gebhart/patrepeval huggingface dataset:
Photoinduced electron transfer between cytochrome c peroxidase and yeast cytochrome c labeled at Cys 102 with (4-bromomethyl-4'-methylbipyridine)[bis(bipyridine)]ruthenium2+ (1991)

The synthesis of (4-bromomethyl-4'-methylbipyridine) [bis(bipyridine)]ruthenium(II) hexafluorophosphate is described. This new reagent was found to selectively label the single sulfhydryl group at Cys-102 on yeast iso-1-cytochrome c to form the (dimethylbipyridine-Cys-102-cytochrome c)[bis(bipyridine)]ruthenium derivative (Ru-102-cyt c). Excitation of Ru-102-cyt c with a short light flash resulted in formation of excited-state Ru(II*), which rapidly transferred an electron to the ferric heme group to form Fe(II). When the cytochrome c peroxidase compound I (CMPI) was present in the solution, electron transfer from photoreduced Fe(II) in Ru-102-cyt c to the radical site in CMPI was observed. At high ionic strength (100 mM sodium phosphate and 25 mM EDTA, pH 7), second-order kinetics were observed with a rate constant of (7.5 +/- 0.7) x 10(7) M-1 s-1. The second-order rate constant for native iso-1-cytochrome c was (6.7 +/- 0.7) x 10(7) M-1 s-1 under these conditions. The second-order rate constant for electron transfer from Ru-102-cyt c to the radical site in CMPI increased as the ionic strength was decreased, reaching a value of (4.8 +/- 0.5) x 10(8) M-1 s-1 in 40 mM EDTA, pH 7. At lower ionic strength, a complex was formed between Ru-102-cyt c and CMPI, and the rate for intracomplex electron transfer to the radical site was found to be greater than 50,000 s-1.(ABSTRACT TRUNCATED AT 250 WORDS)
Multiple features of the p59fyn src homology 4 domain define a motif for immune-receptor tyrosine-based activation motif (ITAM) binding and for plasma membrane localization. (1996)

The src family tyrosine kinase p59fyn binds to a signaling motif contained in subunits of the TCR known as the immune-receptor tyrosine-based activation motif (ITAM). This is a specific property of p59fyn because two related src family kinases, p60src and p56lck, do not bind to ITAMs. In this study, we identify the residues of p59fyn that are required for binding to ITAMs. We previously demonstrated that the first 10 residues of p59fyn direct its association with the ITAM. Because this region of src family kinases also directs their fatty acylation and membrane association (Resh, M.D. 1993, Biochim. Biophys. Acta 1155:307-322; Resh, M.D. 1994. Cell. 76:411-413), we determined whether fatty acylation and membrane association of p59fyn correlates with its ability to bind ITAMs. Four residues (Gly2, Cys3, Lys7, and Lys9) were required for efficient binding of p59fyn to the TCR. Interestingly, the same four residues are present in p56lyn, the other src family tyrosine kinase known to bind to the ITAM, suggesting that this set of residues constitutes an ITAM recognition motif. These residues were also required for efficient fatty acylation (myristoylation at Gly2 and palmitoylation at Cys3), and plasma membrane targeting of p59fyn. Thus, the signals that direct p59fyn fatty acylation and plasma membrane targeting also direct its specific ability to bind to TCR proteins.
Genetically Defined Therapy of Inherited Long-QT Syndrome (1996)

An increase in serum potassium corrects abnormalities of repolarization duration, T-wave morphology, QT/ RR slope, and QT dispersion in patients with chromosome 7-linked LQT.
Transcriptional regulation of genes for ornithine cycle enzymes (1995)

Research Article| December 15 1995 Transcriptional regulation of genes for ornithine cycle enzymes M Takiguchi; M Takiguchi 1Department of Molecular Genetics, Kumamoto University School of Medicine, Kuhonji 4-24-1, Kumamoto 862, Japan Search for other works by this author on: This Site PubMed Google Scholar M Mori M Mori 1Department of Molecular Genetics, Kumamoto University School of Medicine, Kuhonji 4-24-1, Kumamoto 862, Japan Search for other works by this author on: This Site PubMed Google Scholar Biochem J (1995) 312 (3): 649–659. https://doi.org/10.1042/bj3120649 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn MailTo Cite Icon Cite Get Permissions Citation M Takiguchi, M Mori; Transcriptional regulation of genes for ornithine cycle enzymes. Biochem J 15 December 1995; 312 (3): 649–659. doi: https://doi.org/10.1042/bj3120649 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAll JournalsBiochemical Journal Search Advanced Search This content is only available as a PDF. © 1995 The Biochemical Society, London1995 Article PDF first page preview Close Modal You do not currently have access to this content.
Evaluation of body composition and cartilage biomarkers in large-breed dogs fed two foods designed for growth (2010)

