gebhart/patrepeval huggingface dataset:
Enzymatic reduction of benzoyl‐CoA to alicyclic compounds, a key reaction in anaerobic aromatic metabolism (1992)

Different anaerobic bacteria can oxidize a variety of aromatic compounds completely to CO2 via one common aromatic intermediate, benzoyl-CoA. It has been postulated that anaerobically the aromatic nucleus of benzoyl-CoA becomes reduced. An oxygen-sensitive enzyme system is described catalyzing the reduction of benzoyl-CoA to trans-2-hydroxycyclohexanecarboxyl-CoA in a denitrifying Pseudomonas species grown anaerobically on benzoate plus nitrate. The assay mixture consists of cell extract, [U-14C]benzoyl-CoA, a [U-14C]benzoyl-CoA-generating system (consisting of [U-14C]benzoate, purified benzoate-CoA ligase, Mg(2+)-ATP, coenzyme A), an ATP-regenerating system (consisting of phosphoenolpyruvate, pyruvate kinase, myokinase), and a low-potential reductant [titanium(III) citrate]. The optimal pH is about 7, the specific activity 10 nmol benzoyl-CoA reduced min-1 x mg-1 protein. The apparent Km for benzoyl-CoA is below 50 microM. Five major products were found. One product is cyclohex-1-enecarboxyl-CoA which must have been formed by a benzoyl-CoA reductase. The other product is probably trans-2-hydroxycyclohexanecarboxyl-CoA rather than the cis-stereoisomer; this product must have been formed by a cyclohex-1-enecarboxyl-CoA hydratase. Two other products are likely to be intermediates of benzoyl-CoA reduction to cyclohex-1-enecarboxyl-CoA, suggesting that the reduction reaction is more complex. An early formed fifth product is more polar than cyclohexanecarboxyl- or cyclohex-1-enecarboxyl-CoA. The enzyme system is under oxygen control since it was not found in cells grown aerobically on benzoate. It is induced by aromatic compounds since its activity is low in cells grown anaerobically on acetate. The actual inducer is probably benzoyl-CoA rather than benzoate. This conclusion is drawn from the fact that the system is also present in cells grown anaerobically on phenol, phenylacetate, 4-hydroxybenzoate, or 2-aminobenzoate; the anaerobic metabolism of these compounds has been shown in this organism to proceed directly via benzoyl-CoA rather than via free benzoate.
Phylogenetic Analyses of a New Group of Denitrifiers Capable of Anaerobic Growth on Toluene and Description of Azoarcus tolulyticus sp. nov. (1995)

To understand the phylogeny and taxonomy of eight new toluene-degrading denitrifying isolates, we performed a 16S rRNA sequence analysis and a gas chromatographic analysis of their cellular fatty acids and examined some of their biochemical and physiological features. These isolates had 16s rRNA sequence signatures identical to those of members of the beta subclass of the Proteobacteria. The levels of similarity were as follows: 97.9 to 99.9% among the new isolates; 91.2 to 92.4% between the new isolates and Azoarcus sp. strain S5b2; 95.3 to 96.2% between the new isolates and Azoarcus sp. strain BH72; and 94.8 to 95.3% between the new isolates and Azoarcus indigens VB32T (T = type strain). Phylogenetic trees constructed by using the distance matrix, maximum-parsimony, and maximum-likelihood methods showed that our eight denitrifying isolates form a phylogenetically coherent cluster which represents a sister lineage of the previously described Azoarcus species. Furthermore, the fatty acid profiles, the cell morphology, and several physiological and nutritional characteristics of the eight isolates and the previously described members of the genus Azoarcus were also similar. In contrast to the previously described members of the genus Azoarcus, the eight new isolates were capable of degrading toluene under denitrifying conditions. We concluded that these toluene-degrading denitrifiers are members of a new species of the novel nitrogen-fixing genus Azoarcus. We propose the name Azoarcus tolulyticus for these toluene-degrading denitrifying isolates and designate strain Tol-4 the type strain.
Self-Oscillating Gel (1996)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTSelf-Oscillating GelRyo Yoshida, Toshikazu Takahashi, Tomohiko Yamaguchi, and Hisao IchijoView Author Information National Institute of Materials and Chemical Research, 1-1, Higashi Tsukuba, Ibaraki 305, JapanCite this: J. Am. Chem. Soc. 1996, 118, 21, 5134–5135Publication Date (Web):May 29, 1996Publication History Received24 January 1996Published online29 May 1996Published inissue 1 January 1996https://pubs.acs.org/doi/10.1021/ja9602511https://doi.org/10.1021/ja9602511rapid-communicationACS PublicationsCopyright © 1996 American Chemical SocietyRequest reuse permissionsArticle Views6225Altmetric-Citations602LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Absorption,Oscillation,Phase transitions,Polymers,Redox reactions Get e-Alerts
Monitoring guidance for patients with hypophosphatasia treated with asfotase alfa (2017)

