gebhart/patrepeval huggingface dataset:
Purification and characterization of a novel, distinct isoform of prostaglandin endoperoxide synthase induced by human chorionic gonadotropin in granulosa cells of rat preovulatory follicles. (1992)

To purify and characterize the isoform of prostaglandin endoperoxide synthase (rPGSi) induced by human chorionic gonadotropin in granulosa cells of rat preovulatory follicles, solubilized cell extracts were subjected to anionic exchange chromatography, column fractions were resolved by one-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and rPGSi was visualized by immunoblotting and silver staining techniques. Immunoreactive rPGSi and peroxidase activity co-eluted at pH 6.5 and 6.0. Amino-terminal amino acid sequence of three immunoreactive rPGSi bands (Mr = 72,000, 70,000, and 59,000) were identical, Mr = 59,000 being a proteolytic fragment. Alignment of the amino-terminal sequences of rPGSi with those of ovine PGS (oPGS) indicated that only 15 of 26 residues were identical (58% identity). In contrast, rPGSi was closely related to the deduced amino acid sequence of PGS-related cDNA clones isolated from chicken and mouse cell lines, with 77% (20/26 residues) and 96% (25/26 residues) identity, respectively. Whereas tryptic digests of oPGS generated fragments of Mr = 38,000 and Mr = 33,000, only a small peptide appeared cleaved from the carboxyl terminus of rPGSi. Peroxidase activity of partially purified rPGSi exhibited lower apparent Km and maximal velocity than that of oPGS. Collectively, these results document the existence of a novel rat PGS isoform (based on purification, enzymatic activity, and amino-terminal amino acid sequence) which is hormonally induced and obligatory for a known biological process, ovulation.
Beta-lactamases as fully efficient enzymes. Determination of all the rate constants in the acyl-enzyme mechanism. (1990)

The rate constants for both acylation and deacylation of beta-lactamase PC1 from Staphylococcus aureus and the RTEM beta-lactamase from Escherichia coli were determined by the acid-quench method [Martin & Waley (1988) Biochem. J. 254, 923-925] with several good substrates, and, for a wider range of substrates, of beta-lactamase I from Bacillus cereus. The values of the acylation and deacylation rate constants for benzylpenicillin were approximately the same (i.e. differing by no more than 2-fold) for each enzyme. The variation of kcat./Km for benzylpenicillin with the viscosity of the medium was used to obtain values for all four rate constants in the acyl-enzyme mechanism for all three enzymes. The reaction is partly diffusion-controlled, and the rate constant for the dissociation of the enzyme-substrate complex has approximately the same value as the rate constants for acylation and deacylation. Thus all three first-order rate constants have comparable values. Here there is no single rate-determining step for beta-lactamase action. This is taken to be a sign of a fully efficient enzyme.
Bayesian automatic relevance determination algorithms for classifying geneexpression data (2002)

We demonstrate the effectiveness of the algorithms on three gene expression datasets for cancer, showing they compare well with alternative kernel-based techniques. By automatically incorporating feature selection, accurate classifiers can be constructed utilizing very few features and with minimal hand-tuning. We argue that the feature selection is meaningful and some of the highlighted genes appear to be medically important.
Inquiry into the Formation of Cyclic Carbonates during the (Salen)CrX Catalyzed CO2/Cyclohexene Oxide Copolymerization Process in the Presence of Ionic Initiators (2007)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTInquiry into the Formation of Cyclic Carbonates during the (Salen)CrX Catalyzed CO2/Cyclohexene Oxide Copolymerization Process in the Presence of Ionic InitiatorsDonald J. Darensbourg, Paolo Bottarelli, and Jeremy R. AndreattaView Author Information Department of Chemistry, Texas A&M University, College Station, Texas 77843 Cite this: Macromolecules 2007, 40, 21, 7727–7729Publication Date (Web):September 18, 2007Publication History Received29 May 2007Revised27 July 2007Published online18 September 2007Published inissue 1 October 2007https://pubs.acs.org/doi/10.1021/ma071206ohttps://doi.org/10.1021/ma071206obrief-reportACS PublicationsCopyright © 2007 American Chemical SocietyRequest reuse permissionsArticle Views1382Altmetric-Citations87LEARN 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 SUBJECTS:Copolymerization,Copolymers,Depolymerization,Inorganic carbon compounds,Oxides Get e-Alerts
Amplified Expression, Purification and Functional Reconstitution of the Dipeptide and Tripeptide Transport Protein of Lactococcus Lactis (1997)

