gebhart/patrepeval huggingface dataset:
Epitope spreading to citrullinated antigens in mouse models of autoimmune arthritis and demyelination (2008)

Our results suggest that anti-citrulline antibody responses develop in the early stages of CIA and EAE, and that autoimmune inflammation results in citrullination of joint proteins in CIA and brain proteins in EAE, thereby creating neoantigens that become additional targets in epitope spreading of autoimmune responses.
Involvement of Fas and Fas Ligand in ConA Induced Hepatitis (1997)

Ksontini, R.; Colagiovanni, D.; Vauthey, J. N.; Solorzano, C. C.; Abdalla, E. K.; Josephs, M. D.; Moshyedi, A. K.; Lazarus, D. L.; Kieft, G.; MacKay, S. L.D.; Copeland, E. M. III; Edwards, C. K. III; Moldawer, L. L. Author Information
Diabetic nephropathy: the role of inflammation in fibroblast activation and kidney fibrosis (2013)

Kidney disease associated with diabetes mellitus is a major health problem worldwide. Although established therapeutic strategies, such as appropriate blood glucose control, blood pressure control with renin-angiotensin system blockade, and lipid lowering with statins, are used to treat diabetes, the contribution of diabetic end-stage kidney disease to the total number of cases requiring hemodialysis has increased tremendously in the past two decades. Once renal function starts declining, it can result in a higher frequency of renal and extra-renal events, including cardiovascular events. Therefore, slowing renal function decline is one of the main areas of focus in diabetic nephropathy research, and novel strategies are urgently needed to prevent diabetic kidney disease progression. Regardless of the type of injury and etiology, kidney fibrosis is the commonly the final outcome of progressive kidney diseases, and it results in significant destruction of normal kidney structure and accompanying functional deterioration. Kidney fibrosis is caused by prolonged injury and dysregulation of the normal wound-healing process in association with excess extracellular matrix deposition. Kidney fibroblasts play an important role in the fibrotic process, but the origin of the fibroblasts remains elusive. In addition to the activation of residential fibroblasts, other important sources of fibroblasts have been proposed, such as pericytes, fibrocytes, and fibroblasts originating from epithelial-to-mesenchymal and endothelial-to-mesenchymal transition. Inflammatory cells and cytokines play a vital role In the process of fibroblast activation. In this review, we will analyze the contribution of inflammation to the process of tissue fibrosis, the type of fibroblast activation and the therapeutic strategies targeting the inflammatory pathways in an effort to slow the progression of diabetic kidney disease.
Investigation of dry-etch-induced defects in &gt;600 V regrown, vertical, GaN, p-n diodes using deep-level optical spectroscopy (2019)

The impact of dry-etch-induced defects on the electrical performance of regrown, c-plane, GaN p-n diodes where the p-GaN layer is formed by epitaxial regrowth using metal-organic, chemical-vapor deposition was investigated. Diode leakage increased significantly for etched-and-regrown diodes compared to continuously grown diodes, suggesting a defect-mediated leakage mechanism. Deep level optical spectroscopy (DLOS) techniques were used to identify energy levels and densities of defect states to understand etch-induced damage in regrown devices. DLOS results showed the creation of an emergent, mid-gap defect state at 1.90 eV below the conduction band edge for etched-and-regrown diodes. Reduction in both the reverse leakage and the concentration of the 1.90 eV mid-gap state was achieved using a wet chemical treatment on the etched surface before regrowth, suggesting that the 1.90 eV deep level contributes to increased leakage and premature breakdown but can be mitigated with proper post-etch treatments to achieve &amp;gt;600 V reverse breakdown operation.
Small‐Angle Neutron Scattering and Magnetically Heterogeneous State in Sr2FeMoO6–δ (2019)

