gebhart/patrepeval huggingface dataset:
Local control of peptide conformation: Stabilization ofcis proline peptide bonds by aromatic proline interactions (1998)

In the native state of proteins there is a marked tendency for an aromatic amino acid to precede a cis proline. There are also significant differences between the three aromatic amino acids with Tyr exhibiting a noticeably higher propensity than Phe or Trp to precede a cis proline residue. In order to study the role that local interactions play in these conformation preferences, a set of tetrapeptides of the general sequence acetyl-Gly-X-Pro-Gly-carboxamide (GXPG), where X = Tyr, Phe, Trp, Ala, or cyclohexyl alanine, were synthesized and studied by nmr. Analysis of the nmr data shows that none of the peptides adopt a specific backbone structure. Ring current shifts, the equilibrium constant, the Van't Hoff enthalpy, and the measured rate of cis-trans isomerization all indicate that the cis proline conformer is stabilized by favorable interactions between the aromatic ring and the proline residue. Analysis of the side chain conformation of the aromatic residue and analysis of the chemical shifts of the pyrrolidine ring protons shows that the aromatic side chain adopts a preferred conformation in the cis form. The distribution of rotamers and the effect of an aromatic residue on the cis-trans equilibrium indicate that the preferred conformation is populated to approximately 62% for the Phe containing peptide, 67% for the Tyr containing peptide, and between 75 and 80% for the Trp containing peptide. The interaction is unaffected by the addition of 8M urea. These local interactions favor an aromatic residue immediately preceding a cis proline, but they cannot explain the relative propensities for Phe-Pro, Tyr-Pro, and Trp-Pro cis peptide bonds observed in the native state of proteins. In the model peptides the percentage of the cis proline conformer is 21% GYPG while it is 17% for GFPG. This difference is considerably smaller than the almost three to one preponderance observed for cis Tyr-Pro peptide bonds vs cis Phe-Pro peptide bonds in the protein database.
Compatibility of Ceramics with Liquid Na and Li (1976)

A thermodynamic criterion was developed for predicting the compatibility of insulating ceramics with liquid Na and Li. Nonmetallic impurities in liquid metals were shown to have a profound effect on the compatibility behavior of ceramics. Attempts were made to identify the structural parameters which affect the corrosion behavior of ceramics in liquid Na and Li.
Effect of annealing on magnetic exchange coupling in CoPt/Co bilayer thin films (2000)

Thin film CoPt/Co bilayers have been prepared as a model system to investigate the relationship between microstructure and exchange coupling in two-phase nanocomposite permanent magnets. The bilayers were prepared by magnetron sputter deposition of near-equiatomic CoPt with a thickness of 25 nm onto oxidized Si wafers. In the as-deposited state, CoPt had the A1 (fcc) structure and was magnetically soft. Before reinsertion into the sputtering chamber for the deposition of 2.8–16.7 nm thick Co layers, the CoPt films were annealed at 700 °C for 120 min to produce the magnetically hard, fully ordered L10 phase. The presence of exchange coupling in the bilayers was verified by magnetic hysteresis and recoil measurements and showed that only for Co thicknesses below 6.3 nm was this layer (in its as-deposited state) coupled through its full thickness to the CoPt layer. Annealing the bilayer samples at 300 and 550 °C for 20 min resulted in improvement of the interlayer magnetic coupling and produced clear differences in the magnetic reversal coherency and the recoil curves. However, for some samples, the improved coupling resulted in a decrease in coercivity, indicating that there is an optimum in the coupling strength for the attainment of high coercivity. Transmission electron microscopy studies of the bilayers in plan view showed that the increased interlayer coupling with annealing was a result of improved granular epitaxy of Co to CoPt.
Cloning, Sequence, and Transcriptional Regulation of the Operon Encoding a Putative N -Acetylmannosamine-6-Phosphate Epimerase ( <i>nanE</i> ) and Sialic Acid Lyase ( <i>nanA</i> ) in <i>Clostridium perfringens</i> (1999)

