gebhart/patrepeval huggingface dataset:
Facile Atom Transfer Radical Polymerization of Methoxy-Capped Oligo(ethylene glycol) Methacrylate in Aqueous Media at Ambient Temperature (2000)

We report the facile atom transfer radical polymerization (ATRP) of a commercially available hydrophilic monomer, methoxy-capped oligo(ethylene glycol) methacrylate (OEGMA), under remarkably mild conditions. Various bromide-based initiators, in conjunction with a copper-based catalyst, allow rapid homopolymerization of OEGMA in water at 20 °C. Good living character was achieved with two ligands, namely 2,2‘-bipyridine (bpy) and 1,1,4,7,10,10-hexamethyltriethylenetetramine (HMTETA). Kinetic studies confirm that, for bpy, 90% conversion is typically achieved within 20 min, and the polymerization is first order even up to very high conversions. Molecular weight increases linearly with conversion and is close to the target molecular weight in all cases. Polydispersities remain narrow (Mw/Mn = 1.15−1.30) throughout the polymerization. It is possible to lower the copper catalyst by a factor of 10 (i.e., [Cu(I)]/[initiator] = 0.10) without significant loss of control over the polymerization, which is good evidence for the highly active nature of the copper catalyst. To investigate the role played by the water in promoting rapid ATRP, selected bulk polymerizations were also carried out. With the bpy ligand it was found that the polymerization was living but slow: 90% conversion required 15 h at 20 °C even though the monomer, initiator, and catalyst concentrations were significantly higher in the bulk than in aqueous ATRP. Remarkably, the polydispersity of the final polymer isolated from this slow bulk polymerization was relatively high at 1.30, whereas typical final polydispersities for aqueous ATRP are 1.20−1.25. There are several factors that may account for the unexpectedly rapid, yet controlled, aqueous ATRP of OEGMA at 20 °C. The highly polar nature of water is believed to promote the formation of a very active mononuclear [Cu(bpy)2]+ catalyst. Furthermore, since OEGMA is a sterically congested monomer, its termination rate constant is several orders of magnitude lower than that of conventional methacrylates, which is expected to lead to improved living character. A third possibility is that the amphiphilic nature of the OEGMA monomer may lead to micellar polymerization, but no evidence was found for monomer micelles prior to ATRP. Finally, the cationic copper catalyst is easily removed from the aqueous reaction solution using silica chromatography, and the nonionic OEGMA homopolymer is readily isolated as a colorless solid.
Human breast cancer cells generated by oncogenic transformation of primary mammary epithelial cells (2001)

A number of genetic mutations have been identified in human breast cancers, yet the specific combinations of mutations required in concert to form breast carcinoma cells remain unknown. One approach to identifying the genetic and biochemical alterations required for this process involves the transformation of primary human mammary epithelial cells (HMECs) to carcinoma cells through the introduction of specific genes. Here we show that introduction of three genes encoding the SV40 large-T antigen, the telomerase catalytic subunit, and an H-Ras oncoprotein into primary HMECs results in cells that form tumors when transplanted subcutaneously or into the mammary glands of immunocompromised mice. The tumorigenicity of these transformed cells was dependent on the level of ras oncogene expression. Interestingly, transformation of HMECs but not two other human cell types was associated with amplifications of the c-myc oncogene, which occurred during the in vitro growth of the cells. Tumors derived from the transformed HMECs were poorly differentiated carcinomas that infiltrated through adjacent tissue. When these cells were injected subcutaneously, tumors formed in only half of the injections and with an average latency of 7.5 weeks. Mixing the epithelial tumor cells with Matrigel or primary human mammary fibroblasts substantially increased the efficiency of tumor formation and decreased the latency of tumor formation, demonstrating a significant influence of the stromal microenvironment on tumorigenicity. Thus, these observations establish an experimental system for elucidating both the genetic and cell biological requirements for the development of breast cancer.
Inhibition of replication of hepatitis B virus by cytallene in vitro (1997)

