gebhart/patrepeval huggingface dataset:
MutS as a tool for mutation detection. (2005)

MutS, a DNA mismatch-binding protein, seems to be a promising tool for mutation detection. We present three MutS based approaches to the detection of point mutations: DNA retardation, protection of mismatched DNA against exonuclease digestion, and chimeric MutS proteins. DNA retardation in polyacrylamide gels stained with SYBR-Gold allows mutation detection using 1-3 microg of Thermus thermophilus his6-MutS protein and 50-200 ng of a PCR product. The method enables the search for a broad range of mutations: from single up to several nucleotide, as mutations over three nucleotides could be detected in electrophoresis without MutS, due to the mobility shift caused by large insertion/deletion loops in heteroduplex DNA. The binding of DNA mismatches by MutS protects the complexed DNA against exonuclease digestion. The direct addition of the fluorescent dye, SYBR-Gold, allows mutation detection in a single-tube assay. The limited efficiency of T4 DNA polymerase as an exonuclease hampers the application of the method in practice. The assay required 300-400 ng of PCR products in the range of 200-700 bp and 1-3 microg of MutS. MutS binding to mismatched DNA immobilised on a solid phase can be observed thanks to the activity of a reporter domain linked to MutS. We obtained chimeric bifunctional proteins consisting of T. thermophilus MutS and reporter domains, like beta-galactosidase or GFP. Very low detection limits for beta-galactosidase could theoretically enable mutation detection not only by the examination of PCR products, but even of genomic DNA.
The reaction of 1,3-dichloro-1,1,3,3-tetraisopropyldisiloxane with cytosine arabinoside and 1-(6-deoxy-α-L-talofuranosyl)uracil (1980)

1,3-dichloro-1,1,3,3-tetraisopropyldisiloxane ( I ) reacts with cytosine arabinoside ( II ) in pyridine under the formation of 3',5'-O-(tetraisopropyldisiloxane-1,3-diyl)cytosine arabinoside ( IIIa ) and with 1-(6'-deoxy-α-L-talofuranosyl)uracil ( V ) under the formation of 2',3'-O-(tetraisopropyldisiloxane-1,3-diyl) 1-(6-deoxy-α-L-talofuranosyl)uracil ( VIa ).
Regulation of resting and cycling human B lymphocytes via surface IgM and the accessory molecules interleukin-4, CD23 and CD40. (1989)

Experiments were designed in order to compare directly the ability of a new and potent monoclonal anti-mu chain antibody to initiate or maintain stimulation in resting and cycling B lymphocytes, respectively. Resting B cells could be stimulated by soluble anti-mu only in the presence of additional signals; these could be supplied by a high dose of phorbol ester or a combination of interleukin-4 (IL-4) and the CD40 antibody, G28-5. Immobilization of anti-mu not only increased the magnitude of the resting B-cell response but also diminished the co-factor requirements. The 'background' stimulation obtained when using a high concentration of immobilized anti-mu was unexpectedly reduced in the presence of IL-4 alone. The duration, but not the magnitude, of the IL-4 signal required for promoting optimal responses varied with the co-stimulation applied. Importantly, the threshold concentrations of soluble anti-mu needed to trigger the resting B cells were reduced upon the addition of each co-stimulant. With actively cycling B cells, both soluble and immobilized anti-mu were now capable of sustaining stimulation which could be prolonged on the addition of IL-4 and/or G28-5. In both resting and cycling populations, a strong correlation was noted between the magnitude of stimulation elicited when IL-4 was present and the release of the soluble CD23 molecule. Moreover, IL-4-promoted, but not other, stimulations could be augmented up to 10-fold by the inclusion of the CD23 antibody MHM6. Both the resting and cycling B-cell populations were found to secrete IgM in direct response to IL-4 and G28-5; this factor-driven production of IgM was differentially modulated by soluble and immobilized anti-mu in the two populations.
Total assignment of the proton and carbon NMR spectra of the alkaloid quindoline — utilization of HMQC‐TOCSY to indirectly establish protonated carbon‐protonated carbon connectivities (1991)

Abstract The reisolation of the indoloquinoline alkaloid quindoline (also known as norcryptolepine) from Cryptolepis sanguinolenta is reported. The structure was unequivocally confirmed by two‐dimensional nmr methods; the proton and carbon spectra were assigned for the first time. Because of congestion in the proton spectrum HMQC‐TOCSY was used as an alternative to the more familiar COSY experiment. In addition to establishing proton‐proton connectivities, HMQC‐TOCSY affords the added benefit of providing, in an indirect sense, connectivity information between protonated carbons.
Drug Therapy for Atrial Fibrillation: What Will Its Role Be in the Era of Increasing Use of Catheter Ablation? (2008)

