gebhart/patrepeval huggingface dataset:
Gonadal steroid regulation of oxytocin and oxytocin receptor gene expression. (1995)

By Northern blot analysis and in situ hybridization, we have determined that, at term, the rat uterine epithelium represents a major site of oxytocin (OT) gene expression. OT mRNA levels increase > 150-fold during pregnancy and, at term, exceed hypothalamic OT mRNA by a factor of 70. By cryoultramicroscopy, OT immunoreactivity was localized to transport vesicles in the apical compartment of uterine epithelial cells. Estrogens (E) act as a strong inducer of uterine OT gene expression in vivo, and this effect is potentiated 7-fold by concomitant progesterone (P) administration. We have also cloned the rat OT receptor (OTR) gene and developed a polymerase chain reaction (PCR)-based assay to measure OTR mRNA. Whereas OTR mRNA is strongly induced by E, P does not potentiate but slightly attenuates the E-induced rise. However, E-induced OT binding is completely reversed by concomitant P administration, suggesting an additional post-transcriptional effect of P. The mechanisms of E-induction of the uterine OT gene remain unclear, inasmuch as the OTR gene promoter does not contain a classical estrogen response element (ERE). Moreover, transfection analysis of a 3.1 kb OTR gene promoter fragment linked to a luciferase reporter gene indicates that promoter activity is induced 5-fold by calcium ionophore A23187 but not by E.
Principles of Virology: Molecular Biology, Pathogenesis, and Control (1999)

Part I: The Science of Virology1. Foundations of Virology2. Virus Cultivation, Detection, and Genetics Part II: Molecular Biology3. Virus Structure4. Virus Attachment to Host Cells5. Virus Entry into Cells6. Genome Replication and mRNA Production by RNA Viruses7. Reverse Transcription and Integration: Hallmarks of the Retroid Viruses8. Transcription Strategies: DNA Templates9. Genome Replication Strategies: DNA Viruses10. Processing of Viral Pre-mRNA11. Translational Control of Viral Gene Expression12. Intracellular Transport of Viral Components: Prelude to Assembly13. Assembly, Exit, and Maturation of Progeny Virions Part III: Pathogenesis and Control14. Virus Offense Meets Host Defense15. Patterns of Infection: a Delicate Balance16. Viral Transformation and Oncogenesis17. Viral Pathogenesis18. Multiple Facets of HIV Pathogenicity19. Prevention and Control of Viral Diseases20. Virus Evolution and the Emergence of New Viruses Appendix: Structure, Genome Organization, and Infectious Cycles of Animal Viruses Discussed in This Book
Bombesin, vasopressin, and endothelin stimulation of tyrosine phosphorylation in Swiss 3T3 cells. Identification of a novel tyrosine kinase as a major substrate. (1992)

Neuropeptide-stimulated tyrosine phosphorylation of specific components in Swiss 3T3 cells was investigated using monoclonal antibodies directed against the src transformation-associated substrates p125 focal adhesion kinase (FAK), a novel type of cytosolic tyrosine kinase, and p130. Treatment of Swiss 3T3 cells with the mitogenic peptides bombesin, vasopressin, and endothelin caused a striking increase in the tyrosine phosphorylation of p125FAK, as judged either by anti-phosphotyrosine (anti-Tyr(P)) Western blots of anti-p125FAK immunoprecipitates, or by anti-p125FAK immunoblots of anti-Tyr(P) immunoprecipitates. Bombesin-stimulated tyrosine phosphorylation of p125FAK was detectable within seconds and concentration-dependent (half-maximum effect of 0.3 nM). Neuropeptides also stimulated the tyrosine phosphorylation of a second component of M(r) 130,000, previously identified as the major p130 phosphotyrosyl protein in src-transformed cells. Bombesin stimulated p130 tyrosine phosphorylation with kinetics and concentration dependence similar to those observed for p125FAK. This is the first report to identify substrates for neuropeptide-stimulated tyrosine phosphorylation; the finding that one of these substrates is a tyrosine kinase suggests the existence of a novel signal transduction pathway in the action of mitogenic neuropeptides.
Study of Cell Antigens and Intracellular DNA by Identification of Element-Containing Labels and Metallointercalators Using Inductively Coupled Plasma Mass Spectrometry (2008)

