gebhart/patrepeval huggingface dataset:
T cell receptor-mediated protein geranylgeranylation controls transforming growth factor-beta-induced Foxp3 expression by regulating the induction of Smad6/7 (50.40) (2009)

Abstract TGF- β plays a critical role as a differentiation factor for the generation of Foxp3+ induced T regulatory cells (iTregs) from naïve T cells. To evaluate the potential role of the mevalonate pathway in the control of iTreg development, we have used the mevalonate pathway inhibitor, Simvastatin. When CD4+Foxp3- T cells were activated with anti-CD3/CD28, the addition of Simvastatin increased the induction of Foxp3+ T cells. A marked synergistic induction of Foxp3 expression was observed when Simvastatin was added to the induction cultures with a suboptimal concentration of TGF-β. The action of Simvastatin was not mediated by enhancement of Smad3 phosphorylation, but was associated with marked inhibition of induction of the Smad 6/7 proteins. The synergistic effect was mediated at the level of mRNA transcription and was associated with increased DNA demethylation of the Foxp3 promoter. The effects of Simvastatin and TGF-βon the induction of Foxp3 expression were reproduced by the addition of an inhibitor of protein geranylgeranylation, but not an inhibitor of protein farnesylation. These studies demonstrate that protein geranylgeranylation represents of one of the key regulatory steps in the generation of iTregs by TGF-β. Pharmacologic manipulation of the mevalonate pathway may represents one mechanism for the induction of iTregs in vivo.
Expression of Pannexin Isoforms in the Systemic Murine Arterial Network (2012)

We conclude that the specific localized expression of Panx channels throughout the vasculature points towards an important role for these channels in regulating the release of ATP throughout the arterial network.
Bone Morphogenetic Proteins 2 and 5 Are Down-regulated in Adrenocortical Carcinoma and Modulate Adrenal Cell Proliferation and Steroidogenesis (2009)

Bone morphogenetic proteins (BMP) have been shown to affect tumorigenesis in a variety of tumors. Quantitative PCR analysis revealed down-regulation of BMP2 and BMP5 in tissue samples from adrenocortical carcinoma and adrenocortical tumor cell lines compared with normal adrenal glands. Integrity of BMP-dependent pathways in these cell lines could be shown by activation of the Smad1/5/8 pathway with subsequent increase of ID protein expression upon incubation with BMP2 or BMP5. On a functional level, BMP treatment resulted in inhibition of cell proliferation and viability in a dose- and time-dependent manner. This growth inhibitory effect was associated with BMP-dependent reduction of AKT phosphorylation under baseline conditions and under insulin-like growth factor costimulation. Furthermore, steroidogenic function, including melanocortin-2 receptor and steroidogenic enzyme expressions, was profoundly reduced. In vitro demethylation treatment and overexpression of GATA6 resulted in reactivation of BMP-dependent pathways with concomitant modulation of steroidogenesis. Taken together, we show that loss of expression of members of the BMP family of ligands is a common finding in adrenocortical tumors and we provide evidence that BMP-dependent pathways are likely to be involved in the modulation of the malignant and functional phenotype of adrenocortical cancer cells.
ChemInform Abstract: Unique Stereocontrol in Europium(III)‐Catalyzed Cyanosilylation of Chiral α‐Alkoxy and α‐Amino Aldehydes. (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Hysteresis loops of ferroelectric bilayers and superlattices (2000)

A ferroelectric superlattice with an antiferroelectric interfacial coupling is considered; the same model describes a bilayer with antiferroelectric coupling. By mapping minimum points in the Landau free energy expression and plotting them against the applied electric field, a triple hysteresis loop pattern is obtained. The loop patterns vary between typically ferroelectric and typically antiferroelectric depending on the layer thicknesses and the magnitude of the interfacial-coupling constant. This work suggests the possibility of designing multilayer elements for computer memories with four or more different storage states.
Soluble factors from Lactobacillus GG activate MAPKs and induce cytoprotective heat shock proteins in intestinal epithelial cells (2005)

