gebhart/patrepeval huggingface dataset:
Unusual amino acids VI. Substituted arylamino acids by asymmetric hydrogenation ofN-Cbz andN-Boc protected dehydroamino acid derivatives (1996)

Substituted N-Cbz and N-Boc protected arylamino acrylic acids and esters have been prepared and used in asymmetric hydrogenations catalyzed by PROPRAPHOSRh. Stereoselectivities > 90% ee could be achieved, the rate of which is dependent on the position of the substituent in the aromatic ring. The N-Boc derivatives provide advantages compared with the N-Cbz analogues. The amino acid derivatives were fully characterized by 19F, 13C, and 1H NMR spectroscopy. © 1996 Wiley-Liss, Inc.
Recovery of therapeutic proteins from inclusion bodies: problems and process strategies (1990)

Conference Article| April 01 1990 Recovery of therapeutic proteins from inclusion bodies: problems and process strategies DAVID R. THATCHER DAVID R. THATCHER 1ICI Pharmaceuticals, Alderley Park, Macclesfield SK10 4TG, U.K. Search for other works by this author on: This Site PubMed Google Scholar Author and article information Publisher: Portland Press Ltd Received: October 10 1989 Online ISSN: 1470-8752 Print ISSN: 0300-5127 © 1990 Biochemical Society1990 Biochem Soc Trans (1990) 18 (2): 234–235. https://doi.org/10.1042/bst0180234 Article history Received: October 10 1989 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Facebook Twitter LinkedIn Email Cite Icon Cite Get Permissions Citation DAVID R. THATCHER; Recovery of therapeutic proteins from inclusion bodies: problems and process strategies. Biochem Soc Trans 1 April 1990; 18 (2): 234–235. doi: https://doi.org/10.1042/bst0180234 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 Society Transactions Search Advanced Search This content is only available as a PDF. © 1990 Biochemical Society1990 Article PDF first page preview Close Modal You do not currently have access to this content.
High-Mobility Group Box 1, Oxidative Stress, and Disease (2010)

Oxidative stress and associated reactive oxygen species can modify lipids, proteins, carbohydrates, and nucleic acids, and induce the mitochondrial permeability transition, providing a signal leading to the induction of autophagy, apoptosis, and necrosis. High-mobility group box 1 (HMGB1) protein, a chromatin-binding nuclear protein and damage-associated molecular pattern molecule, is integral to oxidative stress and downstream apoptosis or survival. Accumulation of HMGB1 at sites of oxidative DNA damage can lead to repair of the DNA. As a redox-sensitive protein, HMGB1 contains three cysteines (Cys23, 45, and 106). In the setting of oxidative stress, it can form a Cys23-Cys45 disulfide bond; a role for oxidative homo- or heterodimerization through the Cys106 has been suggested for some of its biologic activities. HMGB1 causes activation of nicotinamide adenine dinucleotide phosphate oxidase and increased reactive oxygen species production in neutrophils. Reduced and oxidized HMGB1 have different roles in extracellular signaling and regulation of immune responses, mediated by signaling through the receptor for advanced glycation end products and/or Toll-like receptors. Antioxidants such as ethyl pyruvate, quercetin, green tea, N-acetylcysteine, and curcumin are protective in the setting of experimental infection/sepsis and injury including ischemia-reperfusion, partly through attenuating HMGB1 release and systemic accumulation.
Neuritogenesis and the Nerve Growth Factor-induced Differentiation of PC-12 Cells Requires Annexin II-mediated Plasmin Generation (2001)

