gebhart/patrepeval huggingface dataset:
<i>N</i>‐Acetylcysteine enhances the action of anti‐inflammatory drugs as suppressors of prostaglandin production in monocytes (2002)

The anti-inflammatory effect of non-steroidal anti-inflammatory drugs (NSAIDs) is associated with inhibition of cyclooxygenase (COX), the rate-limiting enzyme responsible for the synthesis of prostaglandins. Since oxygen free radicals can act as second cellular messengers, especially to modulate the metabolism of arachidonic acid and the prostaglandin tract, it seems plausible that antioxidants might affect the production of prostaglandin by activated cells. This research is focused on the effect of the antioxidant N-acetylcysteine (NAC) on the inhibition of prostaglandin E(2) formation in activated monocytes by specific and non-specific COX inhibitors. We found that lipopolysaccharide-induced prostaglandin E(2) formation was significantly reduced by rofecoxib and by diclofenac, two NSAIDs. Addition of NAC to each of these drugs enhanced the effect of the NSAIDs. These results suggest that one might expect either a potentiation of the anti-inflammatory effect of COX inhibitors by their simultaneous administration with NAC, or obtaining the same anti-inflammatory at lower drug levels.
Explanted embryo culture: In vitro and in ovo techniques for domestic fowl (1987)

Abstract 1. Embryos of the domestic fowl (72 h old) have been explanted into shell‐less cultures or ‘surrogate’ eggshells, in order to investigate the possibility of rearing these embryos to hatching. 2. Rocking embryo cultures during the first half of incubation enhanced embryo growth. 3. Embryos explanted into ‘surrogate’ eggshells of either other individuals or other species have been successfully ‘hatched’. 4. A normal chorioallantois is formed in these surrogate eggshells. This enables a functional albumen sac to form and eggshell resorption to be achieved. 5. Embryos grown in ‘surrogate’ eggshells are slightly smaller than controls but otherwise normal. 6. The technique provides opportunities for genetic engineering experiments.
MiR-93-5p enhances growth and angiogenesis capacity of HUVECs by down-regulating EPLIN (2017)

Tumor angiogenesis is essential in delivering oxygen and nutrients to growing tumors, and therefore considered as a hallmark of cancer. MicroRNAs (miRNAs) have been shown to play important roles in regulating tumor angiogenesis. MicroRNA-93-5p (miR-93-5p) has been identified as an oncogenic miRNA in a variety of human malignancies and involved in tumor angiogenesis in astrocytoma. However, the direct effect(s) of miR-93-5p on the biological behaviors of endothelial cells have not been investigated. Thus, in the present study we investigated the role(s) of miR-93-5p in regulating the functions of human umbilical vein endothelial cells (HUVECs). We found that triple negative breast cancer (TNBC) tissues with higher levels of miR-93-5p showed higher blood vessel density. Overexpression of miR-93-5p accelerated HUVECs proliferation and migration and promoted HUVECs lumen formation and sprouting <i>in vitro</i>, while blockade of miR-93-5p suppressed HUVECs migration and angiogenic capacity. The mechanistic studies revealed that miR-93-5p can promote angiogenic process through inhibiting epithelial protein lost in neoplasm (EPLIN) expression in HUVECs. In sum, our results have indicated that miR-93-5p promoted angiogenesis through down-regulating EPLIN and therefore represented a promising target for developing novel anti-angiogenic therapeutics.
Hardware-accelerated execution of Pi-calculus reconfiguration schedules (2011)

The π-calculus is a process algebra originally designed for modelling communicating systems. In this work, it is applied to the design of schedules for partial dynamic reconfiguration, which denote when modules become active and which channels they use for communication. While the execution of the π-calculus in software is possible, a direct execution in hardware is desirable for two reasons: Firstly, direct hardware execution removes the requirement to use a softcore processor. As will be shown in this paper, π-calculus processes only have a tiny hardware footprint. Secondly, the π-calculus is inherently concurrent, and its execution on dedicated hardware can thus be greatly accelerated. This can be used in order to speed up the simulation of schedules. The acceleration of π-calculus simulation may have applications in other fields, since the π-calculus has been used for modelling systems in a wide range of disciplines, for instance in computational biology. The paper shows how π-calculus primitives can be translated into corresponding hardware modules. Since this is difficult to do manually, a tool was created which automatically maps complete processes into synthesizable VHDL code.
How Entanglement of Different Physicochemical Properties Complicates the Prediction of <i>in Vitro</i> and <i>in Vivo</i> Interactions of Gold Nanoparticles (2018)

