gebhart/patrepeval huggingface dataset:
A Classification of SQL-Injection Attacks and Countermeasures (2006)

Differentiation in habitat selection among sympatric species may depend on niche partitioning, species interactions, selection mechanisms and scales considered. In a mountainous area in Sweden, we explored hierarchical habitat selection in Global Positioning System-collared individuals of two sympatric large carnivore species; an obligate predator, the Eurasian lynx (Lynx lynx), and a generalist predator and scavenger, the wolverine (Gulo gulo). Although the species' fundamental niches differ widely, their ranges overlap in this area where they share a prey base and main cause of mortality. Both lynx and wolverines selected for steep and rugged terrain in mountainous birch forest and in heaths independent of scale and available habitats. However, the selection of lynx for their preferred habitats was stronger when they were forming home ranges and they selected the same habitats within their home ranges independent of home range composition. Wolverines displayed a greater variability when selecting home ranges and habitat selection also varied with home range composition. Both species selected for habitats that promote survival through limited encounters with humans, but which also are rich in prey, and selection for these habitats was accordingly stronger in winter when human activity was high and prey density was low. We suggest that the observed differences between the species result primarily from different foraging strategies, but may also depend on differences in ranging and resting behaviour, home range size, and relative density of each species. Our results support the prediction that sympatric carnivores with otherwise diverging niches can select for the same resources when sharing main sources of food and mortality.
Reduction of in‐source collision‐induced dissociation and thermolysis of sulopenem prodrugs for quantitative liquid chromatography/electrospray ionization mass spectrometric analysis by promoting sodium adduct formation (2008)

Six chromatographically resolved sulopenem prodrugs were monitored for their potential to undergo both in-source collision-induced dissociation (CID) and thermolysis. Initial Q1 scans for each prodrug revealed the formation of intense [Prodrug2 + H]+, [Prodrug2 + Na]+, [Prodrug + Na]+, and [Sulopenem + Na]+ ions. Non-adduct-associated sulopenem ([Sulopenem + H]+) along with several additional lower mass ions were also observed. Product ion scans of [Prodrug3 + Na]+ showed the retention of the sodium adduct in the collision cell continuing down to opening of the beta-lactam ring. In-source CID and temperature experiments were conducted under chromatographic conditions while monitoring several of the latter ion transitions (i.e., adducts, dimers and degradants/fragments) for a given prodrug. The resulting ion profiles indicated the regions of greatest stability for temperature and declustering potential (DP) that provided the highest signal intensity for each prodrug and minimized in-source degradation. The heightened stability of adduct ions, relative to their appropriate counterpart (i.e., dimer to dimer adduct and prodrug to prodrug adduct ions), was observed under elevated temperature and DP conditions. The addition of 100 microM sodium to the mobile phase further enhanced the formation of these more stable adduct ions, yielding an optimal [Prodrug + Na]+ ion signal at temperatures from 400 to 600 degrees C. A clinical liquid chromatography/tandem mass spectrometry (LC/MS/MS) assay for sulopenem prodrug PF-04064900 in buffered whole blood was successfully validated using sodium-fortified mobile phase and the [PF-04064900 + Na]+ ion for quantitation. A conservative five-fold increase in sensitivity from previously validated preclinical assays using the [PF-04064900 + H]+ precursor ion was achieved.
FGF21 Requires βklotho to Act In Vivo (2012)

FGF21 has gradually become a focal point in metabolic research given its intriguing and complex biology and relevance to drug discovery. Despite the large amount of accumulated data, there remains a dearth of understanding of FGF21 physiology at the molecular/whole organism level. The scaffold protein βklotho (KLB) has previously been demonstrated in vitro to function as a co-factor permitting FGF21 mediated FGF receptor activation. However, the requirement for KLB in the propagation of FGF21 action in living animals has yet to be evaluated. To answer this question, we tested FGF21 in mice with total body ablation of KLB (KLBKO) and found no detectable activity. Firstly, we demonstrate that the disruption of KLB entirely abrogates acute FGF21 signaling in adipose tissue. We go on to show that this signaling defect translates to the absence of FGF21 mediated metabolic improvements in DIO mice. Indeed, KLBKO mice are totally refractory to FGF21-induced normalization of glucose homeostasis, attenuation of dyslipidemia, elevation of energy expenditure and weight loss. The lack of FGF21-driven effects was further substantiated at the transcriptional level with no FGF21 target gene signature detectable in adipose tissue and liver of KLBKO animals. Taken together our data show that KLB is a vital component of the FGF21 in vivo signaling machinery and is critically required for FGF21 action at the whole organism level.
Facile, Fast and Safe Process Development of Nitration and Bromination Reactions Using Continuous Flow Reactors (2009)