Clostridium perfringens can obtain sialic acid from host tissues by the activity of sialidase enzymes on sialoglycoconjugates. After sialic acid is transported into the cell, sialic acid lyase (NanA) then catalyzes the hydrolysis of sialic acid into pyruvate and N-acetylmannosamine. The latter is converted for use as a biosynthetic intermediate or carbohydrate source in a pathway including an epimerase (NanE) that converts N-acetylmannosamine-6-phosphate to N-acetylglucosamine-6-phosphate. A 4.0-kb DNA fragment from C. perfringens NCTC 8798 that contains the nanE and nanA genes has been cloned. The identification of the nanA gene product as sialic acid lyase was confirmed by overexpressing the gene and measuring sialic acid lyase activity in a nanA Escherichia coli strain, EV78. The nanA gene product was also shown to restore growth to EV78 in minimal medium with sialic acid as the sole carbon source. By using Northern blot experiments, it was demonstrated that the nanE and nanA genes comprise an operon and that transcription of the operon in C. perfringens is inducible by the addition of sialic acid to the growth medium. The Northern blot experiments also showed that there is no catabolite repression of nanE-nanA transcription by glucose. With a plasmid construct containing a promoterless cpe-gusA gene fusion, in which beta-glucuronidase activity indicated that the gusA gene acted as a reporter for transcription, a promoter was localized to the region upstream of the nanE gene. Primer extension experiments then allowed us to identify a sialic acid-inducible promoter located 30 bp upstream of the nanE coding sequence.
A validated high performance liquid chromatography method for the analysis of thymol and carvacrol in Thymus vulgaris L. volatile oil (2010)

Thymus vulgaris L. (Lamiaceae) is a well-known medicinal plant that contains important compounds such as thymol and carvacrol and it has been used in many pharmaceutical dosage forms. Thymol and carvacrol in essential oils are often quantified by gas chromatography (GC) technique but in this work, a validated and reliable high performance liquid chromatography (HPLC) method has been developed for the analysis of these two components in T. vulgaris essential oil. The essential oil of the plant was analyzed by HPLC and GC techniques. The HPLC system consisted of ACE C(18) column and an isocratic acetonitrile:water (50:50) as the mobile phase which was kept at a flow rate of 1 ml/min. The method was validated for selectivity, linearity (r(2) > 0.997 for both thymol and carvacrol), precision (intra-day 0.8-1.9, 1.7-2.6; and inter-day 3.5-4.5, 3.6-4.7) and recovery (97.7%, 97.6%) for thymol and carvacrol, respectively. The limits of detection (LODs) and limits of quantization (LOQs) were calculated to be 2.8, 0.6 µg/ml and 8.6, 1.8 µg/ml for thymol and carvacrol, respectively. The GC system consisted of flame ionization detector (FID) and CP-SIL 8 column. The concentrations of thymol and carvacrol in essential oil obtained by HPLC (41.2%, 4.3%) and GC (40.7%, 4.2%) were compared by statistical methods and they showed good agreement.
D-serine dehydratase from Escherichia coli. DNA sequence and identification of catalytically inactive glycine to aspartic acid variants. (1988)

We have identified two glycyl residues whose integrity is essential for the catalytic competence of a model pyridoxal 5'-phosphate requiring enzyme, D-serine dehydratase from Escherichia coli. This was accomplished by isolating and sequencing the structural gene from wild type E. coli and from two mutant strains that produce inactive D-serine dehydratase. DNA sequencing indicated the presence of a single glycine to aspartic acid replacement in each variant. The amino acid replacements lie in a glycine-rich region of D-serine dehydratase well removed from pyridoxal 5'-phosphate-binding lysine 118 in the primary structure of the enzyme. The striking effect of these two glycine to aspartic acid replacements on catalytic activity, the conservation of the glycine-rich region in several pyridoxal 5'-phosphate-dependent enzymes that catalyze alpha/beta-eliminations, and the placement of similar glycine-rich sequences in well-characterized active site structures suggest that the glycine-rich region interacts with the cofactor at the active site of the enzyme.
Dynamic Interaction of the Measles Virus Hemagglutinin with Its Receptor Signaling Lymphocytic Activation Molecule (SLAM, CD150) (2008)

