gebhart/patrepeval huggingface dataset:
Visualizing Functional Group Distribution in Solid-Support Beads by Using Optical Analysis (1999)

Detection of the interior functionalization of fluorescently labeled ArgoPore, glass, polystyrene, and Tentagel beads is made possible by the use of optical analysis (see diagram). This analysis is useful for the evaluation of both the polymerization and amino-funtionalization processes that are relevant to the reactivity of these resins during solid-phase synthesis.
Enhancement of spatial resolution of roentgenographic methods using deconvolution (2008)

The spatial resolution of X-ray micro radiography (alike any other imaging method) is the crucial parameter, which determines the span of possible applications. Its improvement remains a major experimental and data processing challenge. From theoretical principles the lower limit of the spatial resolution of a radiographic method is given by the size of the so-called point spread function (PSF) of the imaging system. Hence, details in the radiograms smaller than the size of the PSF cannot be theoretically distinguished. In the case of high geometrical magnification, the X-ray spot size becomes the most important factor for PSF determination. We have successfully measured in 2-D the X-ray spot shape and using deconvolution the spatial resolution has been improved for high-contrast object up to three-fold. We have successfully illustrated the approach for real biological and material structure investigations. Another possibility for resolution enhancement is sub-pixel micro-shifting of the X-ray detector used. Although this approach is quite common for optical imaging, it has not been fully investigated for X-ray imaging. In our measurements we have used sub-pixel micro-shifts of the Medipix2 detector. The method is successfully presented on real objects.
Disrupting the Entry Barrier and Attacking Brain Tumors: The Role of the Neisseria Lipobox-Containing H.8 Epitope and the Laz Protein (2006)

Azurin is a periplasmic 128 amino acid protein in Pseudomonas aeruginosa, termed Paz, which has been shown to enter preferentially and induce apoptosis in cancer cells such as human melanoma or breast cancer. Its effectiveness against brain tumors such as glioblastomas has not been studied. The meningitis-causing bacterium Neisseria meningitidis also harbors an azurin-like protein. Unlike all other known azurins, Neisserial azurin, termed Laz, is surface-exposed and has in its N-terminal region a 39 amino acid epitope called H.8. Upstream of this H.8 moiety is a lipobox that results in the truncation of the protein at the N-terminal cysteine residue with modification by a lipid group. No function of Laz is known. We demonstrate that while Paz is deficient in entering glioblastoma cells and exhibits low cytotoxicity, Laz is much more proficient in entering glioblastoma cells and shows a higher level of cytotoxicity. When the Neisserial H.8 moiety containing the lipobox is fused in frame with Paz either in its N-terminal (H.8-Paz) or in its C-terminal (Paz-H.8), both had high cytotoxicity for glioblastoma cells and a higher level of internalization. When expressed in E. coli, H.8-Paz was much more exposed on the surface than Paz-H.8. The replacement of the Laz N-terminal cysteine residue involved in acylation with an alanine residue abolished the surface display, but had no effect on cytotoxicity or entry in glioblastoma cells, suggesting a role of the H.8 moiety, but not its lipidation, in disrupting the entry barrier in brain tumor cells.
Surface topography induces 3D self-orientation of cells and extracellular matrix resulting in improved tissue function (2009)

The organization of cells and extracellular matrix (ECM) in native tissues plays a crucial role in their functionality. However, in tissue engineering, cells and ECM are randomly distributed within a scaffold. Thus, the production of engineered-tissue with complex 3D organization remains a challenge. In the present study, we used contact guidance to control the interactions between the material topography, the cells and the ECM for three different tissues, namely vascular media, corneal stroma and dermal tissue. Using a specific surface topography on an elastomeric material, we observed the orientation of a first cell layer along the patterns in the material. Orientation of the first cell layer translates into a physical cue that induces the second cell layer to follow a physiologically consistent orientation mimicking the structure of the native tissue. Furthermore, secreted ECM followed cell orientation in every layer, resulting in an oriented self-assembled tissue sheet. These self-assembled tissue sheets were then used to create 3 different structured engineered-tissue: cornea, vascular media and dermis. We showed that functionality of such structured engineered-tissue was increased when compared to the same non-structured tissue. Dermal tissues were used as a negative control in response to surface topography since native dermal fibroblasts are not preferentially oriented in vivo. Non-structured surfaces were also used to produce randomly oriented tissue sheets to evaluate the impact of tissue orientation on functional output. This novel approach for the production of more complex 3D tissues would be useful for clinical purposes and for in vitro physiological tissue model to better understand long standing questions in biology.
Antigenic cross-reactivity between outer membrane proteins of Neisseria meningitidis and commensal Neisseria species (2000)

