gebhart/patrepeval huggingface dataset:
Transparent flexible organic thin-film transistors that use printed single-walled carbon nanotube electrodes (2006)

Electrodes based on printed networks of single-walled carbon nanotubes (SWNTs) are integrated with ultrathin layers of the organic semiconductor pentacene to produce bendable, transparent thin-film transistors on plastic substrates. The physical and structural properties of the SWNTs lead to the remarkably good electrical contacts with the pentacene. Optical transmittances of ∼70%, device mobilities &amp;gt;0.5cm2V−1s−1, ON/OFF ratios &amp;gt;105 and tensile strains as large as 1.8% are achieved in devices of this type. These characteristics indicate promise for applications in power conserving flexible display systems and other devices.
Kin28, the TFIIH-Associated Carboxy-Terminal Domain Kinase, Facilitates the Recruitment of mRNA Processing Machinery to RNA Polymerase II (2000)

The cotranscriptional placement of the 7-methylguanosine cap on pre-mRNA is mediated by recruitment of capping enzyme to the phosphorylated carboxy-terminal domain (CTD) of RNA polymerase II. Immunoblotting suggests that the capping enzyme guanylyltransferase (Ceg1) is stabilized in vivo by its interaction with the CTD and that serine 5, the major site of phosphorylation within the CTD heptamer consensus YSPTSPS, is particularly important. We sought to identify the CTD kinase responsible for capping enzyme targeting. The candidate kinases Kin28-Ccl1, CTDK1, and Srb10-Srb11 can each phosphorylate a glutathione S-transferase-CTD fusion protein such that capping enzyme can bind in vitro. However, kin28 mutant alleles cause reduced Ceg1 levels in vivo and exhibit genetic interactions with a mutant ceg1 allele, while srb10 or ctk1 deletions do not. Therefore, only the TFIIH-associated CTD kinase Kin28 appears necessary for proper capping enzyme targeting in vivo. Interestingly, levels of the polyadenylation factor Pta1 are also reduced in kin28 mutants, while several other polyadenylation factors remain stable. Pta1 in yeast extracts binds specifically to the phosphorylated CTD, suggesting that this interaction may mediate coupling of polyadenylation and transcription.
Serum microRNAs as non-invasive biomarkers for cancer (2010)

Human serum and other body fluids are rich resources for the identification of novel biomarkers, which can be measured in routine clinical diagnosis. microRNAs are small non-coding RNA molecules, which have an important function in regulating RNA stability and gene expression. The deregulation of microRNAs has been linked to cancer development and tumor progression. Recently, it has been reported that serum and other body fluids contain sufficiently stable microRNA signatures. Thus, the profiles of circulating microRNAs have been explored in a variety of studies aiming at the identification of novel non-invasive biomarkers. In this review, we discuss recent findings indicating that circulating microRNAs are useful as non-invasive biomarkers for different tumor types. Additionally, we summarize the knowledge about the mechanism of microRNA release and the putative functional roles of circulating microRNAs. Although several challenges remain to be addressed, circulating microRNAs have the potential to be useful for the diagnosis and prognosis of cancer diseases.
B-Domain Deleted Recombinant Coagulation Factor VIII Modified with Monomethoxy Polyethylene Glycol (2000)

Recombinant coagulation factor VIII (r-VIII SQ) was chemically modified with monomethoxy poly(ethylene glycol) (mPEG). Three mPEG derivatives were used for coupling to the r-VIII SQ lysines, a mixed anhydride of monomethoxy poly(ethylene glycol) succinic acid (mPEG-SAH), monomethoxy poly(ethylene glycol) succinimidyl succinate (mPEG-SS), and monomethoxy poly(ethylene glycol) tresylate (mPEG-TRES). A consequence of the modification with all derivatives was a substantial reduction in coagulant activity, even at very low degrees of modification. A method was developed with the purpose of avoiding conjugation at certain important biological sites on the factor VIII and thereby producing conjugates with better retained activity. This was achieved by immobilizing the protein onto a solid matrix during the modification reaction. Characterization of conjugates by SDS-PAGE, western blots, interaction with von Willebrand factor (vWf), and thrombin activation/inactivation analyses was undertaken. The SDS-PAGE and western blots revealed coupling heterogeneity regarding degree of modification. The amount of factor VIII able to bind to vWf decreased with the conjugation. Thrombin activated the modified factor VIII to essentially the same extent as the reference preparation of r-VIII SQ. Inactivation of the modified factor VIII was, however, slower than inactivation of the unmodified protein. Finally, an in vitro study was performed to evaluate the influence of the mPEG modification on the protein stability in extract of porcine tissue. Despite that conjugates with low degrees of modification were included in the study, the coagulant activity was preserved to a significantly higher extent in all incubation mixtures containing conjugates compared to that with unmodified protein.
Improving clinical trial design for Duchenne muscular dystrophy (2015)

