gebhart/patrepeval huggingface dataset:
The autophagy receptor SQSTM1/p62 mediates anti-inflammatory actions of the selective NR3C1/glucocorticoid receptor modulator compound A (CpdA) in macrophages (2018)

Glucocorticoids are widely used to treat inflammatory disorders; however, prolonged use of glucocorticoids results in side effects including osteoporosis, diabetes and obesity. Compound A (CpdA), identified as a selective NR3C1/glucocorticoid receptor (nuclear receptor subfamily 3, group C, member 1) modulator, exhibits an inflammation-suppressive effect, largely in the absence of detrimental side effects. To understand the mechanistic differences between the classic glucocorticoid dexamethasone (DEX) and CpdA, we looked for proteins oppositely regulated in bone marrow-derived macrophages using an unbiased proteomics approach. We found that the autophagy receptor SQSTM1 but not NR3C1 mediates the anti-inflammatory action of CpdA. CpdA drives SQSTM1 upregulation by recruiting the NFE2L2 transcription factor to its promoter. In contrast, the classic NR3C1 ligand dexamethasone recruits NR3C1 to the Sqstm1 promoter and other NFE2L2-controlled gene promoters, resulting in gene downregulation. Both DEX and CpdA induce autophagy, with marked different autophagy characteristics and morphology. Suppression of LPS-induced Il6 and Ccl2 genes by CpdA in macrophages is hampered upon Sqstm1 silencing, confirming that SQSTM1 is essential for the anti-inflammatory capacity of CpdA, at least in this cell type. Together, these results demonstrate how off-target mechanisms of selective NR3C1 ligands may contribute to a more efficient anti-inflammatory therapy.
The influence of the p-n junction induced electric field on the optical properties of InGaN/GaN/AlGaN light emitting diode (1999)

The temperature dependence of photoluminescence measurement was performed on an undoped In0.126Ga0.874N/GaN multiple quantum well (MQW) structure and a light emitting diode (LED) structure using this MQW as an active region. The emission energy of the LED structure showed a red shift of about 230 meV at room temperature compared with the undoped In0.126Ga0.874N/GaN MQW. This behavior of the LED structure is attributed to the quantum-confined Stark effect due to its p-n junction induced electric field. This conclusion was confirmed by a calculation and a detailed discussion based on the theory of the quantum-confined Stark effect.
Interleukin –18 and other inflammatory cytokines as independent predictors of diabetic nephropathy in patients with type 2 diabetes mellitus. (2003)

Diabetes Mellitus is a very common cause of glomerular disease in adults and is a very common cause of end stage renal failure. The pathogenesis of diabetic nephropathy is not completely understood dispite extensive investigations. Involvement of the kidneys in patients with diabetes mellitus includes not only hyperglycemia, advanced glycosylation products but also activation of proinflammatory cytokines. Data about the relationship of inflammation to nephropathy in type 2 diabetes mellitus are scarce. Our study was conducted to compare levels of interleukin - 18 ( IL- 18), tumor necrosis factor-alpha.( TNF- α ) and interleukin- 6 (IL-6) in serum of diabetic patients with various degrees of nephropathy. The study included 50 patients and 35 normal control subjects presented at Ain Shams University Hospitals. The diabetic subjects were divided into 3groups according to urinary albumin excretion ( UAE): o Group I : included 22 subjects with UAE < 30 μg/mg creatinine i.e diabetic patients with normoalbuminuria. o Group II : included 20 subjects. with UAE 30 to 300 μg/mg creatinine i.e. diabetic patients with microalbuminuria . o Group III : Included 8 subjects with UAE > 300 μg/mg creatinine i.e. diabetic patients with macroalbuminuria. The serum levels of IL–18, TNF- α and IL-6 were measured for the control group to determine the normal values and for all diabetic subjects with various degrees of nephropathy . The results revealed highly significant statistical differences in serum levels of IL-18, TNF-α and IL-6 between the patients and control subjects. In addition, IL-18 levels were increased in diabetic patients with proteinuria as compared with those without proteinuria. Also TNF-α and IL-6 in diabetic patients with microalbuminuria and clinical albuminuria were significantly increased as compared with diabetic patients without albuminuria. These results suggest that serum levels of IL-18, TNF- α and IL-6 may have etiopathogenic roles in diabetic nephropathy and are independent predictors of UAE in type 2 diabetes mellitus. So, in addition to metabolic and hemodynamic factors, it is possible to consider the participation of inflammation on the pathogenesis of diabetic nephropathy.
Multi-factor combined biomarker screening strategy to rapidly diagnose Alzheimer's disease and evaluate drug effect based on a rat model (2022)

