gebhart/patrepeval huggingface dataset:
Elucidation of the deficiency in two yeast coenzyme Q mutants. Characterization of the structural gene encoding hexaprenyl pyrophosphate synthetase. (1990)

The assembly of a polyisoprenoid side chain and its transfer to para-hydroxybenzoate are the first two steps of coenzyme Q biosynthesis. In yeast these reactions are catalyzed by hexaprenyl pyrophosphate synthetase and PHB:polyprenyltransferase, respectively. We have screened nine complementation groups of yeast coenzyme Q mutants for the activities of these two enzymes and found two strains deficient in either activity. The strain deficient in hexaprenyl pyrophosphate synthetase activity, C296-LH3, is complemented by the plasmid pG3/T1. When C296-LH3 was transformed with a shuttle vector containing a 2,187-base pair fragment from the genomic insert of pG3/T1, both glycerol growth and hexaprenyl pyrophosphate synthetase activity were restored. The activity of the latter enzyme was higher than that seen in wild-type yeast. The increase in activity could be attributed to a gene dosage effect of the multi-copy plasmid. A 1,419-base pair open reading frame encoding a 52,560-dalton protein was found on the genomic fragment. The size of the RNA transcript and the location of transcriptional initiation indicate that the entire open reading frame is contained within the mRNA. Comparison of the hexaprenyl pyrophosphate synthetase amino acid sequence with amino acid sequences from the related enzyme farnesyl pyrophosphate synthetase show the presence of three highly conserved domains. Within two of the domains is an aspartate-rich motif found invariantly in the amino acid sequences of farnesyl pyrophosphate synthetase from three species and the hexaprenyl pyrophosphate synthetase amino acid sequence reported here. These aspartic acid motifs may comprise binding sites for the allylic and homoallylic substrates. The hydrophobicity profiles of the hexaprenyl pyrophosphate synthetase sequence and the farnesyl pyrophosphate synthetase sequence from rat appear similar. Furthermore, the hydrophobicity correlation coefficient of the comparison of these two sequences indicate with a high degree of confidence (p less than 0.001) that the two proteins will fold into similar three-dimensional structures.
Use of statistical criteria for screening potential homologies in nucleic acid sequences (1984)

We proposed a simple formula to assess the statistical significance of homologous segments found in comparison of two nucleic acid sequences (Goad and Kanehisa, Nucleic Acids Res. 10, 247-263, 1982). This paper clarifies the basic assumptions of the formula and its reliability is examined by Monte Carlo calculations. The results were satisfactory for random sequences. The formula is a useful measure for screening potentially interesting homologies and it can be implemented in any search algorithms. Examples are given for the screening procedure in the graphic display version of the Goad-Kanehisa algorithm.
Temporal coupled-mode theory and the presence of non-orthogonal modes in lossless multimode cavities (2004)

We develop a general temporal coupled-mode theory for multimode optical resonators. This theory incorporates a formal description of a direct transmission pathway, and is therefore capable of describing Fano interference phenomena in multimode cavities. Using this theory, we prove a general criterion that governs the existence of nonorthogonal modes. The presence of nonorthogonal modes creates interesting transport properties which can not be obtained in normal resonator systems. We validate our theory by comparing its predictions with first-principles finite-difference time-domain simulations and obtaining excellent agreement between the two.
Picture coding: A review (1980)

This paper presents a review of techniques used for digital encoding of picture material. Statistical models of picture signals and elements of psychophysics relevant to picture coding are covered first, followed by a description of the coding techniques. Detailed examples of three typical systems, which combine some of the coding principles, are given. A bright future for new systems is forecasted based on emerging new concepts, technology of integrated circuits and the need to digitize in a variety of contexts.
Interference with Pseudomonas quinolone signal synthesis inhibits virulence factor expression by Pseudomonas aeruginosa (2001)

