gebhart/patrepeval huggingface dataset:
Plasmid transfer by conjugation fromEscherichia colito Gram-positive bacteria (1987)

We have developed a vector strategy that allows transfer of plasmid DNA by conjugation from Escherichia coli to various Gram-positive bacteria in which transformation via natural competence has not been demonstrated. The prototype vector constructed, pAT187, contains the origins of replication of pBR322 and of the broad host range streptococcal plasmid pAMβ1, a kanamycin resistance gene known to be expressed in both Gram-negative and Gram-positive bacteria, and the origin of transfer of the IncP plasmid RK2. This shuttle plasmid can be mobilised efficiently by the self-transferable IncP plasmid pRK212.1 co-resident in the E. coli donors, and was successfully transferred by filter matings at frequencies of 2 × 10−8 to 5 × 10−7 to Enterococcus faecalis, Streptococcus lactis, Streptococcus agalactiae, Bacillus thuringiensis, Listeria monocytogenes and Staphylococcus aureus.
High-speed indoor wireless communications at 60 GHz with coded OFDM (1999)

A high-speed indoor wireless communication system using coded orthogonal frequency-division multiplexing (OFDM) and working at 60 GHz is proposed and analyzed. An actual propagation environment consisting of a medium sized research laboratory, characterized by means of a ray-tracing technique, is considered for the analysis. In this contest the paper investigates and discusses the effects of frequency diversity, antenna sectorization, OFDM clustering, and different block coding strategies. Moreover, to characterize the communication between stationary indoor terminals at millimeter waves, a new definition of coverage is introduced. In order to evaluate the performance of the coded system in the actual environment, a suitable semianalytical algorithm is defined and applied. In the results the feasibility of a coded OFDM system for 155 Mbit/s packet transmission is checked. It is shown that all the line-of-sight (LOS) positions and 70% of the no LOS points can be covered in the scenario considered with a transmitted power of 10 dBm.
ICl/Ar electron cyclotron resonance plasma etching of III–V nitrides (1996)

Electron cyclotron resonance plasma etch rates for GaN, InN, InAlN, AlN, and InGaN were measured for a new plasma chemistry, ICl/Ar. The effects of gas chemistry, microwave and rf power on the etch rates for these materials were examined. InN proved to be the most sensitive to the plasma composition and ion density. The GaN, InN, and InGaN etch rates reached ∼13 000, 11 500, and ∼7000 Å/min, respectively, at 250 W rf (−275 V dc) and 1000 W microwave power. The etched surface of GaN was found to be smooth, with no significant preferential loss of N from the surface at low rf powers, and no significant residue on the surface after etching.
Nucleoside conjugates. 11. Synthesis and antitumor activity of 1-.beta.-D-arabinofuranosylcytosine and cytidine conjugates of thioether lipids (1990)

Five 1-beta-D-arabinofuranosylcytosine conjugates and two cytidine conjugates of thioether lipids (1-S-alkylthioglycerols) linked by a pyrophosphate diester bond have been prepared and their antitumor activity against an ara-C2 sensitive (L1210/0) and two ara-C resistant L1210 lymphoid leukemia sublines in mice were evaluated. These prodrugs of ara-C include ara-CDP-rac-1-S-hexadecyl-2-O-palmitoyl-1-thioglycerol (8a), ara-CDP-rac-1-S-octadecyl-2-O-palmitoylthioglycerol (8b), and ara-CDP-rac-1-S-octadecyl-2-O-methyl(or -ethyl, -hexadecyl)thioglycerols (8c-e). The cytidine conjugates include CDP-rac-1-S-octadecyl-2-O-palmitoyl(or -methyl)- 1-thioglycerols (9a and 9b). Sonicated solutions of the conjugates existed in the form of micellar disks (size 0.01-0.04 microns). Single doses (200-400 mg/kg) of 8a and 8b produced significant increase in life span (257-371%) in mice bearing ip implanted L1210/0 leukemia. In contrast, conjugates 8c-e were less effective (ILS 19-75%) and cytidine conjugates (9a and 9b) were ineffective. Even though 8a and 8b were found to be curative in a high percentage of mice bearing ip implanted partially ara-C resistant L1210 subline [L1210/ara-C(I)], they were completely ineffective against deoxycytidine kinase deficient ara-C resistant L1210 subline [L1210/ara-C(II)]. However, the present results, together with the previous, demonstrate that 8a and 8b are promising new prodrugs of ara-C with improved efficacy.
Synthesis of Phenol, Aromatic Ether, and Benzofuran Derivatives by Copper‐Catalyzed Hydroxylation of Aryl Halides (2009)

