gebhart/patrepeval huggingface dataset:
Integrated device for optical stimulation and spatiotemporal electrical recording of neural activity in light-sensitized brain tissue (2009)

Neural stimulation with high spatial and temporal precision is desirable both for studying the real-time dynamics of neural networks and for prospective clinical treatment of neurological diseases. Optical stimulation of genetically targeted neurons expressing the light sensitive channel protein Channelrhodopsin (ChR2) has recently been reported as a means for millisecond temporal control of neuronal spiking activities with cell-type selectivity. This offers the prospect of enabling local delivery of optical stimulation and the simultaneous monitoring of the neural activity by electrophysiological means, both in the vicinity of and distant to the stimulation site. We report here a novel dual-modality hybrid device, which consists of a tapered coaxial optical waveguide ('optrode') integrated into a 100 element intra-cortical multi-electrode recording array. We first demonstrate the dual optical delivery and electrical recording capability of the single optrode in in vitro preparations of mouse retina, photo-stimulating the native retinal photoreceptors while recording light-responsive activities from ganglion cells. The dual-modality array device was then used in ChR2 transfected mouse brain slices. Specifically, epileptiform events were reliably optically triggered by the optrode and their spatiotemporal patterns were simultaneously recorded by the multi-electrode array.
Protective cytotoxic T lymphocytes are induced during murine infection with Chlamydia trachomatis. (1994)

T cell responses are often an important component in immunity to organisms that replicate intracellularly. Cytotoxic T lymphocyte (CTL) recognition of peptide Ag in the context of MHC class I molecules results in lysis of infected cells and the release of cytokines including IFN-gamma. Members of the genus Chlamydia are obligate intracellular pathogens that cause blindness and sexually transmitted disease worldwide. Even though it replicates within a membrane-bound vacuole, Chlamydia trachomatis may elicit a CTL response if Chlamydia Ags are present in the cytoplasmic compartment where they can be processed for presentation and bound by MHC class I. In this study, we characterized a CTL line derived from mice infected with C. trachomatis. This CTL line is specific for, and able to lyse, Chlamydia-infected cells. The peptide epitope recognized by this CTL line is present on infected cells, and is presented to the CTL by the classical MHC class I molecule H-2 Ld. Adoptive transfer of this CTL line into an infected mouse affords protection, and this protection requires the activity of IFN-gamma.
Immune response hinders therapy for lysosomal storage diseases (2008)

Enzyme replacement therapy (ERT) for the lysosomal storage disease mucopolysaccharidosis I (MPS I) involves i.v. injection of alpha-l-iduronidase, which can be taken up by cells throughout the body. While a significant immune response to ERT has been shown in patients with MPS I, little is known about what effect anti-enzyme antibodies have on treatment efficacy. In this issue of the JCI, Dickson et al. demonstrate that anti-enzyme antibodies inhibit enzyme uptake and substantially limit the therapeutic efficacy of ERT in canines with MPS I (see the related article beginning on page 2868). Furthermore, the induction of immune tolerance--via oral delivery of cyclosporine A and azathioprine for two months at the time of initiation of ERT with recombinant human alpha-L-iduronidase--improved enzyme uptake in organs. Therefore, transient immunosuppression may enhance ERT for lysosomal storage diseases.
Josephson Persistent-Current Qubit (1999)

A qubit was designed that can be fabricated with conventional electron beam lithography and is suited for integration into a large quantum computer. The qubit consists of a micrometer-sized loop with three or four Josephson junctions; the two qubit states have persistent currents of opposite direction. Quantum superpositions of these states are obtained by pulsed microwave modulation of the enclosed magnetic flux by currents in control lines. A superconducting flux transporter allows for controlled transfer between qubits of the flux that is generated by the persistent currents, leading to entanglement of qubit information.
Attenuated Glial Reactions and Photoreceptor Degeneration after Retinal Detachment in Mice Deficient in Glial Fibrillary Acidic Protein and Vimentin (2007)

