gebhart/patrepeval huggingface dataset:
ChemInform Abstract: Nucleic‐Acid Analogues with Restricted Conformational Flexibility in the Sugar‐Phosphate Backbone (“Bicyclo‐DNA”). Part 6. Probing the Influence of Torsion Angle γ on DNA‐Duplex Stability: Synthesis and Properties of Oligodeoxynucleotides Containing ((3′S,5′S)‐2′‐Deoxy‐ 3′,5′‐ethano‐β‐D‐ribofuranosyl)adenine and ‐thymine (“5′‐Epi‐ bicyclodeoxynucleosides”). (1996)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Adaptive echo compensation applied to the hands-free telephone problem (2002)

The requirements of a loudspeaker-enclosure-microphone system model are reviewed. It is shown that decoupling of the loudspeaker and the microphone requires an adaptive system with an impulse response of several-hundred-microsecond duration. Means to solve the adaptation problem are described.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Regulation of prelamin A endoprotease activity by prelamin A (1997)

The maturation of lamin A is completed by the endoproteolytic cleavage of its farnesylated precursor protein, prelamin A. In the absence of this cleavage, prelamin A can neither give rise to lamin A nor assemble into the nuclear lamina. We call the enzyme which catalyzes this endoproteolytic step the 'prelamin A endoprotease'. In this study, we begin characterization of the regulation of prelamin A endoprotease. In particular, we address the question as to whether prelamin A endoprotease activity is constitutive in cells or responds to expression of prelamin A. To do this, we compared the activity of this novel endoprotease in cells which express prelamin A with those that do not. Our data shows that the enzymatic activity of prelamin A endoprotease is enhanced by the expression of prelamin A.
Virtual Texturing with WebGL (2012)

Until recently, achieveing hardware accelerated 3D content on web sites have only been accessible through third party plugins. The new HTML5 standard eliminates this restriction\nby adding native 3D rendering through the WebGL API. This technology brings established desktop applications online, bridging the gap between software platforms.\nThis thesis investigates how to implement Virtual Texturing for web browsers using WebGL and how to maintain high performance. Virtual Texturing is a recent approach\nto texture mapping that enables support for theoretically infinite image dimensions. In this thesis, Virtual Texturing is implemented with the help of several elements new to the HTML5 specification, such as Web Workers and Web Sockets. The thesis provides an introduction to the required browser features, an overview of relevant WebGL features,as well as a performance analysis. Results show that Virtual Texturing in WebGL is a viable approach for websites with high resource demands.
Endogenous Formation of Carbon Monoxide in Man Under Normal and Pathological Conditions (1949)

(1949). Endogenous Formation of Carbon Monoxide in Man Under Normal and Pathological Conditions. Scandinavian Journal of Clinical and Laboratory Investigation: Vol. 1, No. 3, pp. 201-214.
Relationship Between Intraocular Pressure and Primary Open Angle Glaucoma Among White and Black Americans (1991)

A detailed ocular examination, including perimetry, was conducted on 5308 black and white subjects aged 40 years and older in a population-based prevalence survey in east Baltimore, Md. Repeated, detailed examinations were carried out on selected subjects. Roughly half of all subjects with optic nerve damage from primary open angle glaucoma, regardless of race, were unaware that they had the condition. The average intraocular pressure (IOP) among black patients with glaucoma who were receiving treatment was virtually identical to that in those black patients who were not receiving treatment (median IOP, 20 mm Hg); treated eyes of white patients had a lower IOP than those eyes of white patients who were not receiving treatment (mean [+/- SD] IOP, 18.69 +/- 3.23 mm Hg vs 24.15 +/- 5.23 mm Hg; P less than .001). The risk of glaucomatous optic nerve damage increased with the height of the screening IOP, particularly at levels of 22 to 29 and 30 mm Hg and above (relative rate compared with IOP of 15 mm Hg or lower, 12.8 and 40.1 mm Hg, respectively). More than half of all glaucomatous eyes had a screening IOP below 21 mm Hg, whether these eyes were receiving treatment or not. The IOP in glaucomatous eyes tended to rise on follow-up, in contrast with nonglaucomatous eyes in which the IOP was as likely to rise as to fall. Results confirmed that IOP is an important factor in glaucoma, but did not support the traditional distinction between "normal" and "elevated" pressure, nor its corollaries, "low-tension" glaucoma and "high-tension" glaucoma.
Fluorescence in situ hybridization with human chromosome-specific libraries: detection of trisomy 21 and translocations of chromosome 4. (1988)