The BAP activity, osteocalcin concentration, and CTXII concentration were greater during growth than at 18 months of age. The food that was proportionately higher in protein, calcium, n-3 fatty acids, and antioxidants increased lean body mass and may have positively affected cartilage turnover as maturity was attained. Whether the rate of cartilage turnover during growth affects development of orthopedic disease or arthritis in adulthood has yet to be determined.
Solution Structure of Bovine Neutrophil .beta.-Defensin-12: The Peptide Fold of the .beta.-Defensins Is Identical to That of the Classical Defensins (1995)

The solution structure is reported for bovine neutrophil beta-defensin-12 (BNBD-12), a member of the beta-defensin family of antimicrobial peptides. Structural constraints in the form of proton-proton distances, dihedral angles, and hydrogen bond constraints were derived from two-dimensional, homonuclear magnetic resonance spectroscopy experiments. The three-dimensional structure of BNBD-12 was calculated using distance geometry and restrained molecular dynamics. An ensemble of structures with low NOE constraint violation energies revealed a precisely defined triple-stranded, antiparallel beta-sheet as the structural core of the peptide. The N-terminal beta-strand and three locally well-defined tight turns form a hydrophobic face. Conserved isoleucine and glycine residues form a beta-bulge structure which initiates a beta-hairpin secondary structure motif composed of the second and C-terminal beta-strands. The beta-hairpin contains numerous charged residues and forms the cationic face of BNBD-12. The N-terminal residues were found to be disordered, due to an absence of tertiary NOEs. The triple-stranded beta-sheet, the beta-bulge preceding the hairpin, and the cationic/hydrophobic amphiphilic character are definitive features of all defensin structures determined to date. Further, we predict that the tracheal antimicrobial peptide (TAP) and the recently described gallinacins will have tertiary structures similar to that of BNBD-12.
Anaerotruncus (2015)

Abstract An.ae.ro.trun'cus. Gr. pref. an without; Gr. masc. n. aer air; L. masc. n. truncus stick; N.L. masc. n. Anaerotruncus a stick that lives without air. Thin rod‐shaped cells . Gram positive and sporeforming. Strictly anaerobic and catalase negative . Glucose is fermented. End products of metabolism from peptone/yeast extract broth are acetic and butyric acids . Gelatin is not hydrolyzed. Urease negative. Nitrate is not reduced to nitrite. Indole positive. Based on 16S rRNA sequence and phylogenetic analysis, this genus belongs to the Clostridium leptum rRNA super cluster (Cluster IV). Isolated from human feces and blood. DNA G + C content ( mol %): 53–54. Type species : Anaerotruncus colihominis Lawson, Song, Liu, Molitoris, Vaisanen, Collins and Finegold 2004, 415 VP . Taxonomic and Nomenclature Notes According to the List of Prokaryotic names with Standing in Nomenclature (LPSN), the taxonomic status of the genus Anaerotruncus is: correct name (last update, February 2025) * . LPSN classification: Bacteria / Bacillati / Bacillota / Clostridia / Eubacteriales / Oscillospiraceae / Anaerotruncus The genus Anaerotruncus can also be recovered in the Genome Taxonomy Database (GTDB) as g__Anaerotruncus (version v220) ** . GTDB classification: d__Bacteria / p__Bacillota_A / c__Clostridia / o__Oscillospirales / f__Ruminococcaceae / g__Anaerotruncus * Meier‐Kolthoff et al. ( 2022 ). Nucleic Acids Res , 50 , D801 – D807 ; DOI: 10.1093/nar/gkab902 ** Parks et al. ( 2022 ). Nucleic Acids Res , 50 , D785 – D794 ; DOI: 10.1093/nar/gkab776
Aminozucker‐Synthesen, II. Benzyl‐2.6‐didesoxy‐2.6‐diamino‐α‐D‐glucosid (1961)

Abstract Ausgehend vom Benzyl‐ N ‐carbobenzoxy‐3.4‐diacetyl‐α‐ D ‐glucosaminuron‐säurenitril (II) konnte über mehrere Zwischenstufen das Benzyl‐2.6‐didesoxy‐2.6‐diamino‐α‐ D ‐glucosid (VII) als Bis‐hydrochlorid gewonnen werden. Sein Bis‐ N ‐carbobenzoxy‐(V) sowie sein Bis‐ N ‐benzoyl‐Derivat (VI) werden beschrieben.
Dependency parsing by belief propagation (2008)

