gebhart/patrepeval huggingface dataset:
Design and synthesis of naltrexone-derived affinity labels with nonequilibrium opioid agonist and antagonist activities. Evidence for the existence of different .mu. receptor subtypes in different tissues (1984)

A series of beta-funaltrexamine (2, beta-FNA) analogues (3-14) were synthesized that contain a variety of electrophilic groups attached at the 6 beta-position of the opiate. The opioid agonist and antagonist activities of these ligands were evaluated in the guinea pig ileum (GPI) and mouse vas deferens (MVD) in vitro assays. Several of the compounds behaved like beta-FNA in that they exhibited reversible agonist activity at kappa opioid receptors and irreversible antagonist activity at mu opioid receptors. The rank order of irreversible antagonism for a series of related Michael acceptors did not parallel their intrinsic chemical reactivity, confirming that the degree of covalent binding is in part dependent on the spatial disposition of the electrophilic center relative to the receptor nucleophile (secondary recognition). The maleimidoacetamide 8 behaved very differently from beta-FNA in that it exhibited considerably greater irreversible mu antagonism in MVD relative to the mu blockage in the GPI. This suggests that different proportions of mu receptor subtypes exist in the two tissues. Several of the agents tested, including some nonreactive control compounds, displayed an unusual type of persistent kappa agonist activity in the GPI. This activity, which was reversed by addition of naloxone, reappeared upon washing. Receptor models have been presented to explain this effect. A few of the reactive ligands displayed a true nonreversible kappa agonist activity, suggesting a covalent association with the receptor. Of note in this regard was the propiolamide 6, which appeared to be an irreversible mixed agonist-antagonist at kappa and mu receptors.
Synthesis and Characterization of Enzymatically-Cross-Linked Poly(ethylene glycol) Hydrogels (1997)

We demonstrate formation of a hydrogel network by cross-linking functionalized poly(ethylene glycol) (PEG) and a lysine-containing polypeptide through the action of a natural tissue enzyme, transglutaminase. The enzyme reaction rate using a PEG-modified peptide substrate is the same as the reaction rate for free substrate. Both the ratio and total concentration of the two macromers determine whether gelation will occur and the nature of the gel which forms. Under suitable conditions, clear gels form and swell to give a final composition which is 90% water. Diffusion coefficients of small proteins and albumin in the gel are comparable to those in free solution. Gelation proceeds under mild conditions and thus these gels hold potential for forming highly hydrated networks around living cells.
An alternative approach to monitoring cancer patient survival (1996)

Despite some limitations with respect to the ease of data interpretation. period monitoring offers a useful supplement to existing methods of monitoring patient survival.
Intergroup Rhabdomyosarcoma Study: Update for Pathologists (1998)

Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma of childhood, and 75% of such cases in the United States are reviewed at the Pathology Center for the Intergroup Rhabdomyosarcoma Study Group (IRSG). The first four generations of IRSG therapeutic trials (IRS I-IV) and supportive pathologic studies have generated a new International Classification of Rhabdomyosarcoma (ICR) that offers new morphologic concepts to the practicing pathologist. The objective of this report is to clearly define emerging histopathologic categories of RMS as defined by the ICR, and to emphasize correlative immunohistochemical or molecular studies. Emerging ICR variants of RMS place the patient in widely divergent prognostic categories (superior, botryoid or spindle cell variants; poor, solid alveolar or diffusely anaplastic variants). The cardinal histopathologic features of the ICR combined with results of studies of fusion genes seen with t(1;13) and t(2;13) will help delineate therapeutic subgroups of RMS for the fifth generation (IRS V) of IRSG studies. Consequently, it is imperative for the practicing pathologist to be familiar with the practical workup and diagnosis of RMS in childhood.
Chemoattractant Signaling between Tumor Cells and Macrophages Regulates Cancer Cell Migration, Metastasis and Neovascularization (2009)

