gebhart/patrepeval huggingface dataset:
Enhanced radiation response in radioresistant MCF-7 cells by targeting peroxiredoxin II (2013)

In our previous study, we identified that a protein target, peroxiredoxin II (PrxII), is overexpressed in radioresistant MCF+FIR3 breast-cancer cells and found that its expression and function is associated with breast-cancer radiation sensitivity or resistance. Small interference RNA (siRNA) targeting PrxII gene expression was able to sensitize MCF+FIR3 radioresistant breast-cancer cells to ionizing radiation. The major focus of this work was to investigate how the radiation response of MCF+FIR3 radioresistant cells was affected by the siRNA that inhibits PrxII gene expression. Our results, presented here, show that silencing PrxII gene expression increased cellular toxicity by altering cellular thiol status, inhibiting Ca(2+) efflux from the cells, and perturbing the intracellular Ca(2+) homeostasis. By combining radiotherapy and siRNA technology, we hope to develop new therapeutic strategies that may have potential to enhance the efficacy of chemotherapeutic agents due to this technology's property of targeting to specific cancer-related genes.
On the concept and the interest of virtual power plant: Some results from the European project Fenix (2009)

In order to manage distributed generation and to enhance its valorization within electrical distribution systems, the concept of virtual power plant (VPP) has emerged and is used by many research teams worldwide. It consists in aggregating various small size generating units to form a ldquosingle virtual generating unitrdquo that can behave as a conventional one. Such a concept is under development within the EU project FENIX. Two types of aggregation are considered by the FENIX project: the commercial virtual power plant (CVPP) that tackles the aggregation of small generating units with respect to market integration and the technical virtual power plant (TVPP) that tackles aggregation of these units with respect to services that can be offered to the grid. The voltage and congestion management of network are the two major services that are detailed in this paper.
In Support of Commercial Applications of Miniemulsion Polymerization (2022)

This paper is not meant as a review of miniemulsion polymerization, but as a personal commentary from one who has seen its development at close range, on the potential of this technology for further commercialization. The paper discusses its advantages and disadvantages (over conventional emulsion polymerization), misconceptions about the technology, and specific areas in which its implementation might be highly beneficial.
Targeted Next-Generation Sequencing Identifies Pathogenic Variants in Diabetic Kidney Disease (2021)

Our findings suggest that rare variants in kidney disease-related genes in a diabetic background may play a role in the pathogenesis of DKD and NDKD in patients with diabetes.
Color image contrast enhacement method based on differential intensity/saturation gray-levels histograms (2013)

Histogram equalization (HE) is a simple and effective method for contrast enhancement as it can automatically define the gray-levels transformation function based on the distribution of gray-levels included in the image. HE fails to produce satisfactory results for a broad variety of low-contrast images because the HE does not use a spatial feature included in the input image. The differential gray-levels histogram which is contained edge information of the input image, were defined. Furthermore, the differential gray-levels histogram equalization (DHE) has been proposed. The DHE shows better enhancement results compared to the HE results for many kinds of images. In this paper, we propose a DHE method for color images. In the case of color images, two differential gray-level histograms can be defined. One is intensity gray-levels histogram, the other is saturation gray-levels histogram. The differential histogram for color image is defined in combination with two gray-levels histograms. The DHE method is extended to the color image processing by using the differential gray-levels histogram for color image. The proposed method has one parameter and the emphasis property of color images can be controlled by the parameter. The guideline for decision of the parameter which is agreed in a human sense is shown.
Semi-supervised Bi-dictionary Learning Using Smooth Representation-Based Label Propagation (2015)

Due to heavy clutters and occlusions of complex background, natural images contain complex features in data structure which often cause errors in image classification. In this paper, we propose semi-supervised bi-dictionary learning for image classification with smooth representation-based label propagation (SRLP) which extends reconstruction-based classification in a probabilistic manner. First, we jointly learn a discriminative dictionary in the feature space and its corresponding soft label in the label space. Then, we utilize the learnt bi-dictionary in image classification based on SRLP. Experimental results demonstrate that the proposed SRLP is capable of learning the discriminative bi-dictionary for image classification and outperforms the-state-of-the-art reconstruction-based classification methods.
Crystal Structure of the Mitotic Spindle Kinesin Eg5 Reveals a Novel Conformation of the Neck-linker (2001)