One of the key morphological changes associated with the nerve growth factor (NGF)-induced differentiation of rat adrenal pheochromocytoma (PC-12) cells is the growth of axon-like processes called neurites. A growing body of evidence suggests that this process may be dependent upon plasmin, a serine protease generated from plasminogen (Plg) by either urokinase Plg activator (u-PA) or tissue Plg activator (t-PA). Prior work in our laboratory has identified annexin II (Ann-II) as a co-receptor for Plg and t-PA that promotes and localizes plasmin generation near the cell surface. In the present study, we report a 3-9-fold increase in Ann-II protein and message levels in NGF-treated PC-12 cells. Message stability and nuclear run-on assays suggest that this induction occurs at the level of gene transcription. Neurite outgrowth assays on and within a three-dimensional matrix demonstrate the inhibition of NGF-induced PC-12 cell differentiation by polyclonal and monoclonal antibodies directed against Ann-II as well as by the overexpression of antisense Ann-II mRNA. Neuritogenesis is also impaired by alpha(2)-plasmin inhibitor, antibodies directed against t-PA and u-PA, and epsilon-aminocaproic acid, a lysine analog that inhibits Plg activation and the binding of Plg to Ann-II. Plasmin generation assays reveal a 2-fold increase in plasmin production on NGF-treated PC-12 cells, which can be blocked by a polyclonal antibody directed against the tail region of Ann-II. From these data, we conclude that Ann-II is transcriptionally up-regulated by NGF and that Ann-II-mediated plasmin generation may play an important role during neurite development in the differentiating PC-12 cell.
Structural basis for the enantiospecificities of R‐ and S‐specific phenoxypropionate/α‐ketoglutarate dioxygenases (2006)

(R)- and (S)-dichlorprop/alpha-ketoglutarate dioxygenases (RdpA and SdpA) catalyze the oxidative cleavage of 2-(2,4-dichlorophenoxy)propanoic acid (dichlorprop) and 2-(4-chloro-2-methyl-phenoxy)propanoic acid (mecoprop) to form pyruvate plus the corresponding phenol concurrent with the conversion of alpha-ketoglutarate (alphaKG) to succinate plus CO2. RdpA and SdpA are strictly enantiospecific, converting only the (R) or the (S) enantiomer, respectively. Homology models were generated for both enzymes on the basis of the structure of the related enzyme TauD (PDB code 1OS7). Docking was used to predict the orientation of the appropriate mecoprop enantiomer in each protein, and the predictions were tested by characterizing the activities of site-directed variants of the enzymes. Mutant proteins that changed at residues predicted to interact with (R)- or (S)-mecoprop exhibited significantly reduced activity, often accompanied by increased Km values, consistent with roles for these residues in substrate binding. Four of the designed SdpA variants were (slightly) active with (R)-mecoprop. The results of the kinetic investigations are consistent with the identification of key interactions in the structural models and demonstrate that enantiospecificity is coordinated by the interactions of a number of residues in RdpA and SdpA. Most significantly, residues Phe171 in RdpA and Glu69 in SdpA apparently act by hindering the binding of the wrong enantiomer more than the correct one, as judged by the observed decreases in Km when these side chains are replaced by Ala.
TGFbeta1 signaling via alphaVbeta6 integrin. (2003)

Our data provide support for the existence of an alternate TGFbeta1 signaling pathway that is independent of the known SMAD pathway. This alternate pathway involves alphaVbeta6 integrin and the Ras/MAP kinase pathway and does not employ an RGD motif in TGFbeta1-sensitive tumor cells. The combined action of these two pathways seems to be necessary to elicit a complete TGFbeta1 signal.
Comparison of Sphingosine 1-Phosphate–Induced Intracellular Signaling Pathways in Vascular Smooth Muscles (2002)

Sphingosine 1-phosphate (S1P), a lipid released from activated platelets, influences physiological processes in the cardiovascular system via activation of the endothelial differentiation gene (EDG/S1P) family of 7 transmembrane G protein-coupled receptors. In cultured vascular smooth muscle (VSM) cells, S1P signaling has been shown to stimulate proliferative responses; however, its role in vasoconstriction has not been examined. In the present study, the effects of S1P and EDG/S1P receptor expression were determined in rat VSM from cerebral artery and aorta. S1P induced constriction of cerebral artery, which was partly dependent on activation of p160(ROCK) (Rho-kinase). S1P also induced activation of RhoA in cerebral artery with a similar time course to contraction. In aorta, S1P did not produce a constriction or RhoA activation. In VSM myocytes from cerebral arteries, stimulation with S1P gives rise to a global increase in [Ca2+]i, initially generated via Ca2+ release from the sarcoplasmic reticulum by an inositol 1,4,5-trisphosphate-dependent pathway. In aorta VSM, a small increase in [Ca2+]i was observed after stimulation at higher concentrations of S1P. S1P induced activation of p42/p44(mapk) in aorta and cerebral artery VSM. Subtype-specific S1P receptor antibodies revealed that the expression of S1P3/EDG-3 and S1P2/EDG-5 receptors is 4-fold higher in cerebral artery compared with aorta. S1P(1)/EDG-1 receptor expression was similar in both types of VSM. Therefore, the ability of S1P to act as a vasoactive mediator is dependent on the activation of associated signaling pathways and may vary in different VSM. This differential signaling may be related to the expression of S1P receptor subtypes.
New controller for functional electrical stimulation systems (2001)