Tumor-associated macrophages are known to influence cancer progression by modulation of immune function, angiogenesis, and cell metastasis, however, little is known about the chemokine signaling networks that regulate this process. Utilizing CT26 colon cancer cells and RAW 264.7 macrophages as a model cellular system, we demonstrate that treatment of CT26 cells with RAW 264.7 conditioned medium induces cell migration, invasion and metastasis. Inflammatory gene microarray analysis indicated CT26-stimulated RAW 264.7 macrophages upregulate SDF-1alpha and VEGF, and that these cytokines contribute to CT26 migration in vitro. RAW 264.7 macrophages also showed a robust chemotactic response towards CT26-derived chemokines. In particular, microarray analysis and functional testing revealed CSF-1 as the major chemoattractant for RAW 264.7 macrophages. Interestingly, in the chick CAM model of cancer progression, RAW 264.7 macrophages localized specifically to the tumor periphery where they were found to increase CT26 tumor growth, microvascular density, vascular disruption, and lung metastasis, suggesting these cells home to actively invading areas of the tumor, but not the hypoxic core of the tumor mass. In support of these findings, hypoxic conditions down regulated CSF-1 production in several tumor cell lines and decreased RAW 264.7 macrophage migration in vitro. Together our findings suggest a model where normoxic tumor cells release CSF-1 to recruit macrophages to the tumor periphery where they secrete motility and angiogenic factors that facilitate tumor cell invasion and metastasis.
Dynamical Charge Tensors and Infrared Spectrum of AmorphousSiO2 (1997)

Using a model structure consisting of a network of corner sharing tetrahedra, we calculate the infrared spectrum of amorphous ${\mathrm{SiO}}_{2}$ within a first-principles approach and find good agreement with experiment both for the positions and the intensities of the main peaks. In addition to the vibrational properties, this required the dynamical charge tensors, which were obtained applying the recent quantum polarization theory. The relative intensities in the spectrum depend sensitively on the charge tensors and their anisotropic components are crucial to obtain good agreement with experiment. We find that the Born charges can be correlated to the local structural properties.
A protocol for building and evaluating predictors of disease state based on microarray data (2005)

An important contribution of this work is the description of a principled training and validation protocol, which allows objective evaluation of the complete methodology for constructing a predictor. We review the possible choices of computational approaches, with specific emphasis on predictor choice and reporter selection strategies. Employing this training-validation protocol, we evaluated different reporter selection strategies and predictors on six gene expression datasets of varying degrees of difficulty. We demonstrate that simple reporter selection strategies (forward filtering and shrunken centroids) work surprisingly well and outperform partial least squares in four of the six datasets. Similarly, simple predictors, such as the nearest mean classifier, outperform more complex classifiers. Our training-validation protocol provides a robust methodology to evaluate the performance of new computational approaches and to objectively compare outcome predictions on different datasets.
Rat brain expresses an alternatively spliced form of the dihydropyridine-sensitive L-type calcium channel alpha 2 subunit. (1992)

We have cloned and sequenced a cDNA (rB-alpha 2) encoding an alpha 2 subunit of the voltage-sensitive L-type calcium channel (dihydropyridine receptor) of rat brain. The cDNA (3823 base pairs) encodes a protein of 1091 amino acids with a Mr of 123,822. The deduced amino acid sequence of rB-alpha 2 cDNA is highly similar (95% amino acid identity) to that of rabbit skeletal muscle alpha 2 subunit. The rB-alpha 2 protein is distinct from the previously cloned skeletal muscle alpha 2-subunit protein [Ellis, S. B., Williams, M. E., Ways, N. R., Brenner, R., Sharp, A. H., Leung, A. T., Campbell, K. P., McKenna, E., Koch, W., Hui, A., Schwartz, A. & Harpold, M. M. (1988) Science 241, 1661-1664] because it contains an insertion of 7 amino acid residues and a deletion of a 19-amino acid segment between putative transmembrane domains 1 and 2. We show that the rB-alpha 2 and skeletal muscle alpha 2-subunit transcripts are the variants produced by alternative splicing of the primary transcript and that they are differentially expressed in brain and skeletal muscle, respectively.
Anti-Idiotypic Antibody Facilitates scFv Chimeric Immune Receptor Gene Transduction and Clonal Expansion of Human Lymphocytes for Tumor Therapy (2003)