Transport of hydrophilic dipeptides and tripeptides into Lactococcus lactis is mediated by a proton-motive-force-driven peptide-transport protein (DtpT) that shares similarity to eukaryotic peptide transporters, e.g. from yeasts, plants, and the kidney and small intestine of rabbit, man and rat. The expression level of DtpT protein in L. lactis was increased (20-40-fold) to approximately 10% of total integral membrane protein by means of a low-copy-number vector and selecting the appropriate growth conditions. Membrane vesicles bearing the DtpT-His6 protein (containing a C-terminal factor-Xa cleavage site and a six-histidine-tag) showed a Pro-Ala uptake activity that was half that of membranes containing the wild-type protein. The activity in the DtpT-His6 membrane vesicles increased at least 50% upon removal of the His6 tag from the protein. More than 95% DtpT was solubilized from L. lactis membranes in the presence of 1% (mass/vol.) n-dodecyl-beta-D-maltoside, and approximately 2 mg DtpT-His6 was purified by Ni2+-chelate affinity chromatography from 100 mg membrane protein. Purified DtpT-His6 was reconstituted unidirectionally into detergent-saturated formed liposomes, which were prepared from Escherichia coli phospholipid and egg phosphatidylcholine; the detergent was removed by adsorption to polystyrene beads. The highest uptake activities were obtained when DtpT was incorporated into liposomes that were treated with a low amount of n-dodecyl-beta-D-maltoside (onset of liposome solubilization). The uptake activity could be improved by addition of NaCl (200 mM) and lipids (2 mg/ml) during the solubilization, purification and reconstitution steps.
Enantiomeric Z- and E-crotyldiisopinocampheylboranes. Synthesis in high optical purity of all four possible stereoisomers of .beta.-methylhomoallyl alcohols (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEnantiomeric Z- and E-crotyldiisopinocampheylboranes. Synthesis in high optical purity of all four possible stereoisomers of .beta.-methylhomoallyl alcoholsHerbert C. Brown and Krishna S. BhatCite this: J. Am. Chem. Soc. 1986, 108, 2, 293–294Publication Date (Print):January 1, 1986Publication History Published online1 May 2002Published inissue 1 January 1986https://pubs.acs.org/doi/10.1021/ja00262a017https://doi.org/10.1021/ja00262a017research-articleACS PublicationsRequest reuse permissionsArticle Views3580Altmetric-Citations301LEARN 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
Thermostable DNA polymerase from Thermus thermophilus B35: influence of divalent metal ions on the interaction with deoxynucleoside triphosphates. (2000)

The interaction of DNA polymerase from Thermus thermophilus B35 (Tte-pol) with deoxynucleoside triphosphates in the presence of different divalent metal ions has been studied. DNA synthesis and competitive inhibition of the polymerase reaction by non-complementary dNTPs are described with corresponding kinetic schemes. The co-factor properties of some metals (Mg2+, Mn2+, Co2+, Ni2+, Cu2+, Ca2+, Cd2+, and Zn2+) were investigated, and their activating concentration ranges were determined. It was found that kcat values are significantly decreased and Km values slowly decrease when Mn2+ displaces Mg2+. The value of Kd for DNA template-primer is Me2+-independent, whereas Kd values for non-complementary dNTPs decrease in the presence of Mn2+. Tte-pol processivity but not DNA synthesis efficiency is Me2+-type independent.
BXR, an embryonic orphan nuclear receptor activated by a novel class of endogenous benzoate metabolites (1998)

