gebhart/patrepeval huggingface dataset:
On the selectivity of superoxide dismutase mimetics and its importance in pharmacological studies (2003)

The list of pathophysiological conditions associated with the overproduction of superoxide expands every day. Much of the knowledge compiled on the role of this radical in disease has been gathered using the native superoxide dismutase enzyme and, more recently, by the use of superoxide dismutase knockout models or transgenic models that overexpress the various isoforms of the enzyme. Although the native enzyme has shown promising anti-inflammatory properties in both preclinical and clinical studies, there were drawbacks and issues associated with its use as a therapeutic agent and pharmacological tool. Based on the concept that removal of superoxide modulates the course of inflammation, synthetic, low-molecular-weight mimetics of the superoxide dismutase enzymes that could overcome some of the limitations associated with the use of the native enzyme have been designed. In this review, we will discuss the advances made using various superoxide dismutase mimetics that led to the proposal that superoxide (and/or the product of its interaction with nitric oxide, peroxynitrite) is an important mediator of inflammation, and to the conclusion that superoxide dismutase mimetics can be utilized as therapeutic agents in diseases of various etiologies. The importance of the selectivity of such compounds in pharmacological studies will be discussed.
Nonsteroidal Selective Glucocorticoid Modulators:  The Effect of C-10 Substitution on Receptor Selectivity and Functional Potency of 5-Allyl-2,5-dihydro-2,2,4-trimethyl-1H-[1]benzopyrano[3,4-f]quinolines (2003)

The preparation and characterization of a series of C-10 substituted 5-allyl-2,5-dihydro-2,2,4-trimethyl-1H-[1]benzopyrano[3,4-f]quinolines as a novel class of selective ligands for the glucocorticoid receptor is described. Substitution at the C-10 position of the tetracyclic core with linear, two-atom appendages (OCH(3), OCF(2)H, NHMe, SMe, CH=CH(2), Ctbd1;CH, CH(2)OH) provided molecules of high affinity (K(i) = 2-8 nM) for the human glucocorticoid receptor (hGR) with limited cross-reactivity with other steroid receptors (PR, MR, AR, ER). Optimal analogues showed slightly less potent but highly efficacious E-selectin repression with reduced levels of GRE activation efficacy in reporter gene assays relative to prednisolone. Preliminary SAR of analogues containing substitution at the C-9 and C-10 positions identified the 9-OH, 10-OMe analogue 50 and the 9-OH, 10-Cl analogue 58 as compounds that demonstrated potent, GR-mediated inhibition in a conconavalin A stimulated T-cell proliferation assay in both rodent and human whole blood monocytes. When evaluated for their in vivo effects in carrageenan-induced paw edema in rats, 50, 58, and 10-OCF(2)H analogue 35 showed dose-dependent anti-inflammatory effects (50, ED(50) = 16 mg/kg; 58, ED(50) = 15 mg/kg; 35, ED(50) = 21 mg/kg vs ED(50) = 15 mg/kg for 18 and ED(50) = 4 mg/kg for prednisolone).
Surface photovoltage measured capacitance: Application to semiconductor/electrolyte system (1983)

Surface photovoltage measured capacitance (SPMC), a novel technique for determining the properties of semiconducting materials, is introduced. SPMC permits the determination of a semiconductor depletion layer capacitance by measuring changes of the surface potential barrier induced by low intensity chopped light whose photon energy exceeds the band-gap energy. The theory of the SPMC technique is derived, and an equivalent circuit for analyzing the measurements is described. The present technique is compared with the conventional current measured capacitance method, and it is shown that using SPMC the separation of the depletion layer capacitance from the influence of the surface states can be performed by measurements at only one frequency of light modulation. This is a simpler procedure than the frequency dispersion measurement required of conventional capacitance techniques. Measurements of the capacitance-voltage characteristics of a semiconductor/electrolyte system, in particular n-type WS2 exposed to an inert electrolyte, are used as examples to illustrate the capabilities of SPMC.
Generation of osteoclasts from isolated hematopoietic progenitor cells (1989)

