gebhart/patrepeval huggingface dataset:
Innate cellular fluorescence reflects alterations in cellular proliferation (1997)

Background and Objective The objective of this study was to examine the question of whether unique spectral patterns were associated with cell proliferation and could be identified by comparing the fluorescence pattern of slow to rapid growing cells. Study Design/Materials and Methods: Three in vitro model systems, (A431 cells inhibited by EGF, serum-starved 3T3 fibroblasts, and normal oral epithelial cells exposed to TGFβ), were analyzed using fluorescence spectroscopy. Growth status was monitored by cell number, 3H-thymidine incorporation, and flow cytometry. Results The excitation spectra (λex 240–430 nm, λem 450 nm) effectively distinguished slow and rapid growing cells in all three systems. Statistical analysis of the ratios of the main broad peak (320–350 nm) to a point on the down-slope of the curve at 370 nm was statistically significant. Ratios in the emission scan (λex 340 nm, λem 360–660 nm) could separate slow and rapid growing A431 and oral epithelial cells (P=0.0001 and P=0.023, respectively), but not slow and fast growing 3T3 cells (P=0.56). Conclusion Innate cellular fluorescence has the potential to discriminate proliferating and nonproliferating cell populations. Lasers Surg. Medicine 20:319–331, 1997. © 1997 Wiley-Liss, Inc.
A Transmissible Antigen Detected in Two Cell Lines Derived from Human Tumours (1974)

SUMMARY Vesicular stomatitis virus (VSV) can form ‘pseudotype’ particles with neutralization antigen(s) derived from mouse or chicken leukaemia viruses. These pseudotype particles contain the genome of VSV, but show neutralization, host-range and interference specificity of the corresponding oncornavirus. Pseudotypes were also detected following the growth of VSV in two established cell lines derived from human tumours: in MaTu derived from mammary carcinoma and in Tu-135 derived from a sarcoma. No virus-like particles were detected in these cells by labelling with [3H]-uridine followed by sucrose density gradient sedimentation. Media from these cultures did not contain DNA polymerase. Nevertheless, the capacity to produce VSV pseudotype was transmitted to some pseudotype-negative cells following their co-cultivation with X-irradiated, pseudotype-positive cells. Cell-free filtrates did not transmit the property. An antigen detected by immunofluorescence was also consistently transmitted. The VSV pseudotype produced in cells infected by co-cultivation possessed the same neutralization specificity as VSV pseudotype produced in the original tumour cells.
Control of mammalian translation by mRNA structure near caps (2006)

The scanning model of RNA translation proposes that highly stable secondary structures within mRNAs can inhibit translation, while structures of lower thermal stability also affect translation if close enough to the 5' methyl G cap. However, only fragmentary information is available about the dependence of translation efficiency in live mammalian cells on the thermodynamic stability, location, and GC content of RNA structures in the 5'-untranslated region. We devised a two-color fluorescence assay for translation efficiency in single live cells and compared a wide range of hairpins with predicted thermal stabilities ranging from -10 to -50 kcal/mol and 5' G cap-to-hairpin distances of 1-46 bases. Translation efficiency decreased abruptly as hairpin stabilities increased from deltaG = -25 to -35 kcal/mol. Shifting a hairpin as little as nine bases relative to the 5' cap could modulate translation more than 50-fold. Increasing GC content diminished translation efficiency when predicted thermal stability and cap-to-hairpin distances were held constant. We additionally found naturally occurring 5'-untranslated regions affected translation differently in live cells compared with translation in in vitro lysates. Our study will assist scientists in designing experiments that deliberately modulate mammalian translation with designed 5' UTRs.
Exciton Primer-mediated SNP detection in SmartAmp2 reactions (2010)

