gebhart/patrepeval huggingface dataset:
Assessment of viral RNA in idiopathic pulmonary fibrosis using RNA-seq (2020)

To the best of our knowledge, this is the first publication that employs RNA-seq to assess whether viral infections are linked to the pathogenesis of IPF. Our results do not address the role of viral infection in acute exacerbations of IPF, however, this analysis patently did not support an association between herpes virus detection and IPF.
Nonlinear dynamics in aluminum nitride contour-mode resonators (2013)

In this work we discuss the self-heating dynamics of aluminum nitride contour mode resonators. The self-heating introduces a quadratic coupling between the resonator motion and its temperature. This coupling produces a nonlinear frequency response identical to the Duffing resonator in steady-state. However, since the thermal relaxation rate is much smaller than the mechanical relaxation rate the dynamics of the resonator differ from the conventional Duffing resonator.
Land Seismic Data Acquisition Using Rotation Sensors (2012)

A 2D land seismic data acquisition method that combines measurements of the vertical component particle velocity and the horizontal rotation rate of the wavefield is presented. It is shown that the station spacing of such a survey can be increased to beyond that corresponding to the spatial Nyquist wavenumber. An algorithm is described that can separate once-aliased data from the vertical component wavefield data. The separated data can be used for wavefield interpolation. A field experiment shows that rotation rate sensors can directly measure at the free surface, the required horizontal gradient of the vertical component of the wavefield. A synthetic data set is used to demonstrate the algorithm for the separation and interpolation of regularly spaced aliased data.
Painful Lumbar End-Plate Disruptions: A Significant Discographic Finding (1988)

Of the 692 discs injected during lumbar discograms, end-plate disruptions with leakage of contrast material into the vertebral bodies were noted in 14 discs. Although gentle pressure was applied during the injections, severe fully concordant pain was reproduced in four (28.3%) discs, moderately severe and fully concordant pain in nine (64.3%) discs, and mild discordant pain in one (7.4%) disc. This is compared to 11.2% of the remaining 678 discs without end-plate disruption that reproduced severe concordant pain, 31.1% with moderately severe concordant pain, 17.1% with mild pain, and 40.6% without any pain reproduction. The difference between pain frequency in discs with end-plate disruption and those without is statistically significant (P less than .001). This suggests that end-plate disruptions may be related to painful segments.
A survey of polyvinylphenol blend miscibility (1994)

Abstract The effect of polymer structure on blend miscibility with polyvinylphenol (PVPh) has been studied for at least one polymer from a variety of polymer classes with potential hydrogen‐bond accepting groups: polyesters (aliphatic and aromatic), polycarbonates, polyimides, polyamides, polysulfones, polyurethanes, polyethers, polysiloxanes, poly(amideimides), and cellulose esters. Many of the polyesters, polyamides, and cellulose esters showed evidence of interaction and miscibility with PVPh. In most of the other cases, there was no sign of miscibility. Generally good correlation exists between thermal behavior and infrared spectral data. Where there is significant interaction seen between the polymers by FTIR, substantial miscibility is seen by DSC analysis. In some cases, the phase behavior depended on the blend preparation scheme. © 1994 John Wiley &amp; Sons, Inc.
Clinical, genomic, and metagenomic characterization of oral tongue squamous cell carcinoma in patients who do not smoke: Clinical and genomic study of nonsmokers with oral tongue cancer (2020)

Evidence suggests the incidence of oral tongue squamous cell carcinoma is increasing in young patients, many who have no history of tobacco use.
Prospective trial evaluating immunocytochemical-based sputum techniques for early lung cancer detection: Assays for promotion factors in the bronchial lavage (1993)