The acyclic cytosine nucleoside analog cytallene [1-(4'-hydroxy-1',2'-butadienyl)cytosine], which has both (+)- and (-)-enantiomers, was evaluated for its anti-hepatitis B virus (HBV) activity in 2.2.15 cells and was found to have potent activity against HBV DNA synthesis. The R-(-)-enantiomer was found to be the more active of the cytallene enantiomers, with a 50% inhibition concentration against HBV synthesis (HBIC50) of 0.08 microM. Its antiviral activity could be reversed by deoxycytidine (dC) and less efficiently by cytidine. Upon removal of the R-(-)-enantiomer from culture medium, the synthesis of HBV DNA could reinitiate, which suggested that the antiviral action is reversible. The R-(-)-enantiomer was also found to be more cytotoxic than the S-(+)-enantiomer. The degree of cytotoxicity varied among the cell lines, with a 50% inhibition of cell growth at greater than 10 microM. The R-(-)-enantiomer had no effect on HBV RNA synthesis and mitochondrial DNA synthesis at a concentration of 10 times or more than the HBIC50. The two enantiomers cannot be deaminated by dC deaminase, and they can be phosphorylated by cytoplasmic dC kinase. The R-(-)-enantiomer of cytallene is the first acyclic cytosine analog with potent inhibitory activity against HBV similar to those of other L-(-)-ddC analogs.
Vagal Nerve Stimulation and Reflux (2007)

To the Editor: Recently, Hatton et al. (1) described a number of side effects of vagal nerve stimulator (VNS) implantation related to vagal efferent control of the gastrointestinal tract via the parasympathetic nervous system. Dyspepsia occurring in 12.6% can be explained by the action of the vagus nerve, which stimulates increased gastric acid secretion as well as promotes gastric emptying. However, the cause of dyspepsia may be multifactorial resulting from gastric hypersecretion (previously treated surgically with vagotomy and accompanied by pyloroplasty due to the vagotomy causing gastric stasis) or gastroparesis or delayed gastric emptying. We are writing to illustrate a further effect of the VNS on gastric motility. A gentleman attended our neurosurgical unit for replacement of his VNS battery. He had experienced seizures since childhood; suffering 7–10 episodes each week despite best medical management. VNS was placed in October 2000 resulting in improved seizure control. The seizures had increased in frequency 7 months before admission for this procedure, and interrogation of the electronics confirmed end of battery life. Upon routine preoperative anesthetic assessment, we discovered that he had also experienced dyspepsia over these 7 months. Relief was attained by taking a proton pump inhibitor. The gentleman attributed his dyspepsia to VNS failure. He underwent unremarkable day-case anesthesia and battery replacement. Telephone conversation, 2 weeks later, confirmed that the symptoms of reflux had ceased after reinstitution of VNS. This demonstrates a gastrointestinal effect of VNS, which was advantageous to our patient. It may be that VNS could offer an alternative solution to dyspepsia resulting from impaired gastric emptying. Rohna Sinclair, MRCP, FRCA Specialist Registrar in Anaesthetics Rahul R. Bajekal, MD, FRCA Consultant Anaesthetist Department of Anaesthesia Newcastle General Hospital Newcastle Upon Tyne, UK [email protected]
Skin autofluorescence as a biological UVR dosimeter (2004)

Background/Purpose: Collagen is one of the major endogenous skin fluorophores. Alteration in the structure of collagen due to chronic ultraviolet radiation (UVR) exposure may influence the intensity of the autofluorescence. The aim of this study was to investigate the relation between collagen‐linked autofluorescence and sun exposure to clarify whether the skin can be used as a biological UVR dosimeter. Methods: We conducted an in vivo study with 131 healthy volunteers. Fluorescence was measured from sun‐exposed (dorsal forearm, forehead and shoulder) and sun‐protected (buttock) skin and corrected for the impact of pigmentation and redness. The excitation wavelengths (Ex) and emission wavelengths (Em) were: Ex330:Em370, Ex330:Em455 and Ex370:Em455 nm. Individual UVR exposure data were collected both retrospectively and prospectively using questionnaires and electronic personal UVR dosimeters for a summer period. Results: Age, but not sex, skin type or smoking habits correlated significantly positively with skin autofluorescence at Ex370:Em455 at all body sites ( P &lt;0.001, r 2 =0.08–0.26), and at Ex330:Em455 only at the buttock ( P =0.001, r 2 =0.08), whereas age was not correlated with Ex330:Em370. Sun‐protected buttock skin had significantly higher autofluorescence than sun‐exposed skin ( P ‐values&lt;0.0001). Because of great between‐subject differences in autofluorescence at different body sites, and because the autofluorescence at the unexposed buttock represents the baseline value, individual correction of skin autofluorescence measurement with that of the buttock was performed. Different measures of individual chronic cumulative UVR doses correlated significantly negatively with the skin autofluorescence ratio ( F ratio ), but the correlations were poor ( r 2 =0.03–0.10). Conclusion: The results indicate that the collagen‐linked skin F ratio might be best to use as a measure of individual photodamage, a UVR dose effect, and that it is also a better marker of individual cumulative UVR dose than the used UVR exposure measurements. The methods used to obtain UVR exposure data might not be sensitive and specific enough.
A new diet for yeast to improve biofuel production (2011)