The interaction of measles virus with its receptor signaling lymphocytic activation molecule (SLAM) controls cell entry and governs tropism. We predicted potential interface areas of the measles virus attachment protein hemagglutinin to begin the investigation. We then assessed the relevance of individual amino acids located in these areas for SLAM-binding and SLAM-dependent membrane fusion, as measured by surface plasmon resonance and receptor-specific fusion assays, respectively. These studies identified one hemagglutinin protein residue, isoleucine 194, which is essential for primary binding. The crystal structure of the hemagglutinin-protein localizes Ile-194 at the interface of propeller blades 5 and 6, and our data indicate that a small aliphatic side chain of residue 194 stabilizes a protein conformation conducive to binding. In contrast, a quartet of residues previously shown to sustain SLAM-dependent fusion is not involved in binding. Instead, our data prove that after binding, this quartet of residues on propeller blade 5 conducts conformational changes that are receptor-specific. Our study sets a structure-based stage for understanding how the SLAM-elicited conformational changes travel through the H-protein ectodomain before triggering fusion protein unfolding and membrane fusion.
Practical limitations of Talbot imaging with microlens arrays (1997)

The Talbot effect which also appears for the foci of microlens arrays can, in principle, be used for array illuminators. In particular, the multiplication of the foci in the fractional Talbot planes seems to be promising. Certainly, in practice there are three effects which limit the application of the fractional Talbot effect for microlens arrays. Theoretical, numerical and experimental results are given to demonstrate these limitations.
A homogeneous type II DNA topoisomerase from HeLa cell nuclei. (1981)

Using kinetoplast DNA networks as a substrate in a decatenation assay, we have purified to apparent homogeneity a type II DNA topoisomerase from HeLa cell nuclei. The most pure preparations contain a single polypeptide of 172,000 daltons as determined by sodium dodecyl sulfate-gel electrophoresis. The molecular weight of the native protein, based on sedimentation and gel filtration analyses, is estimated to be 309,000. These results suggest that the enzyme is a dimer of 172,0090-dalton subunits. The enzyme is a type II topoisomerase as demonstrated by its ability to change the linking number of DNA circles in steps of two and to decatenate or unknot covalently closed DNA circles. No gyrase activity is detectable. ATP is required for the relaxation, decatenation, and unknotting of DNA, and a DNA-dependent ATPase activity is present in the most pure fractions. ATP is hydrolyzed to ADP in this properties to T4 DNA topoisomerase (Liu, L. F., Liu, C. C., and Alberts, B. M. (1979) Nature 281, 456-461).
Sampling Piecewise Sinusoidal Signals With Finite Rate of Innovation Methods (2009)

We consider the problem of sampling piecewise sinusoidal signals. Classical sampling theory does not enable perfect reconstruction of such signals since they are not band-limited. However, they can be characterized by a finite number of parameters, namely, the frequency, amplitude, and phase of the sinusoids and the location of the discontinuities. In this paper, we show that under certain hypotheses on the sampling kernel, it is possible to perfectly recover the parameters that define the piecewise sinusoidal signal from its sampled version. In particular, we show that, at least theoretically, it is possible to recover piecewise sine waves with arbitrarily high frequencies and arbitrarily close switching points. Extensions of the method are also presented such as the recovery of combinations of piecewise sine waves and polynomials. Finally, we study the effect of noise and present a robust reconstruction algorithm that is stable down to SNR levels of 7 [dB].
Synthesis of oligonucleotides containing 2′-deoxy-6-thioguanosine at a predetermined site (1991)

A new approach has been devised for the synthesis of oligonucleotides containing 2'-deoxy-6-thioguanosine [d(s6G)]. The synthesis of oligonucleotides containing d(s6G) requires special protection and deprotection strategies to prevent the thione functionality from undergoing oxidation and hydrolysis. Previous attempted syntheses have neglected to address this problem. By using the cyanoethyl protecting group for the thione and phenoxyacetyl for the exocyclic amino group, it was possible to deprotect oligonucleotides with a mixture of sodium hydroxide and sodium hydrogen sulfide without any significant conversion of d(s6G) to deoxyguanosine. Application of this strategy will allow investigation of the structural as well as biological activity of d(s6G)-containing oligonucleotides.
Combination of rapamycin and 17-allylamino-17-demethoxygeldanamycin abrogates Akt activation and potentiates mTOR blockade in breast cancer cells (2008)