Here, we review some key points that should be considered when designing clinical trials for these new therapies. First, younger patients have more functional abilities and more muscle fibers to preserve than older patients and therefore are better subjects for trials designed to demonstrate the success of new treatments. Second, the inclusion of patients on corticosteroids both in the treatment and placebo groups is of concern because the positive effect of corticosteroids might mask the effect of the treatment being tested. Additionally, the reasonable expectation from these therapies is the slowing of disease progression rather than improvement. Therefore, the appropriate clinical endpoints are the prolongation of the ability to stand from the floor, climb stairs, and walk, not an increase in muscle strength or function. Hence, the time frames for the detection of new dystrophin, which occurs within months, and the ability to demonstrate a slowing of disease progression, which requires years, are strikingly different. Finally, placebo-controlled trials are difficult to manage if years of blindness are required to demonstrate a slowing of disease progression. Thus, accelerated/conditional approval for new therapies should be based on surrogate biochemical outcomes: the demonstration of de novo dystrophin production and of its beneficial effect on the functional recovery of muscle fiber. These data suggest that clinical trials for DMD patients must be adapted to the particular characteristics of the disease in order to demonstrate the expected positive effect of new treatments.
Towards the Creation of Story Sharing Network of Research Supervisors (2011)

The function of the supervisor is therefore significant in the entire research endeavour; and it has beenargued that a major cause of failure to complete postgraduate degree is due to inadequate supervision(Welford, 2008). Recent investigations conducted in the USA by the Council of Graduate Schoolsrevealed that mentoring/advising is the second highest (65%) factor contributing to respondents’ PhDcompletion; second only to financial support (80%) (Kirby, Sowell, Bell, &amp; Naftel, 2009). The central rolethat supervisors play in students’ postgraduate expertise makes it necessary for supervisors to usetheir ability, knowledge, and the experiences of their colleagues to provide students the bestsupervision necessary.
Cone Resynthesis ECO Methodology for Multi-Million Gate Designs (2009)

In this paper, we talk about techniques to incrementally resynthesize logic cones within a large design impacted by multiple RTL changes in order to accommodate a late functional ECO. In design methodologies where the RTL is hierarchical and the post route netlist is flat, mapping a change in the behavioral description to the post layout netlist is very complicated and may not even be feasible if the RTL is not written in a synthesis friendly manner. We try to attack this problem by introducing a technique that causes minimum perturbation to the gate level netlist, thereby retaining to a large degree, the goodness metrics of timing convergence, routability and layout cleanliness that were achieved during the various design milestones. This paper talks about the cone resynthesis ECO methodology in detail and highlights its usefulness during tight product deliverable schedules.
Molecular Basis of Enhanced Activity in Factor VIIa-Trypsin Variants Conveys Insights into Tissue Factor-mediated Allosteric Regulation of Factor VIIa Activity (2015)

The complex of coagulation factor VIIa (FVIIa), a trypsin-like serine protease, and membrane-bound tissue factor (TF) initiates blood coagulation upon vascular injury. Binding of TF to FVIIa promotes allosteric conformational changes in the FVIIa protease domain and improves its catalytic properties. Extensive studies have revealed two putative pathways for this allosteric communication. Here we provide further details of this allosteric communication by investigating FVIIa loop swap variants containing the 170 loop of trypsin that display TF-independent enhanced activity. Using x-ray crystallography, we show that the introduced 170 loop from trypsin directly interacts with the FVIIa active site, stabilizing segment 215-217 and activation loop 3, leading to enhanced activity. Molecular dynamics simulations and novel fluorescence quenching studies support that segment 215-217 conformation is pivotal to the enhanced activity of the FVIIa variants. We speculate that the allosteric regulation of FVIIa activity by TF binding follows a similar path in conjunction with protease domain N terminus insertion, suggesting a more complete molecular basis of TF-mediated allosteric enhancement of FVIIa activity.
IL-6 pathway in the liver: From physiopathology to therapy (2016)