Most commonly used intercalating fluorescent dyes in DNA detection are lacking any sequence specificity, whereas so-called Exciton Primers can overcome this limitation by functioning as "sequence-specific dyes." After hybridization to complementary sequences, the fluorescence of Exciton Primers provides sequence-specific signals for real-time monitoring of amplification reactions. Applied to the SmartAmp2 mutation detection process, Exciton Primers show high signal strength with low background leading to a superior specificity and sensitivity compared to SYBR Green I. Signal strength can be further enhanced using multiple dyes within one Exciton Primer or use of multiple Exciton Primers in the same amplification reaction. Here we demonstrate the use of Exciton Primers for genotyping a single nucleotide polymorphism (SNP) in the VKORC1 locus (-1639G>A) relevant for Warfarin dosing as an example for Exciton Primers mediated genotyping by SmartAmp2. The genotyping assay can use only one labeled Exciton Primer for endpoint detection, or simultaneously by real-time monitoring detect wild-type and mutant alleles in a one-tube reaction using two Exciton Primers having different dyes. Working directly from blood samples, Exciton Primer mediated genotyping by SmartAmp2 offers superior solutions for rapid point-of-care testing.
In vivo albumin labeling and lymphatic imaging (2014)

The ability to accurately and easily locate sentinel lymph nodes (LNs) with noninvasive imaging methods would assist in tumor staging and patient management. For this purpose, we developed a lymphatic imaging agent by mixing fluorine-18 aluminum fluoride-labeled NOTA (1,4,7-triazacyclononane-N,N',N''-triacetic acid)-conjugated truncated Evans blue ((18)F-AlF-NEB) and Evans blue (EB) dye. After local injection, both (18)F-AlF-NEB and EB form complexes with endogenous albumin in the interstitial fluid and allow for visualizing the lymphatic system. Positron emission tomography (PET) and/or optical imaging of LNs was performed in three different animal models including a hind limb inflammation model, an orthotropic breast cancer model, and a metastatic breast cancer model. In all three models, the LNs can be distinguished clearly by the apparent blue color and strong fluorescence signal from EB as well as a high-intensity PET signal from (18)F-AlF-NEB. The lymphatic vessels between the LNs can also be optically visualized. The easy preparation, excellent PET and optical imaging quality, and biosafety suggest that this combination of (18)F-AlF-NEB and EB has great potential for clinical application to map sentinel LNs and provide intraoperative guidance.
Physical Studies of Conformational Plasticity in a Recombinant Prion Protein (1997)

PrP(Sc) is known to be the major, if not the only, component of the infectious prion. Limited proteolysis of PrP(Sc) produces an N-terminally truncated polypeptide of about 142 residues, designated PrP 27-30. Recently, a recombinant protein (rPrP) of 142 residues corresponding to the Syrian hamster PrP 27-30 was expressed in Escherichia coli and purified (Mehlhorn et al., 1996). rPrP has been refolded into both alpha-helical and beta-sheet structures as well as various intermediates in aqueous buffers. The beta-sheet state and two pH-dependent alpha-helical states were characterized by CD and NMR. The alpha-helical conformation occurred only after the formation of an intramolecular disulfide bond, whereas the beta-sheet form was accessible either with or without the disulfide. Of the different alpha-helical forms studied, only those refolded in the pH range 5-8 were substantially soluble at physiological pH, exhibiting similar conformations and monomeric analytical sedimentation profiles throughout the above pH range. Furthermore, refolded alpha-rPrP showed NMR chemical shift dispersion typical of proteins with native conformations, although 2D NMR indicated large segments of conformational flexibility. It displayed a cooperative thermal denaturation transition; at elevated temperatures, it converted rapidly and irreversibly to the thermodynamically more stable beta-sheet form. Unfolding of alpha-rPrP by GdnHCl revealed a two-phase transition with a relatively stable folding intermediate at 2 M GdnHCl. The deltaG values were estimated to be 1.9 +/- 0.4 kcal/mol for the first phase and 6.5 +/- 1.2 kcal/mol for the second, consistent with a folding core surrounded by significant segments of flexible conformation. By NMR, alpha-rPrP(acid) isolated at pH 2 without refolding exhibited heterogeneous line widths, consistent with an acid-denatured molten globular state. We conclude that to the extent that rPrP constitutes a relevant folding domain of PrP(C), the various conformations exhibited by rPrP suggest that the PrP sequence may be intrinsically plastic in its conformations; indeed, portions of PrP(C) may possess a relatively open conformation which makes it susceptible to conversion into PrP(Sc) under appropriate conditions.
A role for Id-1 in the aggressive phenotype and steroid hormone response of human breast cancer cells. (2000)