Increased Akt phosphorylation was reported in cancer cell lines and tumor tissues of patients exposed to rapamycin, a response likely contributing to the attenuated antitumor activity of rapamycin. It is, therefore, necessary to develop and validate combination strategies to reverse rapamycin-induced Akt signaling. We now report that Akt activation in response to rapamycin is abrogated by 17-allylamino-17-demethoxygeldanamycin (17-AAG), a heat shock protein 90 (HSP90) inhibitor. Rapamycin/17-AAG combination results in an enhanced antiproliferative activity in both MCF-7 and MDA-MB-231 breast cancer cells. In combination 17-AAG confers potent suppression of Raf-MEK-extracellular signal-regulated kinase signaling, a pathway that is otherwise not inhibited by rapamycin individually. Importantly, 17-AAG cooperates with rapamycin to block the phosphorylation of the mammalian target of rapamycin at Ser2448, as well as its downstream effectors ribosomal p70 S6 kinase and eukaryotic initiation factor 4E binding protein 1, which is accompanied by a substantial reduction in cyclins D1 and E. The potency of rapamycin/17-AAG combination is not affected by the activation of insulin-like growth factor 1 receptor signaling, which has been previously shown to diminish the antiproliferative activity of rapamycin. Rapamycin/17-AAG combination alleviates the induction of HSP90 protein, a heat shock response frequently associated with 17-AAG monotherapy. Our findings establish a mechanistic rationale for a combination approach using rapamycin and 17-AAG in the treatment of breast cancer.
Improved energy compensation for time-of-flight mass spectrometry (1994)

A model for improved energy compensation in time-of-flight (TOF) mass spectrometry has been developed and tested. This model includes effects of both the acceleration and drift region on mass resolution for surface desorption TOP mass spectrometers that employ ion mirrors to improve mass resolution. Appropriate placement of an additional stage onto the conventional one- and two-stage mirrors provides compensation for flight time spreads, caused by initial ion kinetic energy distributions, in both regions. Experimental results that validate the model calculations are presented for a modified commercial two-stage ion mirror. For example, m/†m for Na(+) was improved from ∼ 100 to ∼ 200 using only a 200-eV drift energy and a 58-cm drift path.
Barley Mutants Lacking Chloroplast Glutamine Synthetase—Biochemical and Genetic Analysis (1987)

Eight mutants of barley (Hordeum vulgare cv Maris Mink) lacking the chloroplast isozyme of glutamine synthetase (EC 6.3.1.2.) were isolated by their inability to grow under photorespiratory conditions. The cytoplasmic isozyme of glutamine synthetase was present in the leaves of all the mutants, with activities comparable to the wild-type (10-12 nanokatals per gram fresh weight). The mutant plants developed normally and were fully fertile under conditions that minimize photorespiration. In 1% O(2) the rate of CO(2) fixation in leaves of one of the mutants, RPr 83/32, was the same as the wild-type, but in air this rate declined to 60% of the wild-type after 30 minutes. During this time the ammonia concentration in leaves of the mutant rose from 1 to 50 micromoles per gram fresh weight. Such ammonia accumulation in air was found in all the mutant lines. In back-crosses with the parent line, F(1) plants were viable in air. In the F(2) generation, nonviability in air and the lack of chloroplast glutamine synthetase co-segregated, in both the lines tested. These two lines and four others proved to be allelic; we designate them gln 2a-f. The characteristics of these mutants conclusively demonstrate the major role of chloroplast glutamine synthetase in photorespiration and its associated nitrogen recycling.
Anisotropic Activation Spread in Heart Cell Monolayers Assessed by High-Resolution Optical Mapping (1996)

The role of tissue discontinuities in anisotropic impulse propagation was assessed in two-dimensional anisotropic monolayers of neonatal rat myocytes cultured on a growth-directing substrate of collagen. Activation spread and distribution of maximal upstroke rate of rise (Vmax) of the action potential were measured with an optical system using a voltage-sensitive fluorescent dye (RH-327) and a 10x10 photodiode array with a spatial resolution ranging from 7 to 15 microns. Activation maps were compared with the cellular architecture and the distribution of gap junctions obtained from immunostaining the gap junction protein connexin43 (Cx43). Four types of structures were studied: (1) dense cell cultures, (2) cultures with anisotropic intercellular clefts of variable size, (3) discontinuities created by inclusion of nonmyocyte cells, and (4) discontinuities resulting from nonuniform expression of gap junctions. In dense monolayers, activation spread was continuous with microinhomogeneities in both longitudinal and transverse directions. The average cell dimensions in such monolayers were smaller than in adult canine myocardium. However, the degree of cellular anisotropy (length-to-width ratio of 5.3 +/- 1.4) and connectivity were similar. The presence of small intercellular clefts (less than one cell in length) did not disturb the general pattern of transverse or longitudinal activation spread, but it was associated with wave front microcollisions during transverse propagation and a concomitant increase of Vmax beyond the cleft. Long intercellular clefts caused discontinuous transverse propagation. Conduction velocity and Vmax decreased significantly at narrow isthmuses formed by closely apposed clefts, rendering such sites susceptible for conduction block. In contrast Vmax increased when the wave front faced the borders of the clefts. Nonmyocyte cells were electrically connected to myocytes and served as sinks for electrotonic currents, thereby producing localized conduction slowing and a decrease in Vmax. Localized inhomogeneity in Cx43 distribution correlated accurately with circumscribed conduction block and changes in Vmax. Our results provide direct experimental evidence that the cellular structure and gap junction distribution correlate with action potential propagation and distribution of Vmax. We suggest that in tissue with a nonuniform anisotropy, connective tissue separating fiber bundles or sites of inhomogeneous connexin distribution may represent predilective sites for block in transverse direction.
Effect of local hyperthermia on blood flow and microenvironment: a review. (1984)

