gebhart/patrepeval huggingface dataset:
Pathway for Unfolding of Ubiquitin in Sodium Dodecyl Sulfate, Studied by Capillary Electrophoresis (2008)

This paper characterizes the complexes formed by a small protein, ubiquitin (UBI), and a negatively charged surfactant, sodium dodecyl sulfate (SDS), using capillary electrophoresis (CE), circular dichroism (CD), and amide hydrogen-deuterium exchange (HDX; as monitored by mass spectroscopy, MS). Capillary electrophoresis of complexes of UBI and SDS, at apparent equilibrium, at concentrations of SDS ranging from sub-micellar and sub-denaturing to micellar and denaturing, revealed multiple complexes of UBI and SDS of the general composition UBI-SDS(n). Examination of electrophoretic mobilities of complexes of UBI and SDS as a function of the concentration of SDS provided a new way to characterize the interaction of this protein with SDS and established key characteristics of this system: e.g., the reversibility of the formation of the complexes, their approximate chemical compositions, and the pathway of SDS binding to UBI. The work identified, in addition to SDS-saturated UBI, at least six groups of complexes of UBI with SDS, within which four groups were populated with complexes of distinct stoichiometries: UBI-SDS(approximately 11), UBI-SDS(approximately 25), UBI-SDS(approximately 33), and UBI-SDS(approximately 42). CD spectroscopy and amide HDX of the UBI-SDS(n) complexes suggested that many of the UBI-SDS(n) complexes (n > 11) have greater alpha-helical content than native UBI. Capillary electrophoresis provides a level of detail about interactions of proteins and SDS that has not previously been accessible, and CE is an analytical and biophysical method for studies of interactions of proteins and surfactants that is both convenient and practical. This study sheds light on the formation of the enigmatic protein-SDS complexes formed during SDS polyacrylamide gel electrophoresis and brings a new tool to the study of proteins and detergents.
Alternative splicing‐regulated protein of hepatitis B virus hacks the TNF‐α‐stimulated signaling pathways and limits the extent of liver inflammation (2015)

Hepatitis B splicing-regulated protein (HBSP) of the hepatitis B virus (HBV) was uncovered a few years ago but its function remains unknown. HBSP expression occurs from a spliced viral transcript that increases during the course of liver disease. This study aimed at characterizing the impact of HBSP on cellular signaling pathways in vitro and on liver pathogenesis in transgenic (Tg) mice. By RT-qPCR array, NF-κB-inducible genes appeared modulated in HepG2 cells transduced with a HBSP-encoding lentivirus. Using luciferase and Western blot assays, we observed a decreased activation of the NF-κB pathway in HBSP-expressing cells following TNF-α treatment, as illustrated by lower levels of phosphorylated IκB-α. Meanwhile, the level of phosphorylated JNK increased together with the sensitivity to apoptosis. The contrasting effects on JNK and IκB-α activation upon TNF-α stimulation matched with a modulated maturation of TGF-β-activated kinase 1 (TAK1) kinase, assessed by 2-dimensional SDS-PAGE. Inhibition of the NF-κB pathway by HBSP was confirmed in the liver of HBSP Tg mice and associated with a significant decrease of chemically induced chronic liver inflammation, as assessed by immunohistochemistry. In conclusion, HBSP contributes to limit hepatic inflammation during chronic liver disease and may favor HBV persistence by evading immune response.
Decellularization combined with enzymatic removal of N‐linked glycans and residual DNA reduces inflammatory response and improves performance of porcine xenogeneic pulmonary heart valves in an ovine in vivo model (2019)

Functional xenogeneic heart valve substitutes with a low immunologic load can be produced by decellularization combined with enzymatic removal of DNA and partial deglycosylation of dpPHV.
Resonant frequency selectable induction heating targets (2004)

This paper examines a scheme for developing frequency selectable induction heating targets for stimulating temperature sensitive polymer actuators. "Frequency selectable" implies that each target has a frequency at which it heats preferentially compared to other remaining targets. Resonant RLC circuits that are inductively coupled to a primary induction coil are examined. One way to achieve selectivity with frequency is to design each target to have a different resonant frequency. In this way, a target driven at its resonant frequency will heat preferentially when compared to the remaining targets.
CFD Heat Transfer Investigation Into the Convective Coefficient of a Perforated Plate (2005)