To confirm the results of a previous report on the use of monoclonal antibodies in immunocytochemical assays of sputums for the early detection of lung cancer, we designed a new prospective trial in an independent clinical trial population. Since well-characterized Stage I resected non-small cell lung cancer patients have a low rate of tumor relapse and a high (1-3%/year) chance of developing a second primary lung cancer, they comprise a very favorable group for conducting an early lung cancer detection trial. The rate of new lung cancer is about 10-fold in excess of a standard "high" risk population of smokers. To optimize the chance for a favorable outcome, all of the technical components for the trial have been systematically evaluated to ensure that optimal procedures are employed. For example, automated immunostaining of the sputum specimens will be performed. Bronchial lavages will be analyzed in a subset of the trial participants to define additional targets for early lung cancer detection. Two markers will be quantitated, including gastrin releasing peptide and peptidyl glycine alpha-amidating monooxygenase activity. These two markers assess the epithelium's capacity to produce growth factors which may be central to the biology of tumor promotion. Since these assays have not been performed in this context before, we attempted to optimize the specimen handling to permit the receipt of the material from a range of collaborating clinical sites in a condition that permits accurate quantitation of these two biomarkers. Efforts to standardize the assay endpoint stimulated the development of computer-assisted methods of immunocytochemical analysis.(ABSTRACT TRUNCATED AT 250 WORDS)
Abstract 17087: VNS Induced Early Suppression of the Excessive Inflammatory Response May Contribute to its Beneficial Effects on Chronic Heart Failure (2015)

Background: The inflammatory response plays a pivotal role in the pathogenesis of chronic heart failure (CHF). Although vagal nerve stimulation (VNS) improves CHF, the central mechanism remains unclear. Since VNS exerts powerful anti-inflammatory effects, we investigated how VNS impacts on the inflammatory regulation and the development of CHF. Methods: In 8 weeks old Sprague-Dawley rats, we created large myocardial infarction (MI) and started VNS 2 weeks after MI. We adjusted the intensity of VNS below the threshold of bradycardia (20 Hz, 1.5±0.9 volts, 10 sec on, 50 sec off). In the first group (EARLY) (CHF: n=8, VNS: n=13), we continued VNS for 3 days and evaluated the early impact of VNS on inflammation on the 3rd day. In the second group (LATE) (CHF: n=13, VNS: n=13), we continued VNS for 4 weeks and evaluated cardiac remodeling and function on the last day. Results: In EARLY, hemodynamic parameters or plasma BNP as an index of CHF did not change significantly. In contrast, VNS halved the invasion of CD 68 positive cells in the left ventricle (LV) (CHF: 295.1±142.1, VNS: 110.7±59.6 counts/mm2, p&lt;0.01), and markedly reduced interleukin-1β (IL-1β) not only in plasma (CHF: 75.7±27.6, VNS: 32.9±6.8 pg/mL, p&lt;0.01) but also in the heart (CHF: 13.2±4.6, VNS: 9.3±2.4 pg/mg, p&lt;0.05) and spleen (CHF: 170.2±65, VNS: 115.4±58.8 pg/mg, p&lt;0.05). TNF-α, IL-6, HMGB-1 and CRP remained unchanged. In addition, VNS significantly reduced the expression of TGF-β in LV which is a key mediator of fibroblast activation (CHF: 31±4.0, VNS: 16.6±2.0 %, p&lt;0.01). In LATE, VNS significantly decreased cardiac fibrosis (Masson’s trichrome stain) (CHF: 4.4±0.7, VNS: 2.9±1.1 %, p&lt;0.01), heart weight (CHF: 3.7±0.5, VNS: 3.2±0.5 g/kg, p&lt;0.01) and LVEDP (CHF: 24.2±5.0, VNS: 17.5±7.1 mmHg, p&lt;0.01), suggesting that VNS prevented cardiac remodeling and preserved LV function. Conclusion: VNS significantly decreased the invasion of macrophage, IL-1β and TGF-β production from the beginning of VNS initiation, and resulted in the decrease of cardiac fibrosis and the improvement of cardiac remodeling as well as cardiac function. VNS induced early suppression of the excessive inflammatory response may lead to its late beneficial effects on CHF.
Dynamic UL/DL Mode Selection and Resource Allocation in Multi-Cell MIMO TDD Systems (2019)

This paper considers joint uplink/downlink mode selection and resource allocation problem in multi-cell systems for flexible TDD frame structures. To combat the difficult interference characteristics of such systems, a dynamic mode selection and resource allocation scheme is derived using Lyapunov optimization. The result is a cross-layer optimization scheme, where a long-term time-average utility function of flow rates and interference penalty is optimized by solving a series of instantaneous subproblems. The proposed dynamic algorithm provides a solution for the UL/DL mode selection and resource allocation, guided by the accumulating network layer queues and virtual queues. Furthermore, a heuristic method is considered to decouple the difficult power constraint in the resource allocation subproblem.
Balancing Ethanol Cosolvent Concentration with Product Performance in 134a-Based Pressurized Metered Dose Inhalers (2003)