Pseudomonas aeruginosa is an opportunistic pathogen that controls numerous virulence factors through intercellular signals. This bacterium has two quorum-sensing systems (las and rhl), which act through the intercellular signals N-(3-oxododecanoyl)-l-homoserine lactone (3-oxo-C(12)-HSL) and N-butyryl-l-homoserine lactone (C(4)-HSL), respectively. P. aeruginosa also produces a third intercellular signal that is involved in virulence factor regulation. This signal, 2-heptyl-3-hydroxy-4-quinolone [referred to as the Pseudomonas quinolone signal (PQS)], is a secondary metabolite that is part of the P. aeruginosa quorum-sensing hierarchy. PQS can induce both lasB (encodes LasB elastase) and rhlI (encodes the C(4)-HSL synthase) in P. aeruginosa and is produced maximally during the late stationary phase of growth. Because PQS is an intercellular signal that is part of the quorum-sensing hierarchy and controls multiple virulence factors, we began basic studies designed to elucidate its biosynthetic pathway. First, we present data that strongly suggest that anthranilate is a precursor for PQS. P. aeruginosa converted radiolabeled anthranilate into radioactive PQS, which was bioactive. We also found that an anthranilate analog (methyl anthranilate) would inhibit the production of PQS. This analog was then shown to have a major negative effect on elastase production by P. aeruginosa. These data provide evidence that precursors of intercellular signals may provide viable targets for the development of therapeutic treatments that will reduce P. aeruginosa virulence.
Concerted elimination dynamics from highly excited states (1997)

Photoinduced molecular detachment has been investigated for methylene iodide (CH2I2) and several related compounds (CH2Br2, CH2Cl2 and CF2Br2). Multiphoton excitation of these molecules at 310 nm gives rise to halogens in the D′ state. Femtosecond pump-probe experiments on the dissociation of these compounds indicate that the process is extremely fast (<60 fs) and proceeds without an intermediate. In addition to the characteristic D′→A′ fluorescence at 342 nm, photodissociation of CH2I2 also produces several fluorescence bands in the 260–290 nm region. The CH2I2 transients show characteristic I2 vibrational coherence. Time resolved data collected by detection at 272 nm also demonstrate clear, fast decaying rotational anisotropy, analysis of which reveals a distribution of rather high rotational levels of I2. Based on analysis of the dissociation time, rotational anisotropy and vibrational coherence, and on the estimated partitioning of energy in the fragments, an I2 concerted molecular detachment mechanism has been proposed.
Ascidians: producers of amino acid-derived metabolites (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAscidians: producers of amino acid-derived metabolitesBradley S. DavidsonCite this: Chem. Rev. 1993, 93, 5, 1771–1791Publication Date (Print):July 1, 1993Publication History Published online1 May 2002Published inissue 1 July 1993https://pubs.acs.org/doi/10.1021/cr00021a006https://doi.org/10.1021/cr00021a006research-articleACS PublicationsRequest reuse permissionsArticle Views1240Altmetric-Citations310LEARN 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
Detection of angiotensin I and II in cultured rat cardiac myocytes and fibroblasts (1992)

Angiotensin II (ANG II) is a stimulus for positive chronotropic and inotropic effects, protein synthesis, and hypertrophic growth in cardiac tissue. These short- and long-term effects of ANG II are mediated through specific plasma membrane receptors. Indirect evidence suggests that ANG II synthesized in the myocardium may be important in regulating cardiac function. The cell types in the myocardium that produce components of the renin-angiotensin system have not been determined. In this study, we evaluated whether cultured cardiomyocytes and fibroblasts obtained from ventricles of neonatal rat hearts were capable of synthesizing ANG I and II. Both cardiomyocytes and fibroblasts were found to have immunofluorescent staining for ANG I, ANG II, and angiotensin-converting enzyme (ACE). The amounts of ANG I and II in cell extracts and conditioned media obtained from cardiomyocytes and fibroblasts were quantified by radioimmunoassay. The amounts of ANG I and II detected in cardiomyocyte cultures (1.48 x 10(6) cells/dish) were 32.2 +/- 16.2 (n = 4) and 6.2 +/- 2.9 (n = 4) ng/10(6) cells, respectively. The amounts of ANG I and II detected in the media conditioned by a 48-h exposure to cardiomyocytes were 5.2 +/- 1.2 (n = 3) and 2.1 +/- 1.2 (n = 3) ng/10(6) cells, respectively. The amounts of ANG I and II detected in fibroblast cultures (5.38 x 10(6) cells/dish) were 34.8 +/- 4.9 (n = 4) and 8.0 +/- 3.5 (n = 4) ng/10(6) cells, respectively. The amounts of ANG I and II obtained from media conditioned by a 48-h exposure to fibroblasts were 4.7 +/- 0.6 (n = 4) and 3.3 +/- 2.1 (n = 4) ng/10(6) cells, respectively. The identity of the radioimmunoassayable materials as ANG I and II peptides was confirmed in cardiomyocytes using an in vitro bioassay based on displacement of 125I-ANG II from receptor binding sites in cardiac membranes prepared from neonatal pig heart. Identification of ANG I and II and ACE in vitro in cultures of cardiac myocytes and fibroblasts supports the hypothesis that there is an intracardiac renin-angiotensin system that produces these peptides.
Intestinal colonization of neonatal animals by Campylobacter fetus subsp. jejuni (1981)