A variety of studies have shown that osteoclasts originate from bone marrow, but their exact progenitors and differentiation pathway remain unclear. The treatment of mice with a high dose of 5-fluorouracil (5- FU) results in an enrichment for primitive hematopoietic progenitors; using this procedure, we prepared a new class of murine hematopoietic colonies that had very high secondary plating efficiencies in vitro. When spleen cells from mice pretreated in vivo with 5-FU were cultured in the presence of methylcellulose medium containing recombinant interleukin-3 (rIL-3), small colonies consisting of blast cells with little sign of differentiation developed on day 7 of culture. We lifted these blast colonies, pooled them, and replated them as secondary methylcellulose cultures in the presence of rIL-3 and erythropoietin. Approximately 60% of the cells formed colonies comprising various combinations of neutrophils, macrophages, eosinophils, mast cells, megakaryocytes, and erythroblasts. We replated such blast cells into microtiter wells and cultured them in the presence of rIL-3 (100 U/mL) or recombinant granulocyte-macrophage colony stimulating factor (GM- CSF) (100 U/mL) plus 1.25(OH)2D3 (10(-7) mol/L). Multinucleated cells appeared from day 14 of culture and approximately 100 giant cells per well were scored on day 21 of culture. Parathyroid hormone (1 U/mL) also induced the multinucleated cell formation. May-Grunwald-Giemsa staining revealed the large cells containing many nuclei in their cytoplasm, which is characteristic of bone-resorbing cells or osteoclasts. These cells showed a tartrate-resistant acid phosphatase (TRAP) activity. Calcitonin caused a striking shape change in these cells and suppressed the formation of multinucleated cells. Moreover, electron microscopy shows that these cells were able to resorb fetal calvariae. In the presence of r granulocyte-colony stimulating factor, r macrophage-colony stimulating factor, or r interleukin-6 plus 1.25(OH)2D3, formation of TRAP-positive multinucleated cells was lower compared with the support of rIL-3 or rGM-CSF. Mature macrophages collected from colonies did not form the multinucleated cells as described above, even in the presence of rIL-3 and 1.25(OH)2D3. Moreover, to exclude the possibility that osteoclasts generated from non-blast cells, we performed a cloning experiment from one isolated blast cell and demonstrated that single cells differentiate into osteoclasts or macrophages in the presence of rIL-3 with or without 1.25(OH)2D3. This system will provide a useful model for further analysis of osteoclast formation in vitro.
Evaluation of radiation effects against C6 glioma in combination with vaccinia virus-p53 gene therapy. (1998)

The primary objective of this study was to evaluate the antitumor effects of recombinant vaccinia virus-p53 (rVV-p53) in combination with radiation therapy against the C6 rat glioma, a p53 deficient tumor that is relatively radioresistant. VV-LIVP, the parental virus (Lister strain), was used as a control. Localized treatment of subcutaneous C6 tumors in athymic mice with either rVV-p53 or VV-LIVP together with tumor irradiation resulted in low tumor incidence and significantly slower tumor progression compared to the agents given as single modalities. Assays of blood and spleen indicated that immune system activation may account, at least partly, for the enhance tumor inhibition seen with combined treatment. No overt signs of treatment-related toxicity were noted.
An evaluation of human protein-protein interaction data in the public domain (2006)

Given the importance of PPIs, we suggest that submission of PPIs to repositories be made mandatory by scientific journals at the time of manuscript submission as this will minimize annotation errors, promote standardization and help keep the information up to date. We hope that our analysis will help guide biomedical scientists in selecting the most appropriate database for their needs especially in light of the dramatic differences in their content.
Expression of human cytokines dramatically improves reconstitution of specific human-blood lineage cells in humanized mice (2009)