Alzheimer's disease (AD) represents the main form of dementia; however, valid diagnosis and treatment measures are lacking. The discovery of valuable biomarkers through omics technologies can help solve this problem. For this reason, metabolomic analysis using ultra-performance liquid chromatography coupled with quadrupole time-of-flight tandem mass spectrometry (UPLC-Q-TOF-MS) was carried out on plasma, hippocampus, and cortex samples of an AD rat model. Based on the metabolomic data, we report a multi-factor combined biomarker screening strategy to rapidly and accurately identify potential biomarkers. Compared with the usual procedure, our strategy can identify fewer biomarkers with higher diagnostic specificity and sensitivity. In addition to diagnosis, the potential biomarkers identified using our strategy were also beneficial for drug evaluation. Multi-factor combined biomarker screening strategy was used to identify differential metabolites from a rat model of amyloid beta peptide 1-40 (Aβ<sub>1-40</sub>) plus ibotenic acid-induced AD (compared with the controls) for the first time; lysophosphatidylcholine (LysoPC) and intermediates of sphingolipid metabolism were screened as potential biomarkers. Subsequently, the effects of donepezil and pine nut were successfully reflected by regulating the levels of the abovementioned biomarkers and metabolic profile distribution in partial least squares-discriminant analysis (PLS-DA). This novel biomarker screening strategy can be used to analyze other metabolomic data to simultaneously enable disease diagnosis and drug evaluation.
Complex-valued hough transforms for circles (2015)

This paper proposes the use of complex variables to represent votes in the Hough transform for circle detection. Replacing the positive numbers classically used in the parameter space of the Hough transforms by complex numbers allows cancellation effects when adding up the votes. Cancellation and the computation of shape likelihood via a complex number's magnitude square lead to more robust solutions than the “classic” algorithms, as shown by computational experiments on synthetic and real datasets. We note a resemblance to methods used in quantum theory.
Formulation, Pharmacokinetic, and Efficacy Studies of Mannosylated Self-Emulsifying Solid Dispersions of Noscapine (2016)

Mannosylated noscapine self-emulsifying solid dispersions (Mann-Nos_SESDs) are bioavailable and potentiate the antineoplastic effect of cisplatin-based chemotherapy in cisplatin-resistant NSCLC.
Statistical Pitfalls in Brain Age Analyses (2020)

Abstract Over the past decade, there has been an abundance of research on the difference between age and age predicted using brain features, which is commonly referred to as the “brain age gap”. Researchers have identified that the brain age gap, as a linear transformation of an out-of-sample residual, is dependent on age. As such, any group differences on the brain age gap could simply be due to group differences on age. To mitigate the brain age gap’s dependence on age, it has been proposed that age be regressed out of the brain age gap. If this modified brain age gap (MBAG) is treated as a corrected deviation from age, model accuracy statistics such as R 2 will be artificially inflated. Given the limitations of proposed brain age analyses, further theoretical work is warranted to determine the best way to quantify deviation from normality. Highlights The brain age gap is an out-of-sample residual, and as such varies as a function of age. A recently proposed modification of the brain age gap, designed to mitigate the dependence on age, results in inflated model accuracy statistics if used incorrectly. Given these limitations, we suggest that new methods should be developed to quantify deviation from normal developmental and aging trajectories.
Bioactive bone cement: Effect of surface curing properties on bone-bonding strength (2000)