Chromosomes can be specifically stained in metaphase spreads and interphase nuclei by in situ hybridization with entire chromosome-specific DNA libraries. Unlabeled human genomic DNA is used to inhibit the hybridization of sequences in the library that bind to multiple chromosomes. The target chromosome can be made at least 20 times brighter per unit length than the others. Trisomy 21 and translocations involving chromosome 4 can be detected in metaphase spreads and interphase nuclei by using this technique.
Conformal Coating on Ultrahigh-Aspect-Ratio Nanopores of Anodic Alumina by Atomic Layer Deposition (2003)

Anodic alumina (AA) membranes are composed of highly uniform, nanometer-scale pores arranged in a hexagonal close-packed array. Depositing conformal films inside the nanopores is extremely difficult because the nanopores have an ultrahigh aspect ratio of L/d ≈ 103. Atomic layer deposition (ALD) is a thin film growth technique that can deposit highly uniform films on high-aspect-ratio substrates with monolayer thickness control. In this study, AA membranes were coated with Al2O3 and ZnO ALD films and subsequently analyzed using cross-sectional scanning electron microscopy (SEM) and electron probe microanalysis (EPMA). SEM analysis of individual nanopores revealed that the AA membranes with nanopore diameters of d = 65 nm and lengths of L = 50 μm could be coated conformally by Al2O3 ALD using sufficient reactant exposure times. Zn concentration profiles measured by EPMA following ZnO ALD showed the progressive infiltration of the ZnO ALD into the nanopores with increasing exposure times for aspect ratios as high as L/d ∼5000. Monte Carlo simulation of the experimental results assuming Knudsen diffusion accurately reproduced the experimental Zn concentration profiles and predicted the minimum ALD reactant exposures necessary to achieve conformal films. The Monte Carlo simulation also predicted that the diffusion-limited deposition will become reaction-limited given a sufficiently low ALD reaction probability. To test this idea, Fourier transform infrared absorption measurements were performed during the coating of the AA membranes by Al2O3 and SiO2 ALD. The surface reactions during Al2O3 ALD have a relatively high reaction probability of ∼10-3. In contrast, the surface reactions during SiO2 ALD have a very low reaction probability of ∼10-8. In agreement with the predictions, diffusion-limited behavior with a t1/2 time dependence was observed during Al2O3 ALD. Reaction-limited behavior with a t1 time dependence was observed during SiO2 ALD.
Non-Abelian Operations on Majorana Fermions via Single-Charge Control (2011)

We demonstrate that non-Abelian rotations within the degenerate ground-state manifold of a set of Majorana fermions can be realized by the addition or removal of single electrons, and propose an implementation using Coulomb blockaded quantum dots. The exchange of electrons generates rotations similar to braiding, though not in real space. Unlike braiding operations, rotations by a continuum of angles are possible, while still being partially robust against perturbations. The quantum dots can also be used for readout of the state of the Majorana system via a charge measurement.
Rationally Engineered Therapeutic Proteins with Reduced Immunogenicity (2005)

Chronic administration of protein therapeutics may elicit unacceptable immune responses to the specific protein. Our hypothesis is that the immunogenicity of protein drugs can be ascribed to a few immunodominant helper T lymphocyte (HTL) epitopes, and that reducing the MHC binding affinity of these HTL epitopes contained within these proteins can generate drugs with lower immunogenicity. To test this hypothesis, we studied the protein therapeutic erythropoietin (Epo). Two regions within Epo, designated Epo 91-120 and Epo 126-155, contained HTL epitopes that were recognized by individuals with numerous HLA-DR types, a property common to immunodominant HTL epitopes. We then engineered analog epitopes with reduced HLA binding affinity. These analog epitopes were associated with reduced in vitro immunogenicity. Two modified forms of Epo containing these substitutions were shown to be bioactive and nonimmunogenic in vitro. These findings support our hypothesis and demonstrate that immunogenicity of protein drugs can be reduced in a systematic and predictable manner.
One‐pot synthesis of symmetrically disubstituted 3H‐phenoxazin‐3‐ones by selective oxidative condensation with LTA (2007)