Conditioned media from the probiotic Lactobacillus GG (LGG-CM) induce heat shock protein (Hsp) expression in intestinal epithelial cells. LGG-CM induces both Hsp25 and Hsp72 in a time- and concentration-dependent manner. These effects are mediated by a low-molecular-weight peptide that is acid and heat stable. DNA microarray experiments demonstrate that Hsp72 is one of the most highly upregulated genes in response to LGG-CM treatment. Real-time PCR and electrophoretic mobility shift assay confirm that regulation of Hsp induction is at least in part transcriptional in nature, involving heat shock factor-1. Although Hsps are not induced for hours after exposure, transient exposure to LGG-CM is sufficient to initiate the signal for Hsp induction, suggesting that signal transduction pathways may be involved. Experiments confirm that LGG-CM modulates the activity of certain signaling pathways in intestinal epithelial cells by activating MAP kinases. Inhibitors of p38 and JNK block the expression of Hsp72 normally induced by LGG-CM. Functional studies indicate that LGG-CM treatment of gut epithelial cells protects them from oxidant stress, perhaps by preserving cytoskeletal integrity. By inducing the expression of cytoprotective Hsps in gut epithelial cells, and by activating signal transduction pathways, the peptide product(s) secreted by LGG may contribute to the beneficial clinical effects attributed to this probiotic.
The Fortran 90 bindings for OpenGL (1999)

It is important to provide a good Fortran interface to OpenGL and related libraries for scientific visualization in mathematical software. OpenGL has had FORTRAN 77 bindings for some time, however these bindings rely upon several extensions to the FORTRAN 77 standard. By using the new features of Fortran 90 it is possible to define bindings for OpenGL that do not depend on any extensions to the standard and provide access to the full functionality of OpenGL.
Analysis of printed transmission lines for monolithic integrated circuits (1982)

Planar transmission lines formed with MIS and Schottky barrier contacts are analysed based on the spectral domain technique. Depending on the frequency and the resistivity of the substrates, three different types of fundamental modes are predicted. The calculated slow-wave factors and attenuation constants agree well with experimental results.
Ionic liquids new technologies (2012)

Novel methylimidazolium and pyridinium ionic liquids (ILs), derivatives of 3,4-dimethoxy-3,4-methylenedioxy- and 3,4-dihydroxy- mandelic acid, have been synthesised to serve as low-toxic and biodegradable solvents for catalytic asymmetric reactions. These ILs were prepared with three types of counteranion (halide, OctOSO3−, NTf2−) via a simple 3-5 step scalable synthetic route. The stability of the prepared ILs on aqueous conditions was studied. Although of the prepared ILs were chiral, they were obtained as racemic mixtures. Various methods were attempted to obtain ILs in the optically pure form and with the use of a chiral auxiliary approach, a diastereomerically enriched IL was obtained. Further synthetic work involved the optimisation and large scale (40-120 g) preparation of known achiral and chiral ILs. Both optically pure and achiral ILs were obtained in a 3-4 step synthesis, without the need for chromatographic purification. Preliminary ecotoxicological assessment of novel ILs was carried out; including, antimicrobial and antifungal screening as well as biodegradation studies. The majority of the ILs tested proved to be of low toxicity towards microorganisms and two ILs proved to be non-toxic towards bacteria at concentration as high as 100 mM. In the biodegradation test of halide ILs, one IL was found to pass the test (66 %) and for the remaining ILs values between 13–52 % were reached in the 28 day test. Selected ILs were tested as solvents in asymmetric reactions with chiral catalysts. With the use of organic co-solvents, very good eantioselectivities, short reaction times and catalyst recycling were achieved. In the presence of the novel ILs, derivatives of 3,4-disubstituted mandelic acids, asymmetric hydrogenation of the enamide double bond, together with aromatic ring reduction, was achieved at very mild conditions.
Proteomics of renal disorders: Urinary proteome analysis by two-dimensional gel electrophoresis and MALDI-TOF mass spectrometry (2002)

