gebhart/patrepeval huggingface dataset:
Regulation of Bone Cell Development and Function: Implications for Renal Osteodystrophy (2001)

<h3>Introduction</h3> The burden of chronic heart failure (HF) is rising owing to an increased survivorship after myocardial infarction (MI). Pulmonary structural remodelling in patients with HF may protect against oedema while causing dyspnoea, the predominant symptom associated with HF. The cellular and molecular mechanisms underlying these processes in HF are poorly understood. We hypothesised that pulmonary venous hypertension (PVH) following MI provides a mechanical stimulus for structural remodelling of the lung via monocyte chemoattractant protein-1 (MCP-1). <h3>Methods</h3> Human lung microvascular endothelial cells (HLMVEC) and Ea.Hy 926 cells exposed to cyclic mechanical strain (CMS) in vitro were analysed for MCP-1 expression and activation of signalling intermediates. HF was induced in Sprague–Dawley rats 16 weeks after MI; a cohort was rescued with AAV9.SERCA2a gene therapy to reduce PVH. <h3>Results</h3> HLMVEC and Ea.Hy 926 cells exposed to CMS upregulated MCP-1 gene expression and protein release in an extracellular-signal-regulated kinase (ERK) 1/2 dependent manner. Supernatants from these experiments stimulated fibroblast (human fetal lung fibroblast -1) and pulmonary artery smooth muscle cell proliferation and differentiation. Total lung collagen, a marker of structural remodelling, and MCP-1 gene expression were increased in the lungs of rats with post-MI HF. SERCA2a gene therapy that attenuated PVH after MI was associated with lower levels of lung collagen and MCP-1 gene expression in the lung. <h3>Conclusions</h3> Mechanical strain associated with PVH may stimulate pulmonary structural remodelling through ERK 1/2 dependent induction of MCP-1. These findings provide insights into the pathophysiology of lung remodelling in HF and highlight novel, potential therapeutic targets.
Development of <i>o</i>-Chlorophenyl Substituted Pyrimidines as Exceptionally Potent Aurora Kinase Inhibitors (2012)

The o-carboxylic acid substituted bisanilinopyrimidine 1 was identified as a potent hit (Aurora A IC(50) = 6.1 ± 1.0 nM) from in-house screening. Detailed structure-activity relationship (SAR) studies indicated that polar substituents at the para position of the B-ring are critical for potent activity. X-ray crystallography studies revealed that compound 1 is a type I inhibitor that binds the Aurora kinase active site in a DFG-in conformation. Structure-activity guided replacement of the A-ring carboxylic acid with halogens and incorporation of fluorine at the pyrimidine 5-position led to highly potent inhibitors of Aurora A that bind in a DFG-out conformation. B-Ring modifications were undertaken to improve the solubility and cell permeability. Compounds such as 9m with water-solubilizing moieties at the para position of the B-ring inhibited the autophosphorylation of Aurora A in MDA-MB-468 breast cancer cells.
Collagen as a scaffold for biomimetic mineralization of vertebrate tissues (2005)

Collagen is a well known protein component that has the capacity to mineralize in a variety of vertebrate tissues. In its mineralized form, collagen potentially can be utilized as a biomimetic material for a variety of applications, including, for example, the augmentation and repair of damaged, congenitally defective, diseased or otherwise impaired calcified tissues such as bone and cartilage. In order to effect an optimal response in this regard, the manner in which collagen becomes mineralized is critically important to understand. This paper provides details concerning collagen–mineral interaction and its implications with respect to designing biomimetic mineralizing collagen that will be functionally competent in its biological, chemical, and biomechanical properties.
Simulation of higher harmonics generation in tapping-mode atomic force microscopy (2001)

In tapping-mode atomic force microscopy, nonlinear tip–sample interactions give rise to higher harmonics of the cantilever vibration. We present an electrical circuit to model the atomic force microscope cantilever with its first three flexural eigenmodes. An electrical circuit simulator is used to simulate the tapping-mode operation. Amplitude and phase responses of the third flexural eigenmode are obtained for different sample properties. It is found that amplitude and phase of higher harmonics depend highly on sample properties.
Overexpression of Nodal induces a metastatic phenotype in pancreatic cancer cells via the Smad2/3 pathway (2015)

