gebhart/patrepeval huggingface dataset:
Expression of the <i>Brachyury</i> gene during mesoderm development in differentiating embryonal carcinoma cell cultures (1994)

When aggregated and treated with dimethyl sulfoxide (DMSO), P19 embryonal carcinoma cells differentiate into cell types normally derived from the mesoderm and endoderm including epithelium and cardiac and skeletal muscle. The Brachyury gene is expressed transiently in these differentiating cultures several days before the appearance of markers of the differentiated cell types. The expression of Brachyury is not affected by DMSO but is induced by cell aggregation, which requires extracellular calcium. Expression of Brachyury is also induced by various members of the TGF beta family such as activin and bone morphogenetic proteins. D3 is a mutant clone of P19 cells selected for its failure to differentiate when aggregated in DMSO. Aggregated D3 cells express Brachyury mRNA suggesting that the mutation(s) responsible for the phenotype of D3 cells is downstream of the chain of events initiated by Brachyury expression.
Power Efficiency of Millimeter Wave Transmission Systems with Large Number of Antennas (2016)

Large scale antenna systems (LSAS) in the mmWave bands provide a solution to the problems of spectrum shortage experienced in the conventional microwave bands. In a practical large scale antenna deployment, implementation of hybrid beamforming structures is very important as it provides high array gains to overcome the high path loss and achieve sufficient link margins. However, while implementing this we encounter the challenges such as complexity, cost and energy consumption. In this paper a power consumption model for the large scale antenna mmWave system is presented and analysed. From the power consumption model we maximize the energy efficiency of the overall system. Optimization of energy efficiency is a crucial factor in system optimization and design of the powerhungry devices. But with increasing energy efficiency, the spectral efficiency decreases. Thus analysis of the relation between energy and spectral efficiency becomes a critical task and we optimize energy efficiency at a fixed spectral efficiency. The results can then be utilized to guide the practical energy/spectrum efficiency trade-off for the LSAS design.
Cloning, sequencing, and expression in Escherichia coli of lcnB, a third bacteriocin determinant from the lactococcal bacteriocin plasmid p9B4-6 (1992)

On the bacteriocin plasmid p9B4-6 of Lactococcus lactis subsp. cremoris 9B4, a third bacteriocin determinant was identified. The genes encoding bacteriocin production and immunity resided on a 1.2-kb CelII-ScaI fragment and were located adjacent to one of two previously identified bacteriocin operons (M. J. van Belkum, B. J. Hayema, R. E. Jeeninga, J. Kok, and G. Venema, Appl. Environ. Microbiol. 57:492-498, 1991). The fragment was sequenced and analyzed by deletion and mutation analyses. The bacteriocin determinant consisted of two genes which were transcribed as an operon. The first gene (lcnB), containing 68 codons, was involved in bacteriocin activity. The second gene (lciB) contained 91 codons and was responsible for immunity. The specificity of this novel bacteriocin, designated lactococcin B, was different from that of the other two bacteriocins specified by p9B4-6. Part of the nucleotide sequence of the lactococcin B operon was similar to a nucleotide sequence also found in the two other bacteriocin operons of p9B4-6. This conserved region encompassed a nucleotide sequence upstream of the bacteriocin gene and the 5' part of the gene. When the lactococcin B operon was expressed in Escherichia coli by using a T7 RNA polymerase-specific promoter, antagonistic activity could be detected.
Lysine-specific demethylase 1 inhibitors protect cochlear spiral ganglion neurons against cisplatin-induced damage (2015)