Nuclear receptors are ligand-modulated transcription factors that respond to steroids, retinoids, and thyroid hormones to control development and body physiology. Orphan nuclear receptors, which lack identified ligands, provide a unique, and largely untapped, resource to discover new principles of physiologic homeostasis. We describe the isolation and characterization of the vertebrate orphan receptor, BXR, which heterodimerizes with RXR and binds high-affinity DNA sites composed of a variant thyroid hormone response element. A bioactivity-guided screen of embryonic extracts revealed that BXR is activatable by low-molecular-weight molecules with spectral patterns distinct from known nuclear receptor ligands. Mass spectrometry and 1H NMR analysis identified alkyl esters of amino and hydroxy benzoic acids as potent, stereoselective activators. In vitro cofactor association studies, along with competable binding of radiolabeled compounds, establish these molecules as bona fide ligands. Benzoates comprise a new molecular class of nuclear receptor ligand and their activity suggests that BXR may control a previously unsuspected vertebrate signaling pathway.
Widespread CD4+ T-cell reactivity to novel hTERT epitopes following vaccination of cancer patients with a single hTERT peptide GV1001 (2012)

Understanding the basis of a successful clinical response after treatment with therapeutic cancer vaccines is essential for the development of more efficacious therapy. After vaccination with the single telomerase (hTERT) 16-mer peptide, GV1001, some patients experienced clinical responses and long-term survival. This study reports in-depth immunological analysis of the T-cell response against telomerase (hTERT) in clinically responding patients compared with clinical non-responders following vaccination with the single hTERT 16-mer peptide, GV1001. Extensive characterization of CD4+ T-cell clones specific for GV1001 generated from a lung cancer patient in complete remission after vaccination demonstrated a very broad immune response to this single peptide vaccine with differences in fine specificity, HLA restriction, affinity and function. Some CD4+ T-cell clones were cytotoxic against peptide-loaded target cells and also recognized processed recombinant hTERT protein. Furthermore, T-cell responses against several unrelated hTERT epitopes, some of which are novel, were detected, indicating extensive epitope spreading which was confirmed in other clinical responders. In contrast, patients responding immunologically, but not clinically, after vaccination did not display this intramolecular epitope spreading. Multifunctional CD4+ T-cell clones specific for novel hTERT epitopes were generated and shown to recognize a melanoma cell line. Pentamer analysis of T cells in peripheral blood also demonstrated the presence of an important CD8+ T-cell response recognizing an HLA-B7 epitope embedded in GV1001 not previously described. These results indicate that the highly diverse hTERT-specific T-cell response, integrating both T helper and CTL responses, is essential for tumor regression and the generation of long-term T-cell memory.
Molecular analysis of the interaction between protein A of Staphylococcus aureus and von Willebrand factor (2007)

THESIS 8435%%%%Staphylococcus aureus continues to be a major cause of infection in normal as well as
immunocompromised hosts, and the increasing prevalence of highly virulent community acquired
methicillin-resistant strains is a public health concern. Protein A (Spa) is a surface associated
protein of S. aureus best known for its ability to bind to the Fc region of IgG. This
interaction is of importance in resistance of S. aureus to phagocytosis. Spa also binds strongly
to the Fab region of the immunoglobulins bearing Vh3 heavy chains and more recently has
been shown to bind von Willebrand factor (vWF) and tumour necrosis factor receptor-1
(TNFR1). Each Spa domain is organized into a three helix bundle and binding sites for Fc and
VH3 Fab have been identified.
Immunomodulatory Drugs and Active Immunotherapy for Chronic Lymphocytic Leukemia (2012)

