gebhart/patrepeval huggingface dataset:
Globotriaosylceramide-Expressing Burkitt's Lymphoma Cells Are Committed to Early Apoptotic Status by Rhamnose-Binding Lectin from Catfish Eggs (2009)

Silurus asotus (catfish) egg lectin (SAL) has a strong affinity to Gal alpha-linked carbohydrate chains of not only glycoproteins but also glycosphingolipids such as globotriaosylceramide (Gb3). SAL uniformly bound to surfaces of Gb3-expressing (Gb3+) Burkitt's lymphoma cells, while Gb3 molecules were interspersed on the surfaces of Gb3+ cells. After a short period of treating Raji and Daudi cells with SAL, each cell size was 10 and 25% smaller than that of untreated cells, respectively. Treatment of Gb3+ cells with SAL caused an increase in binding of annexin V, however, neither caspase activation nor DNA fragmentation was observed after treatment with SAL for 22 h. Since SAL did not induce cell death in Gb3+ cells, SAL may function as an inducer of early apoptotic signal. We have revealed that SAL did not bind to D-threo-1-phenyl-2-decanoylamino-3-morphorino-1-propanol (D-PDMP)-treated Raji cells, and no cell shrinkage was observed in Gb3-deficient Raji cells treated with SAL, indicating that Gb3 localized in the glycosphingolipid-enriched microdomain (GEM) was involved in SAL-induced cell shrinkage through activation of voltage-gated potassium channel Kv1.3, and that the glycoprotein ligands on Gb3-deficient Raji cells treated with SAL were not included in this phenomenon. These results suggest that SAL leads the cells to early apoptotic status via binding to Gb3 existing in GEM, and that this binding is a prerequisite condition to induce early stage of apoptosis.
Pertussis toxin-sensitive G proteins mediate carbachol-induced REM sleep and respiratory depression (1995)

Microinjecting cholinomimetics into the medial pontine reticular formation (mPRF) of conscious cats causes a rapid eye movement (REM) sleep-like state and state-dependent respiratory depression. Muscarinic receptors within the mPRF have been shown to mediate this state-dependent respiratory depression, but the specific signal transduction mechanisms remain poorly understood. This study tested the hypothesis that the cholinergically induced REM sleep-like state and state-dependent respiratory depression are mediated by guanine nucleotide binding proteins (G proteins). Cholera toxin, pertussis toxin, 5'-guanylylimidodiphosphate, and forskolin were microinjected alone and in combination with carbachol into the mPRF of intact unanesthetized cats. All of the G protein-altering compounds significantly reduced the ability of carbachol to produce the REM sleep-like state. Pertussis toxin caused the greatest decrease in the percent of time spent in the carbachol-evoked REM sleep-like state, showing for the first time mediation by a pertussis toxin-sensitive (Gi- or G(o)-like) G protein. Cholera toxin blocked the carbachol-induced respiratory depression, indicating mediation by a Gs-like G protein. Forskolin significantly decreased carbachol-evoked REM sleep. These data provide the first demonstration that adenylyl cyclase within the mPRF contributes to the carbachol induction of REM sleep and respiratory depression.
Total Synthesis and Determination of the Absolute Configuration of Guadinomines B and C2 (2008)

This article describes the determination of the absolute configurations of the guadinomines, which are novel cyclic guanidyl natural products that are inhibitors of the type III secretion system (TTSS) of bacteria. Any compound that interrupts the TTSS of bacteria is potentially an ideal anti-infectious drug. The reliable asymmetric synthesis of guadinomines has revealed their absolute configurations, which could not have been defined without this synthetic approach. Our report not only describes the asymmetric total synthesis of the title compounds, but also demonstrates the novel concise synthesis of tri-substituted piperazinone cores as optically pure forms. The novel feature of our method is an intramolecular S(N)2 cyclization that uses PPh(3) and I(2) to construct the unique 5-membered cyclic guanidine substructure.
Post-traumatic hypoxia exacerbates neurological deficit, neuroinflammation and cerebral metabolism in rats with diffuse traumatic brain injury (2011)

Altogether, aggravated behavioural deficits observed in rats with diffuse TAI combined with hypoxia may be induced by enhanced neuroinflammation, and a prolonged period of metabolic dysfunction.
Molecular cloning of the three base restriction endonuclease R.CviJI from eukaryotic Chlorella virus IL-3A (1996)

