gebhart/patrepeval huggingface dataset:
Purification and characterization of the dihydropyridine-sensitive voltage-dependent calcium channel from cardiac tissue. (1987)

The dihydropyridine-sensitive voltage-dependent Ca2+ channel from cardiac tissue was purified 900-fold using DEAE-Sephadex A-25, concanavalin A-Sepharose, and wheat germ agglutinin-Sepharose. The purified preparation was highly enriched in a peptide of 140,000 daltons when electrophoresed on sodium dodecyl sulfate gels in the presence of 2-mercaptoethanol, or 170,000 when electrophoresed in the presence of iodoacetamide. Polyclonal antibodies raised against the purified subunits of the rabbit skeletal muscle Ca2+ channel recognized the 170-kDa protein in preparations electrophoresed under nonreducing conditions, and the large peptide of 140 kDa and smaller peptides of 29-32 kDa in preparations analyzed under reducing conditions. Monoclonal antibodies, which were raised against the native Ca2+ channel from skeletal muscle, immunoprecipitated [3H]PN 200-110 binding activity from solubilized cardiac membranes and immunoprecipitated 125I-labeled peptides (from the purified cardiac Ca2+ channel preparation) which migrated as a single species of 170 kDa under nonreducing conditions, or as 140, 32, and 29 kDa under reducing conditions. The results show that the purified cardiac Ca2+ channel, like that previously purified from skeletal muscle, consists of a major component of 170 kDa which is comprised of a 140-kDa peptide linked by disulfide bonds to smaller peptides of 32-29 kDa. Peptide maps of the 140-kDa peptide purified from cardiac and skeletal muscle preparations were strikingly similar, suggesting a high degree of homology in their primary sequence.
Structure and Functional Properties of Ulvan, a Polysaccharide from Green Seaweeds (2007)

With today's interest in novel renewable chemicals and polymers, the underexploited marine green algae belonging to species of Ulva and Entermorpha stimulated interest as sources of polysaccharides with innovative structure and functional properties. These algae are common on all seashores and can produce in time an important amount of biomass in nutrient-enriched waters. The major water-soluble polysaccharide, ulvan, extracted from the cell wall represents about 8-29% of the algae dry weight. The original physicochemical, rheological, and biological properties recently unraveled for this complex sulfated aldobiouronan open the way for novel potential applications.
Glycolytic activity in human red cell populations separated by a combination of density and counterflow centrifugation. Evidence for an improved separation of red cells according to age (1986)

Human red blood cells were separated by a discontinuous Percoll density gradient into fractions of increasing density. Red cells comprising the lowest and highest density fractions, respectively, were subsequently separated according to mean cell volume (MCV) by means of counterflow centrifugation. The activities of 4 red cell age-dependent enzymes (hexokinase (HK), pyruvate kinase (PK), glucose-6-phosphate dehydrogenase (G6PD) and aspartate aminotransferase (ASAT) were highest in the red cell fraction with low density/large MCV, although the difference from red cell enzyme activities in the total low density fraction was not significant. These 4 enzyme activities were lowest in the fraction of red cells with high density/small MCV. The relative activities of the enzymes in the high density/small MCV fraction, as compared to the unseparated cell population, were: HK (58%), PK (49%), G6PD (53%) and ASAT (28%). These activities were all significantly lower than those measured in the total high density red cell fraction. The rates of lactate production in the low density/large MCV cells (0.89 +/- 0.15 mumol X min-1 X 10(-11) cells) is approximately 3-fold higher than in high density/small MCV cells (0.33 +/- 0.03 mumol X min-1 X 10(-11) cells). This latter value is 1.8-fold lower than the rate of lactate production in the total high density red cell fraction (0.59 +/- 0.14 mumol X min-1 X 10(-11) cells) and is, in contrast to lactate production in other density/size fractions, insensitive to phosphate as a metabolic stimulus. It is argued that the combination of density gradient and counter-flow centrifugation offers a greater potential for obtaining an old red cell population than classical red cell density centrifugation alone.
Antimicrobial susceptibility of Neisseria gonorrhoeae strains isolated in Guangzhou, China, 1996-2001 (2003)