We formulate dependency parsing as a graphical model with the novel ingredient of global constraints. We show how to apply loopy belief propagation (BP), a simple and effective tool for approximate learning and inference. As a parsing algorithm, BP is both asymptotically and empirically efficient. Even with second-order features or latent variables, which would make exact parsing considerably slower or NP-hard, BP needs only O(n3) time with a small constant factor. Furthermore, such features significantly improve parse accuracy over exact first-order methods. Incorporating additional features would increase the runtime additively rather than multiplicatively.
Privacy behaviors of lifeloggers using wearable cameras (2014)

A number of wearable 'lifelogging' camera devices have been released recently, allowing consumers to capture images and other sensor data continuously from a first-person perspective. Unlike traditional cameras that are used deliberately and sporadically, lifelogging devices are always 'on' and automatically capturing images. Such features may challenge users' (and bystanders') expectations about privacy and control of image gathering and dissemination. While lifelogging cameras are growing in popularity, little is known about privacy perceptions of these devices or what kinds of privacy challenges they are likely to create.
Multipitch estimation and sound separation by the spectral smoothness principle (2002)

A processing principle is proposed for finding the pitches and separating the spectra of concurrent musical sounds. The principle, spectral smoothness, is used in the human auditory system which separates sounds partly by assuming that the spectral envelopes of real sounds are continuous. Both theoretical and experimental evidence is presented for the vital importance of spectral smoothness in resolving sound mixtures. Three algorithms of varying complexity are described which successfully implement the new principle. In validation experiments, random pitch and sound source combinations were analyzed in a single time frame. The number of simultaneous sounds ranged from one to six, the database comprising sung vowels and 26 musical instruments. Usage of a specific yet straightforward smoothing operation corrected approximately half of the pitch errors that occurred in a system which was otherwise identical but did not use the smoothness principle. In random four-voice mixtures, pitch error rate reduced from 18 % to 8.1 %.
Sunlight Triggers Cutaneous Lupus through a CSF-1-Dependent Mechanism in MRL-Fas lpr Mice (2008)

Sunlight (UVB) triggers cutaneous lupus erythematosus (CLE) and systemic lupus through an unknown mechanism. We tested the hypothesis that UVB triggers CLE through a CSF-1-dependent, macrophage (Mø)-mediated mechanism in MRL-Fas(lpr) mice. By constructing mutant MRL-Fas(lpr) strains expressing varying levels of CSF-1 (high, intermediate, none), and use of an ex vivo gene transfer to deliver CSF-1 intradermally, we determined that CSF-1 induces CLE in lupus-susceptible MRL-Fas(lpr) mice, but not in lupus-resistant BALB/c mice. UVB incites an increase in Møs, apoptosis in the skin, and CLE in MRL-Fas(lpr), but not in CSF-1-deficient MRL-Fas(lpr) mice. Furthermore, UVB did not induce CLE in BALB/c mice. Probing further, UVB stimulates CSF-1 expression by keratinocytes leading to recruitment and activation of Møs that, in turn, release mediators, which induce apoptosis in keratinocytes. Thus, sunlight triggers a CSF-1-dependent, Mø-mediated destructive inflammation in the skin leading to CLE in lupus-susceptible MRL-Fas(lpr) but not lupus-resistant BALB/c mice. Taken together, CSF-1 is envisioned as the match and lupus susceptibility as the tinder leading to CLE.
Holographic refractive index detector for application in microchip-based separation systems (1998)

A novel detection scheme for capillary electrophoresis on planar glass microchips is presented. The application of a holographic-based refractive index detector to the electrophoretic separation of carbohydrates is described. The microchip device consists of a cyclic (square) separation channel having a circumference of 80 mm, a width of 40 µm and a depth of 10 µm. The volume of the injection scheme is approximately 16 pl. Separation and refractive index detection of a mixture of sucrose, N-acetylglucosamine and raffinose, each at a concentration of 33 mM, was achieved within 17 s of injection. Preliminary results demonstrate the feasibility of using hologram-based refractive index detectors in microchip separation systems. Although the initial detection limits are poor in comparison with alternative techniques, the potential of a universal detector of this kind is clear.
Counting Processes and Survival Analysis. (1992)

