gebhart/patrepeval huggingface dataset:
Long-term persistence of plasmid DNA and foreign gone expression in mouse muscle (1992)

Plasmid pRSVL persisted and expressed luciferase for at least 19 months in mouse skeletal muscle after intramuscular injection. Other injected plasmids also stably expressed long-term suggesting that any plasmid DNA could stably persist and express in muscle. Plasmid DNA was demonstrated by quantitative PCR in some of the muscle DNA samples for at least 19 months after injection. The methylation pattern of the plasmid DNA remained in its bacterial form indicating that the foreign DNA did not replicate in the muscle cells. The electroporation of total cellular DNA from injected muscles into bacteria indicated that the plasmid DNA was extrachromosomal. Chromosomal integration of plasmid DNA was searched for by electroporating the injected muscle DNA into bacteria after restriction enzyme digestion and ligation. No plasmids containing plasmid/chromosome junctions were observed in over 1800 colonies examined. Lack of integration increases the theoretical safety of this gene transfer technique. Long-term stability of plasmid DNA in muscle indicates that muscle is an attractive target tissue for the introduction of extrachromosomal plasmid or viral DNA for the purpose of gene therapy.
Stereoselective Synthesis of Tilivalline1 (1998)

Tilivalline 1, a metabolite from Klebsiella pneumoniae var. ocytoca, was easily synthesized in five steps from (S)-proline and 3-(benzyloxy)isatoic anhydride 4g. This synthesis is based on modified Curtius reactions of 3-substituted phthalic anhydrides 11 to 3-substituted isatoic anhydrides 4, conversion of lactams 6 to the acyliminium precursors 7 and stereoselective introduction of indole from the less hindered side of 7.
Cranberry components inhibit interleukin‐6, interleukin‐8, and prostaglandin E2 production by lipopolysaccharide‐activated gingival fibroblasts (2007)

Periodontitis is a chronic inflammatory disease that affects the tooth supporting tissues. Gingival fibroblasts are the most abundant cells in periodontal tissues and participate actively in the host inflammatory response to periodontopathogens, which is known to mediate local tissue destruction in periodontitis. The aim of this study was to investigate the effect of a proanthocyanidin-enriched cranberry fraction, prepared from cranberry juice concentrate, on inflammatory mediator production by gingival fibroblasts stimulated by the lipopolysaccharide (LPS) of Aggregatibacter actinomycetemcomitans. Interleukin (IL)-6, IL-8, and prostaglandin E(2) (PGE(2)) production by fibroblasts treated with the cranberry fraction and stimulated by A. actinomycetemcomitans LPS was evaluated by enzyme-linked immunosorbent assay. Changes induced by A. actinomycetemcomitans LPS and the cranberry fraction in the expression and phosphorylation state of fibroblast intracellular signaling proteins were characterized by antibody microarrays. The LPS-induced IL-6, IL-8, and PGE(2) responses of gingival fibroblasts were inhibited by treatment with the cranberry fraction. This fraction was found to inhibit fibroblast intracellular signaling proteins, a phenomenon that may lead to a down-regulation of activating protein-1 activity. Cranberry components also reduced cyclooxygenase 2 expression. This study suggests that cranberry juice contains molecules with interesting properties for the development of new host-modulating therapeutic strategies in the adjunctive treatment of periodontitis.
Ultrafast Radiationless Deactivation of Organic Dyes:  Evidence for a Two-State Two-Mode Pathway in Polymethine Cyanines (2000)

CASSCF quantum chemical calculations (including dynamics) have been used to investigate the ultrafast photoisomerization of three symmetric cyanine dye models of different chain lengths. For the “model” trimethine cyanine, the photochemical isomerization path can be divided into two phases: initial barrierless skeletal stretching coupled with torsional motion and the decay process that takes place in the region of the twisted intramolecular charge-transfer (TICT) minimum state with an adjacent conical intersection. The path is consistent with both biexponential decay of fluorescence without rise time at short wavelengths and the rise time followed by monoexponential decay at long wavelengths observed in time-resolved experiments. For penta- and heptamethine cyanines, the photoisomerization about different C−C bonds is shown to be an activated process, where the torsional reaction path terminates, again, at a TICT state and the decay takes place at a twisted S1/S0 conical intersection. In agreement with the experimental results, the activation energies increase with the length of the polymethine chain. In contrast to the differences in the potential energy surface between short and long cyanines, we demonstrate that the excited state evolution of these systems can be understood in terms of the same two-state two-mode model of the reaction coordinate previously reported for the (isoelectronic) retinal protonated Schiff base models.
Synthesis of 1-Benzyl-3-(5‘-hydroxymethyl-2‘-furyl)indazole Analogues as Novel Antiplatelet Agents (2001)

