gebhart/patrepeval huggingface dataset:
Synthesis of (−)-Tetracycline (2005)

We describe a convergent, enantioselective synthesis of (-)-tetracycline (1) from benzoic acid (17 steps, 1.1% yield). Benzoic acid was transformed into the AB precursor 2 in 10 steps (11% yield), as previously described, and the latter compound was activated toward Diels-Alder cycloaddition by the introduction of an alpha-phenylthio group (two steps, 66% yield). Heating of the resulting alpha-(phenylthio)enone (3) with the triethylsilyloxybenzocyclobutene derivative 4 at 85 degrees C gave the endo-Diels Alder adduct 5 in 64% yield. Deprotection and oxidation of the latter intermediate gave the 2-(phenylthio)-1,3-diketone 7, which was oxidized with m-chloroperoxybenzoic acid in the presence of trifluoroacetic acid. The sulfoxide intermediate(s) formed eliminated upon warming to 35 degrees C to give the anyhydrotetracycline derivative 8. Intermediate 8 underwent spontaneous autoxidation at 23 degrees C to form the hydroperoxide keto-9 stereoselectively. Without isolation, hydrogenolysis of 9 in the presence of palladium black gave (-)-tetracycline (42% yield from 7), indistinguishable from an authentic sample.
Inhibition of angiogenesis (2013)

Arctigenin, a functional ingredient of several traditional Chinese herbs, has been reported to have potential antitumor activity. However, its mechanisms of action are still not well elucidated. Because the establishment and metastatic spread of tumors is crucially dependent on angiogenesis, here we investigated whether arctigenin inhibits tumor growth by disturbing blood vessel formation. For this purpose, human dermal microvascular endothelial cells were exposed to different arctigenin doses to study their viability, proliferation, protein expression, migration, and tube formation compared with vehicle-treated controls. In addition, arctigenin action on vascular sprouting was analyzed in an aortic ring assay. Furthermore, we studied direct arctigenin effects on CT26.WT colon carcinoma cells. Spheroids of these tumor cells were transplanted into the dorsal skinfold chamber of arctigenin-treated and vehicle-treated BALB/c mice for the in-vivo analysis of tumor vascularization and growth by intravital fluorescence microscopy, histology, and immunohistochemistry. We found that noncytotoxic doses of arctigenin dose dependently reduced the proliferation of human dermal microvascular endothelial cells without affecting their migratory and tube-forming capacity. Arctigenin treatment also resulted in a decreased cellular expression of phosphorylated serine/threonine protein kinase AKT, vascular endothelial growth factor receptor 2, and proliferating cell nuclear antigen and inhibited vascular sprouting from aortic rings. In addition, proliferation, but not secretion of vascular endothelial growth factor, was decreased in arctigenin-treated tumor cells. Finally, arctigenin suppressed the vascularization and growth of engrafting CT26.WT tumors in the dorsal skinfold chamber model. Taken together, these results show for the first time an antiangiogenic action of arctigenin, which may contribute considerably toward its antitumor activity.
Blending parametric surfaces (1989)

A blending surface is a surface that smoothly connects two given surfaces along two arbitrary curves, one on each surface. This is particularly useful in the modeling operations of filleting a sharp edge between joining surfaces or connecting disjoint surfaces. In this paper we derive a new surface formulation for representing surfaces which are blends of parametric surfaces. The formulation has the advantage over the traditional rational polynomial approach in that point and normal values have no gaps between the blending surface and the base surfaces. Shape control parameters that control the cross-sectional shape of the blending surface are also available. In addition, the base surfaces are not restricted to any particular type of surface representation as long as they are parametrically defined and have a well-defined and continuous normal vector at each point. The scheme is extensible to higher orders of geometric continuity, although we concentrate on G 1 .
Expression of human telomerase reverse transcriptase gene and protein, and of estrogen and progesterone receptors, in breast tumors: Preliminary data from neo-adjuvant chemotherapy (2005)

