of J.C. Dunn (1974)) for which the condition of uniqueness has already been established is derived. Using this relationship, the existence of a unique fuzzy c-partition produced by the fuzzy validity function is also proved. Examples of applications to segmentation of color image for IC defects give encouraging results.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A Highly Conserved Arginine Is Critical for the Functional Folding of Inhibitor of Apoptosis (IAP) BIR Domains (2002)

The inhibitor of apoptosis (IAP) proteins are found in all animals and regulate apoptosis (programmed cell death) by binding and inhibiting caspase proteases. This inhibition is overcome by several apoptosis stimulators, including Drosophila Hid and mammalian Smac/DIABLO, which bind to 65-residue baculovirus IAP repeat (BIR) domains found in one to three copies in all IAPs. Virtually all BIRs contain three Cys and a His that bind zinc, a Gly in a tight turn, and an Arg. The functional and structural role of the Arg was investigated in isolated BIR domains from the baculovirus Orgyia pseudotsugata Op-IAP and the Drosophila DIAP1 proteins. Mutation of the Arg to either Ala or Lys abolished Hid and Smac binding to BIRs, despite the Hid/Smac binding site being located on the opposite side of the BIR domain from the Arg. The mutant BIR domains also exhibited weakened zinc binding, increased sensitivity to limited proteolysis, and altered circular dichroism spectra indicative of perturbed domain folding. Examination of known BIR structures indicates that the Arg side chain makes simultaneous bridging hydrogen bonds and a cation-pi interaction for which the Arg guanidino group is uniquely well suited. These interactions are likely critical for stabilizing the tertiary fold of BIR domains in all IAPs, explaining the conservation of this residue.
Dual bioluminescence and near-infrared fluorescence monitoring to evaluate spherical nucleic acid nanoconjugate activity in vivo (2017)

RNA interference (RNAi)-based gene regulation platforms have shown promise as a novel class of therapeutics for the precision treatment of cancer. Techniques in preclinical evaluation of RNAi-based nanoconjugates have yet to allow for optimization of their gene regulatory activity. We have developed spherical nucleic acids (SNAs) as a blood-brain barrier-/blood-tumor barrier-penetrating nanoconjugate to deliver small interfering (si) and micro (mi)RNAs to intracranial glioblastoma (GBM) tumor sites. To identify high-activity SNA conjugates and to determine optimal SNA treatment regimens, we developed a reporter xenograft model to evaluate SNA efficacy in vivo. Engrafted tumors stably coexpress optical reporters for luciferase and a near-infrared (NIR) fluorescent protein (iRFP670), with the latter fused to the DNA repair protein O<sup>6</sup>-methylguanine-DNA-methyltransferase (MGMT). Using noninvasive imaging of animal subjects bearing reporter-modified intracranial xenografts, we quantitatively assessed MGMT knockdown by SNAs composed of MGMT-targeting siRNA duplexes (siMGMT-SNAs). We show that systemic administration of siMGMT-SNAs via single tail vein injection is capable of robust intratumoral MGMT protein knockdown in vivo, with persistent and SNA dose-dependent MGMT silencing confirmed by Western blotting of tumor tissue ex vivo. Analyses of SNA biodistribution and pharmacokinetics revealed rapid intratumoral uptake and significant intratumoral retention that increased the antitumor activity of coadministered temozolomide (TMZ). Our study demonstrates that dual noninvasive bioluminescence and NIR fluorescence imaging of cancer xenograft models represents a powerful in vivo strategy to identify RNAi-based nanotherapeutics with potent gene silencing activity and will inform additional preclinical and clinical investigations of these constructs.
Secretion bySaccharomyces cerevisiaeof Human Apolipoprotein E as a Fusion to Serum Albumin (1995)

For secretion of human apolipoprotein E (hApoE) by Saccharomyces cerevisiae, the hApoE gene was fused to truncated human serum albumin (HSA)-encoding sequences and expressed under the control of the GAL7 promoter. When the mature region of the hApoE gene was fused to the HSA-encoding sequence without its pro-region and expressed in galactose-containing medium, the HSA-hApoE fusion protein was efficiently secreted into the medium at a maximum yield of 6.3 mg per liter.