gebhart/patrepeval huggingface dataset:
High miR203a-3p and miR-375 expression in the airways of smokers with and without COPD (2022)

Smoking is a leading cause of chronic obstructive pulmonary disease (COPD). It is known to have a significant impact on gene expression and (inflammatory) cell populations in the airways involved in COPD pathogenesis. In this study, we investigated the impact of smoking on the expression of miRNAs in healthy and COPD individuals. We aimed to elucidate the overall smoking-induced miRNA changes and those specific to COPD. In addition, we investigated the downstream effects on regulatory gene expression and the correlation to cellular composition. We performed a genome-wide miRNA expression analysis on a dataset of 40 current- and 22 ex-smoking COPD patients and a dataset of 35 current- and 38 non-smoking respiratory healthy controls and validated the results in an independent dataset. miRNA expression was then correlated with mRNA expression in the same patients to assess potential regulatory effects of the miRNAs. Finally, cellular deconvolution analysis was used to relate miRNAs changes to specific cell populations. Current smoking was associated with increased expression of three miRNAs in the COPD patients and 18 miRNAs in the asymptomatic smokers compared to respiratory healthy controls. In comparison, four miRNAs were lower expressed with current smoking in asymptomatic controls. Two of the three smoking-related miRNAs in COPD, miR-203a-3p and miR-375, were also higher expressed with current smoking in COPD patients and the asymptomatic controls. The other smoking-related miRNA in COPD patients, i.e. miR-31-3p, was not present in the respiratory healthy control dataset. miRNA-mRNA correlations demonstrated that miR-203a-3p, miR-375 and also miR-31-3p expression were negatively associated with genes involved in pro-inflammatory pathways and positively associated with genes involved in the xenobiotic pathway. Cellular deconvolution showed that higher levels of miR-203a-3p were associated with higher proportions of proliferating-basal cells and secretory (club and goblet) cells and lower levels of fibroblasts, luminal macrophages, endothelial cells, B-cells, amongst other cell types. MiR-375 expression was associated with lower levels of secretory cells, ionocytes and submucosal cells, but higher levels of endothelial cells, smooth muscle cells, and mast cells, amongst other cell types. In conclusion, we identified two smoking-induced miRNAs (miR-375 and miR-203a-3p) that play a role in regulating inflammation and detoxification pathways, regardless of the presence or absence of COPD. Additionally, in patients with COPD, we identified miR-31-3p as a miRNA induced by smoking. Our identified miRNAs should be studied further to unravel which smoking-induced inflammatory mechanisms are reactive and which are involved in COPD pathogenesis.
New Pb–Pb bonds: syntheses and molecular structures of hexabiphenyldiplumbane and tri(trisbiphenylplumbyl)plumbate (2004)

Reaction of lead(II) chloride with biphenylmagnesium bromide yields Bp(3)Pb-PbBp(3) and [(THF)(3)Mg(mu-Cl)(3)Mg(THF)(3)][Pb(PbBp(3))(3)](Bp = biphenyl), which, upon single crystal X-ray crystallographic analysis, reveals an interesting variation of Pb-Pb bond distances.
BKCa and hEag1 Channels Regulate Cell Proliferation and Differentiation in Human Bone Marrow‐Derived Mesenchymal Stem Cells (2013)

Human bone marrow-derived mesenchymal stem cells (MSCs) serve as a reservoir for the continuous renewal of various mesenchymal tissues; however, cellular physiology of ion channels is not fully understood. The present study investigated potential roles of large-conductance Ca(2+) -activated potassium (BKCa ) channels and ether-à-go-go potassium (hEag1 or Kv10.1) channels in regulating cell proliferation and differentiation in human MSCs. We found that inhibition of BKCa with paxilline or hEag1 with astemizole, or knockdown of BKCa with shRNAs targeting KCa1.1 or hEag1 channels with shRNAs targeting KCNH1 arrested the cells at G0/G1 phase. In addition, silencing BKCa or hEag1 channels significantly reduced adipogenic differentiation with decrease of lipid accumulation and expression of the adipocyte marker PPARγ, and decreased osteogenic differentiation with reduction of mineral precipitation and osteocalcin. These effects were accompanied with a reduced cyclin D1, cyclin E, p-ERK1/2, and p-Akt. Our results demonstrate that BKCa and hEag1 channels not only regulate cell proliferation, but also participate in the adipogenic and osteogenic differentiations in human MSCs, which indicates that BKCa and hEag1 channels may be essential in maintaining bone marrow physiological function and bone regeneration.
A study to assess the feasibility of undertaking a randomized controlled trial of adherence with eye drops in glaucoma patients (2013)