The proteomes of urinary samples from patients with different renal conditions were analysed by two dimensional electrophoresis and MALDI-TOF technology. Samples from three different renal conditions, namely kidney failure, nephrotic syndrome and microalbuminuria, were included in the analysis. Apart from the presence of albumin, the profiles of protein spots found in these urine samples were quite distinct. While kidney failure patients showed predominantly low molecular weight proteins, the nephrotic syndrome patients showed an abundance of relatively high molecular weight proteins clustering in the acidic range of the 2-D gels. Two different protein spots from kidney failure patients, four from nephrotic syndrome patients and three from micro-albuminuria patients were identified by in-gel protease digestions and analysis of resulting peptides by MALDI-TOF. The proteins identified were albumin, alpha-1-antitrypsin, alpha-1-acid glycoprotein 2, Zn-alpha-2-glycoprotein and alpha-1-microglobulin. Among these, only one was common between the proteomes of renal failure and nephrotic syndrome patients. Among the limited proteins found in microalbuminuria patients, three were common with the proteome of nephrotic syndrome. Overall profiles were, however, quite different. Our study showed that urinary proteomes of different renal conditions were different and emphasized the potential of urinary proteome analysis to augment existing tools in the diagnosis of renal disorders.
A Controlled Phase Ii Trial Assessing Three Doses of Enfuvirtide (T-20) in Combination with Abacavir, Amprenavir, Ritonavir and Efavirenz in Non-Nucleoside Reverse Transcriptase Inhibitor-Naive HIV-Infected Adults (2003)

Enfuvirtide is a novel antiretroviral that blocks HIV-1 cell fusion and viral entry. This Phase II, controlled, open-label, randomized, multicentre dose-ranging trial explored the safety, antiviral activity and pharmacokinetics of enfuvirtide, administered by subcutaneous (s.c.) injection, in 71 HIV-1-infected, protease inhibitor-experienced, non-nucleoside reverse transcriptase inhibitor (NNRTI)-naive adults for 48 weeks. Study participants were randomized to receive enfuvirtide at a deliverable dose of 45, 67.5 or 90 mg twice daily; the 45 mg twice daily dose required 2 injections/day, while the higher doses required 4 injections/day. A background oral antiretroviral (ARV) regimen of abacavir (300 mg twice daily), amprenavir (1200 mg twice daily), ritonavir (200 mg twice daily) and efavirenz (600 mg once daily) was provided with enfuvirtide. A control group received the background ARV regimen alone. All potential participants underwent an HIV genotype at screen to ensure a homogenous population and to exclude patients with evidence of genotypic resistance to NNRTIs. Overall, the tolerability of the combination of abacavir, amprenavir, ritonavir, efavirenz and enfuvirtide was generally comparable to control through 48 weeks. No enfuvirtide dose-dependent adverse events (AEs) were observed across treatment groups. Injection site reactions (ISRs) occurred at least once in 68.5% of the enfuvirtide-treated population, and most ISRs were mild to moderate in severity, with no apparent dose relationship. Excluding ISRs, the most common treatment-emergent AEs were nausea, diarrhoea, dizziness and fatigue; with no clinically significant differences in the incidence of AEs observed between the control and enfuvirtide groups. Each treatment group benefited from ARV therapy, with a trend of increasing antiviral and immunological activity associated with increasing enfuvirtide dose. At 48 weeks, the median HIV-1 RNA change from baseline for the ITT population was -2.24 log10 copies/ml for the combined enfuvirtide groups compared with -1.87 log10 copies/ml for the control group. In addition, 54.9% of patients in the enfuvirtide group achieved HIV-1 RNA < or = 400 copies/ml versus 36.8% of patients in the control group. These results indicate that enfuvirtide has a favourable safety profile and is a promising new antiviral agent for HIV-infected patients who have been on previously failing ARV regimens.
“Compatibilizing effect” in interpenetrating polymer networks (1995)

Abstract α,ω‐Acrylate terminated poly(1,3‐dioxolane) (polyDXL) was copolymerized with methyl acrylate and methyl methacrylate for the synthesis of block copolymer networks. It was shown by dynamic mechanical thermal analysis (DMTA) that the presence of covalent bonds between poly DXL and the polyacrylate leads to a high degree of compatibility. In contrast, the combination of the same two components in network form, leading to sequential interpenetrating polymer networks (IPN's), resulted in phase‐separated materials. When the above‐mentioned block copolymer structures, in which one of the blocks is chemically identical to the polyacrylate used in the second network, were applied in the first network of the IPN, an increase of miscibility between the two types of polymers was observed. DMTA analysis revealed that the morphology of these IPN's could be varied from phase‐separated to homogeneous materials by increasing the polyacrylate fraction in the first block copolymer network. The possibility to degrade the poly DXL segments in an acid environment allows the complete degradation and extraction of one network in the IPN's and hence provided an interesting approach to the study of domain characteristics by optical microscopy.
Can Cellular Phototoxicity be Accurately Predicted on the Basis of Sensitizer Photophysics? (1999)