Two mouse sera against outer membrane proteins from a pathogenic Neisseria meningitidis strain and a commensal N. lactamica strain and two human sera from patients recovering from meningococcal meningitis were used to identify antigens common to pathogenic and commensal Neisseria species. Two major antigens of 55 kDa and 32 kDa, present in all N. meningitidis and N. lactamica strains tested, were demonstrable with all the sera used; the 55-kDa protein was iron-regulated. Demonstration of other common antigens was dependent on the serum used: a 65-kDa antigen was visualised with the human and the mouse anti-N. lactamica sera; a 37-kDa antigen identified as the meningococcal ferric binding protein (FbpA) was only detected with the mouse sera, and two antigens of 83 kDa and 15 kDa were only shown with the mouse anti-N. meningitidis serum. The results demonstrate the existence of several outer membrane antigens common to N. lactamica and N. meningitidis strains, in agreement with the hypothesis that natural immunity against meningitis is partially acquired through colonisation by commensal species, and open new perspectives for the design of vaccine formulations and the development of strategies for vaccination against meningitis.
Interactive spoken-language processing in a hybrid connectionist system (1996)

Our SCREEN (Symbolic Connectionist Robust Enterprise for Natural Language) system analyzes real-world utterances and can be used for relatively large and complex tasks. SCREEN learns a robust flat syntax, semantics, and pragmatics representation. The system also deals with uncommon syntactic and semantic language irregularities. The system is able to produce many utterance hypotheses based on spoken input and can determine which hypotheses are most likely. SCREEN's ability to analyze spoken language, despite encountering mistakes and uncertainties, demonstrates the system's robustness and potential. Because SCREEN is a German spoken-language system, the example of spoken language that we analyze is in German. We provide a literal and, where appropriate, a more easily understood English translation of any German words and sentences that we use.
Robust Pacemaking in Substantia Nigra Dopaminergic Neurons (2009)

Dopaminergic neurons of the substantia nigra pars compacta are autonomous pacemakers. This activity is responsible for the sustained release of dopamine necessary for the proper functioning of target structures, such as the striatum. Somatodendritic L-type Ca2+ channels have long been viewed as important, if not necessary, for this activity. The studies reported here challenge this viewpoint. Using a combination of optical and electrophysiological approaches in brain slices, it was found that antagonism of L-type Ca2+ channel effectively stopped dendritic Ca2+ oscillations but left autonomous pacemaking unchanged. Moreover, damping intracellular Ca2+ oscillations with exogenous buffer had little effect on pacemaking rate. Although not necessary for pacemaking, L-type channels helped support pacemaking when challenged with cationic channel blockers. Simulations suggested that the insensitivity to antagonism of L-type channels reflected the multichannel nature of the pacemaking process. The robustness of pacemaking underscores its biological importance and provides a framework for understanding how therapeutics targeting L-type Ca2+ channels might protect dopaminergic neurons in Parkinson's disease without compromising their function.
Cognitive interventions post acquired brain injury (2007)

Future research should explore functional outcome measures and long-term effects of treatment interventions through follow-up.
Bisimidazoacridones: 2. Steady-state and Time-resolved Fluorescence Studies of Their Diverse Interactions with DNA¶§ (2003)