The helix-loop-helix protein Id-1 inhibits the activity of basic helix-loop-helix transcription factors, and is an important regulator of cell growth and tissue-specific differentiation. We have shown (P. Y. Desprez et al., Mol. Cell. Biol., 18: 4577-4588, 1998) that ectopic expression of Id-1 inhibits differentiation and stimulates the proliferation and invasiveness of mouse mammary epithelial cells, and that there is a correlation between the levels of Id-1 protein and the aggressiveness of several human breast cancer cell lines. Here, we show that aggressive and metastatic breast cancer cells express high levels of Id-1 mRNA because of a loss of serum-dependent regulation that is mediated by a 2.2-kb region of the human Id-1 promoter. Three lines of evidence suggest that unregulated Id-1 expression may be an important regulator of the aggressive phenotype of a subset of human breast cancer cells: (a) a constitutively expressed Id-1 cDNA, when introduced into a nonaggressive breast cancer cell line (T47D), conferred a more aggressive phenotype, as measured by growth and invasiveness; (b) Id-1 was an important mediator of the effects of sex steroid hormones on T47D cell proliferation. Estrogen stimulated proliferation and induced Id-1 expression, whereas progesterone inhibited proliferation and repressed Id-1 expression. Progesterone repressed Id-1 expression, at least in part by repressing transcription. Most importantly, an antisense oligonucleotide that reduced Id-1 protein levels reduced the ability of estrogen to stimulate cell proliferation, whereas constitutive Id-1 expression rendered cells refractory to growth inhibition by progesterone; and (c) using a limited number of breast cancer biopsies, we showed that Id-1 was more frequently expressed in infiltrating carcinomas compared with ductal carcinomas in situ. Our results suggest that Id-1 can control the malignant progression of breast cancer cells, particularly that mediated by sex steroid hormones. Moreover, Id-1 has the potential to serve as a marker for aggressive breast tumors.
Nutrition in Advanced Cancer: Anorexia as an Outcome Variable and Target of Therapy (1992)

The endpoints used as outcome variables in clinical cancer treatment trials, including nutrition intervention studies, should contain items that are meaningful to the patient. Variables to consider are appetite, food intake, physical performance, psychological and social functioning, response to cancer therapies, survival time, nutrition status, associated morbidity, and costs. Ideally, the design and conduct of nutrition trials should be carried out by a multidisciplinary team comprising medical oncologists, physician specialists in nutrition, dietitians, and social scientists. Anorexia has not been a focus of nutrition support trials in the past partly because of the lack of effective strategies to reverse it. Anorexia is one important cause of cancer starvation, and it also causes patient discomfort. This paper describes outcome variables that include patient derived subjective factors such as anorexia, and outlines new strategies to reverse anorexia. Pharmacologic strategies tested to reverse anorexia include corticosteroids, anabolic steroids, cyproheptadine, hydrazine sulfate, cannabinoids, and megestrol acetate. Of these, only the latter has been consistently well tolerated and effective, with significant improvements in appetite and food intake demonstrated in large-scale, randomized, controlled trials involving more than 600 cancer patients. Dose-response studies have demonstrated increasing efficacy with increasing doses of megestrol acetate from 160 to 800 mg/day. Doses in excess of 800 mg/day are not currently recommended. The mechanisms of action of megestrol acetate involve both behavioral and metabolic effects, and its impact on energy expenditure, appetite, body composition, endocrine function, and lipid metabolism is the subject of ongoing research.(ABSTRACT TRUNCATED AT 250 WORDS)
Olefin Metathesis with 1,1-Difluoroethylene (2001)