R.CviJI is unique among site-specific restriction endonucleases in that its activity can be modulated to recognize either a two or three base sequence. Normally R.CviJI cleaves RGCY sites between the G and C to leave blunt ends. In the presence of ATP R.CviJI* cleaves RGCN and YGCY sites, but not YGCR sites. The gene encoding R.CviJI was cloned from the eukaryotic Chlorella virus IL-3A and expressed in Escherichia coli. The primary E.coli cviJIR gene product is a 278 amino acid protein initiated from a GTG codon, rather than the expected 358 amino acid protein initiated from an in-frame upstream ATG codon. Interestingly, the 278 amino acid protein displays the normal restriction activity but not the R.CviJI* activity of the native enzyme. Nine restriction and modification proteins which recognize a central GC or CG sequence share short regions of identity with R.CviJI amino acids 144-235, suggesting that this region is the recognition and/or catalytic domain.
A two-metal ion mechanism operates in the hammerhead ribozyme-mediated cleavage of an RNA substrate (1998)

Evidence for a two-metal ion mechanism for cleavage of the HH16 hammerhead ribozyme is provided by monitoring the rate of cleavage of the RNA substrate as a function of La3+ concentration in the presence of a constant concentration of Mg2+. We show that a bell-shaped curve of cleavage activation is obtained as La3+ is added in micromolar concentrations in the presence of 8 mM Mg2+, with a maximal rate of cleavage being attained in the presence of 3 microM La3+. These results show that two-metal ion binding sites on the ribozyme regulate the rate of the cleavage reaction and, on the basis of earlier estimates of the Kd values for Mg2+ of 3.5 mM and > 50 mM, that these sites bind La3+ with estimated Kd values of 0.9 and > 37.5 microM, respectively. Furthermore, given the very different effects of these metal ions at the two binding sites, with displacement of Mg2+ by La3+ at the stronger (relative to Mg2+) binding site activating catalysis and displacement of Mg2+ by La3+ at the weaker (relative to Mg2+) (relative to Mg2+) binding site inhibiting catalysis, we show that the metal ions at these two sites play very different roles. We argue that the metal ion at binding site 1 coordinates the attacking 2'-oxygen species in the reaction and lowers the pKa of the attached proton, thereby increasing the concentration of the attacking alkoxide nucleophile in an equilibrium process. In contrast, the role of the metal ion at binding site 2 is to catalyze the reaction by absorbing the negative charge that accumulates at the leaving 5'-oxygen in the transition state. We suggest structural reasons why the Mg(2+)-La3+ ion combination is particularly suited to demonstrating these different roles of the two-metal ions in the ribozyme cleavage reaction.
The YeastSaccharomyces cerevisiaeContains Two Glutaredoxin Genes That Are Required for Protection against Reactive Oxygen Species (1998)

Glutaredoxins are small heat-stable proteins that act as glutathione-dependent disulfide oxidoreductases. Two genes, designated GRX1 and GRX2, which share 40-52% identity and 61-76% similarity with glutaredoxins from bacterial and mammalian species, were identified in the yeast Saccharomyces cerevisiae. Strains deleted for both GRX1 and GRX2 were viable but lacked heat-stable oxidoreductase activity using beta-hydroxyethylene disulfide as a substrate. Surprisingly, despite the high degree of homology between Grx1 and Grx2 (64% identity), the grx1 mutant was unaffected in oxidoreductase activity, whereas the grx2 mutant displayed only 20% of the wild-type activity, indicating that Grx2 accounted for the majority of this activity in vivo. Expression analysis indicated that this difference in activity did not arise as a result of differential expression of GRX1 and GRX2. In addition, a grx1 mutant was sensitive to oxidative stress induced by the superoxide anion, whereas a strain that lacked GRX2 was sensitive to hydrogen peroxide. Sensitivity to oxidative stress was not attributable to altered glutathione metabolism or cellular redox state, which did not vary between these strains. The expression of both genes was similarly elevated under various stress conditions, including oxidative, osmotic, heat, and stationary phase growth. Thus, Grx1 and Grx2 function differently in the cell, and we suggest that glutaredoxins may act as one of the primary defenses against mixed disulfides formed following oxidative damage to proteins.
Phase I and pharmacokinetic study of a low‐clearance, unilamellar liposomal formulation of lurtotecan, a topoisomerase 1 inhibitor, in patients with advanced leukemia (2004)