Cisplatin is a widely used chemotherapeutic drug, but one of its side effects is ototoxicity. Epigenetic-related drugs, such as lysine-specific demethylase 1 (LSD1) inhibitors, have been reported to protect against cisplatin-induced hair cell loss by preventing demethylation of histone H3K4 (H3K4me2). However, the protective effect of LSD1 inhibitors in spiral ganglion neurons (SGNs) remains unclear. To investigate whether LSD1 inhibitors exert similar protective effects on SGNs, we treated mouse cochlear explant cultures with LSD1 inhibitors (2PCPA, S2101, or CBB1007) together with cisplatin. Low concentrations of cisplatin damaged SGNs much more than high concentrations, and blocking the demethylation of H3K4me2 with LSD1 inhibitors prevented the SGNs from injury. Reactive oxygen species are also involved in the injury process, and LSD1 inhibitors protected SGNs by increasing the expression level of the antioxidant gene Slc7a11 and decreasing the level of the pro-oxidant gene lactoperoxidase (Lpo). Our findings show that LSD1 inhibitors prevent cisplatin-induced SGN loss by regulating the demethylation of H3K4 and preventing increases of reactive oxygen species levels, which might provide a potential therapeutic strategy for cisplatin-induced hearing loss.
Activation of the Luteinizing Hormone Receptor Following Substitution of Ser-277 with Selective Hydrophobic Residues in the Ectodomain Hinge Region (2000)

Glycoprotein hormone receptors are G protein-coupled receptors with ligand-binding ectodomains consisting of leucine-rich repeats. The ectodomain is connected by a conserved cysteine-rich hinge region to the seven transmembrane (TM) region. Gain-of-function mutants of luteinizing hormone (LH) and thyroid-stimulating hormone receptors found in patients allowed identification of residues important for receptor activation. Based on constitutively active mutations at Ser-281 in the hinge region of the thyroid-stimulating hormone receptor, we mutated the conserved serine in the LH (S277I) and follicle-stimulating hormone receptors (S273I) and observed increased basal cAMP production and ligand affinity by mutant receptors. For the LH receptor, conversion of Ser-277 to all natural amino acids led to varying degrees of receptor activation. Hydropathy index analysis indicated that substitution of neutral serine with selective nonpolar hydrophobic residues (Leu>Val>Met>Ile) confers constitutive receptor activation whereas serine deletion or substitution with charged Arg, Lys, or Asp led to defective receptor expression. Furthermore, mutation of the angular proline near Ser-273 to flexible Gly also led to receptor activation. The findings suggest the ectodomain of glycoprotein hormone receptors constrain the TM region. Point mutations in the hinge region of these proteins, or ligand binding to these receptors, could cause conformational changes in the TM region that result in G(s) activation.
Color image enhancement via chromaticity diffusion (2001)

A novel approach for color image denoising is proposed in this paper. The algorithm is based on separating the color data into chromaticity and brightness, and then processing each one of these components with partial differential equations or diffusion flows. In the proposed algorithm, each color pixel is considered as an n-dimensional vector. The vectors' direction, a unit vector, gives the chromaticity, while the magnitude represents the pixel brightness. The chromaticity is processed with a system of coupled diffusion equations adapted from the theory of harmonic maps in liquid crystals. This theory deals with the regularization of vectorial data, while satisfying the intrinsic unit norm constraint of directional data such as chromaticity. Both isotropic and anisotropic diffusion flows are presented for this n-dimensional chromaticity diffusion flow. The brightness is processed by a scalar median filter or any of the popular and well established anisotropic diffusion flows for scalar image enhancement. We present the underlying theory, a number of examples, and briefly compare with the current literature.
1-(Aminoalkyl)-6-aryl-4H-s-triazolo[4,3-a][1,4]benzodiazepines with antianxiety and antidepressant activity (1980)

A series of 1-(aminoalkyl)-6-aryl-4H-s-triazolo[4,3-a][1,4]benzodiazepines has been prepared and evaluated for central nervous system activity. We have found that members of this series have activity in pharmacological test systems designed to detect both anxiolytic and antidepressant activity. Each type of activity could be varied independently by appropriate substituent selections.
Typical Enteroaggregative <i>Escherichia coli</i> Is the Most Prevalent Pathotype among <i>E. coli</i> Strains Causing Diarrhea in Mongolian Children (2004)

