gebhart/patrepeval huggingface dataset:
Phosphorylation at Serine 10, a Major Phosphorylation Site of p27 , Increases Its Protein Stability (2000)

The association of the p27(Kip1) protein with cyclin and cyclin-dependent kinase complexes inhibits their kinase activities and contributes to the control of cell proliferation. The p27(Kip1) protein has now been shown to be phosphorylated in vivo, and this phosphorylation reduces the electrophoretic mobility of the protein. Substitution of Ser(10) with Ala (S10A) markedly reduced the extent of p27(Kip1) phosphorylation and prevented the shift in electrophoretic mobility. Phosphopeptide mapping and phosphoamino acid analysis revealed that phosphorylation at Ser(10) accounted for approximately 70% of the total phosphorylation of p27(Kip1), and the extent of phosphorylation at this site was approximately 25- and 75-fold greater than that at Ser(178) and Thr(187), respectively. The phosphorylation of p27(Kip1) was markedly reduced when the positions of Ser(10) and Pro(11) were reversed, suggesting that a proline-directed kinase is responsible for the phosphorylation of Ser(10). The extent of Ser(10) phosphorylation was markedly increased in cells in the G(0)-G(1) phase of the cell cycle compared with that apparent for cells in S or M phase. The p27(Kip1) protein phosphorylated at Ser(10) was significantly more stable than the unphosphorylated form. Furthermore, a mutant p27(Kip1) in which Ser(10) was replaced with glutamic acid in order to mimic the effect of Ser(10) phosphorylation exhibited a marked increase in stability both in vivo and in vitro compared with the wild-type or S10A mutant proteins. These results suggest that Ser(10) is the major site of phosphorylation of p27(Kip1) and that phosphorylation at this site, like that at Thr(187), contributes to regulation of p27(Kip1) stability.
Treatment of Avascular Necrosis of the Femoral Head by a Combination of Bone Grafting, Decompression, and Electrical Stimulation (1984)

The goal in the treatment of avascular necrosis is to preserve, not replace, the femoral head. Although many methods have been proposed, none has proved completely satisfactory. Electrical stimulation as a supplement to bone grafting and decompression is an attractive approach to this problem because it combines the desirable features of other procedures, each of which has shown a certain degree of effectiveness in stimulating bone growth and repair. Preliminary results indicate that patients treated with decompression and grafting alone and those in whom electrical stimulation was added to these had better results than patients treated by "conservative" means. The effectiveness of the electrical stimulation itself, however, has not yet been established and remains an important area for investigation. Further improvements in delivery systems and techniques are required to develop better methods for the treatment of avascular necrosis.
Understanding the flow behaviour of copolymer and associative polymers in porous media using extensional viscosity characterization: Effect of hydrophobic association (2018)

Associative polymer (AP) and hydrolyzed polyacrylamide (HPAM), the two commonly used polymers for heavy oil recovery, are reported to exhibit very different flow behaviour in porous media despite having similar shear viscosity. The kind of hydrophobic association (intramolecular or intermolecular) that AP exhibit is concentration dependent and will influence both shear and elongational flow in the porous media. To understand flow behaviour of these two polymers in porous media, the role of hydrophobic association on shear and extensional rheology and its effect on the resistance factor (RF) and residual resistance factor in porous media are investigated over a non‐associating HPAM polymer. The results suggest that shear rheology and the Deborah number cannot explain the porous media flow behaviour. However, direct measurements of extensional properties using a capillary breakup extensional rheometer have shown the marginal difference between two polymers at a lower concentration (1000 ppm) and the considerable difference at a higher concentration (2000 ppm), indicating an intramolecular and intermolecular association, respectively. These results are in accordance with porous media observations where both polymers have shown a similar RF at 1000 ppm. Whereas, at 2000 ppm AP showed a much higher RF at low/intermediate fluxes, and a similar RF at high flux, suggesting the transformation from intermolecular association to intramolecular association. The significant drop in the extensional viscosity at high strain rates after exhibiting the maxima explains this behaviour.
A scaffold immune microenvironment (2016)