Hypophosphatasia (HPP) is a rare, inherited, systemic, metabolic disorder caused by autosomal recessive mutations or a single dominant-negative mutation in the gene encoding tissue-nonspecific alkaline phosphatase (TNSALP). The disease is associated with a broad range of signs, symptoms, and complications, including impaired skeletal mineralization, altered calcium and phosphate metabolism, recurrent fractures, pain, respiratory problems, impaired growth and mobility, premature tooth loss, developmental delay, and seizures. Asfotase alfa is a human, recombinant enzyme replacement therapy that is approved in many countries for the treatment of patients with HPP. To address the unmet need for guidance in the monitoring of patients receiving asfotase alfa, an international panel of physicians with experience in diagnosing and managing HPP convened in May 2016 to discuss treatment monitoring parameters. The panel discussions focused on recommendations for assessing and monitoring patients after the decision to treat with asfotase alfa had been made and did not include recommendations for whom to treat. Based on the consensus of panel members, this review provides guidance on the monitoring of patients with HPP during treatment with asfotase alfa, including recommendations for laboratory, efficacy, and safety assessments and the frequency with which these should be performed during the course of treatment. Recommended assessments are based on patient age and include regular monitoring of biochemistry, skeletal radiographs, respiratory function, growth, pain, mobility and motor function, and quality of life. Because of the systemic presentation of HPP, a coordinated, multidisciplinary, team-based, patient-focused approach is recommended in the management of patients receiving asfotase alfa. Monitoring of efficacy and safety outcomes must be tailored to the individual patient, depending on medical history, clinical manifestations, availability of resources in the clinical setting, and the clinician's professional judgment.
Conversation system for natural communication with robot partner (2014)

This paper proposes a conversation system for verbal communication between a human and a robot partner. The system has three main components. In the first one, the conversation system uses the relationship between utterance sentences and perceptual information. Additionally, human utterance patterns are also used to realize a scenario-like conversation. Similarity information between verbs and adjectives of different sentences are also utilized. The second component is the sentence building module which is based on predefined set of rules. Therefore, the robot can also respond using sentence creation. In the third module, the robot can select sentence based on time dependent information. We show experimental results of the proposed method using a real robot partner.
Bivalent Cholesterol-Based Coupling of Oligonucletides to Lipid Membrane Assemblies (2004)

By mimicking Nature's way of utilizing multivalent interactions, we introduce in the present work a novel method to improve the strength of cholesterol-based DNA coupling to lipid membranes. The bivalent coupling of DNA was accomplished by hybridization between a 15-mer DNA and a 30-mer DNA, being modified with cholesterol in the 3' and 5' end, respectively. Compared with DNA modified with one cholesterol moiety only, the binding strength to lipid membranes appears to be significantly stronger and even irreversible over the time scale investigated ( approximately 1 hr). First, this means that the bivalent coupling can be used to precisely control the number of DNA per lipid-membrane area. Second, the strong coupling is demonstrated to facilitate DNA-hybridization kinetics studies. Third, exchange of DNA between differently DNA-modified vesicles was demonstrated to be significantly reduced. The latter condition was verified via site-selective and sequence-specific sorting of differently DNA-modified lipid vesicles on a low-density cDNA array. This means of spatially control the location of different types of lipid vesicles is likely to find important applications in relation to the rapid progress currently made in the protein chip technology and the emerging need for efficient ways to develop membrane protein arrays.
Yield-reliability modeling for fault tolerant integrated circuits (2002)