The blood flow in tumors varies considerably among different tumor types. Even in the same tumor, the distribution of vasculature and blood flow is quite heterogeneous. The tumor blood flow generally decreases as the tumors grow larger, owing partially to progressive deterioration of vascular beds and to the rapid growth of tumor cell population relative to vascular beds. Contrary to the general notion that blood flow is less in tumors than in normal tissues, blood flow in many tumors, particularly in small tumors, is actually greater than that in surrounding normal tissues at normothermic conditions. Compared to the normal tissue blood flow, however, the capacity of tumor blood flow to increase upon heating appears to be rather limited. Consequently, the heat dissipation by blood flow in tumors is slower than that in normal tissues, and thus the temperature of tumor rises higher than that in normal tissue during heating. Preferential heating of tumors, however, may not be achieved all the time because the relative blood perfusion in some tumors remains greater than that in the surrounding normal tissues despite the profound increase in normal tissue blood flow during heating. The vasculature in tumor can be significantly damaged at temperatures which may alter but do not damage the vasculature of normal tissue. Upon heating, the intratumor environment becomes acidic, hypoxic, and nutritionally deprived due probably to vascular damage. Such a suboptimal environment in the heated tumors potentiates the response of tumor cells to hyperthermia, inhibits the repair of thermal damage, and also interferes with the development of thermal tolerance. The acidic environment also appears to potentiate the response of tumor cells to certain drugs at elevated temperatures. The changes in oxygenation of tumors and normal tissues caused by the changes in blood flow may have significant implications in the effectiveness of different sequences of hyperthermia and radiotherapy in the combined use of these two modalities. Changes in the distribution of drugs in tumors and normal tissues due to changes in blood flow will also determine the optimal use of hyperthermia in conjunction with chemotherapy.
Antibiotic resistance mechanisms in<i>Salmonella</i>species causing bacteraemia in Malawi and Kenya (1996)

In two studies on the causative agents of bacteraemia in Malawi and Kenya, 33 Salmonella strains were isolated. Fourteen strains of Salmonella typhimurium and Salmonella enteritidis were found to exhibit resistance to amoxicillin, amoxicillin/clavulanic acid and cotrimoxazole as well as decreased susceptibility to a range of aminoglycosides. The resistant strains were studied to establish their resistance mechanisms. Beta-lactamase co-focusing with TEM-1 was present in 12 strains. In two strains, both S. typhimurium from Kenya, an OXA-1 beta-lactamase was detected. The aminoglycoside-modifying enzyme ANT(2") was found in 10 strains. The presence of the encoding genes was confirmed by PCR. For comparison, susceptibility records of 73 Salmonella strains isolated during the past 14 years in our hospital were studied retrospectively. Only one of these strains was resistant to amoxicillin. This resistance was acquired during therapy.
A conductivity-based selective etching for next generation GaN devices (2010)

Electrochemical etching having large selectivity based on the conductivity of n-type GaN was investigated to demonstrate the feasibility of novel optical and microelectromechanical system devices. The electrochemical etching exhibited two regimes with different etching characteristics, i.e., nanoporous and electropolishing, depending on the doping concentration and applied voltage. For photonic applications, GaN microdisks and distributed Bragg reflectors were fabricated where optical index contrast can be achieved by selective etching or nanoporous formation of GaN. Stimulated emission of GaN microdisk was observed under pulsed optical pumping. In addition, a GaN cantilever was formed and its resonance frequency was measured at ∼120 kHz.