Preface. 0. The Applied Setting. 1. The Counting Process and Martingale Framework. 2. Local Square Integrable Martingales. 3. Finite Sample Moments and Large Sample Consistency of Tests and Estimators. 4. Censored Data Regression Models and Their Application. 5. Martingale Central Limit Theorem. 6. Large Sample results of the Kaplan-Meier Estimator. 7. Weighted Logrank Statistics. 8. Distribution Theory for Proportional Hazards Regression. Appendix A: Some Results from stieltjes Integration and Probability Theory. Appendix B: An Introduction to Weak convergence. Appendix C: The Martingale Central Limit Theorem: Some Preliminaries. Appendix D: Data. Appendix E: Exercises. Bibliography. Notation. Author Index. Subject Index.
Mapping tRNA structure in solution using double-strand-specific ribonuclease V1from cobra venom (1981)

A method for mapping all base-paired stems in both elongation and initiator tRNAs is described using double-strand-specific ribonuclease V 1 from the venom of the cobra Naja naja oxiana . 32 p-end-labeled RNA is first partially digested with double-strand-specific V 1 nuclease under near physiological conditions, and the resultant fragments are then electrophoretically fractionated by size in adjacent lanes of a polyacrylamide gel run in 90% formamide. After autoradiography, the base-paired nucleotides are definitively located by comparing V 1 generated bands with fragments of known length produced by both Neurospora endonuclease and base-specific ribonucleases. Using the substrates yeast tRNA Phe and E. coli tRNA Met of known three-dimensional structure, we find V 1 nuclease to cleave entirely within every base-paired stem. Our studies also reveal that nuclease V 1 will digest paired nucleotides not hydrogen-bonded by standard Watson-Crick base-pairing. In yeast tRNA Phe cleavage of both wobble base-pairs and nucleotides involved in tertiary base-base hydrogen bonding is demonstrated.
Effect of vitamin E and beta-carotene on DNA strand breakage induced by tobacco-specific nitrosamines and stimulated human phagocytes. (1997)

The tobacco-specific nitrosamines (TSNAs), nitrosonornicotine (NNN) and 4-(N-methyl-N-nitrosamino)-1-(3-pyridyl)-1-butanone (NNK), are metabolites of nicotine and are major carcinogens in cigarette smoke. Chronic inflammation may promote the carcinogenic effect of these nitrosamines through the generation of oxygen radicals. To evaluate the effect of oxygen radicals on TSNA-induced genetic damage, cultured human lung cells treated with NNN or NNK were exposed to stimulated human phagocytes and assayed for single-strand DNA breaks. TSNAs or stimulated phagocytes alone cause a significant increase in strand breakage which is augmented in an additive fashion when the two are combined. Pretreating the cells with vitamin E or beta carotene provided significant protection against the induction of DNA damage but vitamin E was significantly more effective than beta carotene. These data suggest a possible approach to the chemoprevention of tobacco-induced carcinogenesis.
Efficacy of Deuterium Oxide to Estimate Body Composition of Growing Swine (1983)

An experiment involving 73 pigs was conducted to evaluate the efficacy of the deuterium oxide (D2O) dilution procedure for in vivo estimation of body composition in swine. Pigs were infused with known quantities of D2O at 6.4 and 18 kg and then at approximately 18 kg increments to 145 kg body weight. Postinfusion blood D2O concentrations were partitioned into early- and total-equilibrating pools. Results from D2O analyses were compared with empty (ingesta-free) and total body water values obtained from chemical analysis of the ground animals. Both early- and total-equilibrating D2O pools seemed to be good estimators of empty body weight. Total body D2O space was similar to total body water at 6.4 kg, but consistently overestimated body water (averaged 20%) as the pigs attained heavier weights. Early- or total-body D2O pool measurements accurately predicted chemically determined components with residual coefficients of variation below 5% and R2 greater than or equal to .90. However, total body D2O space provided as accurate an estimate of empty body water as the early-pool technique and may be easier to use because catheterization of blood vessels is not required. The incorporation of live weight and sex in multiple regression equations did not improve the accuracy of empty body water prediction over that obtained from D2O measurements alone. A method to estimate total body composition (water, protein, fat, ash) from the total body D2O space measurements is presented.
Human gene therapy for melanoma: CT-guided interstitial injection. (1997)

CT provides a safe, accurate, and efficacious way to monitor and assess tumor progression and response, and it provides guidance for biopsies and intratumoral injections during gene therapy. Significant responses in injected tumors of six of the 10 patients in our study suggest that further clinical trials of this gene therapy are warranted.
Design and Analysis of a Flipping Controller for RHex (2003)