Diarrhea remains one of the main sources of morbidity and mortality in the world, and a large proportion is caused by diarrheagenic Escherichia coli. In Mongolia, the epidemiology of diarrheagenic E. coli has not been well studied. A total of 238 E. coli strains from children with sporadic diarrhea and 278 E. coli strains from healthy children were examined by PCR for 10 virulence genes: enteropathogenic E. coli (EPEC) eae, tir, and bfpA; enterotoxigenic E. coli (ETEC) lt and st; enteroinvasive E. coli (EIEC) ipaH; enterohemorragic E. coli stx1 and stx2; and enteroaggregative E. coli (EAEC) aggR and astA. EAEC strains without AggR were identified by the HEp-2 cell adherence test. The detection of EAEC, ETEC, EPEC, and EIEC was significantly associated with diarrhea. The incidence of EAEC (15.1%), defined by either a molecular or a phenotypic assay, was higher in the diarrheal group than any other category (0 to 6.0%). The incidence of AggR-positive EAEC in the diarrheal group was significantly higher than in the control group (8.0 versus 1.4%; P = 0.0004), while that of AggR-negative EAEC was not (7.1 versus 4.3%). Nineteen AggR-positive EAEC strains harbored other EAEC virulence genes-aggA, 2 (5.5%); aafA, 4 (11.1%); agg-3a, 5 (13.8%); aap, 8 (22.2%); aatA, 11 (30.5%); capU, 9 (25.0%); pet, 6 (16.6%); and set, 3 (8.3%)-and showed 15 genotypes. EAEC may be an important pathogen of sporadic diarrhea in Mongolian children. Genetic analysis showed the heterogeneity of EAEC but illustrated the importance of the AggR regulon (denoting typical EAEC) as a marker for virulent EAEC strains.
In-Situ 3D Nano-Printing of Freeform Coupling Elements for Hybrid Photonic Integration (2018)

Hybrid photonic integration exploits complementary strengths of different material platforms, thereby offering superior performance and design flexibility in comparison to monolithic approaches. This applies in particular to multi-chip concepts, where components can be individually optimized and tested on separate dies before integration into more complex systems. The assembly of such systems, however, still represents a major challenge, requiring complex and expensive processes for high-precision alignment as well as careful adaptation of optical mode profiles. Here we show that these challenges can be overcome by in-situ nano-printing of freeform beam-shaping elements to facets of optical components. The approach is applicable to a wide variety of devices and assembly concepts and allows adaptation of vastly dissimilar mode profiles while considerably relaxing alignment tolerances to the extent that scalable, cost-effective passive assembly techniques can be used. We experimentally prove the viability of the concept by fabricating and testing a selection of beam-shaping elements at chip and fiber facets, achieving coupling efficiencies of up to 88 % between an InP laser and an optical fiber. We also demonstrate printed freeform mirrors for simultaneously adapting beam shape and propagation direction, and we explore multi-lens systems for beam expansion. The concept paves the way to automated fabrication of photonic multi-chip assemblies with unprecedented performance and versatility.
Worst case fair beamforming for multiple multicast groups in multicell networks (2018)

The design problem associated with robust downlink beamforming in multicast, multigroup, multicell wireless systems is addressed. The channel state information (CSI) of users is assumed to be imperfect and the uncertainty of CSI is modelled using the Frobenius norm. The objective is to optimise the signal‐to‐interference‐plus‐noise ratio over all users with a constraint on the maximum total transmitted power. This was achieved through a robust solution using the successive convex approximation (SCA) method. The beamforming problem is treated as a bi‐convex problem, which is solved using the iterate‐alternative convex technique. Here, the CSI uncertainty is addressed using a convex package through the non‐monotone spectral projected gradient method and the beamforming vector is extracted using the SCA method. Also, the authors offer the required condition to extract the beamform vector using the SCA method through a suboptimal solution that always addressed before using different beamforming methods. Their simulation results examine all proposed system parameters in order to show convergence and feasibility of the solution. They also compare the solution with a suboptimal solution and the quality of service method for imperfect CSI in downlink beamforming. Numerical results show that the robust solution achieves the best power efficiency for practical solutions.
Melatonin protects against 6‐OHDA‐induced neurotoxicity in rats: a role for mitochondrial complex I activity (2001)