A smooth operator: The copper-catalyzed synthesis of phenols from aryl halides was carried out under relatively mild reaction conditions. Alkyl aryl ethers and benzofurans could also be prepared smoothly by one-pot domino protocols based on hydroxylation of aryl iodides (see scheme). Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Optimal electrode placement for noninvasive electrical stimulation of human abdominal muscles (2006)

Abdominal muscles are the most important expiratory muscles for coughing. Spinal cord-injured patients have respiratory complications because of abdominal muscle weakness and paralysis and impaired ability to cough. We aimed to determine the optimal positioning of stimulating electrodes on the trunk for the noninvasive electrical activation of the abdominal muscles. In six healthy subjects, we compared twitch pressures produced by a single electrical pulse through surface electrodes placed either posterolaterally or anteriorly on the trunk with twitch pressures produced by magnetic stimulation of nerve roots at the T(10) level. A gastroesophageal catheter measured gastric pressure (Pga) and esophageal pressure (Pes). Twitches were recorded at increasing stimulus intensities at functional residual capacity (FRC) in the seated posture. The maximal intensity used was also delivered at total lung capacity (TLC). At FRC, twitch pressures were greatest with electrical stimulation posterolaterally and magnetic stimulation at T(10) and smallest at the anterior site (Pga, 30 +/- 3 and 33 +/- 6 cm H(2)O vs. 12 +/- 3 cm H(2)O; Pes 8 +/- 2 and 11 +/- 3 cm H(2)O vs. 5 +/- 1 cm H(2)O; means +/- SE). At TLC, twitch pressures were larger. The values for posterolateral electrical stimulation were comparable to those evoked by thoracic magnetic stimulation. The posterolateral stimulation site is the optimal site for generating gastric and esophageal twitch pressures with electrical stimulation.
Conductive Differences in Electrodes Used with Transcutaneous Electrical Nerve Stimulation Devices (1991)

The purpose of this study was to document conductive differences among commercially available electrodes used with transcutaneous electrical nerve stimulation (TENS) devices. Impedance within a model system involving a human subject was calculated from oscilloscopic tracings of the pulse waveform for each of 25 different electrode types. Impedance values ranged from 1,000 to 7,800 omega Possible reasons for these differences are discussed. The observation that electrodes vary in their impedance and can thereby affect the stimulus applied to the skin raises the question of whether electrode choice might affect the clinical effectiveness of TENS. Attention is drawn to the skin electrodes as a variable that may affect the results of clinical and basic studies involving TENS.
MicroRNA-199b-5p Impairs Cancer Stem Cells through Negative Regulation of HES1 in Medulloblastoma (2009)

Despite advances in our understanding of the pathogenesis of MB, one-third of these patients remain incurable and current treatments can significantly damage long-term survivors. Here we show that miR-199b-5p expression correlates with metastasis spread, identifying a new molecular marker for a poor-risk class in patients with MB. We further show that in a xenograft model, MB tumor burden can be reduced, indicating the use of miR199b-5p as an adjuvant therapy after surgery, in combination with radiation and chemotherapy, for the improvement of anti-cancer MB therapies and patient quality of life. To date, this is the first report that expression of a miRNA can deplete the tumor stem cells, indicating an interesting therapeutic approach for the targeting of these cells in brain tumors.
The response of the lens to trauma. (1982)

The results of a number of investigations into traumatic cataract and after-cataract are presented. The traumatic cataract has been studied both in human lenses and experimentally. Light and electron microscopy, quantitative microradiography and an extracellular tracer--procion dye, were used to follow the cellular changes during cataract progression. The influence of wound size and wound healing as well as the lens fibre response to trauma were followed. Furthermore, tissue culture was used to study the proliferation of lens epithelial cells on the lens capsule. The after-cataract formed in tissue culture as well as experimental traumatic cataracts in rats and rabbits were compared to different stages of human traumatic cataract. Traumatic cataract has a subcapsular distribution and the importance of an intact functioning epithelium for lens transparency is emphasized.
Can Androgen Therapy Replete Lean Body Mass and Improve Muscle Function in Wasting Associated With Human Immunodeficiency Virus Infection? (1999)