The effects of formulation parameters on the product performance characteristics of solution metered dose inhalers (MDIs) were determined using ethanol as the cosolvent and HFA 134a as the propellant. Solubility of beclomethasone dipropionate (BDP) was determined in various blends of 134a and ethanol and was shown to increase with ethanol concentration. Product performance was assessed using the APS Model 3306 Impactor Inlet in conjunction with APS Model 3320 Aerodynamic Particle Sizer (APS). Nine solution formulations containing various BDP and ethanol concentrations were studied. Chemical analysis of the Impactor Inlet was performed in order to determine the "respirable" deposition of the MDI system. With increased ethanol concentration, the throat deposition and plate deposition increased and the respirable deposition decreased. The mass median aerodynamic diameter (MMAD) increased with the increasing drug concentration, but did not show a significant increase with an increase in ethanol concentration. This indicates that the efficiency of solution MDIs decreases with increased ethanol concentration. A Maximum Respirable Mass (MRM) was calculated based on the drug solubility at a particular ethanol concentration and the respirable deposition for a 50mcl valve and QVAR actuator for that ethanol concentration. The MRM represents the maximum amount of a given drug that can be delivered to the lungs theoretically and is very sensitive to the solubility profile of the drug. The MRM increased with the increasing ethanol concentration in the formulation until a plateau was reached at an ethanol concentration of 10-15% w/w. The MRM initially increases with increase in ethanol concentration due to the increase in drug solubility. However, at higher ethanol concentrations the increase in drug solubility was negated by a decrease in the respirable deposition. This study illustrates the importance of considering both formulation properties and product performance characteristics when optimizing a metered dose inhaler drug delivery system.
Synthesis of 1-aryl-1-phenylpropenes using an alkylation-rearrangement-methylation-isomerization one-pot reaction sequence (2011)

Abstract (Z/E)-1-(2-Methoxyaryl)-1-phenylpropenes have been prepared in good yields by heating a mixture of a phenolic substrate, cinnamyl chloride, tetramethylammonium chloride and K2CO3 in polyethyleneglycol at 180°C. The one-pot synthesis proceeds through four discrete reaction steps: alkylation of the phenol with cinnamyl chloride, Claisen rearrangement, O-methylation and double-bond migration. The configuration of one crystalline product was determined using a single-crystal X-ray diffraction analysis. The thermodynamic and structural features of the products were evaluated using computational chemistry techniques.
Factor IX Expressed in Lettuce Chloroplasts Induces Oral Tolerance in Hemophilia B Mice (2015)

Abstract Inhibitor formation represents a major complication of factor replacement therapy for hemophilia. There are currently no prophylactic protocols against this antibody response. To address this problem, we sought to develop an antigen-specific immune tolerance protocol that does not rely on immune suppressive drugs and that would be feasible in pediatric patients. Oral tolerance fits these requirements but is hampered by vulnerability of the protein antigen to degradation in the stomach, cost of production, and inadequate delivery across the gut epithelium to the immune system (the gut-associated lymphoid tissue or GALT). We had hypothesized that transgenic expression of coagulation factors fused to a transmucosal carrier in the chloroplasts of plant cells would provide high level and cost-effective antigen production, bioencapsulation, and transmucosal delivery. Although we demonstrated this concept by of expression cassettes for factor VIII (FVIII) and factor IX (FIX) antigens fused to cholera toxin B (CTB) subunit in tobacco, further advancement of this system to the clinic is not feasible. Translation of this approach would require generation of transgenic edible plant cells expressing these fusion proteins. Therefore, in this study, we expressed CTB-FIX using species-specific chloroplast vectors regulated by endogenous psbA sequences, a requirement for optimal transgene expression (Plant Physiology 152: 2088-2104). Transplastomic plants were homoplasmic (inserted into all copies of chloroplast genomes in each plant cell) as evidenced by Southern blots. CTB-FIX antigen levels reached ~1mg antigen/g of lyophilized leaf cells and was stable with proper folding, disulfide bond formation, and CTB pentamer assembly when stored at ambient temperature for up to 2 years. Oral gavage of these cells (twice per week for 2 months) to hemophilia B mice (FIX gene deletion, C3H/HeJ background, n=7-11/experimental group) delivered CTB-FIX efficiently to the gut epithelium and immune system (as shown by immunohistochemistry), and induced LAP+ regulatory T cells in response to intravenous challenge with recombinant FIX protein. Moreover, FIX-CTB antigen doses of 1.5 mg, 5 mg, or 15 mg all effectively prevented inhibitor/IgG formation against intravenous FIX and averted anaphylaxis and associated fatal reactions by suppression of FIX-specific IgE production. Average inhibitor titers were 15-fold lower for CTB-FIX fed compared to control mice. Of orally treated mice, &gt;80% had inhibitor titers that were undetectable to &lt;2 BU, while controls formed high-titer inhibitors that were &gt;5BU, with 9/11 showing &gt;10 BU. Induction of tolerance in such a broad dose range should greatly facilitate translation of the approach. Our results support initiation of clinical studies on oral tolerance for hemophilia B using transplastomic lettuce. Disclosures Herzog: Spark Therapeutics: Patents &amp; Royalties: Patent licenses; Novo Nordisk: Research Funding. Daniell:Novo Nordisk: Research Funding.
Laser Ablation Surface Treatment of Structural Aerospace Composites and Metal Alloys for Adhesive Bonding (2018)