1-Benzyl-3-(5'-hydroxymethyl-2'-furyl)indazole (28, YC-1) was selected as the lead compound for systemic structural modification. After screening for antiplatelet activity, SARs of YC-1 analogues were established. Among these potent active derivatives, compounds 29, 30, 31, 44, and 45 functioned as potent activators of sGC and inhibitors of PDE5 with potency comparable to that of YC-1. In addition, compound 58 was found to be a selective and potent inhibitor of protease-activated receptor type 4 (PAR4)-dependent platelet activation.
Design and facile production of recombinant resilin-like polypeptides: gene construction and a rapid protein purification method (2007)

Resilin is an elastic protein found in specialized regions of the cuticle of insects, which displays unique resilience and fatigue lifetime properties. As is the case with many elastomeric proteins, including elastin, gliadin and spider silks, resilin contains distinct repetitive domains that appear to confer elastic properties to the protein. Recent work within our laboratory has demonstrated that cloning and expression of exon 1 of the Drosophila melanogaster CG15920 gene, encoding a putative resilin-like protein, results in a recombinant protein that can be photochemically crosslinked to form a highly resilient, elastic biomaterial (Rec1 resilin). The current study describes a recursive cloning strategy for generating synthetic genes encoding multiple copies of consensus polypeptides, based on the repetitive domains within resilin-like genes from D. melanogaster and Anopheles gambiae. A simple non-chromatographic purification method that can be applied to these synthetic proteins and Rec1 is also reported. These methods for the design and purification of resilin-like periodic polypeptides will facilitate the future investigation of structural and functional properties of resilin, and the development of novel highly resilient biomaterials.
Oral Supplementation of Lutein/Zeaxanthin and Omega-3 Long Chain Polyunsaturated Fatty Acids in Persons Aged 60 Years or Older, with or without AMD (2008)

The addition of omega-3 LCPUFA to oral supplementation of lutein/zeaxanthin did not change the serum levels of lutein and zeaxanthin. A long-term large clinical trial is necessary to investigate the benefits and adverse effects of these factors for the treatment of AMD.
Histone deacetylase inhibitor, Trichostatin A induces ubiquitin-dependent cyclin D1 degradation in MCF-7 breast cancer cells (2006)

We have demonstrated that rapid TSA-induced cyclin D1 degradation in MCF-7 cells requires GSK3beta-mediated Thr-286 phosphorylation and the ubiquitin-dependent 26S proteasome pathway. Drug induced cyclin D1 repression contributes to the inhibition of breast cancer cell proliferation and can sensitize cells to CDK and Akt inhibitors. In addition, anti-cyclin D1 therapy may be highly specific for treating human breast cancer. The development of potent and effective cyclin D1 ablative agents is therefore of clinical relevance. Our findings suggest that HDAC inhibitors may have therapeutic potential as small-molecule cyclin D1 ablative agents.
Beyond the Textbook: A First-Year Introduction to Research at a Research I University (1998)

The project "Beyond the Textbook", is designed to provide second semester undergraduate students firsthand exposure to chemical research. In this project, student teams become investigative reporters assigned to learn the workings of a chemistry research group. This project involves interviewing professors, graduate students and postdocs about their research, and where possible shadowing researchers in the laboratory. At the conclusion of this project, student teams write a feature news article and give a fifteen minute oral presentation. By placing students in an active research setting, the educational focus is shifted from the professor "making the subject matter relevant," to the professor providing the opportunity for students to be engaged in relevant subject matter.
Organometallic polymers. XXV. Preparation of polyvinylferrocene (1973)