Local immune cells create conditions that support tissue regeneration [Also see Report by Sadtler et al. ]
Algorithm and Hardware Design of Discrete-Time Spiking Neural Networks Based on Back Propagation with Binary Activations (2017)

We present a new back propagation based training algorithm for discrete-time spiking neural networks (SNN). Inspired by recent deep learning algorithms on binarized neural networks, binary activation with a straight-through gradient estimator is used to model the leaky integrate-fire spiking neuron, overcoming the difficulty in training SNNs using back propagation. Two SNN training algorithms are proposed: (1) SNN with discontinuous integration, which is suitable for rate-coded input spikes, and (2) SNN with continuous integration, which is more general and can handle input spikes with temporal information. Neuromorphic hardware designed in 40nm CMOS exploits the spike sparsity and demonstrates high classification accuracy (>98% on MNIST) and low energy (48.4-773 nJ/image).
Automatic Rule Extraction from Long Short Term Memory Networks (2017)

Although deep learning models have proven effective at solving problems in natural language processing, the mechanism by which they come to their conclusions is often unclear. As a result, these models are generally treated as black boxes, yielding no insight of the underlying learned patterns. In this paper we consider Long Short Term Memory networks (LSTMs) and demonstrate a new approach for tracking the importance of a given input to the LSTM for a given output. By identifying consistently important patterns of words, we are able to distill state of the art LSTMs on sentiment analysis and question answering into a set of representative phrases. This representation is then quantitatively validated by using the extracted phrases to construct a simple, rule-based classifier which approximates the output of the LSTM.
Carrier Suppression of Phase Modulated Beam Using Optical Cavity for Coherent Population Trapping Clock (2010)

We present a method of carrier suppression of a phase-coherent laser beam produced by an electro-optic modulator for coherent population trapping (CPT) clock. To suppress the undesired strong carrier mode of the phase-modulated beam, a Fabry–Perot (FP) cavity is used as an optical filter. The intensity of the carrier mode is reduced by 70% without significant loss of the two first-order side modes for CPT clock. The contrast of the CPT signal is improved by a factor of 1.4 when the carrier-suppressed phase-coherent laser beam is applied to a 87 Rb CPT clock.
Structural Clustering of Machine-Generated Mail (2016)

Several recent studies have presented different approaches for clustering and classifying machine-generated mail based on email headers. We propose to expand these approaches by considering email message bodies. We argue that our approach can help increase coverage and precision in several tasks, and is especially critical for mail extraction. We remind that mail extraction supports a variety of mail mining applications such as ad re-targeting, mail search, and mail summarization. We introduce new structural clustering methods that leverage the HTML structure that is common to messages generated by a same mass-sender script. We discuss how such structural clustering can be conducted at different levels of granularity, using either strict or flexible matching constraints, depending on the use cases.
Label-Free Capacitance-Based Identification of Viruses (2015)

This study was undertaken to quantitate a single virus suspension in culture medium without any pre-processing. The electrical capacitance per virus particle was used to identify the kind of virus present by measuring the suspension (virus plus medium) capacitance, de-embedding the medium contribution, and dividing by the virus count. The proposed technique is based on finding the single virus effective dielectric constant which is directly related to the virus composition. This value was used to identify the virus type accordingly. Two types of viruses thus tested were further quantified by a biochemical technique to validate the results. Furthermore, non-organic nanoparticles with known concentration and capacitance per particle were identified using the proposed method. The selectivity of the method was demonstrated by performing electrical measurements on a third virus, revealing that the proposed technique is specific and sensitive enough to permit detection of a few hundred virus particles per milliliter within a few minutes.
High‐Speed Selective Electroplating with Single Circular Jets (1982)