Die Synthese elektronisch ungesättigter Halogencarbenkomplexe ist das erste Beispiel für eine Olefinmetathese mit einem direkt fluorierten Substrat. Der Rutheniumkatalysator 1 reagiert mit 1,1-Difluorethylen unter Bildung des Methylidens [Ru]=CH2 2 und des Difluorcarbenkomplexes [Ru]=CF2 3. H2IMes=1,3-Dimesityl-4,5-dihydroimidazol-2-yliden; Cy=Cyclohexyl.
Electroplating of Cyclic Multilayered Alloy (CMA) Coatings (1983)

A new technique has been developed for producing laminated composites of cyclic multilayered alloy (CMA) electrodeposits. The thickness and composition of the individual layers of the CMA deposits are altered precisely and conveniently by cyclic modulation of the cathodic current or potential during electrodeposition. It is thus possible to modify the structure to obtain laminated composite coatings which may have desirable engineering properties. Wear and corrosion resistances, mechanical hardness and strength, as well as certain magnetic, optic, and electronic properties of the plated composite alloys should be, in principle, straightforward to design and fabricate. The CMA technique was demonstrated by plating a wide variety of Ag‐Pd CMA structures. Fine structures, with repeat distances as small as 0.05 μm, were obtained. Both square and triangular waveforms were applied to produce sharp or gradual composition variations, respectively. The resulting deposits were found to correspond closely to the intended structures with respect to thickness and composition, when the individual layers were thicker than about 1000Å. The amplitude of the composition modulation diminished rapidly for layer thicknesses below this limit. For the prospective application of Ag‐Pd alloys as a contact finish, CMA structures composed of relatively thin Pd‐rich layers alternating with thick Ag‐rich layers would offer the high corrosion resistance of Pd combined with the low electrical resistance and low cost of Ag. An initial comparison of the CMA deposits with uniform, d‐c plated, Ag‐Pd alloys did not show any clear difference in contact properties. However, both types of deposit proved satisfactory in the tests which were made.
Regulation of transcription of genes required for fatty acid transport and unsaturated fatty acid biosynthesis in Escherichiacoli by FadR (1993)

Fatty acid biosynthesis and fatty acid degradation in Escherichia coli are co-ordinately regulated at the level of transcription by the product of the fadR gene, FadR. In the present work we investigate FadR interaction with the fabA and fadL promoters. The FadR-responsive operator within fabA, OA, was localized to a region -47 to -31 base pairs relative to the start of transcription using DNase I protection studies. The promoter and untranslated leader within fadL had two binding sites for FadR, OL1 at -25 to -9 and OL2 at -1 to +16 relative to the start of transcription. The binding affinity of FadR for OA and OL1 or OL2 was lower than that for the single site within fadB (OB) as measured using protein-DNA gel retention assays. Overall, these experiments demonstrated that the affinity of FadR binding for DNA containing the fadB, fadL and fabA promoters was OB > OL1, OL2 > OA. We could not distinguish separate binding affinities for OL1 or OL2. We demonstrated repression of fadL transcription and activation of fabA transcription in vitro using run-off transcription assays containing purified FadR and RNA polymerase.
Genetic variation in arylN‐acetyltransferase results in significant differences in the pharmacokinetic and safety profiles of amifampridine (3,4‐diaminopyridine) phosphate (2014)