The fact that bisphenol-a-glycidyl methacrylate (bis-GMA)-based cements contain an uncured surface is believed to play an important role when determining the surface curing properties of the cements. Therefore, in the present study, the bone-bonding strength of cement plates having an uncured surface on one side and a cured surface on the other side has been evaluated. These cement plates were composites of a bis-GMA-based resin with either an apatite- and wollastonite-containing glass-ceramic (AW-GC) powder or a hydroxyapatite (HA) powder, respectively designated AWC and HAC. The amount of each of these powders in a composite cement was 70 wt %. We formulate the hypothesis that the uncured surface of a cement plate is bioactive having bone-bonding properties. The goal of the present study was to indicate the bone-bonding strength of the uncured surfaces of AWC and HAC and compare the strength with the respective cured surfaces by a detaching in vivo test, as well as to histologically examine the bone-cement interface. Each plate has been implanted into the tibiae of male Japanese white rabbits, taking care to retain the surface properties, and the so-called "failure load has been measured using a detaching test followed 8 weeks after implantation. The failure load for AWC-plates at the uncured surface (2.05 +/- 1.11 kgf, n = 8) was significantly higher than AWC at its cured surface side (0.28 +/- 0.64 kgf, n = 8). The failure load for HAC-plates at the uncured surfaces (1.40 +/- 0.68 kgf, n = 8) was significantly higher than HAC at its cured surface (0.00 +/- 0.00 kgf, n = 8). Failure loads for AWC at its uncured and cured surfaces were both higher than for HAC, although not significantly. Direct bone formation has been observed histologically for both AWC and HAC on the uncured surfaces, and a Ca-P-rich layer was observed only at the uncured surface of AWC. These findings strongly suggest that uncured surfaces are useful for exposing a bioactive filler on a surface of composites, being very effective in inducing bone bonding.
Implementation of a data acquisition system for contactless conductivity imaging (2002)

A data acquisition system is realized for conductivity imaging via contactless measurements. It is observed that field profiles are good representatives of the conductive objects scanned by the measurement system. Three different data sets are taken with different scanning resolutions. Note that although the scanning resolution is decreased 25 times, it is still possible to observe the conductive object. The data acquisition time is due to the data acquisition time limit of the lock-in amplifier. As might be expected, the secondary voltage profiles spreads. It is possible to employ an image reconstruction algorithm and obtain conductivity images with better resolution. In conclusion, the first results of a promising new medical imaging modality were presented. This system can provide necessary conductivity information for electromagnetic source imaging of the human brain. Moreover, this system can be applicable to brain, breast and lung imaging. Other application areas should further be explored.
In situ biasing TEM investigation of resistive switching events in TiO<inf>2</inf>-based RRAM (2014)

We report the first demonstration of in situ electrical biasing and resifstive switching of TiO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> -based RRAM while observing oxygen vacancy migration under the TEM. Specifically, repeated extension and retraction of Wadsley defects due to the migration of oxygen vacancies was observed to be concurrent with the SET and RESET processes (respectively) in the hysteretic I–V behavior of single-crystal TiO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> devices. Additionally, structural evolution within a 20 nm size grain was observed during SET processes in ALD-grown TiO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> devices using STEM HAADF imaging.
Displacement control device for dynamic tissue deformation in MRI - biomed 2010. (2010)

Several methods have been used to create controlled motion in an MRI bore using traditional motors that operate at a large distance away from the bore. The purpose of this effort is to develop a device to precisely control deflection of tissue while measuring interface loads within an MRI bore. Displacement of a tissue sample is provided via a non-ferromagnetic linear piezoelectric motor mounted on an aluminum sliding stage. A software program is developed to synchronize and gate the motor motion with the pulse sequence of the MRI using signals sent by the MRI controller. The piezoelectric motor has submicron position precision with closed loop encoder control allowing for accurate control. The motor encoder relays position data to the motor control software which is used to calculate the deflection, velocity, strain, and strain rate. An end effecter is mounted to the motor stage and transmits load to the tissue. The end effecter will contain a single axis load cell to record the compression force during displacement. Tissue samples are contained within an acrylic container and immersed in saline solution. The motor stage and container are mounted on a stack of sliding platforms that allow the user to easily move the motor stage and end indenter relative to the container or the motor stage, end effecter, and container relative to the MRI head coil. These degrees of freedom provide the user a means for quick and easy test setup. The device will measure strain, strain rate, and load in time. It will provide a tool to relate external tissue load, strain, and strain rate to internal three-dimensional strain fields which in turn will be used to quantify viscoelastic tissue stiffness.
Hydrocracking of n-Alkane Mixtures on Pt/H−Y Zeolite:  Chain Length Dependence of the Adsorption and the Kinetic Constants (1997)