The physicochemical properties of a set of 21 different gold nanoparticles (spherical and rod-shaped nanoparticles (NPs) of different diameters with three different surface coatings) were studied. Protein corona formation, in vitro uptake, effect on cell viability and proliferation, and in vivo biodistribution of these NPs were determined. The relation of the results of the different NPs was analyzed by hierarchical cluster analysis, which will tell which NPs have the most similar physicochemical properties and biological effects, without having to specify individual physicochemical parameters. The results show that the physicochemical properties of gold nanoparticles (Au NPs) are mainly accounted for by their hydrodynamic diameter and their zeta-potential. The formation of the protein corona is determined by the pH-dependence of their zeta-potential. While several reports found that in vitro uptake and in vivo biodistribution of NPs are correlated to individual physicochemical parameters, e. g., size, shape, or surface chemistry, such direct dependence in the investigated multidimensional set of NPs was not found in our study. This most likely is due to entanglement of the different parameters, which complicates the prediction of the biological effect of NPs in case multiple physicochemical properties are simultaneously varied. The in vitro uptake and in vivo biodistribution of NPs seem to be not directly driven by the protein corona, but the physicochemical properties determine as well the corona as they influence in vitro/ in vivo behaviors, and thus the effect of the protein corona would be rather indirect.
Genetically modified bone marrow continuously supplies anti-inflammatory cells and suppresses renal injury in mouse Goodpasture syndrome (2001)

In chronic inflammation, macrophages and neutrophils, which are derived from bone marrow, play a pivotal role. Therefore, reconstitution of bone marrow with anti-inflammatory stem cells may modify inflammation. In this study, transplantation-based gene therapy was applied to glomerular inflammation for a long-lasting suppression of the glomerular damage seen in chronic nephritis. Bone marrow cells were harvested from male donor mice, which had received 5-fluorouracil 3 days previously, and transduced with an interleukin 1 (IL-1) receptor antagonist (IL-1Ra) or a mock gene using a retrovirus vector. After confirmation that transduced cells possessed the transgene at approximately 0.7 copies per cell and secreted recombinant IL-1Ra, these cells were infused into sublethally irradiated (6 Gy) female recipients once daily for 4 consecutive days. These female recipient mice had the male Y antigen in bone marrow, liver, and spleen, and 10% to 20% of their spleen cells possessed the transgene even 8 weeks after transplantation. Glomerulonephritis was then induced in these mice. Renal function and histology were retarded in the mice whose bone marrow was reconstituted with IL-1Ra-producing cells compared with mock transduced cells. In situ hybridization using a Y painting probe revealed that transplanted donor cells were recruited into the glomerulus upon induction of nephritis, suggesting therapeutic effects were channeled through the secretion of IL-1Ra from these cells. Furthermore, the survival rate after a second challenge with nephrotoxic antibody was significantly improved in the IL-1Ra chimera. These results suggest that reconstitution of bone marrow for continuous supply of anti-inflammatory cells may be a useful strategy for the treatment of chronic inflammation.
A Fluorescent Assay Method for GDP-L-Fuc: N-Acetyl- D- Glucosaminide  1-6Fucosyltransferase Activity, Involving High Performance Liquid Chromatography (1996)