Abstract The synthetic details of solution polymerization in benzene and bulk polymerization of vinylferrocene are reported. In benzene solutions, with azobisisobutyronitrile (AIBN) as the initiator, small yields of low‐polydispersity low molecular weight ( M̄ n ≃ 5000) polyvinylferrocene is obtained. However, high yields can be obtained by continuous or multiple AIBN addition. Higher molecular weight polymers and binodal polymers can be obtained as the monomer concentration is increased. In bulk polymerizations, yields of 80% can be obtained. The molecular weight increases as temperature decreases from 80 to 60°C in bulk polymerizations, and an increasing amount of insoluble polymer results. The soluble portion is often binodal, the higher molecular weight node consisting of an increasingly branched structure. Lower molecular weight polymer was readily fractionated into narrow fractions from benzene–methanol systems, but higher molecular weight polymer proved impossible to fractionate into narrow fractions due to branching.
De Novo Design of Native Proteins:  Characterization of Proteins Intended To Fold into Antiparallel, Rop-like, Four-Helix Bundles (1997)

The de novo design and characterization of a series of 51-residue helix-turn-helix peptides intended to dimerize into antiparallel four-stranded coiled coils is described. The sequence is based on a coiled coil heptad repeat Ncap-(Aa Zb Zc Ld Ze Zf Zg)3-turn- (Xa Zb Zc Ld Ze Zf Zg)3-Ccap-CONH2, where X is either Val or Ala. The overall topology was intended to be similar to that found in the Escherichia coli protein ROP. The design strategy included consideration of geometric complementarity of the packing of side chains within the hydrophobic core as well as the use of specific interfacial interactions, both of which were intended to favor the desired ROP-like topology. Additionally, the sequence was designed to destabilize potential alternative structures that might compete with the desired topology. The peptides (RLP-1, RLP-2, and RLP-3) assemble into stable alpha-helical dimers and exhibit the hallmarks of a native protein as judged by its spectroscopic properties, and the lack of binding to hydrophobic dyes. Also, the enthalpy and heat capacity changes upon denaturation were determined by measuring the temperature dependence of the CD spectra and confirmed by differential scanning calorimetry (DSC). The values determined by the two methods are in excellent agreement and are in the range of those of naturally occurring proteins of this size. These results suggest that it is now possible to design native-like helical proteins that should serve as templates for the further design of functional proteins.
ELECTRON MICROSCOPE RADIOAUTOGRAPHY AS A QUANTITATIVE TOOL IN ENZYME CYTOCHEMISTRY (1967)

Tritiated diisopropylfluorophosphate (DFP) was used to phosphorylate acetylcholinesterase (AChase) in the motor end plate of mouse sternomastoid muscle, and its distribution within the end plate was evaluated quantitatively by electron microscope radioautography. With the use of emulsion layers whose sensitivity to tritium had been calibrated, the density of AChase in different components of the end plate was calculated. The AChase was primarily localized (85%) in the junctional fold region. The concentration of AChase there was more than 20,000 active sites per cubic micron of tissue. The resolution of the technique was not sufficient to determine whether there was some AChase in the nerve end bulb; however, if there is any there, the concentration must be less than 10% of that at the junctional fold region.
Error Mitigation for Short-Depth Quantum Circuits (2017)

Two schemes are presented that mitigate the effect of errors and decoherence in short-depth quantum circuits. The size of the circuits for which these techniques can be applied is limited by the rate at which the errors in the computation are introduced. Near-term applications of early quantum devices, such as quantum simulations, rely on accurate estimates of expectation values to become relevant. Decoherence and gate errors lead to wrong estimates of the expectation values of observables used to evaluate the noisy circuit. The two schemes we discuss are deliberately simple and do not require additional qubit resources, so to be as practically relevant in current experiments as possible. The first method, extrapolation to the zero noise limit, subsequently cancels powers of the noise perturbations by an application of Richardson's deferred approach to the limit. The second method cancels errors by resampling randomized circuits according to a quasiprobability distribution.
Delta endotoxin of Bacillus thuringiensis subsp. israelensis (1985)