Human telomerase reverse transcriptase (hTERT), the catalytic subunit of telomerase, is very closely associated with telomerase activity. Telomerase has been implicated in cellular immortalization and carcinogenesis. In situ detection of hTERT will aid in determining the localization of telomerase-positive cells. The aim of this study was to detect expression of hTERT mRNA, hTERT protein, estrogen receptor (ER) and progesterone receptor (PR) in paraffin-embedded breast tissue samples and to investigate the relationship between hTERT expression and various clinicopathological parameters in breast tumorigenesis. We used in situ hybridization (ISH) to examine hTERT gene expression, and immunohistochemistry (IHC) to examine expression of hTERT protein, ER and PR, in breast tissues including 64 adenocarcinomas, 2 phyllode tumors and their adjacent normal breast tissues. hTERT gene expression was detected by ISH in 56 (88%) carcinomas, but in neither of the 2 phyllode tumors. hTERT protein expression was detected by IHC in 52 (81%) carcinomas, but in neither of the 2 phyllode tumors. Moreover, ER and PR were expressed in 42 (66%) and 42 (66%) carcinomas, respectively, and in neither of the 2 phyllode tumors. In 4 cases of breast carcinoma that strongly expressed hTERT gene and protein before treatment, neo-adjuvant chemotherapy led to disappearance of gene and protein expression in all cases. There was a strong correlation between detection of hTERT gene expression by ISH and of hTERT protein by ICH in tissue specimens from breast tumors. These results suggest that detection of hTERT protein by ICH can be used to distinguish breast cancers as a potential diagnostic and therapeutic marker.
Determination of phosphorus and metals in human brain proteins after isolation by gel electrophoresis by laser ablation inductively coupled plasma source mass spectrometry (2004)

Phosphorus, sulfur, silicon and metal concentrations (Al, Cu and Zn) were determined in human brain proteins by laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) after separation of protein mixtures by two dimensional (2-D) gel electrophoresis. The analysis of phosphorus, silicon and metals in single protein spots in the gel was performed with an optimized microanalytical method using a double-focusing sector field inductively coupled plasma mass spectrometer coupled to a commercial laser ablation system (LA-ICP-MS). Relative ion intensities for P, Si and metals with respect to sulfur in protein spots were determined by LA-ICP-MS. The detection limits for phosphorus and sulfur in protein spots with a silver staining procedure on the 2-D gels were compared with the Coomassie staining technique described previously.
Amodiaquine N‐oxides and other 7‐chloro‐4‐aminoquinoline n‐oxides (1964)

Abstract Oxidation of amodiaquine with perbenzoic acid gave amodiaquine N‐α‐oxide, whereas N 4 ‐methylamodiaquine and amodiaquine 1‐oxide afforded N 4 ‐methylamodiaquine N‐α,1‐dioxide and amodiaquine N‐α, 1‐dioxide, respectively. Amodiaquine 1‐oxide, O ‐methyl‐amodiaquine 1‐oxide, oxychloroquine 1‐oxide, and a variety of other 4 ‐ (7‐chloro‐4‐quinolylamino)‐α‐dialkylamino‐ o ‐cresol 1‐oxides and 7‐chloro‐4‐[(mono‐ and dialkylamino)‐alkylamino]quinoline 1‐oxides were prepared by the condensation of 4, 7‐dichloroquinoline 1‐oxide with a 4‐amino‐α‐(dialkylamino)‐ o ‐cresol, N‐α, N‐α‐diethyl‐6‐methoxytoluene‐α, ‐3‐diamine, or a mono‐ or dialkylaminoalkylamine in phenol or aqueous ethanol. N 4 ‐Methyl‐amodiaquine was synthesized from p ‐ [(7‐chloro‐4‐quinolyl)methylamino]phenol, diethyl‐amine, and paraformaldehyde. Many of the N‐oxides are highly active against the plasmodia of malaria.
Multiple Phosphoinositide 3-Kinase-Dependent Steps in Activation of Protein Kinase B (2002)