Liposomal encapsulation of lurtotecan altered its metabolism significantly. There was no evident correlation between exposure, as measured by plasma pharmacokinetics of lurtotecan, and clinical response or toxicities. OSI-211 merits further study in hematologic malignancies.
Increased rectal mucosal enteroendocrine cells, T lymphocytes, and increased gut permeability following acute Campylobacter enteritis and in post-dysenteric irritable bowel syndrome (2000)

Increased EC, T lymphocytes, and gut permeability are acute changes following Campylobacter enteritis which can persist for more than a year and may contribute to PD-IBS.
Cyclooxygenase-2 dependent expression of angiogenic CXC chemokines, ENA-78/CXCL5 and IL-8/CXCL8, in human non-small cell lung cancer (2004)

4942 Elevated tumor cyclooxygenase 2 (COX-2) activity plays a multifaceted role in non-small cell lung cancer (NSCLC). To elucidate the role of COX-2 in the in vitro and in vivo expression of two known NSCLC angiogenic peptides, CXCL8 and CXCL5, we studied two COX-2 gene modified NSCLC cell lines, A549 and H157. COX-2 overexpression enhanced the in vitro expression of both CXCL8 and CXCL5. In contrast, specific COX-2 inhibition decreased the in vitro production of both peptides. Consistent with the COX-2 in vitro effects, the enhanced tumor growth of COX-2 expressing tumors in a SCID-mouse model of NSCLC was accompanied by elevated levels of CXCL5 and CXCL8. Furthermore, neutralizing anti-CXCL5 and anti-CXCL8 antisera inhibited the tumor growth of COX-2 overexpressing tumors in SCID-mice. In addition, the COX-2 related angiogenic capacity of H157 was efficiently reduced by anti-CXCR2 treatment in a rat corneal pocket model of angiogenesis. In summary, we conclude that COX-2 contributes to the progression of NSCLC tumorigenesis by enhancing the expression of angiogenic chemokines CXCL8 and CXCL5. Further studies will be required to determine if COX-2 inhibitors can regulate angiogenic chemokines in lung cancer patients.
Halo‐substituted (S)‐N‐(2‐benzoylphenyl)‐1‐benzylpyrrolidine‐2‐carboxamides as New Chiral Auxiliaries for the Asymmetric Synthesis of (S)‐α‐Amino Acids. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Detection of Rochalimaea henselae DNA in specimens from cat scratch disease patients by PCR (1994)

A PCR assay was developed by using degenerate primers that allow amplification of a 414-bp fragment of DNA from the rickettsia-like organisms Rochalimaea henselae and R. quintana. Internal oligonucleotides were used as hybridization probes, permitting rapid differentiation of these two Rochalimaea species. DNAs from 12 different isolates of R. henselae were amplified with the PCR primers, and the resulting 414-bp PCR product hybridized only with the R. henselae-specific probe. DNAs from four different isolates of R. quintana were amplified and produced a PCR product of the same size that hybridized only with the R. quintana-specific probe. DNAs from isolates of R. elizabethae, R. vinsonii, Bartonella bacilliformis, and Afipia felis failed to amplify the 414-bp fragment in the PCR assay. This two-step assay was applied to DNAs extracted from 16 fresh (unfixed) lymph node biopsy specimens and nine aspirates from patients with clinical cat scratch disease (CSD) to assay for the presence of R. henselae or R. quintana DNA in these samples. Twenty-one (84%) of 25 lymph node samples from CSD patients were positive for R. henselae, while none were positive for R. quintana. The characteristic 414-bp fragment was not amplified from eight lymph node tissue samples from non-CSD cases. These results provide evidence that R. henselae, and not R. quintana, plays the central role in the etiology of CSD.
Clinical validation of a gene expression signature that differentiates benign nevi from malignant melanoma (2015)

The performance, objectivity, reliability and minimal tissue requirements of this test suggest that it could have clinical application as an adjunct to histopathology in the diagnosis of melanocytic neoplasms.
Characterization of adriamycin-resistant human breast cancer cells which display overexpression of a novel resistance-related membrane protein. (1990)