We report on the design and analysis of a controller that can achieve dynamical self-righting of our hexapedal robot, RHex.We present an empirically tuned controller that works reasonably well on indoor surfaces, using a hybrid energy pumping strategy to overcome torque limitations of its actuators.Subsequent modeling and analysis yields a new controller with a much wider domain of success as well as a preliminary understanding of the hybrid control strategy.Simulation results demonstrate the superiority of the improved control strategy relative to the first generation empirically designed controller.
Novel Method for Detection of β-Lactamases by Using a Chromogenic Cephalosporin Substrate (1972)

A new cephalosporin with a highly reactive beta-lactam ring was found to give an immediate color change in the presence of beta-lactamases from many bacteria, including staphylococci, Bacillus species, Enterobacteriaceae, and Pseudomonas. The reaction is confined to organisms producing beta-lactamases, but it is sufficiently sensitive to indicate the presence of this enzyme is small amounts in strains previously considered not to produce it. The compound has an unusual ultraviolet spectrum, and the color change can be followed quantitatively by measuring changes in absorption which occur in the 380- to 500-nm region, where cephalosporins normally have no absorption. The development of color is thought to be a consequence of the beta-lactam ring being unusually highly conjugated with the 3-substituent. Although in the bacteria only beta-lactamases produce this color change, it was found that serum and tissues from experimental animals also rapidly produced the colored breakdown product, which was then excreted in the urine. The mechanism of the mammalian breakdown was considered to be different from that found in bacteria.
The Oxysterol, 27-Hydroxycholesterol, Links Cholesterol Metabolism to Bone Homeostasis Through Its Actions on the Estrogen and Liver X Receptors (2011)

Osteoporosis and age-related bone loss are important public health concerns. Therefore, there is a high level of interest in the development of medical interventions and lifestyle changes that reduce the incidence of osteoporosis and age-related bone loss. Decreased bone mineral density is associated with high cholesterol, and patients on statins have increased bone mineral densities, strongly implicating cholesterol as a negative regulator of bone homeostasis. In this study, using both molecular and pharmacological approaches, we have been able to demonstrate that the primary cholesterol metabolite, 27-hydroxycholesterol, through its actions on both estrogen receptors and liver X receptors, decreases osteoblast differentiation and enhances osteoclastogenesis, resulting in increased bone resorbtion in mice. Induction of the short heterodimer partner protein by estrogens in osteoblasts can attenuate the liver X receptor-mediated actions of 27-hydroxycholesterol in bone. These data establish a mechanistic link between cholesterol and bone quality, highlight an unexpected target of estrogens in osteoblasts, and define a signaling axis, the therapeutic exploitation of which is likely to yield novel antiosteoporotic drugs.
Repeated Thoracic Discharges From a Stun Device (2007)

Although significant changes in some parameters were seen, these changes were small and of little clinical significance. Lengthy EMI exposures did not cause extreme acidosis or cardiac arrhythmias. These findings may differ from those seen with other EMI devices because of the unique MK63 waveform characteristics or to specific characteristics of the model systems.
Down-regulation of HER2/neu expression induces apoptosis in human cancer cells that overexpress HER2/neu. (2000)

The HER2/neu oncogene is overexpressed in a significant fraction of human tumors; such overexpression is thought to play a role in the aberrant proliferation of cancer cells. The effects of HER2/neu-specific phosphorothioate antisense oligodeoxyribonucleotides on HER2/neu expression, tumor cell proliferation, and activation of apoptotic cell death pathways have been examined. Antisense treatment down-regulates HER2/neu expression in a dose-dependent and sequence-specific manner. HER2/neu antisense treatment specifically inhibits the growth of tumor lines that overexpress HER2/neu, but it has little effect on the growth of tumor cells that express low levels of HER2/neu. Down-regulation of HER2/neu expression is not only cytostatic, but it also results in the activation of apoptotic cell death pathways in cells that overexpress HER2/neu. These results suggest that, in addition to stimulating tumor cell proliferation, HER2/neu overexpression in cancer cells acts as an antiapoptotic cell survival factor.
Codon usage tabulated from the international DNA sequence databases; its status 1999 (1999)

Frequencies for each of the 206 526 complete protein-coding genes (CDS's) have been compiled from taxonomical divisions of the GenBank DNA sequence database. The sum of the codon use of 7434 organisms has also been calculated. These data files can be obtained from anonymous ftp sites of DDBJ, DISC and EBI. The list of the codon usage of genes in an organism as well as the sum of the codon usage of the organism was made searchable by the name of organism through a web site http://www.dna.affrc.go.jp//CUTG.html