gebhart/patrepeval huggingface dataset:
Insights into cyclosporine A-induced atherosclerotic risk in transplant recipients: Macrophage scavenger receptor regulation (2004)

Clinical monitoring of organ-transplant recipients suggests that administration of cyclosporine (CsA) may increase the risk of atherosclerosis when compared with the general population. The purpose of this work is to demonstrate the utility of the in vitro Tamm-Horsfall protein (THP)-1 human monocyte cell culture model for determining drug-related atherosclerotic potential in macrophages. The effect of CsA on the mRNA expression of macrophage scavenger receptor genes including CD36, CD68, scavenger receptor (SR)-A, SR-BII, and lectin-like oxidized low-density lipoprotein receptor (LOX-1); the nuclear hormone receptors, including peroxisome-proliferator activated receptor (PPAR)gamma and liver-X-receptor (LXR)alpha; and the cholesterol efflux pump ABCA1 were investigated as markers of atherosclerotic progression. The THP-1 cells were cultured and differentiated into macrophages. The macrophages were then treated with CsA to assess gene expression. Time- (1, 2, 4, 8, and 24 hours) and dose- (concentrations [mg/L] corresponding to the trough [0.5], peak [1.25] and 4x peak [5]) dependency of CsA was assessed. The treated macrophage mRNA gene expression of CD36, CD68, and PPARgamma were up-regulated in the presence of CsA. Interestingly, SR-A, SR-BII, LOX-1, and LXRalpha expression appeared to be slightly down-regulated, and ABCA1 was relatively unchanged. Immunoblotting studies demonstrated that the protein expression of CD36 was unchanged or increased, PPARgamma was unchanged, and ABCA1 was unchanged or decreased at 4 and 8 hours. The results document CsA-induced mRNA and protein changes in receptors relevant to lipid-laden foam cell formation and demonstrate the utility of THP-1 macrophages for screening of atherosclerotic risk potential.
Adiabatic Solid Effect (2020)

The solid effect (SE) is a two spin dynamic nuclear polarization (DNP) mechanism that enhances the sensitivity in NMR experiments by irradiation of the electron-nuclear spin transitions with continuous wave (CW) microwaves at ω<sub>0S</sub> ± ω<sub>0I</sub>, where ω<sub>0S</sub> and ω<sub>0I</sub> are electron and nuclear Larmor frequencies, respectively. Using trityl (OX063), dispersed in a 60/40 glycerol/water mixture at 80 K, as a polarizing agent, we show here that application of a chirped microwave pulse, with a bandwidth comparable to the EPR line width applied at the SE matching condition, improves the enhancement by a factor of 2.4 over the CW method. Furthermore, the chirped pulse yields an enhancement that is ∼20% larger than obtained with the ramped-amplitude NOVEL (RA-NOVEL), which to date has achieved the largest enhancements in time domain DNP experiments. Numerical simulations suggest that the spins follow an adiabatic trajectory during the polarization transfer; hence, we denote this sequence as an adiabatic solid effect (ASE). We foresee that ASE will be a practical pulsed DNP experiment to be implemented at higher static magnetic fields due to the moderate power requirement. In particular, the ASE uses only 13% of the maximum microwave power required for RA-NOVEL.
Nanocrystalline Hydroxyapatite–Poly(thioketal urethane) Nanocomposites Stimulate a Combined Intramembranous and Endochondral Ossification Response in Rabbits (2019)

Resorbable bone cements are replaced by bone osteoclastic resorption and osteoblastic new bone formation near the periphery. However, the ideal bone cement would be replaced by new bone through processes similar to fracture repair, which occurs through a variable combination of endochondral and intramembranous ossification. In this study, nanocrystalline hydroxyapatite (nHA)-poly(thioketal urethane) (PTKUR) cements were implanted in femoral defects in New Zealand White rabbits to evaluate ossification at 4, 12, and 18 months. Four formulations were tested: an injectable, flowable cement and three moldable putties with varying ratios of calcium phosphate to sucrose granules. New bone formation and resorption of the cement by osteoclasts occurred near the periphery. Stevenel's Blue and Safranin O staining revealed infiltration of chondrocytes into the cements and ossification of the cartilaginous intermediate. These findings suggest that nHA-PTKUR cements support combined intramembranous and endochondral ossification, resulting in enhanced osseointegration of the cement that could potentially improve patient outcomes.
Use of Aspirin Associates with Longer Primary Patency of Hemodialysis Grafts (2011)

