gebhart/patrepeval huggingface dataset:
Midkine Expression in Reed-Sternberg Cells of Hodgkin's Disease (2000)

Midkine (MK) was originally cloned as a product of a retinoic acid-responsive gene. The rationale for studying MK expression is based on previous reports showing that it transforms 3T3 cells, and that it acts as an autocrine growth factor in Wilm's tumors, and that its overexpression has been associated with worse outcome in bladder carcinoma. Besides bladder carcinoma, its expression was reported in various solid tumors. We investigated the expression of MK protein and/or MK gene in biopsied specimens from 40 patients with primary malignant lymphoma, 21 with Hodgkin's disease (HD) and 19 with non-Hodgkin's lymphoma (NHL). Reed-Sternberg (R-S) cells were stained positive in 10 of 16 HD cases evaluated by immunohistochemical method, whereas 18 of 19 NHL cases did not stain, and one B-cell NHL stained weakly positive. Immunostaining analysis was extended to established cell lines and to normal lymphocytes with or without lectin stimulation or with EB virus transformation. Among hematopoietic cells examined, erythro- or megakaryoblastic leukemia cell lines (K562, MEG-01 and UT7) were positive, while normal lymphocytes (except the EB virus-transformed one) and most myeloid and lymphoid cell lines (except Raji cells) were negative. On the contrary, solid tumor cell lines showed high and strongly positive staining including cell lines derived from of lung gastric, colon, and a pancreatic cancer. Using semi-quantitative reverse transcription polymerase chain reaction (RT-PCR), which is suitable for the detection of weakly expressed mRNA, the relative ratio of MK mRNA to beta-actin mRNA of samples was measured and compared in cases where RNA was available. The mean values of relative ratio (MK/beta-actin) of HD were almost twice as those of NHL samples, peripheral blood T cells, and spleen B cells. Our findings showed that MK is expressed in Reed-Sternberg cells of HD, and that MK might play a role in the pathogenesis of HD.
ChemInform Abstract: FeCl3‐Catalyzed Condensation of 2‐Naphthol and Aldehydes under Solvent‐Free Reaction Conditions: An Efficient and Green Alternative for the Synthesis of 14‐Aryl(Alkyl)‐14‐H‐dibenzo[a,j]xanthenes. (2011)

Abstract The title reaction uses an inexpensive and eco‐friendly catalyst without any additives.
Elevation of hemoglobin and work tolerance in iron-deficient subjects. (1981)

Selected parameters related to work tolerance were measured in 31 adult subjects with hemoglobin (Hb) concentration from 2.5 to 14.0 g/100 ml. Work tolerance was closely related to Hb concentration (r = 0.74) regardless of the adequacy of storage iron level. One male and six females with a mean Hb of 3.5 g/ml (27-55 years old) were studied before and 24h after transfusing 570ml of whole blood. The mean maximal work load tolerated increased 83% within 24h after transfusion in these seven subjects. Post-exercise venous blood lactate was markedly lower after transfusion. Work tolerance of these subjects within 24h after transfusion was the same as in other subjects who had had the equivalent Hb level as the post-transfusion subjects presumably for at least several weeks. These data suggest that the decrement in work performance capacity in iron-deficient and anemic subjects is, in a large part, a reflection of the level of anemia rather than other non-Hb related biochemical changes that could accompany prolonged iron deficiency anemia.
Inducible phosphorylation of I kappa B alpha is not sufficient for its dissociation from NF-kappa B and is inhibited by protease inhibitors. (1994)