Abstract magnified image A one‐pot synthesis of some new 2,8‐disubstituted 3 H ‐phenoxazin‐3‐ones from 4‐substituted‐2‐aminophenols through a selective oxidative condensation by lead tetraacetate in acetic acid is described.
Design of a special dielectric lens for concentrating a subnanosecond electromagnetic pulse on a biological target (2009)

Analytical design procedures, numerical simulations and preliminary experimental results of a dielectric lens concentrating the field on a target are discussed. A quarter spherical electromagnetic lens with subsequent layers is used to obtain better focusing, smaller spot size and elimination of the reflection at the second focal point of a prolatespheroidal impulse radiating antenna for skin cancer treatment.
Mammalian Cytosine DNA Methyltransferase Dnmt1: Enzymatic Mechanism, Novel Mechanism-Based Inhibitors, and RNA-directed DNA Methylation (2008)

This is a review of the enzymatic mechanism of DNA methyltransferase Dnmt1 and analysis of its implications on regulation of DNA methylation in mammalian cells and design of novel mechanism-based inhibitors. The methylation reaction by Dnmt1 has different phases that depend on DNA substrate and allosteric regulation. Consequently, depending on the phase, the differences in catalytic rates between unmethylated and pre-methylated DNA can vary between 30-40 fold, 3-6 fold or only 1 fold. The allosteric site and the active site can bind different molecules. Allosteric activity depends on DNA sequence, methylation pattern and DNA structure (single stranded vs. double stranded). Dnmt1 binds poly(ADP-ribose) and some RNA molecules. The results on kinetic preferences, allosteric activity and binding preference of Dnmt1 are combined together in one comprehensive model mechanism that can address regulation of DNA methylation in cells; namely, inhibition of DNA methylation by poly(ADP-ribose), RNA-directed DNA methylation by methylated and unmethylated non-coding RNA molecules, and transient interactions between Dnmt1 and genomic DNA. Analysis of reaction intermediates showed that equilibrium between base-flipping and base-restacking events can be the key mechanism in control of enzymatic activity. The two events have equal but opposite effect on accumulation of early reaction intermediates and methylation rates. The accumulation of early reaction intermediates can be exploited to improve the current inhibitors of Dnmt1 and achieve inhibition without toxic modifications in genomic DNA. [1,2-dihydropyrimidin-2-one]-5-methylene-(methylsulfonium)-adenosyl is described as the lead compound.
Blocking signaling through the gp130 receptor chain by interleukin‐6 and oncostatin M inhibits PC‐3 cell growth and sensitizes the tumor cells to etoposide and cisplatin‐mediated cytotoxicity (1999)

BACKGROUND The mechanisms of drug resistance associated with advanced, hormone-independent prostate carcinoma are poorly understood. The human prostate carcinoma PC-3 cell line, derived from a metastatic tumor and lacking androgen receptors, represents a useful model to investigate drug resistance. METHODS The effects of oncostatin M (OM), antiinterleukin-6 (IL-6) treatment, or interference with the gp130-mediated signaling on etoposide- or cisplatin-mediated cytotoxicity were investigated. RESULTS Both endogenous and exogenous IL-6 and exogenous OM up-regulated cell growth and enhanced resistance of PC-3 tumor cells to both etoposide and cisplatin. The influence of IL-6 is controlled by treating PC-3 tumor cells with anti-IL-6 neutralizing antibody and, more efficiently, by a mutated IL-6, Sant7. Sant7 has a high affinity binding to the IL-6 receptor-α (IL-6Rα) subunit, but does not bind to the signaling subunit gp130; therefore, it behaves as a receptor antagonist. Both IL-6- and OM-mediated effects are inhibited by the treatment of PC-3 with an antisense oligodeoxynucleotide against gp130, the protein kinase inhibitor genistein (GNS), or the monoterpene perillic acid (PA), a posttranslational inhibitor of p21ras isoprenylation. CONCLUSIONS These results demonstrate the protective roles in drug sensitivity of IL-6 and OM through signaling of the common chain gp130 and, most likely, a downstream ras-dependent pathway in PC-3 tumor cells. These findings suggest the potential clinical application of anticytokine therapy or interference with gp130 signaling in the treatment of drug resistant prostate carcinoma. Cancer 1999;85:134–44. © 1999 American Cancer Society.
Survival in BRAF V600–Mutant Advanced Melanoma Treated with Vemurafenib (2012)