Abstract— The phototoxicity of three structurally related photosensitizers (PS), deuteroporphyrin IX (DP) and monobromo (Br‐DP) and dibromo (Br 2 ‐DP) derivatives, was studied in murine L1210 leukemia cells. These compounds were chosen on the basis of heavy‐atom‐induced differences in triplet yield, Φ T , and lifetime, T T , and used as tools to test a model for phototoxicity based on photophysical parameters. All three porphyrins were found to localize preferentially in the plasma membrane of L1210 cells by confocal fluorescence microscopy. A poor correlation was observed between the measured photodynamic efficacies of these PS and a model using photophysical parameters determined by laser flash photolysis in homogeneous solution. However, an excellent correlation was obtained when the same parameters measured directly in the cells were used. The biological microenvironment of the porphyrins in cells induces significant changes in the photophysics of the PS. Reduction in fluorescence yield, φ F , and φ T observed for Br 2 ‐DP in cell suspensions arises from self association of the molecule due to increased hydrophobicity and high local concentrations. The photophysical model was also tested for its ability to handle variations in the oxygen dependence of cellular phototoxicity of these PS. The good correlation achieved between laser flash photolysis data determined in cells and the measured phototoxicity under air, 1.5% and 0.5% O 2 ‐saturated conditions, proves the intermediacy of singlet oxygen. This study gives further credence to the direct use of photophysical techniques to elucidate photochemical mechanisms in biological media while highlighting the potential pitfalls of using solution data to predict photosensitizing potential.
Stochastic geometry analysis of the average error probability of downlink cellular networks (2014)

In this paper, we introduce a mathematical framework for computing the average error probability of downlink cellular networks in the presence of other-cell interference, Rayleigh fading, and thermal noise. A stochastic geometry based abstraction model for the locations of the Base Stations (BSs) is used, hence the BSs are modeled as points of a homogeneous spatial Poisson Point Process (PPP). The Mobile Terminal (MT) is assumed to be served by the BS that is closest to it. The technical contribution of this paper is twofold: 1) we provide an exact closed-form expression of the Characteristic Function (CF) of the aggregate other-cell interference at the MT, which takes into account the shortest distance based cell association mechanism; and 2) by relying on the Gil-Pelaez inversion theorem, we provide an exact closed-form expression of the Average Pairwise Error Probability (APEP), which accounts for Rayleigh fading and for the spatial distribution of the BSs. From the APEP, the Average Symbol Error Probability (ASEP) is obtained by using the Nearest Neighbor (NN) approximation, which is shown to provide accurate estimates. Finally, the mathematical framework is substantiated through extensive Monte Carlo simulations and insights on the achievable performance are discussed.
Author response: Fast bacterial growth reduces antibiotic accumulation and efficacy (2022)

Phenotypic variants that avoid antibiotic accumulation within clonal bacterial populations are a significant contributor to antibiotic treatment failure and can rely on previously unrecognised survival strategies such as fast growth during drug treatment.
Transcatheter Valve Therapy Registry Is A Model For Medical Device Innovation And Surveillance (2015)

Heart valve diseases are increasingly prevalent, especially in people older than age seventy. Many of these elderly people have other comorbid conditions, making them poor candidates for surgical treatment of heart valve diseases. Since 2011 such patients have been eligible to receive new nonsurgical heart valve treatments approved by the Food and Drug Administration (FDA) and covered by Medicare. This article examines the Transcatheter Valve Therapy Registry, which captures clinical information on all US patients undergoing new nonsurgical heart valve treatments. The registry has patient-level data from more than 27,000 patients treated with the novel devices. Patient- and procedure-related data are gathered from hospitals, patient-reported outcomes are assessed pre- and postprocedure, and longer-term data on mortality and repeat hospitalization are provided by linking the registry's data to Medicare patient data. The registry is a model of collaboration among professional societies, the FDA, the Centers for Medicare and Medicaid Services, hospitals, patients, and the medical device industry. It has been used to support Medicare coverage decisions, expand device indications, provide comprehensive device surveillance, and establish national quality benchmarks. Beyond having it serve as a collaborative model, future goals for the registry include shortening the FDA-approval timeline for devices, providing data for decision-making tools for patients, and public reporting of hospital performance.
Conserved and transcript-specific functions of the RESC factors, RESC13 and RESC14, in kinetoplastid RNA editing (2022)