An assay method for GDP-L-Fuc:N-acetyl-beta-D-glucosaminide alpha 1-6fucosyltransferase (alpha 1-6FucT; EC 2.4.1.68) activity has been developed, involving a fluorescent pyridylaminated substrate. A glycopeptide derived from bovine gamma-globulin was coupled with 4-(2-pyridylamino)butylamine (PABA) through the peptide bond, and the following substrate was obtained. [equation: see text] The substrate and guanosine diphospho-fucopyranoside (GDP-Fuc) were incubated with a crude enzyme extract for 2 h, and then the enzymatic product was separated by reversed phase HPLC. Quantitation of the product involved measurement of the fluorescence intensity of the fucosylated pyridylaminated sugar. The structures of both synthesized GnGn-bi-Asn-PABA (substrate), and synthesized GnGnF-bi-Asn-PABA (product) were analyzed by 1H NMR. The enzymatic product was also analyzed by 1H NMR and was found to have alpha 1-6fucose at the reducing end GlcNAc. This method is highly specific for alpha 1-6FucT and is applicable for various experiments, including purification and cell culture ones.
Adaptive Iterative Soft-Input Soft-Output Parallel Decision-Feedback Detectors for Asynchronous Coded DS-CDMA Systems (2005)

The optimum and many suboptimum iterative soft-input soft-output (SISO) multiuser detectors require a priori information about the multiuser system, such as the users' transmitted signature waveforms, relative delays, as well as the channel impulse response. In this paper, we employ adaptive algorithms in the SISO multiuser detector in order to avoid the need for this a priori information. First, we derive the optimum SISO parallel decision-feedback detector for asynchronous coded DS-CDMA systems. Then, we propose two adaptive versions of this SISO detector, which are based on the normalized least mean square (NLMS) and recursive least squares (RLS) algorithms. Our SISO adaptive detectors effectively exploit the a priori information of coded symbols, whose soft inputs are obtained from a bank of single-user decoders. Furthermore, we consider how to select practical finite feedforward and feedback filter lengths to obtain a good tradeoff between the performance and computational complexity of the receiver.
High-Precision Flip-Chip Process Yields E-Band Harmonic Mixers with Potential Sub-10-dB Conversion Loss (2006)

A process in which discrete semiconductor chips are flip-attached by thermocompression bonding to 30-micron-diameter gold bumps on fine-featured passive integrated circuits was employed in the fabrication of diode subharmonic mixers for use over the 71-76 GHz and 81-86 GHz ranges. Incorporated in the substrate were high-precision grounded heat sinks, semi-lumped filters, and matching networks in low-loss microstrip format. Measurements show conversion loss minima of 12 dB, but the frequency response was impaired by inaccuracies in the filter design. Parasitics characteristic of flip-chip technology were not an impediment, and a mixer technology with high performance and low materials cost appears feasible
Fast Exact Search in Hamming Space with Multi-Index Hashing (2013)

There is growing interest in representing image data and feature descriptors using compact binary codes for fast near neighbor search. Although binary codes are motivated by their use as direct indices (addresses) into a hash table, codes longer than 32 bits are not being used as such, as it was thought to be ineffective. We introduce a rigorous way to build multiple hash tables on binary code substrings that enables exact k-nearest neighbor search in Hamming space. The approach is storage efficient and straightforward to implement. Theoretical analysis shows that the algorithm exhibits sub-linear run-time behavior for uniformly distributed codes. Empirical results show dramatic speedups over a linear scan baseline for datasets of up to one billion codes of 64, 128, or 256 bits.
Peyer's patch eosinophils: identification, characterization, and regulation by mucosal allergen exposure, interleukin-5, and eotaxin (2000)

The gastrointestinal immune system is traditionally thought to be composed of lymphocytes located within Peyer's patches and the lamina propria. We have recently reported that eosinophils also reside in the gastrointestinal tract during healthy states, in particular, within the lamina propria, and that these cells substantially increase after oral allergen exposure. We now demonstrate the presence of eosinophils in Peyer's patches and characterize the signals that regulate the accumulation of eosinophils in Peyer's patches. In contrast to the lamina propria, intestinal Peyer's patches have very low levels of eosinophils under healthy states. However, elevated levels of interleukin-5 (IL-5), generated by transgenic or pharmacologic approaches, result in a dramatic increase in eosinophil levels in Peyer's patches. Most eosinophils are located in the outer cortex and interfollicular regions of the Peyer's patches. To dissect the mechanism of eosinophil trafficking to Peyer's patches, the role of eotaxin was examined. Mice transgenic for IL-5 and genetically deficient in eotaxin were found to have reduced levels of eosinophils in Peyer's patches compared with IL-5-transgenic mice. To prove that eosinophils also traffic to Peyer's patches in wild-type mice, allergic hypersensitivity was induced and Peyer's patches were examined. Exposure to mucosal allergen promoted marked accumulation of eosinophils in Peyer's patches and this process was attenuated in eotaxin-deficient mice. In summary, these data demonstrate that elevated levels of IL-5 and mucosal allergen exposure promote eotaxin-dependent eosinophil trafficking to Peyer's patches. These studies suggest that eosinophils may cooperate with lymphocytes in the development of mucosal immune responses in the gastrointestinal tract.
A comparison between the Warren-Averbach method and alternate methods for X-ray diffraction microstructure analysis of polycrystalline specimens (2001)

