gebhart/patrepeval huggingface dataset:
Engineering Clostridium Strain to Accept Unmethylated DNA (2010)

It is difficult to genetically manipulate the medically and biotechnologically important genus Clostridium due to the existence of the restriction and modification (RM) systems. We identified and engineered the RM system of a model clostridial species, C. acetobutylicum, with the aim to allow the host to accept the unmethylated DNA efficiently. A gene CAC1502 putatively encoding the type II restriction endonuclease Cac824I was identified from the genome of C. acetobutylicum DSM1731, and disrupted using the ClosTron system based on group II intron insertion. The resulting strain SMB009 lost the type II restriction endonuclease activity, and can be transformed with unmethylated DNA as efficiently as with methylated DNA. The strategy reported here makes it easy to genetically modify the clostridial species using unmethylated DNA, which will help to advance the understanding of the clostridial physiology from the molecular level.
Stable Isotope Probing with <sup>15</sup> N Achieved by Disentangling the Effects of Genome G+C Content and Isotope Enrichment on DNA Density (2007)

Stable isotope probing (SIP) of nucleic acids is a powerful tool that can identify the functional capabilities of noncultivated microorganisms as they occur in microbial communities. While it has been suggested previously that nucleic acid SIP can be performed with 15N, nearly all applications of this technique to date have used 13C. Successful application of SIP using 15N-DNA (15N-DNA-SIP) has been limited, because the maximum shift in buoyant density that can be achieved in CsCl gradients is approximately 0.016 g ml-1 for 15N-labeled DNA, relative to 0.036 g ml-1 for 13C-labeled DNA. In contrast, variation in genome G+C content between microorganisms can result in DNA samples that vary in buoyant density by as much as 0.05 g ml-1. Thus, natural variation in genome G+C content in complex communities prevents the effective separation of 15N-labeled DNA from unlabeled DNA. We describe a method which disentangles the effects of isotope incorporation and genome G+C content on DNA buoyant density and makes it possible to isolate 15N-labeled DNA from heterogeneous mixtures of DNA. This method relies on recovery of "heavy" DNA from primary CsCl density gradients followed by purification of 15N-labeled DNA from unlabeled high-G+C-content DNA in secondary CsCl density gradients containing bis-benzimide. This technique, by providing a means to enhance separation of isotopically labeled DNA from unlabeled DNA, makes it possible to use 15N-labeled compounds effectively in DNA-SIP experiments and also will be effective for removing unlabeled DNA from isotopically labeled DNA in 13C-DNA-SIP applications.
Theory of Field-Programmed Field-Flow Fractionation with Corrections for Steric Effects (1994)

This paper deals with the principal perturbation to ideal normal-mode elution of particles in field-flow fractionation (FFF). This perturbation is due to the finite size of particles undergoing migration in the FFF channel. The effects of a first-order correction for particle size are examined. Equations are derived for retention time, fractionating power, and steric inversion diameter for operation at constant field strength, as well as under conditions of both exponential and power programmed field decay. Useful limiting equations for fractionating power are derived and their validity is confirmed for typical experimental conditions. The derived equations are necessary for the future development of a systematic optimization strategy for the selection of operating conditions for particle size analysis by FFF. Calculations confirm our previous conclusion that the fractionating power for exponential field programming varies strongly with particle size; this variation is only slightly reduced by steric perturbations. The uniform fractionating power of power programming is slightly disturbed by steric effects although fractionating power remains much more uniform than for exponential programming. It is shown that a higher uniformity in fractionating power can be gained by manipulating the parameters of power programming but that no improvement is possible with exponential programming. Phenomena giving rise to higher order perturbations and to secondary relaxation are discussed and the conditions identified under which these effects are minimized.
Atmospheric Residues of Kuwait Heavy Crude Upgrading: A Pilot Plant and Model Simulation Study (2009)

