gebhart/patrepeval huggingface dataset:
Neural EGF-like protein 1 (NELL-1): Signaling crosstalk in mesenchymal stem cells and applications in regenerative medicine (2017)

Bone tissue regeneration holds the potential to solve both osteoporosis and large skeletal defects, two problems associated with significant morbidity. The differentiation of mesenchymal stem cells into the osteogenic lineage requires a specific microenvironment and certain osteogenic growth factors. Neural EGF Like-Like molecule 1 (NELL-1) is a secreted glycoprotein that has proven, both <i>in vitro</i> and <i>in vivo</i>, to be a potent osteo-inductive factor. Furthermore, it has been shown to repress adipogenic differentiation and inflammation. NELL-1 can work synergistically with other osteogenic factors such as Bone Morphogenic Protein (BMP) -2 and -9, and has shown promise for use in tissue engineering and as a systemically administered drug for the treatment of osteoporosis. Here we provide a comprehensive up-to-date review on the molecular signaling cascade of NELL-1 in mesenchymal stem cells and potential applications in bone regenerative engineering.
CD28 Regulates the Translation of Bcl-xL via the Phosphatidylinositol 3-Kinase/Mammalian Target of Rapamycin Pathway (2005)

In concert with the TCR, CD28 promotes T cell survival by regulating the expression of the antiapoptotic protein Bcl-x(L). The mechanism by which CD28 mediates the induction of Bcl-x(L) remains unknown. We show that although signaling through the TCR is sufficient to stimulate transcription of Bcl-x(L) mRNA, CD28, by activating PI3K and mammalian target of rapamycin, provides a critical signal that regulates the translation of Bcl-x(L) transcripts. We observe that CD28 induced 4E-binding protein-1 phosphorylation, an inhibitor of the translational machinery, and that CD28 costimulation directly augmented the translation of a Bcl-x(L) 5'-untranslated region reporter construct. Lastly, costimulation by CD28 shifted the distribution of Bcl-x(L) mRNA transcripts from the pretranslation complex to the translationally active polyribosomes. These results demonstrate that CD28 relieves the translational inhibition of Bcl-x(L) in a PI3K/mammalian target of rapamycin-dependent manner.
Anti–Programmed Death-1 Synergizes with Granulocyte Macrophage Colony-Stimulating Factor–Secreting Tumor Cell Immunotherapy Providing Therapeutic Benefit to Mice with Established Tumors (2009)

The combination of PD-1 blockade with GM-CSF-secreting tumor cell immunotherapy leads to significantly improved antitumor responses by augmenting the tumor-reactive T-cell responses induced by the cellular immunotherapy. Readministration of the cellular immunotherapy with the anti-PD-1 antibody in subsequent immunotherapy cycles was required to reactivate these T-cell responses.
4-Hydroxytamoxifen binds to and deactivates the estrogen-related receptor γ (2001)

The estrogen-related receptors (ERR alpha, ERR beta, and ERR gamma) form a family of orphan nuclear receptors that share significant amino acid identity with the estrogen receptors, but for which physiologic roles remain largely unknown. By using a peptide sensor assay, we have identified the stilbenes diethylstilbestrol (DES), tamoxifen (TAM), and 4-hydroxytamoxifen (4-OHT) as high-affinity ligands for ERR gamma. In direct binding assays, 4-OHT had a K(d) value of 35 nM, and both DES and TAM displaced radiolabeled 4-OHT with K(i) values of 870 nM. In cell-based assays, 4-OHT binding caused a dissociation of the complex between ERR gamma and the steroid receptor coactivator-1, and led to an inhibition of the constitutive transcriptional activity of ERR gamma. ERR alpha did not bind 4-OHT, but replacing a single amino acid predicted to be in the ERR alpha ligand-binding pocket with the corresponding ERR gamma residue allowed high-affinity 4-OHT binding. These results demonstrate the existence of high-affinity ligands for the ERR family of orphan receptors, and identify 4-OHT as a molecule that can regulate the transcriptional activity of ERR gamma.
Sub-50 fs Yb-doped laser with anomalous-dispersion photonic crystal fiber (2013)