Several bisimidazoacridones (BIA) are potent, selective antineoplastic agents, whereas others have potent anti-human immunodeficiency virus activity. BIA are bifunctional agents that consist of two imidazoacridone (IA) chromophores held together by various linkers. Interaction of BIA with DNA has been postulated to be required for their biological activity. Fluorescence data on free and bound BIA suggest that the binding of BIA and similar drugs to DNA is driven by a transfer of hydrophobic molecules from aqueous media to the more amphiphilic DNA environment. Binding to DNA was sensitive to sequence and depended on the length and rigidity of the linker. Time-resolved fluorescence measurements showed that BIA adopt an extended conformation upon binding and that all of the molecules are tightly associated with DNA. Gel-shift and melting assays indicated that one of the aromatic residues of BIA is intercalated, whereas the other, together with a linker, resides in a groove, probably the minor groove. A continuum of structures may be possible where intercalation and classical minor groove binding are limiting structures. In general, the hypothesis for the mechanism of action of BIA wherein the unintercalated residue, accessible for additional interactions, captures a critical protein involved in repair or transcription, is consistent with this model.
Mutants of monomeric red fluorescent protein mRFP1 at residue 66: Structure modeling by molecular dynamics and search for correlations with spectral properties (2008)

To study the interrelation between the spectral and structural properties of fluorescent proteins, structures of mutants of monomeric red fluorescent protein mRFP1 with all possible point mutations of Glu66 (except replacement by Pro) were simulated by molecular dynamics. A global search for correlations between geometrical structure parameters and some spectral characteristics (absorption maximum wavelength, integral extinction coefficient at the absorption maximum, excitation maximum wavelength, emission maximum wavelength, and quantum yield) was performed for the chromophore and its 6 A environment in mRFP1, Q66A, Q66L, Q66S, Q66C, Q66H, and Q66N. The correlation coefficients (0.81-0.87) were maximal for torsion angles in phenolic and imidazolidine rings as well as for torsion angles in the regions of connection between these rings and chromophore attachment to beta-barrel. The data can be used to predict the spectral properties of fluorescent proteins based on their structures and to reveal promising positions for directed mutagenesis.
Tumor-promoting phorbol diesters cause the phosphorylation of epidermal growth factor receptors in normal human fibroblasts at threonine-654. (1985)

The effect of tumor-promoting phorbol diesters to potentiate the action of epidermal growth factor (EGF) on cell proliferation is associated with phosphorylation of EGF receptors, acute depression of EGF binding, and inhibition of EGF receptor tyrosine kinase activity. In the present studies, normal human fibroblasts and A431 carcinoma cells were labeled with [32P]phosphate and treated with and without 10 nM 4 beta-phorbol 12 beta-myristate 13 alpha-acetate (PMA). The EGF receptors then were isolated by immunoprecipitation and digested with trypsin. Analysis of the labeled receptor phosphopeptides by reversed-phase HPLC revealed that PMA induces the phosphorylation of a unique phosphopeptide containing [32P]phosphothreonine. Comparison of several chemical and physical properties of the 32P-labeled phosphopeptide with the primary structure of the EGF receptor suggested the identify Lys-Arg-Thr(P)-Leu-Arg. This was confirmed by direct demonstration that a synthetic peptide of this structure comigrates during HPLC and electrophoresis with the 32P-labeled phosphopeptide isolated from the EGF receptors of normal human fibroblasts. The phosphorylated site on the peptide corresponds to threonine-654 of the EGF receptor, which is located on the cytoplasmic side of the plasma membrane nine residues distant from the transmembrane domain. These data indicate that phosphorylation of the EGF receptor in human fibroblasts and A431 cells at threonine-654 may regulate the EGF receptor tyrosine kinase activity and the binding of EGF.
Elevation of anions in exercise‐induced acidosis: a study by ion‐exchange chromatography/mass spectrometry (2007)

