gebhart/patrepeval huggingface dataset:
Determination of equilibrium and individual rate constants for subtilisin‐catalyzed transesterification in anhydrous environments (1992)

We report here the first determinations of individual rate constants and equilibrium constants for enzymatic reactions in essentially anhydrous organic solvents. Using the added nucleophile method we have measured the effect of changing solvent on the binding and catalytic steps for subtilisin-catalyzed transesterification of N-protected amino acid esters. The detailed information generated indicates that once the substrate has bound to the enzyme, the catalytic machinery can work at rates equivalent to those in water. The decreased overall rates for subtilisin suspended in anhydrous solvents are merely the result of extremely high values for K(s), in most cases, coupled with low concentrations of nucleophile ( approximately 1.0M in organic solvents, and 55M in water). The method described, which is generally applicable, and straightforward experimentally, will, we believe, enable a clearer understanding of how changing solvent can predictably affect the activity and specificity of the enzyme.
Ki-67 detects a nuclear matrix-associated proliferation-related antigen: II. Localization in mitotic cells and association with chromosomes (1989)

In interphase cells the proliferation-associated antigen recognized by monoclonal antibody Ki-67 is almost exclusively located in the nucleoli. When cells at several stages of mitosis were examined for the localization of the Ki-67 antigen, a striking redistribution could be observed. During prophase the distinct nucleolar Ki-67 fluorescence changed to a bright irregular meshwork throughout the nucleoplasm. At metaphase the antigen appeared to be distributed in a reticulate structure surrounding the condensed chromosomes, while at late telophase a punctated staining of the entire nucleoplasm was observed, which preceded the typical nucleolar localization pattern in each of the two daughter cells. Immunolabelling with Ki-67 of metaphase chromosome spreads revealed a circumferential staining of the individual chromosomes. The Ki-67 antigen is preserved in nuclear matrix preparations obtained after in situ fractionation of interphase cells. When mitotic cells were exposed to such treatments, the obtained fluorescence data suggested that the antigen may be part of the chromosome scaffold. Quantification of the Ki-67 fluorescence signal using flow cytometry revealed the highest staining intensities in mitotic cells. Furthermore, it was shown that nutritionally deprived cells became negative for Ki-67.
Home energy management system based on power line communication (2010)

This paper describes a home energy management system (HEMS) based on power line communication. Smart metering and power line communication can provide detailed information of energy consumption patterns and intelligent controlling to appliances at home. We propose a HEMS that can provide easy-to-access information on home energy consumption in real time, intelligent planning for controlling appliances, and optimization of power consumption at home. The HEMS consists of three modules: an advanced power control planning engine, a device control module, and a power resource management server. Our prototype system reduces the cost of power consumption by about 10%.
Macrophage-Induced Genes of<i>Legionella pneumophila:</i>Protection from Reactive Intermediates and Solute Imbalance during Intracellular Growth (2002)

A promoter-probe strategy was devised to identify genes specifically expressed by Legionella pneumophila during growth within the macrophage. Random fragments from the L. pneumophila chromosome were inserted upstream of a promoterless phage T4 td gene, and fragments that led to complementation of thymine auxotrophy during intracellular growth of the bacterium were identified. Two different selection strategies were employed to eliminate promoters that were also active during extracellular growth of the bacterium. Some of these genes were identified independently by using both of the selection strategies. The factors identified include orthologs of efflux-mediated resistance determinants and transporters, a transporter involved in protection from osmotic stress, a stress response GTP-binding protein, a response regulator, a sensor kinase, and two systems that increase the reducing potential of the bacterium, one of which encodes the L. pneumophila ortholog of ahpC. Five of the clones analyzed here were fusions to promoters that were closely linked to genes encoding three-component chemiosmotic efflux pumps that export heavy metals or toxic organic compounds. Analysis of ahpC gene expression indicates that levels increased at least sevenfold during intracellular growth of the bacterium. Inactivation of several of the genes at their chromosomal loci had no effect on the intracellular growth rate of L. pneumophila in cultured macrophages. This suggests that a number of genes with increased expression during intracellular growth may be part of redundant systems that allow survival and growth under the conditions encountered within host cells.
Real-Time Document Localization in Natural Images by Recursive Application of a CNN (2017)