Chimeric immune receptors (CIR) transduced into lymphocytes link target recognition by single chain antibody Fv (scFv) to activation through CD28/TCRzeta signaling. As surrogate antigens, anti-idiotypic antibodies may facilitate gene-transduction and clonal expansion of human lymphocytes for in vivo tumor therapy. The murine monoclonal antibody (MAb) 8H9 reacts with a novel antigen widely expressed on solid tumors. A CIR consisting of human CD8-leader sequence, 8H9-scFv, CD28 (transmembrane and cytoplasmic domains), and TCR-zeta chain was constructed, ligated into the pMSCVneo vector, and used to transfect the packaging line GP + envAM12 bearing an amphotropic envelope. Rat anti-idiotypic MAb 2E9 (IgG2a) was used to clone retroviral producer line as well as to expand gene-modified primary human lymphocytes. Sequential enrichments using either affinity chromatography or cell sorting using anti-idiotypic MAb 2E9 significantly improved the percentage of producer clones positive for surface 8H9-scFv and the efficiency of their supernatant in transducing the indicator cell line K562. By 3 weeks of in vitro culture, >95% of transduced primary human lymphocytes were CIR-positive. Upon periodic stimulation with 2E9, these lymphocytes underwent >10(6)-fold expansion by 6 months in culture. They mediated antigen-specific non-MHC restricted cytokine release and tumor cytotoxicity, and inhibited human xenograft engraftment in SCID mice. Anti-idiotypic antibody may provide a useful tool for optimizing gene transduction of CIR fusion constructs into primary human lymphocytes and their continual expansion in vitro.
In Vivo Antibacterial Activity of S-3578, a New Broad-Spectrum Cephalosporin: Methicillin-Resistant Staphylococcus aureus and Pseudomonas aeruginosa Experimental Infection Models (2003)

The in vivo antibacterial activity of S-3578, a new parental cephalosporin, was compared with those of cefepime, ceftriaxone, ceftazidime, imipenem-cilastatin, and vancomycin. The efficacy of S-3578 against systemic infections caused by methicillin-resistant Staphylococcus aureus (MRSA) SR3637 (50% effective dose [ED(50)], 7.21 mg/kg of body weight) was almost the same as that of vancomycin. In contrast, cefepime and imipenem-cilastatin were less active against this pathogen (ED(50)s, >100 and >100 mg/kg, respectively). S-3578 was the most effective compound against penicillin-resistant Streptococcus pneumoniae SR20946 (ED(50), 1.98 mg/kg). S-3578 (10 mg/kg) induced a significant reduction in the numbers of viable MRSA SR17764 and Pseudomonas aeruginosa SR10396 organisms in polymicrobial pulmonary infections. The therapeutic efficacy of S-3578 was more potent than that of the combination of vancomycin and ceftazidime. High levels of S-3578 were detected in plasma in vivo, and its efficacy against experimentally induced infections in mice caused by MRSA and P. aeruginosa reflected its potent in vitro activity. We conclude that S-3578 is a promising new cephalosporin for the treatment of infections caused by gram-positive and -negative bacteria, including MRSA and P. aeruginosa.
Fragment Growing and Linking Lead to Novel Nanomolar Lactate Dehydrogenase Inhibitors (2013)

Lactate dehydrogenase A (LDH-A) catalyzes the interconversion of lactate and pyruvate in the glycolysis pathway. Cancer cells rely heavily on glycolysis instead of oxidative phosphorylation to generate ATP, a phenomenon known as the Warburg effect. The inhibition of LDH-A by small molecules is therefore of interest for potential cancer treatments. We describe the identification and optimization of LDH-A inhibitors by fragment-based drug discovery. We applied ligand based NMR screening to identify low affinity fragments binding to LDH-A. The dissociation constants (K(d)) and enzyme inhibition (IC(50)) of fragment hits were measured by surface plasmon resonance (SPR) and enzyme assays, respectively. The binding modes of selected fragments were investigated by X-ray crystallography. Fragment growing and linking, followed by chemical optimization, resulted in nanomolar LDH-A inhibitors that demonstrated stoichiometric binding to LDH-A. Selected molecules inhibited lactate production in cells, suggesting target-specific inhibition in cancer cell lines.
Relationship between peroxisome proliferator‐activated receptors (PPARα and PPARγ) and endothelium‐dependent relaxation in streptozotocin‐induced diabetic rats (2003)