The ubiquitous transcription factor NF-kappa B is regulated by its cytoplasmic inhibitor I kappa B. A variety of cellular stimuli cause the dissociation of NF-kappa B from I kappa B, allowing NF-kappa B to translocate to the nucleus and regulate gene expression. Although the activation of NF-kappa B in vivo is associated with the phosphorylation and degradation of I kappa B alpha, it has remained unclear how each of these events contributes to this process. Recently, studies utilizing protease inhibitors have suggested that the proteolysis of I kappa B alpha is a necessary event in the activation of NF-kappa B. We demonstrate in this study that these and an additional protease inhibitor also completely repress inducible phosphorylation of I kappa B alpha. This surprising result suggests a more complex role of proteases in NF-kappa B activation. In addition, data presented here indicate that many of these inhibitors also directly modify NF-kappa B and inhibit its DNA binding activity. Due to the pleiotropic effects of these protease inhibitors, it is difficult to conclude from their use how I kappa B alpha phosphorylation and degradation contribute to NF-kappa B activation. In the present study, a more direct approach demonstrates that phosphorylation of I kappa B alpha alone is not sufficient for NF-kappa B activation.
Improved compositional abruptness at the InGaAs on GaAs interface by presaturation with In during molecular-beam epitaxy (1995)

Surface segregation of In atoms during molecular beam epitaxy of InGaAs layers greatly influences the composition profile in the vicinity of both the normal and the inverted Ga(Al)As/InGaAs interface, inherently limiting compositional abruptness. We find, for example, that the intended alloy composition in In0.22Ga0.78As is not reached until nearly 35 Å from the InGaAs on GaAs interface for growth at 500 °C. We propose and demonstrate how the compositionally graded region in InGaAs can be eliminated by preadsorbing a fixed amount of In onto the GaAs surface to match the surface segregated layer during steady state, before depositing the InGaAs layer.
Eighteen years follow-up study of the clinical manifestations and progression of Dupuytren's disease (2001)

The incidence of Dupuytren's disease is high in elderly men. Dupuytren's disease is progressive in nature and most operated patients have recurrent finger contractures.
Mammalian Target of Rapamycin Positively Regulates Collagen Type I Production via a Phosphatidylinositol 3-Kinase-independent Pathway (2004)

The mammalian target of rapamycin (mTOR) is a multifunctional protein involved in the regulation of cell growth, proliferation, and differentiation. The goal of this study was to determine the role of mTOR in type I collagen regulation. The pharmacological inhibitor of phosphatidylinositol (PI) 3-kinase, LY294002, significantly inhibited collagen type I protein and mRNA levels. The effects of LY294002 were more pronounced on the collagen alpha1(I) chain, which was inhibited at the transcriptional and mRNA stability levels versus collagen alpha2(I) chain, which was inhibited through a decrease in mRNA stability. In contrast, addition of the PI 3-kinase inhibitor, wortmannin, did not alter type I collagen steady-state mRNA levels. This observation and further experiments using an inactive LY294002 analogue suggested that collagen mRNA levels are inhibited independent of PI 3-kinase. Additional experiments have established that mTOR positively regulates collagen type I synthesis in human fibroblasts. These conclusions are based on results demonstrating that inhibition of mTOR activity using a specific inhibitor, rapamycin, reduced collagen mRNA levels. Furthermore, decreasing mTOR expression by about 50% by using small interfering RNA resulted in a significant decrease of collagen mRNA (75% COL1A1 decrease and 28% COL1A2 decrease) and protein levels. Thus, mTOR plays an essential role in regulating basal expression of collagen type I gene in dermal fibroblasts. Together, our data suggest that the classical PI 3-kinase pathway, which places mTOR downstream of PI 3-kinase, is not involved in mTOR-dependent regulation of type I collagen synthesis in dermal fibroblasts. Because collagen overproduction is a main feature of fibrosis, identification of mTOR as a critical mediator of its regulation may provide a suitable target for drug or gene therapy.
Synthesis of hydrocarbon-strapped porphyrins containing quinone and phenolic groups (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of hydrocarbon-strapped porphyrins containing quinone and phenolic groupsBrian Morgan and David DolphinCite this: J. Org. Chem. 1987, 52, 24, 5364–5374Publication Date (Print):November 1, 1987Publication History Published online1 May 2002Published inissue 1 November 1987https://pubs.acs.org/doi/10.1021/jo00233a011https://doi.org/10.1021/jo00233a011research-articleACS PublicationsRequest reuse permissionsArticle Views639Altmetric-Citations12LEARN 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
The molecular portraits of breast tumors are conserved across microarray platforms (2006)

