gebhart/patrepeval huggingface dataset:
Morbidity and mortality in rheumatoid patients during treatment with adalimumab and infliximab (2004)

Morbidity and mortality in rheumatoid patients during treatment with adalimumab and infliximab SIR, Three anti-tumour necrosis factor (TNF) agents (infliximab, adalimumab and etanercept) have demonstrated impressive efficacy in the treatment of rheumatoid arthritis (RA). They have been remarkably safe in the clinical trials reported to date [1]. The occurrence of serious infection, some fatal, during anti-TNF therapy in three UK centres led Moots et al. [2] to advocate greater caution in the use of these agents. Others have also recently emphasized the risk of serious bacterial infection associated with anti-TNF therapy [3, 4]. As of August 2002, 574 deaths have occurred in 554 372 patient-yr of exposure to infliximab (communication from Schering-Plough). Adalimumab was licensed by the USA Food and Drug Administration in December 2002 and has been available in Ireland from the company on a named patient basis since January 2003. No deaths related to its use have been reported in the literature up to September 2003. However, three deaths possibly related to adalimumab occurred during clinical trials (communication from Abbott UK).
Cascade CRISPR/cas enables amplification-free microRNA sensing with fM-sensitivity and single-base-specificity (2020)

Existing CRISPR/cas-based biosensors usually improve sensitivity by target amplification, which is time-consuming and susceptible to impurities in complex biofluid. Herein, this is the first time a cascade CRISPR/cas (casCRISPR) system has been developed, which can provide a detection limit of 1.33 fM (∼1000 times lower than direct Cas13a-based miRNA detection) and single-base resolution for miR-17 detection without resorting to target amplification. casCRISPR can also be applied to detect miRNA in complicated cell extracts and serum samples. Overall, casCRISPR will provide a heuristic idea for CRISPR/cas based biosensing, and could be a promising tool for miRNA diagnostics.
Distinct Translational Control in CD4+ T Cell Subsets (2013)

Regulatory T cells expressing the transcription factor Foxp3 play indispensable roles for the induction and maintenance of immunological self-tolerance and immune homeostasis. Genome-wide mRNA expression studies have defined canonical signatures of T cell subsets. Changes in steady-state mRNA levels, however, often do not reflect those of corresponding proteins due to post-transcriptional mechanisms including mRNA translation. Here, we unveil a unique translational signature, contrasting CD4(+)Foxp3(+) regulatory T (T(Foxp3+)) and CD4(+)Foxp3(-) non-regulatory T (TFoxp3-) cells, which imprints subset-specific protein expression. We further show that translation of eukaryotic translation initiation factor 4E (eIF4E) is induced during T cell activation and, in turn, regulates translation of cell cycle related mRNAs and proliferation in both T(Foxp3)- and T(Foxp3+) cells. Unexpectedly, eIF4E also affects Foxp3 expression and thereby lineage identity. Thus, mRNA-specific translational control directs both common and distinct cellular processes in CD4(+) T cell subsets.
ChemInform Abstract: Are d0 ML6 Complexes Always Octahedral? The X‐Ray Structure of Trigonal‐Prismatic (Li(tmed))2(ZrMe6). (1989)

Abstract The X‐ray structure of the title complex (I) (Aba2, Z=4) shows that the methyl groups describe a trigonal prism around the Zr center, which is not explicable in terms of ligand field theory and contradicts the octahedral prediction of a simple electrostatic points‐on‐a‐sphere model.
Early Inhibition of MMP Activity in Ischemic Rat Brain Promotes Expression of Tight Junction Proteins and Angiogenesis During Recovery (2013)