The absence of GFAP and vimentin attenuates RD-induced reactive gliosis and, subsequently, limits photoreceptor degeneration. Results of this study indicate that reactive retinal glial cells contribute critically to retinal damage induced by RD and provide a new avenue for limiting photoreceptor degeneration associated with RD and other retinal diseases or damage.
Kinetics of the thermolysis of octamethylcyclotetrasiloxane in the gas phase (1975)

The kinetics of the thermolysis of octamethylcyclotetrasiloxane have been studied in the gas phase between 767 and 925 K. A mechanism has been deduced involving the intermediate Me2SiO, and conclusions are drawn about the stability and chemical behaviour of Me2SiO.
Reactions of Elementary Silicon (1966)

Abstract Elementary silicon is normally treated “dry” with gaseous reactants in a fluidized bed. The apparent inertness of ordinary silicon is due to surface passivation. Non‐passivated silicon reacts as a strongly electropositive element. Finely divided silicon is pyrophoric and forms surface compounds with many substances (e.g. alcohol, water, and metal or organic halides) even at room temperature. An alternative to the “dry” process is a new suspension process, in which finely divided activated silicon, preferably suspended in its liquid reaction products (possibly in the presence of the soluble catalysts) reacts at elevated pressures, generally with liquids. The reactions in suspension can be easily controlled, and al the silicon is consumed. Polysilanes often are the only initial products, and these react further in the homogeneous liquid phase to give monosilanes. For example, dissolution of ordinary silicon in methanol leads smoothly to methoxysilanes, which can add to unsaturated hydrocarbons.
Human glucocorticoid-induced TNF receptor ligand regulates its signaling activity through multiple oligomerization states (2008)

Ligation between glucocorticoid-induced tumor necrosis factor receptor (GITR) and its ligand (GITRL) provides an undefined signal that renders CD4(+)CD25(-) effector T cells resistant to the inhibitory effects of CD4(+)CD25(+) regulatory T cells. To understand the structural basis of GITRL function, we have expressed and purified the extracellular domain of human GITR ligand in Escherichia coli. Chromotography and cross-linking studies indicate that human GITRL (hGITRL) exists as dimers and trimers in solution and also can form a supercluster. To gain insight into the nature of GITRL oligomerization, we determined the crystallographic structures of hGITRL, which revealed a loosely associated open trimer with a deep cavity at the molecular center and a flexible C-terminal tail bent for trimerization. Moreover, a tetramer of trimers (i.e., supercluster) has also been observed in the crystal, consistent with the cross-linking analysis. Deletion of the C-terminal distal three residues disrupts the loosely assembled trimer and favors the formation of a dimer that has compromised receptor binding and signaling activity. Collectively, our studies identify multiple oligomeric species of hGITRL that possess distinct kinetics of ERK activation. The studies address the functional implications and structural models for a process by which hGITRL utilizes multiple oligomerization states to regulate GITR-mediated signaling during T cell costimulation.
Operative and Technical Complications of Vagus Nerve Stimulator Implantation (2010)

VNS therapy is combined with a wide spread of possible complications. Technical problems are to be expected, including electrode fracture, dislocation, and generator malfunction. The major complication in younger patients is the electrode fracture, which might be induced by growth during adolescence. Surgically induced complications of VNS implantation are comparably low. Cardiac symptoms and recurrent nerve palsy need to be taken into consideration.
Privileged Chiral Catalysts (2003)

One of the most active current areas of chemical research is centered on how to synthesize handed (chiral) compounds in a selective manner, rather than as mixtures of mirror-image forms (enantiomers) with different three-dimensional structures (stereochemistries). Nature points the way in this endeavor: different enantiomers of a given biomolecule can exhibit dramatically different biological activities, and enzymes have therefore evolved to catalyze reactions with exquisite selectivity for the formation of one enantiomeric form over the other. Drawing inspiration from these natural catalysts, chemists have developed a variety of synthetic small-molecule catalysts that can achieve levels of selectivity approaching, and in some cases matching, those observed in enzymatic reactions.
Therapeutic potential of inhibiting leukocyte rolling in ischemia/reperfusion. (1995)