Seamless integration of information from digital and paper documents is crucial for efficient knowledge management. One convenient way to achieve this is to digitize a document from a natural image. This requires precise localization of the document in the image. Several methods have been proposed to solve this problem but they rely on traditional image processing techniques which are not robust to extreme viewpoint and background variations. Deep Convolutional Neural Networks (CNNs), on the other hand, have shown to be extremely robust to variations in background and viewpoint in object detection and classification tasks. Inspired by their robustness and generality, we propose a novel CNN based method to accurately localize documents in real-time. We model localization problem as a key point detection problem. The four corners of the documents are jointly predicted by a Deep Convolutional Neural Network. We then refine our prediction using a novel recursive application of a CNN. Performance of the system is evaluated on ICDAR 2015 SmartDoc Competition 1 dataset. The results are comparable to state of the art on simple backgrounds and improve the state of the art to 94% from the previous 86% on the complex background. Code, dataset, and models are available at: https://github.com/KhurramJaved96/Recursive-CNNs.
Micropreparative two‐dimensional electrophoresis allowing the separation of samples containing milligram amounts of proteins (1993)

We describe some simple modifications to the micropreparative two-dimensional (2-D) electrophoresis procedure using immobilized pH gradients in the first dimension and sodium dodecyl sulfate-electrophoresis in the second dimension. The geometry of the immobilized pH gradient strips has been changed to allow the use of large sample application cups that can accommodate greater sample volumes. The use of narrow range immobilized pH gradients with a large sample loading volume allows an efficient resolubilization of polypeptides after the first dimension. As a result, the vertical streaking caused by too high a protein concentration is eliminated in the second dimension. Protein identification by N-terminal sequencing is facilitated by the large protein load (1-15 mg) which can be employed using this modification. Spots not normally detectable on conventional analytical 2-D maps, even with sensitive silver staining, are observed. Results for plasma and liver proteins are shown.
Security-aware ad hoc routing for wireless networks (2001)

We propose a new routing technique called Security-Aware ad hoc Routing (SAR) that incorporates security attributes as parameters into ad hoc route discovery. SAR enables the use of security as a negotiable metric to improve the relevance of the routes discovered by ad hoc routing protocols. We develop a two-tier classification of routing protocol security metrics, and propose a framework to measure and enforce security attributes on ad hoc routing paths. Our framework enables applications to adapt their behavior according to the level of protection available on communicating nodes in an ad hoc network.
AN ADAPTIVE BASEBAND EQUALIZER FOR HIGH DATA RATE BANDLIMITED CHANNELS (2006)

ITC/USA 2006 Conference Proceedings / The Forty-Second Annual International Telemetering Conference and Technical Exhibition / October 23-26, 2006 / Town and Country Resort & Convention Center, San Diego, California
Inhibition of iNOS as a novel effective targeted therapy against triple-negative breast cancer (2015)

Considering the effectiveness of L-NMMA in decreasing tumor growth and enhancing survival rate in TNBC, we propose a targeted therapeutic clinical trial by re-purposing the pan-NOS inhibitor L-NMMA, which has been extensively investigated for cardiogenic shock as an anti-cancer therapeutic.
Improving baculovirus recombination (2003)

Recombinant baculoviruses have established themselves as a favoured technology for the high-level expression of recombinant proteins. The construction of recombinant viruses, however, is a time consuming step that restricts consideration of the technology for high throughput developments. Here we use a targeted gene knockout technology to inactivate an essential viral gene that lies adjacent to the locus used for recombination. Viral DNA prepared from the knockout fails to initiate an infection unless rescued by recombination with a baculovirus transfer vector. Modified viral DNA allows 100% recombinant virus formation, obviates the need for further virus purification and offers an efficient means of mass parallel recombinant formation.
ANTIOXIDANT PROPERTIES OF SOME NANOPARTICLE MAY ENHANCE WOUND HEALING IN T2DM PATIENT (2008)