(1) The aim of the present study was to investigate the causal relationship between peroxisome proliferator-activated receptor (PPAR) and endothelium-dependent relaxation in streptozotocin (STZ)-induced diabetic rats. (2) Acetylcholine (ACh)-induced endothelium-dependent relaxation was significantly weaker in diabetic rats than in age-matched controls. The decreased relaxation in diabetes was improved by the chronic administration of bezafibrate (30 mg kg-1, p.o., 4 weeks). (3) The expressions of the mRNAs for PPARalpha and PPARgamma were significantly decreased in STZ-induced diabetic rats (compared with the controls) and this decrease was restored partially, but not completely, by the chronic administration of bezafibrate. (4) Superoxide dismutase activity in the aorta was not significantly different between diabetic rats and bezafibrate-treated diabetic rats. (5) The expression of the mRNA for the p22phox subunit of NAD(P)H oxidase was significantly higher in diabetics than in controls, but it was lower in bezafibrate-treated diabetic rats than in nontreated diabetic rats. Although the expression of the mRNA for prepro ET-1 (ppET-1) was markedly increased in diabetic rats (compared with controls), this increase was prevented to a significant extent by the chronic administration of bezafibrate. (6) These results suggest that downregulations of PPARalpha and PPARgamma may lead to an increased expression of ppET-1 mRNA in diabetic states and this increment may trigger endothelial dysfunction.
Two‐dimensional NMR studies and secondary structure of cobrotoxin in aqueous solution (1990)

The 1 H‐NMR spectra of cobrotoxin, a neurotoxic protein isolated from Formosan cobra Naja naja atra , have been studied by two‐dimensional NMR techniques. Of 62 amino acid residues in cobrotoxin, the complete assignments of 58 residues have been made. The resonances from several of the remaining residues have been identified but not yet specifically assigned. The secondary structure of an antiparallel triple‐ and double‐stranded β‐sheet has also been determined by observing the NOE.
Induction and segregation of glial intermediate filament expression in the RT4 family of peripheral nervous system cell lines. (1987)

We have found glial fibrillary acidic protein (GFAP), the major component of astrocyte intermediate filaments, to be expressed in cell lines of the RT4 peripheral neurotumor family. The RT4 family is a "stem-cell-like" cell line, RT4-AC, that spontaneously undergoes differentiation in culture to three derivative cell types. This process, termed cell-type conversion, results in a segregation among the derivative cell types of parental cell phenotypes that have been described as neuronal-like or glial-like. We have identified a 50-kDa GFAP-immunoreactive cytoskeletal protein and GFAP mRNA in continuous RT4-AC and RT4-D (glial-type derivative) cell lines, but not in two presumptive neuronal-type cell lines. This result suggests that GFAP gene expression is coordinately coupled with the expression of other glial properties during cell-type conversion. In addition, the RT4-AC and RT4-D sublines were found to significantly express GFAP only at high cell densities and not during logarithmic growth and to express GFAP precociously during morphological differentiation following treatment with 1 mM N6, O2'-dibutyryladenosine 3',5'-cyclic monophosphate. These observations closely reflect reports of glial filament expression in astrocyte cultures, suggesting that a common regulatory mechanism is employed by central and peripheral nervous system glia.
Increased polysomies of chromosomes 7 and 17 during head and neck multistage tumorigenesis. (1993)

Head and neck cancer development has been proposed to represent a multistage process characterized by dysregulation of proliferation and differentiation and driven by an accumulation of genetic alterations in an anatomic field repeatedly exposed to carcinogens. To visualize the accumulation of genetic alterations during head and neck tumorigeneses and to determine the extent of the genetically altered field, we probed 25 squamous cell carcinomas of the head and neck and their adjacent premalignant lesions for numerical chromosome aberrations by nonisotopic, in situ hybridization using chromosome-specific centromeric DNA probes for chromosomes 7 and 17. Normal control oral epithelium from individuals free of cancer showed no chromosome polysomy (i.e., cells with > or = 3 chromosome copies), whereas histologically normal epithelium adjacent to the tumors showed squamous cells with polysomies for chromosomes 7 and 17. Moreover, the frequency of cells with polysomy increased as the tissues passed from histologically normal epithelium to hyperplasia to dysplasia to cancer. The finding of genotypic abnormalities in histologically normal and precancerous regions adjacent to the tumor supports the concept of field cancerization. The finding of progressive genetic changes as the tumor develops supports the concept of multistep carcinogenesis in the head and neck region. Such genotypic parameters could serve as biomarkers in the assessment of the risk of progression to malignancy and as intermediate end points in chemoprevention trials.
TLR4 Signaling Inhibitory Pathway Induced by Green Tea Polyphenol Epigallocatechin-3-Gallate through 67-kDa Laminin Receptor (2010)