Leukocyte rolling has been postulated to be mandatory for subsequent leukocyte adhesion and tissue injury observed during ischemia/reperfusion. The objective of this study was to systematically assess this hypothesis at the microvascular level by examining the effects of various concentrations of a selectin-binding carbohydrate (fucoidin) on the increased rolling and adhesion of leukocytes in postischemic venules. The contribution of L-selectin and/or P-selectin to leukocyte rolling were also assessed in this model. Using intravital microscopy we observed that 60 min of ischemia followed by reperfusion caused a profound increase in leukocyte rolling and adhesion. A high dose of fucoidin (25 mg/kg) reduced leukocyte rolling by > 90% and significantly reduced leukocyte adhesion, whereas a lower dose of fucoidin still reduced leukocyte rolling by 60% but had no effect on leukocyte adhesion. Moreover, despite the profound reduction in leukocyte rolling with fucoidin, the remaining rolling cells were able to firmly adhere via a CD18-dependent mechanism, particularly in those postcapillary venules with reduced (30-50%) shear rates. The increased rolling was also reduced 60% by either an anti-P-selectin antibody, an anti-L-selectin antibody, or a combination of the two antibodies, but this reduction in rolling cells did not translate into significantly reduced leukocyte adhesion. Our data suggest that L-selectin, P-selectin, and a fucoidin-sensitive pathway contribute to the significant increase in reperfusion-induced leukocyte rolling. However, targeting leukocyte rolling as a form of therapy requires very significant efficacy (> 90%) to achieve reasonable (approximately 50%) attenuation in leukocyte adhesion in postischemic venules.
Pattern Recognition and Neural Networks (1996)

This 1996 book is a reliable account of the statistical framework for pattern recognition and machine learning. With unparalleled coverage and a wealth of case-studies this book gives valuable insight into both the theory and the enormously diverse applications (which can be found in remote sensing, astrophysics, engineering and medicine, for example). So that readers can develop their skills and understanding, many of the real data sets used in the book are available from the author's website: www.stats.ox.ac.uk/~ripley/PRbook/. For the same reason, many examples are included to illustrate real problems in pattern recognition. Unifying principles are highlighted, and the author gives an overview of the state of the subject, making the book valuable to experienced researchers in statistics, machine learning/artificial intelligence and engineering. The clear writing style means that the book is also a superb introduction for non-specialists.
Chronic treatment with fluoxetine up-regulates cellular BDNF mRNA expression in rat dopaminergic regions (2005)

During the last few years several studies have highlighted the possibility that major depression can be characterized by a general reduction in brain plasticity and an increased vulnerability under challenging situations. Such dysfunction may be the consequence of reduced expression and function of proteins important for neuroplasticity such as brain-derived neurotrophic factor (BDNF). On this basis, by using a sensitive non-radioactive in-situ hybridization, we evaluated the effects of a chronic treatment with fluoxetine on BDNF expression within rat dopaminergic regions. In fact, besides the well-established role of the hippocampus, increasing evidence indicates that other brain regions may be involved in the pathophysiology of depression and consequently be relevant for the therapeutic action of antidepressant drugs. Our results indicate that 3 wk of fluoxetine administration up-regulates BDNF mRNA levels selectively within structures belonging to the meso-cortico-limbic pathway. The expression of the neurotrophin is significantly increased in the ventral tegmental area, prefrontal cortex, and shell region of the nucleus accumbens, whereas no changes were detected in the substantia nigra and striatum. Moreover, in agreement with previous studies, fluoxetine increased BDNF mRNA levels in the hippocampus, an effect that was limited to the cell bodies without any change in its dendritic targeting. These data show that chronic treatment with fluoxetine increases BDNF gene expression not only in limbic areas but also in dopaminergic regions, suggesting that such an effect may contribute to improve the function of the dopaminergic system in depressed subjects.
N‐terminal domains of native multidomain proteins have the potential to assist de novo folding of their downstream domains in vivo by acting as solubility enhancers (2007)