This study validates the "breast tumor intrinsic" subtype classification as an objective means of tumor classification that should be translated into a clinical assay for further retrospective and prospective validation. In addition, our method of combining existing data sets can be used to robustly validate the potential clinical value of any new gene expression profile.
Auctions and Bidding: A Primer (1989)

The “Winner's Curse,” is just one of the surprising and puzzling conclusions turned up by modern research into auctions. Another is the theoretical proposition that, for example, a sealed-bid Treasury bill auction in which each buyer pays a price equal to the highest rejected bid would yield more revenue to the Treasury than the current procedure in which the winning bidder pays the seemingly higher amount equal to his own bid. There are also subtle results that demonstrate the equivalence of such apparently different institutions as the standard sealed-bid auction and the Dutch auction. Other results explain the use of standard auctions as the selling schemes that maximize the welfare of the bid–taker, or as schemes that lead to efficient allocations, minimize transaction costs, guard against corruption by the bid-taker's agents, or mitigate the effects of collusion among the bidders. Finally, for some environments, the theory makes sharp, testable predictions about the bids and profits of various classes of bidders. This paper relies mainly on theory to study these issues, but it will also review some experimental evidence and recent empirical studies testing the predictions of the theory.
Direct Synthesis and Characterization of Hydrophobic Aluminum-Free Ti−Beta Zeolite (1998)

Incorporation of Ti into the framework of aluminium-free zeolite Beta has been achieved in F- medium and has produced hydrophobic selective oxidation catalysts. The Ti−Beta(F) materials have been characterized by X ray diffraction, infrared, Raman, ultraviolet, XANES, EXAFS, 29Si MAS NMR, and 1H→29Si CP MAS NMR spectroscopies, adsorption microcalorimetry, and catalytic testing. At near neutral pH the incorporation of Ti into the framework appears to present an upper limit of ca. 2.3 Ti/uc, beyond which anatase is detected in the calcined materials. However, at higher pH (ca. 11) larger amounts of Ti can be incorporated without anatase formation. After calcination, Ti incorporation in the framework is characterized by an increase in the unit cell volume, the appearance of one Raman band and three infrared bands in the region near 960 cm-1 and the presence of a strong absorption band in the 205−220 nm ultraviolet spectrum. By 29Si MAS NMR, 1H→29Si CP MAS NMR, and infrared spectroscopies it is concluded that upon contact with ambient humidity there is no hydrolysis of Si−O−Ti bonds in Ti−Beta zeolites prepared by the fluoride route, while it is probably a major feature of those synthesized in OH- medium. XANES and EXAFS spectroscopies of calcined dehydrated Ti−Beta zeolites unambiguously demonstrate the tetrahedral coordination of Ti with a Ti−O bond length of ca. 1.80 Å. Upon hydration, the changes in the XANES and EXAFS spectra are consistent with a change in the coordination of Ti to reach a state which depends on the composition and synthesis route and which ranges from a 5-fold coordination for Al-free Ti−Beta synthesized by the F- method to a highly distorted 6-fold coordination in Ti,Al−Beta synthesized in OH- medium. Adsorption microcalorimetry experiments show the strict hydrophobic nature of pure SiO2 zeolite Beta synthesized in F- medium while evidencing a slight increase in the hydrophilicity of the material upon incorporation of Ti to the framework. This is due to the relatively strong adsorption of precisely one H2O molecule per Ti site. On the contrary, the materials synthesized in OH- medium show an enhanced hydrophilicity. Finally, Ti−Beta(F) is an active and selective catalyst for oxidation of organic substrates with H2O2. A comparison of the activities and selectivities of Ti−Beta(F), Ti−Beta(OH) and TS-1 in the epoxidation of 1-hexene using acetonitrile and methanol as solvents demonstrates that the major differences between Ti−Beta and TS-1 catalysts are intrinsic to each zeolitic structure. Because of its high hydrophobicity, Ti−Beta(F) catalyst can advantageously replace Ti−Beta(OH) in the epoxidation of substrates, like unsaturated fatty acids or esters, which contain a polar moiety.
Oncolytic and immunostimulatory efficacy of a targeted oncolytic poxvirus expressing human GM-CSF following intravenous administration in a rabbit tumor model (2009)