A computational fluid dynamics (CFD) model investigating the heat transfer convective coefficient of the upstream face, the upstream face and the tube face, and the upstream face, tube face, and leeward face of a perforated sheet was developed. This model was based on the hexagonally shaped flow pattern that exists around each of the holes in a perforated sheet of a certain pitch to diameter ratio. The CFD model used in the investigation of the convective heat transfer coefficient involved a single hole in a thin hexagonally shaped sheet with appropriate boundary conditions. Through a series of models varying the inlet velocity, hole diameter, and the plate temperature and then solving for the exit temperature the convective coefficient could be obtained. After obtaining the convective coefficient, the Nusselt number was calculated. These values were then plotted against the Reynolds number and an equation for the line was obtained of the form: Nu=C1·ReC2(1)
c-Jun N-Terminal Kinase Contributes to Aberrant Retinoid Signaling in Lung Cancer Cells by Phosphorylating and Inducing Proteasomal Degradation of Retinoic Acid Receptor α (2005)

Retinoic acid (RA) is the ligand for nuclear RA receptors (RARs and RXRs) and is crucial for normal epithelial cell growth and differentiation. During malignant transformation, human bronchial epithelial cells acquire a block in retinoid signaling caused in part by a transcriptional defect in RARs. Here, we show that activation of c-Jun N-terminal kinase (JNK) contributes to RAR dysfunction by phosphorylating RARalpha and inducing degradation through the ubiquitin-proteasomal pathway. Analysis of RARalpha mutants and phosphopeptide mapping revealed that RARalpha residues Thr181, Ser445, and Ser461 are phosphorylated by JNK. Mutation of these residues to alanines prevented efficient ubiquitination of RARalpha and increased the stability of the protein. We investigated the importance of RARalpha phosphorylation by JNK as a mediator of retinoid resistance in lung cancer. Mice that develop lung cancer from activation of a latent K-ras oncogene had high intratumoral JNK activity and low RARalpha levels and were resistant to treatment with an RAR ligand. JNK inhibition in a human lung cancer cell line enhanced RARalpha levels, ligand-induced activity of RXR-RAR dimers, and growth inhibition by RA. These findings point to JNK as a key mediator of aberrant retinoid signaling in lung cancer cells.
Recombinant baculovirus displayed vaccine (2013)

The rapid evolution of new sublineages of H5N1 influenza in Asia poses the greatest challenge in vaccine development for pre-pandemic preparedness. To overcome the antigenic diversity of H5N1 strains, multiple vaccine strains can be designed based on the distribution of neutralizing epitopes in the globular head of H5 hemagglutinin (HA). Recently, we selected two different HAs of H5N1 strains based on the neutralizing epitopes and reactivity with different neutralizing antibodies. The HAs of selected vaccine strains were individually expressed on the baculovirus envelope (bivalent-BacHA) with its native antigenic configuration. Further, oral delivery of live bivalent-BacHA elicited broadly reactive humoral, mucosal and cell-mediated immune responses and showed complete protection against antigenically distinct H5N1 strains in mice. The strategy for the vaccine strain selection, vaccine design and route of administration will provide an idea for development of a widely protective vaccine against highly pathogenic H5N1 for pre-pandemic preparedness.
Severe Acute Respiratory Syndrome: Radiographic Appearances and Pattern of Progression in 138 Patients (2003)

Predominant peripheral location; common progression pattern from unilateral focal air-space opacity to unilateral multifocal or bilateral involvement during treatment; and lack of cavitation, lymphadenopathy, and pleural effusion are the more distinctive radiographic findings of SARS.
Synthesis of Diverse 11- and 12-Membered Macrolactones from a Common Linear Substrate Using a Single Biocatalyst (2017)

The diversification of late stage synthetic intermediates provides significant advantages in efficiency in comparison to conventional linear approaches. Despite these advantages, accessing varying ring scaffolds and functional group patterns from a common intermediate poses considerable challenges using existing methods. The combination of regiodivergent nickel-catalyzed C-C couplings and site-selective biocatalytic C-H oxidations using the cytochrome P450 enzyme PikC addresses this problem by enabling a single late-stage linear intermediate to be converted to macrolactones of differing ring size and with diverse patterns of oxidation. The approach is made possible by a novel strategy for site-selective biocatalytic oxidation using a single biocatalyst, with site selectivity being governed by a temporarily installed directing group. Site selectivities of C-H oxidation by this directed approach can overcome positional bias due to C-H bond strength, acidity, inductive influences, steric accessibility, or immediate proximity to the directing group, thus providing complementarity to existing approaches.
Design, Synthesis, and Evaluation of (4R)-1-{3-[2-(18F)Fluoro-4-methylpyridin-3-yl]phenyl}-4-[4-(1,3-thiazol-2-ylcarbonyl)piperazin-1-yl]pyrrolidin-2-one ([18F]T-401) as a Novel Positron-Emission Tomography Imaging Agent for Monoacylglycerol Lipase (2019)