The conversion of a mixture of n-hexane, n-heptane, n-octane and n-nonane, in the presence of hydrogen over zeolite Pt/H−Y is modeled using a multicomponent adsorption−reaction scheme. Adsorption parameters for the relevant hydrocarbon molecules are determined using the chromatographic technique. Intrinsic reaction parameters are obtained by the fitting of the model to reaction rate data from catalytic experiments, using the independently determined adsorption parameters. Preferential conversion of the longer n-alkanes in mixtures is caused by competitive adsorption favoring the heavy compounds. Apparent reaction rates in mixtures are controlled by adsorption, increasing with chain length of the n-alkanes, rather than by the individual intrinsic reaction rates of the different n-alkanes, which are similar.
pyKNEEr: An image analysis workflow for open and reproducible research on femoral knee cartilage (2020)

Transparent research in musculoskeletal imaging is fundamental to reliably investigate diseases such as knee osteoarthritis (OA), a chronic disease impairing femoral knee cartilage. To study cartilage degeneration, researchers have developed algorithms to segment femoral knee cartilage from magnetic resonance (MR) images and to measure cartilage morphology and relaxometry. The majority of these algorithms are not publicly available or require advanced programming skills to be compiled and run. However, to accelerate discoveries and findings, it is crucial to have open and reproducible workflows. We present pyKNEEr, a framework for open and reproducible research on femoral knee cartilage from MR images. pyKNEEr is written in python, uses Jupyter notebook as a user interface, and is available on GitHub with a GNU GPLv3 license. It is composed of three modules: 1) image preprocessing to standardize spatial and intensity characteristics; 2) femoral knee cartilage segmentation for intersubject, multimodal, and longitudinal acquisitions; and 3) analysis of cartilage morphology and relaxometry. Each module contains one or more Jupyter notebooks with narrative, code, visualizations, and dependencies to reproduce computational environments. pyKNEEr facilitates transparent image-based research of femoral knee cartilage because of its ease of installation and use, and its versatility for publication and sharing among researchers. Finally, due to its modular structure, pyKNEEr favors code extension and algorithm comparison. We tested our reproducible workflows with experiments that also constitute an example of transparent research with pyKNEEr, and we compared pyKNEEr performances to existing algorithms in literature review visualizations. We provide links to executed notebooks and executable environments for immediate reproducibility of our findings.
Compensatory Link between Fusion and Endocytosis of Human Immunodeficiency Virus Type 1 in Human CD4 T Lymphocytes (2004)