A significant number of men who are infected with the human immunodeficiency virus (HIV) have low testosterone levels. Androgen deficiency in HIV-infected patients is associated with decreased muscle mass and function, and adverse disease outcome. Administration of replacement doses of testosterone to healthy hypogonadal men augments lean body mass, muscle size, and maximal voluntary strength. Recent studies have shown that physiologic testosterone replacement in HIV-infected men with weight loss who have low testosterone levels can also increase muscle mass and effort-dependent strength. However, further studies are needed to determine whether androgen therapy can improve physical function and health-related outcomes in HIV-infected men.
Insulin-like growth factor binding protein 2 promotes ovarian cancer cell invasion. (2005)

We therefore showed that IGFBP2 enhances the invasion capacity of ovarian cancer cells. Blockage of IGFBP2 may thus constitute a viable strategy for targeted cancer therapy.
Nitric oxide and the common cold (2005)

Further studies are warranted to evaluate the role of nitric oxide in colds and to determine whether the administration of nitric oxide donor compounds could be a viable therapeutic approach for viral exacerbations of airway diseases.
Differences in decorin expression by papillary and reticular fibroblasts in vivo and in vitro (1993)

Immunostaining of adult human skin shows that the small dermatan sulphate proteoglycan decorin is abundant in the whole dermal layer but absent from the epidermis. In the papillary layer adjacent to the dermal-epidermal border, more decorin was detected than in the reticular layer of the dermis. Expression of decorin mRNA by cells in the papillary dermis could also be shown by in situ hybridization. In contrast, biglycan, another small chondroitin sulphate/dermatan sulphate proteoglycan, is found only at the dermal-epidermal border. Therefore the biosynthesis of these two proteoglycans by papillary and reticular fibroblasts from two different donors was compared in tissue culture. Papillary fibroblasts secrete up to 5.9 times more decorin than reticular fibroblasts, while the amounts of cell-associated decorin in both cell types are similar. By Northern blot analysis as well as by in situ hybridization it was shown that papillary fibroblasts contain more mRNA coding for decorin than do reticular cells. In addition, no mosaic pattern of decorin expression was found in the cultured cells. The expression and synthesis of biglycan compared with decorin was about 10 times lower and did not show any significant differences for the two cells types. The kinetics of secretion and the rate of endocytosis of decorin were similar for both types of fibroblasts. These results were found with fibroblasts between the 9th and 15th passage from a newborn subject as well as from a 78-year-old donor, indicating that the pattern of decorin synthesis is not age-dependent in the range investigated. These results further show that fibroblasts from different layers of the dermis have a specific pattern of synthesis of small chondroitin sulphate/dermatan sulphate proteoglycans, and they also maintain these patterns in cell culture.
C- and L-band erbium-doped waveguide lasers with wafer-scale silicon nitride cavities (2013)

We report on integrated erbium-doped waveguide lasers designed for silicon photonic systems. The distributed Bragg reflector laser cavities consist of silicon nitride waveguide and grating features defined by wafer-scale immersion lithography and a top erbium-doped aluminum oxide layer deposited as the final step in the fabrication process. The resulting inverted ridge waveguide yields high optical intensity overlap with the active medium for both the 0.98 μm pump (89%) and 1.5 μm laser (87%) wavelengths with a pump-laser intensity overlap of >93%. We obtain output powers of up to 5 mW and show lasing at widely spaced wavelengths within both the C and L bands of the erbium gain spectrum (1536, 1561, and 1596 nm).
Identification of the phosphorylation site in vitro for cAMP-dependent protein kinase on the rat adipocyte cGMP-inhibited cAMP phosphodiesterase. (1994)