Monoacylglycerol lipase (MAGL) is a cytosolic serine hydrolase involved in endocannabinoid and inflammatory signaling. Positron-emission tomography (PET) imaging of MAGL serves to validate target engagement of therapeutic MAGL inhibitors as well as to investigate MAGL levels under normal and disease conditions. However, PET radioligands with reversible binding kinetics for MAGL, which allow quantitative assessment of MAGL, are hitherto unavailable. In this study, we designed and synthesized fluoro-containing PET probes starting from a recently identified piperazinyl pyrrolidine-2-one derivative with reversible binding to MAGL. By tailoring the lipophilicity of the molecule to optimize nonspecific binding and blood-brain barrier permeability, we successfully identified two compounds that show high uptake to regions enriched with MAGL. PET imaging of wild-type and MAGL-deficient mice as well as a macaque monkey indicated that [<sup>18</sup>F]5 ((4 R)-1-{3-[2-(<sup>18</sup>F)fluoro-4-methylpyridin-3-yl]phenyl}-4-[4-(1,3-thiazol-2-ylcarbonyl)piperazin-1-yl]pyrrolidin-2-one, [<sup>18</sup>F]T-401) specifically binds to MAGL with adequate reversibility, yielding a high contrast for MAGL within an appropriate imaging time.
Integrated and computer-aided tool for assembly and ressource planning (1993)

info:eu-repo/semantics/published
Cardiac-Specific Overexpression of CYP2J2 Attenuates Diabetic Cardiomyopathy in Male Streptozotocin-Induced Diabetic Mice (2013)

Cytochrome P450 (CYP) epoxygenases metabolize arachidonic acid to biologically active cis-epoxyeicosatrienoic acids, which have potent vasodilatory, antiinflammatory, antiapoptotic, and antidiabetes properties. Here, we showed the effects of cardiac-specific overexpression of CYP epoxygenase 2J2 (CYP2J2) on diabetic cardiomyopathy and insulin resistance in high-fat (HF) diet fed, low-dose streptozotocin-treated mice. Diabetic cardiomyopathy was induced by HF and streptozotocin in cardiac-specific CYP2J2 transgenic mice. Physiological parameters and systemic metabolic parameters were monitored using ELISA kits. Intraperitoneal injection glucose tolerance test and hyperinsulinemic-euglycemic clamp study were implied to indicate insulin resistance. Cardiac function was assessed by echocardiography and Millar catheter system. Real-time PCR and Western blotting were used in signal pathway detection. αMHC-CYP2J2 transgenic mice showed significantly lower plasma glucose and insulin levels, improved glucose tolerance, and increased cardiac glucose uptake. Furthermore, αMHC-CYP2J2 transgenic mice were significantly protected from HF-streptozotocin-induced diabetic cardiomyopathy. Strikingly, CYP2J2 overexpression attenuated myocardial hypertrophy induced by diabetes. We conclude that cardiac-specific overexpression of CYP2J2 significantly protects against diabetic cardiomyopathy, which may be due to improved cardiac insulin resistance, glucose uptake, and reversal of cardiac hypertrophy. Relevant mechanisms may include up-regulation of peroxisome proliferator-activated receptor γ, activation of insulin receptor and AMP-activated protein kinase signaling pathways, and inhibition of nuclear factor of activated T cells c3 signal by enhanced atrial natriuretic peptide production. These results suggest that CYP2J2 epoxygenase metabolites likely play an important role in plasma glucose homeostasis, and enhancement of epoxyeicosatrienoic acids activation may serve as an effective therapeutic strategy to prevent diabetic cardiomyopathy.
Reply: Subclinical Interstitial Lung Disease: No Place for Crackles? (2012)

From the Authors:

We thank Professors Cottin and Cordier for their thoughtful response to our perspective of subclinical interstitial lung disease (ILD) (1). We agree with the authors that the physical exam is an important skill to be taught and refined and not to be supplanted by more complex physiologic testing but rather supplemented by it. However, the only data addressing the significance of crackles in subclinical ILD that we are aware of is what we have previously shown in individuals with subclinical rheumatoid arthritis–associated ILD (RA-ILD) (2). In this study, we found a statistically significant difference in the percentage of subjects having audible crackles on physical exam when comparing those with subclinical RA-ILD (24%) to those with only RA (4.7%, P = 0.02) or to those with clinically significant RA-ILD (100%, P < 0.001). We did not include physical exam in our diagnostic algorithm as it is unclear if these findings can be extrapolated to other groups affected with subclinical ILD. Despite the above, we agree with Cottin and Cordier that the presence of crackles could improve the assessment of populations at risk of developing subclinical ILD.

We agree with Cottin and Cordier that the identification of subjects with subclinical ILD may come with increased psychological and financial burdens and with a risk of additional radiation exposure. As outlined in our perspective, we believe that future research into subclinical ILD can be structured to minimize these risks while maximizing the benefit of early identification. Longitudinal studies will be crucial in determining which subset of patients with subclinical ILD will go on to develop clinically significant ILD and which individuals may have reversible causes, such as hypersensitivity pneumonitis; it is in this population that a work-up for subclinical ILD would be most justified. More sensitive noninvasive metrics to assess subclinical ILD, such as clinical predictive modeling and biomarker and genetic assays, can also work to reduce the indiscriminate use of imaging. Additionally, an improved understanding of subclinical ILD will hopefully lead to a better understanding of the pathophysiology of ILD and the development of more effective treatments targeted at earlier stages of disease. Our hope is that efforts targeted at early identification will ultimately have a positive impact on the morbidity and mortality of ILD.
Soft-Tissue Balance in Revision Total Knee Arthroplasty (2004)

1 Department of Orthopaedic Surgery, University of California at San Francisco, 500 Parnassus Avenue (MU 320-W), San Francisco, CA 94143. E-mail address: [email protected] 2 The Hospital for Special Surgery, 535 East 70th Street, New York, NY 10021
Effects of transformation on the hemagglutinins of Haemophilus paragallinarum. (1995)

Strain 0083 and two field isolates of H. paragallinarum were previously converted into NAD-independent organisms by the use of crude DNA extractions from naturally occurring NAD-independent H. paragallinarum isolates. Two of these transformed isolates [0083(T) and A745(T)] were used as DNA donors in another transformation experiment in which another field isolate (M85) was used as the DNA recipient. Transformation was confirmed by lack of NAD requirement for growth, by carbohydrate fermentation patterns and by a comparison of the monoclonal antibody patterns of the isolates before and after transformation. Previously, antigenic differences were observed when DNA from an NAD-independent isolate was introduced into strain 0083. Antigenic differences were also seen in the transformed M85 organisms prepared in this work, and these differences were dependent on the antigenic patterns of the DNA donors. It was established by haemagglutination (HA) and haemagglutination inhibition (HI) that the hemagglutinins of 0083, A745/92 and M85 were not affected by transformation. The use of strains transformed to NAD independence for vaccine production appears to be a valid approach, as the transformation appears not to affect the hemagglutinins of the transformed organisms The major advantage would be the alleviation of the requirement for chicken serum or NAD in the bacterial growth medium used for infectious-coryza-vaccine production.
Laser Direct Structured 3D Circuits on Silicone (2022)

Silicone rubber is a biocompatible elastomeric polymer, with great potential for mechanical and biologic sensing applications, if electrical circuits can be reliably integrated. Laser direct structuring is a bottom-up circuit fabrication process, whereby copper is chemically grown on laser exposed regions of a modified substrate, promoting adhesion by laser roughening the circuit tracks. In this Research Article, we successfully demonstrate this process using superflexible biocompatible silicone (30 hardness on Shore 00) with copper chromite additive, cast into both 2D planar and 3D contour substrates. A horseshoe pattern circuit, meander and Hilbert fractal inductors, and a 3D hemispherical helix trace are fabricated and tested. The range of laser power and copper chromite concentration are explored. Mechanical testing is performed to determine breakage strain and elastic modulus. Material stiffness and trace peel strength are shown to increase with copper chromite concentration. Peel strength is measured to be very high, from approximately 1 to 5 kN/m, depending on dopant loading. With high adhesion and conductivity, the simple laser-writing process presented here enables high-quality circuit integration into elastomeric silicone.
Cloud-Point Extraction and Delipidation of Porcine Brain Proteins in Combination with Bottom-Up Mass Spectrometry Approaches for Proteome Analysis (2010)