Success of mitosis depends upon the coordinated and regulated activity of many cellular factors, including kinesin motor proteins, which are required for the assembly and function of the mitotic spindle. Eg5 is a kinesin implicated in the formation of the bipolar spindle and its movement prior to and during anaphase. We have determined the crystal structure of the Eg5 motor domain with ADP-Mg bound. This structure revealed a new intramolecular binding site of the neck-linker. In other kinesins, the neck-linker has been shown to be a critical mechanical element for force generation. The neck-linker of conventional kinesin is believed to undergo an ordered-to-disordered transition as it translocates along a microtubule. The structure of Eg5 showed an ordered neck-linker conformation in a position never observed previously. The docking of the neck-linker relies upon residues conserved only in the Eg5 subfamily of kinesin motors. Based on this new information, we suggest that the neck-linker of Eg5 may undergo an ordered-to-ordered transition during force production. This ratchet-like mechanism is consistent with the biological activity of Eg5.
A RANDOMIZED CONTROLLED TRIAL OF INTRAVESICAL BACILLUS CALMETTE-GUERIN FOR TREATMENT REFRACTORY INTERSTITIAL CYSTITIS (2005)

Although the BCG safety profile was acceptable, the response rate for the primary outcome was low. Effective medical treatment for patients with moderate to severe interstitial cystitis remains elusive.
UV written waveguides for photonic quantum circuits (2009)

Integrated optical circuits provide an important technology within optical telecommunications, and are also major subjects of research in optical chemical and biological sensors. Recently, however, their application in quantum information processing has attracted considerable attention within the research community, as they offer a robust and reliable route to realising experiments on a chip that would require whole optical benches of bulk optics. This talk will provide a background to technologies for creating optical circuitry, review their existing uses within optics, will look at the elements required to achieve meaningful quantum operations, and will highlight the recent uses of laser direct write to create optical waveguides. In particular, the UV direct write approach pioneered at COM in Denmark and at the ORC in Southampton will be shown to allow the creation of low loss, fibre compatible waveguides, enables the fabrication of cross-couplers and allows ready incorporation of Bragg gratings, thermo-optic elements and liquid crystal tunable elements. Results from the application of UV written waveguides to quantum circuits will be presented.
Cardiac Microlesions Form During Severe Bacteremic Enterococcus faecalis Infection (2020)

Enterococcus faecalis is a significant cause of hospital-acquired bacteremia. Herein, the discovery is reported that cardiac microlesions form during severe bacteremic E. faecalis infection in mice. The cardiac microlesions were identical in appearance to those formed by Streptococcus pneumoniae during invasive pneumococcal disease. However, E. faecalis does not encode the virulence determinants implicated in pneumococcal microlesion formation. Rather, disulfide bond forming protein A (DsbA) was found to be required for E. faecalis virulence in a Caenorhabditis elegans model and was necessary for efficient cardiac microlesion formation. Furthermore, E. faecalis promoted cardiomyocyte apoptotic and necroptotic cell death at sites of microlesion formation. Additionally, loss of DsbA caused an increase in proinflammatory cytokines, unlike the wild-type strain, which suppressed the immune response. In conclusion, we establish that E. faecalis is capable of forming cardiac microlesions and identify features of both the bacterium and the host response that are mechanistically involved.
Next Generation Technology-Enhanced Assessment (2017)