The enumeration of absolute cell numbers and cell proliferation in clinical samples is important for diagnostic and research purposes. Detection of cellular DNA with fluorescent dyes is the most commonly used approach for cell enumeration in cytometry. Inductively coupled plasma mass spectrometry (ICPMS) has been recently introduced to the field of protein and cell surface antigen identification via ICPMS-linked immunoassays using element-labeled affinity reagents such as gold and lanthanide-conjugated antibodies. In the present work, we describe novel methods for using metallointercalators that irreversibly bind DNA and low concentrations of rare earth metals added to cell growth media for rapid and sensitive measurement of cell numbers by mass spectrometry. We show that Ir- and Rh-containing metallointercalators are useful reagents for labeling cells and normalizing signals when studying antigen expression on different types and numbers of cells. Results are presented for solution analysis performed by conventional ICPMS and compared to measurements obtained on the novel flow cytometer mass spectrometer (FC-MS) instrument, designed to analyze multiple antigens and DNA simultaneously in single cells.
Glycoform heterogeneity of porcine interferon-gamma expressed in Sf9 cells. (1994)

Porcine interferon-gamma (SfPoIFN-gamma) was expressed with high efficiency in Spodoptera frugiperda (Sf9) cells by means of the baculovirus expression system. Up to 10(5) U/ml of antivirally active SfPoIFN-gamma could be tracked down in the culture medium at 64 h postinfection. Three proteins (17, 19, and 21 kDa), which under nondenaturing conditions primarily exist as mutual-dimeric combinations, were purified by immunoaffinity chromatography. Carbohydrate labeling and kinetic deglycosylation studies suggested that the 19- and 21-kDa proteins are N-glycosylated variants of a single 17-kDa protein carrying no N-linked sugars, in which one respectively two N-glycosylation sequons are occupied by glycans of 2 kDa. Both the quantitative recovery of SfPoIFN-gamma from a Con A column at 0.2 M methyl-alpha-mannopyranoside and the results of lectin blots, revealing strong affinity of the 19- and 21-kDa species for Galanthus nivalis agglutinin, support the presence of N-glycosidically linked high mannose-type chains in the carbohydrate moiety of SfPoIFN-gamma. Intriguingly, both 19- and 21-kDa glycoforms, but not their sialidase-treated derivatives, showed clear reactivity with the Sambucus nigra and Maackia amurensis agglutinins. These agglutinins specifically recognize sialic acid linked alpha(2-6) and alpha(2-3), respectively, to penultimate galactose residues. Their affinity for the larger glycoforms of PoIFN-gamma suggests that the biosynthetic pathways in Sf9 cells are able to modify oligomannose structures to complex or hybrid glycans.
Purification and characterization of two forms of I-DmoI, a thermophilic site-specific endonuclease encoded by an archaeal intron. (1994)

The archaeal intron in the 23 S rRNA gene of the hyperthermophile Desulfurococcus mobilis has previously been shown to encode a site-specific DNA endonuclease that contains the LAGLIDADG motif. The enzyme, I-DmoI, has been shown to be active in two forms when expressed in vitro, from RNAs representing either the linear (I-DmoIl) or circular (I-DmoIc) intron. In this study we have overexpressed I-DmoIl and I-DmoIc and purified the enzymes from Escherichia coli. The optimal conditions for the enzymatic activity in vitro were determined, and the enzyme was used to delimit the recognition boundary on its DNA substrate (14-20 nucleotides), an intronless 23 S rRNA gene. Despite belonging to the archaeal kingdom, and being the product of a hyperthermophile, I-DmoI shares many properties with LAGLIDADG intron and intein endonucleases in other kingdoms. These results support the view that these phylogenetically diverse enzymes, which function to mobilize the DNA sequences that encode them, share a common ancestry.
Histamine Antagonizes Tumor Necrosis Factor (TNF) Signaling by Stimulating TNF Receptor Shedding from the Cell Surface and Golgi Storage Pool (2003)

Tumor necrosis factor (TNF) activates pro-inflammatory functions of vascular endothelial cells (EC) through binding to receptor type 1 (TNFR1) molecules expressed on the cell surface. The majority of TNFR1 molecules are localized to the Golgi apparatus. Soluble forms of TNFR1 (as well as of TNFR2) can be shed from the EC surface and inhibit TNF actions. The relationships among cell surface, Golgi-associated, and shed forms of TNFR1 are unclear. Here we report that histamine causes transient loss of surface TNFR1, TNFR1 shedding, and mobilization of TNFR1 molecules from the Golgi in cultured human EC. The Golgi pool of TNFR1 serves both to replenish cell surface receptors and as a source of shed receptor. Histamine-induced shedding is blocked by TNF-alpha protease inhibitor, an inhibitor of TNF-alpha-converting enzyme, and through the H1 receptor via a MEK-1/p42 and p44 mitogen-activated protein kinase pathway. Cultured EC with histamine-induced surface receptor loss become transiently refractory to TNF. Histamine injection into human skin engrafted on immunodeficient mice similarly caused shedding of TNFR1 and diminished TNF-mediated induction of endothelial adhesion molecules. These results both clarify relationships among TNFR1 populations and reveal a novel anti-inflammatory activity of histamine.
Characterization of rubber particles and rubber chain elongation in Taraxacum koksaghyz (2010)