Atmospheric residue hydrodesufurization (ARDS) is an important hydroprocessing unit in Kuwait refineries to upgrade heavy residues into more valuable and environmental friendly products. To enhance the process cost-effectiveness, it is important to understand the interaction between the catalyst system, process operation conditions, and feedstock properties and the effects on the unit performance. This requires extensive programs of pilot plant work, which is very costly. To minimize the costs, efforts, and time required for experimental work, mathematical modeling is a powerful tool to assist in achieving such targets. Performance life study of an industrial ARDS catalyst system identified as the CAT-B system, which contains five different catalysts, is studied using a downflow pilot plant unit. The feedstock used was the atmospheric residue of Kuwait Heavy Crude (KHC-AR) from the blending of Ratawi/Burgan heavy oils. A portion of the pilot plant data of the life test is used in the parameter estimation for the developed model before model prediction is performed. Model simulation is then applied to predict the performance of the pilot plant life test with KHC-AR as the feedstock. Some discrepancies are found between model predictions and pilot plant life test results. These discrepancies may be attributed to the changes in the activities of the HDM catalysts used in CAT-B.
The mechanism of gold deposition by thermal evaporation (2000)

The charged cluster model states that chemical vapor deposition (CVD) begins with gas phase nucleation of charged clusters followed by cluster deposition on a substrate surface to form a thin film. A two-chambered system, separated by a 1-mm orifice, was used to study gold deposition by thermal evaporation in order to determine if the CCM applies in this case. At a filament temperature of 1523 and 1773 K, the presence of nano-meter sized gold clusters was confirmed by transmission electron microscopy (TEM). The charge on the primary clusters was found to be positive and the cluster size and size distribution increased with increasing temperature. Small clusters were found to be amorphous and they combined with clusters already deposited on a substrate surface to form larger amorphous clusters on the surface. This work revealed that gold thin films deposited on a mica surface are the result of the sticking of 4-10 nm clusters. The topography of these films was similar to those reported previously under similar conditions.
Restoration of Lateral Hand Grasp Using Natural Sensors (1997)

A closed-loop control system for controlling the key grip of a C6 tetraplegic patient was developed. Natural sensors served as the source of the feedback signal. The neural signals from cutaneous receptors were picked up by an implanted cuff electrode placed around the radial branch of the median nerve innervating the lateral part of the index finger. Mechanical stress applied to the skin, like pressure and slips, resulted in an increase in amplitude of the recorded neural signal. The goal of the study was to determine whether the recorded neural signals were able to indicate the slip of an object during lateral grasp and whether the slip could be stopped by increasing the grasp force through functional electrical stimulation of the thumb adductor and flexor.
<title>Comprehensive study of processing parameters influencing the stress and stress gradient of thick polysilicon layers</title> (1997)

Thick polysilicon layers (greater than 10 micrometer), grown in an epitaxial reactor, are highly desirable for surface micromachining applications. The mechanical properties of these layers were studied extensively by characterizing the stress and stress gradient. The stress profile and texture were insensitive to variations of deposition parameters both of the polysilicon seed layer and the epitaxial process, and were influenced to a small degree by doping with phosphorous. Annealing in oxygen ambient resulted in compressive stresses up to 80 MPa and stress gradients of -10 MPa/micrometer. Subsequent annealing in nitrogen reduced the stress and stress gradient, but it can be reversed by re-annealing in oxygen. A model based on diffusion of oxygen is presented explaining the influence of the annealing on stress. Oxygen atoms diffuse into polysilicon during an anneal in the oxygen ambient, introducing compressive stress. Upon annealing in the nitrogen ambient, oxygen is released from the polysilicon layers due to the partial pressure of oxygen at the annealing temperature. The diffusion of oxygen atoms out of the layers results in a partial reversal of the mechanical effects. This insight gives the possibility to tailor the stress of thick polysilicon layers within certain limits to the specific needs of the application.
Development of a novel class of cyclic hexapeptide oxytocin antagonists based on a natural product (1992)