The protein kinase B (PKB)/Akt family of serine kinases is rapidly activated following agonist-induced stimulation of phosphoinositide 3-kinase (PI3K). To probe the molecular events important for the activation process, we employed two distinct models of posttranslational inducible activation and membrane recruitment. PKB induction requires phosphorylation of two critical residues, threonine 308 in the activation loop and serine 473 near the carboxyl terminus. Membrane localization of PKB was found to be a primary determinant of serine 473 phosphorylation. PI3K activity was equally important for promoting phosphorylation of serine 473, but this was separable from membrane localization. PDK1 phosphorylation of threonine 308 was primarily dependent upon prior serine 473 phosphorylation and, to a lesser extent, localization to the plasma membrane. Mutation of serine 473 to alanine or aspartic acid modulated the degree of threonine 308 phosphorylation in both models, while a point mutation in the substrate-binding region of PDK1 (L155E) rendered PDK1 incapable of phosphorylating PKB. Together, these results suggest a mechanism in which 3' phosphoinositide lipid-dependent translocation of PKB to the plasma membrane promotes serine 473 phosphorylation, which is, in turn, necessary for PDK1-mediated phosphorylation of threonine 308 and, consequentially, full PKB activation.
Photodynamic therapy for sarcoma pulmonary metastases: a preclinical toxicity study. (2004)

Histologic and clinical changes associated with interstitial and pleural PDT were acceptable after dosimetry was adjusted. PDT holds promise as an adjuvant treatment for sarcoma pulmonary metastases.
NudgeCam (2010)

NudgeCam is a mobile application that can help users capture more relevant, higher quality media. To guide users to capture media more relevant to a particular project, third-party template creators can show users media that demonstrates relevant content and can tell users what content should be present in each captured media using tags and other meta-data such as location and camera orientation. To encourage higher quality media capture, NudgeCam provides real time feedback based on standard media capture heuristics, including face positioning, pan speed, audio quality, and many others. We describe an implementation of NudgeCam on the Android platform as well as field deployments of the application.
Circulating nucleosomes as epigenetic biomarkers in pancreatic cancer (2015)

The present study suggests that global epigenetic profiling of cfnucleosomes in serum using a simple NuQ(®) immunoassay-based approach can provide novel diagnostic biomarkers in pancreatic cancer.
Ovarialkarzinomzellen unterdrücken anti-tumorale Immunantworten durch extrazelluläre Generierung von Adenosin via CD39 und CD73 (2009)

In humanen Ovarialkarzinomen korreliert die Infiltration durch regulatorische T Zellen (Treg) mit einer ungünstigen Prognose. Treg können im Tumorkontext wünschenswerte Immunantworten inhibieren, indem sie ATP mittels der Ektonukleotidasen CD39 und CD73 zu Adenosin abbauen, das über den Adenosin 2a-Rezeptor (ADORA2A) hemmend auf T und NK Zellen wirkt. Die vorliegende Arbeit untersucht, inwiefern humane Ovarialkarzinomzellen diesen Mechanismus selber zum „tumor immune escape“ nützen können.
Quantitative Methods for Anthocyanins. (1968)

SUMMARY— The method developed consists of extracting the anthocyanins with ethanol‐1.5N hydrochloric acid (85:15) and measuring the O.D. of the extract, diluted with the extracting solvent, at 535 nm. The total anthocyanin content was calculated in absolute quantities with the aid of the extinction coefficients established for the four major cranberry anthocyanins dissolved in the alcoholic solvent system.
Robot localization using a computer vision sextant (2002)

This paper explores the possibility of using Sun altitude for localization of a robot in totally unknown territory. A set of Sun altitudes is obtained by processing a sequence of time-indexed images of the sky. Each altitude constrains the viewer to a circle on the surface of a celestial body, called the circle of equal altitude. A set of circles of equal altitude can be intersected to yield viewer position. We use this principle to obtain the position on Earth. Since altitude measurements are corrupted by noise, a least-square estimate is numerically calculated from the sequence of altitudes. The paper discusses the necessary theory for Sun-based localization, the technical issues of camera calibration and image processing, and presents preliminary results with real data.
Oxygen, Epigenetics and Stem Cell Fate (2005)