The use of technology for workplace and occupational testing blossomed in the early years of this century. This book offers a demonstration that the first generation of these technologies have now been implemented long enough to observe the patterns and issues that emerge when these approaches evolve through technical advancement and successive application. A new set of issues and opportunities has emerged and the next generation of these applications is now coming of age. This book reflects on the last few decades of this evolutionary process from a vantage point of global experience across a wide range of workplace applications, including employment selection, development, and occupational certification. The themes and issues that arise as this broad treatment unfolds provide an essential foundation for students, researchers, and professionals who are involved with the assessment of human capability and potential in organizational and workplace contexts
Monotonic algorithms for transmission tomography (1999)

We present a framework for designing fast and monotonic algorithms for transmission tomography penalized-likelihood image reconstruction. The new algorithms are based on paraboloidal surrogate functions for the log likelihood. Due to the form of the log-likelihood function it is possible to find low curvature surrogate functions that guarantee monotonicity. Unlike previous methods, the proposed surrogate functions lead to monotonic algorithms even for the nonconvex log likelihood that arises due to background events, such as scatter and random coincidences. The gradient and the curvature of the likelihood terms are evaluated only once per iteration. Since the problem is simplified at each iteration, the CPU time is less than that of current algorithms which directly minimize the objective, yet the convergence rate is comparable. The simplicity, monotonicity, and speed of the new algorithms are quite attractive. The convergence rates of the algorithms are demonstrated using real and simulated PET transmission scans.
Oxidized phospholipids inhibit cyclooxygenase-2 in human macrophages via nuclear factor-κB/IκB- and ERK2-dependent mechanisms (2002)

ox-PAPC down-regulates LPS-induced Cox-2 expression in human macrophages by targeting both NF-kappaB/IkappaB and ERK2 pathways. An altered inflammatory response by macrophages within atheromata may contribute to the progression of atherosclerosis.
Ovothiol: a novel thiohistidine compound from sea urchin eggs that confers NAD(P)H-O2 oxidoreductase activity on ovoperoxidase. (1986)

Sea urchin eggs contain a small molecular weight heat-stable factor that confers cyanide-resistant NAD(P)H-O2 oxidoreductase activity on ovoperoxidase (Turner, E., Somers, C. E., and Shapiro, B. M. (1985) J. Biol. Chem. 260, 13163-13171), the enzyme responsible for cross-linking the extracellular protein coat (fertilization membrane) of the egg. Here we report the isolation of the active cofactor and its identification by ultraviolet, NMR, and mass spectroscopy as a new sulfur-containing amino acid derivative, 1-methyl-alpha N,alpha N-dimethyl-4-thiohistidine, or ovothiol. Ovothiol reacts slowly with atmospheric oxygen or rapidly with micromolar concentrations of H2O2 to form ovothiol disulfide, which is inactive as a cofactor for the ovoperoxidase NAD(P)H oxidase. Reduced active ovothiol is regenerated by treatment with disulfide reductants and shows significant differences in its ultraviolet and NMR spectra from oxidized ovothiol. The oxidoreductase activity of the ovoperoxidase/ovothiol system is similar to that previously characterized with crude cofactor preparations; it is greatly enhanced by Mn2+ and is relatively insensitive to CN-, compared to the peroxidase activity of ovoperoxidase. The ovothiol content of eggs is estimated as 1.8 pmol/egg or an intracellular concentration of 6.8 mM. This concentration exceeds the amount of reductant needed for the CN-(-)insensitive oxygen consumption following fertilization and used in the production of H2O2 for fertilization membrane cross-linking. Whether ovothiol is involved in the cross-linking reaction, protects the egg from damage from H2O2, or has another role in development remains unclear.
All-semiconductor plasmonic gratings for biosensing applications in the mid-infrared spectral range (2016)