High‐speed selective electroplating of circular deposits with a jet system was investigated by both experimental and theoretical studies. Direct measurement of current distribution was made with a sectioned electrode made of concentric rings. Three systems were studied, including alkaline ferricyanide reduction, copper deposition from acidified sulfate solution, and copper deposition from an acidified sulfate solution that also contained a ferric/ferrous redox couple. In these systems, current distribution data were obtained upon controlled variation of jet Reynolds number, electrolyte conductivity, reactant concentration, and applied total current. A mathematical model of the process was developed that included mass transfer, ohmic resistance, charge transfer, cell geometry, and multiple electrode reactions. The mathematical model was used to generate dimensionless contour maps indicating generalized conditions under which selective high‐speed electroplating can be accomplished.
List-mode maximum likelihood reconstruction of Compton scatter camera images in nuclear medicine (2002)

A Maximum Likelihood (ML) image reconstruction technique using list-mode data has been applied to Compton scattering camera imaging. List-mode methods are appealing in Compton camera image reconstruction because the total number of data elements in the list (the number of detected photons) is significantly smaller than the number of possible combinations of position and energy measurements, leading to a much smaller problem than that faced by traditional iterative reconstruction techniques. For a realistic size device, the number of possible detector bins can be as large as 10 billion per pixel of the image space, while the number of counted photons would typically be a very small fraction of that. The primary difficulty in applying the list-mode technique is in determining the parameters which describe the response of the imaging system. In this work, a simple method for determining the required system matrix coefficients is employed, in which a back-projection is performed in list-mode, and response coefficients determined for only tallied pixels. Projection data has been generated for a representative Compton camera system by Monte Carlo simulation for disk sources with hot and cold spots and energies of 141, 364, and 511 keV, and reconstructions performed.
Predictive screening of M1 and M2 macrophages reveals the immunomodulatory effectiveness of post spinal cord injury azithromycin treatment (2017)

Spinal cord injury (SCI) triggers a heterogeneous macrophage response that when experimentally polarized toward alternative forms of activation (M2 macrophages) promotes tissue and functional recovery. There are limited pharmacological therapies that can drive this reparative inflammatory state. In the current study, we used in vitro systems to comprehensively defined markers of macrophages with known pathological (M1) and reparative (M2) properties in SCI. We then used these markers to objectively define the macrophage activation states after SCI in response to delayed azithromycin treatment. Mice were subjected to moderate-severe thoracic contusion SCI. Azithromycin or vehicle was administered beginning 30 minutes post-SCI and then daily for 3 or 7 days post injury (dpi). We detected a dose-dependent polarization toward purportedly protective M2 macrophages with daily AZM treatment. Specifically, AZM doses of 10, 40, or 160 mg/kg decreased M1 macrophage gene expression at 3 dpi while the lowest (10 mg/kg) and highest (160 mg/kg) doses increased M2 macrophage gene expression at 7 dpi. Azithromycin has documented immunomodulatory properties and is commonly prescribed to treat infections in SCI individuals. This work demonstrates the utility of objective, comprehensive macrophage gene profiling for evaluating immunomodulatory SCI therapies and highlights azithromycin as a promising agent for SCI treatment.
Efficient luminescent solar cells based on tailored mixed-cation perovskites (2016)

We report on a new metal halide perovskite photovoltaic cell that exhibits both very high solar-to-electric power-conversion efficiency and intense electroluminescence. We produce the perovskite films in a single step from a solution containing a mixture of FAI, PbI2, MABr, and PbBr2 (where FA stands for formamidinium cations and MA stands for methylammonium cations). Using mesoporous TiO2 and Spiro-OMeTAD as electron- and hole-specific contacts, respectively, we fabricate perovskite solar cells that achieve a maximum power-conversion efficiency of 20.8% for a PbI2/FAI molar ratio of 1.05 in the precursor solution. Rietveld analysis of x-ray diffraction data reveals that the excess PbI2 content incorporated into such a film is about 3 weight percent. Time-resolved photoluminescence decay measurements show that the small excess of PbI2 suppresses nonradiative charge carrier recombination. This in turn augments the external electroluminescence quantum efficiency to values of about 0.5%, a record for perovskite photovoltaics approaching that of the best silicon solar cells. Correspondingly, the open-circuit photovoltage reaches 1.18 V under AM 1.5 sunlight.
Investigation of leucine‐rich repeat kinase 2 (2008)