The fusion of soluble partner to the N terminus of aggregation-prone polypeptide has been popularly used to overcome the formation of inclusion bodies in the E. coli cytosol. The chaperone-like functions of the upstream fusion partner in the artificial multidomain proteins could occur in de novo folding of native multidomain proteins. Here, we show that the N-terminal domains of three E. coli multidomain proteins such as lysyl-tRNA synthetase, threonyl-tRNA synthetase, and aconitase are potent solubility enhancers for various C-terminal heterologous proteins. The results suggest that the N-terminal domains could act as solubility enhancers for the folding of their authentic C-terminal domains in vivo. Tandem repeat of N-terminal domain or insertion of aspartic residues at the C terminus of the N-terminal domain also increased the solubility of fusion proteins, suggesting that the solubilizing ability correlates with the size and charge of N-terminal domains. The solubilizing ability of N-terminal domains would contribute to the autonomous folding of multidomain proteins in vivo, and based on these results, we propose a model of how N-terminal domains solubilize their downstream domains.
Hydrogen Sensing by Enzyme-Catalyzed Electrochemical Detection (2005)

Hydrogen (H2) is a possible future alternative to current fossil-based transportation fuels; however, its lower explosive limit in air requires a reliable sensor to detect leaks wherever H2 is produced, stored, or used. Most current H2 sensors employ palladium or its alloy as the sensing element, featuring high operating temperature and limited selectivity. In this study, we report using soluble hydrogenase (SH) of aerobic beta-proteobacterium Ralstonia eutropha strain H16 to accomplish ambient, electrochemical detection of H2. Gas samples were collected in a solution containing SH that catalyzed the oxidation of H2. The electrons released during the H2 oxidation reaction were accepted by benzyl viologen (BV2+). The product of the redox reaction, BV+, was then detected using chronoamperometry. Using this sensing scheme, we demonstrate detection of H2 ranging from 1 to 100%. In addition, enzyme kinetics and the effect of oxygen on signal response were studied. Our results indicate that it is feasible to develop a sensor to detect H2 in the atmosphere that is based on enzyme-catalyzed electrochemical detection.
The Rationale for Inhibiting 5α-Reductase Isoenzymes in the Prevention and Treatment of Prostate Cancer (2008)

The inhibition of 5alpha-reductase represents a valid target for prostate cancer risk reduction and treatment strategies. The greater suppression of dihydrotestosterone observed with agents that inhibit each 5alpha-reductase isoenzyme may translate into enhanced outcomes and studies are under way to test this hypothesis.
Targeting the autolysis loop of urokinase-type plasminogen activator with conformation-specific monoclonal antibodies (2011)

Tight regulation of serine proteases is essential for their physiological function, and unbalanced states of protease activity have been implicated in a variety of human diseases. One key example is the presence of uPA (urokinase-type plasminogen activator) in different human cancer types, with high levels correlating with a poor prognosis. This observation has stimulated efforts into finding new principles for intervening with uPA's activity. In the present study we characterize the so-called autolysis loop in the catalytic domain of uPA as a potential inhibitory target. This loop was found to harbour the epitopes for three conformation-specific monoclonal antibodies, two with a preference for the zymogen form pro-uPA, and one with a preference for active uPA. All three antibodies were shown to have overlapping epitopes, with three common residues being crucial for all three antibodies, demonstrating a direct link between conformational changes of the autolysis loop and the creation of a catalytically mature active site. All three antibodies are potent inhibitors of uPA activity, the two pro-uPA-specific ones by inhibiting conversion of pro-uPA to active uPA and the active uPA-specific antibody by shielding the access of plasminogen to the active site. Furthermore, using immunofluorescence, the conformation-specific antibodies mAb-112 and mAb-12E6B10 enabled us to selectively stain pro-uPA or active uPA on the surface of cultured cells. Moreover, in various independent model systems, the antibodies inhibited tumour cell invasion and dissemination, providing evidence for the feasibility of pharmaceutical intervention with serine protease activity by targeting surface loops that undergo conformational changes during zymogen activation.
SpyCon: Emulating User Activities to Detect Evasive Spyware (2007)