Neonatal mice (2.3 to 2.8 g) were inoculated intragastrically with different human isolates of Campylobacter fetus subsp. jejuni. At weekly intervals thereafter, mice were sacrificed and dilution plate counts were performed on segments of the gastrointestinal tract. Mice were uniformly colonized by some strains for 2 weeks, whereas other strains were being cleared at that time. One strain (BO216) persisted in some mice for 3 weeks. The greatest number of organisms (10(7)) was recovered from the cecum and large intestine. The small intestine had from 10(2) to 10(5) colony-forming units. Colonization of the stomach was not found consistently. One strain killed 13% of the infected mice. Deaths occurred between 1 and 5 days postinfection. Two other strains killed a smaller percentage of challenged animals, and two additional strains killed none. Retarded weight gain was noticed in some, but not all, of the infected mice. The intestines of neonatal rats and rabbits were colonized much the same as those of mice, whereas hamsters were resistant to colonization. Preweanling mice, up to about 6.5 to 7.0 g, could be colonized with C. fetus subsp. jejuni after intragastric challenge, but weanling mice of larger weight (9.8 g) and young adult mice (18.3 g) could not. Scanning electron photomicrographs of the lower ileum showed campylobacters in and below the dried mucous gel that lines the intestines. The use of this model for additional studies is discussed.
Expression and pharmacological characterization of the human M1 muscarinic receptor in Saccharomyces cerevisiae (1990)

The yeast S. cerevisiae has been examined as a heterologous host for the expression of mammalian neurotransmitter receptors which couple to guanine nucleotide regulatory (G) proteins. A cloned gene encoding the M1 subtype of human muscarinic receptor (HM1) was transformed into S. cerevisiae on a high copy plasmid under the control of the promoter for the yeast alcohol dehydrogenase (ADH) gene. Northern blotting demonstrated the presence of HM1 transcripts in transformants, and crude membranes prepared from these cells showed saturable binding of the muscarinic antagonist [3H]N-methyl scopolamine with a Kd of 179 pM and Bmax of 20 fmol/mg protein. Competition binding studies revealed pharmacological properties for these sites which were comparable to those reported for the M1 site in mammalian tissues. Yeast expressing HM1 did not exhibit high affinity agonist binding or cell-cycle arrest in the presence of muscarinic agonists, indicating that the mammalian receptor did not couple to the endogenous yeast G protein.
DRB1*0401-restricted human T cell clone specific for the major proinsulin73-90 epitope expresses a down-regulatory T helper 2 phenotype (2006)