T. koksaghyz rubber particles are similar to those described for H. brasiliensis. They contain very pure, high molecular mass poly(cis-1,4-isoprene) and the chain elongation process can be studied ex vivo. Because of their localization on rubber particles and their activity in yeast, we propose that the recently described T. koksaghyz CPTs are the major rubber chain elongating enzymes in this species. T. koksaghyz is amenable to genetic analysis and modification, and therefore could be used as a model species for the investigation and comparison of rubber biosynthesis.
Ketone-DNA:  A Versatile Postsynthetic DNA Decoration Platform (2001)

[reaction: see text] A general strategy for the functional diversification of DNA oligonucleotides under physiological conditions was developed. We describe the synthesis of DNA molecules bearing ketone ports (ketone-DNA) and the efficient postsynthetic decoration of ketone-DNA with structurally diverse aminooxy compounds.
Glassy Chimeras Could Be Blind to Quantum Speedup: Designing Better Benchmarks for Quantum Annealing Machines (2014)

Recent benchmarking of the computational speedup of quantum ``annealing'' machines of the D-Wave-2 type shows that they do not perform faster than a standard desktop computer. A timely theoretical study of the computational tests used in the benchmarking explains why that may be the case.
CD151 enhances cell motility and metastasis of cancer cells in the presence of focal adhesion kinase (2001)

We have examined the role of the protein CD151 in cell motility, invasion and metastasis of cancer cells by using CD151-overexpressing cells prepared by transfection of CD151 cDNA into three cancer cell lines established from different origins; a human colon cancer RPMI4788, a human glioblastoma A172 and a human fibrosarcoma HT1080. Invasion into Matrigel and cell motility of all 3 CD151-overexpressing cancer cells were enhanced significantly when compared to control parental cells. Pulmonary metastasis of 2 metastatic CD151-overexpressing cancer cell lines, RPMI4788/CD151 and HT1080/CD151, was higher than that of control parental cells and was markedly inhibited by anti-CD151 monoclonal antibody (MAb), SFA1.2B4. To examine whether focal adhesion kinase (FAK) is associated with promotion of cell motility and invasion of cancer cells through CD151, we transfected human CD151 cDNA into FAK (+/+) or FAK (-/-) fibroblasts that were isolated from embryos in FAK-deficient mice and compared invasion into Matrigel and cell motility between each CD151-transfected cells and controls. The invasion into Matrigel and cell motility of CD151-transfected FAK (+/+) fibroblasts increased significantly above those of parental cells and were inhibited by anti-CD151 MAb, whereas those of CD151-transfected FAK (-/-) fibroblasts were not enhanced at all and were not blocked by anti-CD151 MAb. These findings indicate that the CD151 molecule enhances cell motility, invasion and metastasis of cancer cells and that FAK is needed for these events through CD151.
Transcriptional Control and Cell Type Specificity of HPV Gene Expression (1994)

An intricate interplay between cellular and viral transcription factors is a prerequisite for epithelial specificity, physiologic responses, and persistence of papillomavirus infections.
Isolation and characterization of an esterified form of steryl glucoside (1964)

A hitherto unreported esterified form of steryl glucoside has been isolated from potato tuber lipids and soybean phosphatides. It is composed of sterol, glucose, and fatty acid in the molar ratio 1:1:1. Four components of the sterol moiety have been detected ; they include Β-sitosterol and stigmasterol (identified by gas–liquid chromatography). Fatty acids are palmitic, stearic, oleic, linoleic, and linolenic acids. As demonstrated by infrared analysis and periodate oxidation, the fatty acid is located on C6 of the sugar portion.
3‐Phenacylidene‐3,4‐dihydro‐1H‐pyrido[2,3‐b]pyrazin‐2‐ones and 2‐Phenacylidene‐1,2‐dihydro‐4H‐pyrido[2,3‐b]pyrazin‐3‐ones (1995)