Acidosis is a major factor that determines the upper limit of exercise endurance. We have previously shown that anions usually associated with intermediary metabolism are elevated in critically ill patients with metabolic acidosis and contribute significantly to acidosis generation. This study was to determine whether volunteers with normal metabolism would exhibit similar elevations in anions associated with intermediate metabolism when exposed to a short-term physiological stress leading to a brief lactic acidosis. Physiological stress was induced on five healthy male subjects by means of a ramped exercise protocol. Blood was obtained immediately prior to and post-exercise, plasma ultrafiltrate was prepared and analysed immediately both by enzyme assay and liquid chromatography coupled to electrospray-mass spectrometry (LC/ESI-MS). Metabolic acidosis concomitant with a significant increase in blood lactate occurred in each subject, but in addition, anions normally associated with intermediate metabolism were significantly elevated after exercise. The contribution of these anions to generating an acidosis, and thus potentially limiting the extent of exercise, has never been acknowledged.
Nitrogen-Containing and Carbohydrate-Containing Antigen from Actinomyces bovis (1965)

Pirtle, E. C. (National Animal Disease Laboratory, Ames, Iowa), P. A. Rebers, and W. W. Weigel. Nitrogen-containing and carbohydrate-containing antigen from Actinomyces bovis. J. Bacteriol. 89:880-888. 1965.-Water-soluble, heat-stable antigens have been isolated from the supernatant fluids of broth cultures of Actinomyces bovis ATCC 10048 after 8 days of growth in a broth medium composed of Casamino Acids, yeast extract, Tween 80 (polyoxyethylene sorbitan monooleate), sodium thioglycolate, dextrose, and sodium chloride. The antigens were precipitated from the culture supernatant fluid with alcohol and purified by fractional precipitation with alcohol in the presence of calcium or zinc and by chromatography on diethylaminoethyl Sephadex. Two serologically active substances which differed in chemical composition and size were characterized. The larger one contained 71% hexose and 2.8% nitrogen, and the smaller one contained 45% hexose and 5.4% nitrogen. Heterogeneity of these fractions could not be demonstrated by electrophoresis in free solution at pH 7.8 or 2, by ultracentrifugal analysis, by double diffusion in agar, or by immunoelectrophoresis. Despite their differences in chemical composition and size, they appeared identical in activity as antigens in complement fixation and in double-diffusion tests in agar. Each was found to contain mannose as its chief component after hydrolysis and paper chromatography with three solvent systems. A small percentage of the total nitrogen may be attributed to the presence of amino sugars but the remainder is as yet unidentified.
Chromosome aberrations induced in vitro by low doses of radiation: nondisjunction in lymphocytes of young adults. (1975)

Epidemiological studies suggest radiation exposure as a cause of meiotic non-disjunction in humans, but experimental evidence with cytological proof has been lacking. Our results indicate that mitotic nondisjunction of lymphocyte chromosomes can also be induced by exposure to a low dose of radiation. Abnormal segregation can be induced not only when the cells are irradiated but also when nonirradiated cells are incubated with irradiated cell-free plasma or serum. The X and no. 21 chromosomes appear particularly susceptible to nondisjunction.
Extremely Bendable, High-Performance Integrated Circuits Using Semiconducting Carbon Nanotube Networks for Digital, Analog, and Radio-Frequency Applications (2012)

Solution-processed thin-films of semiconducting carbon nanotubes as the channel material for flexible electronics simultaneously offers high performance, low cost, and ambient stability, which significantly outruns the organic semiconductor materials. In this work, we report the use of semiconductor-enriched carbon nanotubes for high-performance integrated circuits on mechanically flexible substrates for digital, analog and radio frequency applications. The as-obtained thin-film transistors (TFTs) exhibit highly uniform device performance with on-current and transconductance up to 15 μA/μm and 4 μS/μm. By performing capacitance-voltage measurements, the gate capacitance of the nanotube TFT is precisely extracted and the corresponding peak effective device mobility is evaluated to be around 50 cm(2)V(-1)s(-1). Using such devices, digital logic gates including inverters, NAND, and NOR gates with superior bending stability have been demonstrated. Moreover, radio frequency measurements show that cutoff frequency of 170 MHz can be achieved in devices with a relatively long channel length of 4 μm, which is sufficient for certain wireless communication applications. This proof-of-concept demonstration indicates that our platform can serve as a foundation for scalable, low-cost, high-performance flexible electronics.
Polar Dibenzocyclooctynes for Selective Labeling of Extracellular Glycoconjugates of Living Cells (2012)