Single‐phase strontium ferromolybdate (Sr 2 FeMoO 6–δ ) samples with different degrees of the superstructural ordering of the Fe/Mo cations ( P ) are obtained from partially reduced SrFeO 3–х , SrMoO 4 precursors by the solid‐state technology. The study of the temperature dependences of the magnetization measured in the field‐cooling and zero‐field‐cooling modes indicated an inhomogeneous magnetic state of the samples. The presence of magnetic regions of different nature has also been revealed by the small‐angle neutron scattering. For the Sr 2 FeMoO 6–δ samples with different P values and for all values of the magnetic field induction up to 1.5 T and of the scattering vector in the interval 0.1 &gt; q &gt; 0.002 Å −1 , the analytical dependence I ∼ q – α obeys the Porod law ( α ≈ 4), which corresponds to an object with a smooth and well‐marked surface and polydisperse grain size. Deviations from the Porod law in the q &gt; 0.1 Å −1 region and a weakening of the neutron scattering in applied magnetic fields may be ascribed to magnetic inhomogeneities with diameters D &lt; 6 nm, which are partially destroyed/oriented by magnetic fields В ≥ 1.5 T. It is established that the magnetic homogeneity of the Sr 2 FeMoO 6–δ compound is enhanced with increasing superstructural ordering of the Fe/Mo cations.
The Pentratricopeptide Repeat Protein DELAYED GREENING1 Is Involved in the Regulation of Early Chloroplast Development and Chloroplast Gene Expression in Arabidopsis (2008)

An Arabidopsis (Arabidopsis thaliana) mutant that exhibited a delayed greening phenotype (dg1) was isolated from a population of activation-tagged Arabidopsis lines. Young, inner leaves of dg1 mutants were initially very pale, but gradually greened and mature outer leaves, more than 3 weeks old, appeared similar to those of wild-type plants. Sequence and transcription analyses showed that DG1 encodes a chloroplast protein consisting of eight pentratricopeptide repeat domains and that its expression depends on both light and developmental status. In addition, analysis of the transcript profiles of chloroplast genes revealed that plastid-encoded polymerase-dependent transcript levels were markedly reduced, while nucleus-encoded polymerase-dependent transcript levels were increased, in dg1 mutants. Thus, DG1 is probably involved in the regulation of plastid-encoded polymerase-dependent chloroplast gene expression during early stages of chloroplast development.
Potential of adult neural stem cells for cellular therapy. (2007)

Cellular therapy is the replacement of unhealthy or damaged cells or tissues by new ones. Because neurodegenerative diseases, cerebral strokes, and traumatic injuries to the central nervous system (CNS) produce neurological deficits that result from neuronal loss, cell therapy is a prominent area of investigation for the treatment of neurological diseases and injuries. Neural progenitor and stem cells generate the main phenotyes of the nervous system, and offer a model of choice for cellular therapy in the CNS. With the confirmation that neurogenesis occurs in the adult brain, and the recent isolation and characterization in vitro of neural progenitor and stem cells from the adult CNS, new strategies are being devised and have the potential to treat a broad range of CNS diseases and injuries.
Predictive Medicine: Computational Techniques in Therapeutic Decision-Making (1999)

The current paradigm for surgery planning for the treatment of cardiovascular disease relies exclusively on diagnostic imaging data to define the present state of the patient, empirical data to evaluate the efficacy of prior treatments for similar patients, and the judgement of the surgeon to decide on a preferred treatment. The individual variability and inherent complexity of human biological systems is such that diagnostic imaging and empirical data alone are insufficient to predict the outcome of a given treatment for an individual patient. We propose a new paradigm of predictive medicine in which the physician utilizes computational tools to construct and evaluate a combined anatomidphysiologic model to predict the outcome of alternative treatment plans for an individual patient. The predictive medicine paradigm is implemented in a software system developed for Simulation-Based Medical Planning. This system provides an integrated set of tools to test hypotheses regarding the effect of alternate treatment plans on blood flow in the cardiovascular system of an individual patient. It combines an internet-based user interface developed using Java and VRML, image segmentation, geometric solid modeling, automatic finite element mesh generation, computational fluid dynamics, and scientific visualization techniques. This system is applied to the evaluation of alternate, patient-specific treatments for a case of lower extremity occlusive cardiovascular disease.
Therapeutic inhibition of BCL-2 and related family members (2017)