Vemurafenib induces clinical responses in more than half of patients with previously treated BRAF V600-mutant metastatic melanoma. In this study with a long follow-up, the median overall survival was approximately 16 months. (Funded by Hoffmann-La Roche; ClinicalTrials.gov number, NCT00949702.).
Proliferative senescence in hematopoietic stem cells during ex-vivo expansion. (2005)

The good outcome of hematopoietic stem cell (HSC) transplantation is hampered by low doses of CD34+ cell infusion. Transplanted HSCs undergo a replicative stress that causes accelerated senescence due to rapid telomere shortening. The expansion of human cord blood HSCs is instrumental in obtaining a large number of "good quality" cells, in terms of telomere length and telomerase activity compared to adult HSCs.
Volatilidad y Crecimiento en Países en Desarrollo: El Rol del Crédito y la Política Fiscal (2008)

El objetivo de este artículo es examinar el rol del crédito, el gasto en I+D y, la disciplina fiscal en su contribución a reducir la volatilidad, y al ajuste ante los shocks. Este aspecto es de especial relevancia para economías emergentes como la chilena, que están frecuentemente expuestas a las turbulencias internacionales. Además, por su condición de transición al desarrollo, estas economías enfrentan mayores distorsiones en el mercado de créditos que las economías maduras. Utilizando un análisis empírico de datos de panel para 72 países entre 1950 y 2004, se encuentra una correlación positiva entre crecimiento, desarrollo financiero, gasto en I+D y disciplina fiscal, y negativa entre volatilidad y las mismas variables. Los resultados son bastantes robustos para confirmar estas relaciones, así como una mayor velocidad de ajuste en economías con mejor acceso al crédito y mayor disciplina fiscal.
Structural analysis of two genes encoding divergent forms of yeast cytochrome c oxidase subunit V. (1987)

In Saccharomyces cerevisiae, subunit V of the inner mitochondrial membrane protein complex cytochrome c oxidase is encoded by two nonidentical genes, COX5a and COX5b. Both genes are present as single copies in S. cerevisiae and in several other Saccharomyces species. Nucleotide sequencing studies with the S. cerevisiae COX5 genes reveal that they encode proteins of 153 and 151 amino acids, respectively. Overall, the coding sequences of COX5a and COX5b have nucleotide and protein homologies of 67 and 66%, respectively. They are saturated for nucleotide substitutions that result in a synonomous codon, indicating a long divergence time between these two genes. Nucleotide sequences flanking the COX5a and COX5b coding regions exhibit no significant homology. The COX5a protein, pre-subunit Va, contains a 20-amino-acid leader peptide, whereas the COX5b protein, pre-subunit Vb, contains a 17-amino-acid leader peptide. These two leader peptides exhibit only 45% homology in the primary sequence, but have similar predicted secondary structures. By analyzing the RNA transcripts from both genes we have found that COX5a is a contiguous gene but that COX5b contains an intron. Surprisingly, the COX5b intron interrupts the AUG codon that initiates translation of the pre-subunit Vb polypeptide and contains a 5' donor splice sequence that differs from that normally found in yeast introns.
Direct transfection of viral and plasmid DNA into the liver or spleen of mice. (1984)