Extended-release dipyridamole plus low-dose aspirin (ERDP/ASA) prolongs primary unassisted graft patency of newly created hemodialysis arteriovenous grafts, but the individual contributions of each component are unknown. Here, we analyzed whether use of aspirin at baseline associated with primary unassisted graft patency among participants in a randomized trial that compared ERDP/ASA and placebo in newly created grafts. We used Cox proportional hazards regression, adjusting for prespecified baseline comorbidities and covariates. Of all participants, 43% reported use of aspirin at baseline; of these, 82% remained on nonstudy aspirin (i.e., excluding ERDP/ASA) at 1 year. After 1 year of follow-up, the incidence of primary unassisted patency among participants using aspirin at baseline was 30% (95% CI: 24 to 35%) and among those not using aspirin was 23% (95% CI: 18 to 27%). Use of aspirin at baseline associated with a dose-dependent prolongation of primary unassisted graft patency that approached statistical significance (adjusted HR, 0.83; 95% CI: 0.68 to 1.01; P=0.06). Use of aspirin at baseline did not associate with prolongation of cumulative graft patency or participant survival. In conclusion, use of aspirin associates with a trend toward longer primary unassisted patency of newly placed hemodialysis grafts similar to that observed for ERDP/ASA.
Low-k material cryoetch using high boiling point organic compounds to reduce plasma induced damage (2018)

International audience
Correlative Microscopy for the Identification of Intracellular Nanoparticles and their Cellular Processing (2023)

Journal Article Correlative Microscopy for the Identification of Intracellular Nanoparticles and their Cellular Processing Get access Ingo Lieberwirth, Ingo Lieberwirth Max-Planck Institute for Polymer Research, Mainz, Germany Corresponding author: lieberw@mpip-mainz.mpg.de Search for other works by this author on: Oxford Academic Google Scholar Shen Han, Shen Han Max-Planck Institute for Polymer Research, Mainz, Germany Search for other works by this author on: Oxford Academic Google Scholar Anke Kaltbeitzel, Anke Kaltbeitzel Max-Planck Institute for Polymer Research, Mainz, Germany Search for other works by this author on: Oxford Academic Google Scholar Gunnar Glaßer, Gunnar Glaßer Max-Planck Institute for Polymer Research, Mainz, Germany Search for other works by this author on: Oxford Academic Google Scholar Katharina Landfester Katharina Landfester Max-Planck Institute for Polymer Research, Mainz, Germany Search for other works by this author on: Oxford Academic Google Scholar Microscopy and Microanalysis, Volume 29, Issue Supplement_1, 1 August 2023, Page 1955, https://doi.org/10.1093/micmic/ozad067.1012 Published: 22 July 2023
Progression of subtle motor signs in PINK1 mutation carriers with mild dopaminergic deficit (2010)

Our findings strengthen the hypothesis that heterozygous PINK1 mutations act as a susceptibility factor to develop at least subtle Parkinson disease motor and nonmotor signs, as supported by the finding of a reduced striatal dopaminergic FDOPA uptake not only in homozygous but also, albeit to a lesser extent, in heterozygous mutation carriers.
Hepatitis C Virus Infects and Perturbs Liver Stem Cells (2021)

Summary Hepatitis C virus (HCV) is the leading cause of death from liver disease. How HCV infection causes lasting liver damage and increases cancer risk beyond viral clearance remains unclear. We identify bipotent liver stem cells as novel targets for HCV infection, and their erroneous differentiation as the potential cause of impaired liver regeneration and cancer development. We show 3D organoids generated from liver stem cells from actively HCV-infected individuals carry replicating virus and maintain low-grade infection over months. Organoids can be infected with a primary HCV isolate. Virus-inclusive single-cell RNA-sequencing uncovered extensive transcriptional reprogramming in HCV + cells supporting hepatocytic differentiation, cancer stem cell development and viral replication while stem cell proliferation and interferon signaling are disrupted. Our data adds a pathogenesis factor – infection of liver stem cells – to the biology of HCV infection that explains persistent liver damage and enhanced cancer risk through an altered stem cell state.
Education Committee Activities at the 2014 Antennas and Propagation Symposium [Education Column] (2014)