All questionnaires other than the Short Form-12 were considered to be valuable measures and use of a Medical Events Monitoring System device was considered to be an objective surrogate measure for adherence with eye drops. A multicenter, randomized, controlled equivalence trial of group versus individualized education using adherence as the primary outcome is the next step.
Easy directions of magnetization in ternary R&lt;inf&gt;2&lt;/inf&gt;(Co, Fe)&lt;inf&gt;17&lt;/inf&gt;phases (1972)

The magnetocrystalline symmetry and the Curie temperature of six families of quasi-binary rare earth-cobalt-iron intermetallic phases were studied. Investigated were the phases R <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> (Co <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1-x</inf> Fe <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x</inf> ) <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">17</inf> of the light rare-earth elements R = Ce, Pr, Nd, Sm, and Y and also of Ce-rich mischmetal (MM). In the Sm system, the terminal compound Sm <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> Co <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">17</inf> has an easy c axis and the easy-axis symmetry persists up to <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x \approx 0.5</tex> . The Nd alloys have an easy basal plane for all values of x. In the other systems, small iron substitutions change the easy-plane behavior of the R <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> Co <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">17</inf> to an easy-axis anisotropy. The easy-axis ranges are <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x \approx 0.05</tex> to 0.45 for Ce, <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x \approx 0.2</tex> to 0.6 for Pr, <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x \approx 0.1</tex> to 0.5 for Y, and <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">x \approx 0.1</tex> to 0.45 for MM. The Curie temperatures are high, between 600°C and 940°C, in these ranges. It is concluded that some of the alloys investigated are promising candidate materials for use in improved "rare earth-cobalt" magnets.
Performance of Advanced Materials during Earthquake Loading Tests of a Bridge System (2012)

Three unconventional details for the plastic hinge regions of bridge columns subjected to seismic loads were developed, designed, and implemented in a large-scale, four-span RC bridge. Superelastic shape memory alloys (SMAs), engineered cementitious composites (ECCs), posttensioned columns, and elastomeric bearings were used in three different piers to improve the seismic performance of the bridge in terms of minimizing damage and reducing residual displacements. The bridge model was subjected to a series of biaxial earthquake excitations with increasing amplitudes. The experimental results showed that, besides being effective in reducing permanent displacement of the bridge, the high-performance materials and details substantially reduced the damage at plastic hinge regions and modified significantly other response parameters of the bents compared with conventional RC construction. Higher ductility was observed in the pier with the SMA/ECC combination, and larger load capacity was exhibited by the pier with elastomeric pads. While rotations at the plastic hinges with high-performance materials were significantly larger than those measured at plastic hinges made of conventional RC, the measured residual strains in the longitudinal reinforcement in the plastic hinges with innovative details were smaller than those observed in RC plastic hinges.
A layered adaptive verification platform for simulation, test, and emulation (2004)

This adaptive architecture for structuring testbenches accommodates various models of a design, from transaction to silicon. Moreover, the adapter-based architecture supports the execution of design models on different simulators (high level, RTL, gate level, and switch level), hardware emulators (the testbench runs entirely on the emulator), and even testers. Here, we present a modular, layered testbench (MLTB) approach to building a testbench. This approach is similar to platform-based design. It consists of a generic testbench kernel (TBK), connected through a bus to testbench elements. Our verification platform also satisfies another meaning of platform: a set of connected tools or a powerful tool environment, normally with an attached database, that acts as a platform for verification.
Combining MR elastography and diffusion tensor imaging for the assessment of anisotropic mechanical properties: A phantom study (2012)