Metastasis is the major cause for the high mortality rate of pancreatic cancer. Human embryonic stem cell (hESC) associated genes frequently correlate with malignant disease progression. Recent studies have demonstrated that the embryonic protein Nodal, which plays a critical role during embryonic development, is re-expressed in several types of tumors and promotes cancers progression. However, little is known about the role of Nodal in pancreatic cancer. Here, we show that Nodal expression is upregulated in human pancreatic cancer tissues. Moreover, Nodal expression levels correlate well with the grade of pancreatic cancer differentiation. In addition, we present clear evidence that Nodal induces signal transduction through the Smad2/3-dependent pathway in vitro. Furthermore, we show that Nodal promotes pancreatic cancer cell migration and invasion, induces epithelial-mesenchymal transition (EMT) and enhances the expression of matrix metalloproteinase-2 (MMP2) and CXC chemokine receptor 4 (CXCR4). Using an in vivo liver metastasis model of pancreatic cancer, we observed that blocking Nodal signaling activity with the small-molecule inhibitor SB431542 decreases the number and size of liver metastases. Taken together, our results suggest that Nodal overexpression induces a metastatic phenotype in pancreatic cancer cells, and that targeting Nodal signaling may be a promising therapeutic strategy for pancreatic cancer.
THERMOCHEMICAL AND PHOTOCHEMICAL KINETICS IN COOLER HYDROGEN-DOMINATED EXTRASOLAR PLANETS: A METHANE-POOR GJ436b? (2011)

We introduce a thermochemical kinetics and photochemical model. We use high-temperature bidirectional reaction rates for important H, C, O, and N reactions (most importantly for CH_4 to CO interconversion), allowing us to attain thermochemical equilibrium, deep in an atmosphere, purely kinetically. This allows the chemical modeling of an entire atmosphere, from deep-atmosphere thermochemical equilibrium to the photochemically dominated regime. We use our model to explore the atmospheric chemistry of cooler (T_(eff) < 10^3 K) extrasolar giant planets. In particular, we choose to model the nearby hot-Neptune GJ436b, the only planet in this temperature regime for which spectroscopic measurements and estimates of chemical abundances now exist. Recent Spitzer measurements with retrieval have shown that methane is driven strongly out of equilibrium and is deeply depleted on the day side of GJ436b, whereas quenched carbon monoxide is abundant. This is surprising because GJ436b is cooler than many of the heavily irradiated hot Jovians and thermally favorable for CH_4, and thus requires an efficient mechanism for destroying it. We include realistic estimates of ultraviolet flux from the parent dM star GJ436, to bound the direct photolysis and photosensitized depletion of CH_4. While our models indicate fairly rich disequilibrium conditions are likely in cooler exoplanets over a range of planetary metallicities, we are unable to generate the conditions for substantial CH_4 destruction. One possibility is an anomalous source of abundant H atoms between 0.01 and 1 bars (which attack CH_4), but we cannot as yet identify an efficient means to produce these hot atoms.
Etude structurale et fonctionnelle des antigenes d'histocompatibilite de lasse i murins (1991)

Clean cooking fuels promise substantial health benefits for rural households, but almost three billion people continue to rely on traditional biomass for their cooking needs. We explore the role of gender in the adoption of LPG, a clean cooking fuel, in rural India. Given that women are responsible for most households' cooking needs, we propose that gender inequality is an obstacle to LPG adoption because men may fail to appreciate the full benefits of clean cooking fuels. Using data for 8,563 households from the ACCESS survey, we demonstrate that households where women participant in decison-making are more likely to adopt LPG for cooking than households in which a man is the sole decision-maker. We extend our analytic framework to evaluate the relationship between household characteristics and LPG and firewood use. Access and cylinder costs were both negatively associated with LPG use and while LPG adoption reduced firewood use, fuel stacking remains the norm in study households. This study has implications for future policy designs to increase LPG adoption and use to obtain the multiple benefits of cleaner cooking.
Characterization of microwave integrated circuits using an optical phase-locking and sampling system (2002)