Resistance to penicillin and ciprofloxacin increased greatly during 1996-2001. Ceftriaxone and spectinomycin should be used as the first line agents in treating gonorrhoea. It is of great importance to continuously survey the susceptibilities of N gonorrhoeae to antibiotics in controlling the spread of gonococcal infections.
Impact of anemia correction on the production of the circulating morphogenetic protein α-Klotho in patients with Stages 3B—4 chronic kidney disease: A new direction of cardionephroprotection (2016)

The serum level of the protein Klotho is not only a marker for the severity of CKD and its complications (anemia, left ventricular hypertrophy, and heart failure), but also a pathogenetic factor of CKD progression. Anemia correction with erythropoiesis stimulants has been shown to enhance the renal and extrarenal production of α-Klotho.
Promoter Methylation in Head and Neck Squamous Cell Carcinoma Cell Lines Is Significantly Different than Methylation in Primary Tumors and Xenografts (2011)

Studies designed to identify novel methylation events related to cancer often employ cancer cell lines in the discovery phase of the experiments and have a relatively low rate of discovery of cancer-related methylation events. An alternative algorithm for discovery of novel methylation in cancer uses primary tumor-derived xenografts instead of cell lines as the primary source of nucleic acid for evaluation. We evaluated DNA extracted from primary head and neck squamous cell carcinomas (HNSCC), xenografts grown from these primary tumors in nude mice, HNSCC-derived cell lines, normal oral mucosal samples, and minimally transformed oral keratinocyte-derived cell lines using Illumina Infinum Humanmethylation 27 genome-wide methylation microarrays. We found >2,200 statistically significant methylation differences between cancer cell lines and primary tumors and when comparing normal oral mucosa to keratinocyte cell lines. We found no statistically significant promoter methylation differences between primary tumor xenografts and primary tumors. This study demonstrates that tumor-derived xenografts are highly accurate representations of promoter methylation in primary tumors and that cancer derived cell lines have significant drawbacks for discovery of promoter methylation alterations in primary tumors. These findings also support use of primary tumor xenografts for the study of methylation in cancer, drug discovery, and the development of personalized cancer treatments.
Distribution of enzyme activities within the developing maize (<i>Zea mays</i>) kernel in relation to starch, oil and protein accumulation (1990)

The association of enzyme activities in developing kernels with specific storage product accumulation at maturity was analyzed in different parts of Zea mays inbred OH43 kernels. Maize kernels were harvested at 20 and 55 days post‐pollination and dissected into basal region, pericarp, embryo, lower endosperm, middle endosperm and upper endosperm. Mature (55 days pos(‐pollination) kernel parts were analyzed for starch, total protein, zein and oil content. Immature (20 days post‐pollination) kernel parts were assayed for activities of 15 enzymes of sugar and amino acid metabolism. Statistical analyses of the data suggested that glucokinase (EC 2.7.1.2) fructokinase (EC 2.7.1.4) and phosphofructokinase (EC 2.7.1.1 11) activities were primarily associated with oil accumulation, whereas ADP′‐glueose pyrophosphorylasc (EC 2.7.7.27) and sucrose synthase (EC 2.4.1.13) activities were associated with starch accumulation. The results suggest that oil biosynthesis utilizes inveitase‐mediated sucrose degradation in a pathway not requiring pyrophosphatc. whereas starch biosynthesis utilizes a sucrose synthase‐mediated pathway of sucrose degradation in a pathway requiring pyrophosphatc. Additional groups of enzyme activities were associated with each oilier but not with any specific storage product and appeared to be associated with general metabolic activity.
RNA recognition by designed peptide fusion creates "artificial" tRNA synthetase (2003)