Epigallocatechin-3-gallate (EGCG), a major active polyphenol of green tea, has been shown to downregulate inflammatory responses in macrophages; however, the underlying mechanism has not been understood. Recently, we identified the 67-kDa laminin receptor (67LR) as a cell-surface EGCG receptor that mediates the anticancer action of EGCG at physiologically relevant concentrations (0.1-1 microM). In this study, we show the molecular basis for the downregulation of TLR4 signal transduction by EGCG at 1 microM in macrophages. Anti-67LR Ab treatment or RNA interference-mediated silencing of 67LR resulted in abrogation of the inhibitory action of EGCG on LPS-induced activation of downstream signaling pathways and target gene expressions. Additionally, we found that EGCG reduced the TLR4 expression through 67LR. Interestingly, EGCG induced a rapid upregulation of Toll-interacting protein (Tollip), a negative regulator of TLR signaling, and this EGCG action was prevented by 67LR silencing or anti-67LR Ab treatment. RNA interference-mediated silencing of Tollip impaired the TLR4 signaling inhibitory activity of EGCG. Taken together, these findings demonstrate that 67LR plays a critical role in mediating anti-inflammatory action of a physiologically relevant EGCG, and Tollip expression could be modulated through 67LR. These results provide a new insight into the understanding of negative regulatory mechanisms for the TLR4 signaling pathway and consequent inflammatory responses that are implicated in the development and progression of many chronic diseases.
MDM2 Protein Overexpression Promotes Proliferation and Survival of Multiple Myeloma Cells (1997)

The murine double minute 2 (MDM2) protein facilitates G1 to S phase transition by activation of E2F-1 and can enhance cell survival by suppressing wild-type p53 (wtp53) function. In this study, we examined MDM2 expression and function in multiple myeloma (MM) cells. MDM2 is strongly and constitutively expressed in MM cell lines (ARH-77, RPMI 8226, and OCI-My5) and in the cells of plasma cell leukemia (PCL) patients, but is not expressed in normal bone marrow mononuclear cells (BM MNCs). Treatment of MM cells with MDM2 antisense, but not sense, nonsense, or scrambled, oligodeoxyribonucleotides (ODNs) decreased DNA synthesis and cell viability; it also induced G1 growth arrest, as evidenced by propidium iodide (PI) staining and induction of retinoblastoma protein (pRB) to E2F-1 binding. Moreover, inhibition of MDM2 using antisense ODNs also triggered MM cell apoptosis as evidenced by acridine orange-ethidium bromide staining. We next studied the association of MDM2 with wtp53 and/or mutant p53 (mtp53), E2F-1, CDK4, and p21. MDM2 constitutively binds to E2F-1 in all MM cells, to both wtp53 and mtp53, and to p21 in tumor cells lacking p53. These data suggest that MDM2 may enhance cell-cycle progression in MM cells both by activating E2F-1 and by downregulating cell-cycle inhibitory proteins (wtp53 and p21). Overexpression of MDM2 may therefore contribute to both growth and survival of MM cells, suggesting the potential utility of treatment strategies targeting MDM2 in MM.
The Mask of Janus: A Re-analysis of the Concept of Pollution in the New Guinea Highlands (1981)

In the New Guinea Highlands the concert of pollution is utilized rather narrowly by anthropologists within the context of male/female relations and intersexual opposition; as such it has come to signify the capacity women have to endanger and contaminate males. Various structural features such as the separation of the sexes, male initiation ceremonies, and secret cults are commonly cited as evidence of the dangerous effects of females on males. In this paper I demonstrate that pollution beliefs cannot be reduced to a simplistic male/female dichotomy, as previously maintained in the literature, for such an opposition has no overall relevance for an understanding of pollution beliefs in the Highlands. The ability to contaminate another is a transitory phenomenon that is not transmitted solely along sex lines; it is neither a capacity residing only in women, nor are all women considered polluting. Instead, pollution beliefs must be viewed as embedded in a larger system of ideas concerning the life process itself.
Diazo Esters as Dienophiles in Intramolecular (4 + 2) Cycloadditions: Computational Explorations of Mechanism (2017)

The first experimental examples of Diels-Alder (DA) reactions of diazo compounds as heterodienophiles with dienes have been studied with density functional theory (DFT) using the M06-2X functional. For comparison, the reactivities of diazo esters as dienophiles or 1,3-dipoles with 1,3-dienes in intermolecular model systems have been analyzed by the distortion/interaction model. The 1,3-dipolar cycloaddition is strongly favored for the intermolecular system. The intramolecular example is unique because the tether strongly favors the (4 + 2) cycloaddition.