Development of multidrug resistance due to overexpression of P-glycoprotein (Pgp), a cell membrane drug efflux pump, occurs commonly during in vitro selections with adriamycin (Adr). Pgp-mediated drug resistance can be overcome by the calcium channel blocker verapamil (Vp), which acts as a competitive inhibitor of drug binding and efflux. In order to identify other mechanisms of Adr resistance, we isolated an Adr-resistant subline by selecting the human breast cancer cell line MCF-7 with incremental increases of Adr in the presence of 10 microgram/ml verapamil. The resultant MCF-7/AdrVp subline is 900-fold resistant to Adr, does not overexpress Pgp, and does not exhibit a decrease in Adr accumulation. It exhibits a unique cross-resistance pattern: high cross-resistance to the potent Adr analogue 3'-deamino-3'-(3-cyano-4-morpholinyl)doxorubicin, lower cross-resistance to the alkylating agent melphalan, and a sensitivity similar to the parental cell line to vinblastine. The levels of glutathione and glutathione S-transferase are similar in the parental line and the Adr-resistant subline. Topoisomerase II-DNA complexes measured by the potassium-sodium dodecyl sulfate precipitation method shows a 2-3 fold decrease in the resistant subline. The MCF-7/AdrVp cells overexpress a novel membrane protein with an apparent molecular mass of 95 kDa. Polyclonal antibodies raised against the P-95 protein demonstrate a correaltion between the level of expression and Adr resistance. Removal of Adr but not verapamil from the selection media results in a decline in P-95 protein levels that parallels a restoration of sensitivity to Adr. Immunohistochemistry demonstrates localization of the P-95 protein on the cell surface. The demonstration of high levels of the protein in clinical samples obtained from patients refractory to Adr suggests that this protein may play a role in clinical drug resistance.
Clomethiazole Acute Stroke Study (CLASS) (1999)

Clomethiazole had no adverse or beneficial effect on long-term outcome for all patients but produced sedation. The hypothesis that clomethiazole is effective in patients with large strokes will be tested in a further study.
Synthesis and Properties of Di‐Chain Esterquat Surfactants (2014)

Abstract A series of cationic surfactants, di‐chain esterquat surfactants (EQs), were synthesized from N ‐methyl diethanolamine, hydrochloric acid, ethylene oxide, and caprylic acid, decylic acid, or lauric acid by a three‐step process. The synthesized surfactants were characterized by IR, MS, and 1 HNMR. Surface properties, antibacterial activity, and biodegradability of the synthesized surfactants were investigated. The results showed that synthesized EQs exhibit high surface activities and good biodegradability. Further, the synthesized surfactant, N , N ‐di‐[ O ‐decanoyl‐2‐hydroxyethyl]‐ N ‐hydroxyethyl‐ N ‐methylammonium chloride, exhibits excellent antibacterial activity against E. coli and S. aureus .
Adsorbents for affinity chromatography. Use of N-hydroxysuccinimide esters of agarose (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAdsorbents for affinity chromatography. Use of N-hydroxysuccinimide esters of agarosePedro Cuatrecasas and Indu ParikhCite this: Biochemistry 1972, 11, 12, 2291–2299Publication Date (Print):June 6, 1972Publication History Published online1 May 2002Published inissue 6 June 1972https://pubs.acs.org/doi/10.1021/bi00762a013https://doi.org/10.1021/bi00762a013research-articleACS PublicationsRequest reuse permissionsArticle Views2082Altmetric-Citations379LEARN 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
Imaging molecular interactions by multiphoton FLIM (2004)

The spatio-temporal localisation of molecular interactions within cells in situ and in particular in vivo is of great importance in elucidating the key mechanisms in regulation of fundamental process within the cell. Measurements of such near-field localisation of protein complexes may be achieved by the detection of fluorescence (or Förster) resonance energy transfer (FRET) between protein-conjugated fluorophores. The use of fluorescence lifetime imaging microscopy (FLIM) to determine both intra- and intermolecular FRET has become an important and powerful technique for investigating biological systems. In this review we focus on the time-domain-based fluorescence lifetime sensing, using time-correlated single photon counting multiphoton microscopy. We give a description of the technique, including data acquisition and analysis, and discuss the different biological applications of this technology.
2-D phase unwrapping and phase aliasing (1993)