NASA Langley Research Center (LaRC) has been involved over the past decade in the development of laser ablation as a method to surface treat aerospace structural fiber reinforced composites (CFRPs) and metal alloys. [1- 18] Laser surface treatment has been shown to be a rapid, high precision, and reproducible method for surface treatment of these materials, and is amenable to automation. The laser ablation process removes surface contamination such as silicones, creates surface roughness, and chemically activates a surface for bonding. The degree of ablation is controllable by adjusting laser parameters. In the case of CFRPs, ablation can be performed without damage to any underlying carbon fibers. In the case of metal alloys, ablation is possible without surface embrittlement, heat damage or creation of undesirable grain structures or morphologies. The optimum laser treatment conditions are substrate dependent and generally are influenced by laser wavelength and pulse duration (typically fixed for a laser system), and laser power. In the case of metal alloys such as Ti-6Al-4V, the laser ablation process eliminates the need for several steps of the conventional processes, including hydrofluoric (HF) acid and caustic treatment. These steps are often conducted in dip tanks and require costly facilities and environmentally unfriendly liquids. In addition, the laser can create nano-porosity on the Ti-6Al-4V alloy surface allowing for sol-gel penetration and thereby creating a gradient interface with improved temperature and mechanical performance. NASA LaRC has also been involved with the development of in-line characterization methods compatible with the laser treatment process to rapidly determine the presence of key contaminates such as silicones that, even at very low concentrations, are a threat to adhesive bonding. A spectroscopic technique called micro-laser induced breakdown spectroscopy (u-LIBS) has been developed to rapidly detect silicones at concentrations below those known to cause bonding problems. This technique requires no sample preparation, vacuum or inert atmosphere, has no practical size limitations, and provides nearly instantaneous feedback to the operator. This presentation will give an overview and update of these developments with specific examples highlighted.
Hemorrhage-Induced Interleukin-1 Receptor Pathway in Lung Is Suppressed by 3,5-Bis(2-Fluorobenzylidene)-4-Piperidone in a Rat Model of Hypovolemic Shock (2014)

Severe blood loss in victims of trauma creates an exaggerated inflammatory background that contributes to the development of intravascular coagulopathy and multiple organ dysfunction syndrome. We hypothesized that treatment with diphenyldifluoroketone EF24, an inhibitor of nuclear factor kappa-B, would have salutary effects in hemorrhagic shock. The objective of this study was to investigate the effect of EF24 on the expression of the interleukin-1 receptor (IL-1R) superfamily in a rat model of hypovolemic shock. Hypovolemia was induced by gradually withdrawing approximately 50% of circulating blood, and EF24 was administered intraperitoneally (0.2 mg/kg) in 50 μL of saline. After 6 h of shock, lung tissue was probed immunohistochemically and by immunoblotting to study the expression of Toll-like receptor 4 (TLR4), IL-1R, suppression of tumorigenicity 2 (ST2), and single immunoglobulin IL-1R-related (SIGIRR). The tissue-associated pro-inflammatory cytokines, tumor necrosis factor alpha (TNF-α) and IL-6, were measured by enzyme-linked immunosorbent assay. We observed a reduction in immunoreactive TLR4 and IL-1R1 in lung tissue of rats treated with EF24. Simultaneously, the pulmonary expression of ST2 and SIGIRR (the putative down-regulators of the pro-inflammatory IL-1R pathway) was increased in EF24-treated hemorrhaged rats. The concentration of hemorrhage-induced TNF-α and IL-6 in lung tissue homogenates was also reduced by EF24 treatment. These results confirm our previous in vitro observations in lipopolysaccharide-stimulated dendritic cells that EF24 beneficially modulates the IL-1R pathway and suggest that it could be investigated as an adjunct therapeutic in managing inflammation associated with hemorrhagic shock.
Supplementary Table S4 from The Master Neural Transcription Factor BRN2 Is an Androgen Receptor–Suppressed Driver of Neuroendocrine Differentiation in Prostate Cancer (2023)