Using an optical technique, phase-locked microwave signals of up to 15 GHz from voltage-controlled oscillators have been achieved. Combining this technique with a photoconductive switch, a novel microwave waveform sampling system that displays the characteristics of oscillators and amplifiers has been demonstrated. The approach has potential applications for optically phase-locked microwave subsystems and monolithic integrated circuit characterizations.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Neural Networks For Pattern Recognition In Medical Diagnosis (2005)

Neural network simulation systems have been adapted for two types of pattern recognition analyses, utilizing up to 400 input quantitative diagnostic findings in each of 850 output medical diagnostic categories, leading to the correct selection of one in up to 400 competing output diagnoses per trained neural network, in a total of 6 trained d iagnostic neural networks. The input data was either entered quantitatively within i ndividual pixels, or semi-quant ita tively within larger data fields. The output medical diagnoses were displayed either in text or in 3-5 digit ICD-9-CM diagnostic codes.
Development and operation of a solid-state switch for thyratron replacement (2005)

A solid-state switch consisting of 22 reverse conducting thyristors, has been designed to operate at 20 kV hold-off voltage, 1500 A peak, 57 ARMS, 1.0 /spl mu/s pulse-width, and 4500 pps. To date, 70 switches have been fielded, accumulating over 330,000 unit hours with a demonstrated MTBF of over 6000 hours. The previously thyratrons have all been replaced since the solid-state swtch has proven to be more reliable. In addition, the solid-state switch is more cost effective due to its ability to be repaired. This paper discusses the design, construction, triggering, operation, reliability, and failure modes of the switch.
Two-dimensional elastic full waveform inversion using Born and Rytov formulations in the frequency domain (2006)

We perform the full elastic waveform inversion in the frequency domain in a 2-D geometry. This method allows imaging of two physical seismic parameters, using vertical and horizontal field components. The forward problem is discretized using finite difference, allowing to simulate the full elastic wavefield propagation. Moreover, it is solved in the frequency domain, a fast approach for multisource and multireceiver acquisition. The non-linear inversion is based on a pre-conditioned gradient method, where Born and Rytov formulations are used to compute Frchet derivatives. Parameter perturbations linearly depend on fields perturbations in the Born kernel, and on the generalized complex phases of fields in the Rytov kernel, giving different Frchet derivatives. The gradient is pre-conditioned with the diagonal part of the inverse Hessian matrix, allowing to better estimate the stepping in the optimization direction. Nonlinearity is taken into account by updating parameters at each iteration and proceeding from low to high frequencies. The latter allows as well to progressively introduce smaller wavelengths in parameter images. On a very simple synthetic example, we examine the way the inversion determines the V p (P-wave velocity) and V s (S-wave velocity) images. We highlight that, with a transmission acquisition, final parameter images weakly depend on the chosen formulation to compute Frchet derivatives and on the inverted parameters choice. Of course, convergence strongly depends on the medium wavenumber illumination which is related somehow to the acquisition geometry. With a reflection acquisition, the Born formulation allows to better recover scatterers. Moreover, the medium anomalies are not well reconstructed when surface waves propagate in the medium. This may be due to the evanescent nature of surface waves. By selecting first body waves and then surface waves, we improve the convergence and properly reconstruct anomalies. This shows us that preparation of the seismic data before the inversion is as critical as the initial model selection.
Neuroprotection of retinal ganglion cells by a novel gene therapy construct that achieves sustained enhancement of brain-derived neurotrophic factor/tropomyosin-related kinase receptor-B signaling (2018)

Previous studies have demonstrated that intravitreal delivery of brain-derived neurotrophic factor (BDNF) by injection of recombinant protein or by gene therapy can alleviate retinal ganglion cell (RGC) loss after optic nerve injury. BDNF gene therapy can improve RGC survival in experimental models of glaucoma, the leading cause of irreversible blindness worldwide. However, the therapeutic efficacy of BDNF supplementation alone is time limited at least in part due to BDNF receptor downregulation. Tropomyosin-related receptor kinase-B (TrkB) downregulation has been reported in many neurological diseases including glaucoma, potentially limiting the effect of sustained or repeated BDNF delivery.Here, we characterize a novel adeno-associated virus (AAV) gene therapy (AAV2 TrkB-2A-mBDNF) that not only increases BDNF production but also improves long-term neuroprotective signaling by increasing expression of the BDNF receptor (TrkB) within the inner retina. This approach leads to significant and sustained elevation of survival signaling pathways ERK and AKT within RGCs over 6 months and avoids the receptor downregulation which we observe with treatment with AAV2 BDNF alone. We validate the neuroprotective efficacy of AAV2 TrkB-2A-mBDNF in a mouse model of optic nerve injury, where it outperforms conventional AAV2 BDNF or AAV2 TrkB therapy, before showing powerful proof of concept neuroprotection of RGCs and axons in a rat model of chronic intraocular pressure (IOP) elevation. We also show that there are no adverse effects of the vector on retinal structure or function as assessed by histology and electroretinography in young or aged animals. Further studies are underway to explore the potential of this vector as a candidate for progression into clinical studies to protect RGCs in patients with glaucoma and progressive visual loss despite conventional IOP-lowering treatment.
Role of Chloride for a Simple, Non-Grignard Mg Electrolyte in Ether-Based Solvents (2016)