BCL-2 proteins are key players in the balance of cell life and death. Their roles in the development and biology of cancer have been well established and continue to be investigated. Understanding the mechanisms by which these proteins regulate apoptosis has led to the development of small molecule targeted therapies that act to overcome the cell's ability to evade programmed cell death. Areas covered: The biology of the intrinsic apoptotic pathway is reviewed with attention to the varied roles of the anti-apoptotic members of the BCL-2 family. BH3 profiling is reviewed. Historical therapeutic agents are addressed, and currently investigated BH3 mimetics are described with attention to clinical significance. The limitations of BCL-2 family targeted drugs with regard to on-target and off-target toxicities are explored. Agents under development for targeting MCL-1 and other BCL-2 family members are discussed. Expert opinion: ABT-199 (venetoclax) and other BH3 mimetics have entered the clinical arena and show promising results in both hematologic and solid malignancies. Use of agents targeting this system will likely expand, and likely a number of malignant diseases will be successfully targeted resulting in improved treatment responses and patient survival.
Evaporation induced diameter control in fiber crystal growth by micro‐pulling‐down technique: Bi4Ge3O12 (2006)

Abstract Diameter self‐control was established in Bi 4 Ge 3 O 12 fiber crystal growth by micro‐pulling‐down technique. In accordance with Bi 2 O 3 ‐GeO 2 phase diagram, the diameter was controlled due to compensation of solidification with evaporation of volatile Bi 2 O 3 self‐flux charged into the crucible with excess. The crucibles had capillary channels of 310 or 650 μm in outer diameter. The crystals up to 400 mm long and 50‐300 μm in diameter were grown at pulling‐down rates of 0.04‐1.00 mm/min. The melt composition and the pulling rate were generally only two parameters determining solidification rate. As a result, crystals with uniform (± 10%) diameter and aspect ratio up to 10 4 were produced without automation of the process. (© 2006 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
On the Structural Design Synthesis of Certifiable Aircraft Engine Pylons (2019)

Thesis (Ph.D.)--University of Washington, 2019
Determining the distribution of probes between different subcellular locations through automated unmixing of subcellular patterns (2010)

Many proteins or other biological macromolecules are localized to more than one subcellular structure. The fraction of a protein in different cellular compartments is often measured by colocalization with organelle-specific fluorescent markers, requiring availability of fluorescent probes for each compartment and acquisition of images for each in conjunction with the macromolecule of interest. Alternatively, tailored algorithms allow finding particular regions in images and quantifying the amount of fluorescence they contain. Unfortunately, this approach requires extensive hand-tuning of algorithms and is often cell type-dependent. Here we describe a machine-learning approach for estimating the amount of fluorescent signal in different subcellular compartments without hand tuning, requiring only the acquisition of separate training images of markers for each compartment. In testing on images of cells stained with mixtures of probes for different organelles, we achieved a 93% correlation between estimated and expected amounts of probes in each compartment. We also demonstrated that the method can be used to quantify drug-dependent protein translocations. The method enables automated and unbiased determination of the distributions of protein across cellular compartments, and will significantly improve imaging-based high-throughput assays and facilitate proteome-scale localization efforts.
High-efficiency, large-bandwidth silicon-on-insulator grating coupler based on a fully-etched photonic crystal structure (2010)

A grating coupler for interfacing between single-mode fibers and photonic circuits on silicon-on-insulator is demonstrated. It consists of columns of fully etched photonic crystal holes, which are made in the same lithography and etching processes used for making the silicon-on-insulator wire waveguide. The holes have a diameter of around 143 nm, and are defined with electron-beam lithography. A peak coupling efficiency of 42% at 1550 nm and 1 dB bandwidth of 37 nm, as well as a low back reflection, are achieved. The performance of the proposed fully etched grating coupler is comparable to that based on the conventional shallowly etched grating, which needs additional fabrication steps.
Corrosion-resistant coatings for ceramic heat-exchanger tubes operating in highly corrosive environments. Annual report, September 1, 1988-August 31, 1989 (1989)