In cerebral ischemia, matrix metalloproteinases (MMPs) have a dual role by acutely disrupting tight junction proteins (TJPs) in the blood-brain barrier (BBB) and chronically promoting angiogenesis. Since TJP remodeling of the neurovascular unit (NVU) is important in recovery and early inhibition of MMPs is neuroprotective, we hypothesized that short-term MMP inhibition would reduce infarct size and promote angiogenesis after ischemia. Adult spontaneously hypertensive rats had a transient middle cerebral artery occlusion with reperfusion. At the onset of ischemia, they received a single dose of the MMP inhibitor, GM6001. They were studied at multiple times up to 4 weeks with immunohistochemistry, biochemistry, and magnetic resonance imaging (MRI). We observed newly formed vessels in peri-infarct regions at 3 weeks after reperfusion. Dynamic contrast-enhanced MRI showed BBB opening in new vessels. Along with the new vessels, pericytes expressed zonula occludens-1 (ZO-1) and MMP-3, astrocytes expressed ZO-1, occludin, and MMP-2, while endothelial cells expressed claudin-5. The GM6001, which reduced tissue loss at 3 to 4 weeks, significantly increased new vessel formation with expression of TJPs and MMPs. Our results show that pericytes and astrocytes act spatiotemporally, contributing to extraendothelial TJP formation, and that MMPs are involved in BBB restoration during recovery. Early MMP inhibition benefits neurovascular remodeling after stroke.
Biosynthesis of subunits of the soybean 7S storage protein. (1981)

Biosynthesis of the alpha', alpha, and beta subunits of the soybean 7S storage protein (conglycinin) was studied by in vivo and in vitro experiments. One hour in vivo labeling produced polypeptides of 72 kilodaltons (kD) and 78 kD which, in a subsequent 1-h chase period, gave rise to a heterodisperse band of polypeptides of 76-83 kD, the apparent molecular weights of mature alpha and alpha', respectively. After a 3-h chase period only mature alpha and alpha' were labeled. The pre-alpha' (80 kD) and pre-alpha (78 kD) polypeptides produced by in vitro translation of total seed poly(A)+ RNA did not coelectrophorese with polypeptides labeled in vivo. The mature beta-subunit (53 kD), produced in vivo during the 1-h chase period, apparently was translated as a 50 kD polypeptide in vitro. The data suggest that, in vivo, primary translation products undergo both cotranslational and posttranslational modifications during the formation of mature subunits. cDNA clones complementary to soybean seed poly(A)+ RNA were prepared and subsequently identified by hybrid-release and immunoprecipitation experiments. Clone pGmc 236 (550 base pairs) (bp) was shown to contain sequences complementary to mRNAs for the alpha', alpha, and beta subunits on the basis of hybrid-release experiments, corroborating tryptic fingerprints that demonstrate that these subunits are closely related to each other. Although selected by a single cDNA clone, the mRNAs are not identical because the alpha' mRNA was eluted from the filter-bound cDNAs at a lower temperature than were the alpha beta mRNAs, pGmc 236 hybridized on Northern blots to mRNAs of approximately 2500 nucleotides, sufficient size to code for the alpha' or alpha subunit of the 7S storage protein.
Narrowband tunable optical filter for channel selection in densely packed WDM systems (1986)

Stimulated Brillouin amplification is used for channel selection in a densely packed WDM direct-detection lightwave experiment. Data at 45 Mbit/s were detected error-free with a similar interfering channel as close as 140 MHz away.
Nogo-A Activates NF-κB Through Its N-Terminal Proline Rich Domain (2009)

Nogo-A is a myelin derived neurite outgrowth inhibitor which is not only highly expressed in mature oligodendrocytes, but also in various kinds of neurons in the central nervous system.However, the function of neuronal Nogo-A remains unclear.To investigate the function of Nogo-A in neurons, human embryonic kidney cell line 293FT was used as a model, along with the pathway profiling reporter system to check the involvement of Nogo-A in regulating the intracellular signaling pathway.It was found that over-expression of Nogo-A could activate NF-κB signaling specifically, then followed by using different Nogo-A alternative splicing isoforms and a serial of truncations, it was confirmed that the activation of NF-κB by Nogo-A relied on its N-terminal proline rich domain.Furthermore, by co-expressing the dominant negative mutants of some NF-κB pathway associated proteins, it revealed that the IκBα,TRAF6, Rac/Cdc42 were involved in Nogo-A inducing activation of NF-κB.Above all, these results indicate that Nogo-A could significantly activate NF-κB, and this activation depended primarily on its N-terminal proline rich domain.
Bridging Between Si and Few-Mode Fiber Higher Order Modes (2020)

We show a mode converter between silicon and polymer waveguides compatible with few-mode fibers for mode-division multiplexing. We convert 4 TE modes of a silicon waveguide to the TE11, TMii, TE21, TM21 modes of a polymer waveguide.
Recombinant A17 Lys human insulin: purification and characterization. (1995)

