gebhart/patrepeval huggingface dataset:
SJG-136 (NSC 694501), a Novel Rationally Designed DNA Minor Groove Interstrand Cross-Linking Agent with Potent and Broad Spectrum Antitumor Activity (2004)

SJG-136 (NSC 694501) is a rationally designed pyrrolobenzodiazepine dimer that binds in the minor groove of DNA. It spans 6 bp with a preference for binding to purine-GATC-pyrimidine sequences. The agent has potent activity in the National Cancer Institute (NCI) anticancer drug screen with 50% net growth inhibition conferred by 0.14 to 320 nmol/L (7.4 nmol/L mean). Sensitive cell lines exhibit total growth inhibition and 50% lethality after treatment with as little as 0.83 and 7.1 nmol/L SJG-136, respectively. COMPARE and molecular target analysis of SJG-136 data versus that of >60,000 compounds tested in the NCI 60 cell line screen shows that, although the agent has similarity to other DNA binding agents, the pattern of activity for SJG-136 does not fit within the clusters of any known agents, suggesting that SJG-136 possesses a distinct mechanism of action. Testing in the NCI standard hollow fiber assay produced prominent growth inhibition in 20 of 24 i.p. and 7 of 24 s.c. test combinations with 5 of 12 cell lines exhibiting cell kill. In addition, SJG-136 produced antitumor activity in mice bearing CH1 and CH1cisR xenografts, a cisplatin-resistant human ovarian tumor model, and also in mice bearing LS174T xenografts, a human colon tumor model. SJG-136 produces DNA interstrand cross-links between two N-2 guanine positions on opposite strands and separated by 2 bp. In human tumor cell lines, the cross-links form rapidly and persist compared with those produced by conventional cross-linking agents such as nitrogen mustards. In mice bearing the LS174T human colon xenograft, DNA interstrand cross-links can be detected in tumor cells using a modification of the single cell gel electrophoresis (comet) assay after administration of a therapeutic dose. Cross-links in the tumor increase with dose and are clearly detectable at 1 hour after i.v. administration. The level of cross-linking persists over a 24-hour period in this tumor in contrast to cross-links produced by conventional cross-linking agents observed over the same time period.
Development of a Human IgG4 Bispecific Antibody for Dual Targeting of Interleukin-4 (IL-4) and Interleukin-13 (IL-13) Cytokines (2013)

Human bispecific antibodies have great potential for the treatment of human diseases. Although human IgG1 bispecific antibodies have been generated, few attempts have been reported in the scientific literature that extend bispecific antibodies to other human antibody isotypes. In this paper, we report our work expanding the knobs-into-holes bispecific antibody technology to the human IgG4 isotype. We apply this approach to generate a bispecific antibody that targets IL-4 and IL-13, two cytokines that play roles in type 2 inflammation. We show that IgG4 bispecific antibodies can be generated in large quantities with equivalent efficiency and quality and have comparable pharmacokinetic properties and lung partitioning, compared with the IgG1 isotype. This work broadens the range of published therapeutic bispecific antibodies with natural surface architecture and provides additional options for the generation of bispecific antibodies with differing effector functions through the use of different antibody isotypes.
An IP-10 (CXCL10)-Derived Peptide Inhibits Angiogenesis (2012)

Angiogenesis plays a critical role in processes such as organ development, wound healing, and tumor growth. It requires well-orchestrated integration of soluble and matrix factors and timely recognition of such signals to regulate this process. Previous work has shown that newly forming vessels express the chemokine receptor CXC receptor 3 (CXCR3) and, activation by its ligand IP-10 (CXCL10), both inhibits development of new vasculature and causes regression of newly formed vessels. To identify and develop new therapeutic agents to limit or reverse pathological angiogenesis, we identified a 21 amino acid fragment of IP-10, spanning the α-helical domain residues 77-98, that mimic the actions of the whole IP-10 molecule on endothelial cells. Treatment of the endothelial cells with the 22 amino acid fragment referred to as IP-10p significantly inhibited VEGF-induced endothelial motility and tube formation in vitro, properties critical for angiogenesis. Using a Matrigel plug assay in vivo, we demonstrate that IP-10p both prevented vessel formation and induced involution of nascent vessels. CXCR3 neutralizing antibody was able to block the inhibitory effects of the IP-10p, demonstrating specificity of the peptide. Inhibition of endothelial function by IP-10p was similar to that described for IP-10, secondary to CXCR3-mediated increase in cAMP production, activation of PKA inhibiting cell migration, and inhibition of VEGF-mediated m-calpain activation. IP-10p provides a novel therapeutic agent that inhibits endothelial cell function thus, allowing for the modulation of angiogenesis.
Bond- and mode-specific reactivity of methane on Ni(100) (2005)