Rat adipocyte cGMP-inhibited cAMP phosphodiesterase (cGI-PDE) appears to be dually regulated in intact cells by serine phosphorylations induced by isoprenaline and insulin, respectively (Degerman, E., Smith, C. J., Tornqvist, H., Vasta, V., Belfrage, P., and Manganiello, V. C. (1990) Proc. Natl. Acad. Sci. U.S.A. 87, 533-537; Smith, C. J., Vasta, V., Degerman, E., Belfrage, P., and Manganiello, V. C. (1991) J. Biol. Chem. 266, 13385-13390). Since cAMP-dependent protein kinase (cAMP-PK) catalyzes the beta-adrenergic effects, the site in the isolated cGI-PDE phosphorylated by this kinase was explored. A peptide, LRRSSGASGLLTSEHHSR (P18), corresponding to the amino acid sequence Leu423-Arg440 in the putative regulatory domain of the rat adipocyte cGI-PDE was synthesized. It contains a consensus substrate sequence -RRXS- for cAMP-PK within two tryptic cleavage sites and was readily phosphorylated by cAMP-PK. Two phosphopeptides, identified as RS-[32P]SGASGLLTSEHHSR and S-[32P]SGASGLLTSEHHSR, were obtained after stoichiometric phosphorylation and trypsinization of the peptide. These two peptides and the two main tryptic phosphopeptides obtained from immunoisolated [32P]cGI-PDE phosphorylated with cAMP-PK in a solubilized crude adipocyte membrane fraction were immuno-precipitated by an affinity-purified polyclonal antibody raised against P18 and exhibited the same chromatographic and electrophoretic profiles in three different separation systems. Similar radiosequencing profiles indicated that the second most N-terminal serine, corresponding to Ser-427 in the intact cGI-PDE, was phosphorylated by cAMP-PK in both P18 and authentic cGI-PDE. It is concluded that serine 427 is the target for cAMP-PK phosphorylation of the rat adipocyte cGI-PDE in vitro.
Autophagy promotes MHC class II presentation of peptides from intracellular source proteins (2005)

MHC-peptide complexes mediate key functions in adaptive immunity. In a classical view, MHC-I molecules present peptides from intracellular source proteins, whereas MHC-II molecules present antigenic peptides from exogenous and membrane proteins. Nevertheless, substantial crosstalk between these two pathways has been observed. We investigated the influence of autophagy on the MHC-II ligandome and demonstrated that peptide presentation is altered considerably upon induction of autophagy. The presentation of peptides from intracellular and lysosomal source proteins was strongly increased on MHC-II in contrast with peptides from membrane and secreted proteins. In addition, autophagy influenced the MHC-II antigen-processing machinery. Our study illustrates a profound influence of autophagy on the class II peptide repertoire and suggests that this finding has implications for the regulation of CD4(+) T cell-mediated processes.
CRISPR/Cas9 Allows Efficient and Complete Knock-In of a Destabilization Domain-Tagged Essential Protein in a Human Cell Line, Allowing Rapid Knockdown of Protein Function (2014)

Although modulation of protein levels is an important tool for study of protein function, it is difficult or impossible to knockdown or knockout genes that are critical for cell growth or viability. For such genes, a conditional knockdown approach would be valuable. The FKBP protein-based destabilization domain (DD)-tagging approach, which confers instability to the tagged protein in the absence of the compound Shield-1, has been shown to provide rapid control of protein levels determined by Shield-1 concentration. Although a strategy to knock-in DD-tagged protein at the endogenous loci has been employed in certain parasite studies, partly due to the relative ease of knock-in as a result of their mostly haploid lifecycles, this strategy has not been demonstrated in diploid or hyperploid mammalian cells due to the relative difficulty of achieving complete knock-in in all alleles. The recent advent of CRISPR/Cas9 homing endonuclease-mediated targeted genome cleavage has been shown to allow highly efficient homologous recombination at the targeted locus. We therefore assessed the feasibility of using CRISPR/Cas9 to achieve complete knock-in to DD-tag the essential gene Treacher Collins-Franceschetti syndrome 1 (TCOF1) in human 293T cells. Using a double antibiotic selection strategy to select clones with at least two knock-in alleles, we obtained numerous complete knock-in clones within three weeks of initial transfection. DD-TCOF1 expression in the knock-in cells was Shield-1 concentration-dependent, and removal of Shield-1 resulted in destabilization of DD-TCOF1 over the course of hours. We further confirmed that the tagged TCOF1 retained the nucleolar localization of the wild-type untagged protein, and that destabilization of DD-TCOF1 resulted in impaired cell growth, as expected for a gene implicated in ribosome biogenesis. CRISPR/Cas9-mediated homologous recombination to completely knock-in a DD tag likely represents a generalizable and efficient strategy to achieve rapid modulation of protein levels in mammalian cells.
Imaging gene expression in the brain in vivo in a transgenic mouse model of Huntington's disease with an antisense radiopharmaceutical and drug-targeting technology. (2002)