The Education Committee sponsored an exciting mix of student-focused events and programs at the Society's annual Symposium in Memphis, Tennessee, USA, July 6-11, 2014. The Student Design Contest finalist demonstrations were held in the exhibit hall. Enthusiastic student competitors showcased their work on innovative antennas for RFID applications. The first prize went to a team from the Instituto de Telecomunicaéïes in Portugal, and second place was a tie between teams from the Indian Institute of Technology Kan pur in India, and Aalto University in Finland.
Screening for Compounds That Affect the Interaction Between Bacterial Two-Component Signal Transduction Response Regulator Protein and Cognate Promoter DNA (2007)

Bacterial signal transduction systems can be used as drug targets. The signal transduction targets fall into two groups--sensor kinases and response regulators. Previously reported studies describe hits that were thought to inactivate sensor kinases but on closer examination were found to act elsewhere instead; a possible reason for this is that full-length sensor kinases are integral membrane proteins whose activity might reflect interaction with the cell membrane or with membrane components. We describe a model system that instead is based on the interaction between a test compound and a response regulator in a homogeneous phase reaction. In this system, response regulator-DNA complex formation and its inhibition by a test compound are measured by fluorescence polarization. The model system should be readily adaptable to drug discovery based on other bacterial two-component s transduction systems.
The use of polymers in Li‐S batteries: A review Part A Polymer chemistry (2017)

Recent developments in the use of polymeric materials as device components in lithium sulfur (Li‐S) batteries are reviewed. Li‐S batteries have generated tremendous interest as a next generation battery exhibiting charge capacities and energy densities that greatly exceed Li‐ion battery technologies. In this Highlight, the first comprehensive review focusing on the use of polymeric materials throughout these devices is provided. The key role polymers play in Li‐S technology is presented and organized in terms of the basic components that comprise a Li‐S battery: the cathode, separator, electrolyte, and anode. After a straightforward introduction to the construction of a conventional Li‐S device and the mechanisms at work during cell operation, the use of polymers as binders, protective coatings, separators, electrolytes, and electroactive materials in Li‐S batteries will be reviewed. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2017, 55, 1635–1668
Rate-distortion-optimal subband coding without perfect-reconstruction constraints (2001)

We investigate the design of subband coders without the traditional perfect-reconstruction constraint on the filters. The coder uses scalar quantizers, and its filters and bit allocation are designed to optimize a rate-distortion criterion. Using convexity analysis, we show that optimality can be achieved using filterbanks that are the cascade of a (paraunitary) principal component filterbank for the input spectral process and a set of pre and postfilters surrounding each quantizer. Analytical expressions for the pre and postfilters are then derived. An algorithm for computing the globally optimal filters and bit allocation is given. We also develop closed-form solutions for the special case of two-channel coders under an exponential rate-distortion model. Finally, we investigate a constrained-length version of the filter design problem, which is applicable to practical coding scenarios. While the optimal filterbanks are nearly perfect-reconstruction at high rates, we demonstrate an apparently surprising advantage of optimal FIR filterbanks; they significantly outperform optimal perfect-reconstruction FIR filterbanks at all bit rates.
Supplementary Figure S1 from Ubiquitinated PCNA Drives USP1 Synthetic Lethality in Cancer (2023)

&lt;p&gt;I-138 inhibits USP1-UAF1 - related to Figure 1&lt;/p&gt;
Numerical modeling of collinear mixing of compressional and shear waves in nonlinear elastic media using the iterative nonlinear contrast source method (2019)

In nondestructive testing, nonlinear wave mixing could be used to obtain the nonlinearity parameters of an elastic medium and thereby get information about its state, e.g., aging and fatigue. To better understand the mixing mechanisms and optimize the design of measurement setups, a physics-oriented tool for the simulation of nonlinear elastic wave propagation would be valuable. In this presentation, we extend the iterative nonlinear contrast source method (INCS) to study the nonlinear mixing of two plane, collinear bulk waves (one compressional, one shear) in a homogeneous, isotropic, elastic medium with two independent coefficients of nonlinearity (βL and βT). The method successfully captured the resonant wave generated due to the mixing (one-way and two-way) of primary waves of different frequencies. The obtained results for the resonant wave were in good agreement with the results reported in the literature. In addition, the contrast source allowed the propagating and evanescent components of the scattered wave field to be studied in the wavenumber-frequency domain, which provides physical insight into the mixing process and explains the propagation direction of the scattered wave. Thus, the INCS method seems to be a useful tool to investigate and predict wave mixing in nonlinear elastic media.
ChemInform Abstract: Hymenamides C‐E, New Cyclic Heptapeptides with Two Proline Residues from the Okinawan Marine Sponge Hymeniacidon sp. (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.
Genetic Markers for Western Corn Rootworm Resistance to Bt Toxin (2015)