A method for the direct transfection of polyoma viral DNA and polyoma-plasmid recombinant DNA into the liver or spleen of newborn or adult mice was developed. Calcium phosphate-precipitated DNA was injected directly into mouse organs in combination with hyaluronidase and collagenase. Transfected DNA was shown to replicate at moderate efficiency, relative to direct infection of organs with virus. Transfection with viral DNA rapidly led to an acute infection. A polyoma-bacterial plasmid recombinant DNA also was shown to replicate when transfected into mice. With this plasmid, however, genomic-length polyoma DNA rapidly recombined away from the bacterial component and replicated as viral DNA. This method should allow the direct determination of the biological activity of a cloned DNA within a mouse organ.
Cysteine sulfenic Acid as an Intermediate in Disulfide Bond Formation and Nonenzymatic Protein Folding (2010)

As a posttranslational protein modification, cysteine sulfenic acid (Cys-SOH) is well established as an oxidative stress-induced mediator of enzyme function and redox signaling. Data presented herein show that protein Cys-SOH forms spontaneously in air-exposed aqueous solutions of unfolded (disulfide-reduced) protein in the absence of added oxidizing reagents, mediating the oxidative disulfide bond formation process key to in vitro, nonenzymatic protein folding. Molecular oxygen (O(2)) and trace metals [e.g., copper(II)] are shown to be important reagents in the oxidative refolding process. Cys-SOH is also shown to play a role in spontaneous disulfide-based dimerization of peptide molecules containing free cysteine residues. In total, the data presented expose a chemically ubiquitous role for Cys-SOH in solutions of free cysteine-containing protein exposed to air.
Chip-Scale Universal Detection Based on Backscatter Interferometry (2000)

An on-chip detector based on backscatter interferometry has been developed to perform subnanoliter-volume refractive index measurements. The detection system consists of a simple, folded optical train based on the interaction of a laser beam and an etched channel, consisting of two radii joined by a flat portion, thus defining a curved surface in the shape of a hemisphere in a silica (glass) plate. The backscattered light from the channel takes on the form of a high-contrast interference pattern that contains information related to the bulk properties of the fluid contained within the probe volume. Positional changes of the interference pattern (fringes) allow for the determination of deltan at the 10(-6) level, corresponding to 743 microM or 139 x 10(-15) mol or 12.8 x 10(-12) g of sucrose, in a probe volume of only 188 x 10(-12) L. A theoretical model of the on-chip backscatter interferometric detector has also been developed, evaluated, and found to be in agreement with experimental data. It is shown that the model can be used to predict general system performance for changes in the optical train such as the chip's wall thickness and channel diameter.
Revisiting the structures of several antibiotics bound to the bacterial ribosome (2010)

The increasing prevalence of antibiotic-resistant pathogens reinforces the need for structures of antibiotic-ribosome complexes that are accurate enough to enable the rational design of novel ribosome-targeting therapeutics. Structures of many antibiotics in complex with both archaeal and eubacterial ribosomes have been determined, yet discrepancies between several of these models have raised the question of whether these differences arise from species-specific variations or from experimental problems. Our structure of chloramphenicol in complex with the 70S ribosome from Thermus thermophilus suggests a model for chloramphenicol bound to the large subunit of the bacterial ribosome that is radically different from the prevailing model. Further, our structures of the macrolide antibiotics erythromycin and azithromycin in complex with a bacterial ribosome are indistinguishable from those determined of complexes with the 50S subunit of Haloarcula marismortui, but differ significantly from the models that have been published for 50S subunit complexes of the eubacterium Deinococcus radiodurans. Our structure of the antibiotic telithromycin bound to the T. thermophilus ribosome reveals a lactone ring with a conformation similar to that observed in the H. marismortui and D. radiodurans complexes. However, the alkyl-aryl moiety is oriented differently in all three organisms, and the contacts observed with the T. thermophilus ribosome are consistent with biochemical studies performed on the Escherichia coli ribosome. Thus, our results support a mode of macrolide binding that is largely conserved across species, suggesting that the quality and interpretation of electron density, rather than species specificity, may be responsible for many of the discrepancies between the models.