Mutations in leucine-rich repeat kinase 2 (LRRK2) comprise the leading cause of autosomal dominant Parkinson's disease, with age of onset and symptoms identical to those of idiopathic forms of the disorder. Several of these pathogenic mutations are thought to affect its kinase activity, so understanding the roles of LRRK2, and modulation of its kinase activity,may lead to novel therapeutic strategies for treating Parkinson's disease. In this study, highly purified, baculovirus-expressed proteins have been used,for the first time providing large amounts of protein that enable a thorough enzymatic characterization of the kinase activity of LRRK2.Although LRRK2 undergoes weak autophosphorylation, it exhibits high activity towards the peptidic substrate LRRKtide, suggesting that it is a catalytically efficient kinase. We have also utilized a time-resolved fluorescence resonance energy transfer (TR-FRET) assay format (Lantha-ScreenTM) to characterize LRRK2 and test the effects of nonselective kinase inhibitors. Finally, we have used both radiometric and TR-FRETassays to assess the role of clinical mutations affecting LRRK2's kinase activity. Our results suggest that only the most prevalent clinical mutation,G2019S, results in a robust enhancement of kinase activity with LRRKtideas the substrate. This mutation also affects binding of ATP to LRRK2,with wild-type binding being tighter (Km,app of 57 lm) than with theG2019S mutant (Km,app of 134 lm). Overall, these studies delineate the catalytic efficiency of LRRK2 as a kinase and provide strategies by which a therapeutic agent for Parkinson's disease may be identified.
Self-adjusting nuclei segmentation (SANS) of Hematoxylin-Eosin stained histopathological breast cancer images (2016)

Hematoxylin-Eosin (H&E) stained breast cancer (BC) histopathological images are widely used in breast cancer diagnosis, for which segmenting the cells/nuclei from the images is a major operation. However, most of current methods are sensitive to the characteristics of the images. In this paper, we propose a self-adjusting method for adaptive cell/nuclei segmentation from HE BC images, which works on BC images of different types and quality. To deal with the diversity of nuclei sizes, our approach employs an ellipse detector to estimate nuclei size, which is essential for noise elimination and for addressing the cell overlap issue. Then we propose a novel seed detection method based on the topological skeleton model in the marker-controlled watershed transform framework. The experiment result shows that our method is effective and efficient, and outperforms the state-of-the-art approaches on various types of HE BC images.
Double hysteresis loop in (Pb0.90La0.10)Ti0.975O3∕Pb(Zr0.20Ti0.80)O3 bilayer thin films (2007)

( Pb 0.90 La 0.10 ) Ti 0.975 O 3 ∕ Pb ( Zr 0.20 Ti 0.80 ) O 3 bilayer thin films were fabricated using radio frequency magnetron sputtering with a PbOx buffer layer. The x-ray diffraction patterns show that the bilayers possess highly (100) orientation. Polarization hysteresis and capacitance-voltage characteristics of the bilayers show clear antiferroelectric (AFE) characteristics. The related mechanism for double hysteresis loop was also discussed. The competition among the intrinsic ferroelectric coupling at the interface between bilayers gives rise to an AFE polarization behavior.
HydDB: A web tool for hydrogenase classification and analysis (2016)

H<sub>2</sub> metabolism is proposed to be the most ancient and diverse mechanism of energy-conservation. The metalloenzymes mediating this metabolism, hydrogenases, are encoded by over 60 microbial phyla and are present in all major ecosystems. We developed a classification system and web tool, HydDB, for the structural and functional analysis of these enzymes. We show that hydrogenase function can be predicted by primary sequence alone using an expanded classification scheme (comprising 29 [NiFe], 8 [FeFe], and 1 [Fe] hydrogenase classes) that defines 11 new classes with distinct biological functions. Using this scheme, we built a web tool that rapidly and reliably classifies hydrogenase primary sequences using a combination of k-nearest neighbors' algorithms and CDD referencing. Demonstrating its capacity, the tool reliably predicted hydrogenase content and function in 12 newly-sequenced bacteria, archaea, and eukaryotes. HydDB provides the capacity to browse the amino acid sequences of 3248 annotated hydrogenase catalytic subunits and also contains a detailed repository of physiological, biochemical, and structural information about the 38 hydrogenase classes defined here. The database and classifier are freely and publicly available at http://services.birc.au.dk/hyddb/.
CHLOROSULFONATION OF 9-ARYL 3,3,6,6-TETRAMETHYLOCTAHYDROXANTHEN-1,8-DIONES (1993)