This study has demonstrated the feasibility of the proposed imaging technique for characterizing mechanical anisotropy of anisotropic materials and biological tissues, and validated the mechanical anisotropy results.
Highly Efficient Metal‐Free Visible Light Driven Photocatalyst: Graphene Oxide/Polythiophene Composite (2017)

Abstract Graphene oxide/polythiophene (GO/PTh) composites were synthesized by in‐situ polymerization of thiophene (Th) monomers on GO surfaces. Remarkable performance of GO/PTh composites for methylene blue (MB) photo‐degradation under visible light has been achieved by tuning GO/Th ratio and graphene oxidation degrees. 100 % MB degradation was achieved by the composite within 30 min under visible light, its catalytic activity (0.1149 min −1 ) is 382 and 41 times higher than that of PTh (0.0003 min −1 ) and GO (0.0028 min −1 ), respectively. The results of MB adsorption experiment, ultraviolet‐visible (UV‐vis) and photoluminescence (PL) spectra show that combination of GO and PTh increases MB adsorption, decreases the band gap and enhances photo‐electron transfer. The composite with 36 % PTh (at the fed GO/Th weight ratio of 1:2) shows the highest catalytic activity where MB adsorption ability by GO and photo‐electron producing ability by PTh in the composite is well matched. The catalytic activity can be further enhanced by changing graphene oxidation degree by controlling graphite/KMnO 4 ratio and post‐reaction time during GO preparation. Fourier transform infrared (FTIR) spectroscopy and X‐ray photo‐electron (XPS) spectroscopy analyses have shown that increasing oxidation degree of GO leads to a stronger π‐π interaction between GO and PTh and a more electron‐rich PTh, resulting in higher catalytic activity.
CD8+ T‐cell recognition of a synthetic epitope formed by t‐butyl modification (2014)

We set out to clone Bax-specific CD8<sup>+</sup> T-cells from peripheral blood samples of primary chronic lymphocytic leukemia patients. A number of clones were generated using a Bax peptide pool and their T-cell epitope was mapped to two peptides sharing a common 9-aa sequence (LLSYFGTPT), restricted by HLA-A*0201. However, when these T-cell clones were tested against highly purified syntheses (>95%) of the same peptide sequence, there was no functional response. Subsequent mass spectrometric analysis and HPLC fractionation suggested that the active component in the original crude peptide preparations (77% pure) was a peptide with a tert-butyl (tBu) modification of the tyrosine residue. This was confirmed by modification of the inactive wild type (wt) sequence to generate functionally active peptides. Computer modeling of peptide:HLA-A*0201 structures predicted that the tBu modification would not affect interactions between peptide residues and the HLA binding site. However these models did predict that the tBu modification of tyrosine would result in an extension of the side chain out of the peptide-binding groove up towards the TCR. This modified product formed <1% of the original P603 crude peptide preparation and <0.05% of the original 23 peptide mixture used for T-cell stimulation. The data presented here, illustrates the potential for chemical modifications to change the immunogenicity of synthetic peptides, and highlights the exquisite capacity of TCR to discriminate between structurally similar peptide sequences. Furthermore this study highlights potential pitfalls associated with the use of synthetic peptides for the monitoring and modulating of human immune responses. This article is protected by copyright. All rights reserved.
Main group mechanochemistry: from curiosity to established protocols (2019)