Coordinated interactions between the embryo/fetus and its environment are critical for proper development. In addition to acting as metabolic substrates for cellular homeostasis, basic physiological factors, such as oxygen tension, have a profound influence on developmental outcomes. Since the mammalian embryo resides in a physiologically hypoxic environment during gestation, understanding its responses to oxygen deprivation on a cellular level is critical. In this review, we analyze interactions between the hypoxia-inducible factor family of transcriptional regulators and epigenetic mechanisms governing chromatin structure. The ability of hypoxia-inducible factors to interact physically with histone deacetylase (HDAC) enzymes and modulate nuclear HDAC activities places them in the pivotal position of integrating physiological and epigenetic effectors. Multiple embryonic and extra-embryonic stem cell populations in mice and humans rely on this interaction--an important determinant of stem cell fate. Dissection of the pathways involved will provide novel insights into the metabolic as well as molecular determinants of the stem cell niches that allow self-renewal of progenitors in an undifferentiated state.
Observations of a gel phase in binary mixtures of semifluorinated n-alkanes with hydrocarbon liquids (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleObservations of a gel phase in binary mixtures of semifluorinated n-alkanes with hydrocarbon liquidsRobert J. Twieg, Thomas P. Russell, R. Siemens, and John F. RaboltCite this: Macromolecules 1985, 18, 6, 1361–1362Publication Date (Print):June 1, 1985Publication History Published online1 May 2002Published inissue 1 June 1985https://pubs.acs.org/doi/10.1021/ma00148a060https://doi.org/10.1021/ma00148a060research-articleACS PublicationsRequest reuse permissionsArticle Views291Altmetric-Citations100LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Enhanced Anti-Tumor Effects with Microencapsulated c- myc Antisense Oligonucleotide (1999)

A phosphorothioate c-myc antisense oligonucleotide was complexed with zinc and encapsulated into injectable biodegradable microspheres. The efficacy of this novel formulation was compared with intravenous administration of the unencapsulated drug in human melanoma and leukemia xenografts in immunocompromised mice. The microencapsulated formulation was more effective as shown by reduced tumor growth, a decreased number of metastases, reduced c-myc expression, and increased survival in the melanoma model, and decreased metastatic potential and increased survival in the leukemia model. These results show that, as has been demonstrated previously with protein and peptide drugs, greater therapeutic efficacy can be obtained when antisense oligonucleotides are delivered from sustained-release formulations.
Visible Progress Made in Three-Dimensional Photonic ‘Crystals’ (1999)

Spurred by the success of the semiconductor industry, researchers are trying to push circuit devices to higher speeds and greater functionality by using photons rather than electrons. At the heart of the semiconductor technology is the electronic bandgap, a range of energies within which electrons cannot propagate through a material. It turns out that certain material structures can have a photonic bandgap. a range of forbidden frequencies within which light cannot be transmitted. The electronic bandgap results from the periodic arrangement of atoms in the semiconductor; the photonic analog stems from a regular array of dielectric material, known as a photonic crystal.
Peptide Aptamer Libraries (2008)

Peptide aptamers are molecules that bind to protein targets and are able to interfere with their functions. In the past, important achievements have been made using such peptide aptamers in different approaches and for various purposes. Peptide aptamers are comprised of a variable peptide region of 8 to 20 amino acids in length, which is displayed by a scaffold protein. An overview of the numerous scaffold proteins that have been investigated for their suitability to present peptide aptamers will be given. To identify peptide aptamers efficiently and specifically binding to a predetermined target, two eukaryotic systems have been used in multiple studies: a modified version of the Gal4 yeast-two-hybrid system and the optimized LexA interaction trap system. The two yeast systems are compared and the design of high-complexity peptide aptamer libraries for these systems is described. Although the yeast-two-hybrid system is based on intracellular interactions mammalian screens, performed in cell culture experiments, are sometimes preferred or required. We will give an overview of the mammalian selection systems available, which are based on the expression of peptide aptamers in retroviral or lentiviral vectors. We will show that the isolation and use of peptide aptamers as inhibitors of individual signaling components represents a new challenge for drug development.
Optimization of Substrate Doping for Back-Gate Control in SOI T-RAM Memory Technology (2006)

This paper presents various considerations for substrate doping optimization in SOI T-RAM technology. Back gate (substrate voltage) control is used in an SOI T-RAM technology for optimizing cell characteristics. However, it is reported for the first time that typical low-doped substrates used in SOI logic technologies can create unusually slow transient effects in T-RAM cell. It is also demonstrated that the optimization of substrate doping resolves this slow transient problem and improves back gate control of SOI T-RAM memory arrays.
Production of Ethanol by Continuous Fermentation and Liquid-Liquid Extraction (1996)