A new structural class of cyclic hexapeptide oxytocin antagonists derived from Streptomyces silvensis and typified by L-365,209 (cyclo-[L-prolyl1-D-phenylalanyl2-L- isoleucyl3-D-dehydropiperazyl4-L-dehydroperazyl5-D-(N- methyl)phenylalanyl6]) was recently reported. In this paper we further delineate the structure-activity profile for this new class by systematic study of L-365,209 analogs obtained by total synthesis. The optimal combination of cyclic amino acid ring sizes at positions 1, 4, and 5 and the role of the N-alkyl substituent at position 6 was elucidated. The lipophilic amino acids at positions 2 and 3 and the unusual amino acid D-dehydropiperazic acid at position 4 were found to be the most critical residues for obtaining good oxytocin receptor affinity. Analogs containing a basic side chain at the less critical 5- and 6-positions maintained good receptor affinity and also had useful levels of water solubility for intravenous formulation. By combining potency- and solubility-enhancing substitutions, several analogs were identified that have the desired combination of properties in vitro (22, cyclo-[L-prolyl-D-tryptophanyl-L-isoleucyl-D-pipecolyl-L-pipeco lyl-D- histidyl]; 25, cyclo-[L-prolyl-D-2-naphthylalanyl-L-isoleucyl-D-pipecolyl-L -pipecolyl-D- histidyl]; 26, cyclo-[L-prolyl-D-tryptophanyl-L-isoleucyl-D-dehydropiperazyl-L-++ pipecolyl-D-histidyl]; 33, cyclo-[L-prolyl-D-tryptophanyl-L-isoleucyl-D-pipecolyl-L- piperazinylcarboxy-D-(N-methyl)phenylalanyl]; 34, cyclo-[L-prolyl-D-phenylalanyl-L-isoleucyl-D-dehydropiperazyl-L-or nithyl- D-(N-methyl)phenylalanyl]). In general, this class exhibited good selectivity for binding to the oxytocin receptor versus the arginine vasopressin V1a and V2 receptor subtypes, although increased V2 receptor affinity was observed in one case (32, cyclo[L-prolyl-D-2-naphthylalanyl-L-isoleucyl-D-pipecolyl-L- lysyl-D-(N- methyl)phenylalanyl]). Unexpectedly, compound 33 was found to stimulate contractions of the isolated rat uterus via activation of the uterine bradykinin receptor. Compounds 22, 25, 26, 33, and 34 were found to be potent antagonists of oxytocin-stimulated contraction of the rat uterus in vitro and in vivo. Compounds 22 and 25 were additionally characterized as potent antagonists of oxytocin-stimulated uterine contractions in the near-term pregnant rhesus monkey. These studies thus demonstrate the selectivity and efficacy of certain members of this novel class of antagonists and suggest their use as pharmacological tools in further defining the role of oxytocin in both term and preterm labor.
Generation of high intensity cw stimulated Raman scattering in a single-mode fiber (1988)

The first two orders of stimulated Raman scattering have been observed by pumping a single-mode fiber with a cw Nd:YAG laser. Broadband first Stokes with intensity of up to a few watts has been observed as a function of the input power. The critical powers have been measured.
Potential serum biomarkers from a metabolomics study of autism (2015)

Two metabolites have potential as biomarkers for the clinical diagnosis and evaluation of autism.
Purification and characterization of a branched-chain amino acid aminotransferase from Lactobacillus paracasei subsp. paracasei CHCC 2115 (2004)

The findings of this work contribute to the knowledge of transamination performed by cheese-related bacteria, and in the understanding and control of amino acid catabolism and the production of aroma compounds.
Charge Transfer Dynamics from Photoexcited Semiconductor Quantum Dots (2016)

Understanding photoinduced charge transfer from nanomaterials is essential to the many applications of these materials. This review summarizes recent progress in understanding charge transfer from quantum dots (QDs), an ideal model system for investigating fundamental charge transfer properties of low-dimensional quantum-confined nanomaterials. We first discuss charge transfer from QDs to weakly coupled acceptors within the framework of Marcus nonadiabatic electron transfer (ET) theory, focusing on the dependence of ET rates on reorganization energy, electronic coupling, and driving force. Because of the strong electron-hole interaction, we show that ET from QDs should be described by the Auger-assisted ET model, which is significantly different from ET between molecules or from bulk semiconductor electrodes. For strongly quantum-confined QDs on semiconductor surfaces, the coupling can fall within the strong coupling limit, in which case the donor-acceptor interaction and ET properties can be described by the Newns-Anderson model of chemisorption. We also briefly discuss recent progress in controlling charge transfer properties in quantum-confined nanoheterostructures through wavefunction engineering and multiple exciton dissociation. Finally, we identify a few key areas for further research.
Some Relations between Chemical Structure and Antifungal Effects of Griseofulvin Analogues (1964)