Abstract Condensation of 2,3‐diaminopyridine ( 1 ) with ethyl o‐, m ‐ and p ‐substituted benzoylpyruvates 2–9 gave two isomeric products. The preferential formation of one or the other isomer has been achieved by different reaction conditions. All the products appear to exist in the enamine form as evidenced by their 1 H nmr and ir spectra.
Fc-Silent Anti-CD154 Domain Antibody Effectively Prevents Nonhuman Primate Renal Allograft Rejection (2017)

The advent of costimulation blockade provides the prospect for targeted therapy with improved graft survival in transplant patients. Perhaps the most effective costimulation blockade in experimental models is the use of reagents to block the CD40/CD154 pathway. Unfortunately, successful clinical translation of anti-CD154 therapy has not been achieved. In an attempt to develop an agent that is as effective as previous CD154 blocking antibodies but lacks the risk of thromboembolism, we evaluated the efficacy and safety of a novel anti-human CD154 domain antibody (dAb, BMS-986004). The anti-CD154 dAb effectively blocked CD40-CD154 interactions but lacked crystallizable fragment (Fc) binding activity and resultant platelet activation. In a nonhuman primate kidney transplant model, anti-CD154 dAb was safe and efficacious, significantly prolonging allograft survival without evidence of thromboembolism (Median survival time 103 days). The combination of anti-CD154 dAb and conventional immunosuppression synergized to effectively control allograft rejection (Median survival time 397 days). Furthermore, anti-CD154 dAb treatment increased the frequency of CD4<sup>+</sup> CD25<sup>+</sup> Foxp3<sup>+</sup> regulatory T cells. This study demonstrates that the use of a novel anti-CD154 dAb that lacks Fc binding activity is safe without evidence of thromboembolism and is equally as potent as previous anti-CD154 agents at prolonging renal allograft survival in a nonhuman primate preclinical model.
Oscillator strengths, quantum efficiencies, and laser cross sections of Yb3+ and Er3+ in III-V compounds (1989)

An absolute oscillator strength is obtained for the first time for a rare earth in a III-V compound semiconductor. The value for Yb3+ in InP is f=(3±1)×10−6. It is of same order as for insulating ionic hosts, confirming what available theory can predict. From observed emission spectra, laser cross sections of 10−21 cm2 for Yb3+ at 1.0 μm and &amp;lt;1.4×10−20 cm2 for Er3+ at 1.54 μm are obtained. Yb3+, entering III-V compounds more covalently, presents a quantum efficiency for direct photon excitation two orders of magnitude smaller than Er3+. Predicted laser gains are in the range of 10−2 to a few 10−1 cm−1, showing that gains will be marginal in semiconductor devices of usual dimensions.
The race‐specific elicitor AVR9 of the tomato pathogen Cladosporium fulvum: a cystine knot protein (1997)

The secondary structure and global fold of the AVR9 elicitor protein of Cladosporium fulvum has been determined by 2D NMR and distance-geometry protocols. The protein consists of three anti-parallel strands forming a rigid region of beta-sheet. On the basis of the NMR-derived parameters and distance geometry calculations, it is evident that the AVR9 protein is structurally very homologuous to carboxy peptidase inhibitor (CPI) of which the X-ray structure is known. The AVR9 protein reveals the presence of a cystine knot, which consists of a ring formed by two disulfide bridges and the interconnecting backbone through which the third disulfide bridge penetrates. This structural motif is found in several small proteins such as proteinase inhibitors, ion channel blockers and growth factors. The implications of the structural relationship between AVR9 and other biologically active proteins are discussed.
Progress report of combined chemoradiotherapy versus radiotherapy alone in patients with esophageal cancer: an intergroup study. (1997)

We conclude that cisplatin and 5FU infusion given during and post-RT of 50 Gy is statistically superior to standard 64-Gy RT alone in patients with locally advanced esophageal cancer.
C4 Isoform of NADP-Malate Dehydrogenase (cDNA Cloning and Expression in Leaves of C4, C3, and C3-C4 Intermediate Species of Flaveria) (1995)