We report on the generation of 42 fs pulses at 1 μm in a completely fiber-integrated format, which are, to the best of our knowledge, the shortest from all-fiber-integrated Yb-doped fiber lasers to date. The ring fiber cavity incorporates anomalous-dispersion, solid-core photonic crystal fiber with low birefringence, which acts as a broadband, in-fiber Lyot filter to facilitate mode locking. The oscillator operates in the stretched-pulse regime under slight normal net cavity dispersion. The cavity generates 4.7 ps long pulses with a spectral bandwidth of 58.2 nm, which are dechirped to 42 fs via a grating pair compressor outside of the cavity. Relative intensity noise (RIN) of the laser is characterized, with the integrated RIN found to be 0.026% in the 3 Hz-250 kHz frequency range.
Microcellular polymer processing and the design of a continuous sheet processing system (1994)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Mechanical Engineering, 1994.
Novel Combretastatin Analogues Effective against Murine Solid Tumors:  Design and Structure−Activity Relationships (1998)

A series of combretastatin A-4 (CA-4) analogues were synthesized, and their cytotoxic effects against murine Colon 26 adenocarcinoma and inhibitory activity on tubulin polymerization were evaluated. Since CA-4 has limited aqueous solubility, the target compounds were designed to improve solubility by introduction of a nitrogen-containing group. Among the compounds synthesized, those with an amino moiety in place of the phenolic OH of CA-4 showed potent antitubulin activity and cytotoxicity against murine Colon 26 adenocarcinoma in vitro. Some of the compounds which were potent in vitro were evaluated in the murine tumor model Colon 26 in vivo. Among these, 13bHCl, 21aHCl, and 21bHCl showed significant antitumor activity in the animal model, while CA-4 was ineffective. 13bHCl and 21aHCl were further evaluated in two murine tumor models (Colon 38 and 3LL) and human xenografts HCT-15. These compounds showed potent antitumor activity comparable or superior to that of CDDP. The structure-activity relationships of this series of compounds are also discussed.
Dry Reforming of Methane – Review of Feasibility Studies (2012)

International audience
Comparing in vitro , in situ , and in vivo experimental data in a three-dimensional model of mammalian cochlear mechanics (1999)

Normal mammalian hearing is refined by amplification of the motion of the cochlear partition. This partition, comprising the organ of Corti sandwiched between the basilar and tectorial membranes, contains the outer hair cells that are thought to drive this amplification process. Force generation by outer hair cells has been studied extensively in vitro and in situ, but, to understand cochlear amplification fully, it is necessary to characterize the role played by each of the components of the cochlear partition in vivo. Observations of cochlear partition motion in vivo are severely restricted by its inaccessibility and sensitivity to surgical trauma, so, for the present study, a computer model has been used to simulate the operation of the cochlea under different experimental conditions. In this model, which uniquely retains much of the three-dimensional complexity of the real cochlea, the motions of the basilar and tectorial membranes are fundamentally different during in situ- and in vivo-like conditions. Furthermore, enhanced outer hair cell force generation in vitro leads paradoxically to a decrease in the gain of the cochlear amplifier during sound stimulation to the model in vivo. These results suggest that it is not possible to extrapolate directly from experimental observations made in vitro and in situ to the normal operation of the intact organ in vivo.
Induction of Cytoplasmic Accumulation of p53: A Mechanism for Low Levels of Arsenic Exposure to Predispose Cells for Malignant Transformation (2008)

Although epidemiologic studies have linked arsenic exposure to the development of human cancer, the mechanisms underlying the tumorigenic role of arsenic remain largely undefined. We report here that treatment of cells with sodium arsenite at the concentrations close to environmental exposure is associated with the up-regulation of Hdm2 and the accumulation of p53 in the cytoplasm. Through the mitogen-activated protein kinase pathway, arsenite stimulates the P2 promoter-mediated expression of Hdm2, which then promotes p53 nuclear export. As a consequence, the p53 response to genotoxic stress is compromised, as evidenced by the impaired p53 activation and apoptosis in response to UV irradiation or 5FU treatment. The ability of arsenite to impede p53 activation is further demonstrated by a significantly blunted p53-dependent tissue response to 5FU treatment when mice were fed with arsenite-containing water. Together, our data suggests that arsenic compounds predispose cells to malignant transformation by up-regulation of Hdm2 and subsequent p53 inactivation.
A Novel Thrombelastograph?? Tissue Factor/Kaolin Assay of Activated Clotting Times for Monitoring Heparin Anticoagulation During Cardiopulmonary Bypass (2004)