The use of IMiDs alone or in combination with immunotherapy represents a treatment option for relapsed/refractory or treatment-naive patients. Mature data and further studies are needed to validate overall and progression-free survival. The toxicity profile of lenalidomide might limit its use and delay further studies. Immunotherapy offers another potential alternative, but further understanding of the immunogenicity of CLL cells and the mechanisms of tumor fl are reaction is needed to improve the outcomes in this field.
Linkers designed to intercalate the double helix greatly facilitate DNA alkylation by triplex-forming oligonucleotides carrying a cyclopropapyrroloindole reactive moiety (1999)

Triplex-forming oligonucleotides (TFOs) bind sequence-specifically in the major groove of double-stranded DNA. Cyclopropapyrroloindole (CPI), the electrophilic moiety that comprises the reactive subunit of the antibiotic CC-1065, gives hybridization-triggered alkylation at the N-3 position of adenines when bound in the minor groove of double-stranded DNA. In order to attain TFO-directed targeting of CPI, we designed and tested linkers to 'thread' DNA from the major groove-bound TFO to the minor groove binding site of CPI. Placement of an aromatic ring in the linker significantly enhanced the site-directed reaction, possibly due to a 'threading' mechanism where the aromatic ring is intercalated. All of the linkers containing aromatic rings provided efficient alkylation of the duplex target. The linker containing an acridine ring system, the strongest intercalator in the series, gave a small but clearly detectable amount of non-TFO-specific alkylation. An equivalent-length linker without an aromatic ring was very inefficient in DNA target alkylation.
Blunted ACTH and Cortisol Responses to Systemic Injection of Corticotropin‐Releasing Hormone (CRH) in Fibromyalgia (2002)

Thirteen female patients suffering from fibromyalgia (FM) and thirteen female age-matched controls were intravenously injected with a bolus dose of 100 microg corticotropin-releasing hormone (CRH), and the evoked secretion pattern of ACTH, cortisol, somatostatin, and growth hormone (GH) was followed up for two hours, together with the plasma levels of CRH. The increases of ACTH and cortisol following CRH were not significantly different between controls and FM patients. The increase of plasma CRH following its injection was significantly higher in FM patients and lasted about 45 min, paralleled by an increase of somatostatin with a similar time course. Basal GH levels were significantly lower in FM patients. GH increased in FM patients 90 min after injection of CRH, coincident with decreasing CRH and somatostatin levels, while GH levels in controls rather decreased with the lowest values occurring 90 min after CRH. The results support the concept that the hormonal secretion pattern frequently observed in FM patients is primarily caused by CRH, possibly as a response to chronic pain and stress. The elevated levels of CRH in the circulation of FM patients suggest elevated levels of CRH-binding protein, which could explain why the levels of ACTH and cortisol between controls and FM following CRH do not differ.
Structure of Molecular Tweezer Complexes in the Solid State:  NMR Experiments, X-ray Investigations, and Quantum Chemical Calculations (2007)

The structure of supramolecular complexes formed by a naphthalene-spaced tweezer molecule as host and 1,4-dicyanobenzene (DCNB), 1,2,4,5-tetracyanobenzene (TCNB), and 7,7,8,8-tetracyano-p-quinodimethane (TCNQ) as aromatic, electron-deficient guests is investigated by solid-state NMR and X-ray diffraction measurements. Quantum chemical calculations using linear scaling methods are applied to predict and to assign the 1H NMR chemical shifts of the complexes. By combining experiment and theory, insights into intra- and intermolecular effects influencing the proton chemical shifts of the host-guest system are provided in the solid state.
Genetic Transformation of Drosophila with Transposable Element Vectors (1982)

Exogenous DNA sequences were introduced into the Drosophila germ line. A rosy transposon (ry1), constructed by inserting a chromosomal DNA fragment containing the wild-type rosy gene into a P transposable element, transformed germ line cells in 20 to 50 percent of the injected rosy mutant embryos. Transformants contained one or two copies of chromosomally integrated, intact ry1 that were stably inherited in subsequent generations. These transformed flies had wild-type eye color indicating that the visible genetic defect in the host strain could be fully and permanently corrected by the transferred gene. To demonstrate the generality of this approach, a DNA segment that does not confer a recognizable phenotype on recipients was also transferred into germ line chromosomes.
Pentacene-based organic thin-film transistors (1997)