Recombinant A17 Lys human insulin precursor expressed in yeast cells was isolated from the culture medium. After purification, the precursor was converted into A17 Lys human insulin. A17 Lys human insulin can be crystallized but has much lower receptor-binding and biological activities than porcine or human insulin where A17 is Glu. It is proposed that the A17 Glu residue may be involved in the receptor-binding or the active site of human insulin.
Crystallization of nanostructured cobalt hydroxide carbonate at ambient conditions: a key precursor of Co<sub>3</sub>O<sub>4</sub> (2016)

Abstract Crystals of Co 2 CO 3 (OH) 2 have been synthesized under ambient conditions, in contrast to hydrothermal methods reported previously. We have developed a simple but efficient methodology to obtain an initial amorphous phase that evolves to a crystalline cobalt hydroxide carbonate after one week of maturation. X-ray diffraction analysis indicates that this phase crystallizes in the space group P 2 1 / a ( a = 12.886(6), b = 9.346(3), c = 3.156(1) Å, β = 110.358(6)°). The platelet morphology of Co 2 CO 3 (OH) 2 agrees with its lamellar crystal structure. High-resolution transmission electron microscopy (HRTEM) reveals that each individual platelet is comprised of nanodomains disoriented with respect to their neighbours. The kinetics and the activation energy (E a = 6.26 kJ mol –1 ) of the transformation process have been estimated using the rate constant method. The precipitation of solids leads to a decrease in the cobalt concentration in the solution (∼88%) reaching values of ∼150 ppm, which can be considered a successful reduction from the perspective of water quality. The calcination in air of the synthetized platelets produced exclusively Co 3 O 4 . The thermo-X-ray difraction results confirm that Co 2 CO 3 (OH) 2 is transformed over a small range of temperatures (225–235°C) into pure Co 3 O 4 . HRTEM images show that the lamellar nanomorphology is preserved in the Co 3 O 4 phase. Therefore, understanding the crystallization behaviour of Co 2 CO 3 (OH) 2 can help to minimize environmental problems caused by cobalt pollution and may facilitate the management of methods to obtain phases with specific nanomorphologies used widely in material sciences.
Inhibition Effect of AC-Treated, Mixed Self-Assembled Film of Phenylthiourea and 1-Dodecanethiol on Copper Corrosion (2003)

A new method for preparing effective inhibition film on copper has been developed. Phenylthiourea was first adsorbed to a copper surface to form a self-assembled film. 1-Dodecanethiol was then self-assembled on the surface for subsequent modification. Finally, ac voltage was loaded on copper covered with the mixed film to further modify the film. After these procedures, an effective inhibition film was obtained as indicated by the low corrosion current density in polarization curves. High charge-transfer resistance in electrochemical impedance spectra reveals that the film hinders corrosion electrochemical reaction between the copper surface and NaCl solution. Film coverage on the copper surface is more than 99.0%, and inhibition efficiency is more than 97.2% in NaCl solutions. The mixed films before and after ac treatment are stable in a wide region of potentials. X-ray photoelectron spectroscopy analysis reveals that the effect of ac treatment may associate with the formation of a new complex compound. © 2003 The Electrochemical Society. All rights reserved.
Compiler-based graph representations for deep learning models of code (2020)

In natural language processing, novel methods in deep learning, like recurrent neural networks (RNNs) on sequences of words, have been very successful. In contrast to natural languages, programming languages usually have a well-defined structure. With this structure compilers can reason about programs, using graphs such as abstract syntax trees (ASTs) or control-data flow graphs (CDFGs). In this paper, we argue that we should use these graph structures instead of sequences for learning compiler optimization tasks. To this end, we use graph neural networks (GNNs) for learning predictive compiler tasks on two representations based on ASTs and CDFGs. Experiments show that this improves upon the state-of-the-art in the task of heterogeneous OpenCL mapping, while providing orders of magnitude faster inference times, crucial for compiler optimizations. When testing on benchmark suites not included for training, our AST-based model significantly outperforms the state-of-the-art by over 12 percentage points in terms of accuracy. It is the only one to perform clearly better than a random mapping. On the task of predicting thread coarsening factors, we show that all of the methods fail to produce an overall speedup.
Antimicrobial, antiadhesive and antibiofilm potential of lipopeptides synthesised by Bacillus subtilis, on uropathogenic bacteria (2015)