A continuous pilot plant was constructed for fermentation production of ethanol, using liquid–liquid extraction to remove the product and with recycle of the fermented broth raffinate. The plant was operated for up to 18 days with feed glucose concentrations in the range 10·0–45·8% (w/w). The solvent was n-dodecanol and immobilised yeast was used to overcome the problem of emulsification. The concentration of by-products in the fermented broth had no adverse effect on the rate of ethanol production. A mathematical model to predict the time required for achievement of 99% of the steady-state by-products concentrations was shown to be in good agreement with the experimentally determined concentration of the main by-product, glycerol. At a feed glucose concentration of 45·8% (w/w), the aqueous purge was equivalent to 2·8 m3 of effluent per m3 of ethanol produced and represented a 78% reduction in the volume of the aqueous purge compared with using a feed containing 10% (w/w) glucose.
Immunological Optimization of a Generic Hydrophobic Pocket for High Affinity Hapten Binding and Diels–Alder Activity (2004)

Antibody 1E9, which binds a tetrachloronorbornene derivative with subnanomolar affinity and catalyzes the Diels-Alder reaction between tetrachlorothiophene dioxide and N-ethylmaleimide with high efficiency, arose from a family of highly restricted germ-line immunoglobulins that bind diverse hydrophobic ligands. Two somatic mutations, one at position L89 in the light chain (SerL89Phe) and another at position H47 in the heavy chain (TrpH47Leu), have been postulated to be responsible for the unusually high degree of shape and chemical complementarity observed in the crystal structure of 1E9 complexed with its hapten. To test this hypothesis, the germ-line sequence at these two positions was restored by site-directed mutagenesis. The ensuing 160 to 3900-fold decrease in hapten affinity and the complete loss of catalytic activity support the hypothesis that these somatic mutations substantially remodel the antibody binding pocket. Mutation of the highly conserved hydrogen-bond donor AsnH35, which sits at the bottom of the active site and is a hallmark of this family of antibodies, is also catastrophic with respect to hapten binding and catalysis. In contrast, residues in the CDR H3 loop, which contributes a significant fraction of the hapten-contacting protein surface, have a more subtle influence on the properties of 1E9. Interestingly, while most changes in this loop have neutral or modestly deleterious effects, replacement of MetH100b at the floor of the pocket with phenylalanine leads to a significant sevenfold increase in catalytic activity. The latter result is surprising given the unusually close fit of the parent antibody to the transition-state analogue. Further fine-tuning of the interactions between 1E9 and its ligands by introducing mutations outside the active site could conceivably yield substantially more active catalysts.
Linear inversion for source signatures from ministreamer data (2000)

Estimation of the source signature, an old and important problem in exploration seismology, is becoming even more important. Areas where this knowledge is potentially of great value are onboard source array QC, deconvolution, multiple attenuation, tying reflection data to wells, modeling and inversion, AVO analysis, reservoir monitoring, and analysis of marine multicomponent recordings.
Identification of differentially expressed genes in human prostate cancer using subtraction and microarray. (2000)

We have identified human prostate cancer- and tissue-specific genes using cDNA library subtraction in conjunction with high throughput microarray screening. Subtracted cDNA libraries of prostate tumors and normal prostate tissue were generated. Characterization of subtracted libraries showed enrichment of both cancer- and tissue-specific genes. Highly redundant clones were eliminated by colony hybridization. The remaining clones were selected for microarray to determine gene expression levels in a variety of tumor and normal tissues. Clones showing overexpression in prostate tumors and/or normal prostate tissues were selected and sequenced. Here we report the identification of two genes, P503S and P504S, from subtracted libraries and a third gene, P510S, by subtraction followed by microarray screening. Their expression profiles were further confirmed by Northern blot, real-time PCR (TaqMan), and immunohistochemistry to be overexpressed in prostate tissues and/or prostate tumors. Full-length cDNA sequences were cloned, and their subcellular locations were predicted by a bioinformatic algorithm, PSORT, to be plasma membrane proteins. The genes identified through these approaches are potential candidates for cancer diagnosis and therapy.