Targeted oncolytic poxviruses hold promise for the treatment of cancer. Arming these agents with immunostimulatory cytokines (for example, granulocyte-monocyte colony-stimulating factor; GM-CSF) can potentially increase their efficacy and/or alter their safety. However, due to species-specific differences in both human GM-CSF (hGM-CSF) activity and poxviruses immune avoidance proteins, the impact of hGM-CSF expression from an oncolytic poxvirus cannot be adequately assessed in murine or rat tumor models. We developed a rabbit tumor model to assess toxicology, pharmacodynamics, oncolytic efficacy and tumor-specific immunity of hGM-CSF expressed from a targeted oncolytic poxvirus JX-963. Recombinant purified hGM-CSF protein stimulated a leukocyte response in this model that paralleled effects of the protein in humans. JX-963 replication and targeting was highly tumor-selective after i.v. administration, and intratumoral replication led to recurrent, delayed systemic viremia. Likewise, hGM-CSF was expressed and released into the blood during JX-963 replication in tumors, but not in tumor-free animals. hGM-CSF expression from JX-963 was associated with significant increases in neutrophil, monocyte and basophil concentrations in the peripheral blood. Finally, tumor-specific cytotoxic T lymphocytes (CTL) were induced by the oncolytic poxvirus, and expression of hGM-CSF from the virus enhanced both tumor-specific CTL and antitumoral efficacy. JX-963 had significant efficacy against both the primary liver tumor as well as metastases; no significant organ toxicity was noted. This model holds promise for the evaluation of immunostimulatory transgene-armed oncolytic poxviruses, and potentially other viral species.
Differentiation of Osteoblasts and in Vitro Bone Formation from Murine Embryonic Stem Cells (2001)

Pluripotent embryonic stem (ES) cells have the potential to differentiate to all fetal and adult cell types and might represent a useful cell source for tissue engineering and repair. Here we show that differentiation of ES cells toward the osteoblast lineage can be enhanced by supplementing serum-containing media with ascorbic acid, beta-glycerophosphate, and/or dexamethasone/retinoic acid or by co-culture with fetal murine osteoblasts. ES cell differentiation into osteoblasts was characterized by the formation of discrete mineralized bone nodules that consisted of 50-100 cells within an extracellular matrix of collagen-1 and osteocalcin. Dexamethasone in combination with ascorbic acid and beta-glycerophosphate induced the greatest number of bone nodules and was dependent on time of stimulation with a sevenfold increase when added to ES cultures after, but not before, 14 days. Co-culture with fetal osteoblasts also provided a potent stimulus for osteogenic differentiation inducing a fivefold increase in nodule number relative to ES cells cultured alone. These data demonstrate the application of a quantitative assay for the derivation of osteoblast lineage progenitors from pluripotent ES cells. This could be applied to obtain purified osteoblasts to analyze mechanisms of osteogenesis and for use of ES cells in skeletal tissue repair.
Role of interleukin-6 in mediating the acute phase protein response and potential as an early means of severity assessment in acute pancreatitis. (1993)