SUMMARY: Inhibitory effects of more than 300 analogues of griseofulvin against six dermatophytic fungi and eight plant pathogenic fungi were determined in an investigation of relations between chemical structure and biological activity. The influence of chemical structure on physical properties of the analogues appeared dominant, but optimum requirements for in vitro performance were somewhat different from those required in vivo for effective control of plant pathogenic or dermatophytic fungi.
Insulin and Glycogen Synthase (1972)

The present status of the molecular nature of the enzyme glycogen synthase from rabbit skeletal muscle is reviewed. It is shown that per 90,000 Dalton subunit there are six phosphorylatable sites and six sulfhydryl groups. No pyridoxal phosphate is present. The enzyme has a hexagonal subunit visible in the electron microscope which associates to tetramers and higher forms as well. Insulin brings about a shift from dependent (D) to independent (I) form in all sensitive tissues. This is accompanied by a shift in the kinase from an I to D form. Although under certain conditions a decreased cyclic AMP concentration may be observed, under other conditions no change is observed. The combination of an altered kinase sensitivity to cyclic AMP together with a potential decrease in cyclic AMP concentration suggests a decreased kinase activity and explains the D to I shift in synthase. The question of a new intermediate related to cyclic AMP whose formation is stimulated by insulin is introduced as a hypothesis.
Post-translational protein modification and expression of ankyrin-binding site(s) in GP85 (Pgp-1/CD44) and its biosynthetic precursors during T-lymphoma membrane biosynthesis. (1991)

In this study, we have investigated the biosynthesis and processing of GP85 (Pgp-1/CD44), a lymphoma transmembrane glycoprotein known to contain ankyrin-binding site(s). Using a standard pulse-chase protocol, we have detected a 52-kDa polypeptide precursor (p52) within the first 5 min of pulse labeling which contains a high mannose-type N-linked oligosaccharide chains. The conversion of p52 to GP85 requires further glycosylation (both complex type N-linked and O-linked) which takes place in the Golgi complex within 10-20 min after p52 is synthesized. GP85 is then incorporated into the plasma membrane where its turnover rate is relatively slow, a t1/2 of approximately 8 h. Following tunicamycin treatment, we have detected two other precursor proteins: p42 which is unglycosylated and p58 which is O-glycosylated. p42 appears to be an immediate precursor of p52 because p52 is converted to p42 upon deglycosylation. Therefore, the biosynthesis of GP85 appears to occur in the following sequence: p42 in equilibrium to p52 in equilibrium to GP85. Further analysis reveals that all of the GP85 precursors (i.e. p42, p52, and p58) contain ankyrin-binding site(s). Chemical composition analysis of GP85 indicates that this molecule contains approximately 3 N-linked and 4-5 O-linked oligosaccharide chains. Although neither N-glycosylation nor O-glycosylation appears to play an important role in the formation of ankyrin-binding site(s), O-glycosylation (and to a lesser extent N-glycosylation) of GP85 is required for T-lymphoma cell surface interaction with both collagen and hyaluronic acid. These findings suggest that GP85 (Pgp-1/CD44) and its biosynthetic precursors play a pivotal role in regulating adhesion functions such as lymphocyte homing and binding to the extracellular matrix.
For effective facilities planning: layout optimization then simulation, or vice versa? (2005)

It is widely accepted that simulation is an integral part of any effective facilities planning or layout study. Traditional approaches claim that layout optimization produces strategic results and therefore should precede simulation analysis, which focuses on operational issues. On the other hand, more recent studies suggest that running simulation models prior to conducting layout optimization produces more realistic layouts. In this paper, we contrast these two paradigms, with respect to the general assumptions and the types of applications that advocates from each paradigm have used to support their claim. In addition, we propose guidelines on which approach to pursue according to the layout study objectives and the characteristics of the system under consideration.
Three sensitive assays do not provide evidence for circulating HuD-specific T cells in the blood of patients with paraneoplastic neurological syndromes with anti-Hu antibodies (2012)