Adoptive transfer of human hematopoietic stem cells (HSCs) into mice lacking T, B and natural killer (NK) cells leads to development of human-blood lineage cells in the recipient mice (humanized mice). Although human B cell reconstitution is robust and T cell reconstitution is reasonable in the recipient mice, reconstitution of NK cells and myeloid cells is generally poor or undetectable. Here, we show that the poor reconstitution is mainly the result of a deficiency of appropriate human cytokines that are necessary for the development and maintenance of these cell lineages. When plasmid DNA encoding human IL-15 and Flt-3/Flk-2 ligand were delivered into humanized mice by hydrodynamic tail-vein injection, the expression of the human cytokine lasted for 2 to 3 weeks and elevated levels of NK cells were induced for more than a month. The cytokine-induced NK cells expressed both activation and inhibitory receptors, killed target cells in vitro, and responded robustly to a virus infection in vivo. Similarly, expression of human GM-CSF and IL-4, macrophage colony stimulating factor, or erythropoietin and IL-3 resulted in significantly enhanced reconstitution of dendritic cells, monocytes/macrophages, or erythrocytes, respectively. Thus, human cytokine gene expression by hydrodynamic delivery is a simple and efficient method to improve reconstitution of specific human-blood cell lineages in humanized mice, providing an important tool for studying human immune responses and disease progression in a small animal model.
Experimental Methods for Quantifying the Activity of Platinum Electrocatalysts for the Oxygen Reduction Reaction (2010)

A tutorial is provided for methods to accurately and reproducibly determine the activity of Pt-based electrocatalysts for the oxygen reduction reaction in proton exchange membrane fuel cells and other applications. The impact of various experimental parameters on electrocatalyst activity is demonstrated, and explicit experimental procedures and measurement protocols are given for comparison of electrocatalyst activity to fuel cell standards. (To listen to a podcast about this article, please go to the Analytical Chemistry multimedia page at pubs.acs.org/page/ancham/audio/index.html.).
De Novo Design and Structural Characterization of Proteins and Metalloproteins (1999)

De novo protein design has recently emerged as an attractive approach for studying the structure and function of proteins. This approach critically tests our understanding of the principles of protein folding; only in de novo design must one truly confront the issue of how to specify a protein's fold and function. If we truly understand proteins, it should be possible to design receptors, enzymes, and ion channels from scratch. Further, as this understanding evolves and is further refined, it should be possible to design proteins and biomimetic polymers with properties unprecedented in nature.
90K (Mac-2 BP) gene expression in breast cancer and evidence for the production of 90K by peripheral-blood mononuclear cells (1998)

The tumor-derived antigen 90K (Mac-2 BP) is a widely expressed, secreted glycoprotein found in the serum of healthy individuals and at elevated levels in the serum of patients with breast cancer and other types of cancer. The precise function of 90K, particularly in the context of tumor-host relationships, has not yet been established. In this study, the clinical significance of 90K mRNA expression was studied in relation to other established prognostic parameters in 86 patients with primary breast carcinoma. The 2.2-kb 90K message was detected in all tumor samples, but there was marked variation in expression levels from tumor to tumor. Patients were classified into 2 groups on the basis of 90K expression: group 1 (n = 62) included patients with low expression, and group 2 (n = 24) consisted of patients with high expression. An inverse significant correlation was found between the levels of 90K mRNA expression and overexpression of c-erbB2/Neu receptor kinase, a marker of poor prognosis for patients with breast cancer. There was no significant difference between the groups with respect to tumor size, number of involved axillary lymph nodes, hormone-receptor status, p53 expression or proliferation activity as estimated by Ki-67 count. Similarly, no association was found between the level of 90K expression and the risk of death from breast cancer. These data are at variance with published findings showing that high serum 90K levels are associated with poor survival. Significantly, investigation of 90K-gene expression in peripheral-blood mononuclear cells (PBMC) revealed higher levels of 90K message in PBMC of breast-cancer patients than in healthy individuals. This new finding suggests that PBMC activated in response to tumor growth and progression may be an important source of serum 90K in breast cancer.
NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries (2013)

Source code, user guide and example data are available from https://github.com/richardmleggett/nextclip/.
The lunar laser communications demonstration (2011)