In the last few decades, mechanochemistry has become rapidly established as a powerful tool enabling environmentally-benign and sustainable chemical syntheses. Not only have these techniques been demonstrated as viable alternatives to traditional solution-based syntheses, but they have also received attention for their ability to enable new reactivity and "unlocking" novel compounds inaccessible by conventional methods. Reflecting the rising popularity of mechanochemistry, many excellent reviews highlighting its benefits have recently been published. Whilst the scope of most of these focuses on organic chemistry, transition-metal catalysis, porous framework materials, coordination compounds and supramolecular synthesis, few have addressed the use of mechanochemical ball milling for the synthesis of compounds containing s- and p-block elements. This tutorial review turns the spotlight towards mechanochemical research in the field of inorganic main group chemistry, highlighting significant advantages that solid-state inorganic reactions often possess, and the potential for these to drive the development of greener methodologies within the modern main group arena.
Inverse relation of C-reactive protein levels to heart rate variability in patients after acute myocardial infarction. (2007)

Increased levels of circulating CRP after acute myocardial infarction are associated with attenuated HRV indices, suggesting a possible relationship between inflammation and cardiac autonomic balance.
Antimicrobial peptides: a review of how peptide structure impacts antimicrobial activity (2004)

Antimicrobial peptides (AMPs) have been discovered in insects, mammals, reptiles, and plants to protect against microbial infection. Many of these peptides have been isolated and studied exhaustively to decipher the molecular mechanisms that impart protection against infectious bacteria, fungi, and viruses. Unfortunately, the molecular mechanisms are still being debated within the scientific community but valuable clues have been obtained through structure/function relationship studies<sup>1</sup>. Biophysical studies have revealed that cecropins, isolated from insects and pigs, exhibit random structure in solution but undergo a conformational change to an amphipathic &#945;-helix upon interaction with a membrane surface<sup>2</sup>. The lack of secondary structure in solution results in an extremely durable peptide able to survive exposure to high temperatures, organic solvents and incorporation into fibers and films without compromising antibacterial activity. Studies to better understand the antimicrobial action of cecropins and other AMPs have provided insight into the importance of peptide sequence and structure in antimicrobial activities. Therefore, enhancing our knowledge of how peptide structure imparts function may result in customized peptide sequences tailored for specific applications such as targeted cell delivery systems, novel antibiotics and food preservation additives. This review will summarize the current state of knowledge with respect to cell binding and antimicrobial activity of AMPs focusing primarily upon cecropins.
Gallium Arsenide detectors for X-ray and electron (beta particle) spectroscopy (2016)

Results characterizing GaAs p+-i-n+ mesa photodiodes with a 10 µm i layer for their spectral response under illumination of X-rays and beta particles are presented. A total of 22 devices, having diameters of 200 µm and 400 µm, were electrically characterized at room temperature. All devices showed comparable characteristics with a measured leakage current ranging from 4 nA/cm2 to 67 nA/cm2 at an internal electric field of 50 kV/cm. Their unintentionally doped i layers were found to be almost fully depleted at 0 V due to their low doping density. 55Fe X-ray spectra were obtained using one 200 µm diameter device and one 400 µm diameter device. The best energy resolution (FWHM at 5.9 keV) achieved was 625 eV using the 200 µm and 740 eV using the 400 µm diameter device, respectively. Noise analysis showed that the limiting factor for the energy resolution of the system was the dielectric noise; if this noise was eliminated by better design of the front end of the readout electronics, the achievable resolution would be 250 eV. 63Ni beta particle spectra obtained using the 200 µm diameter device showed the potential utility of these detectors for electron and beta particle detection. The development of semiconductor electron spectrometers is important particularly for space plasma physics; such devices may find use in future space missions to study the plasma environment of Jupiter and Europa and the predicted electron impact excitation of water vapor plumes from Europa hypothesized as a result of recent Hubble Space Telescope (HST) UV observations.
An object-oriented and constraint-based knowledge representation system for design object modeling (2002)