The aim of this study was to investigate the antimicrobial effect of lipopeptide biosurfactants from surfactin, iturin and fengycin families, synthesised by the Bacillus subtilis I'1a strain, on uropathogenic bacteria, including the effects on planktonic growth, processes of biofilm formation and dislodging. Antimicrobial activity was tested against 32 uropathogenic strains belonging to 12 different species of Gram-negative and Gram-positive bacteria. The sensitivity of 25 tested bacterial strains to the B. subtilis I'1a filtrate was confirmed by an agar diffusion assay. None of the strains seemed to be sensitive to pure surfactin at concentrations ranging from 0.1 mg × ml(-1) to 0.4 mg ml(-1). After the treatment of uropathogens with B. subtilis lipopeptides, the metabolic activity of planktonic cells was inhibited by 88.05±3.96% in the case of 21 studied uropathogens, the process of biofilm formation was reduced by 88.15±4.77% in the case of 24 uropathogens and mature biofilms of 18 strains were dislodged by about 81.20±4.72%. Ten strains of uropathogenic bacteria were selected to study the antimicrobial activity of surfactin (concentrations 0.1, 0.2 and 0.4 mg × ml(-1)). Surfactin had no influence on the metabolic activity of planktonic forms of uropathogens, however, biofilms of 5 tested strains were reduced by 64.77±9.05% in the presence of this biosurfactant at the concentration 0.1 mg × ml(-1). The negative effect of the compound on the biofilm formation process was observed at all concentrations used. The above-described results were fully confirmed by CLSM. It could suggest that synergistic application of biosurfactants could be efficient in uropathogen eradication.
Self-propagating high-temperature synthesis as a process for joining materials (1996)

Self-propagating high-temperature synthesis or SHS is a process that allows production of a wide variety of ceramic and intermetallic compounds by highly exothermic reactions. It has been successfully used for simultaneous net-shape production, as well as joining, albeit the process of joining is in an embryonic state of understanding. In this study, the Gleeble{reg_sign} was employed for the systematic evaluation of the effects of heating rate (0.5 to 2 C/s), processing temperature (500 to 1,300 C), hold time (2 to 60 min), and applied pressure (8.8 to 82.7 MPa), as well as minor variations of reactant composition, on the degree of reaction, joining integrity, and filler metal density and homogeneity in a model system of 3Ni + Al > Ni{sub 3}Al reacted in situ between Alloy 600 end elements. For all temperatures above the reaction ignition temperature (T{sub i}), where a liquid phase is formed (639.9 C), joining integrity was good. The degree of reaction, as well as product homogeneity and density, were all increased most by increased processing temperatures, with more modest effects from longer hold times and higher applied pressures. Heating rate had no apparent effect, although the range was narrow. Composition around the perfect stoichiometric ratio hadmore » a modest effect on density.« less
Design and performance of tunnel collector HBTs for microwave power amplifiers (2003)

AlGaAs/GaAs/GaAs and GaInP/GaAs/GaAs n-p-n heterojunction bipolar transistors (HBTs) are now in widespread use in microwave power amplifiers. In this paper, improved HBT structures are presented to address issues currently problematic for these devices: high offset and knee voltages and saturation charge storage. Reduced HBT offset and knee voltages (V/sub CE,os/ and V/sub k/) are important to improve the power amplifier efficiency. Reduced saturation charge storage is desirable to increase gain under conditions when the transistor saturates (such as in over-driven Class AB amplifiers and switching mode amplifiers). It is shown in this paper that HBT structures using a 100-/spl Aring/-thick layer of GaInP between the GaAs base, and collector layers are effective in reducing V/sub CE,os/ to 30 mV and V/sub k/ measured at a collector current density of 2/spl times/10/sup 4/ A/cm/sup 2/ to 0.3 V (while for conventional HBTs V/sub CE,os/=0.2 V and V/sub k/=0.5 V are typical). A five-fold reduction in saturation charge storage is simultaneously obtained.
Impact of Food Components on in vitro Calcitonin Gene-Related Peptide Secretion—A Potential Mechanism for Dietary Influence on Migraine (2016)