The fundamental parameters approach is used to simulate the instrument contribution to the X-Ray diffraction profile. This procedure eliminates the need to experimentally prepare a reference sample of the studied crystalline material when using the Warren-Averbach method to investigate microstrutural parameters. The Warren-Averbach method is also compared to the Balzar and Enzo methods, two other popular methods of size-strain analysis. The analysis was carried out using bohmite powder having two different nominal average crystallite sizes, 80 Å and 200 Å. A 50%-50% mixture of these materials was used as a third sample. The proposed simulation procedure provides good results and is much faster to implement than the usual procedure that includes the preparation of a reference. For larger crystallite sizes, the results calculated from the Warren-Averbach method for the volume-weighted average crystallite size differs significantly from the ones obtained from the Balzar and Enzo methods. The limitations of the Balzar and Enzo methods are also discussed.
Type-Specific Detection of Echovirus 30 Isolates Using Degenerate Reverse Transcriptase PCR Primers (2001)

ABSTRACT Following an approach used to specifically identify polioviruses and enterovirus 71, we have developed reverse transcriptase (RT) PCR primers containing mixed-base residues or deoxyinosine at positions of codon degeneracy. These primers permit specific RT-PCR amplification of echovirus 30 (E30) sequences by targeting sites that encode conserved amino acid motifs within the major capsid protein, VP1. All 221 E30 strains tested, isolated in 16 countries over a 44-year period, yielded the predicted 158-bp PCR product. No specific products were obtained by PCR assays containing templates from any of the other 63 EV serotypes. Inosine-containing degenerate primers may be widely applicable to the identification of echovirus serotypes by PCR.
Plasma‐Strengthened Lithiophilicity of Copper Oxide Nanosheet–Decorated Cu Foil for Stable Lithium Metal Anode (2019)

Lithium metal is the most ideal anode for next-generation lithium-ion batteries. However, the formation of lithium dendrites and the continuous consumption of electrolyte during cycling lead to a serious safety problems. Developing stable lithium metal anode with uniform lithium deposition is highly desirable. Herein, a nitrogen plasma strengthening strategy is proposed for copper oxide nanosheet-decorated Cu foil as an advanced current collector, and deep insights into the plasma regulating mechanism are elaborated. The plasma-treated electrode can maintain a high coulombic efficiency of 99.6% for 500 cycles. The symmetric cell using the lithium-plated electrode can be cycled for more than 600 h with a low-voltage hysteresis (23.1 mV), which is much better than those of electrodes without plasma treatment. It is well confirmed that this plasma-induced nitrogen doping method can provide sufficient active sites for lithium nucleation to enhance the stability of lithium deposition on copper oxide nanosheets decorated on Cu foil and improve the electrical conductivity to greatly reduce the overpotential of the lithium nucleation, which can be extended to other modified current collectors for stable lithium metal anode.
Biomass as renewable feedstock in standard refinery units. Feasibility, opportunities and challenges (2012)