FREEDOM (Framework for Representing and Elaborating Design Object Models), a system for design object modeling, is presented. An object model, represented as a set of objects in this system, is not a mere data structure but an active entity which works to solve design problems. The knowledge representation provided in the system, based on the object-oriented paradigm, makes it possible to describe constraints in declarative form. A class hierarchy is represented with links, and a class-instance relation can be changed dynamically. These features are useful for top-down refinement. The problem-solving mechanism of the system is based on constraint-satisfaction techniques. Constraints are declared statically and can be added to the objects dynamically. An object has a function, to keep its state satisfying given constraints. By this function, values of attributes and classes of objects that satisfy design requirements can be found. The constraint-satisfaction method is based on the technique of constraint logic programming and constraint propagation among objects. FREEDOM is implemented using the ESP language on a PSI machine.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Guided Policy Search with Delayed Senor Measurements. (2016)

Guided policy search is a method for reinforcement learning that trains a general policy for accomplishing a given task by guiding the learning of the policy with multiple guiding distributions. Guided policy search relies on learning an underlying dynamical model of the environment and then, at each iteration of the algorithm, using that model to gradually improve the policy. This model, though, often makes the assumption that the environment dynamics are markovian, e.g., depend only on the current state and control signal. In this paper we apply guided policy search to a problem with non-markovian dynamics. Specifically, we apply it to the problem of pouring a precise amount of liquid from a cup into a bowl, where many of the sensor measurements experience non-trivial amounts of delay. We show that, with relatively simple state augmentation, guided policy search can be extended to non-markovian dynamical systems, where the non-markovianess is caused by delayed sensor readings.
Macromol. Rapid Commun. 12/2011 (2011)

Front Cover: (Meth)acrylates (white circle) and vinyl ethers (yellow circle) are copolymerized under controlled manner in the presence of organoheteroatom chain transfer agents, such as an organotellurium compound shown in the middle. Alternating copolymerization occurs by employing an excess amount of vinyl ethers over (meth)acrylates. Further details can be found in the article by E. Mishima and S. Yamago* on page 893.
Postprandial incorporation of EPA and DHA from transgenic Camelina sativa oil into blood lipids is equivalent to that from fish oil in healthy humans (2019)

EPA and DHA are important components of cell membranes. Since humans have limited ability for EPA and DHA synthesis, these must be obtained from the diet, primarily from oily fish. Dietary EPA and DHA intakes are constrained by the size of fish stocks and by food choice. Seed oil from transgenic plants that synthesise EPA and DHA represents a potential alternative source of these fatty acids, but this has not been tested in humans. We hypothesised that incorporation of EPA and DHA into blood lipids from transgenic Camelina sativa seed oil (CSO) is equivalent to that from fish oil. Healthy men and women (18-30 years or 50-65 years) consumed 450 mg EPA + DHA from either CSO or commercial blended fish oil (BFO) in test meals in a double-blind, postprandial cross-over trial. There were no significant differences between test oils or sexes in EPA and DHA incorporation into plasma TAG, phosphatidylcholine or NEFA over 8 h. There were no significant differences between test oils, age groups or sexes in postprandial VLDL, LDL or HDL sizes or concentrations. There were no significant differences between test oils in postprandial plasma TNFα, IL 6 or 10, or soluble intercellular cell adhesion molecule-1 concentrations in younger participants. These findings show that incorporation into blood lipids of EPA and DHA consumed as CSO was equivalent to BFO and that such transgenic plant oils are a suitable dietary source of EPA and DHA in humans.
Experimental microvenous thrombosis following anastomosis with a knotted suture (1995)

An experimental model for producing venous thrombosis was developed in end-to-end anastomoses of femoral veins in rats. The anastomoses were performed using a suture (9-0 suture-70 microns needle) with a knot 1 cm from the needle. The knot was formed by making either six or eight half-hitches in one throw of the suture. Vessel patency was assessed through the direct "milking test" at 20 min and 24 hrs. The incidence of thrombosis when using one knot with six half-hitches ranged from 20% to 40% and with eight half-hitches, from 50% to 70%. The incidence of femoral vein thrombosis varied directly with the presence and size of the knot. In this model, thrombosis was induced by exaggerating vessel injuries that may occur when performing routine microvascular anastomoses. This study demonstrates a reproducible thrombogenic model which mimics clinical practice and may be used to study the effects of local and systemic antithrombogenic agents.