A novel, self-contained controller for functional electrical stimulation systems has been designed. The development was motivated by the need to have a general purpose, easy to use controller capable of stimulating many muscle groups, thus restoring complex motor functions (e.g. standing, walking, reaching, and grasping). The designed controller can regulate the frequency, pulse duration, and charge balance on up to 16 channels, and execute pre-programmed and sensory-driven control operations. The controller supports up to eight analog and six digital sensors, and comprises a memory block for including history of the sensory data (time series). Five independent timers provide the basis for the multi-modal and multi-level control of movement. The PC compatible interface is realised via an IR serial communication channel. The PC based software is user friendly and fully menu driven. This paper also presents a case study where the controller was implemented to restore walking in a paraplegic subject. The assistive system comprised the novel controller, the power and output stages of an eight-channel FES system (IEEE Trans Rehabil Eng, TRE-2 (1994) 234), ankle-foot orthoses, and a rolling walker. Stimulation was applied with surface electrodes positioned over the motoneurons that innervate muscles responsible for the hip and knee flexion and extension. The sensory system included goniometers at knee and hip joints, force-sensing resistors built in the shoe insoles, and digital accelerometers at the hips. A rule-based control algorithm was generated following a two-step procedure: (1) simulation and (2) machine learning as described in earlier studies (IEEE Trans Rehab Eng, TRE-7 (1999) 69). The paraplegic subject walked faster, and with less physiological effort, when automatic control was applied as compared to hand-control. This case study, as well as a previous one for assisting grasping (The design and testing of a new programmable electronic stimulator. N. Fisekovic, MS thesis. University of Belgrade, Belgrade, 2000) indicate that the novel control unit is effectively applicable to FES systems.
Sewage reflects the distribution of human faecal L achnospiraceae (2013)

Faecal pollution contains a rich and diverse community of bacteria derived from animals and humans, many of which might serve as alternatives to the traditional enterococci and Escherichia coli faecal indicators. We used massively parallel sequencing (MPS) of the 16S rRNA gene to characterize microbial communities from wastewater treatment plant (WWTP) influent sewage from 12 cities geographically distributed across the USA. We examined members of the Clostridiales, which included the families Clostridiaceae, Lachnospiraceae and Ruminococcaceae for their potential as sewage indicators. Lachnospiraceae was one of the most abundant groups of faecal bacteria in sewage, and several Lachnospiraceae high-abundance sewage pyrotags occurred in at least 46 of 48 human faecal samples. Clone libraries targeting Clostridium coccoides (C. coccoides) in sewage samples demonstrated that Lachnospiraceae-annotated V6 pyrotags encompassed the previously reported C. coccoides group. We used oligotyping to profile the genus Blautia within Lachnospiraceae and found oligotypes comprised of 24 entropy components that showed patterns of host specificity. These findings suggest that indicators based on Blautia might have the capacity to discriminate between different faecal pollution sources. Development of source-specific alternative indicators would enhance water quality assessments, which leads to improved ecosystem health and reduced human health risk due to waterborne disease.
Small Catalytic RNAs (1992)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
Molecular recognition among alcohols and amines: super-tetrahedral crystal architectures of linear diphenol–diamine complexes and aminophenols (1994)