The genetic code was established through aminoacylations of RNA substrates that emerged as tRNAs. The 20 aminoacyl-tRNA synthetases (one for each amino acid) are ancient proteins, the active-site domain of which catalyzes formation of an aminoacyl adenylate that subsequently reacts with the 3' end of bound tRNA. Binding of tRNA depends on idiosyncratic (to the particular synthetase) domains and motifs that are fused to or inserted into the conserved active-site domain. Here we take the domain for synthesis of alanyl adenylate and fuse it to "artificial" peptide sequences (28 aa) that were shown previously to bind to the acceptor arm of tRNAAla. Certain fusions confer aminoacylation activity on tRNAAla and on hairpin microhelices modeled after its acceptor stem. Aminoacylation was sensitive to the presence of a specific G:U base pair known to be a major determinant of tRNAAla identity. Aminoacylation efficiency and specificity also depended on the specific peptide sequence. The results demonstrate that barriers to RNA-specific aminoacylations are low and can be achieved by relatively simple peptide fusions. They also suggest a paradigm for rationally designed specific aminoacylations based on peptide fusions.
Microwave absorption by an array of carbon nanotubes: A phenomenological model (2006)

A simple model to explain microwave-induced heating of carbon nanotubes (CNTs) through transformation of electromagnetic energy into mechanical vibrations is proposed and analyzed. The model provides a way to understand recent observations of heating of CNTs exposed to microwaves in the range of $2--20\phantom{\rule{0.3em}{0ex}}\mathrm{GHz}$. It is shown that transverse vibrations of CNTs during microwave irradiation can be associated with parametric resonance, as occurs in the analysis of acoustic experiments on forced longitudinal vibrations of a stretched elastic string. For carbon nanotubes [single wall nanotube (SWNT), double wall nanotube (DWNT), multiwall nanotube (MWNT), ropes, and strands] the resonant parameters are shown to be located in a region of instability of the Mathieu's equation. Wave equations with cubic nonlinearity were used to qualitatively describe the effects of phonon-phonon interactions and energy transfer from microwaves to CNTs at a rate much exceeding the traditional Joule heating via electron-phonon interaction.
Myths, Facts and the RAAF Force Structure (2004)

What we observe today in force structure planning for the RAAF combat fleet, and its supporting rationale, is a fundamental realignment to a force structure which priorities battlefield air interdiction and close air support capabilities over the long established doctrine of prioritising air superiority and strategic strike capabilities. This unstated doctrine will expose Australia to pressure by regional nations, and increase dependency on US combat assets in an unprecedented fashion. The reasoning which justifies this change is underpinned largely by mythology, as proper analysis was never performed. Politically and strategically less painful alternatives exploiting the F-111 and F/A-22A all vanish as the current JSF-centric plan is implemented. This paper explores many of these myths.
The MPTP Model of Parkinson’s Disease (2007)

In his monograph “The case of the frozen addicts,” William Langston reported the story of six patients, who, in 1982, in California, developed mysterious symptoms provoked by 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) that were reminiscent of Parkinson’s disease (PD). Since that time, MPTP has been recognized as a highly selective neurotoxin; in reality, this compound has a much longer history (1). Apparently, the synthesis of MPTP was first reported by Ziering and his colleagues in 1947 as part of a series of papers on meperidine derivatives (2), and, using these methods, it was shown that piperidols may be acylated with a propionic group to produce MPPP (1-methyl-4-phenyl-4-propionoxypiperidine), a compound 25 times more potent than morphine in the rat (2,3). Since then, MPTP has been used extensively as a synthetic intermediate in meperidine chemistry and has become commercially available (Aldrich Chemical Company, Milwaukee, Wisconsin) for this purpose long before it had been identified as a potent neurotoxin.
Optimal observers for a class of continuous linear time-varying stochastic systems (1977)

A simple method is presented for avoiding the use of signal differentiation in the design of a least-squares estimator for the state of a linear finite-dimensional time-varying stochastic system when the system outputs are unobscured by additive noise.
Peptide potencial energy surfaces and protein folding (2006)