Atrial fibrillation (AF) is an increasingly important disorder. In most patients the treatment of AF usually employs anti-arrhythmic drugs (AADs). Despite the widespread utilization of AADs for the conversion of atrial fibrillation and maintenance of normal sinus rhythm, their use is limited by modest efficacy, frequent intolerance, and the potential for serious ventricular proarrhythmia and organ toxicity. In addition to AADs, ablations for AF have come into vogue. If ablation techniques improve, one might ask whether there will still be a role for AADs, and, if so, what will it be and what agents will be used. This manuscript will attempt to answer these questions.
Synthesis and Identification of [1,3,5]Triazine-pyridine Biheteroaryl as a Novel Series of Potent Cyclin-Dependent Kinase Inhibitors (2005)

On the basis of previous studies, we identified pyrazine-pyridine A as a potent vascular endothelial growth factor inhibitor and pyrimidine-pyridine B as a moderately potent cyclin dependent kinase (CDK) inhibitor. A proposed combination of CGP-60474 and compound B led to the discovery of [1,3,5]triazine-pyridine as a new series of potent CDK inhibitors. Palladium-catalyzed C-C bond formation reactions, particularly the Negishi coupling reaction, were used to assemble various triazine-heteroaryl analogues effectively. Among them, compound 20 displayed high inhibitory potency at CDK1 (IC(50) = 0.021 microM), CDK2, and CDK5 and submicromolar potency at CDK4, CDK6, and CDK7. Compound 20 also displayed high potency at GSK-3beta. It demonstrated potent antiproliferative activity on various tumor cell lines, including HeLa, HCT-116, U937, and A375. When 20 was administered intraperitoneally at 150 and 125 mg/kg to nude mice bearing human A375 xenografts, the compound produced a significant survival increase. Molecular docking studies were conducted in an attempt to enhance the understanding of the observed structure-activity relationship.
Human Embryonic Stem Cells: An Introduction to the Science and Therapeutic Potential (2003)

This single reference provides basic information on the multiple disciplines of science as they pertain to the science of stem cells.
RhoA is required for monocyte tail retraction during transendothelial migration (2001)

Transendothelial migration of monocytes is the process by which monocytes leave the circulatory system and extravasate through the endothelial lining of the blood vessel wall and enter the underlying tissue. Transmigration requires coordination of alterations in cell shape and adhesive properties that are mediated by cytoskeletal dynamics. We have analyzed the function of RhoA in the cytoskeletal reorganizations that occur during transmigration. By loading monocytes with C3, an inhibitor of RhoA, we found that RhoA was required for transendothelial migration. We then examined individual steps of transmigration to explore the requirement for RhoA in extravasation. Our studies showed that RhoA was not required for monocyte attachment to the endothelium nor subsequent spreading of the monocyte on the endothelial surface. Time-lapse video microscopy analysis revealed that C3-loaded monocytes also had significant forward crawling movement on the endothelial monolayer and were able to invade between neighboring endothelial cells. However, RhoA was required to retract the tail of the migrating monocyte and complete diapedesis. We also demonstrate that p160ROCK, a serine/threonine kinase effector of RhoA, is both necessary and sufficient for RhoA-mediated tail retraction. Finally, we find that p160ROCK signaling negatively regulates integrin adhesions and that inhibition of RhoA results in an accumulation of beta2 integrin in the unretracted tails.
Isolation and Characterization of a Shigella flexneri Invasin Complex Subunit Vaccine (2000)

The invasiveness and virulence of Shigella spp. are largely due to the expression of plasmid-encoded virulence factors, among which are the invasion plasmid antigens (Ipa proteins). After infection, the host immune response is directed primarily against lipopolysaccharide (LPS) and the virulence proteins (IpaB, IpaC, and IpaD). Recent observations have indicated that the Ipa proteins (IpaB, IpaC, and possibly IpaD) form a multiprotein complex capable of inducing the phagocytic event which internalizes the bacterium. We have isolated a complex of invasins and LPS from water-extractable antigens of virulent shigellae by ion-exchange chromatography. Western blot analysis of the complex indicates that all of the major virulence antigens of Shigella, including IpaB, IpaC, and IpaD, and LPS are components of this macromolecular complex. Mice or guinea pigs immunized intranasally with purified invasin complex (invaplex), without any additional adjuvant, mounted a significant immunoglobulin G (IgG) and IgA antibody response against the Shigella virulence antigens and LPS. The virulence-specific response was very similar to that previously noted in primates infected with shigellae. Guinea pigs (keratoconjunctivitis model) or mice (lethal lung model) immunized intranasally on days 0, 14, and 28 and challenged 3 weeks later with virulent shigellae were protected from disease (P<0.01 for both animal models).
Matriptase-2 (TMPRSS6): a proteolytic regulator of iron homeostasis (2009)