ABSTRACT Uridine insertion/deletion RNA editing is an extensive post-transcriptional modification of mitochondrial mRNAs in kinetoplastid organisms, including Trypanosoma brucei . This process is carried out using trans -acting gRNAs and complex protein machinery. The essential RNA Editing Substrate Binding Complex (RESC) serves as the scaffold that modulates protein and RNA interactions during editing, and contains the Guide RNA Binding Complex (GRBC), the RNA Editing Mediator Complexes (REMCs), and organizer proteins. Despite the importance of RESC in editing, the functions of each protein comprising this complex are not completely understood. Here, we further define the roles of a REMC protein, RESC13, and a RESC organizer, RESC14, using high-throughput sequencing on two large pan-edited mRNAs, A6 and COIII. When comparing our analyses to that of a previously published small pan-edited mRNA, RPS12, we find that RESC13 has conserved functions across the three transcripts with regards to editing initiation, gRNA utilization, gRNA exchange, and restricting the formation of long mis-edited junctions that likely arise from its ability to modulate RNA structure. However, RESC13 does have transcript-specific effects on the types of long junctions whose formation it restricts. RESC14 has a conserved effect on gRNA utilization across the three transcripts analyzed, but has transcript-specific effects on editing initiation, gRNA exchange, and junction formation. Our data suggest that transcript-specific effects of both proteins are due to differences in transcript length and sequences as well as transcript-specific protein interactions. These findings highlight the importance of studying multiple transcripts to determine the function of editing factors.
Shear Yielding in Blown Oriented Polystyrene Films (2000)

Control over orientation is important for polystyrene (PS) films since it can affect brittleness in these materials. These authors discuss how the film morphology can be varied by orientation processing in amorphous bubble-blown PS films and how it influences the properties and performance of the film. The Figure shows the film morphology resulting from straining along the transverse direction of the blown bubble.
Supplementary Material and Method, Supplementary Tables 1-2, and Figure Legends from Efficacy of AKT Inhibitor ARQ 092 Compared with Sorafenib in a Cirrhotic Rat Model with Hepatocellular Carcinoma (2023)

&lt;p&gt;Supplementary Table 1: IC20 and IC50 values of ARQ 092 and sorafenib in Hep3B, Huh-7, HepG2, PLC/PRF/5 and HR4 cell lines after 48h of exposure; Supplementary Table 2: List of significantly different phospho-kinases from ARQ 092 treated rats compared to control group.&lt;/p&gt;
Advances in the robotic production of radiopharmaceuticals (1994)

A variety of robotic systems, including Zymark, Hudson Control Group, Anotech, and Questech formerly U.M.I, have been used as a reliable and safe way to produce radiopharmaceuticals. A robotic system`s ability allows it to produce a variety of radiopharmaceuticals on a routine basis including final preparation and quality control. With proper scheduling, a single robotic system can synthesize {sup 18}F-fluorodeoxyglucose, {sup 18}F-estradiol, {sup 11}C-acetate, {sup 68}Ga-citrate and at the same time control black box type syntheses such as {sup 15}O-butanol in a single day. A robotic system`s flexibility allows it to be used in designing and testing new syntheses, thus making the development of the new radiopharmaceuticals safer for the chemist. The development of Windows, a multi-tasking operating system for PC computers, allows a robot controlled by that computer to function simultaneously with a large variety of other systems. This increases the system`s ability to communicate with other systems and it allows for change without replacing the entire system. Improvements in robot technology has increased their reliability while making them competitive in price to other means of automation. Today a robotic system to produce {sup 18}F-fluorodeoxyglucose can cost as little as $55,000 U.S. depending on the cost of the hotmore » cell.« less