In 2010, our group announced the discovery of two cellodextrin transporter families from the cellulolytic fungus, Neurospora crassa. Furthermore, we demonstrated the utility of these transporters in the production of lignocellulosic biofuels. This discovery was made possible by a decision to systematically study cell wall degradation by N. crassa. The identified transport pathway has opened up a new way of thinking about microbial fermentation of hexoses as well as pentoses derived from plant cell walls. Integrating this pathway with the endogenous metabolism and signaling networks of S. cerevisiae is now a major goal of our group.
Detection and modulation in vivo of helix-loop-helix protein-protein interactions. (1993)

Studies are described that allow for the in vivo detection of helix-loop-helix (HLH) protein-protein interaction. The assay used requires HLH protein-protein interaction to reconstitute a functional GAL4 transcriptional activator, which in turn activates a reporter gene placed downstream of GAL4 DNA binding sequences. Using this assay, we are able to detect intracellular heterodimerization but not homodimerization of the MyoD, E12, and Id gene products. In addition, using this system we are unable to detect stable heterodimerization between MyoD and c-Jun. We also show that expression of activated rasH gene product does not inhibit and may stabilize HLH protein-protein interaction. This system may be of general utility in studying the modulation of transcription factor interactions.
Optical and electro‐optical properties of bimesogenic organosiloxane antiferroelectric liquid crystals with molecular tilt approaching 45 degrees (2005)

We have studied the optical and electro‐optical properties of three different bimesogenic siloxane materials. The dimers are symmetrical and the two mesogenic groups are connected by a siloxane unit containing three Si atoms and methylene spacers. The mesogens contain F, Cl and Br substituents, respectively, laterally attached to the phenyl ring lying closest to the chiral centre of the mesogen. These materials each exhibited a broad temperature range antiferroelectric phase and large molecular tilt, which is almost temperature‐independent. We have shown that, at low temperatures, the molecular tilt in the antiferroelectric phase is the same as the apparent molecular tilt in the field‐induced ferroelectric state and is close to 45°. It was found that the antiferroelectric phase of these compounds, aligned in such way that the dimeric molecules were lying in a plane parallel to the confining substrates, exhibited very low in‐plane birefringence. For this reason, samples of the compounds inserted between crossed polarizers in the antiferroelectric state exhibited an extremely dark state, with contrast ratios as high as 1000:1, which did not change noticeably on rotating the sample between the crossed polarizers. It was shown that the optically isotropic siloxane moiety did not contribute to the optical properties, viz. birefringence or tilt angle, but served to enhance the promotion of the antiferroelectric phase and the temperature independent properties. We also showed the existence of a linear electro‐optic response in the pretransitional region of the antiferroelectric phase of these compounds over a moderate range of fields.
Involvement of Nuclear Factor-κB in the Inhibition of Pro-Inflammatory Mediators by Pinosylvin (2006)

Nuclear factor-kappaB (NF-kappaB) is a critical transcription factor for maximal expression of many of the cytokines that are involved in the pathogenesis of inflammatory diseases. In this study, we found that pinosylvin, a natural stilbenoid that is a component of the pine leaf (Pinus densiflora), significantly inhibited LPS-induced NF-kappaB activation in a concentration-dependent manner. Additionally, pinosylvin was found to inhibit the LPS-induced phosphorylation and degradation of IkappaB alpha in THP-1 cells. Therefore, we have attempted to determine whether pinosylvin can inhibit the expression of cytokines possessing NF-kappaB binding sites in their promoter regions. In a consistent result, pinosylvin inhibited LPS-induced production of TNF alpha and interleukin-8 (IL-8). Taken together, these results show that pinosylvin suppresses the production of pro-inflammatory mediators through the inhibition of the NF-kappaB signaling pathway.
Atomic force microscopy of mica surface after ion replacement (1991)