Abstract The 9-aryl-3,3,6,6-tetramethyloctahydroxanthendiones (4-20) react with chlorosulfonic acid to give the sulfonyl chlorides (25, 34, 43, 53, 55, 59, 63 and 65). The xanthendione (7) from m-anisaldehyde afforded the bis-sulfonyl chloride (30). The products were converted into 35 sulfonamides, 4-hydrazides (48, 56, 57, 69a) and 2 hydrazones (49, 69b) required for screening as potential pesticides. Dimedone (1) (2 moles) and cinnamaldehyde (1 mole) in ethanol-piperidine (catalyst) afforded an abnormal product probably (76), however an equimolar reaction with cinnamaldehyde or the α-methyl derivative in pyridine gave the 2-phenylpyrans (78, 79). Dimedone with salicylaldehyde or o-vanillin afforded the pyran derivatives (72, 73); the former reacted with chlorosulfonic acid to give the sulfonyl chloride (74), characterized as the morpholidate (75). The xanthendione (15) with chlorosulfonic acid afforded the chloride (70), characterized as the morpholidate (71). Attempted chlorosulfonation of the substrates (16, 77, 78 and 79) all gave impure products and 13 failed to react. The NMR spectral data of the compounds are briefly discussed.
On the Decreasing Power of Kernel and Distance based Nonparametric Hypothesis Tests in High Dimensions (2014)

This paper is about two related decision theoretic problems, nonparametric two-sample testing and independence testing. There is a belief that two recently proposed solutions, based on kernels and distances between pairs of points, behave well in high-dimensional settings. We identify different sources of misconception that give rise to the above belief. Specifically, we differentiate the hardness of estimation of test statistics from the hardness of testing whether these statistics are zero or not, and explicitly discuss a notion of "fair" alternative hypotheses for these problems as dimension increases. We then demonstrate that the power of these tests actually drops polynomially with increasing dimension against fair alternatives. We end with some theoretical insights and shed light on the \textit{median heuristic} for kernel bandwidth selection. Our work advances the current understanding of the power of modern nonparametric hypothesis tests in high dimensions.
Biodegradable Chitosan Nanoparticle Coatings on Titanium for the Delivery of BMP-2 (2015)

A simple method for the functionalization of a common implant material (Ti6Al4V) with biodegradable, drug loaded chitosan-tripolyphosphate (CS-TPP) nanoparticles is developed in order to enhance the osseointegration of endoprostheses after revision operations. The chitosan used has a tailored degree of acetylation which allows for a fast biodegradation by lysozyme. The degradability of chitosan is proven via viscometry. Characteristics and degradation of nanoparticles formed with TPP are analyzed using dynamic light scattering. The particle degradation via lysozyme displays a decrease in particle diameter of 40% after 4 days. Drug loading and release is investigated for the nanoparticles with bone morphogenetic protein 2 (BMP-2), using ELISA and the BRE luciferase test for quantification and bioactivity evaluation. Furthermore, nanoparticle coatings on titanium substrates are created via spray-coating and analyzed by ellipsometry, scanning electron microscopy and X-ray photoelectron spectroscopy. Drug loaded nanoparticle coatings with biologically active BMP-2 are obtained in vitro within this work. Additionally, an in vivo study in mice indicates the dose dependent induction of ectopic bone growth through CS-TPP-BMP-2 nanoparticles. These results show that biodegradable CS-TPP coatings can be utilized to present biologically active BMP-2 on common implant materials like Ti6Al4V.