In this study, temperature-induced phase fractionation also known as cloud-point extraction (CPE) with the nonionic surfactant Triton X-114 was used to simultaneously extract hydrophobic and hydrophilic proteins from porcine brain tissue. Various protein precipitation/delipidation procedures were investigated to efficiently remove lipids and detergents while retaining maximum protein recoveries. The best performing delipidation method was then used in combination with CPE to compare three different mass spectrometry (MS) based “bottom-up” proteomic approaches for protein analysis of the porcine brain. In the first approach, the intact proteins were initially separated by one-dimensional (1D) gel electrophoresis. The excised protein bands were digested with trypsin, and the peptides were separated by reversed phase nanoliquid chromatography (RP-nanoLC) followed by electrospray ionization (ESI) tandem mass spectrometry (MS/MS) analysis. The other bottom-up proteomic approaches were based on first enzymatical digestion of the proteins followed by RP-nanoLC separation in combination with matrix assisted laser desorption/ionization time-of-flight tandem mass spectrometry (MALDI-TOF/TOF MS) or on the combination of in-solution isoelectric focusing (IEF) with ESI−nanoLC−MS/MS of the IEF separated peptides. In total, we found and unambiguously identified 331 unique proteins. The overlap between different techniques was about 10%, showing that the use of multiple proteomic approaches is beneficial to yield a better coverage of the proteome. Furthermore, the overlap between the CPE extracted hydrophilic and hydrophobic proteins was rather small (9−16%), indicating an efficient sample preparation technique to extract and separate hydrophilic and hydrophobic proteins from brain tissue. The percentage of identified membrane proteins was 27%, which is in accordance to the fact that about one-third of all genes in various organisms encode for this class of proteins. The results indicate that cloud point extraction is a promising sample preparation tool, which allows simultaneous in depth studies of brain derived membrane proteins as well as hydrophilic proteins. This technique can be very useful when studying human central nervous system (CNS) tissue or animal models of neurological diseases.
Levosimendan Improves Hemodynamics and Exercise Tolerance in PH-HFpEF (2021)

Six weeks of once-weekly levosimendan infusion did not affect exercise-PCWP but did reduce PCWP incorporating data from rest and exercise, in tandem with increased 6MWD. Further study of levosimendan is warranted as a therapeutic option for PH-HFpEF. (Hemodynamic Evaluation of Levosimendan in Patients With PH-HFpEF [HELP]; NCT03541603).
Enantioselective Synthesis of 2‐Aryl‐4‐piperidones via Rhodium/Phosphoramidite‐Catalyzed Conjugate Addition of Arylboroxines. (2005)

The highly enantioselective synthesis of 2-aryl-4-piperidones by rhodium/phosphoramidite-catalyzed conjugate addition of arylboroxines to\n2,3-dihydro-4-pyridones is described. Both enantiomers of a variety of products with sterically and electronically different R substituents were\nobtained in high isolated yield and with excellent enantioselectivity up to 99%.
Clutter-free doppler detection of signed velocity based on legendre seires expansion (2005)

A clutter-free velocimetry based on Legendre polynomial series expansion, which can fully utilize the unique low-frequency cut-off characteristic of the polynomial regression filter, is conceived. A set of complex I/Q Doppler signals, with a packet size of N, is expanded into a series of Legendre polynomials, obtaining expansion coefficients, L(n), (n=0, ..., N-1). Complex Legendre coefficients, C(/spl plusmn/n), are then formed by linearly combining the Legendre coefficients as C(/spl plusmn/n)=L(n-1)/spl plusmn/jL(n) for an odd number of n and C(/spl plusmn/n)=L(n)/spl plusmn/jL(n-1) for an even number of n. The spectrum of the signed velocity can thereby be obtained from the absolute magnitudes of C(/spl plusmn/n). The cut-off characteristic of the polynomial regression filter can be obtained by excluding C(/spl plusmn/n) of small numbers of n.