The Lunar Laser Communications Demonstration represents NASA's first attempt to demonstrate optical communications from a lunar orbiting spacecraft to an Earth-based ground receiver. A low size, weight and power optical terminal will be integrated onto the Lunar Atmosphere and Dust Environment Explorer (LADEE) spacecraft, presently scheduled to launch in 2013. LLCD will demonstrate duplex optical communications between this small space terminal and a multi-aperture photon-counting ground terminal at downlink data rates of up to 622 Mbps and uplink data rates of up to 20 Mbps.
Benign familial neonatal epilepsy with mutations in two potassium channel genes (1999)

The significant progress made over the past year in understanding the basis for a form of neonatal seizures can be attributed to the successful positional cloning of two new voltage-gated potassium channel genes. Expression studies have increased our understanding of the biology of these channels and their role in epilepsy.
Direct Palladium-Catalyzed Phosphinylation of Aryl Triflates with Secondary Phosphines. Its Scope and Limitations:  The Synthesis of Optically Active Carboxylated 2-(Diphenylphosphino)-1,1‘-binaphthalenes (1998)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTDirect Palladium-Catalyzed Phosphinylation of Aryl Triflates with Secondary Phosphines. Its Scope and Limitations: The Synthesis of Optically Active Carboxylated 2-(Diphenylphosphino)-1,1'-binaphthalenesGabriel Martorell, Xavier Garcías, Marcus Janura, and José M. SaáView Author Information Departament de Química, Universitat de les Illes Balears, 07071 Palma de Mallorca, Spain Cite this: J. Org. Chem. 1998, 63, 10, 3463–3467Publication Date (Web):April 30, 1998Publication History Received1 August 1997Published online30 April 1998Published inissue 1 May 1998https://pubs.acs.org/doi/10.1021/jo971428shttps://doi.org/10.1021/jo971428sbrief-reportACS PublicationsCopyright © 1998 American Chemical SocietyRequest reuse permissionsArticle Views771Altmetric-Citations34LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Aromatic compounds,Group 15 compounds,Mixtures,Oxidation,Oxides Get e-Alerts
A novel method for prokaryotic promoter prediction based on DNA stability (2005)

Our analysis clearly shows that the change in stability of DNA seems to provide a much better clue than usual sequence motifs, such as Pribnow box and -35 sequence, for differentiating promoter region from non-promoter regions. To a certain extent, it is more general and is likely to be applicable across organisms. Hence incorporation of such features in addition to the signature motifs can greatly improve the presently available promoter prediction programs.
Efficacy of ICS 205-930, a novel 5-hydroxytryptamine3 (5-HT3) receptor antagonist, in the prevention of migraine attacks. A complex answer to a simple question (1991)

To investigate whether the novel, potent and highly selective 5-hydroxytryptamine3 (5-HT3) receptor antagonist ICS 205-930 can prevent migraine attacks, we conducted simultaneously two randomized, double-blind, placebo-controlled, multicentre, international trials, involving a total of 204 patients, suffering from classic or common migraine. Both trials had the same parallel-group design (1 month baseline observation, followed by 3 months treatment) and both produced remarkably similar results. The primary efficacy parameter was the proportional reduction in attack frequency recorded after 3 months of treatment. Twenty-two patients withdrew prematurely from the trials and could not be assessed for efficacy. Mild to severe constipation was reported by about 50% of the patients on active treatment. None of the doses of ICS 205-930 tested (50 mg, 25 mg and 15 mg daily) produced a statistically significantly better result to reduce attack frequency than did placebo. However, confidence intervals for the difference in effect with placebo were wide, indicating that 15 mg ICS 205-930 may produce a 57% reduction in attack frequency as compared to placebo. The most unusual finding was that, for all efficacy parameters, the best results were obtained with the lowest dose (15 mg), the worst results with the highest dose (50 mg) and an intermediate effect with 25 mg. Such an inverse relation between dose and efficacy suggests a bell-shaped dose-response curve, implying that doses lower than 15 mg might well prove to be more effective. Thus, the present study has produced inconclusive, but intriguing results. Lower doses should be further investigated before drawing any definite conclusion on the efficacy of ICS 205-930 in the prophylactic treatment of migraine.
Xq28-linked noncompaction of the left ventricular myocardium: Prenatal diagnosis and pathologic analysis of affected individuals (1997)