An integrated yield-reliability model for defect tolerant integrated circuits is presented that allows one to estimate the yield following both wafer probe and burn-in testing. The model is based on the long observed clustering of defects and the experimentally verified relation between defects causing wafer probe failures and defects causing infant mortality failures. The two-parameter negative binomial distribution is used to describe the distribution of defects over a semiconductor wafer. The clustering parameter /spl alpha/, while known to play a key role in accurately determining wafer probe yields of defect tolerant chips, is shown for the first time. to play a similar role in determining burn-in fall-out. Numerical results indicate that the number of infant mortality failures predicted by the clustering model can differ significantly from calculations that ignore clustering.
High level expression of soluble glycoproteins in the allantoic fluid of embryonated chicken eggs using a Sendai virus minigenome system (2007)

The simplicity and economy of the Sendai minigenome system, together with the high yield achieved in the allantoic fluid of eggs, makes it an attractive method to express soluble glycoproteins aimed for structural studies.
A Ca(2+)-independent protein kinase C from fission yeast. (1993)

A protein kinase C homologue of Schizosaccharomyces pombe, pkc1+, was isolated from a genomic library by screening with the Saccharomyces cerevisiae PKC1 probe. From its primary sequence and biochemical properties, we conclude that S. pombe pkc1+ encodes a phospholipid-activated Ca(2+)-independent protein kinase, homologous to the delta/epsilon classes of mammalian protein kinase C. Gene disruption experiments show that pkc1+ is not essential for cell viability; however, overexpression of the protein leads to an abnormal cell morphology and a block in cell separation following mitosis suggestive of a role in cell division. In vitro phosphorylation experiments reveal several potential pkc1+ substrates.
Nalmefene: Intravenous safety and kinetics of a new opioid antagonist (1986)

In a placebo-controlled, double-blind study we evaluated the safety and kinetics of a new narcotic antagonist, nalmefene, after 2, 6, 12, and 24 mg intravenous doses to healthy men. At each dose level four subjects received active drug and two received placebo. The drug was well tolerated at all dose levels with only mild and transient side effects, the most common of which was lightheadedness. The plasma concentration-time data were best fit with a triexponential equation, and the terminal elimination phase had a harmonic mean t1/2 of 8 to 9 hours. Only about 5% of the dose was excreted in the urine as intact nalmefene, with up to 60% excreted as nalmefene glucuronide. Although intersubject differences were noted, mean or dose-normalized mean kinetic parameters such as clearance, steady-state volume of distribution, terminal t1/2, and AUC showed no consistent trends related to increasing doses, indicating that nalmefene has linear pharmacokinetics.
Statistical characterization of fiber random birefringence (2000)

The statistical properties of the random birefringence that affects long single-mode fibers are experimentally evaluated by means of a polarization-sensitive optical time-domain reflectometry. The measurements are in good agreement with theoretical predictions and show, for what we believe is the first time, that the components of the local birefringence vector are Gaussian random variables.
Some novel, acid-labile amine protecting groups (1977)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSome novel, acid-labile amine protecting groupsStephen F. Brady, Ralph Hirschmann, and Daniel F. VeberCite this: J. Org. Chem. 1977, 42, 1, 143–146Publication Date (Print):January 1, 1977Publication History Published online1 May 2002Published inissue 1 January 1977https://pubs.acs.org/doi/10.1021/jo00421a030https://doi.org/10.1021/jo00421a030research-articleACS PublicationsRequest reuse permissionsArticle Views862Altmetric-Citations20LEARN 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
Polymeric implants for cancer chemotherapy (1997)