&lt;p&gt;Primer sequences.&lt;/p&gt;
Cytoskeleton stiffness regulates cellular senescence and innate immune response in Hutchinson–Gilford Progeria Syndrome (2020)

Hutchinson-Gilford progeria syndrome (HGPS) is caused by the accumulation of mutant prelamin A (progerin) in the nuclear lamina, resulting in increased nuclear stiffness and abnormal nuclear architecture. Nuclear mechanics are tightly coupled to cytoskeletal mechanics via lamin A/C. However, the role of cytoskeletal/nuclear mechanical properties in mediating cellular senescence and the relationship between cytoskeletal stiffness, nuclear abnormalities, and senescent phenotypes remain largely unknown. Here, using muscle-derived mesenchymal stromal/stem cells (MSCs) from the Zmpste24<sup>-/-</sup> (Z24<sup>-/-</sup> ) mouse (a model for HGPS) and human HGPS fibroblasts, we investigated the mechanical mechanism of progerin-induced cellular senescence, involving the role and interaction of mechanical sensors RhoA and Sun1/2 in regulating F-actin cytoskeleton stiffness, nuclear blebbing, micronuclei formation, and the innate immune response. We observed that increased cytoskeletal stiffness and RhoA activation in progeria cells were directly coupled with increased nuclear blebbing, Sun2 expression, and micronuclei-induced cGAS-Sting activation, part of the innate immune response. Expression of constitutively active RhoA promoted, while the inhibition of RhoA/ROCK reduced cytoskeletal stiffness, Sun2 expression, the innate immune response, and cellular senescence. Silencing of Sun2 expression by siRNA also repressed RhoA activation, cytoskeletal stiffness and cellular senescence. Treatment of Zmpste24<sup>-</sup><sup>/</sup><sup>-</sup> mice with a RhoA inhibitor repressed cellular senescence and improved muscle regeneration. These results reveal novel mechanical roles and correlation of cytoskeletal/nuclear stiffness, RhoA, Sun2, and the innate immune response in promoting aging and cellular senescence in HGPS progeria.
The Discovery of Common Recurrent Transmembrane Protease Serine 2 (TMPRSS2)-Erythroblastosis Virus E26 Transforming Sequence (ETS) Gene Fusions in Prostate Cancer (2009)

Recurrent gene fusions and chromosomal rearrangements were previously thought to be the primary oncogenic mechanism of hematological malignancies and sarcomas. The recent discovery of recurrent gene fusions in a majority of prostate cancers represents a paradigm shift in understanding the molecular mechanisms of one of the most prevalent epithelial malignancies, with important clinical and biologic implications. The prostate cancer gene fusions that have been identified so far are characterized by 5'-genomic regulatory elements, most notably the androgen-controlled prostate specific gene, transmembrane protease serine 2, fused to members of the erythroblastosis virus E26 transforming sequence family of transcription factors, most notably ERG, leading to the overexpression of oncogenic transcription factors. The erythroblastosis virus E26 transforming sequence gene fusions most likely define a distinct class of prostate cancer with potential implications for early diagnosis, prognosis, and rational therapeutic targeting. In this review, we summarize the bioinformatics approach that led to the discovery of gene fusions, the current state of the frequency, and diversity of gene fusions that define the molecular heterogeneity of prostate cancer, their associations with prostate cancer progression and clinical outcome, the subsequent morphological characteristics, and the potential application of gene fusions as biomarkers in the diagnosis and management of prostate cancer.