Motivation. This paper outlines the utility of a 3D→1D transformation of peptide conformation. Although this transformation leads to a linearized notation of protein secondary and tertiary structures that may be used for an objective description and classification of protein folding, nevertheless, the method is intended to be descriptive and is not meant to be predictive. Method. It is established from first principles that the idealized 2D-Ramachandran potential energy surface must have nine minima. It is therefore an obvious question to ask whether all these nine conformations are actually occurring in proteins. An analysis is carried out on 258 proteins with known X-ray structure. These proteins contain 56 495 amino-acid residues with well-defined φ and ψ angles. The minima are identified with the aid of the nine minima of Ac-L-Ala-NHMe determined by ECEPP/2 method allowing a ±40° tolerance in the φ and ψ values. All nine conformations do occur in proteins. Results. L-conformation preference varies as: e > γ > α >> δ > β = 1. Pro is the amino acid with the greatest preference for L-conformation. L-conformation preference varies as: Pro >> Ile > Val > Leu > Thr > Met > Ala > Glu > Phe > Trp > Tyr > Gln > Lys > Ser > Cys > Arg > Asp > His > Asn > Gly. The results relative to achiral Gly shows that the trend-line slope varies as: α >> e > γ >> β = 0 ≈ δ. The strong Pro preference is in agreement with its character of strong α-helix and β-sheet breaker, and β-turn and random-coil former. Conclusions. In XX–XXI centuries, the secondary–tertiary structures of proteins, frequently referred to as protein folding, posed a major problem to medicine, biochemistry, pharmaceutical drug design and related fields. A method is formulated, via a 3D→1D transformation, which allows using a qualitative linearized notation for protein 3D structures, which is based on quantitative geometrical data. It appears that with the present objective method, there is no longer any need to refer to a particular protein segment as unordered, and the description– classification of protein secondary–tertiary structures is now within reach of all protein chemists. L-conformation preferences vary as: e > γ > α >> δ > β = 1, and as: Pro >> Ile > Val > Leu > Thr > Met > Ala > Glu > Phe > Trp > Tyr > Gln > Lys > Ser > Cys > Arg > Asp > His > Asn > Gly. The Pro preference is in agreement with its strong character of α-helix and β-sheet breaker, and β-turn and random-coil former. Availability. The original software used in the investigation is available from the author.
Positive and negative regulation of the erythropoietin gene. (1994)

In order to investigate positive and negative regulatory elements of the erythropoietin (Epo) gene, synthetic oligonucleotides were designed to control Epo transcription by means of an antigen strategy. We devised a new method for detecting regulatory elements of genes that have a weak promoter. Synthetic oligonucleotides were incubated with Hep3B cells in the presence or absence of CoCl2 or hypoxia. To exclude the effect of translational regulation, Epo mRNA concentration was determined by competitive polymerase chain reaction. The addition of antisense oligonucleotide for CACCC elements decreased the production of Epo mRNA in a dose-dependent fashion when cells were stimulated by CoCl2 or hypoxia. In contrast, the addition of antisense oligonucleotide for the GATA element caused a dose-dependent stimulation of Epo mRNA production either in the presence or absence of CoCl2 or hypoxia. Triple helix formation was revealed by electrophoresis. CACCC elements were demonstrated to be positive regulatory elements of the Epo gene, whereas the GATA element was a negative regulatory element. Furthermore, by gel mobility shift assays, we demonstrated evidence for the presence of factors in Hep3B cell nuclear extract that specifically bind to CACCC or GATA elements. Based on these observations, we presented the possibility that triple helix formation could serve as a novel means for transcriptional regulation of the gene.
Transition Boiling Heat Transfer and the Film Transition Regime (1987)

The “Berenson” flat-plate transition-boiling experiment has been re-created with a reduced thermal resistance in the heater, and an improved access to those portions of the transition boiling regime that have a steep negative slope. Tests have been made in Freon-113, acetone, benzene, and n-pentane boiling on horizontal flat copper heaters that have been mirror-polished, “roughened,” or teflon-coated. The resulting data reproduce and clarify certain features observed by Berenson: the modest surface finish dependence of boiling burnout, and the influence of surface chemistry on both the minimum heat flux and the mode of transition boiling, for example. A rational scheme of correlation yields a prediction of the heat flux in what Witte and Lienhard previously identified as the “film-transition boiling” region. It is also shown how to calculate the heat flux at the boundary between the pure-film, and the film-transition, boiling regimes, as a function of the advancing contact angle.
Effects of cinnamic acid derivatives on in vitro growth of Plasmodium falciparum and on the permeability of the membrane of malaria-infected erythrocytes (1992)