Chemists working in a pilot plant often face safety issues during scale-up operations. With the help of emerging microfluidic applications and microdevices, running hazardous, highly exothermic or potentially unstable reactions can be easily transposed into a safe continuous flow mode. This paper describes how a potentially hazardous pyrazole nitration and the bromination of a variety of electron-rich heteroaromatic substrates were efficiently performed using a cheap and easily available system for bench chemists. Advantages of the continuous flow mode in organic synthetic chemistry will be exemplified by the large-scale production of raw materials under safe, green and reproducible conditions.
Effects of an Engineered Human Anti–TNF-α Antibody (CDP571) on Insulin Sensitivity and Glycemic Control in Patients With NIDDM (1996)

Inhibition of tumor necrosis factor (TNF)-alpha action has recently been shown to reverse insulin resistance dramatically and to improve glycemic control in obese rodents. This double-blind study was designed to assess the effects of a recombinant-engineered human TNF-alpha-neutralizing antibody (CDP571) on glucose homeostasis in obese NIDDM patients. Glycemic control and insulin sensitivity were monitored in 21 NIDDM subjects for a 2-week run-in and then for 6 weeks after treatment in a randomized fashion with a single intravenous dose of either CDP571 (5 mg/kg) or an equivalent volume of normal saline. The prolonged half-life of the antibody ensured adequate plasma levels as measured throughout the study. Concentrations of fasting glucose (CDP571: 10.0 +/- 0.8, 10.1 +/- 0.8, 10.0 +/- 1.0; placebo: 8.5 +/- 0.6, 8.1 +/- 0.5, 8.7 +/- 0.8 mmol/l at baseline, day 1, and week 4, respectively), fasting serum insulin (CDP571: 21.2 +/- 2.8, 21.0 +/- 2.8, 24.8 +/- 3.3; placebo: 19.0 +/- 2.8, 20.8 +/- 2.9, 17.5 +/- 2.2 pmol/l, respectively), and C-peptide remained unaffected by the type of treatment throughout the study. The percentage rate of glucose clearance per minute (KITT) during intravenous insulin sensitivity tests was identical in the CDP571 and placebo groups at baseline and also at 1 and 4 weeks after treatment (mean +/- SE; CDP571: 1.33 +/- 0.21, 1.44 +/- 0.25, 1.26 +/- 0.18; placebo: 1.38 +/- 0.15, 1.47 +/- 0.20, 1.52 +/- 0.20; P = 0.85, 0.93, and 0.36, respectively). TNF-alpha neutralization over a period of 4 weeks had no effect on insulin sensitivity in obese NIDDM subjects.
Pharmacokinetics and Safety of Viramidine, a Prodrug of Ribavirin, in Healthy Volunteers (2004)