A number of laboratory and clinical studies have shown that interleukin-6 is the principal mediator of the acute phase protein response. In this study the relationship between serum concentrations of interleukin-6 and C-reactive protein in acute pancreatitis are examined and the ability of interleukin-6 to discriminate between severe and mild attacks is assessed. We have studied 24 patients (10 severe and 14 mild). Serum samples were collected on admission, six hourly for 48 hours and then 12 hourly for a further three days. When the areas under the curves of individual patients were compared there was a strong correlation between the total production of interleukin-6 and C-reactive protein (r = 0.73) (Spearman rank correlation) and peak interleukin-6 and C-reactive protein concentrations (r = 0.75), suggesting a close relationship between interleukin-6 and C-reactive protein production. Both on admission and peak interleukin-6 concentrations were significantly higher in patients with severe than mild disease. There was no significant difference in on admission C-reactive protein concentrations, although significant differences were seen when peak concentrations were considered. Utilising a peak interleukin-6 concentration of > 130 u/ml, we were able to distinguish between severe and mild attacks of acute pancreatitis with a sensitivity of 100% and specificity of 71%. These figures were comparable with those for peak C-reactive protein, a C-reactive protein of > 150 mg/l detecting severe attacks of acute pancreatitis with a sensitivity of 90% and specificity of 79%. In view of the fact that interleukin-6 concentrations peaked earlier than those of C-reactive protein, interleukin-6 is capable of providing comparable, but earlier severity prediction than C-reactive protein.
The Substrate Specificity of a Recombinant Cysteine Protease from Leishmania mexicana: Application of a Combinatorial Peptide Library Approach (2000)

The substrate specificity of CPB2.8DeltaCTE, a recombinant cysteine protease from Leishmania mexicana, was mapped by screening a fluorescence-quenched combinatorial peptide library. Results from library screening indicated a preference for Arg or Lys in the S(3) subsite and for hydrophobic residues, both aliphatic and aromatic, in S(2). The S(1) subsite exhibited a specificity for the basic residues Arg and Lys. Generally, the specificity of the primed subsites was less strict compared with the non-primed side which showed preference for Arg, Lys and Ala in S'(1), Arg, Pro and Gly in S'(2) and Lys, Arg and Ser in S'(4). By contrast, a strict preference for the basic residues Arg and Lys was found for S'(3). Overall, there was a trend for basic residues in alternating subsites and smaller residues in the primed sites compared with the non-primed sites. In addition, there were strict requirements for the amino acids in subsites S(3)--S(1). Fluorescence-quenched peptides from the library with the highest on-resin cleavage were resynthesised and their kinetics of hydrolysis by CPB2.8DeltaCTE assessed in solution phase assays. Several good substrates containing the quintessential dipeptide particular to cathepsin-L-like enzymes, -F-R/K-, in P(2) and P(1) were identified (e.g. Y(NO(2))-EKFR down arrow RGK-K(Abz)G, Abz=2-aminobenzoyl; k(cat)K(m)(-1)=4298 mM(-1)s(-1)). However, novel substrates containing the dipeptide -L/I-Q- in P(2) and P(1) were also well hydrolysed (e.g. Y(NO(2))-YLQ down arrow GIQK-K(Abz)G; k(cat)K(m)(-1)=2583 mM(-1)s(-1)). The effect of utilising different fluorescent donor--quencher pairs on the value of k(cat)K(m)(-1) was examined. Generally, the use of the Abz/Q-EDDnp donor--quencher pair (EDDnp=N-(2,4-dinitrophenyl)ethylenediamine) instead of K(Abz)/Y(NO(2)) resulted in higher k(cat)K(m)(-1) values for analogous substrates.
Electrostatic Interactions in RNA Aminoglycosides Binding (1997)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTElectrostatic Interactions in RNA Aminoglycosides BindingHai Wang and Yitzhak TorView Author Information Department of Chemistry and Biochemistry University of California, San Diego La Jolla, California 92093-0358 Cite this: J. Am. Chem. Soc. 1997, 119, 37, 8734–8735Publication Date (Web):September 17, 1997Publication History Received12 May 1997Published online17 September 1997Published inissue 1 September 1997https://pubs.acs.org/doi/10.1021/ja9715105https://doi.org/10.1021/ja9715105rapid-communicationACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views595Altmetric-Citations84LEARN 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:Carbohydrates,Crystal cleavage,Genetics,Hydroxyls,Reaction products Get e-Alerts