The delayed wound healing is a well known problem with Type 2 diabetic patient (T2DM). Understanding wound healing today involves much more than simply stating that there are three phases: “inflammation, proliferation, and maturation.” Wound healing is a complex series of reactions and interactions among cells and “mediators.” Each year, new mediators are discovered and our understanding of inflammatory mediators and cellular interactions grows. However, the lack of understanding of the molecular mechanisms and pathogenesis of impaired healing in chronic ulcer is a serious health care problem that contributes to excessive limb amputation and mortality. Oxidative stress is a major contributes for delayed wound healing and produce tremendous amount of ROS this is very harmful for surrounding tissue or cells. Recently, it was shown in some literature that few metal oxide nanoparticle like Al2O3, CeO2, Y2O3, act as a ROS scavenger. The essentials of nanoparticle in ROS scavenging system have been presented in this article, which has portrayed current thinking that speculates the use of nanoparticle is another likely to cure of impaired healing of diabetic foot wounds. Thus nanoparticle mediated diabetic wound healing could also be clinically significant.
Reducing Crosstalk of Silicon-based Optical Switch with All-optical Multi-wavelength Regenerator (2017)

Improving crosstalk performance of Mach–Zehnder-interferometer-type optical switches is experimentally investigated by use of an all-optical multi-wavelength regenerator. Extinction ratio and bit error rate of WDM signals are simultaneously improved in proposed regenerative optical switching.
Safety and feasibility of oral immunotherapy to multiple allergens for food allergy (2014)

Clinicaltrial.gov NCT01490177.
Isolation of Breast Cancer Stem Cells by Single-Cell Sorting (2012)

researched by various groups worldwide. Strategies include targeting the self-renewal of BCSCs [30]; [31], indirectly targeting the microenvironment [29]; [50]; [31] and directly killing BCSCs by chemical agents that induce differentiation [25]; [19]; [42]; [43], immunotherapy [4]; [5]; [40] and oncolytic viruses [26]; [34].
Externalization of the leaderless cytokine IL-1F6 occurs in response to LPS/ATP activation of transduced bone marrow derived macrophages (38.10) (2009)

Abstract Interleukin (IL)-1F6, like many members of the IL-1 cytokine family, lacks a signal sequence. Moreover, IL-1F6 does not contain an obvious prodomain or a caspase cleavage site but is somehow released to act on target cells. The mechanism of cellular export of IL-1F6 was compared to that employed by IL-1β. In the case of IL-1β, release of the mature processed cytokine is induced by treating lipopolysaccharide (LPS)-primed monocytes/macrophages with an agonist of the P2X7 receptor, such as adenosine 5’-triphosphate (ATP). Mouse bone marrow derived macrophages (BMDMs) were selected as the model system because they express the P2X7 receptor and because they can be engineered via retroviral transduction to express genes of interest. Stable populations of BMDMs transduced with retroviral vectors encoding full length IL-1F6 or green fluorescent protein (GFP) constitutively expressed IL-1F6 and GFP but did not constitutively release these polypeptides to the medium. Evidence is presented that IL-1F6 can be externalized rapidly in response to sequential LPS and ATP activation via a non-selective process. Therefore, externalization of IL-1F6 from cells engaged in the synthesis of this cytokine proceeds in vitro via a stimulus-coupled mechanism similar to that employed by IL-1β.
Assigning videos to textbooks at appropriate granularity (2014)