In this work, the state-resolved reactivity of methane excited to different C-H stretch vibrations have been measured on a Ni(100) surface. Two kinds of experiments have been performed. In the first series of experiments, we have measured the reactivity of dideutero methane (CD2H2) excited in two different C-H stretch vibrational states which are nearly iso-energetic, but have different vibrational amplitudes. We observed that CD2H2 excited with two quanta of vibrational energy in one C-H bond were more reactive (by as much as a factor 5) than molecules excited with one quantum in each of two C-H bonds. This was the first time that state specificity has been observed in a gas-surface reaction. Our results clearly exclude the possibility of statistical models correctly describing the mechanisms of the methane chemisorption and highlight the importance of the dynamical calculations. We rationalize our results in terms of a spectator model and bond-specific reactivity, where the laser excited bond is broken in the reaction with the surface and the difference in reactivity of the two vibrational states is explained in terms of vibrational energy localized in a single C-H bond. Additionally, we have measured the state-resolved reactivity of CH4 in its totally symmetric C-H stretch vibration (ν1) on Ni(100). The methane molecules were excited to ν1 by stimulated Raman pumping prior the collision with the surface. We observed that the reactivity of the ν1 excited CH4 is about an order of magnitude higher than that of methane excited to the isoenergetic antisymmetric stretch (ν3) reported by Juurlink et al. [Phys. Rev. Lett. 83, 868 (1999)] and is similar to that we have previously observed for the excitation of the first overtone (2ν3). Since all four bonds initially carry vibrational amplitude for both ν1 and ν3, the difference in reactivity between the symmetric and antisymmetric vibrations cannot simply be explained in terms of bond-specific laser excitation. We refer to this reactivity difference as mode-specific. In this case, the relative reactivity between two different vibrational states does not only depend on the quantity of vibrational energy contained in each bond, but it is also influenced by the symmetry of the vibrational state excited. Our results are consistent with predictions of a vibrationally adiabatic model of the methane reaction dynamics [Halonen et al., J. Chem. Phys. 115, 5611 (2001)].
The SWISS-PROT protein sequence database and its supplement TrEMBL in 2000 (2000)

SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domains structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other databases. Recent developments of the database include format and content enhancements, cross-references to additional databases, new documentation files and improvements to TrEMBL, a computer-annotated supplement to SWISS-PROT. TrEMBL consists of entries in SWISS-PROT-like format derived from the translation of all coding sequences (CDSs) in the EMBL Nucleotide Sequence Database, except the CDSs already included in SWISS-PROT. We also describe the Human Proteomics Initiative (HPI), a major project to annotate all known human sequences according to the quality standards of SWISS-PROT. SWISS-PROT is available at: http://www.expasy.ch/sprot/ and http://www.ebi.ac.uk/swissprot/
Procedural and clinical outcomes of the valve‐in‐valve technique for severe aortic insufficiency after balloon‐expandable transcatheter aortic valve replacement (2012)

The valve-in-valve technique is an appropriate bailout measure for patients with acute valvular AI after balloon-expandable TAVR.
Mild and Efficient Conversion of Nitriles to Amides with Basic Urea-Hydrogen Peroxide Adduct (1993)

Abstract The urea-hydrogen peroxide adduct, an inexpensive, stable and easily handled reagent has shown utility for mild and efficient transformation of nitriles into the corresponding aliphatic or aromatic amides. Reaction proceeds in aqueous acetone, within 0.5-2.5h, in the presence of catalytic amount of K2CO3, at room temperature.
Flexure-based Manipulator for Active Handheld Microsurgical Instrument (2005)