Maintaining the body's levels of iron within precise boundaries is essential for normal physiological function. Alterations of these levels below or above the healthy limit lead to a systemic deficiency or overload in iron. The type-two transmembrane serine protease (TTSP), matriptase-2 (also known as TMPRSS6), is attracting significant amounts of interest due to its recently described role in iron homeostasis. The finding of this regulatory role for matriptase-2 was originally derived from the observation that mice deficient in this protease present with anemia due to elevated levels of hepcidin and impaired intestinal iron absorption. Further in vitro analysis has demonstrated that matriptase-2 functions to suppress bone morphogenetic protein stimulation of hepcidin transcription through cell surface proteolytic processing of the bone morphogenetic protein co-receptor hemojuvelin. Consistently, the anemic phenotype of matriptase-2 knockout mice is mirrored in humans with matripase-2 mutations. Currently, 14 patients with iron-refractory iron deficiency anemia (IRIDA) have been reported to harbor various genetic mutations that abrogate matriptase-2 proteolytic activity. In this review, after overviewing the membrane anchored serine proteases, in particular the TTSP family, we summarize the identification and characterization of matriptase-2 and describe its functional relevance in iron metabolism.
Cellular Control of Cortical Actin Nucleation (2014)

The contractile actin cortex is a thin layer of actin, myosin, and actin-binding proteins that subtends the membrane of animal cells. The cortex is the main determinant of cell shape and plays a fundamental role in cell division [1-3], migration [4], and tissue morphogenesis [5]. For example, cortex contractility plays a crucial role in amoeboid migration of metastatic cells [6] and during division, where its misregulation can lead to aneuploidy [7]. Despite its importance, our knowledge of the cortex is poor, and even the proteins nucleating it remain unknown, though a number of candidates have been proposed based on indirect evidence [8-15]. Here, we used two independent approaches to identify cortical actin nucleators: a proteomic analysis using cortex-rich isolated blebs, and a localization/small hairpin RNA (shRNA) screen searching for phenotypes with a weakened cortex or altered contractility. This unbiased study revealed that two proteins generated the majority of cortical actin: the formin mDia1 and the Arp2/3 complex. Each nucleator contributed a similar amount of F-actin to the cortex but had very different accumulation kinetics. Electron microscopy examination revealed that each nucleator affected cortical network architecture differently. mDia1 depletion led to failure in division, but Arp2/3 depletion did not. Interestingly, despite not affecting division on its own, Arp2/3 inhibition potentiated the effect of mDia1 depletion. Our findings indicate that the bulk of the actin cortex is nucleated by mDia1 and Arp2/3 and suggest a mechanism for rapid fine-tuning of cortex structure and mechanics by adjusting the relative contribution of each nucleator.
The mode of action of methotrexate‐monoclonal antibody conjugates (1987)

Drug-monoclonal antibody conjugates have been evaluated for their specificity and toxicity towards tumour cells in vitro and in vivo; however, few studies have investigated their mode of entry into cells and mechanism of action. In this study the uptake and toxic effect of three different Methotrexate-monoclonal antibody (MTX-MoAb) conjugates (MTX-anti-transferrin receptor (TFR), MTX-anti-Ly-2.1 and MTX-anti-L3T4) were examined and compared with free MTX. It was concluded that MTX and these MTX-MoAb conjugates gain entry into tumour cells and are processed by different mechanisms, considering the following results: alterations in temperature had a greater effect on the toxicity of MTX-MoAb than on MTX; in addition, MTX and MTX-MoAb had different rates of action on cells; the specific MTX transport inhibitor, p-chloromercuribenzene sulphonate (pCMS), reduced MTX toxicity but had no effect on specific MTX-MoAb conjugates; the concentration of various ions (Ca2+, Mg2+ and Mn2+) effected the entry of MTX-MoAb but had no effect on free MTX. MTX enters by its own carrier mechanism, while MTX-MoAb conjugates enter by endocytosis with release of MTX at the lysosomal membrane, demonstrated by the ability of chloroquine and NH4Cl (which inhibit lysosomal function) to inhibit the action of MTX-MoAb but not MTX. Therefore, these MTX-MoAb conjugates are not degraded at the surface but bind to their receptor and then enter the cell by endocytosis as one entity; the MTX-MoAb conjugates are then degraded within the lysosomes, resulting in the release of free MTX into the cytoplasm where it acts on dihydrofolate reductase (DHFR) to inhibit cell metabolism.
Pyrimidines. 7. A study of the chlorination of pyrimidines with phosphorus oxychloride in the presence of N,N‐dimethylaniline (1984)