Ribavirin, part of the current first-line combination therapy for the treatment of chronic hepatitis C, has side effects-in particular, hemolytic anemia-that is frequently dose limiting. Based on animal studies, viramidine, a prodrug of ribavirin, is converted to ribavirin in the liver. Viramidine dosing yielded 50% higher ribavirin levels in the monkey liver but only half in plasma and red blood cells compared to ribavirin dosing. At the same dose, it also had a safer profile than ribavirin in a 28-day toxicity study in monkeys. The current study was carried out to evaluate the safety, tolerability, and pharmacokinetics of viramidine in healthy male volunteers (n = 8-18 on viramidine vs. 2 on placebo at each dose level) after oral dosing of viramidine at 200, 600, and 1200 mg. There were no serious adverse events, and most adverse events were mild. The percentages of treatment-emergent events judged to be possibly related to the study drug were 50% in the 1200-mg group, 26% in the 600-mg group, and none in the 200-mg group. Viramidine was orally absorbed and rapidly converted to ribavirin with a t(max) of 1.5 to 3.0 hours for both viramidine and ribavirin in plasma. There was dose proportionality in plasma AUC(0-168 h) and C(max) for viramidine and in plasma AUC(0-168 h) for ribavirin. Plasma AUC(0-168 h) for ribavirin was two to four times higher than plasma AUC(0-168 h) for viramidine, indicating that viramidine is extensively metabolized to ribavirin and is a prodrug of ribavirin in man. Amounts of viramidine and ribavirin excreted in the urine were small (2%-5% of dose), indicating that the main route of elimination for both viramidine and ribavirin is metabolism. Both viramidine and ribavirin were excreted into urine through the mechanism of glomerular filtration. In addition, an evaluation of the effect of a high-fat meal on the pharmacokinetics of viramidine and ribavirin after oral dosing of viramidine at 600 mg was conducted in healthy male volunteers (n = 33-34) in a crossover study design. A high-fat meal increased viramidine plasma AUC(0-168 h) by 44% and C(max) by 20%. It also increased ribavirin plasma AUC(0-168 h) by 19% and C(max) by 43%. The clinical relevance of these increases is unknown.
Construction of a modular dihydrofolate reductase cDNA gene: analysis of signals utilized for efficient expression. (1982)

Dihydrofolate reductase (DHFR) modular genes have been constructed with segments containing the adenovirus major late promoter, a 3' splice site from a variable region immunoglobulin gene, a DHFR cDNA, and portions of the simian virus 40 (SV40) genome. DNA-mediated transfer of these genes transformed Chinese hamster ovary DHFR- cells to the DHFR+ phenotype. Transformants contained one to several copies of the transfected DNA integrated into the host genome. Clones subjected to growth in increasing concentrations of methotrexate eventually gave rise to lines containing several hundred copies of the transforming DNA. Analysis of the DHFR mRNA produced in amplified lines indicated the following. (i) All clones utilize the adenovirus major late promoter for transcription initiation. (ii) A hybrid intron formed by the 5' splice site of the adenovirus major late leader and a 3' splice site from a variable-region immunoglobulin gene is properly excised. (iii) The mRNA is not efficiently polyadenylated at sequences in the 3' end of the DHFR cDNA but rather uses polyadenylation signals downstream from the DHFR cDNA. Three independent clones produce a DHFR mRNA containing SV40 or pBR322 and SV40 sequences, and the RNA is polyadenylated at the SV40 late polyadenylation site. Another clone has recombined into cellular DNA and apparently uses a cellular sequence for polyadenylation. Introduction of a segment containing the SV40 early polyadenylation signal into the 3' end of the DHFR cDNA gene generated a recombinant capable of transforming cells to the DHFR+ phenotype with at least a 10-fold increase in efficiency, demonstrating the necessity for an efficient polyadenylation signal. Attachment of a DNA segment containing the transcription enhancer (72-base pair repeat) of SV40 further increased the biological activity of the modular DHFR gene 50- to 100-fold.
Neurotrophins Elevate cAMP to Reach a Threshold Required to Overcome Inhibition by MAG through Extracellular Signal-Regulated Kinase-Dependent Inhibition of Phosphodiesterase (2003)

Inhibitors of regeneration in myelin, such as myelin-associated glycoprotein (MAG), play an important role in preventing regeneration after CNS injury. Elevation of cAMP, either with dibutyryl-cAMP (db-cAMP) or by priming with a variety of neurotrophins, overcomes inhibition by MAG and myelin. However, activation of cAMP is not generally regarded as a signaling pathway for neurotrophins. Here we show that the NGF-like neurotrophins overcome inhibition by MAG by activating tyrosine kinase receptors. We also show that activation of extracellular signal-regulated kinase (Erk) by BDNF is required to overcome inhibition by MAG, and that activated Erk transiently inhibits phosphodiesterase 4 (PDE4), the enzyme that hydrolyzes cAMP. Inhibition of PDE4 then allows cAMP to increase and so initiates the pathway to overcome inhibition. Furthermore, we also show that basal levels of Erk activation and basal cAMP levels contribute to the effects of db-cAMP by pushing the combined levels of cAMP above a threshold required to overcome inhibition. Together, these results not only show how NGF-like neurotrophins can elevate cAMP and overcome inhibition but also point to a novel mechanism of cross talk in neurons from the Erk to the cAMP signaling pathways.
Transmembrane potential and intracellular potassium ion activity in fetal and maternal liver (1984)