This paper presents the design and initial experimental results of a flexure-based parallel manipulator that is actuated by three piezoelectric stacks. The manipulator is for an active handheld tremor canceling device for microsurgery. By using flexures to approximate pin and ball joints, errors due to friction, backlash, and imperfect assemblies have been eliminated. The results show that the manipulator is capable of tracking motions similar to physiological tremor in amplitude and frequency. The workspace of the manipulator is more than 7 times larger than the tremor space in the x and y axes, and about 1.5 times larger in the z axis. One dimensional and three dimensional tracking tests had rms errors of 6.5 &#956;m and 12.1 &#956;m respectively.
Stereochemical Outcome and Kinetic Effects of Rp- and Sp-Phosphorothioate Substitutions at the Cleavage Site of Vaccinia Type I DNA Topoisomerase (2000)

To probe the mechanism of the reversible DNA phosphodiester bond cleavage and religation mechanism of the type I topoisomerase from vaccinia virus, we have synthesized DNA substrates carrying a single nonbridging Rp- or Sp-phosphorothioate (Ps) modification at the scissile phosphodiester (Pd) bond. Analysis of the stereochemical outcome of the net cleavage and rejoining reaction established that the reaction proceeds with retention of configuration, as expected for a double-displacement mechanism. Single-turnover kinetic studies on irreversible strand cleavage using 18/24 mer suicide substrates showed thio effects (k(Pd)/k(Ps)) of 340- and 30-fold for the Rp-Ps and Sp-Ps stereoisomers, respectively, but approximately 10-fold smaller thio effects for the reverse single-turnover religation reaction (Rp-Ps = 30 and Sp-Ps = 3). As compared to the smaller suicide cleavage substrates, approach-to-equilibrium cleavage studies using 32/32 mer substrates showed 7-9-fold smaller thio effects on cleavage, similar effects on religation, and the same ratio of the Rp to Sp thio effect as the suicide cleavage reaction ( approximately 10). In general, thio effects of 2.4-7.2-fold on the cleavage equilibrium are observed for the wild-type and H265A enzymes, suggesting differences in the interactions of the enzyme with the nonbridging sulfur in the noncovalent and covalent complexes. Studies of the cleavage, religation, and approach-to-equilibrium reactions catalyzed by the H265A active site mutant revealed a stereoselective, 11-fold decrease in the Rp-thio effect on cleavage and religation as compared to the wild-type enzyme. This result suggests that His-265 interacts with the nonbridging pro-Rp oxygen in the transition state for cleavage and religation, consistent with the arrangement of this conserved residue in the crystal structure of the human topoisomerase-DNA complex. In general, the greatest effect of thio substitution and the H265A mutation is to destabilize the transition state, with smaller effects on substrate binding. The interaction of His-265 with the pro-Rp nonbridging oxygen is inconsistent with the proposal that this conserved residue acts as a general acid in the strand cleavage reaction.
A Population-Based Study on Blood Pressure and Brain Atrophy in 85-Year-Olds (1998)

In the general population, mean systolic and diastolic blood pressure increases up to age 75 years but decreases thereafter. The brain has a role in blood pressure regulation; it is not clear whether the cerebral changes that occur with aging contribute to the decline in blood pressure in the very elderly. We examined a population-based sample of 484 85-year-old persons (344 nondemented and 140 demented, 61 with Alzheimer's disease, 65 with vascular dementia, and 14 with other types of dementia) with a neuropsychiatric examination and blood pressure measurements. Dementia was diagnosed according to the criteria proposed in the Diagnostic and Statistical Manual of Mental Disorders, edition 3, revised. Brain atrophy was measured by CT of the brain. In the nondemented group, frontal (r=-0.18, P=0.037) and parietal (r=-0.23, P=0.008) cortical atrophy and bifrontal ratio (r=-0.20, P=0.013) were associated with lower systolic blood pressure, and frontal (r=-0.23, P=0.010) and parietal (r=-0.24, P=0.008) cortical atrophy and bifrontal ratio (r=-0.23, P=0.006) with lower diastolic blood pressure. Systolic blood pressure was lower in subjects with Alzheimer's disease and vascular dementia, and diastolic blood pressure was lower in those with vascular dementia compared with the nondemented. Systolic (r=-0.27, P<0.0001) and diastolic (r=-0.10, P=0.020) blood pressure was negatively correlated to dementia severity. In the demented subjects, frontal cortical atrophy was correlated to lower diastolic blood pressure (r=-0.21, P=0.043). Our findings suggest that age-related changes in brain structure may contribute to the decrease in blood pressure in the very elderly and that low blood pressure in dementia disorders is mainly a secondary phenomenon.
Notice of Retraction: Analysis on application of data mining upon rate making and risk analysis in insurance (2010)