Atomic Force Microscope (AFM), is the newest, and potentially most powerful of the scanning probe microscopes. The (AFM) is capable of resolutions approaching atomic dimensions on ideal surfaces. One of the favorite such surfaces is that of mica. Muscovite mica has a platelike structure consisting of an octahedral alumina sheet sandwiched by two tetrahedral silicate sheets. As a result of this structure, mica cleaves readily along a plane leaving a molecularly smooth surface. Because of the isomorphous substitution of the tetravalent silicon by trivalent aluminium, mica has an excess negative surface charge. This negative surface charge of 2.1-10 14 charges per cm 2 is neutralized by an equal number of positive monovalent ions, mainly potassium ions. The ion-exchangable surface ions of mica, in aqueous solution, can be readily replaced by other monovalent or multivalent ions. This ion exchange alters the surface of the mica. We then follow these changes by imaging with the AFM in air.
Cloning of the cDNa for a Na+/myo-inositol cotransporter, a hypertonicity stress protein. (1992)

Kidney medullary cells in situ, as well as kidney-derived Madin-Darby canine kidney (MDCK) cells accumulate nonperturbing, small organic solutes (osmolytes), including myo-inositol, when bathed in hypertonic media. Accumulation of osmolytes balances the osmolality of extracellular fluid without raising intracellular salts that would perturb cellular functions. In hypertonic media, increased myo-inositol accumulation is the result of increased activity of a Na+/myo-inositol cotransporter. We have isolated a cDNA encoding a Na+/myo-inositol cotransporter from MDCK cells using expression in Xenopus oocytes. The cDNA sequence predicts a protein of 718 amino acids with a significant amino acid sequence similarity to the Na+/D-glucose cotransporters of absorbing epithelia. Transporter mRNA is present in kidney and brain and is markedly induced in MDCK cells by medium hypertonicity, demonstrating that adaptation to hypertonic stress involves up-regulation of transporter mRNA accumulation.
A borehole-to-surface electromagnetic survey (1998)

Abstract The results of a limited field trial confirm the usefulness of borehole-to-surface electromagnetic (EM) measurements for monitoring fluid extraction. A vertical EM profiling experiment was done at the University of California Richmond Field Station, where we simulated a brine spill plume by creating a saline water injection zone at a depth of 30 m. The data acquisition mode was analogous to the reverse vertical seismic profiling (VSP) configuration used for seismic measurements in that the EM transmitter traversed the PVC-cased borehole used for fluid injection and extraction while the receivers were deployed on the surface. The EM measurements were made at 9.6 kHz with an accuracy of 1% in signal amplitude and 1% in signal phase. Observations were taken at 5-m intervals along two intersecting profiles that were centered on the injection well and extended for 60 m on either side of it. The presence of the injected salt water, at the expected 30 m depth, was indicated clearly by differences between the pre-extraction and postextraction data. A limited amount of numerical modeling showed that the experimental data were consistent with the presence of two superposed saline plumes. The uppermost of these, located at 26 m depth, was 2 m thick and had an area of 30 m 2 . The lower plume, located at 30 m, is the major cause of the observed anomaly, as it has an areal extent of 120 m 2 and a thickness of 3 m. Surprisingly, the measurements were very sensitive to the presence of cultural surficial conductivity anomalies. These spurious effects were reduced by spatial filtering of the data prior to interpretation.
Evidence for a Ligand Interaction Site at the Amino-Terminus of the Parathyroid Hormone (PTH)/PTH-related Protein Receptor from Cross-linking and Mutational Studies (1998)