Calcitonin gene-related peptide (CGRP) is a pivotal messenger in the inflammatory process in migraine. Limited evidence indicates that diet impacts circulating levels of CGRP, suggesting that certain elements in the diet may influence migraine outcomes. Interruption of calcium signaling, a mechanism which can trigger CGRP release, has been suggested as one potential route by which exogenous food substances may impact CGRP secretion. The objective of this study was to investigate the effects of foods and a dietary supplement on two migraine-related mechanisms in vitro: CGRP secretion from neuroendocrine CA77 cells, and calcium uptake by differentiated PC12 cells. Ginger and grape pomace extracts were selected for their anecdotal connections to reducing or promoting migraine. S-petasin was selected as a suspected active constituent of butterbur extract, the migraine prophylactic dietary supplement. Results showed a statistically significant decrease in stimulated CGRP secretion from CA77 cells following treatment with ginger (0.2 mg dry ginger equivalent/mL) and two doses of grape pomace (0.25 and 1.0 mg dry pomace equivalent/mL) extracts. Relative to vehicle control, CGRP secretion decreased by 22%, 43%, and 87%, respectively. S-petasin at 1.0 μM also decreased CGRP secretion by 24%. Meanwhile, S-petasin and ginger extract showed inhibition of calcium influx, whereas grape pomace had no effect on calcium. These results suggest that grape pomace and ginger extracts, and S-petasin may have anti-inflammatory propensity by preventing CGRP release in migraine, although potentially by different mechanisms, which future studies may elucidate further.
Analysis of scaling soft information on low density parity check code (2003)

Density evolution is used to analyse the scaling of soft information in the iterative decoding of low density parity check codes. Based on the min-sum algorithm and Gaussian approximation, the thresholds are evaluated with various scaling factors. The optimal scaling factor is found by density evolution and the expected scaling gain matches well with the achievable scaling gain from simulation results.
The stability of ionic crystal surfaces (1979)

When there is a dipole moment in the repeat unit perpendicular to the surface in an ionic crystal, lattice sums in the electrostatic energy diverge and the calculated surface energy is infinite. The cause of this divergence is demonstrated and the surfaces of any ionic or partly ionic material are classified into three types. Type 1 is neutral with equal numbers of anions and cations on each plane and type 2 is charged but there is no dipole moment perpendicular to the surface because of the symmetrical stacking sequence. Both these surfaces should have modest surface energies and may be stable with only limited relaxations of the ions in the surface region. The type 3 surface is charged and has a dipole moment in the repeat unit perpendicular to the surface. This surface can only be stabilised by substantial reconstruction. These conclusions are important for the analysis of the surface structure of ionic crystals.
B-Lymphocyte-Stimulating Polysaccharide from Mushroom Phellinus linteus. (1995)

Hot water extract prepared from the mycelial culture of mushroom Phellinus linteus stimulated polyclonal antibody production in an in vitro culture system. The active fraction PLP was purified from the extract ca. 1030-fold by ethanol precipitation followed by DEAE-cellulose and gel permeation chromatography. PLP contained 13.2% (w/w) peptide and 82.5% (w/w) carbohydrate. About 6.8% (w/w) of the total carbohydrate was uronic acid. The molecular weight distribution of PLP was found to be nearly homogeneous (153 kDa) in gel permeation HPLC analysis. Neutral sugar composition analysis revealed Ara (7.5%), Xyl (3.7%), Glc (21.1%), Gal (24.1%) and Man (44.2%). Uronic acid was identified as a glucuronic acid by gas chromatography. Ten amino acids were detected and Asp and Glu were the major components. In our assay system, the half-maximal concentration of PLP for B-lymphocyte stimulation was ca. 3 micrograms/ml. Partial acid hydrolysis as well as sodium periodate treatment of PLP decreased the activity significantly, suggesting that both the full molecular size and the sugar moiety were essential. However, proteinase K treatment for up to 48 h did not affect the activity.
Fabrication and photoluminescence of zinc silicate/silica modulated ZnO nanowires (2005)

Zinc silicate/silica modulated ZnO nanowires have been successfully prepared by a chemical vapour deposition route. The nanowires have a uniform diameter of similar to 30 nm and length of 1 mu m. Photoluminescence spectra show four peaks at 382, 398, 478 and 520 nm. Two new additional peaks at 398 and 478 nm are assigned to modulation between ZnO and SiO2. The formation mechanism of the surface modified ZnO-based nanowires is also proposed.