The clinical use of amifampridine phosphate for neuromuscular junction disorders is increasing. The metabolism of amifampridine occurs via polymorphic aryl N-acetyltransferase (NAT), yet its pharmacokinetic (PK) and safety profiles, as influenced by this enzyme system, have not been investigated. The objective of this study was to assess the effect of NAT phenotype and genotype on the PK and safety profiles of amifampridine in healthy volunteers (N = 26). A caffeine challenge test and NAT2 genotyping were used to delineate subjects into slow and fast acetylators for PK and tolerability assessment of single, escalating doses of amifampridine (up to 30 mg) and in multiple daily doses (20 mg QID) of amifampridine. The results showed that fast acetylator phenotypes displayed significantly lower C max, AUC, and shorter t 1/2 for amifampridine than slow acetylators. Plasma concentrations of the N-acetyl metabolite were approximately twofold higher in fast acetylators. Gender differences were not observed. Single doses of amifampridine demonstrated dose linear PKs. Amifampridine achieved steady state plasma levels within 1 day of dosing four times daily. No accumulation or time-dependent changes in amifampridine PK parameters occurred. Overall, slow acetylators reported 73 drug-related treatment-emergent adverse events versus 6 in fast acetylators. Variations in polymorphic NAT corresponding with fast and slow acetylator phenotypes significantly affects the PK and safety profiles of amifampridine.
Antiparallel Leucine Zipper-Directed Protein Reassembly:  Application to the Green Fluorescent Protein (2000)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTAntiparallel Leucine Zipper-Directed Protein Reassembly: Application to the Green Fluorescent ProteinIndraneel Ghosh, Andrew D. Hamilton, and Lynne ReganView Author Information Department of Chemistry Department of Molecular Biophysics and Biochemistry Yale University, New Haven, Connecticut 06520 Cite this: J. Am. Chem. Soc. 2000, 122, 23, 5658–5659Publication Date (Web):May 24, 2000Publication History Received20 December 1999Published online24 May 2000Published inissue 1 June 2000https://pubs.acs.org/doi/10.1021/ja994421whttps://doi.org/10.1021/ja994421wrapid-communicationACS PublicationsCopyright © 2000 American Chemical SocietyRequest reuse permissionsArticle Views11590Altmetric-Citations417LEARN 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:Dissection,Fluorescence,Imaging probes,Peptides and proteins Get e-Alerts
Evaluation of inherent gray‐level dynamic range in a digital image using the runs test and join‐count statistics (1993)

The dynamic range of the gray level of a digital image is limited by the noise it contains. Two statistical methods called "runs test" and "join-count statistic" are used to measure the noise level in a digital image. A residual image is formed by subtracting an original image from its smoothed version. Theoretically, the noise level in the residual image should be identical to that in the original image. The noise level is determined by examining each bit plane of the residual image individually starting from the least significant bit up to the bit plane whose statistic does not show a random pattern. Images from three digital modalities: computerized tomography, magnetic resonance, and computed radiography are used to evaluate the gray-level dynamic range. Both methods are easy to implement and fast to perform.
Distinct mechanisms may account for the growth-promoting activity of interleukin 3 on cells of lymphoid and myeloid origin. (1984)

We have investigated whether interleukin 3 (IL-3) supports the growth of cells of different lineages by the same mechanism(s). The experiments were carried out with Ea3 cells, a mouse pre-B cell line, and S-480-3 cells, a mouse basophil cell line, both of which are totally IL-3 dependent. We found that Ea3 lymphocytes but not S-480-3 basophils absorb partially purified IL-3. Both Ea3 and S-480-3 cells respond to IL-3 by increasing anaerobic glycolysis as determined by lactic acid production. S-480-3 cells responded to exogenous ATP by maintaining proliferation and reducing lactic acid production, but Ea3 lymphocytes are refractory to exogenous ATP. We conclude that there may be two distinct mechanisms by which cells respond to IL-3, indicated by early events concerning the binding of IL-3 and the effect of exogenous ATP on respiratory metabolism. One appears to be a ligand-receptor-mediated mechanism in lymphoid cells and the other to be a mechanism that is partially replaceable by exogenous ATP in nonlymphoid cells not associated with lymphoid-like receptors. Our findings may explain (i) the apparent variety of cell lineages promoted by IL-3 by a widely available mechanism that supports glycolysis and, therefore, enables both proliferation and possibly expression of binding sites for lineage specific differentiation factors and (ii) the existence of lymphocytes that express receptors specific for IL-3 and are inducible for other characteristics and functions in a regulated manner.