Abstract The chlorination of 6‐trifluoromethyluracils by phosphorus oxychloride in the presence of N,N ‐dimethylaniline was studied and compared with results obtained with 6‐methyluracils. 6‐Trifluoromethyluracil and its 5‐chloro analog afforded moderate yields of the di‐ and trichloropyrimidines, accompanied by good yields of the 2‐ N ‐methylanilino by‐products, after a 3‐hour reaction time. After 24 hours, the 2‐ N ‐methylanilinopyrimidines were the primary or sole products. A small yield of 2,4‐ bis ( N ‐methylanilino)‐6‐trifluoromethylpyrimidine was also obtained. The 6‐methyluracils afforded high yields of the di‐ and trichloropyrimidines, after 3 and 24 hours, along with minor amounts of the 2‐ N ‐methylanilino by‐products. After 48 hours, the proportion of 2,4‐dichloro‐6‐methylpyrimidine decreased, and the 2‐ N ‐methylanilino product increased. 2‐Chloro‐4‐methylanilino‐6‐methylpyrimidine and bis (2‐ N ‐methylanilino)‐6‐methylpyrimidine were also formed in small amounts. The chlorination products from 5‐chloro‐6‐methyluracil remained constant over 188 hours of reaction time. It appears that the π electron distribution around the ring, as influenced by the substituents, controls the course of the chlorination and by‐product formation. Since the amination by a tertiary amine is a type of Hofmann reaction, the presence of the chlorine in the 5 position of the ring adds steric hindrance and thus enhances the regiospecificity of the formation of by‐products.
Postoperative alteration of arteriovenous exchange of amino acids across the gastrointestinal tract. (1983)

Nitrogen flux across the splanchnic bed is altered following operation, injury, and sepsis, but the individual contributions of gut and liver and their interrelationships remain undefined. Since more than 60% of whole blood amino acid nitrogen is transported as glutamine and alanine, we determined the flux of these amino acids across the gastrointestinal tract and liver in splenectomized, awake dogs during a control period and a 2 and 4 days following a standard laparotomy. Blood flow was measured in all studies and substrate flux calculated from flow and arteriovenous and portovenous concentration differences. Portal blood flow decreased by 25% following operation from a control value of 26 +/- 2 ml/kg body weight . min to 19 +/- 2 (P less than 0.05). Total hepatic blood flow did not change significantly after operation, but the individual contributions of the hepatic artery and portal vein were altered; hepatic artery flow increased from a control value of 10 +/- 1 ml/kg . min to 23 +/- 3 (P less than 0.001). Glutamine uptake by teh gastrointestinal tract nearly doubled from a control value of 0.75 +/- 0.16 microM/kg . min to 1.31 +/- 0.13 (P less than 0.05) on postoperative day 2. This increase in flux occurred despite a diminished arterial concentration and a reduced portal blood flow, indicating that extraction of glutamine by the gastrointestinal tract was not primarily dependent on increased arterial concentration. Alanine, on the other hand, was released by the gut at a rate of 1.97 +/- 0.37 microM/kg . min in controls and decreased to 0.81 +/- 0.13 microM/kg . min (P less than 0.05) in dogs that had operation. Glutamine was released by the liver in control dogs at a rate of 1.59 +/- 0.59 microM/kg . min but switched to an organ of slight glutamine uptake (0.31 +/- 0.31, P less than 0.01) on postoperative day 2. Alanine uptake by the liver doubled from 2.94 +/- 0.29 to 5.46 +/- 0.63 microM/kg . min (P less than 0.05) following surgical stress. The gastrointestinal tract plays an active metabolic role in the processing of amino acids following operation and may be a key regulatory of interorgan substrate flux following injury and infection.
Organically modified silica nanoparticles: A nonviral vector for in vivo gene delivery and expression in the brain (2005)