Isolated noncompaction of the left ventricular myocardium (INVM) is characterized by the presence of numerous prominent trabeculations and deep intertrabecular recesses within the left ventricle, sometimes also affecting the right ventricle and interventricular septum. Familial occurrence of this disorder was described previously. We present a family in which 6 affected individuals demonstrated X-linked recessive inheritance of this trait. Affected relatives presented postnatally with left ventricular failure and arrhythmias, associated with the pathognomonic echocardiographic findings of INVM. The usual findings of Barth syndrome (neutropenia, growth retardation, elevated urinary organic acids, low carnitine levels, and mitochondrial abnormalities) were either absent or found inconsistently. Fetal echocardiograms obtained between 24-30 weeks of gestation in 3 of the affected males showed a dilated left ventricle in one heart, but were not otherwise diagnostic of INVM in any of the cases. Four of the affected individuals died during infancy, one is in cardiac failure at age 8 months, and one is alive following cardiac transplant at age 9 months. The hearts from infants who died or underwent transplantation appeared, on gross examination, to be enlarged, with coarse, deep ventricular trabeculations and prominent endocardial fibroelastosis. Histologically, there were loosely organized fascicles of myocytes in subepicardial and midmyocardial zones of both ventricles, and the myocytes showed thin, often angulated fibers with prominent central clearing and reduced numbers of filaments. Markedly elongated mitochondria were present in some ventricular myocytes from one specimen, but this finding was not reproducible. Genetic linkage analysis has localized INVM to the Xq28 region, where other myopathies with cardiac involvement have been located.
CD4+ Lymphocytes Provide MUC1-Specific Tumor Immunity In Vivo That Is Undetectable In Vitro and Is Absent in MUC1 Transgenic Mice (1998)

A C57BL/6 mouse transgenic for human MUC1 (MUC1.Tg) was developed to evaluate MUC1-specific tumor immunity in an animal that expresses MUC1 as a normal self protein. Previous studies showed that MUC1.Tg mice, challenged with syngeneic tumors expressing MUC1 (B16.MUC1), developed progressively growing MUC1-positive tumors, whereas wild-type C57BL/6 (wt) mice developed MUC1-negative tumors at a significantly slower rate. The results of a limiting dilution CTL frequency assay were not informative, in that similar numbers of MUC1-specific CTL precursors (CTL) were detected in MUC1.Tg and wt mice. Tumor immunity in vivo was characterized by an adoptive transfer method to evaluate the degree of MUC1 or non-MUC1 tumor immunity in wt or MUC1.Tg mice. The results revealed that wt mice developed protective tumor immunity mediated by MUC1-specific CD4+ lymphocytes, while MUC1.Tg mice were functionally tolerant to MUC1 in vivo. The potential of adoptive immunotherapy to provide immunity to tumors expressing MUC1 and to produce undesirable autoimmunity in recipient MUC1.Tg mice expressing MUC1 as a self Ag was evaluated. Adoptive transfer of immune cells from wt mice primed in vivo with B16.MUC1 tumor cells into MUC1.Tg recipients resulted in significant increases in the survival of MUC1.Tg recipients compared with unmanipulated control MUC .Tg mice challenged with B16.MUC1 tumor cells. This response was specific for MUC1 since control tumors developed at equivalent rates in recipient or control MUC1.Tg mice. No gross or histologic evidence of autoimmunity was observed in recipient MUC1.Tg mice, indicating that tumor immune responses mediated by MUC1-specific CD4+ lymphocytes spare nontransformed epithelia-expressing MUC1.
Effects of Lipid-Lowering by Simvastatin on Human Atherosclerotic Lesions (2001)

This in vivo human study demonstrates that effective and maintained lipid-lowering therapy by simvastatin is associated with a significant regression of atherosclerotic lesions. Our observation suggests that statins induce vascular remodeling, as manifested by reduced atherosclerotic burden without changes in the lumen.