Low resolution mutational studies have indicated that the amino-terminal extracellular domain of the rat parathyroid hormone (PTH)/PTH-related protein (PTHrP) receptor (rP1R) interacts with the carboxyl-terminal portion of PTH-(1-34) or PTHrP-(1-36). To further define ligand-receptor interactions, we prepared a fully functional photoreactive analog of PTHrP, [Ile5,Bpa23,Tyr36]PTHrP-(1-36)-amide ([Bpa23]PTHrP, where Bpa is p-benzoyl-L-phenylalanine). Upon photolysis, radioiodinated [Bpa23]PTHrP covalently and specifically bound to the rP1R. CNBr cleavage of the broad approximately 80-kDa complex yielded a radiolabeled approximately 9-kDa non-glycosylated protein band that could potentially be assigned to rP1R residues 23-63, Tyr23 being the presumed amino-terminus of the receptor. This assignment was confirmed using a mutant rP1R (rP1R-M63I) that yielded, upon photoligand binding and CNBr digestion, a broad protein band of approximately 46 kDa, which was reduced to a sharp band of approximately 20 kDa upon deglycosylation. CNBr digestion of complexes formed with two additional rP1R double mutants (rP1R-M63I/L40M and rP1R-M63I/L41M) yielded non-glycosylated protein bands that were approximately 6 kDa in size, indicating that [Bpa23]PTHrP cross-links to amino acids 23-40 of the rP1R. This segment overlaps a receptor region previously identified by deletion mapping to be important for ligand binding. Alanine scanning of this region revealed two residues, Thr33 and Gln37, as being functionally involved in ligand binding. Thus, the convergence of photoaffinity cross-linking and mutational data demonstrates that the extreme amino-terminus of the rP1R participates in ligand binding.
Platelet Preservation in Large Containers (1984)

The influence of the size of the container on platelet concentrate storage at 20-24 °C was examined. Baseline studies were obtained with 50 platelet concentrates in 300-ml PL-146 plastic containers. Experimental studies included 6 platelet concentrates each in 300-, 600- and 2,000-ml containers made of PL-146 plastic. Platelet count, total platelets, pO(2), pCO(2), pH, glucose consumption, lactate production, platelet morphology and recovery by platelets to osmotic stress were monitored during storage. During storage, the best pH and morphology values were observed with 2,000-ml containers. The lowest glucose consumption and lactate production were also associated with the 2,000-ml containers. Intermediate improvement in these parameters was noted in 600- ml containers. Recovery from osmotic stress was better in 2,000- and 600-ml containers as compared to 300-ml containers. In addition, characteristic changes in pO(2) and pCO(2) during storage suggest that improved platelet preservation in larger containers is due to improved gas exchange conditions obtained with increased surface area available for gas exchange.
Electrophoresis of DNA and other polyelectrolytes: Physical mechanisms (2000)

The dramatic recent advances in molecular biology, which have opened a new era in medicine and biotechnology, rely on improved techniques to study large molecules. Electrophoresis is one of the most important of these. Separation of DNA by size, in particular, is at the heart of genome mapping and sequencing and is likely to play an increasing role in diagnosis. This article reviews, from the point of view of a physicist, the mechanisms responsible for electrophoretic separation of polyelectrolytes. This separation is mainly performed in gels, and a wide variety of migration mechanisms can come into play, depending on the polyelectrolyte's architecture, on the electric fields applied, and on the properties of the gel. After a brief review of the thermodynamic and electrohydrodynamic principles relating to polyelectrolyte solutions, the author treats the phenomenology of electrophoresis and describes the conceptual and theoretical tools in the field. The reptation mechanisms, by which large flexible polyelectrolytes thread their way through the pores of the gel matrix, play a prominent role. Biased reptation, the extension of this model to electrophoresis, provides a very intuitive framework within which numerous physical ideas can be introduced and discussed. It has been the most popular theory in this domain, and it remains an inspiring concept for current development. There have also been important advances in experimental techniques such as single-molecule viodeomicroscopy and the development of nongel separation media and mechanisms. These, in turn, form the basis for fast-developing and innovative technologies like capillary electrophoresis, electrophoresis on microchips, and molecular ratchets.
Distinctive functional characteristics of human „T” lymphocytes defined by E rosetting or a monoclonal anti‐T cell antibody (1981)

The properties of human lymphocyte fractions isolated either by sheep red cell(E) rosetting or by fluorescence-activated cell sorting after staining with UCHT1 monoclonal anti-T cell antibody have been compared. Two populations of E+ cells with very different phenotype and function have been identified. E+/UCHT1+ cells respond well to the T cell mitogens phytohemagglutinin and concanavalin A and provide help for an in vitro specific antibody response. They can also suppress the antibody response of allegeneic peripheral blood mononuclear cells. In contrast, the E+/UCHT1- population, which has no other markers characteristic of T cells, fails to respond to mitogens or to provide help or suppression for an antibody response. These cells, however, are highly active natural killers. They possess Fc gamma receptors and have a characteristic staining pattern of nonspecific esterase enzyme activity. It is concluded that not all cells capable of forming E rosettes are thymus-processed cells and that this heterogeneity can be revealed by staining with the monoclonal anti-T cell reagent UCHT1.