Mg battery operates with Chevrel phase (Mo6S8, ∼1.1 V vs Mg) cathodes that apply Grignard-based or derived electrolytes, which allow etching of the passivating oxide coating forms at the magnesium metal anode. Majority of Mg electrolytes studied to date are focused on developing new synthetic strategies to achieve a better reversible Mg deposition. While most of these electrolytes contain chloride as a component, and there is a lack of literature which investigates the fundamental role of chloride in Mg electrolytes. Further, ease of preparation and potential safety benefits have made simple design of magnesium electrolytes an attractive alternative to traditional air sensitive Grignard reagents-based electrolytes. Work presented here describes simple, non-Grignard magnesium electrolytes composed of magnesium bis(trifluoromethane sulfonyl)imide mixed with magnesium chloride (Mg(TFSI)2-MgCl2) in tetrahydrofuran (THF) and diglyme (G2) that can reversibly plate and strip magnesium. Based on this discovery, the effect of chloride in the electrolyte complex was investigated. Electrochemical properties at different initial mixing ratios of Mg(TFSI)2 and MgCl2 showed an increase of both current density and columbic efficiency for reversible Mg deposition as the fraction content of MgCl2 increased. A decrease in overpotential was observed for rechargeable Mg batteries with electrolytes with increasing MgCl2 concentration, evidenced by the coin cell performance. In this work, the fundamental understanding of the operation mechanisms of rechargeable Mg batteries with the role of chloride content from electrolyte could potentially bring rational design of simple Mg electrolytes for practical Mg battery.
Shuffle Reduction Based Sparse Matrix-Vector Multiplication on Kepler GPU (2016)

GPU is the suitable equipment for accelerating computing-intensive applications in order to get the higher throughput for High Performance Computing (HPC). Sparse Matrix-Vector Multiplication (SpMV) is the core algorithm of HPC, so the SpMV's throughput on GPU may affect the throughput on HPC platform. In the paper, we focus on the latency of reduction routine in SpMV included in CUSP, such as accessing shared memory and bank conflicting while multiple threads simultaneously accessing the same bank. We provide shuffle method to reduce the partial results instead of reducing in the shared memory in order to improve the throughput of SpMV on Kepler GPU. Experiments show that shuffle method can improve the throughput up to 9% of the original routine of SpMV in CUSP on average.
Proteasome Inhibitors Protect Against Degeneration of Nigral Dopaminergic Neurons in Hemiparkinsonian Rats (2005)

Parkinson's disease is characterized by dopaminergic neuronal death and the presence of Lewy bodies in the substantia nigra pars compacta (SNpc). alpha-Synuclein and ubiquitin are components of Lewy bodies, but the process of Lewy body formation and the relationship between inclusion formation and dopaminergic neuronal death have not been resolved. In this study, unilateral intranigral microinjection of 6-hydroxydopamine caused a significant loss of tyrosine hydroxylase-immunopositive neurons in both the substantia nigra and striatum and apomorphine-induced contralateral rotation. The co-administration of proteasome inhibitors, such as lactacystin or carbobenzoxy-L-leucyl-L-leucyl-L-leucinal (MG-132), significantly prevented both dopaminergic neurodegeneration and apomorphine-induced rotational asymmetry. Proteasome inhibitors markedly formed intracellular protein inclusions labeled by thioflavin-S in the SNpc. Inclusion-like immunoreactivities for alpha-synuclein and ubiquitin were detected after 4 weeks. These results suggest that proteasome plays an important role in both the early phase of dopaminergic neuronal death and inclusion body formation.
Sequence Conservation in Potential Regulatory Regions of the Mouse and Human Leukocyte Common Antigen Gene (1989)