We used a thrombelastograph (TEG) assay with tissue factor and kaolin (TEG TF/K) to measure activated clotting time (ACT) in 31 patients during cardiopulmonary bypass. For comparison, ACTs were also determined by a Hemochron Jr. Signature and a Hepcon HMS. The TEG TF/K correlated with both the Hepcon (r(2) = 0.789) and Hemochron (r(2) = 0.743) ACTs. The average ACT after heparin was 319 +/- 119 s (mean +/- sd) for the TEG TF/K compared with 624 +/- 118 s for the Hepcon instrument. To evaluate the effects of hemodilution on TEG TF/K and Hemochron assays, ACT assays were performed on blood diluted to 50% and titrated with heparin from 0 to 6 U/mL. Both instruments showed significant (P < 0.01) changes in the ACT-versus-heparin slope, but the 0 heparin intercept for the TEG TF/K ACTs was not significantly changed (P = 0.292), in contrast to that for the Hemochron device (P = 0.041). Both instruments also indicated the same 1.3:1 ratio of protamine to heparin for optimum heparin neutralization, with increasing ACTs at ratios >2.6:1. The TEG TF/K ACT assay rapidly monitors heparin anticoagulation, in addition to the capabilities of this instrument to monitor platelet function, clotting factors, and fibrinolysis.
Fundamental harmonic of ripples in symmetrical Cockcroft–Walton cascade rectifying circuit (1996)

On the basis of a conventional Cockcroft–Walton (C–W) cascade rectifying circuit, an expression is derived for the fundamental harmonic of ripples due to asymmetry of driving voltage in a symmetrical C–W circuit. The expression is validated from good agreement with experimental results of both a low-voltage model circuit and a high-voltage circuit used in an ultrahigh-voltage electron microscope.
A Competitive Nucleotide Binding Inhibitor: In Vitro Characterization of Rab7 GTPase Inhibition (2012)

Mapping the functionality of GTPases through small molecule inhibitors represents an underexplored area in large part due to the lack of suitable compounds. Here we report on the small chemical molecule 2-(benzoylcarbamothioylamino)-5,5-dimethyl-4,7-dihydrothieno[2,3-c]pyran-3-carboxylic acid (PubChem CID 1067700) as an inhibitor of nucleotide binding by Ras-related GTPases. The mechanism of action of this pan-GTPase inhibitor was characterized in the context of the Rab7 GTPase as there are no known inhibitors of Rab GTPases. Bead-based flow cytometry established that CID 1067700 has significant inhibitory potency on Rab7 nucleotide binding with nanomolar inhibitor (K(i)) values and an inhibitory response of ≥97% for BODIPY-GTP and BODIPY-GDP binding. Other tested GTPases exhibited significantly lower responses. The compound behaves as a competitive inhibitor of Rab7 nucleotide binding based on both equilibrium binding and dissociation assays. Molecular docking analyses are compatible with CID 1067700 fitting into the nucleotide binding pocket of the GTP-conformer of Rab7. On the GDP-conformer, the molecule has greater solvent exposure and significantly less protein interaction relative to GDP, offering a molecular rationale for the experimental results. Structural features pertinent to CID 1067700 inhibitory activity have been identified through initial structure-activity analyses and identified a molecular scaffold that may serve in the generation of more selective probes for Rab7 and other GTPases. Taken together, our study has identified the first competitive GTPase inhibitor and demonstrated the potential utility of the compound for dissecting the enzymology of the Rab7 GTPase, as well as serving as a model for other small molecular weight GTPase inhibitors.
COMBINATION OF STATISTICAL AND LANGUAGE PROCESSING METHODS IN NEWS SUMMARIZATION: A CASE STUDY FOR VIETNAMESE NEWS (2016)

Abstract: Automatic summarization refers to a technique of reducing of a text document by a computer program to create a summary that retains the most important points of the original document. Among various kinds of textual documents, news plays an important role in our life, which is always updated sequentially every day in large scale. A technique for automatic creation of new summarization would help readers to quickly capture significant information from vast amount of electronic newspapers available on the Internet nowadays. In this paper, we introduce an approach to handle this issue on Vietnamese news. By combining both statistical and linguistic methods, we are able to produce meaningful summarization of real articles collected from major newspaper channels in Vietnam.
Using Self-Assembled Monolayers to Understand the Interactions of Man-made Surfaces with Proteins and Cells (1996)