Recently, we have identified proinsulin (P-Ins)(73-90) as an immunodominant T cell epitope of HLA-DRB1*0401 (DR4) subjects with beta-islet cell autoimmunity and of HLA-DR4/CD4 double-transgenic mice immunized with human P-Ins. We have compared the fine specificities of one human CD4 T cell clone and two mouse T cell hybridoma clones recognizing this epitope, and, although these three clones all recognized the same core region (LALEGSLQK), there were major differences in how they interacted with the peptide (p)/HLA complex, reflecting the fact that human P-Ins is a foreign antigen in the mouse and an autoantigen in the type 1 diabetes patient. The human T cell clone was forkhead transcription factor 3 (Foxp3)-positive, a marker for regulatory T cell lineages, and secreted predominantly IL-5, IL-10, and low levels of IFNgamma in response to P-Ins(73-90). This finding is compatible with the previously detected regulatory cytokine pattern in subjects with beta-cell autoimmunity. However, added N- or C-terminal amino acids drastically changed HLA and tetramer binding capacity as well as T cell reactivity and the cytokine phenotype of the P-Ins(73-90)-specific human CD4 T cell clone, suggesting a potential for this P-Ins epitope as a target for therapeutic intervention in HLA-DR4-positive humans with beta-islet cell autoimmunity or recent-onset type 1 diabetes.
Ondansetron and meperidine prevent postoperative shivering after general anesthesia. (2011)

Ondansetron can effectively reduce post operative shivering.
Mechanical Properties of Suture Materials In Vitro and after In Vivo Implantation in Horses (1992)

Tensile testing of reproducible loops of size 5 braided polyester, size 2 polyglycolic acid, size 2 monofilament nylon, and size 2 polydioxanone sutures was performed in vitro and after subcutaneous implantation in horses for 7, 14, and 28 days. Maximum breaking strength, energy absorption, and percentage elongation to breakage point were measured. Size 5 braided polyester had the highest maximum breaking strength and energy absorption over 28 days. Polydioxanone had better mechanical performance over 28 days than did polyglycolic acid. On day 28, none of these parameters was measurable in polyglycolic acid. Monofilament nylon had the lowest breaking strength of the three materials tested on day 28.
Epidermal growth factor receptors and adenylate cyclase activity in human thyroid tissues (1990)

Thyroid stimulating hormone (TSH) and epidermal growth factor (EGF) are growth factors for some thyroid cells in cultures. We have previously found more EGF receptors in neoplastic human thyroid tissues than in normal thyroid tissues. We have also found a higher TSH-stimulated adenylate cyclase (AC) activity in neoplastic human thyroid tissues than in normal thyroid tissues. To clarify the relationship between the effect of EGF and TSH on thyroid tissue, we measured the binding of EGF and TSH and the basal, TSH-stimulated and forskolin-stimulated adenylate cyclase activity in 49 normal, hyperplastic and neoplastic human thyroid tissues (5 normal, 2 Hashimoto thyroiditis, 5 Graves' disease, 14 multinodular goiters, 9 follicular adenomas, 5 follicular carcinomas, 8 papillary carcinomas, and 1 undifferentiated carcinoma). Specific binding of EGF and TSH were measured by radioreceptor assays using competitive inhibition of radio-labeled ligand by unlabeled ligand. Basal, maximally (300 mU/ml) TSH-stimulated, and maximally (100 mM) forskolin-stimulated adenylate cyclase activities were also measured in the same membrane particulate fractions from the thyroid tissues. We found: neoplastic thyroid tissues bind more labeled EGF than nonneoplastic thyroid tissues; follicular adenomas and carcinomas have higher EGF binding than other thyroid tissues; a weak but significant correlation between specific EGF binding and specific TSH binding, and between specific EGF binding and TSH-stimulated adenylate cyclase activity of the thyroid membrane preparations. These findings are consistent with the hypothesis that TSH stimulates an increase in thyroid EGF receptors by increasing intracellular cAMP.(ABSTRACT TRUNCATED AT 250 WORDS)
Atrial Flutter Mapping and Ablation I (1996)