Within the present contribution we highlight the feasibility of standard refinery units for the production of biofuels from different biomass-derived feedstock. The energy densification of biomass, as well as it’s logistics and incorporation within the refinery supply chain is thoroughly discussed. Likewise, special attention is focused on the catalytic cracking and hydrotreating of triglyceride-rich biomass feedstock, which is probably the most suitable one for co-processing in conventional refinery conversion units. However, the opportunities of other highly oxygenated feedstocks such as pyrolysis oils and sugars are also discussed. Conversion of different feedstocks into conventional liquid fuels by coupling of aqueous phase reforming (APR) with catalytic systems typical of standard petroleum refineries is also evaluated. Thus, here we review the chemistry, catalysis and challenges involved in the production of biofuels from biomass in conventional refineries.
Collaborative Three-Dimensional Completion of Color and Depth in a Specified Area With Superpixels (2018)

A persistent problem in the three-dimensional (3-D) reconstruction technique is to eliminate blank areas in the 3-D map, which commonly emerges after removing undesired objects, such as dynamic targets or occluded areas. This task is challenging for it is difficult to acquire the coherence between color and depth information, which are both lost for each pixel in the target region. Moreover, creating novel artifacts also needs to be avoided during the completion process. To address these problems, in this paper, we propose a collaborative method to complete the lost area in the color image and its corresponding depth map. In the proposed method, an examplar-based image inpainting technique combined with planarity knowledge is adopted to iteratively repair the texture and structure information. The color completion process provides candidates for plane-fitting on segmented superpixels. The depth filling step extracts image areas requiring reinpainting, which is defined by their gradient differences. The final 3-D map can then be reconstructed from both completed color and depth images. Experiments on real-world scenes demonstrate the success of our method in the completion of 3-D maps.
PointFinder: a novel web tool for WGS-based detection of antimicrobial resistance associated with chromosomal point mutations in bacterial pathogens (2017)

PointFinder proved, with high concordance between phenotypic and predicted antimicrobial susceptibility, to be a user-friendly web tool for detection of chromosomal point mutations associated with antimicrobial resistance.
Residual function of cystic fibrosis mutants predicts response to small molecule CFTR modulators (2018)

Treatment of individuals with cystic fibrosis (CF) has been transformed by small molecule therapies that target select pathogenic variants in the CF transmembrane conductance regulator (CFTR). To expand treatment eligibility, we stably expressed 43 rare missense CFTR variants associated with moderate CF from a single site in the genome of human CF bronchial epithelial (CFBE41o-) cells. The magnitude of drug response was highly correlated with residual CFTR function for the potentiator ivacaftor, the corrector lumacaftor, and ivacaftor-lumacaftor combination therapy. Response of a second set of 16 variants expressed stably in Fischer rat thyroid (FRT) cells showed nearly identical correlations. Subsets of variants were identified that demonstrated statistically significantly higher responses to specific treatments. Furthermore, nearly all variants studied in CFBE cells (40 of 43) and FRT cells (13 of 16) demonstrated greater response to ivacaftor-lumacaftor combination therapy than either modulator alone. Together, these variants represent 87% of individuals in the CFTR2 database with at least 1 missense variant. Thus, our results indicate that most individuals with CF carrying missense variants are (a) likely to respond modestly to currently available modulator therapy, while a small fraction will have pronounced responses, and (b) likely to derive the greatest benefit from combination therapy.
<title>Nonlinear indicators of malignancy</title> (1993)

This paper investigates the use of fractional dimension analysis and nonlinear filters for quantifying the degree of lesion diffusion in mammograms. The fractal method involves computing the fractal dimension over the entire lesion. Based on the observation that malignant lesions usually exhibit rougher intensity profiles and often have more toruous boundaries than benign lesions, the fractal dimension, which is a popular means of quantifying the degree of image/surface roughness, is proposed as a natural tool to assist in the diagnosis of malignancy. In this work, the fractal dimension of the image intensity surface is estimated using the fractional Brownian motion model. The nonlinear analysis was performed on horizontal and vertical lines (one-dimensional data) through the area of interest. These scan lines were also processed by a nonlinear (maximum) transformation as a means of reducing the dimensionality of the data, to aid in clarifying the degree of diffusion present in the data. For benign lesions little diffusion will be present, whereas malignant lesions generally display a higher degree of diffusion. Results of these techniques are applied on several malignant and benign lesions are presented, using mammogram X-rays digitized to a 512 X 512 pixel resolution and 8-bits of gray-scale resolution.