Western corn rootworm (WCR) is a major maize (Zea mays L.) pest leading to annual economic losses of more than 1 billion dollars in the United States. Transgenic maize expressing insecticidal toxins derived from the bacterium Bacillus thuringiensis (Bt) are widely used for the management of WCR. However, cultivation of Bt-expressing maize places intense selection pressure on pest populations to evolve resistance. Instances of resistance to Bt toxins have been reported in WCR. Developing genetic markers for resistance will help in characterizing the extent of existing issues, predicting where future field failures may occur, improving insect resistance management strategies, and in designing and sustainably implementing forthcoming WCR control products. Here, we discover and validate genetic markers in WCR that are associated with resistance to the Cry3Bb1 Bt toxin. A field-derived WCR population known to be resistant to the Cry3Bb1 Bt toxin was used to generate a genetic map and to identify a genomic region associated with Cry3Bb1 resistance. Our results indicate that resistance is inherited in a nearly recessive manner and associated with a single autosomal linkage group. Markers tightly linked with resistance were validated using WCR populations collected from Cry3Bb1 maize fields showing significant WCR damage from across the US Corn Belt. Two markers were found to be correlated with both diet (R2 = 0.14) and plant (R2 = 0.23) bioassays for resistance. These results will assist in assessing resistance risk for different WCR populations, and can be used to improve insect resistance management strategies.
Evaluation of a Safe, Slightly Acidic Tubing Clean-Out Fluid (2003)

Abstract Traditional "Best Practices" completion procedures recommend an acid pickle treatment to clean-out all tubulars in a wellbore prior to pumping an acid treatment or a "solids-free" completion brine system. The potential contaminants (iron oxidation, hydrocarbon deposits and pipe dope) can create formation damage if pumped into the formation during the main treatment. In addition, contamination of "solids-free" completion brine can lead to increased location diatomaceous earth (D.E.) filtration time. Tubing clean-out treatments normally consist of a slug of acid (10 to 15wt% hydrochloric) being pumped inside the tubulars and then reverse circulated back to surface without fluids being lost to the formation. A solvent is typically added to assist in the removal of pipe dope and organic deposits. Inhibitor and a surfactant, to facilitate wetting, are the normal fluid additives. Handling and disposal of this fluid after clean up of the tubulars can be dangerous and very costly due to its corrosive nature (pH &amp;lt;0). A slightly acidic (pH of 5.8-6.3) fluid has been evaluated in the laboratory for use as a pickling fluid to replace the traditional acids. This fluid's capability to remove iron scales on coiled tubing, prevent rust from reforming, clean up commercial pipe dopes and reduce corrosion rates, was compared to traditional hydrochloric acid. This fluid performed as efficiently as 15wt% hydrochloric acid in removing all potential contaminants associated with a workstring, while producing one fifth the corrosion rate. Furthermore, a work string treated with this fluid prior to being laid down on a pipe rack retained a protective coating that resisted re-oxidization for up to 30 days.
Characterization of a New Chronic Lymphocytic Leukemia Cell Line for Mechanistic In Vitro and In Vivo Studies Relevant to Disease (2013)

Studies of chronic lymphocytic leukemia (CLL) have yielded substantial progress, however a lack of immortalized cell lines representative of the primary disease has hampered a full understanding of disease pathogenesis and development of new treatments. Here we describe a novel CLL cell line (OSU-CLL) generated by EBV transformation, which displays a similar cytogenetic and immunophenotype observed in the patient's CLL (CD5 positive with trisomy 12 and 19). A companion cell line was also generated from the same patient (OSU-NB). This cell line lacked typical CLL characteristics, and is likely derived from the patient's normal B cells. In vitro migration assays demonstrated that OSU-CLL exhibits migratory properties similar to primary CLL cells whereas OSU-NB has significantly reduced ability to migrate spontaneously or towards chemokine. Microarray analysis demonstrated distinct gene expression patterns in the two cell lines, including genes on chromosomes 12 and 19, which is consistent with the cytogenetic profile in this cell line. Finally, OSU-CLL was readily transplantable into NOG mice, producing uniform engraftment by three weeks with leukemic cells detectable in the peripheral blood spleen and bone marrow. These studies describe a new CLL cell line that extends currently available models to study gene function in this disease.
Tenascin-C triggers fibrin accumulation by downregulation of tissue plasminogen activator (2011)