From Bacillus thuringiensis subsp. israelensis, a proteinase-resistant protein was purified which exhibited toxicity to larval mosquitoes and cultured mosquito cells, lysed erythrocytes, and was lethal to mice. To extract the protein, a sporulating culture of B. thuringiensis subsp. israelensis was treated with alkali, neutralized, and incubated with trypsin and proteinase K. It was then purified by gel filtration and DEAE column chromatography. Up to 240 micrograms of toxic protein was purified from 1 g (wet weight) of culture pellet. Two closely related forms of toxic protein were obtained: the 25a and 25b proteins. The two forms comigrated near 25,000 daltons in a sodium dodecyl sulfate-polyacrylamide gel, were serologically related, and showed similar partial protease digestion profiles, but were distinguishable by DEAE chromatography and nondenaturing polyacrylamide gel electrophoresis. Protein sequencing data indicated the 25b protein lacked the two amino acids at the amino terminus of the 25a protein. A Western blot enzyme-linked immunosorbent assay of alkali-solubilized proteins that were not treated with proteases suggested the toxic 25a and 25b proteins were proteolytically derived from a larger molecule of about 28,000 daltons. Alkali-solubilized proteins from an acrystalliferous strain of B. thuringiensis subsp. israelensis and from B. thuringiensis subsp. kurstaki failed to cross-react with antibodies to the 25a protein.
Induction of antibodies to the Epstein-Barr virus glycoprotein gp85 with a synthetic peptide corresponding to a sequence in the BXLF2 open reading frame (1988)

Epstein-Barr virus codes for at least three envelope glycoproteins, one of which, gp85, has not yet been mapped to the viral genome. The publication and analysis of the entire Epstein-Barr virus DNA sequence has allowed identification of open reading frames with potential for encoding membrane glycoproteins. To determine whether one of these candidate open reading frames, BXLF2, codes for gp85, an antibody was made to a 17-residue peptide derived from positions 518 to 533 of the predicted BXLF2 protein. The reactivity of the antipeptide antibody was then compared with that of the monoclonal antibody F-2-1, which was originally used to define and characterize gp85. Antipeptide antibody and F-2-1 immunoprecipitated glycosylated molecules with identical electrophoretic mobilities; digestion of the two immunoprecipitated proteins with V8 protease generated comparable peptides; and the antipeptide antibody reacted in Western immunoblots with the gp85 glycoprotein that had been immunoprecipitated by F-2-1 before transfer to nitrocellulose. In addition, a monospecific rabbit antibody, made against native gp85, reacted with the peptide used for immunization. These results are compatible with the hypothesis that the BXLF2 open reading frame codes for gp85.
GOCE Program and its Applications (2005)

Current knowledge of the earth's gravity field, as derived from CHAMP and Grace's data, is incomplete, and the determined geoid can not reach the precision required by geophysics and the subjects related to Earth Science. GOCE (Gravity Field and Stead-state Ocean Circulation Explore), which will be launched by ESA in 2006, is the Earth Explorer Gravity Field and Steady-State Ocean Circulation Core Mission satellite based on CHAMP and GRACE. It can determine the geoid with an accuracy of 1 cm and spatial resolution (half wavelength) at length scales between 200-80 km. This paper briefly introduces the current gravity satellites' developing status and their limitations. The GOCE satellite's instruments, its scientific objectives and surveying principle, the important applications in geophysics field, etc., are discussed in detail in this paper. Finally, the applications of the data sources which are generated by GOCE and other gravity satellites are conceived in our country.
An Anti-CD33 Antibody−Calicheamicin Conjugate for Treatment of Acute Myeloid Leukemia. Choice of Linker (2001)

The anti-CD33 antibody, P67.6, has been chosen to target the potently cytotoxic calicheamicin antitumor antibiotics to acute myeloid leukemia (AML) due to the presence of CD33 on >80% of patient samples and its lack of expression outside the myeloid cell lineages, especially its lack of expression on pluripotent stem cells. Previous calicheamicin conjugates relied on the attachment of a hydrazide derivative to the oxidized carbohydrates that occur naturally on antibodies. This results in a "carbohydrate conjugate" capable of releasing active drug by hydrolysis of a hydrazone bond in the lysozomes where the pH is low. Conjugates have now been made that are formed by reacting a calicheamicin derivative containing an activated ester with the lysines of antibodies. This results in an "amide conjugate" that is stable to hydrolysis, leaving the disulfide that is present in all calicheamicin conjugates as the likely site of drug release from the conjugate. In this article, these two classes of calicheamicin-antibody conjugates are compared for potential use in AML with the anti-CD33 antibody P67.6. Conjugates of P67.6 are shown to require the site of hydrolytic release afforded by the carbohydrate conjugates in order to retain good potency and selectivity in vitro, in vivo, and ex vivo. The P67.6 carbohydrate conjugate of calicheamicin is selectively cytotoxic at <0.006 ng/mL of calicheamicin equivalents (cal equiv) toward HL-60 promyelocytic leukemia cells in tissue culture. Long-term, tumor-free survivors are seen in xenograft models when mice bearing HL-60 subcutaneous tumors are treated with the P67.6 carbohydrate conjugate at a dose of 300 microg/kg cal equiv given three times. This conjugate also selectively inhibits the formation of colonies from AML marrow samples at 2 ng/mL cal equiv. The P67.6 carbohydrate conjugate of calicheamicin therefore appears to have promise as an antibody-targeted chemotherapeutic agent for CD33-positive diseases such as AML.
Crystallographic wet chemical etching of GaN (1998)