The leukocyte common antigen is a family of glycoproteins uniquely expressed by cells of hemopoietic origin. The family is generated by alternative splicing of 3 exons, and individual members are expressed in a cell type-specific fashion. The glycoprotein consists of a heavily glycosylated exterior domain of approximately 100 kDa, a single membrane spanning region, and a cytoplasmic domain that has homology to a protein tyrosine phosphatase of 83 kDa. To further understand the regulation and structure of this family of molecules, genomic clones were isolated from mouse lambda and cosmid libraries. The genomic organization was determined from 20 genomic clones. Eighteen of the clones clustered within a 75-kilobase region, whereas the promoter region, the exons for the 5'-untranslated region, and the leader domain are located an unknown distance further 5' within in an unlinked clone. The gene is composed of 34 exons: two 5'-untranslated exons, 1a and 1b, and 32 exons that encode protein sequence. Exon 2 contains part of the 5'-untranslated region and encodes the 23 amino acids of the leader sequence. Exons 3-15 encode amino acid residues 1-538 of the external domain, exon 16 encodes residues 539-574, encompassing the membrane-spanning domain, and exons 17-33 encode residues 575-1268 of the cytoplasmic domain. Exon 33, the largest exon, contains the 1.1-kilobase 3'-untranslated region. A comparison between mouse and human (Hall, L.R., Streuli, M., Schlossman, S.F., and Saito, H. (1988) J. Immunol. 141, 2781-2787) promoter regions reveals significant homologies 5' to the transcription start site. The relationship between exon structure and glycoprotein structure is discussed.
Comparison of Myopotential Interference in Unipolar‐Bipolar Programmable DDD Pacemakers (1987)

Myopotential interference (MPI) can inhibit or trigger single and dual chamber unipolar pacemakers while bipolar pacemakers are resistant. Twenty units of two different models of dual chamber pacemaker, each capable of being programmed to single chamber or dual chamber and unipolar or bipolar function were tested to provoke myopotential interference. No patient had evidence of myopotential interference at any sensitivity setting in the bipolar configuration either in atrium or in ventricle. All patients (20/20) interfered with pacemaker function at the highest atrial or ventricular sensitivity settings in the unipolar configuration. T wave sensing occurred at the 0.25 mV sensitivity setting in four patients in pacemaker model 925, in both bipolar and unipolar configurations. Twenty-five percent of patients had myopotential interference at the unipolar atrial sensing threshold and did not allow a setting which would reject myopotential interference while providing satisfactory atrial sensing. Twenty percent (2/10) had myopotential caused ventricular inhibition at the least sensitive ventricular channel setting in model 240G so that myopotential interference could not be avoided in that unit no matter how large the electrogram.
A Thin Cathode-Ray Tube (1957)

A new type of cathode-ray tube typically only a few inches thick is described. The beam is injected parallel to one edge of the thin tube and caused to pass through two right-angle deflections: the first sends the beam into the region between the front and back tube surfaces, and the second turns it into the phosphor-coated front surface. A brief analysis of the deflection-focusing action is presented and the sweep-voltage requirements are described. The thin tube can be adapted to multicolor operation or to any other use to which cathode-ray tubes are put; it also has many unique features (in addition to small size), such as the capability of being viewed from both sides of the display screen or being rendered transparent.
SLIDING AND SPREADING OF THIN TWO-DIMENSIONAL DROPS (1981)

Journal Article SLIDING AND SPREADING OF THIN TWO-DIMENSIONAL DROPS Get access L. M. HOCKING L. M. HOCKING Department of Mathematics, University CollegeLondon Search for other works by this author on: Oxford Academic Google Scholar The Quarterly Journal of Mechanics and Applied Mathematics, Volume 34, Issue 1, February 1981, Pages 37–55, https://doi.org/10.1093/qjmam/34.1.37 Published: 01 February 1981 Article history Received: 15 January 1980 Published: 01 February 1981