Cancer chemotherapy is not always effective. Difficulties in drug delivery to the tumor, drug toxicity to normal tissues, and drug stability in the body contribute to this problem. Polymeric materials provide an alternate means for delivering chemotherapeutic agents. When anticancer drugs are encapsulated in polymers, they can be protected from degradation. Implanted polymeric pellets or injected microspheres localize therapy to specific anatomic sites, providing a continuous sustained release of anticancer drugs while minimizing systemic exposure. In certain cases, polymeric microspheres delivered intravascularly can be targeted to specific organs or tumors. This article reviews the principles of chemotherapy using polymer implants and injectable microspheres, and summarizes recent preclinical and clinical studies of this new technology for treating cancer.
The neuron in tissue culture (1999)

KEYNOTE CHAPTERS The Neural Crest Colony Assay: Assessing Molecular Influences on Development in Culture (M. Sieber-Blum) In Vitro Analysis of Neuronal Progenitor Cells from Mouse Olfactory Epithelium (A. Calof, et al.) Analysis of Lineage-Dependent Phenotype Using Retroviral Transduction Techniques in Neural Progenitor Cells (G. Foster & B. Stringer) In Vitro Analysis of Signal Mechanisms Involved in Neuronal Migration (H. Komuro & P. Rakic) Regeneration of Adult Dorsal Root Ganglion Axons in Explant Culture (M. Kasper, et al.) Calcium Homeostasis and Mechanisms of Growth Cone Formation During Neuritogenesis in Cultured Aplysia Neurons (M. Spira, et al.) Mechanical Stimulation of Neurite Assembly in Cultured Neurons (S. Heidemann, et al.) Modulation of Functional Synaptogenesis In Vitro Studied Using Two-Compartment Culture Chambers (P. Nelson, et al.) Morphological and Functional Properties of Embryonic Rat Brainstem Motor Neurons in Organotypic Co-Culture with Tongue Muscle (J. Gueritaud & N. Ferrand) Modulation of Single Developing Synapses Between Neurons and Myocytes of Xenopus Embryos In Vitro (X.-H. Wang & M.-M. Poo) Analysis of Enteric Neural Circuits in Organ Culture of Adult Guinea-Pig (Z.-M. Song, et al.) Role of Cajal-Retzius Cells in the Formation of Neuronal Connections in Entorhinohippocampal Organotypic Slice Cultures (J. Del Rio, et al.) Establishment of Kitten Retinogeniculate Connections in Organotypic Co-Cultures (W. Guido & R. Erzurumlu) Neuroanatomical and Physiological Changes of Avian Forebrain Regions Involved in Acoustic Imprinting in Roller Tube Co-Culture (H. Endepols and K. Braum) High Spatial Resolution Imaging of the Excitation of Single Neurons in Culture (S. Tyc-Dumont & P. Gogan) Interactions Between Peripheral Nerve Axons and Schwann Cells in Myelin-Forming Co-Cultures: Dynamics and Sodium Channel Distribution (S. Marshall & K. Angelides) Fast Imaging of Subcellular Calcium Transients in Dendritic Spines of Cultured Hippocampal Neurons (M. Segal, et al.) Physiology of Mature Crustacean Neurosecretory Neurons in Culture (I. Cooke) Physiology of Identified Neurons from the Cockroach Meso- and Metathoracic Ganglia (E. Howes & P. Smith) Viral Infection Studies in Adult Sensory Neurons (J. Castellanos & H. Hurtado) Use of Spheroid Reaggregate Cultures for In Vitro Study of Brain Pathogenesis (R. Fox & C. Atterwill) Brain Neuropathology in Co-Cultures of Central Nervous System Tissue with Monocytes (K. Dzenko, et al.) PROTOCOLS FOR TISSUE AND CELL CULTURE Nerve Cell Culture Methodology: The Medium Environment (G. Rebel, et al.) Neuronal Apoptosis (M. Mattson, et al.) Use of ECM Proteins to Optimize Neuronal Cell Function In Vitro (A. Goldberger & P. Flaherty) Cell Culture of Neurons of the Peripheral Nervous System of Birds and Mammals (M. Welch, et al.) Cell Culture of Neurons of the Fetal, Neonatal and Adult Central Nervous System of Birds and Mammals (V. Wong, et al.) ...
Fluid Manipulation by Bio-Mimetic Cilia (2007)