In C4 plants of the NADP-malic enzyme type, an abundant, mesophyll cell-localized NADP-malate dehydrogenase (MDH) acts to convert oxaloacetate, the initial product of carbon fixation, to malate before it is shuttled to the bundle sheath. Since NADP-MDH has different but important roles in leaves of C3 and C4 plants, we have cloned and characterized a nearly full-length cDNA encoding NADP-MDH from Flaveria trinervia (C4) to permit comparative structure/expression studies within the genus flaveria. The dicot genus Flaveria includes C3-C4 intermediate species, as well as C3 and C4 species. We show that the previously noted differences in NADP-MDH activity levels among C3, C4, and C3-C4 Flaveria species are in part due to interspecific differences in mRNA accumulation. We also show that the NADP-MDH gene appears to be present as a single copy among different Flaveria species, suggesting that a pre-existing gene has been reregulated during the evolution from C3 to C4 plants to accommodate the abundance and localization requirements of the C4 cycle.
Thermal refocusing method for spaceborne high-resolution optical imagers (2016)

We describe the design of a thermal refocusing method for spaceborne high-resolution imagers where Korsch optical design is usually implemented. The secondary mirror is made of aluminum, a high thermal expansion coefficient material, instead of conventional zero-expansion glass ceramics. In this way, the radius of the curvature can be controlled by means of temperature change of the mirror. Change in the radius of curvature also changes the effective focal length of the camera which is used for compensation of the defocus that occurred in space. We show that the 30 μm despace of the secondary mirror in the optical system can be compensated by an ∼10°C temperature change of the mirror while the image quality is maintained.
Efficient Iron-Catalyzed N-Arylation of Aryl Halides with Amines (2008)

A practical and promising protocol was developed for N-arylations of various amines with differently substituted aryl halides. The processes are efficiently promoted by the catalyst system involving the environmentally benign Fe2O3 and the universal ligand L-proline. The versatility, convenient operation, low cost, and environmental friendliness, in combination with the high yields, render this method viable for use in both laboratory research and larger industrial scales.
A Genetic Framework for the Control of Cell Division and Differentiation in the Root Meristem (2008)

Plant growth and development are sustained by meristems. Meristem activity is controlled by auxin and cytokinin, two hormones whose interactions in determining a specific developmental output are still poorly understood. By means of a comprehensive genetic and molecular analysis in Arabidopsis, we show that a primary cytokinin-response transcription factor, ARR1, activates the gene SHY2/IAA3 (SHY2), a repressor of auxin signaling that negatively regulates the PIN auxin transport facilitator genes: thereby, cytokinin causes auxin redistribution, prompting cell differentiation. Conversely, auxin mediates degradation of the SHY2 protein, sustaining PIN activities and cell division. Thus, the cell differentiation and division balance necessary for controlling root meristem size and root growth is the result of the interaction between cytokinin and auxin through a simple regulatory circuit converging on the SHY2 gene.
Determining Beta-Sheet Crystallinity in Fibrous Proteins by Thermal Analysis and Infrared Spectroscopy (2006)

We report a study of self-assembled beta-pleated sheets in B. mori silk fibroin films using thermal analysis and infrared spectroscopy. B. mori silk fibroin may stand as an exemplar of fibrous proteins containing crystalline beta-sheets. Materials were prepared from concentrated solutions (2−5 wt % fibroin in water) and then dried to achieve a less ordered state without beta-sheets. Crystallization of beta-pleated sheets was effected either by heating the films above the glass transition temperature (Tg) and holding isothermally or by exposure to methanol. The fractions of secondary structural components including random coils, alpha-helices, beta-pleated sheets, turns, and side chains were evaluated using Fourier self-deconvolution (FSD) of the infrared absorbance spectra. The silk fibroin films were studied thermally using temperature-modulated differential scanning calorimetry (TMDSC) to obtain the reversing heat capacity. The increment of the reversing heat capacity ΔCp0(Tg) at the glass transition for the less ordered, noncrystalline, silk fibroin is found to be 0.478 ± 0.005 J/(g K). As crystalline beta-sheets form, the heat capacity increment at Tg is systematically decreased. We find that the heat capacity increment from the TMDSC trace is linearly well correlated (negatively) with beta-sheet content φC determined from FSD, yielding ΔCp = 0.475−0.494φC. The correlation allows the beta-sheet content to be determined from a direct measurement of the heat capacity increment at Tg. This type of analysis can serve as an alternative to X-ray methods and may have wide applicability to other crystalline beta-sheet forming proteins.
1-pm spectrally narrowed compact ArF excimer laser for microlithography (1996)

Summary form only given. We demonstrated 1-pm spectral narrowing with the compact ArF excimer laser. We achieved a high narrowing efficiency of 9% due to the design of the short resonator length with a short round-trip time, and the high excitation power density with high gain. This spectrally narrowed ArF excimer laser will be used in basic microlithography experiments with small exposure fields. The MOPA configuration using this laser as a master oscillator is useful for applications that require higher average power.