Although strain-promoted alkyne-azide cycloadditions (SPAAC) have found wide utility in biological and material sciences, the low polarity and limited water solubility of commonly used cyclooctynes represent a serious shortcoming. To address this problem, an efficient synthetic route has been developed for highly polar sulfated dibenzocyclooctynylamides (S-DIBO) by a Friedel-Crafts alkylation of 1,2-bis(3-methoxyphenyl)ethylamides with trichlorocyclopropenium cation followed by a controlled hydrolysis of the resulting dichlorocyclopropenes to give bis(3-methoxyphenyl)cyclooctacyclopropenones, which were subjected to methoxy group removal of the phenols, O-sulfation, and photochemical unmasking of the cyclopropenone moiety. Accurate rate measurements of the reaction of benzyl azide with various dibenzylcyclooctyne derivatives demonstrated that aromatic substitution and the presence of the amide function had only a marginal impact on the rate constants. Biotinylated S-DIBO 8 was successfully used for labeling azido-containing glycoconjugates of living cells. Furthermore, it was found that the substitution pattern of the dibenzylcyclooctynes influences subcellular location, and in particular it has been shown that DIBO derivative 4 can enter cells, thereby labeling intra- and extracellular azido-modified glycoconjugates, whereas S-DIBO 8 cannot pass the cell membrane and therefore is ideally suited for selective labeling of cell surface molecules. The ability to selectively label cell surface molecules will yield unique opportunities for glycomic analysis and the study of glycoprotein trafficking.
A Frequency-Domain Approach to Multichannel Upmix (2004)

A series of upmixing techniques for generating multichannel audio from stereo recordings are proposed. The techniques use a common analysis framework based on a comparison between the short-time Fourier transforms of the left and right stereo signals. An interchannel coherence measure is used to identify time-frequency regions consisting mostly of ambience components, which can then be weighted via a nonlinear mapping function, and extracted to synthesize ambience signals. A similarity measure is used to identify the panning coefficients of the various sources in the mix in the time-frequency plane, and different heuristic mapping functions are applied to unmix (extract) one or more sources, and perceptually based functions to repan the signals into an arbitrary number of channels. We illustrate the application of the various techniques in the design of a two-to-five channel upmix system.
Complications from silicon‐polymer intubulation of nerves (1989)

Three cases are reported to illustrate the potential danger of silicon-polymer intubulation of nerve for either nerve repair or following neurolysis. Since silicon-polymer intubulation of nerve is now a proven model for producing chronic nerve compression, its use clinically may be contraindicated where neural regeneration is the desired goal.
Rényi Divergence Variational Inference (2016)

This paper introduces the variational Rényi bound (VR) that extends traditional variational inference to Rényi's alpha-divergences. This new family of variational methods unifies a number of existing approaches, and enables a smooth interpolation from the evidence lower-bound to the log (marginal) likelihood that is controlled by the value of alpha that parametrises the divergence. The reparameterization trick, Monte Carlo approximation and stochastic optimisation methods are deployed to obtain a tractable and unified framework for optimisation. We further consider negative alpha values and propose a novel variational inference method as a new special case in the proposed framework. Experiments on Bayesian neural networks and variational auto-encoders demonstrate the wide applicability of the VR bound.
Wetting Properties of the Multiscaled Nanostructured Polymer and Metallic Superhydrophobic Surfaces (2006)

A superhydrophobic surface is produced from industrial grade polymer materials. The surface comprises partly disordered triple-scaled arrays of polyvinylidene fluoride (PVDF) globules. An inherently superhydrophobic metallic surface is produced with polymer template. The mathematical model based on the Cassie-Baxter hypothesis of air trapping under a water drop is built, which gives the apparent contact angle on the manifold-scaled interface. The presence of several scales itself is not a sufficient condition of hydrophobicity of inherently wettable surfaces. The geometrical features favoring the increase of the vapor-water interface fraction are necessary for this phenomenon.