Hydroxy and amino groups are complementary as regards hydrogen-bond donors and acceptors. This is expected to lead to molecular recognition among alcohols and primary amines, i.e., to a propensity towards formation of 1 : 1 alcohol–amine complexes, driven by a 50% increase of the number of hydrogen bonds as compared with the uncomplexed constituents. Possible hydrogen-bonded architectures of such complexes are suggested, and the concept is successfully exploited for crystal engineering purposes by drawing upon linear diphenols, aromatic diamines, and aminophenols as supramolecular partners. Specifically, the crystal-structural chemistry is reported of the 1 : 1 molecular complexes between hydroquinone and p-phenylenediamine, hydroquinone and benzidine, 4,4′-dihydroxybiphenyl and p-phenylenediamine, 4,4′-dihydroxybiphenyl and benzidine, as well as of p-aminophenol, and of 4,4′-hydroxyaminobiphenyl. The diphenol–diamine complexes form hyderogen-bonded super-diamond lattices with 1.5 O(H) N bonds per oxygen and nitrogen atoms, respectively. Again exclusively via O(H)N bonds, the aminophenol structures are also supertetrahedral but after the manner of the polar wurtzite variant. Some similar reported structures are analysed in the light of the present concepts and results, and implications are discussed of the finding that molecular recognition is possible among molecules as standard as simple alcohols and amines.
Presentation sensei (2007)

In this paper we present a presentation training system that observes a presentation rehearsal and provides the speaker with recommendations for improving the delivery of the presentation, such as to speak more slowly and to look at the audience. Our system "Presentation Sensei" is equipped with a microphone and camera to analyze a presentation by combining speech and image processing techniques. Based on the results of the analysis, the system gives the speaker instant feedback with respect to the speaking rate, eye contact with the audience, and timing. It also alerts the speaker when some of these indices exceed predefined warning thresholds. After the presentation, the system generates visual summaries of the analysis results for the speaker's self-examinations. Our goal is not to improve the content on a semantic level, but to improve the delivery of it by reducing inappropriate basic behavior patterns. We asked a few test users to try the system and they found it very useful for improving their presentations. We also compared the system's output with the observations of a human evaluator. The result shows that the system successfully detected some inappropriate behavior. The contribution of this work is to introduce a practical recognition-based human training system and to show its feasibility despite the limitations of state-of-the-art speech and video recognition technologies.
Role of Nitric Oxide in Acute Renal Failure (1997)

Nitric oxide synthase has been identified in several epithelial cells in the kidney, including proximal tubular cells, thick ascending limb, inner medullary collecting duct, and interstitial cells. Nitric oxide (NO) plays an important role in renal hemodynamics and sodium tubular transport. We have demonstrated that NO participates in hypoxia/reoxygenation (H/R) injury in isolated rat proximal tubules (PT) suspensions. In this in vitro model L-arginine addition enhanced H/R injury while L-NAME almost completely prevented injury. These effects were less intense in chronic supplemented rats with L-arginine and L-NAME, suggesting that NO synthase manipulation had interfered with PT susceptibility to H/R injury. In contrast, L-arginine protected IMCD cells in culture from hypercholesterolemic rats against hypoxia. Moreover, acute infusion of L-arginine before bilateral renal artery clamping was protective while L-arginine chronic administration and L-NAME were deleterious in this ARF model. The L-arginine protection was not observed in unilateral renal clamping plus contralateral nephrectomy in normal rats, but L-arginine was protective in hypercholesterolemic rats. Taken together, these results suggest that the net effect of NO stimulation is variable, and that it is the result of a balance between beneficial hemodynamic effects and cytotoxicity.
Heterodyne Fourier domain optical coherence tomography for full range probing with high axial resolution (2006)

One of the main drawbacks of Fourier domain optical coherence tomography (FDOCT) is the limited measurement depth range. Phase shifting techniques allow reconstructing the complex sample signal resulting in a doubled depth range. In current complex FDOCT realizations the phase shift is introduced via a reference path length modulation, which causes chromatic phase errors especially if broad bandwidth light sources are employed. With acousto-optic frequency shifters in the reference and sample arm, and the detector being locked to the resulting beating frequency, the signal is quadrature detected at high speed. The beating signal frequency is the same for all wavelengths allowing for achromatic complex reconstruction. With a Ti:Sapphire laser at 800nm and spectral width of 130nm, a heterodyne complex FDOCT system is realized with 20kHz line rate and an axial resolution of 4mum.
Genetic Studies with Herpes Simplex Virus Type 1. The Isolation of Temperature-sensitive Mutants, their Arrangement into Complementation Groups and Recombination Analysis Leading to a Linkage Map (1973)