Self-assembled monolayers (SAMs) formed on the adsorption of long-chain alkanethiols to the surface of gold or alkylsilanes to hydroxylated surfaces are well-ordered organic surfaces that permit control over the properties of the interface at the molecular scale. The ability to present molecules, peptides, and proteins at the interface make SAMs especially useful for fundamental studies of protein adsorption and cell adhesion. Microcontact printing is a simple technique that can pattern the formation of SAMs in the plane of the monolayer with dimensions on the micron scale. The convenience and broad application offered by SAMs and microcontact printing make this combination of techniques useful for studying a variety of fundamental phenomena in biointerfacial science.
Substituent Effects on Twisted Internal Charge Transfer Excited States of N-Borylated Carbazoles and (Diphenylamino)boranes (2012)

N-Boryl-substituted carbazoles (carBR(2)) and (diphenylamino)boranes (Ph(2)NBR(2)) with R = Mes (mesityl) and FMes [tris(trifluoromethyl)phenyl] substituents on boron exhibit large UV/vis Stokes shifts. To investigate the substituent effect on the magnitude of the Stokes shifts, we studied the electronic structure and spectroscopic properties of carBR(2) and Ph(2)NBR(2) with R = H, Mes, and FMes using hybrid density functional theory (B3LYP) and time-dependent density functional theory (TD-B3LYP) for ground and low-lying excited states. The lowest lying excited state with a nonvanishing oscillator strength is a twisted internal charge transfer (TICT) (1)A state in the C(2) point group, owing to a single-electron excitation from the nitrogen lone pair to the unoccupied boron p(z) AO, Nlp → Bp(z). Emission from these (1)A excited states are predicted to be much brighter than from the energetically close (1)B excited states that are not directly related to CT excitation from N to B, due to symmetry. An analysis of geometrical relaxations in the excited state and the state energies relative to the ground state energy of the equilibrium geometry reveals that (a) the carbazole skeleton induces a general red shift in UV/vis spectra, (b) bulky boryl substituents reduce the predicted Stokes shifts of TICT states, and (c) the presence of electron-withdrawing functional groups induces a further general red shift in UV/vis spectra but does not significantly alter Stokes shifts.
Renal Arteriolar C4d Deposition (2013)

Arteriolar C4d deposition may be a pathologic marker of TA-TMA, implicating localized complement fixation in HSCT recipients with kidney disease secondary to small vessel injury. Further studies to better characterize the preferential arteriolar C4d staining may identify a renal compartment of injury, possibly explaining the dramatic hypertension seen in TA-TMA.
Studies on the Synthesis of (2R,4′R,8′R)‐α‐Tocopherol Alternative Syntheses of 2‐Chroman‐acetic Acid Intermediates (1978)

Abstract As an extension of previous studies on the total synthesis of (2R,4′R,8′R)‐α‐tocopherol ( 1 ) [1] [2], (S)‐(−)‐2‐(6‐benzyloxy‐2,5,7,8‐tetramethylchroman)acetic acid ( 6 ), a pivotal intermediate, possessing the absolute configuration required for construction of 1 was prepared by optical resolution of the racemic modification 11 . the latter substance was obtained by two routes, one emanating from the hydroxy acetal 7 [1] and the other based upon the Lewis acid mediated cycloaddition of trimethylhydroquinone to rac.‐3‐hydroxy‐3‐methylpent‐4‐en‐l‐yl acetate ( 16 ) giving rac. ethyl 2‐(6‐hydroxy‐2,5,7,8‐tetramethyl‐chroman)acetate ( 12 ).
New Heteroaromatic Complexing Agents and Luminescence of Their Europium(III) and Terbium(III) Chelates (1992)

Abstract Twelve heteroaromatic complexing agents 9a–I were synthesized with the purpose to develop suitable labels for time‐resolved luminescence‐based bioaffinity assays. The relative luminescence yields, excitation maxima, and emission decay constants of their europium(III) and terbium(III) chelates were determined. According to these results, 2,2′,2″,2‴‐[(2,2′‐bipyridine‐6,6′‐diyl)bis(methylenenitrilo)]tetrakis (acetic acid) ( 9e ) and 2,2′,2″,2‴‐[(2,2′:6′,2″‐terpyridine‐6,6″‐diyl)bis(methylenenitrilo)] tetrakis(acetic acid) ( 91 ) are the most promising agents.
Optical-fibre surface-plasmon-wave polarisers with enhanced performance (1989)