We have compared transmembrane potentials (Em) of maternal liver with Em of fetal liver, and as an initial step to account for differences in Em, we have measured intracellular potassium ion activities (aiK) in both tissues. Paired segments of maternal and fetal (day 17) mouse liver were suffused (15 ml/min) with Krebs' physiologic salt solution equilibrated with 95% 02-5% CO2 (pH 7.3-7.4) at 37 degrees C. To measure Em, cells were impaled with open-tip microelectrodes filled with 0.5 M KCl. Intracellular voltage recordings that were stable +/- 2 mV for at least 10 s were considered valid impalements. Maternal liver mean Em = -41 +/- 1 (SEM) mV, n = V 10 animals. In contrast, fetal liver mean Em = -23 +/- 1 (SEM) mV, n = 10 animals. In the same segments we measured aiK with potassium-selective liquid ion-exchanger microelectrodes. Maternal liver mean aik = 95 +/- 7 (SEM) mM and fetal liver mean aiK = 62 +/- 4 (SEM) mM. in addition, Em and aiK of fetal liver increased to values comparable to those of maternal liver during the first 8 days of neonatal life. The differences of Em and aik between fetal and maternal liver, and the changes in these values that occur in the neonate, may result from activity of a membrane Na-K exchange pump that increases with tissue development.
The chiral bilayer effect stabilizes micellar fibers (1987)

Dihelical fibers several micrometers in length and gels were obtained by spontaneous aggregation of octyl L- and D-gluconamides. The single strands have the thickness of a bimolecular layer. No fibers are formed from the racemate. The tendency of the chiral amphiphiles to aggregate to very long fibers instead of three-dimensional crystals is rationalized with a “chiral bilayer effect”. This effect is caused by the slowness of rearrangements from tail-to-tail hydrophobic bilayers to crystals, in which the molecular sheets are arranged in a head-to-tail fashion. Thermograms which indicate slow rearrangements in ageing gels are also reported.
Properties of Frequency Difference Detectors (1985)

Among other applications, frequency-tracking loops are employed in digital-data receivers, either as a frequency-acquisition aid for phase-locked coherent reception, or as the sole carrier-frequency control for noncoherent reception. This article provides details of design and performance of the frequency-difference detector that lies at the heart of the loop.
A new superfamily of protein-O-fucosyltransferases, 2-fucosyltransferases, and 6-fucosyltransferases: phylogeny and identification of conserved peptide motifs (2003)

The presence of three conserved peptide motifs shared by alpha2-fucosyltransferases, alpha6-fucosyltransferases, the protein-O-fucosyltransferase family 1 (POFUT1) and a newly identified protein-O-fucosyltransferase family 2 (POFUT2), together with evidence that the present genes encoding for these enzymes have originated from a common ancestor by duplication and divergent evolution, suggests that they constitute a new superfamily of fucosyltransferases.
Inhibition of G-Protein Signaling by Dominant Gain-of-Function Mutations in Sst2p, a Pheromone Desensitization Factor in Saccharomyces cerevisiae (1995)

Genetic analysis of cell-cell signaling in Saccharomyces cerevisiae has led to the identification of a novel factor, known as Sst2p, that promotes recovery after pheromone-induced growth arrest (R. K. Chan and C. A. Otte, Mol. Cell. Biol. 2:11-20, 1982). Loss-of-function mutations lead to increased pheromone sensitivity, but this phenotype is partially suppressed by overexpression of the G protein alpha subunit gene (GPA1). Suppression is allele specific, however, suggesting that there is direct interaction between the two gene products. To test this model directly, we isolated and characterized several dominant gain-of-function mutants of SST2. These mutations block the normal pheromone response, including a loss of pheromone-stimulated gene transcription, cell cycle growth arrest, and G protein myristoylation. Although the SST2 mutations confer a pheromone-resistant phenotype, they do not prevent downstream activation by overexpression of G beta (STE4), a constitutively active G beta mutation (STE4Hpl), or a disruption of GPA1. None of the SST2 alleles affects the expression or stability of G alpha. These results point to the G protein alpha subunit as being the direct target of Sst2p action and underscore the importance of this novel desensitization factor in G-protein-mediated signaling.
Memory optimization by counting points in integer transformations of parametric polytopes (2006)