Unilateral injection into the right substantia nigra of the catecholaminergic neurotoxin 6-hydroxydopamine (6-OHDA) produces extensive loss of dopaminergic cells ('hemi-parkinsonian rat'). The pineal hormone melatonin, which is a potent antioxidant against different reactive oxygen species and has been reported to be neuroprotective in vivo and in vitro, was evaluated for potential anti-Parkinson effects in this model. Imbalance in dopaminergic innervation between the striata produced by intranigral administration of 6-OHDA results in a postural asymmetry causing rotation away from the nonlesioned side. Melatonin given systemically prevented apomorphine-induced circling behavior in 6-OHDA-lesioned rats. Reduced activity of mitochondrial oxidative phosphorylation enzymes has been suggested in some neurodegenerative diseases; in particular, selective decrease in complex I activity is observed in the substantia nigra of Parkinson's disease patients. Analysis of mitochondrial oxidative phosphorylation enzyme activities in nigral tissue from 6-OHDA-lesioned rats by a novel BN-PAGE histochemical procedure revealed a clear loss of complex I activity, which was protected against in melatonin-treated animals. A good correlation between behavioral parameters and enzymatic (complex I) analysis was observed independent of melatonin administration. A deficit in mitochondrial complex I could conceivably contribute to cell death in parkinsonism via free radical mechanisms, both directly via reactive oxygen species production and by decreased ATP synthesis and energy failure. Melatonin may have potential utility in the treatment of neurodegenerative disorders where oxidative stress is a participant.
The Effects of a Parametric Variation of the Rim Seal Geometry on the Interaction Between Hub Leakage and Mainstream Flows in High Pressure Turbines (2013)

The objective of this work was to assess and understand the effects of a parametric variation performed on a typical overlapping rim seal geometry. The datum geometry has been the focus of a detailed experimental investigation employing a large-scale linear cascade subjected to a range of the mass flow rates and swirl velocities of the leakage air. The parametric variations described in this paper were examined using validated computational fluid dynamics (CFD). As a part of the parametric studies, both the axial and the radial seal clearance between the rotor fin (angel wing) and stator platform were varied as well as the length of the overlap between stator and rotor platforms. In addition, the effects of forward and backward facing annulus steps were also investigated. It has been found that a backward-facing annulus step was detrimental for all conditions considered, while a forward-facing step offered improvements for smaller step heights and/or lower leakage fractions. Tightening of the seal clearances closer to the annulus line improved the sealing effectiveness but often at the expense of increased losses. On the other hand, increasing the overlap length led to improvements in the sealing effectiveness with very small effects on the overall losses. Moving the rim seal away from the blade-leading edges reduced the pressure asymmetry at the rim seal and increased the flow uniformity of the leakage air. However, this led to an increased cross-passage flow (more negative skew) and higher losses at all but lowest leakage fractions. The results presented in this paper highlight the fact that there may not be an optimum rim seal solution that would offer an improvement for the full range of leakage fractions and that, for different rim sealing flows, there may be a different optimum geometry. In addition, rotor disk movements in radial and axial directions at various off-design conditions should be considered as a part of the design process. Based on the presented results, it may be of a benefit to the turbine designer to consider rotor disk designs that would be more biased towards the upstream and outward disk movements, which would result in tightening of the seal clearances and avoidance of a backward-facing annulus step.
A Benchmark of Objective Quality Metrics for HLG-Based HDR/WCG Image Coding (2020)

In this work, we study the suitability of high dynamic range, wide color gamut (HDR/WCG) objective quality metrics to assess the perceived deterioration of compressed images encoded using the Hybrid Log-Gamma (HLG) method, which is the standard for HDR television. — Several image quality metrics have been developed to deal specifically with HDR content, although in previous work we showed that the best results (i.e., better matches to the opinion of human expert observers) are obtained by an HDR metric that consists simply in applying a given standard dynamic range metric, called visual information fidelity (VIF), directly to HLG-encoded images. — However, all these HDR metrics ignore the chroma components for their calculations, i.e., they just consider the luminance channel. For this reason, in the current work, we conduct subjective evaluation experiments in a professional setting using compressed HDR/WCG images encoded with HLG and analyze the ability of the best HDR metric to detect perceivable distortions in the chroma components, as well as the suitability of popular color metrics (including ΔITP <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">R</sub> , which supports parameters for HLG) to correlate with the opinion scores. Our first contribution is to show that there is a need to consider the chroma components in HDR metrics, as there are color distortions that subjects perceive but that the best HDR metric fails to detect. Our second contribution is the surprising result that VIF, which utilizes only the luminance channel, correlates much better with the subjective evaluation scores than the metrics that do consider the color components.
EXAFS study of hydrogen intercalation into ReO<sub>3</sub>using the evolutionary algorithm (2014)