In this paper, we analysis data of insurance on motor vehicles of some branch of PICC P&C(Peoples Insurance Company of China). We compare the results of data mining approach and traditional approach, to demonstrate the advantage of the former. Data mining approach can process some parts of rate making automatically, adjust rate structure and build a rational rate making system in insurance. In addition, It contributes to the recognition of high-risk customer, thus the loss rate will be controlled.
Rap1 Affects the Length and Heterogeneity of Human Telomeres (2003)

Telomere length is controlled in part by cis-acting negative regulators that limit telomere extension by telomerase. In budding yeast, the major telomere length regulator scRap1 binds to telomeric DNA and acts to inhibit telomere elongation in cis. Because the human Rap1 ortholog hRap1 does not bind to telomeric DNA directly but is recruited to telomeres by TRF2, we examined its role in telomere length control. The data are consistent with hRap1 being a negative regulator of telomere length, indicating functional conservation. Deletion mapping confirmed that hRap1 is tethered to telomeres through interaction of its C terminus with TRF2. The telomere length phenotypes of hRap1 deletion mutants implicated both the BRCT and Myb domain as protein interaction domains involved in telomere length regulation. By contrast, scRap1 binds to telomeres with its Myb domains and uses its C terminus to recruit the telomere length regulators Rif1 and Rif2. Together, our data show that although the role of Rap1 at telomeres has been largely conserved, the domains of Rap1 have undergone extensive functional changes during eukaryotic evolution. Surprisingly, hRap1 alleles lacking the BRCT domain diminished the heterogeneity of human telomeres, indicating that hRap1 also plays a role in the regulation of telomere length distribution.
Autocrine transformation of hemopoietic cells resulting from cytokine message stabilization after intracisternal A particle transposition. (1993)

Cell lines that no longer require exogenous interleukin 3 (IL-3) for growth were isolated from an IL-3-dependent cell line that possesses characteristics of early lymphoid cells. Unlike the parental cells (FL5.12), these autocrine transformed lines (FL-IL3-R) constitutively secreted IL-3, were rearranged at the IL-3 locus and formed tumors upon injection into syngeneic mice. The rearrangement and IL-3 expression resulted from the transposition of an intracisternal A particle (IAP) provirus into the 3' untranslated region of the IL-3 gene. This region contained ATTTA sequence motifs that have been associated with cytokine and oncogene mRNA instability. IL-3 transcripts from the autocrine transformed cell lines had a longer half-life than similar transcripts isolated from either phorbol ester-stimulated T cells or the WEHI-3B myelomonocytic cell line. IAP proviral transposition did not alter the transcription rate of the IL-3 gene in FL-IL3-R cells. Therefore, IAP proviral transposition can activate IL-3 gene expression by prolonging mRNA stability, and this mechanism can contribute to the autocrine transformation of the hemopoietic cells.
Regiospecific electrophilic substitution of aminopyridines: ortho lithiation of 2-, 3-, and 4-(pivaloylamino)pyridines (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRegiospecific electrophilic substitution of aminopyridines: ortho lithiation of 2-, 3-, and 4-(pivaloylamino)pyridinesJames A. TurnerCite this: J. Org. Chem. 1983, 48, 20, 3401–3408Publication Date (Print):October 1, 1983Publication History Published online1 May 2002Published inissue 1 October 1983https://pubs.acs.org/doi/10.1021/jo00168a007https://doi.org/10.1021/jo00168a007research-articleACS PublicationsRequest reuse permissionsArticle Views2597Altmetric-Citations133LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Tolerogenic Dendritic Cells (2003)