Memory size reduction and memory accesses optimization are crucial issues for embedded systems. In the context of affine programs, these two challenges are classically tackled by array linearization, cache access optimization and memory size computation. Their formalization in the polyhedral model reduce to solving the following problem: count the number of solutions of a Presburger formula.In this paper we propose a novel algorithm that answers this question. We solve the Presburger formula whose solution is a union of parametric Z-polytopes and we propose an algorithm to count points in such a union of parametric Z-polytopes. These algorithms were implemented and we compare them to other existing methods.
Functional significance of dystrophin positive fibres in Duchenne muscular dystrophy. (1993)

The age when boys lose the ability to walk independently is one of the milestones in the progression of Duchenne muscular dystrophy (DMD). We have used this as a measure of disease severity in a group of 30 patients with DMD and six patients with intermediate Duchenne/Becker dystrophy (D/BMD). Dystrophin analysis was performed on tissue sections and western blots of muscle biopsy specimens from these patients and the relationships that were found between clinical severity and abundance of dystrophin labelling are reported. All patients with intermediate D/BMD had dystrophin labelling that was detected on sections and blots. Weak dystrophin labelling was found in sections from 21/30 DMD cases and on blots in 18/30 cases. Two non-exclusive patterns of dystrophin labelling were observed on sections: very clear labelling on a small percentage of fibres (usually < 1%) or very weak labelling on a much higher proportion (about 25%). The mean age at loss of mobility among the DMD patients with no dystrophin labelling on tissue sections was 7.9 years (range 6.3-9.5) while the mean age among those with some labelling was 9.9 years (range 8.0-11.9); this is a significant difference. Quantitative estimates of dystrophin abundance were obtained from densitometric analysis of dystrophin bands on blots. In the whole group of 36 patients, a significant positive relationship was found between the abundance of dystrophin and the age at loss of independent mobility. It is concluded that even the very low concentrations of dystrophin found in DMD patients may have some functional significance.
Phase noise in capacitively coupled micromechanical oscillators (2005)

Phase noise in capacitively coupled microresonator-based oscillators is investigated. A detailed analysis of noise mixing mechanisms in the resonator is presented, and the capacitive transduction is shown to be the dominant mechanism for low-frequency 1/f-noise mixing into the carrier sidebands. Thus, the capacitively coupled micromechanical resonators are expected to be more prone to the 1/f-noise aliasing than piezoelectrically coupled resonators. The analytical work is complemented with simulations, and a highly efficient and accurate simulation method for a quantitative noise analysis in closed-loop oscillator applications is presented. Measured phase noise for a microresonator-based oscillator is found to agree with the developed analytical and simulated noise models.
Excitotoxic Cytopathology, Progression, and Reversibility of Thiamine Deficiency-induced Diencephalic Lesions (1995)

The present study examined the cytopathological changes within diencephalon of a rat model of Wernicke's encephalopathy and determined whether administration of thiamine at various intervals after onset of neurological signs can arrest or reverse the cytopathological process. Electron microscopic examination of the brains from animals sacrificed at four progressively severe stages of pyrithiamine-induced thiamine deficiency (PTD) revealed neurocytopathological changes identical to those that have been described in glutamate-induced excitotoxic lesions. These degenerative changes occurred in gelatinosus (Ge) and anteroventral ventrolateral (AVVL) nuclei at an early symptomatic stage and in the ventroposterolateral (VPL), ventroposteromedial (VPM), and ventrolateral (VL) nuclei at slightly later stages of PTD. Light microscopic evaluation of separate groups of PTD rats administered thiamine at each of the same four neurologic stages and allowed to recover for 1 week demonstrated that thiamine treatment is more effective when administered at earlier stages. However, Ge, AVVL, and VPL nuclei sustain severe damage even when thiamine is administered prior to acute neurologic signs. Furthermore, pathologic changes in the mammillary and several midline intralaminar nuclei begin after thiamine administration and reinstitution of thiamine-replete diet to animals in more severe stages of thiamine deficiency. These and other recent findings suggest that excitotoxic and possibly apoptotic mechanisms may mediate neuronal degeneration in the PTD rat model of Wernicke's encephalopathy, and that multiple factors conducive to excitotoxicity may act in concert to produce this syndrome.