Anti-Hu antibody-associated paraneoplastic neurological syndromes (Hu-PNSs) are severe and often precede the detection of a malignancy, usually small-cell lung cancer. In Hu-PNS, it is hypothesized that neuronal cells are destroyed by T cells targeted against HuD, a protein expressed by small-cell lung cancer cells and neurons. There is only limited evidence for the existence of HuD-specific T cells. To detect these T cells in the blood of Hu-PNS patients, we employed 3 highly sensitive assays that included T cell stimulation with dendritic cells (DCs) to specifically expand the number of any HuD-specific T cells. A total of 17 Hu-PNS patients were tested with 1 or more of the following 3 assays: (1) tetramer staining after stimulation of T cells with conventionally generated DCs (n = 9), (2) interleukin (IL)-13 enzyme-linked immunosorbent spot (ELISpot; n = 3), IL-4 and IL-5 and interferon (IFN)-γ multiplex cytokine bead array (n = 2) to assay cytokine production by T cells after stimulation with conventionally generated DCs, and (iii) IFN-γ ELISpot and tetramer staining after T cell stimulation with accelerated co-cultured DCs (n = 11). No circulating HuD-specific T cells were found. We suggest that either autoaggressive T cells in Hu-PNS are not targeted against HuD or that their numbers in the blood are too low for detection by highly sensitive techniques.
COMPARISON OF THE ACTIONS OF OCTOPAMINE AND CATECHOLAMINES ON SINGLE NEURONES OF THE RAT CEREBRAL CORTEX (1978)

1. The technique of microelectrophoresis was used to compare the actions of octopamine, noradrenaline and dopamine on single cortical neurones of the rat. 2. Octopamine both excited and depressed neurones of the cortex. Frequently cells depressed by noradrenaline were excited by octopamine; occasionally the converse was true. The time courses of action of the two amines also differed. Dopamine-elicited excitations were observed, but also were not correlated with octopamine-elicited effects. 3. When octopamine and noradrenaline both caused depressant effects, octopamine frequently was of less apparent potency than noradrenaline. When these amines were excitatory, octopamine appeared at least as and sometimes more potent than noradrenaline. 4. Octopamine was only weakly effective on cortical neurones identified by antidromic stimulation of the pyramidal tract, or synaptically excited by stimulation of the ventrobasal thalamus. 5. alpha-Flupenthixol and propranolol were without effect on octopamine-elicited changes in firing rate at doses which were effective in blocking the actions of dopamine and noradrenaline respectively. Metoclopramide did not block the actions of any of the three agonists, but had strong effects of its own. 6. The results suggest that receptors sensitive to octopamine, and which appear to be pharmacologically distinct from those previously categorized as noradrenaline and dopamine receptors, may exist on central neurones of the rat.
vnews: a multicast, multimedia news service with virtual messages (2002)

We describe the vnews news service, an alternative to the USENET news service that provides full read compatibility with USENET news. vnews allows the posting of binary (8-bit) messages without extra encoding. An interface is provided to metaviewer, a utility for displaying multimedia mail messages which can be composed as a series of attachments. Multicast network transport is used to provide efficiency and automatic connection of new news servers to the news feed. The vnews protocol detects and corrects some classes of errors, such as corrupt packets, lost packets, and incorrectly vnews also provides virtual message for storage efficiency.
Automated interstudy image registration technique for SPECT and PET. (1996)

Our registration method (a) provided accurate registrations for phantom and clinical SPECT and PET studies, (b) is fully automated, (c) simplifies comparison of data sets obtained at different times and with different modalities, and (d) can be applied retrospectively.
Real‐time black‐blood MRI using spatial presaturation (2001)

A real-time interactive black-blood imaging system is described. Rapid blood suppression is achieved by exciting and dephasing slabs outside the imaging slice before each imaging excitation. Sharp-profiled radio frequency saturation pulses placed close to the imaging slice provide good blood suppression, even in views containing slow through-plane flow. In vivo results indicate that this technique improves endocardial border definition during systole in real-time cardiac wall-motion studies. Phantom and animal results indicate that this technique nearly eliminates flow artifacts in real-time intravascular studies. J. Magn. Reson. Imaging 2001;13:807-812.