Organic thin-film transistors using the fused-ring polycyclic aromatic hydrocarbon pentacene as the active electronic material have shown mobility as large as 0.7 cm/sup 2//V-s and on/off current ratio larger than 10/sup 8/; both values are comparable to hydrogenated amorphous silicon devices. On the other hand, these and most other organic TFT's have an undesirably large subthreshold slope. We show here that the large subthreshold slope typically observed is not an intrinsic property of the organic semiconducting material and that devices with subthreshold slope similar to amorphous silicon devices are possible.
Sepsis and Acute Kidney Injury (2011)

Sepsis is a severe and dysregulated inflammatory response to infection characterized by end-organ dysfunction distant from the primary site of infection. Development of acute kidney injury (AKI) during sepsis increases patient morbidity, predicts higher mortality, has a significant effect on multiple organ functions, is associated with an increased length of stay in the intensive care unit, and hence consumes considerable healthcare resources. When compared with AKI of nonseptic origin, septic AKI is characterized by a distinct pathophysiology and therefore requires a different approach. Despite impressive advances in several fields of medicine, the pathophysiology, diagnostic procedures, and appropriate therapeutic interventions in sepsis are still highly debatable. Numerous immunomodulatory agents showing promise in preclinical studies fail to reduce the overwhelmingly high mortality rate of sepsis and provoke AKI when compared with other critically ill patients. Major impediments to progress in understanding, early diagnosis, and application of appropriate therapeutic modalities in sepsis-induced AKI include limited histopathologic information, few animal models that closely mimic human sepsis, and a relative shortage of specific diagnostic tools. Here we discuss the most recent advances in understanding the fundamental mechanisms of sepsis-induced AKI, characteristics of relevant animal models available, and potential therapies.
IL-13 induces proliferation, Ig isotype switching, and Ig synthesis by immature human fetal B cells. (1994)

In this study it is demonstrated that the novel T cell-derived cytokine IL-13 induces proliferation, Ig isotype switching, and Ig synthesis by human immature B cells derived from fetal bone marrow (BM). IL-13 induced proliferation and IgM, total IgG, IgG4, and IgE synthesis when total fetal BM cells or highly purified s mu+, CD10+, CD19+ fetal B cells were cultured in the presence of anti-CD40 mAb or activated CD4+ T cells. Although the ratios of the different isotypes produced in response to IL-13 were similar to those induced by IL-4, the levels of Ig produced in response to IL-13 were generally 5- to 15-fold lower, indicating that IL-13 is less potent than IL-4. In addition, in co-cultures of fetal B cells and CD4+ T cell clones IL-13 was effective only in the presence of IL-7, which may be due to the fact that IL-13, in contrast to IL-4, does not act on T cells. IL-13- and IL-4-induced IgE synthesis by s mu+, CD19+ fetal B cells was enhanced by IL-6 and inhibited by IL-12, IFN-alpha, IFN-gamma, and transforming growth factor-beta, suggesting that IL-13 and IL-4 induce IgE synthesis via similar signaling pathways. Like IL-4, IL-13 also induced Ig production, including IgG4 and IgE synthesis, by highly purified s mu-, CD10+, CD19+ pre-B cells co-cultured in the presence of activated cloned CD4+ T cells and IL-7. However, in contrast to IL-4, IL-13 did not enhance CD23, CD40, and HLA-DR expression on cultured s mu- pre-B cells in the absence of other stimuli, suggesting that IL-13 alone does not activate pre-B cells. Taken together, our data indicate that IL-13 induces proliferation, Ig isotype switching, and Ig production by immature fetal B cells in the presence of costimulatory signals provided by activated CD4+ T cells or anti-CD40 mAb. IL-13 is another cytokine that, in addition to IL-4, can induce isotype switching to IgG4 and IgE synthesis in immature human B cells.