We explored novel functions of tenascin-C by comparing mouse embryonic fibroblasts (MEFs) proficient or deficient in tenascin-C expression. Transcript profiling analysis identified tissue plasminogen activator (tPA) as the most consistently over-expressed gene in all tenascin-C deficient MEFs. This was confirmed by real-time PCR as well as by protein expression analysis. In agreement with these observations, tenascin-C deficient MEFs had an increased capacity to digest fibrin in situ. Consistently, tenascin-C expression in vivo was found to correlate with fibrin deposition in several diseases associated with tenascin-C overexpression such as fibrosis, asthma and cancer. In conclusion, the present study suggests a new role of tenascin-C as a regulator of the fibrinolytic system.
Phase I dose-escalation and expansion study of intratumoral CV8102, a RNA-based TLR- and RIG-1 agonist in patients with advanced solid tumors (2018)

Background: Local activation of innate immune signaling pathways, such as Toll-like Receptors (TLRs) or RIG-I-like Receptors (RLRs), is a promising cancer immunotherapeutic approach to overcome the tumor immunosuppressive microenvironment and to induce/restore anti-tumor immunity. CV8102 consists of a single-stranded, non-coding RNA complexed with a cationic peptide and acts as an agonist to human TLR-7, -8 and RLRs. Local administration of CV8102 was shown to induce upregulation of inflammatory cytokines, chemokines and IFN-y related genes at the injection site followed by activation of T, NK, NKT cells and migratory dendritic cells in the draining lymph node (Heidenreich 2015; Ziegler 2017). In a syngeneic murine model, intratumoral (IT) delivery of CV8102 induced dose-dependent anti-tumor activity and synergized with systemic anti-PD1 antibody treatment. Trial design: This phase I study is evaluating IT injection of CV8102 alone or in combination with a systemic anti-PD-1 antibody in patients with advanced solid tumors. Patients with advanced inoperable melanoma, cutaneous/head and neck squamous cell or adenoid cystic carcinoma and at least one lesion accessible for IT injection are eligible. After determination of the maximum tolerated/ recommended dose of CV8102 alone and in combination with an anti-PD1 antibody, expansion cohorts are planned in different indications. A Bayesian logistic regression model with overdose control will be used to guide the dose escalation. Patients in each cohort will receive up to 8 injections into a single tumor lesion over a 12 weeks period. The primary objective is to determine safety and tolerability, secondary/explorative objectives are to evaluate tumor response and changes in tumor tissue and blood-based biomarkers. The study has been initiated and enrollment is ongoing. Clinical trial identification: NCT03291002. Legal entity responsible for the study: CureVac AG, Paul-Ehrlich-Str. 15, 72076 Tübingen, Germany. Funding: Has not received any funding. Disclosure: P. Terheyden: Honoraria, Travel expenses: Novartis, Merck, Roche, BMS, Biofrontera; Advisory board: Roche, BMS, Sanofi Novartis, Merck. L. Heinzerling: Consultant: CureVac AG PI in clinical study at site Erlangen. P. Mohr: Consultant or advisory role: Merck, Roche, GSK, BMS, Novartis, SciBase, LEO; Honoraria: GSK, Roche, Merck, BMS, Novartis, LEO, SciBase; Research funding: Merck. F. Kiecker: Payments, Travel grants for symposia, Advisory boards, Meetings: Amgen, BMS, Merck-Serono, MSD, Novartis, Pierre-Fabre, Regeneron, Roche. J.C. Becker: Speaker honoraria: Amgen, MerckSerono and Pfizer; Advisory board honoraria: Amgen, CureVac, eTheRNA, Lytix, MerckSerono, Novartis, Rigontec, Takeda; Research funding: Boehringer Ingelheim, BMS, MerckSerono. U. Gnad-Vogt: Stock, Other ownership interests: Bristol-Myers Squibb. All other authors have declared no conflicts of interest.
Abnormal lateralization of functional connectivity between language and default mode regions in autism (2014)

Abnormal language lateralization in autism may be due to abnormal language development rather than to a deficit in hemispheric specialization of the entire brain.