Virions of the type 1 human immunodeficiency virus (HIV-1) can enter target cells by fusion or endocytosis, with sharply different functional consequences. Fusion promotes productive infection of the target cell, while endocytosis generally leads to virion inactivation in acidified endosomes or degradation in lysosomes. Virion fusion and endocytosis occur equally in T cells, but these pathways have been regarded as independent because endocytosis of HIV virions requires neither CD4 nor CCR5/CXCR4 engagement in HeLa-CD4 cells. Using flow cytometric techniques to assess the binding and entry of green fluorescent protein (GFP)-Vpr-labeled HIV virions into primary peripheral blood mononuclear cells, we have found that HIV fusion and endocytosis are restricted to the CD4-expressing subset of cells and that both pathways commonly require the initial binding of HIV virions to surface CD4 receptors. Blockade of CXCR4-tropic HIV virion fusion with AMD3100, a CXCR4-specific entry inhibitor, increased virion entry via the endocytic pathway. Similarly, inhibition of endosome acidification with bafilomycin A1, concanamycin A, or NH(4)Cl enhanced entry via the fusion pathway. Although fusion remained dependent on CD4 and chemokine receptor binding, the endosome inhibitors did not alter surface expression of CD4 and CXCR4. These results suggest that fusion in the presence of the endosome inhibitors likely occurs within nonacidified endosomes. However, the ability of these inhibitors to impair vesicle trafficking from early to late endosomes in some cells could also increase the recycling of these virion-containing endosomes to the cell surface, where fusion occurs. In summary, our results reveal an unexpected, CD4-mediated reciprocal relationship between the pathways governing HIV virion fusion and endocytosis.
Measuring Service Solution Quality in Services Outsourcing Projects Using Value Driver Tree Approach (2012)

In this paper, we present a framework to model and measure the quality of an information technology (IT) service solution in services outsourcing domain. Our three main contributions in this paper are as follows. First, we present a systematic method to identify the drivers of Information Technology (IT) service solution quality based on the lifecycle phases of IT services projects; Second, we present ten service quality measurement dimensions and the associated metrics for measuring these dimensions organized as Value Driver Trees (VDTs); Third, we present a qualitative and quantitative analytical approach for modeling IT service quality metrics and for predicting the quality of service solutions using Value Driver Trees (VDTs). To the best of our knowledge our work is the first of its kind for measuring IT service solution quality in services outsourcing projects from IT service provider point-of-view. We are currently implementing these metrics at a large IT services outsourcing services provider.
Electrochemical Reduction of Li[sub 2]FeS[sub 2] in Solid Electrolyte (2001)

The nature of the product of the electrochemical reduction of has been investigated. This product was completely reoxidized in intimate contact with a lithium ion-conducting solid electrolyte. The product is regarded as α-Fe, although usually, Fe is electrochemically inactive in contact with a solid electrolyte. In order to understand the reason for this discrepancy, the product was investigated by X-ray diffraction and Mössbauer spectroscopy. Its diffraction pattern did not show clear peaks and its Mössbauer spectrum was attributed to superparamagnetic These results suggest that the reduction product consists of noncrystalline, small particles of Fe dispersed in Because of the small particle size, most of the Fe atoms are in contact with This environment is considered to permit the continuous reoxidation to resulting in its electrochemical activity. © 2001 The Electrochemical Society. All rights reserved.
Trans-illumination fluorescence imaging of deep-seated tumors in small animals (2014)

Abstract Background: Fluorescence diffuse tomography (FDT) is the most accurate technique for the imaging of labeled tumors in the small animal body. However, the procedure for reconstruction of the spatial distribution of the fluorophore requires a high signal-to-noise ratio due to the ill-condition of the inverse problem. Therefore, the FDT technique is ineffective for imaging tumors of small size or with dim fluorophores because of the low intensity of their fluorescence compared with the high level of tissue autofluorescence. In these cases, the size and position of a marked tumor in the animal body can be estimated from two-dimensional fluorescence images obtained using trans- or epi-illumination techniques. Material and methods: A versatile system for small animal fluorescence imaging which combines planar epi- and trans-illumination geometries of the light source and of the fluorescence receiver was created and tested. For epi-illumination imaging, light-emitting diode sources were used to provide homogeneous and stable illumination of the experimental animal, in combination with a cooled CCD camera which covers the entire illuminated area. For trans-illumination imaging, mechanical raster-scanning devices modulated at a low frequency were used for the laser source, together with a cooled photomultiplier tube, which provided outstanding sensitivity. Results: Monitoring the orthotopic tumor growth in animal bodies has demonstrated the efficacy of trans-illumination imaging in comparison with the epi-illumination technique. The results obtained also showed that the effective use of the trans-illumination technique requires Born normalization of the fluorescence signal and the exclusion of lateral illumination by surrounding the animal with additional light absorption material using light-absorption pads on both sides of the body.