We propose 1D periodic, highly doped InAsSb gratings on GaSb substrates as biosensing platforms applicable for surface plasmon resonance and surface enhanced infrared absorption spectroscopies. Based on finite-difference time-domain simulations, the electric field enhancement and the sensitivity on refractive index variations are investigated for different grating geometries. The proposed, optimized system achieves sensitivities of 900 nm RIU<sup>-1</sup>. A clear red shift of the plasmon resonance as well as the enhancement of an absorption line are presented for 2 nm thin adlayers in simulations. We experimentally confirm the high sensitivity of the InAsSb grating by measurements of the wavelength shift induced by a 200 nm thin polymethylmethacrylate layer and demonstrate an enhancement of vibrational signals. A comparison to a gold grating with equivalent optical properties in the mid-infrared is performed. Our simulations and experimental results underline the interest in the alternative plasmonic material InAsSb for highly sensitive biosensors for the mid-infrared spectral range.
Ionic Liquid-in-Water Emulsions Stabilized by Molecular and Polymeric Surfactants (2023)

Ionic liquids have drawn notable attention for their unique solvent properties and use in applications such as batteries and chemical separations. While many ionic liquids are water-soluble, there are numerous examples of ionic liquids that are sufficiently hydrophobic to remain phase separated from water. However, relatively little is known about the stability and properties of ionic liquid-in-water emulsions. Here, we survey a series of ionic liquid-in-water emulsions stabilized by a range of ionic and nonionic molecular surfactants and polymers. To assess droplet stability and dynamics, we characterize the ionic liquid-surfactant interfacial tension, describe qualitative coarsening rates, and quantify droplet solubilization rate. In some instances, we observe unexpected spontaneous formation of complex double and triple emulsions. Our observations highlight approaches for ionic liquid emulsion formulation and provide insight into how to address challenges surrounding stabilization of ionic liquid-in-water droplets with molecular surfactants.
Personal Health Records: Definitions, Benefits, and Strategies for Overcoming Barriers to Adoption (2005)

Recently there has been a remarkable upsurge in activity surrounding the adoption of personal health record (PHR) systems for patients and consumers. The biomedical literature does not yet adequately describe the potential capabilities and utility of PHR systems. In addition, the lack of a proven business case for widespread deployment hinders PHR adoption. In a 2005 working symposium, the American Medical Informatics Association's College of Medical Informatics discussed the issues surrounding personal health record systems and developed recommendations for PHR-promoting activities. Personal health record systems are more than just static repositories for patient data; they combine data, knowledge, and software tools, which help patients to become active participants in their own care. When PHRs are integrated with electronic health record systems, they provide greater benefits than would stand-alone systems for consumers. This paper summarizes the College Symposium discussions on PHR systems and provides definitions, system characteristics, technical architectures, benefits, barriers to adoption, and strategies for increasing adoption.
Feature enhancement based on generative-discriminative hybrid approach with gmms and DNNS for noise robust speech recognition (2015)

This paper presents a technique that combines generative and discriminative approaches with Gaussian mixture models (GMMs) and deep neural networks (DNNs) for model-based feature enhancement. Typical model-based feature enhancement employs a generative model approach. The enhanced features are obtained by using the weighted sum of linear transformations given by each Gaussian component contained in GMMs and corresponding posterior probabilities. The computation of posterior probabilities is a crucial factor for this kind of feature enhancement, and can also be formulated as the class discrimination problem of observed noisy features. The prominent discriminability of DNNs is a well-known solution to this discrimination problem. Therefore, we propose the use of DNNs for computing posterior probabilities. The proposed method incorporates the benefit of the discriminative approach into the generative approach. For AURORA2 task evaluations, the proposed method provided noticeable improvements compared with results obtained using the conventional generative model approach.
A novel platform for the production of nonhydroxylated gelatins based on the methylotrophic yeastHansenula polymorpha (2007)