The success of any spyware is determined by its ability to evade detection. Although traditional detection methodologies employing signature and anomaly based systems have had reasonable success, new class of spyware programs emerge which blend in with user activities to avoid detection. One of the latest anti-spyware technologies consists of a local agent that generates honeytokens of known parameters (e.g., network access requests) and tricks spyware into assuming it to be legitimate activity. In this paper, as a first step, we address the deficiencies of static honeytoken generation and present an attack that circumvents such detection techniques. We synthesize the attack by means of data mining algorithms like associative rule mining. Next, we present a randomized honeytoken generation mechanism to address this new class of spyware. Experimental results show that (i) static honeytokens are detected with near 100% accuracy, thereby defeating the state-of-the-art anti-spyware technique, (ii) randomized honeytoken generation mechanism is an effective anti-spyware solution.
Monitoring proton dissociation and solution conformation of chiral ytterbium complexes with near‐IR CD (2005)

The ytterbium complex [Yb((S)-THP)](3+) ((S)-THP = (1S,4S,7S,10S-tetrakis(2-hydroxypropyl)-1,4,7,10-tetraazacyclododecane) is investigated in solution through NMR, near-IR absorption, and CD spectroscopy. Quantitative analysis of the paramagnetic pseudocontact NMR shift shows Lambda helicity of the ligand cage around the metal. The NIR CD spectrum recorded at acidic pH is found to be very similar to that of [Yb((R)-DOTMA)](-) ((R)-DOTMA = (1R,4R,7R,10R)-alpha,alpha',alpha'',alpha'''-tetramethyl-1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid), which in solution assumes a twisted square antiprism (TSA) conformation. The similarity of the NIR CD spectra is discussed, and it is the first proof of the Lambda(lambda,lambda,lambda,lambda) conformation of [Yb((S)-THP)](3+). NIR CD spectra recorded in the pH range of 2-9 allow one to easily follow proton dissociation and to calculate the pK of this equilibrium in water (pK(A) = 6.4 +/- 0.1). This value agrees well with that determined for [Lu((S)-THP)](3+) using potentiometric methods. This demonstrates once again that NIR CD spectroscopy is a powerful technique for investigating the solution structure and dynamics of these complexes.
Electron Transfer Dynamics in Nanocrystalline Titanium Dioxide Solar Cells Sensitized with Ruthenium or Osmium Polypyridyl Complexes (2000)

The electron transfer dynamics in solar cells that utilize sensitized nanocrystalline titanium dioxide photoelectrodes and the iodide/triiodide redox couple have been studied on a nanosecond time scale. The ruthenium and osmium bipyridyl complexes Ru(H2L‘)2(CN)2, Os(H2L‘)2(CN)2, Ru(H2L‘)2(NCS)2, and Os(H2L‘)2(NCS)2, where H2L‘ is 4,4‘-dicarboxylic acid 2,2‘-bipyridine, inject electrons into the semiconductor with a rate constant >108 s-1. The effects of excitation intensity, temperature, and applied potential on the recombination reaction were analyzed using a second-order kinetics model. The rates of charge recombination decrease with increasing driving force to the oxidized sensitizer, indicating that charge recombination occurs in the Marcus inverted region. The electronic coupling factors between the oxidized sensitizer and the injected electrons in TiO2 and the reorganization energies for the recombination reaction vary significantly for the different metal complexes. The charge recombination rates are well described by semiclassical electron transfer theory with reorganization energies of 0.55−1.18 eV. Solar cells sensitized with Ru(H2L‘)2(CN)2, Os(H2L‘)2(CN)2, and Ru(H2L‘)2(NCS)2 have favorable photoelectrochemical characteristics, and iodide is oxidized efficiently. In contrast, iodide oxidation limits the efficiency of cells based on sensitization of TiO2 with Os(H2L‘)2(NCS)2. The observation that charge recombination occurs in the Marcus inverted region has important implications for the design of molecular sensitizers in nanocrystalline solar cells operated under our experimental conditions.
Real-Time Extraction of Maximally Stable Extremal Regions on an FPGA (2007)

This paper describes the implementation of a realtime maximally stable extremal region (MSER) detector. In order to reach real-time performance, both algorithmic and memory issues have been addressed. The union-find algorithm, which is the heart of the MSER detector, is extended to create linked regions that significantly decrease the time to extract MSERs. Hash indexed memory structures are used to locate stored regions fast while keeping the amount of stored data low. The design is verified by including it in a demonstrator circuit. Timing and memory requirements are presented for the demonstrator and as a function of image resolution