These results support the hypothesis that gene expression in vivo can be quantitated with antisense radiopharmaceuticals, providing these molecules are reformulated with drug-targeting technology. Drug targeting enables access of the antisense agent to endogenous transport pathways, which permits passage across the cellular barriers that separate blood and intracellular compartments of target tissues.
Zinc-α-2-Glycoprotein: A Candidate Biomarker for Colon Cancer Diagnosis in Chinese Population (2014)

Zinc-α-2-glycoprotein (AZGP1) is a 41-kDa secreted glycoprotein, which has been detected in several malignancies. The diagnostic value of AZGP1 in serum of prostate and breast cancer patients has been reported. Analyzing "The Cancer Genome Atlas" data, we found that in colon cancer AZGP1 gene expression was upregulated at transcriptional level. We hypothesized that AZGP1 could be used as a diagnostic marker of colon cancer. First, we confirmed AZGP1 expression was higher in a set of 28 tumor tissues than in normal colonic mucosa tissues by real-time quantitative PCR and western blot in a Chinese population. We verified that serum concentration of AZGP1 was higher in 120 colon cancer patients compared with 40 healthy controls by ELISA (p < 0.001). Then receiver-operating characteristic (ROC) curve analysis was used to evaluate the predictive diagnostic value of AZGP1 in serum. The area under the curve (AUC) of AZGP1 was 0.742 (p < 0.001, 95% confidence interval (CI) = 0.656-0.827) in between the AUC of carcinoembryonic antigen (CEA) and the AUC of CA19-9, suggesting that predictive diagnostic value of AZGP1 is between CEA and Carbohydrate 19-9 (CA19-9). The combination of AZGP1 with traditional serum biomarkers, CEA and CA19-9, could result in better diagnostic results. To further validate the diagnostic value of AZGP1, a tissue microarray containing 190 samples of primary colon cancer tissue paired with normal colonic tissue was analysed and the result showed that AZGP1 was significantly upregulated in 68.4% (130 of 190) of the primary cancer lesions. In contrast, there was a weakly positive staining in 29.5% (56 of 190) of the normal colonic tissue samples (p < 0.001). Leave-one-out cross-validation was performed on the serum data, and showed that the diagnostic value of AZGP1 had 63.3% sensitivity and 65.0% specificity. Combination of AZGP1, CEA and CA19-9 had improved diagnosis value accuracy with 74.2% sensitivity and 72.5% specificity. These results suggest that AZGP1 is a useful diagnostic biomarker in tissues and serum from a Chinese population.
Chemistry, Biology, and Medicine of the Glycopeptide Antibiotics (1999)

The war against infectious bacteria is not over! Although vancomycin and glycopeptide antibiotics have provided a strong last line of defence against many drug-resistant bacteria, their overuse has given rise to more dangerous strains of bacteria. An understanding of the chemistry and biology of these highly complex glycopeptides are destined to play a crucial role in the discovery of new antibiotics.
Possible involvement of IFNT in lymphangiogenesis in the corpus luteum during the maternal recognition period in the cow (2011)

The corpus luteum (CL), which secretes large amounts of progesterone and is thus essential for establishing pregnancy, contains various types of immune cells that may play essential roles in CL function by generating immune responses. The lymphatic system is the second circulation system and is necessary for immune function, but the lymphatic system of the bovine CL has not been characterized in detail. We collected bovine CLs on days 12 and 16 of the estrous cycle (C12 and C16) and days 16 and 40 of early pregnancy (P16 and P40). Lymphatic endothelial hyaluronan receptor 1 (LYVE1) protein was detected in the CL by immunohistochemistry and western blotting and increased at P40 compared with C16. The mRNA expression levels of lymphangiogenic factors, such as vascular endothelial growth factor-C (VEGFC), VEGFD, and their common receptor VEGFR3, as well as the lymphatic endothelial cell (LyEC) marker podoplanin, increased in P16 and P40 CLs. Thus, it is suggested that the lymphatic system of the bovine CL reconstitutes during early pregnancy. Interferon tau (IFNT) from the conceptus in the uterus is a candidate for activating luteal lymphangiogenesis during the maternal recognition period (MRP). We found that treatment of LyECs isolated from internal iliac lymphatic vessels with IFNT stimulated LyEC proliferation and significantly increased mRNA expression of VEGFC and IFN-stimulated gene 15. Moreover, both IFNT and VEGFC induced LyECs to form capillary-like tubes in vitro. In conclusion, it is suggested that new lymphangiogenesis in the bovine CL begins during the MRP and that IFNT may mediate this novel phenomenon.