Cinnamic acid derivatives (CADs) are known inhibitors of monocarboxylate transport across plasma and mitochondrial membranes. All derivatives were found to inhibit the growth of intraerythrocytic Plasmodium falciparum in culture, which is in correlation with their hydrophobic character. Parasites at the ring and trophozoite stages were equally susceptible to the different derivatives. This result could be attributed to their inhibition of the transport of lactate, the major product of parasite energy metabolism. However, unexpectedly, it was found that all derivatives also inhibit the translocation of carbohydrates and amino acids across the new permeability pathways induced in the host cell membrane by the parasite. This impediment correlated strictly with CADs' effect on parasite growth. Parasites residing in cells permeabilized by means of Sendai virus were less susceptible to the different drugs, a result which implies that in addition to the direct effect on parasite viability, the drugs may have inhibited some process in the host cell whose function may be vital for parasite growth. The effect of CADs on the ATP levels in infected cells, in virus-treated cells, and in the two cellular compartments of the infected cell revealed that the drugs caused a significant decline in ATP level in the parasite compartment, while they provoked only a small effect on ATP level in the intact cells and the host cell compartment. These observations suggest that CADs inhibit ATP production in the parasite and its utilization by the host cell.
Correction of metabolic alkalosis by HCl and acetazolamide: effects on extracellular and intracellular acid‐base status in rats<i>in vivo</i> (1986)

Extracellular plasma pH (pHe) of nephrectomized male or female Sprague-Dawley rats was changed by infusion of either sodium bicarbonate or HCl to predetermined values in the pH range of 7.53-7.14, and then held constant for 2 h. Intracellular pH (pHi) of the liver, heart, brain, and two skeletal muscle groups as calculated from the distribution of 14C-labelled DMO (5.5-dimethyl-2,4-oxazolidinedione) was compared to corresponding tissues of a control group and rats treated with the carbonic anhydrase inhibitor acetazolamide (Diamox). When compared to control, changes of the extracellular pH in male or female rats were followed by similar effects on pHi in the investigated tissues. At the same extracellular pH there were no statistical differences between pHi values of HCl or acetazolamide treated rats, though the arterial PCO2 following acetazolamide administration was significantly increased when compared to control or the corresponding HCl group. This study shows that administration of acetazolamide or HCl results in a dose-dependent decrease of plasma and tissue pH, and that both agents may be used as a logical and safe therapy during severe metabolic alkalosis in rats.
Low-cost high-speed pseudo-random bit sequence characterization using nonuniform periodic sampling in the presence of noise (2012)

In this paper, we propose a wideband signal reconstruction scheme for testing high-speed pseudo random bit sequences (PRBSs) in the presence of jitter noise using incoherent sampling. The proposed approach exploits synchronous multirate sampling (SMRS) hardware and multicoset back-end signal processing algorithms. The SMRS hardware consists of multiple analog-to-digital converters (ADCs) whose sampling frequencies are synchronized with a common frequency reference and can be individually configured. The optimal sampling frequency of each ADC is chosen based on the input signal information and sampling hardware specifications. As compared to other sampling hardware used for multicoset signal reconstruction, the proposed approach uses less number of ADCs and does not require accurate sampling clock phase adjustment. In the digital signal reconstruction, the input waveform is reconstructed by the multicoset signal processing algorithms and the phase noise of each tone of the PRBS test signal is measured.
N-Acetylglucosamine: Production and Applications (2010)

N-Acetylglucosamine (GlcNAc) is a monosaccharide that usually polymerizes linearly through (1,4)-β-linkages. GlcNAc is the monomeric unit of the polymer chitin, the second most abundant carbohydrate after cellulose. In addition to serving as a component of this homogeneous polysaccharide, GlcNAc is also a basic component of hyaluronic acid and keratin sulfate on the cell surface. In this review, we discuss the industrial production of GlcNAc, using chitin as a substrate, by chemical, enzymatic and biotransformation methods. Also, newly developed methods to obtain GlcNAc using glucose as a substrate in genetically modified microorganisms are introduced. Moreover, GlcNAc has generated interest not only as an underutilized resource but also as a new functional material with high potential in various fields. Here we also take a closer look at the current applications of GlcNAc, and several new and cutting edge approaches in this fascinating area are thoroughly discussed.