Dendritic cells (DCs) have several functions in innate and adaptive immunity. In addition, there is increasing evidence that DCs in situ induce antigen-specific unresponsiveness or tolerance in central lymphoid organs and in the periphery. In the thymus DCs generate tolerance by deleting self-reactive T cells. In peripheral lymphoid organs DCs also induce tolerance to antigens captured by receptors that mediate efficient uptake of proteins and dying cells. Uptake by these receptors leads to the constitutive presentation of antigens on major histocompatibility complex (MHC) class I and II products. In the steady state the targeting of DC antigen capture receptors with low doses of antigens leads to deletion of the corresponding T cells and unresponsiveness to antigenic rechallenge with strong adjuvants. In contrast, if a stimulus for DC maturation is coadministered with the antigen, the mice develop immunity, including interferon-gamma-secreting effector T cells and memory T cells. There is also new evidence that DCs can contribute to the expansion and differentiation of T cells that regulate or suppress other immune T cells. One possibility is that distinct developmental stages and subsets of DCs and T cells can account for the different pathways to peripheral tolerance, such as deletion or suppression. We suggest that several clinical situations, including autoimmunity and certain infectious diseases, can be influenced by the antigen-specific tolerogenic role of DCs.
CD1d-Restricted and TCR-Mediated Activation of V α 14 NKT Cells by Glycosylceramides (1997)

Natural killer T (NKT) lymphocytes express an invariant T cell antigen receptor (TCR) encoded by the Valpha14 and Jalpha281 gene segments. A glycosylceramide-containing alpha-anomeric sugar with a longer fatty acyl chain (C26) and sphingosine base (C18) was identified as a ligand for this TCR. Glycosylceramide-mediated proliferative responses of Valpha14 NKT cells were abrogated by treatment with chloroquine-concanamycin A or by monoclonal antibodies against CD1d/Vbeta8, CD40/CD40L, or B7/CTLA-4/CD28, but not by interference with the function of a transporter-associated protein. Thus, this lymphocyte shares distinct recognition systems with either T or NK cells.
Human Immunodeficiency Virus Type 1 Reverse Transcriptase Mutation Selection during In Vitro Exposure to Tenofovir Alone or Combined with Abacavir or Lamivudine (2004)

Mutations selected or deselected during passage of human immunodeficiency virus strain HXB2 or resistant variants with tenofovir (TFV), abacavir (ABC), and lamivudine (3TC) differed depending on the drug combination and virus genotype. In the wild-type virus, TFV-ABC and TFV-3TC selected K65R (with reduced susceptibility to all three inhibitors) and then Y115F. TFV-containing regimens might increase K65R selection, which confers multiple nucleoside reverse transcriptase inhibitor resistance.
Serum Level of Interferon-.GAMMA. in Autoimmune Diseases. (1991)

Interferon-gamma is one of the cytokines which have various immunoregulatory functions. In the present study, the serum interferon-gamma level was determined in autoimmune diseases. It was increased in the active cases of systemic lupus erythematosus (SLE) and mixed connective tissue disease (MCTD). Since there was a positive correlation between the serum interferon-gamma level and the rate of peripheral mononuclear cells positive for HLA-DR antigen in systemic lupus erythematosus, circulating interferon-gamma might have a biological functions as suggested by many in vitro studies. In rheumatoid arthritis and Sjögren's syndrome, there was no correlation between the serum interferon-gamma level and the clinical findings. These data suggest that interferon-gamma might be associated with the pathogenesis of autoimmune diseases such as SLE and MCTD, and it can be one of the indices for their disease activity.
Unimolecular Micelles Based On Hydrophobically Derivatized Hyperbranched Polyglycerols: Ligand Binding Properties (2008)

This paper discusses the binding and release properties of hydrophobically modified hyperbranched polyglycerol-polyethylene glycol copolymers that were originally developed as human serum albumin (HSA) substitutes. Their unimolecular micellar nature in aqueous solution has been proven by size measurements and other spectroscopic methods. These polymers aggregate weakly in solution, but the aggregates are broken down by low shear forces or by encapsulating a hydrophobic ligand within the polymer. The small molecule binding properties of these polymers are compared with those of HSA. The preliminary in vitro paclitaxel release studies showed very promising sustained drug release characteristics achieved by these unimolecular micelles.