Endocardial mapping has led to a detailed knowledge of reentry mechanisms in atrial flutter. Multipolar and deflecting tip catheters allow recording local electrograms from multiple areas of the right atrium, and from the coronary sinus. In common flutter, with the typical "sawtooth" pattern, there is circular activation of the right atrium in a "counterclockwise" direction, descending in the anterior and lateral walls, and ascending in the septum and posterior wall. Superior and inferior vena cava, linked by a "line" of functional block in the posterolateral wall, make the central obstacle for circular activation. The cranial and caudal turning points are the atrial "roof," and the isthmus between the inferior vena cava and the tricuspid valve. Complex conduction patterns, probably including slow conduction are detectable in the low septal area, around the coronary sinus. Atypical flutter, without the sharp negative deflections of common flutter, sometimes shows circular activation in the right atrium, rotating in the opposite direction of common flutter (clockwise). Other atypical flutters show no circular right atrial activation, and only partial data from coronary sinus activation, combined with the response to atrial stimulation (entrainment) allow the diagnosis of left atrial reentry, without a precise delimitation of the circuits. In patients having undergone cardiac surgery, atypical flutter may be based on reentry around surgical scars. To our knowledge, the mechanism of type II flutter has not been disclosed in humans.
Lentivector-mediated clonal tracking reveals intrinsic heterogeneity in the human hematopoietic stem cell compartment and culture-induced stem cell impairment (2003)

Knowledge of the composition and interrelationship of the various hematopoietic stem cells (HSCs) that comprise the human HSC pool and the consequence of culture on each class is required for effective therapies based on stem cells. Clonal tracking of retrovirally transduced HSCs in nonobese diabetic/severe combined immunodeficient (NOD/SCID) mice revealed heterogeneity in the repopulation capacity of SCID-repopulating cells (SRCs). However, it is impossible to establish whether HSC heterogeneity is intrinsic or whether the culture conditions required for retroviral transduction induce qualitative and quantitative alterations to SRCs. Here, we report establishment of a clonal tracking method that uses lentivectors to transduce HSCs with minimal manipulation during overnight culture without cytokine stimulation. By serial bone marrow (BM) sampling of mice receiving transplants, short-term SRCs (ST-SRCs) and long-term SRCs (LT-SRCs) were identified on the basis of repopulation dynamics demonstrating that their existence is not an experimental artifact but reflects the state of the HSC pool. However, 4 days of culture in conditions previously used for SRC retroviral transduction significantly reduced SRC number as assessed by clonal analysis. These studies provide a foundation to understand the molecular and cellular determinants of human HSC development and to develop therapies targeted to specific HSC classes.
Relationship of brain tryptophan and serotonin in improving cognitive performance in rats. (2006)

Brain function can be affected by the availability of dietary precursors of neurotransmitters. The diet induced increase in tryptophan (TRP) availability has been shown to increase brain serotonin synthesis and various related behaviors. Evidence shows that TRP and serotonin (5HT; 5 Hydroxytryptamine) play a significant role in memory function. Enhanced brain serotonin activity has been shown to improve cognitive performance in animals and human whereas decreasing brain 5HT levels by acute TRP depletion has been shown to impair cognition. A number of methods have been used for the assessment of memory in animals. In the present study, the radial arm maze and the passive avoidance was used for the assessment of memory in rats following long-term TRP administration. TRP at doses of 50 and 100 mg/kg body weight was orally administered for 6 weeks. The present study shows a significant improvement in memory of rats following both doses of tryptophan. Plasma TRP, brain TRP, 5HT and 5 hydroxy indol acetic acid (5HIAA) levels were increased significantly following administration of TRP. The results of the present study suggest that increase in brain 5HT metabolism following long term TRP administration may be involved in enhancement of memory.
Comparing Analysis Methods for Mutation-Accumulation Data (2004)

T HE genomic deleterious mutation rate (U) and the different algorithms to locate maxima (or minima) in the multidimensional parameter space. ML employs nudistribution of mutational effects for fitness, f(s), merical integration to compute likelihood of data as a are important parameters for several theoretical issues function of U and f(s) and combines grid searches with in evolution (Charlesworth and Charlesworth 1998), the simplex algorithm (Nelder and Mead 1965; Press and there has been much recent work on the problem et al. 1992) to attempt to locate the global maximum of their estimation. There are currently three statistical likelihood. Convergence is declared when the relative approaches to infer U and f(s) on the basis of the districhange in likelihood between successive iterations is bution of fitness estimates among inbred mutation acculess than a user-defined threshold. The algorithm is mulation (MA) lines maintained under relaxed selection: guaranteed to converge (although not necessarily to the minimum distance (MD; Garc a-Dorado 1997), tradiglobal maximum) and to produce parameter estimates tional maximum likelihood (ML; Keightley 1994), and