Abstract The phase of complex signals is measured modulo-2pi (wrapped phase); continuous-phase information is obtained by adding properly chosen multiples of 2pi shift to the wrapped phase. Unwrapping searches for the 2pi combinations that minimize the discontinuity of the unwrapped phase as only the unwrapped phase can be analyzed and interpreted by further processing. The key problem of phase unwrapping is phase aliasing, a condition mainly caused by rapid phase variations. The extension of the one-dimensional (1-D) phase unwrapping algorithms to a two-dimensional (2-D) domain by 1-D slicing gives unsatisfactory results even in the presence of low-phase aliasing, whereas 2-D phase unwrapping deals with the complete problem, overcoming the limitations of 1-D unwrapping.The 2-D unwrapped phase is obtained as the solution of a variational problem that minimizes the differences between the gradients of the wrapped and unwrapped phase. The Euler equation is then integrated using the boundary conditions obtained from the wrapped phase. In addition to determining a unique unwrapped phase, this approach has the advantage that it limits the influence of phase aliasing. It is also more attractive than iterative 1-D unwrapping since it limits the propagation of unwrapping errors.Error propagation in phase unwrapping can strongly influence the result of any phase processing. Examples in this paper apply 2-D phase unwrapping to problems of refraction statics and interferometrical imaging using a remote system (SAR) and demonstrate how limited error propagation allows phase processing.
The nature of bone morphogenetic protein (BMP) fractions derived from bovine bone matrix gelatin. (1983)

A bone morphogenetic protein (BMP) fraction consisting of 17.5K, as well as three other low MW components, was extracted from demineralized bovine bone matrix gelatin under dissociative conditions in 4 M GuHCl. This BMP fraction induces differentiation of mesenchymal cells into cartilage and bone when implanted in the thigh muscles of mice. The 17.5K component is a prime candidate for BMP, but the relationship to the 34K, 24K, and 14K components is not established completely. The 24K component is of special interest, because, when it is present in combination with 17.5K and other components, the resultant preparation has high biologic activity. The 24K component, when isolated from the 17.5K component, had no BMP activity. The 14K component, when isolated from the 17.5K component and all components, had no BMP activity. A 22K components completely isolated by CMC chromatography had no BMP activity. The tasks ahead are to examine further the conditions controlling aggregation of the four low MW glycoproteins and to determine whether it is possible to isolate a single 17.5K homogeneous polypeptide with BMP activity.
Gluconeogenesis and Intrahepatic Triose Phosphate Flux in Response to Fasting or Substrate Loads. APPLICATION OF THE MASS ISOTOPOMER DISTRIBUTION ANALYSIS TECHNIQUE WITH TESTING OF ASSUMPTIONS AND POTENTIAL PROBLEMS (1995)

We measured gluconeogenesis (GNG) in rats by mass isotopomer distribution analysis, which allows enrichment of the true biosynthetic precursor pool (hepatic cytosolic triose phosphates) to be determined. Fractional GNG from infused [3-13C]lactate, [1-13C]lactate, and [2-13C]glycerol was 88 +/- 2, 89 +/- 3, and 87 +/- 2%, respectively, after 48 h of fasting. [2-13C]Glycerol was the most efficient label and allowed measurement of rate of appearance of intrahepatic triose phosphate (Ra triose-P), by dilution. IV fructose (10-15 mg/kg/min) increased absolute GNG by 81-147%. Ra triose-P increased proportionately, but endogenous Ra triose-P was almost completely suppressed, suggesting feedback control. Interestingly, 15-17% of fructose was directly converted to glucose without entering hepatic triose-P. IV glucose reduced GNG and Ra triose-P. 24-h fasting reduced hepatic glucose production by half, but absolute GNG was unchanged due to increased fractional GNG (51-87%). Reduced hepatic glucose production was entirely due to decreased glycogen input, from 7.3 +/- 1.8 to 1.1 +/- 0.2 mg/kg/min. Ra triose-P fell during fasting, but efficiency of triose-P disposal into GNG increased, maintaining GNG constant. Secreted glucuronyl conjugates and plasma glucose results correlated closely. In summary, GNG and intrahepatic triose-P flux can be measured by mass isotopomer distribution analysis with [2-13C]glycerol.