The use of yeast as a host for heterologous expression of proteins that are normally derived from animal tissue is a promising way to ensure defined products that are devoid of potential harmful animal side products. Here we report on the production and secretion of a custom-designed gelatin, Hu3-His8, by the yeast Hansenula polymorpha. We observed that Hu3-His8 was poorly secreted by the heterologous Saccharomyces cerevisiae invertase secretion signal. In contrast, the S. cerevisiae mating factor alpha prepro sequence efficiently directed secretion into the culture medium. However, at higher copy numbers, intracellular accumulation of Hu3-His8 precursors occurred. Overproduction of Erv29p, a protein required for packaging of the glycosylated pro-alpha factor into COPII vesicles, did not improve gelatin secretion in the multicopy strain. Previously, H. polymorpha was reported to hydroxylate proline residues in gelatinous sequences. In contrast, we were unable to detect hydroxyprolines in the secreted Hu3-His8. Also, we failed to identify a gene encoding prolyl-4-hydroxylase in the H. polymorpha genome.
Measurements of Islet Function and Glucose Metabolism with the Dipeptidyl Peptidase 4 Inhibitor Vildagliptin in Patients with Type 2 Diabetes (2007)

Vildagliptin improves islet function in T2DM and improves glucose metabolism in peripheral tissues.
Inhibition of bacterial aminopropyltransferases by S‐adenosyl‐1,8‐diamino‐3‐thiooctane and by dicyclohexylamine (1983)

Bacterial aminopropyltransferases from Escherichia coli, Serratia marcescens and Pseudomonas aeruginosa were strongly inhibited by S-adenosyl-1,8-diamino-3-thiooctane (AdoDATO) and by dicyclohexylamine. The sensitivity to these drugs in vitro was comparable to that of mammalian spermidine synthase, but AdoDATO was much less potent in reducing spermidine content in the bacteria than in mammalian cells. Although AdoDATO was a stronger inhibitor than dicyclohexylamine in vitro, dicyclohexylamine was more active in reducing bacterial spermidine levels in vivo, suggesting that it is taken up better or is more stable in the cell and is the preferable compound for in vivo studies in microorganisms. The strong inhibition of spermidine synthases by AdoDATO which is a transition state analog supports the concept that these enzymes proceed by a single displacement reaction, rather than by a ping-pong mechanism.
The Hypervariable Immunodominant NP418-426Epitope from the Influenza A Virus Nucleoprotein Is Recognized by Cytotoxic T Lymphocytes with High Functional Avidity (2006)

Recently it was shown that influenza A viruses can accumulate mutations in epitopes associated with escape from recognition by human virus-specific cytotoxic T lymphocytes (CTL). It is unclear what drives diversification of CTL epitopes and why certain epitopes are variable and others remain conserved. It has been shown that simian immunodeficiency virus-specific CTL that recognize their epitope with high functional avidity eliminate virus-infected cells efficiently and drive diversification of CTL epitopes. T-cell functional avidity is defined by the density of major histocompatibility complex class I peptide complexes required to activate specific CTL. We hypothesized that functional avidity of CTL contributes to epitope diversification and escape from CTL also for influenza viruses. To test this hypothesis, the functional avidity of polyclonal CTL populations specific for nine individual epitopes was determined. To this end, peripheral blood mononuclear cells from HLA-A- and -B-genotyped individuals were stimulated in vitro with influenza virus-infected cells to allow expansion of virus-specific CTL, which were used to determine the functional avidity of CTL specific for nine individual epitopes in enzyme-linked immunospot assays. We found that the functional avidity for the respective epitopes varied widely. Furthermore, the functional avidity of CTL specific for the hypervariable NP(418-426) epitope was significantly higher than that of CTL recognizing other epitopes (P < 0.01). It was speculated that the high functional avidity of NP(418-426)-specific CTL was responsible for the diversification of this influenza A virus CTL epitope.
Incoherent digital holography system utilizing single-shot phase-shifting interferometry (2017)

We propose single-shot incoherent digital holography with a common-path configuration and single-shot four-step phase-shifting interferometry and construct a system based on the proposal. Space-division multiplexing and states of the polarizations of the waves are utilized to implement single-shot phase-shifting interferometry. A common-path setup is constructed to capture an incoherent hologram easily with a compact system. An instantaneous and three-dimensional object image is obtained without undesired diffraction waves by phase-shifting interferometry from a single recorded image. The validity of the proposed technique is experimentally investigated for an object with a diameter of 1 mm.