We demonstrate well-controlled crystallographic etching of wurtzite GaN grown on c-plane sapphire using H3PO4, molten KOH, KOH dissolved in ethylene glycol, and NaOH dissolved in ethylene glycol between 90 and 180 °C, with etch rates as high as 3.2 μm/min. The crystallographic GaN etch planes are {0001}, {101̄0}, {101̄ 1̄}, {101̄ 2̄}, and {101̄3}. The vertical {101̄0} planes appear perfectly smooth when viewed with a field-effect scanning electron microscope. The activation energy is 21 kcal/mol, indicative of reaction-rate limited etching.
Outcomes after allogeneic hematopoietic cell transplantation with nonmyeloablative or myeloablative conditioning regimens for treatment of lymphoma and chronic lymphocytic leukemia (2007)

Allogeneic conventional hematopoietic cell transplantation (HCT) can be curative treatment for lymphoid malignancies, but it has been characterized by high nonrelapse mortality (NRM). Here, we compared outcomes among patients with lymphoma or chronic lymphocytic leukemia given either nonmyeloablative (n = 152) or myeloablative (n = 68) conditioning. Outcomes were stratified by the HCT-specific comorbidity index. Patients in the nonmyeloablative group were older, had more previous treatment and more comorbidities, more frequently had unrelated donors, and more often had malignancy in remission compared with patients in the myeloablative group. Patients with indolent versus aggressive malignancies were equally distributed among both cohorts. After HCT, patients without comorbidities both in the nonmyeloablative and myeloablative cohorts had comparable NRM (P = .74), overall survival (P = .75), and progression-free survival (P = .40). No significant differences were observed (P = .91, P = .89, and P = .40, respectively) after adjustment for pretransplantation variables. Patients with comorbidities experienced lower NRM (P = .009) and better survival (P = .04) after nonmyeloablative conditioning. These differences became more significant (P < .001 and .007, respectively) after adjustment for other variables. Further, nonmyeloablative patients with comorbidities had favorable adjusted progression-free survival (P = .01). Patients without comorbidities could be enrolled in prospective randomized studies comparing different conditioning intensities. Younger patients with comorbidities might benefit from reduced conditioning intensity.
Amyloid‐β(1‐42) alters structure and function of retinal pigmented epithelial cells (2009)

Age-related macular degeneration (AMD) is characterized by the formation of drusen, extracellular deposits associated with atrophy of the retinal pigmented epithelium (RPE), disturbance of the transepithelial barrier and photoreceptor death. Amyloid-beta (Abeta) is present in drusen but its role during AMD remains unknown. This study investigated the in vitro and in vivo effects of the oligomeric form of Abeta(1-42) - OAbeta(1-42) - on RPE and found that it reduced mitochondrial redox potential and increased the production of reactive oxygen species, but did not induce apoptosis in RPE cell cultures. It also disorganized the actin cytoskeleton and halved occludin expression, markedly decreasing attachment capacity and abolishing the selectivity of RPE cell transepithelial permeability. Antioxidant pretreatment partially reversed the effects of OAbeta(1-42) on mitochondrial redox potential and transepithelial permeability. Subretinally injected OAbeta(1-42) induced pigmentation loss and RPE hypertrophy but not RPE cell apoptosis in C57BL/6 J mice. Rapid OAbeta(1-42)-induced disorganization of cytoskeletal actin filaments was accompanied by decreased RPE expression of the tight junction proteins occludin and zonula occludens-1 and of the visual cycle proteins cellular retinaldehyde-binding protein and RPE65. The number of photoreceptors decreased by half within a few days. Our study pinpoints the role of Abeta in RPE alterations and dysfunctions leading to retinal degeneration and suggests that targeting Abeta may help develop selective methods for treating diseases involving retinal degeneration, such as AMD.