SUMMARY Nine 5-bromodeoxyuridine-induced temperature-sensitive (ts) mutants were isolated from stocks of a syncytial plaque type mutant (syn) itself derived from the non-syncytial wild-type (syn +) of the glasgow strain 17 of herpes simplex virus type 1. The nine ts mutants have been assigned to eight cistrons on the basis of different complementation tests. Non-syncytial revertants isolated from the original ts syn mutants were used in reciprocal three-factor crosses of the type: tsX syn × tsY syn + and tsX syn + × tsY syn. With recombination data from these crosses a linkage map has been constructed. The provisional map which locates nine cistrons is linear and spans about 25 recombination units. The regular occurrence of plaques with mixed syn/syn + morphology in the progeny from crosses is reported.
Morphological Reconstruction and Ordering in Films of Sphere-Forming Block Copolymers on Striped Chemically Patterned Surfaces (2008)

The morphology of thin films of sphere-forming block copolymers on striped chemically patterned surfaces was investigated as a function of thickness and commensurability of the pattern period (Ls) and the lattice spacing of the spherical structure (Lo), using scanning electron microscopy and atomic force microscopy. In all cases, a linear wetting layer forms on the chemical pattern. As the film thickness increases from 10 to 25 nm, protuberances in the wetting layer appear. In 57 nm thick films, when Ls and Lo are sufficiently commensurate, the protuberances in the knurled, linear wetting domain and the spheres in the overlying layer of P(S-b-MMA) coordinate during equilibration, resulting in an ordered hexagonal array of partial spherical domains. The range of commensurability over which such an ordered hexagonal structure is achieved decreases when the film thickness is increased to 70 nm. In general, the process leads to a pattern transformation from a series of parallel lines at the substrate surface to an ordered, hexagonal array of spots at the free surface of the film as the block copolymer starts to reconstruct its bulk morphology away from the chemically patterned surface.
Comparative Analysis of Virulence and Toxin Expression of Global Community‐Associated Methicillin‐ResistantStaphylococcus aureusStrains (2010)

The current pandemic of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) skin infections is caused by several genetically unrelated clones. Here, we analyzed virulence of globally occurring CA-MRSA strains in a rabbit skin infection model. We used rabbits because neutrophils from this animal species have relatively high sensitivity to Panton-Valentine leukocidin (PVL), a toxin epidemiologically correlated with many CA-MRSA infections. Virulence in the rabbit model correlated with in vitro neutrophil lysis and transcript levels of phenol-soluble modulin α and α-toxin, but not PVL genes. Furthermore, abscesses caused by USA300 and its PVL-negative progenitor USA500 were comparatively large and similar in size, suggesting that PVL has played a limited role in the evolution of USA300 virulence in the context of skin infections. Our study indicates a major but not exclusive impact of virulence on the epidemiological success of USA300 and other CA-MRSA strains and emphasizes the importance of core genome-encoded toxins in CA-MRSA skin infections.
Evaluating associativity in CPU caches (1989)

The authors present new and efficient algorithms for simulating alternative direct-mapped and set-associative caches and use them to quantify the effect of limited associativity on the cache miss ratio. They introduce an algorithm, forest simulation, for simulating alternative direct-mapped caches and generalize one, which they call all-associativity simulation, for simulating alternative direct-mapped, set-associative, and fully-associative caches. The authors find that although all-associativity simulation is theoretically less efficient than forest simulation or stack simulation (a commonly used simulation algorithm), in practice it is not much slower and allows the simulation of many more caches with a single pass through an address trace. The authors also provide data and insight into how varying associatively affects the miss ratio.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Evaluation of the anti-angiogenic properties of the new selective αVβ3 integrin antagonist RGDechiHCit (2011)

Our data indicate the importance of RGDechiHCit in the selective inhibition of endothelial αVβ3 integrin in vitro and in vivo. Such inhibition opens new fields of investigation on the mechanisms of angiogenesis, offering clinical implications for treatment of pathophysiological conditions such as cancer, proliferative retinopathy and inflammatory disease.