This article reports on the application of organically modified silica (ORMOSIL) nanoparticles as a nonviral vector for efficient in vivo gene delivery. Highly monodispersed, stable aqueous suspension of nanoparticles, surface-functionalized with amino groups for binding of DNA, were prepared and characterized. Stereotaxic injections of nanoparticles, complexed with plasmid DNA encoding for EGFP, into the mouse ventral midbrain and into lateral ventricle, allowed us to fluorescently visualize the extensive transfection of neuronal-like cells in substantia nigra and areas surrounding the lateral ventricle. No ORMOSIL-based toxicity was observed 4 weeks after transfection. The efficiency of transfection equaled or exceeded that obtained in studies using a viral vector. An in vivo optical imaging technique (a fiber-based confocal fluorescent imaging system) provided an effective means to show the retention of viability of the transfected cells. The ORMOSIL-mediated transfections also were used to manipulate the biology of the neural stem/progenitor cells in vivo. Transfection of a plasmid expressing the nucleus-targeting fibroblast growth factor receptor type 1 resulted in significant inhibition of the in vivo incorporation of bromodeoxyuridine into the DNA of the cells in the subventricular zone and the adjacent rostral migratory stream. This in vivo approach shows that the nuclear receptor can control the proliferation of the stem/progenitor cells in this region of the brain. The results of this nanomedicine approach using ORMOSIL nanoparticles as a nonviral gene delivery platform have a promising future direction for effective therapeutic manipulation of the neural stem/progenitor cells as well as in vivo targeted brain therapy.
Wide gamut device-independent colour image interchange (1994)

The article discusses some aspects of colour reproduction in CRT cameras and displays, photography and offset printing. It explains how colour data can be coded in calibrated, nonlinear RGB values in order to take advantage of accurate colour interchange, and how colours outside the gamut of RGB primaries can be conveyed using an extension of RGB coding.
Bidirectional wavelength-division-multiplexing self-healing passive optical network (2005)

We demonstrate a bidirectional wavelength-division-multiplexing (WDM) self-healing passive optical network (PON), which can provide 1+1 protection capability. In this network, self-healing can be achieved within 8 ms against any fiber cut of the feeder fiber and the distribution fiber.
Functional results of percutaneous laser discectomy. (1996)

The purpose of the study was to evaluate laser disc decompression with the KTP 532 laser, used in conjunction with a percutaneous technique, in contained, small to moderately sized lumbar disc herniation. Sixty-three patients who had a contained herniated nucleus pulposus (HNP) and underwent percutaneous laser disc decompression were prospectively studied. Sixty-one were available for follow-up. Access to the disc space was attained with an 18-gauge probe, followed by dilating cannulas guided with an image intensifier. Discography was not performed. The power was set at 10 W, and laser pulses were delivered for 0.2 seconds, with an interval of 0.5 seconds. A total of 1250 J was delivered to the disc space. The average follow-up was 31.75 months (range, 20 to 45 months). Overall, 44 patients (72%) achieved relief of radicular pain, and 33 patients (54%) achieved relief of low back pain. Thirty-six of 61 patients (59%) returned to work by postoperative week 4. Fourteen patients failed treatment, experiencing persistent symptoms (with scores on the Andrews and Lavyne rating scale of < or = 3). In this study group, optimal results were obtained when symptoms were treated within 1 year of presentation. Results from a historical control group are provided for comparison.
Efficient generation of retinal progenitor cells from human embryonic stem cells (2006)

The retina is subject to degenerative conditions, leading to blindness. Although retinal regeneration is robust in lower vertebrates, regeneration does not occur in the adult mammalian retina. Thus, we have developed efficient methods for deriving retinal neurons from human embryonic stem (hES) cells. Under appropriate culture conditions, up to 80% of the H1 line can be directed to the retinal progenitor fate, and express a gene expression profile similar to progenitors derived from human fetal retina. The hES cell-derived progenitors differentiate primarily into inner retinal neurons (ganglion and amacrine cells), with functional glutamate receptors. Upon coculture with retinas derived from a mouse model of retinal degeneration, the hES cell derived retinal progenitors integrate with the degenerated mouse retina and increase in their expression of photoreceptor-specific markers. These results demonstrate that human ES cells can be selectively directed to a neural retinal cell fate and thus may be useful in the treatment of retinal degenerations.