The effect of a thin metal film with positive dielectric permittivity on the performance of an optical-fibre surfaceplasmon-wave polariser is presented. A dramatic improvement has been achieved with polarisation extinction ratios in excess of 45 dB over an extended range of superstrate refractive indices.
Conservation of DNA regions adjacent to nifKDH homologous sequences in diverse slow-growing Rhizobium strains. (1983)

Restriction endonuclease-digested deoxyribonucleic acid (DNA) from 17 slow-growing Rhizobium strains was hybridized with 32P-labeled DNA of the Klebsiella pneumoniae nitrogenase structural gene (nifKDH) region. Sixteen of these strains contained two or more fragments that were homologous to K. pneumoniae nifKDH after cleavage with EcoRI or HindIII. Hybridization with nifKDH subclones revealed that most of the Rhizobium fragments were homologous to the HindIII-EcoRI portion of nifKDH (corresponding to the nifDH region), although fragments homologous to the EcoRI-HindIII portion of nifKDH (corresponding to the nifK region) were also present. Comigrating nif-homologous restriction endonuclease fragments were observed for strains isolated from different geographic locations and from nodules of different plant species. Nearly identical hybridization patterns were obtained for five R. japonicum strains which clearly differed in the pattern of restriction endonuclease fragments from their chromosomal DNA. This indicates that there is a high degree of conservation of DNA sequence surrounding the region of nif homology in these strains.
Single-Chain Fragment Variable Passive Immunotherapies for Neurodegenerative Diseases (2013)

Accumulation of misfolded proteins has been implicated in a variety of neurodegenerative diseases including prion diseases, Alzheimer's disease (AD), Parkinson's disease (PD), and Huntington's disease (HD). In the past decade, single-chain fragment variable (scFv) -based immunotherapies have been developed to target abnormal proteins or various forms of protein aggregates including Aβ, SNCA, Htt, and PrP proteins. The scFvs are produced by fusing the variable regions of the antibody heavy and light chains, creating a much smaller protein with unaltered specificity. Because of its small size and relative ease of production, scFvs are promising diagnostic and therapeutic reagents for protein misfolded diseases. Studies have demonstrated the efficacy and safety of scFvs in preventing amyloid protein aggregation in preclinical models. Herein, we discuss recent developments of these immunotherapeutics. We review efforts of our group and others using scFv in neurodegenerative disease models. We illustrate the advantages of scFvs, including engineering to enhance misfolded conformer specificity and subcellular targeting to optimize therapeutic action.
Immunoblotting Analysis of Anti‐Rickettsial Antibodies Produced in Patients of Tsutsugamushi Disease (1988)

The reactivity of sera from patients of Tsutsugamushi disease (scrub typhus) with the antigenic polypeptides of Rickettsia tsutsugamushi was analyzed by the immunoblotting method. The reactivity varied greatly among the sera of individual patients tested. IgG and IgM antibodies of most patients reacted with the 54-56 kilodalton (54-56K) polypeptide located on the rickettsial surface, suggesting that this polypeptide is a predominant antigen in the infection. Other polypeptides of 60K, 50-52K, 46-47K, 35K, and 21-25K were reactive with some but not all sera. From the reactivity of these polypeptides, it was suggested that the 54-56K polypeptide is both strain-specific and group-specific, the 60K polypeptide is group-specific, and the 35K and 21-25K polypeptides are subgroup-specific. IgG antibodies seem to be more cross-reactive with polypeptides of multiple strains than IgM antibodies and have a tendency of increased cross-reactivity that was observed in the sera obtained at the later stage of illness.
Calcium phosphate plasma‐sprayed coatings and their stability: An in vivo study (1994)

Several factors playing a possible role in determining coating stability and bone tissue response were studied in in vivo experiments. These factors involving the plasmaspray coating procedure were as follows: 1) plasmaspray powder port 2 or 6; 2) particle size distribution; 3) hydroxylapatite versus fluorapatite coatings; and 4) the effect of post-heat treatment. Coating stability and bone tissue response were examined by measuring coating thickness, coating length, and bone apposition against the coatings. The result was that heat treatment influenced coating stability significantly. Also, bone formation was more intense. Fluorapatite proved to be more stable than hydroxylapatite, which was in agreement with our previous reports.
Prophage Genomics (2003)

Both occurrences of "315.5"should read "315.6," and both occurrences of