The emergence of tablet devices, cloud computing, and abundant online multimedia content presents new opportunities to transform traditional paper-based textbooks into tablet-based electronic textbooks, and to further augment the educational experience by enriching them with relevant supplementary materials. Given a candidate set of relevant educational videos for augmenting an electronic textbook, how do we assign the videos at the appropriate granularity (a collection of logical units in the book)? We propose a rigorous formulation of the video assignment problem and present an algorithm for assigning each video to the optimum subset of logical units. Our experimental evaluation using a diverse collection of educational videos relevant to multiple chapters in a textbook demonstrates the efficacy of the proposed techniques for inferring the granularity at which a relevant video should be assigned.
Probucol promotes endogenous antioxidants and provides protection against adriamycin-induced cardiomyopathy in rats. (1994)

These data provide evidence that ADR cardiomyopathy is associated with an antioxidant deficit. Improved cardiac function resulting from treatment with probucol may be related to the maintenance of the antioxidant status of the heart. The study suggests potential usefulness of antioxidant (probucol) therapy in ADR cardiomyopathy.
monocyte CC chemokine receptor selective for MIP-la, MIP-1 3, and RANTES (2015)

Abstract: We have cloned a human cDNA for a novel CC chemokine receptor (CC CMI) designated cc CKR5 that has 48-75 % amino acid identity to other CC CKRs. CC CKR5 mRNA was detected constitutively in primary adherent monocytes but not in primary neutrophils or eosinophils. Macrophage inflammatory protein-la (MIP-la), MIP-13, and RANTES were all potent agonists for CC CKR5 (EC50 = 3-30 nM) when calcium flux was measured in transfected HEK 293 cells, yet the apparent binding affinities of the corresponding iodinated chemokines to intact cells expressing the receptor were low (1C50 o.olOO nM). The calcium flux responses were com-pletely blocked by treatment of transfected cells with pertussis toxin. These data suggest that CC CKR5 is a G1-coupled receptor that may mediate monocyte
Direct patterning of complex oxides by pulsed laser deposition through stencils (2007)

The possibilities to grow isolated structures of complex oxides by pulsed laser deposition through stencils were investigated. A stencil consisting of a SiN membrane with apertures of several hundred nanometers embedded in a Si chip is placed in front of a heated substrate (up to 750 degrees Celsius). Deposition through these apertures results in resistless, direct patterning by local deposition of complex oxides like ferroelectric Lead Zirconate Titanate. The created isolated structures were analyzed by AFM imaging. Under-deposition, in this work called broadening, is inevitable during stencil deposition and is depending on deposition parameters, especially pressure. Different causes of broadening are mapped and discussed.
Systematic review: primary and secondary prevention of gastrointestinal cancers with antioxidant supplements (2008)

We could not find evidence that the studied antioxidant supplements prevented gastrointestinal cancers. On the contrary, they seem to increase overall mortality.
Epstein-Barr virus-specific cytotoxic T lymphocytes as probes of HLA polymorphism. Heterogeneity of T cell-restricting determinants associated with the serologically defined HLA-A2 antigen. (1983)

Epstein-Barr (EB) virus-specific effector T cell lines were established from nine virus-immune donors positive for the serologically defined HLA-A2 antigen; of these, four lines contained a demonstrable A2-restricted cytotoxic component. When these four effector populations were each tested on the same panel of EB virus-transformed lines from 20 HLA-A2-positive individuals, 16 of the target cell lines were consistently killed at levels above 25% of the relevant autologous cell lysis. Cytotoxicity appeared to be mediated through a restricting determinant associated with the 'common A2' antigen that these lines shared; indeed the lysis could be specifically blocked by high concentrations of an HLA-A2-specific monoclonal antibody. In contrast, 4 out of 20 target cell lines were not killed by HLA-A2-restricted effector cells, even though they did express the serologically defined A2 antigen and were found in other tests to be susceptible to EB virus-specific cytolysis restricted through other HLA-A or -B antigens on their surface. These results suggest that EB virus-specific cytotoxic T cells can distinguish between serologically identical HLA-A2 molecules via the heterogeneity of their T cell-restricting determinants. Data from one of the effector cell populations further suggested that a serologically defined cross-reaction between the otherwise distinct HLA-A2 and -Bw57 antigens might also be reflected in a cross-reactivity of T cell-restricting determinants.
4 × 20  Gbit/s mode division multiplexing over free space using vector modes and a q-plate mode (de)multiplexer (2015)