Ten ceramic oxide coating systems, including single-layered mullite and multilayered coatings of mullite, zircon, alumina, yttria, and yttria-stabilized zirconia, were exposed to a simulated aluminum reclamation environment at temperatures ranging from 760-1204 C (1400-2200 F) for 2000 hours plus 10 thermal cycles. Corrosion of the silicon carbide tubes increased with decreasing temperature from 1204 C (2200 F) to 760 C (1400 F). Single layer mullite coatings showed superior corrosion resistance, particularly mullite coatings containing a vitreous phase ceramic seal coating on the outer surface. Measurement of silicon carbide tube wall recessions indicated that the coatings which withstood the 2000 hours exposure test without spalling from the substrate were protective, as compared to uncoated silicon carbide tube sections.
Syntheses of Organofluorine Derivatives by a New Radical Process (2007)

New routes to organofluorine derivatives based on the powerful xanthate radical transfer technology are described. A special emphasis is placed on the synthesis of trifluoromethylsubstituted structures, including trifluoromethylketones and fluorinated aromatic and heteroaromatic substances of interest to the pharmaceutical and agrochemical industries
Overexpression ofMUC5 genes is associated with early post-operative metastasis in non-small-cell lung cancer (1996)

Mucin glycoprotein can promote tumor-cell invasion metastasis and modulate the immune recognition of cancer. This study aimed to elucidate the clinical significance of mucin gene overexpression in lung cancer. We collected 60 lung cancer samples and paired non-tumorous lung portions of varying types and stages. Slot-blot analysis with specific anti-sense oligonucleotide probes derived from tandem repeat sequence of MUC1, -2, -3, -4, 5B and 5AC were utilized to compare the amount of mucin gene mRNA in tumor samples with that of the non-tumorous counterparts. A ratio higher than 1.5 for each specific mucin mRNA amount was considered to indicate mucin gene overexpression in tumors. Immunohistochemical staining of monoclonal antibodies against mature airway mucin (17Q2) and MUC1 mucin protein (HMFG2) were also used to analyze mucin protein. The study showed that overexpression of mucin genes frequently occurred in lung cancer (25 out of 60, 41.7%), but that there was no preferential expression of a particular mucin gene or a combination of mucin genes in these tumors. The overexpression of mucin genes and mucin protein had no correlation with tumor stage, nodal stage, histology or pathological differentiation grade. Tumors of smokers had higher MUC5B and MUC5AC mRNA expression ratios than those of non-smokers. Tumors with increased expression of mucin genes tended to be associated with post-operative relapse, especially when MUC5B and MUC5AC genes were overexpressed (p = 0.015 and 0.025, respectively). The study suggests that overexpression of novel tracheobronchial mucin genes may result in an increased likelihood of post-operative lung-cancer recurrence or metastases.
A fine-grained, controllable, user-to-user delegation method in RBAC (2005)

This paper addresses the issues surrounding user-to-user delegation in RBAC. We show how delegations can be incorporated into the RBAC model in a simple and straightforward manner. A special feature of the model is that it allows fine-grained control over what rights a user wishes to delegate as opposed to delegation at the role level where all the rights of a role must be delegated. In addition, the model provides a rich set of controls regarding further delegations of a right, generic constraints that further control delegations, and an innovative model for revocations. Properties of both delegation and revocation are discussed, and our work is compared with other related research.
Determination of phosphorus in water using iron hydroxide assisted laser-induced breakdown spectroscopy (2023)

Phosphorus (P) in water could be selectively detected using iron hydroxide assisted laser-induced breakdown spectroscopy.
A low-frequency paradox in binaural pitch (2001)