In this study we have investigated the influence of hydrogen intercalation on the local atomic structure of rhenium trioxide using a new approach to EXAFS data analysis, based on the evolutionary algorithm (EA). The proposed EA-EXAFS method is an extension of the conventional reverse Monte Carlo approach but is computationally more efficient. It allows one to perform accurate analysis of EXAFS data from distant coordination shells, taking into account both multiple-scattering and disorder (thermal and static) effects. The power of the EA-EXAFS method is first demonstrated on an example of the model system, pure ReO3, and then it is applied to an in situ study of hydrogen bronze HxReO3 upon hydrogen intercalation. The obtained results allow us to detect changes in the lattice dynamics and correlation of atomic motion, and to follow the structural development at different stages of the reaction.
Metabolic engineering to produce phytochromes with phytochromobilin, phycocyanobilin, or phycoerythrobilin chromophore in <i>Escherichia coli</i> (2006)

By co-expression of heme oxygenase and various bilin reductase(s) in a single operon in conjunction with apophytochrome using two compatible plasmids, we developed a system to produce phytochromes with various chromophores in Escherichia coli. Through the selection of different bilin reductases, apophytochromes were assembled with phytochromobilin, phycocyanobilin, and phycoerythrobilin. The blue-shifted difference spectra of truncated phytochromes were observed with a phycocyanobilin chromophore compared to a phytochromobilin chromophore. When the phycoerythrobilin biosynthetic enzymes were co-expressed, E. coli cells accumulated orange-fluorescent phytochrome. The metabolic engineering of bacteria for the production of various bilins for assembly into phytochromes will facilitate the molecular analysis of photoreceptors.
Stable lightwave frequency synthesis over 1-THz span using Fabry-Perot cavity containing polarization-rotation elements and actively controlled tunable bandpass filter (2000)

We realized a lightwave synthesized frequency sweeper which has a >1-THz sweep span and operates stably. We employed an actively controlled tunable bandpass filter together with a Fabry-Perot cavity, which consisted of a Faraday rotator mirror and a polarization rotation mirror. We confirmed that the frequency information of an input pulse was preserved after 1000 round-trips in the cavity and that signal pulses could circulate stably for 12 h.
Effect of device layout on the switching of enhancement mode GaN HEMTs (2018)

In this study, a comparison of the on-state and switching performance of different die layout configurations of GaN HEMTs is given. Devices with different layout designs are shown to exhibit varying degrees of susceptibility to oscillatory behaviour when switching. This is demonstrated to be related to the level of source inductance and the unbalances of such inductances within the die rather than the package; this behaviour was quantified using a 3D electromagnetic simulation software. SPICE simulations were used to further support these findings.
Endotoxins—the Invisible Companion in Biomaterials Research (2013)

Metal implants and polymeric devices for the application in the clinical treatment of orthopedic tissue injuries are increasingly coated with bioactive biomaterials derived from natural substances to induce desirable biological effects. Many metals and polymers used in biomaterials research show high affinity for endotoxins, which are abundant in the environment. Endotoxin contamination is indicated in the pathology of periodontitis and aseptic implant loosening, but may also affect the evaluation of a biomaterial's bioactivity by inducing strong inflammatory reactions. In this review, we discuss the high affinity of three commonly used implant biomaterials for endotoxins and how the contamination can affect the outcome of the orthopedic fixation. The chemical nature of bacterial endotoxins and some of the clinical health implications are described, as this knowledge is critically important to tackle the issues associated with the measurement and removal of endotoxins from medical devices. Commonly used methods for endotoxin testing and removal from natural substances are examined and the lack of standard guidelines for the in vitro evaluation of biomaterials is discussed.