Vector modes are spatial modes that have spatially inhomogeneous states of polarization, such as, radial and azimuthal polarization. In this work, the spatially inhomogeneous states of polarization of vector modes are used to increase the transmission data rate of free-space optical communication via mode division multiplexing. A mode (de)multiplexer for vector modes based on a liquid crystal q-plate is introduced. As a proof of principle, four vector modes each carrying a 20-Gbit/s quadrature phase shift keying signal (aggregate 80 Gbit/s) on a single wavelength channel (λ∼1550 nm) were transmitted ∼1 m over the lab table with <-16.4 dB mode crosstalk. Bit error rates for all vector modes were measured at the 7% forward error correction threshold with power penalties <3.41 dB.
Performance of titanium oxide–polymer insulation in superconducting coils made of Bi-2212/Ag-alloy round wire (2013)

Conductor insulation is one of the key components needed to make Ag-alloy clad Bi2Sr2CaCu2O8+x (Bi-2212/Ag) superconducting round wire (RW) successful for high field magnet applications, as dielectric standoff and high winding current densities (Jw) directly depend on it. In this study, a TiO2–polymer insulation coating developed by nGimat LLC was applied to test samples and a high field test coil. The insulation was investigated by differential thermal analysis (DTA), thermo-gravimetric analysis (TGA), scanning electron microscopy (SEM), dielectric property measurement, and transport critical current (Ic) property measurement. About 29% of the insulation by weight is polymer. When the Bi-2212/Ag wire is fully heat treated, this decomposes with slow heating to 400 ° C in pure O2. After the full reaction, we found that the TiO2 did not degrade the critical current properties, adhered well to the conductor, and provided a breakdown voltage of more than 100 V, which allowed the test coil to survive quenching in 31.2 T background field, while providing a 2.6 T field increment. For Bi-2212/Ag RW with a typical diameter of 1.0–1.5 mm, this ∼15 μm thick insulation allows a very high coil packing factor of ∼0.74, whereas earlier alumino-silicate braid insulation only allows packing factors of 0.38–0.48.
CTH09-4: A Lattice-Reduction-Aided Soft Detector for Multiple-Input Multiple-Output Channels (2006)

Lattice basis reduction is a powerful technique that enables a hard-output detector for a multiple-input multiple-output channel to approach maximum-likelihood performance with low complexity. In this work we propose a soft-output detector that combines lattice- reduction-aided detection and list decoding. The proposed algorithm performs nearly as well as the list-sphere detector but with much lower complexity. Numerical results reveal that the complexity per bit for the proposed algorithm decreases as the size of the QAM alphabet increases.
Solving the sorting network problem using iterative optimization with evolved hypermutations (2009)

This paper presents an application of a prototype optimization with evolved improvement steps algorithm (POEMS) to the well-known problem of optimal sorting network design. The POEMS is an iterative algorithm that seeks the best variation of the current solution in each iteration. The variations, also called hypermutations, are evolved by means of an evolutionary algorithm. We compared the POEMS to two mutation-based optimizers, namely the (\mu+\lambda)- and (1+\lambda)-evolution strategies. For experimental evaluation 10-input, 12-input, 14-input and 16-input instances of the sorting network problem were used. Results show that the proposed POEMS approach clearly outperforms both compared algorithms. Moreover, POEMS was able to find several perfect networks that are equivalent w.r.t. the number of comparators to the best known solutions for the 10-input, 12-input, 14-input, and 16-input problems. Finally, we propose a modification to the POEMS approach that might further improve its performance.