Binaural pitches, such as the Huggins pitch and binaural coherence edge pitch (BICEP), can be approached in terms of a model network of binaural neurons that are tuned in frequency and in interaural delay [e.g., Raatgever and Bilsen, J. Acoust. Soc. Am. 80, 429–441 (1986)]. The basic rule of binaural combination resembles addition. Binaural pitches appear as peaks or edge features in the frequency-delay plane. The characteristic frequency of a feature determines the pitch, and the internal delay of the feature determines the lateralization of the pitch image. Because delay lines become sparser with increasing delay, the model predicts that binaural pitches of very low frequency should be more difficult to hear the more they are lateralized. However, our Huggins pitch and BICEP discrimination and detection experiments show that the reverse is true. These experiments favor a model in which the basic rule of binaural combination resembles subtraction. However, the predictions of the subtractive model disagree with the observed lateralization. Furthermore, the low-frequency discrimination and detection experiments do not agree with a model in which additive and subtractive binaural combinations are alternative options. This is the low-frequency paradox. [Work supported by NIDCD.]
Adsorption and Desorption of Oxytetracycline and Carbamazepine by Multiwalled Carbon Nanotubes (2009)

We investigated the adsorption-desorption by multiwalled carbon nanotubes (MWCNTs) of two pharmaceuticals, oxytetracycline (OTC) and carbamazepine (CBZ). The pharmaceuticals demonstrated relatively fast sorption kinetics on MWCNTs. All adsorption isotherms were nonlinear and fit the Polanyi-Manes model (PMM). The single point adsorption coefficient (K) values for OTC were more than 1 order of magnitude higher than those for CBZ on corresponding MWCNTs. The adsorbed volume capacity (Q(0)) and K values of PMM showed a significant relationship with surface areas and the meso- and micropore volume of MWCNTs for both chemicals. Depending on the MWCNT outer diameter, 13.8-25.2% and 62.7-90.6% of initially adsorbed OTC and CBZ, respectively, were desorbed after 200 h. The rate of desorption of both OTC and CBZ depended upon pH and the quantity of initially adsorbed pharmaceuticals, as well as aggregation in the case of OTC.
Contribution of p16INK4aand p21CIP1pathways to induction of premature senescence of human endothelial cells: permissive role of p53 (2005)

We have previously found that nonenzymatically glycated collagen I (GC), mimicking diabetic microenvironment, can induce senescent phenotype in early passage human umbilical vein endothelial cells (HUVECs). In the present study, we explored the functional involvement of cell cycle checkpoint pathways in initiating GC-induced premature endothelial cell senescence. When compared with native collagen, early passage HUVECs showed increased p53, p21(CIP1) (p21), and p16(INK4a) (p16) mRNA expression after exposure to GC. Twenty-four hours after transfection of p16, p21, and p53-enhanced green fluorescent protein (EGFP) recombinant plasmids, HUVECs entered G(1)-phase cell cycle arrest. By days 3 and 5, HUVECs transfected with p16-EGFP showed an increased proportion of senescent cells, and this increase was more prominent in the GFP-positive cell population, which exhibited 68% of senescent cells. Transfection of p21 also induced senescence but only by day 5. Cotransfection of p16 and p21 showed no additive effect. Transfection of p21 or p53 induced apoptosis in HUVECs. Next, we suppressed endogenous p53, p21, p16, or retinoblastoma (Rb) gene expression through small interference RNA strategy and investigated their influence in p16- and p21-initiated endothelial cell senescence. Analysis indicated that suppression of p53 expression can abolish senescence induced by p16 overexpression. Paradoxically, this effect was not observed when p21 was suppressed. On the other hand, suppression of Rb eliminated senescence initiated by either p16 or p21 overexpression. In summary, the p53/p21 pathway is mainly responsible for GC-induced apoptosis, but the coordinated activation of the p53/p21 and p16 pathway is responsible for GC-induced endothelial cell senescence through a Rb-dependent mechanism.