This paper describes the fabrication and actuation of bio-mimetic cilia for fluid manipulation. High aspect ratio cilia made of polydimethylsiloxane (PDMS) were successfully assembled in a microfluidic device by our novel fabrication method. This method was to release the PDMS cilia from a Si mold and assemble the cilia in a device. All the process was performed under water in order to avoid the stiction and pairing of the PDMS cilia. The underwater assembly method enabled a high aspect ratio PDMS structure assembly in a fluidic device. The PDMS cilia were actuated in air and water by lead-zirconate-titanate (PZT) microstage. In the fabricated device, the maximum displacement of the cilia was observed at 120Hz in air and at 50Hz in de-ionized (DI) water with our experimental condition. The actuated cilia in a solution produced convective and propulsive fluid flow near the cilia structure. The developed device can be used for precise handling of small volume sample (e.g., 1 μL).
Distinguish protein decoys by Using a scoring function based on a new AMBER force field, short molecular dynamics simulations, and the generalized born solvent model (2004)

Recent works have shown the ability of physics-based potentials (e.g., CHARMM and OPLS-AA) and energy minimization to differentiate the native protein structures from large ensemble of non-native structures. In this study, we extended previous work by other authors and developed an energy scoring function using a new set of AMBER parameters (also recently developed in our laboratory) in conjunction with molecular dynamics and the Generalized Born solvent model. We evaluated the performance of our new scoring function by examining its ability to distinguish between the native and decoy protein structures. Here we present a systematic comparison of our results with those obtained with use of other physics-based potentials by previous authors. A total of 7 decoy sets, 117 protein sequences, and more than 41,000 structures were evaluated. The results of our study showed that our new scoring function represents a significant improvement over previously published physics-based scoring functions.
Measuring Influenza Neuraminidase Inhibition Antibody Titers by Enzyme-linked Lectin Assay (2016)

Antibodies to neuraminidase (NA), the second most abundant surface protein on influenza virus, contribute toward protection against influenza. Traditional methods to measure NA inhibiting (NI) antibody titers are not practical for routine serology. This protocol describes the enzyme-linked lectin assay (ELLA), a practical alternative method to measure NI titers that is performed in 96 well plates coated with a large glycoprotein substrate, fetuin. NA cleaves terminal sialic acids from fetuin, exposing the penultimate sugar, galactose. Peanut agglutinin (PNA) is a lectin with specificity for galactose and therefore the extent of desialylation can be quantified using a PNA-horseradish peroxidase conjugate, followed by addition of a chromogenic peroxidase substrate. The optical density that is measured is proportional to NA activity. To measure NI antibody titers, serial dilutions of sera are incubated at 37 °C O/N on fetuin-coated plates with a fixed amount of NA. The reciprocal of the highest serum dilution that results in ≥50% inhibition of NA activity is designated as the NI antibody titer. The ELLA provides a practical format for routine evaluation of human antibody responses following influenza infection or vaccination.
An Aberrant Transcription Factor Network Essential for Wnt Signaling and Stem Cell Maintenance in Glioblastoma (2013)

Glioblastoma (GBM) is thought to be driven by a subpopulation of cancer stem cells (CSCs) that self-renew and recapitulate tumor heterogeneity yet remain poorly understood. Here, we present a comparative analysis of chromatin state in GBM CSCs that reveals widespread activation of genes normally held in check by Polycomb repressors. These activated targets include a large set of developmental transcription factors (TFs) whose coordinated activation is unique to the CSCs. We demonstrate that a critical factor in the set, ASCL1, activates Wnt signaling by repressing the negative regulator DKK1. We show that ASCL1 is essential for the maintenance and in vivo tumorigenicity of GBM CSCs. Genome-wide binding profiles for ASCL1 and the Wnt effector LEF-1 provide mechanistic insight and suggest widespread interactions between the TF module and the signaling pathway. Our findings demonstrate regulatory connections among ASCL1, Wnt signaling, and collaborating TFs that are essential for the maintenance and tumorigenicity of GBM CSCs.