Interleukin 6 (IL-6) is a pleiotropic four-helix-bundle cytokine that exerts multiple functions in the body. In the liver, IL-6 is an important inducer of the acute phase response and infection defense. IL-6 is furthermore crucial for hepatocyte homeostasis and is a potent hepatocyte mitogen. It is not only implicated in liver regeneration, but also in metabolic function of the liver. However, persistent activation of the IL-6 signaling pathway is detrimental to the liver and might ultimately result in the development of liver tumors. On target cells IL-6 can bind to the signal transducing subunit gp130 either in complex with the membrane-bound or with the soluble IL-6 receptor to induce intracellular signaling. In this review we describe how these different pathways are involved in the physiology and pathophyiology of the liver. We furthermore discuss how IL-6 pathways can be selectively inhibited and therapeutically exploited for the treatment of liver pathologies.
LPS induces apoptosis in macrophages mostly through the autocrine production of TNF-α (2000)

The deleterious effects of lipopolysaccharide (LPS) during endotoxic shock are associated with the secretion of tumor necrosis factor (TNF) and the production of nitric oxide (NO), both predominantly released by tissue macrophages. We analyzed the mechanism by which LPS induces apoptosis in bone marrow-derived macrophages (BMDM). LPS-induced apoptosis reached a plateau at about 6 hours of stimulation, whereas the production of NO by the inducible NO-synthase (iNOS) required between 12 and 24 hours. Furthermore, LPS-induced early apoptosis was only moderately reduced in the presence of an inhibitor of iNOS or when using macrophages from iNOS -/-mice. In contrast, early apoptosis was paralleled by the rapid secretion of TNF and was almost absent in macrophages from mice deficient for one (p55) or both (p55 and p75) TNF-receptors. During the late phase of apoptosis (12-24 hours) NO significantly contributed to the death of macrophages even in the absence of TNF-receptor signaling. NO-mediated cell death, but not apoptosis induced by TNF, correlated with the induction of p53 and Bax genes. Thus, LPS-induced apoptosis results from 2 independent mechanisms: first and predominantly, through the autocrine secretion of TNF-alpha (early apoptotic events), and second, through the production of NO (late phase of apoptosis). (Blood. 2000;95:3823-3831)
Circulating nucleic acids in plasma and serum: applications in diagnostic techniques for noninvasive prenatal diagnosis (2013)

The analysis of fetal nucleic acids in maternal blood 13 years ago has led to the initiation of noninvasive methods for the early determination of fetal gender, rhesus D status, and a number of aneuploid disorders and hemoglobinopathies. Subsequently, a comparatively large quantity of fetal DNA and RNA has been demonstrated in amniotic fluid as well as small amounts in premature infant saliva. The DNA and RNA in amniotic fluid has permitted an analysis of core transcriptomes, whilst the DNA and RNA in saliva allows the early detection and treatment monitoring of fetal developmental problems. These aspects are discussed together with the methodology and limits of analysis for noninvasive prenatal diagnosis in predictive, preventive, and personalized medicine.
Toward Mechanically-Robust Omniphobic Composite Coatings using Fluoroalkyl-Modified Silica (Preprint) (2009)

Abstract : The wide applicability of non-wetting materials has generated a surge in commerical, military, and academic materials research. Previous studies have elucidated three parameters useful in the development of non-wetting surfaces: chemical functionality (high fluorine content), multiple scales of surface roughness (nano and micro), and surface geometry (re-entrant curvature). These parameters have been used in the development of materials that are superhydrophobic and superoleophobic. Although many of these surfaces exhibit the desired omniphobic character, a simple method to produce mechanically robust non-wetting coatings on various substrates has not been reported. Various nanoparticles, such as nanosilica, have been shown to provide the required surface roughness for non-wetting character in polymer systems. In the present work, a fluoroalkyl-modified nanosilica is developed and investigated to help achieve both the surface roughness and low surface energy demands of an omniphobic polymer coating. The fluoroalkyl-modification has the added benefit of increasing dispersion and compatibility in a crosslinkable fluoropolymer matrix, which is thought to be needed to produce a mechanically-robust coating. Substitution of the silanol groups on the surface of silica has been well documented using vanous types of coupling agents, including chlorosilanes. The present work reports the modification of a previously reported two-step, amine promoted method for modifying the surface of silica.
<title>Fiber optic chemical microsensors employing optically active silica microspheres</title> (1995)

Dye-doped porous silica microspheres can be prepared from liquid solution at temperatures near ambient. Microsphere diameter can be controlled between approximately 5.0 microns to in excess of a millimeter. The resulting microspheres can be attached to the distal end of an optical fiber in which the proximal end is attached to a spectrophotometer. Depending upon the organic species doped into the microsphere, a wide variety of sensing functions are possible. In this paper, the use of microsensors for measuring pH, temperature, and solvent content of aqueous solutions is demonstrated. Potential utility of this type of sensor to heavy metals detection and biomedical diagnostics is also discussed.
SonoVue<sup>®</sup> (BR1), a New Long-Acting Echocontrast Agent, Improves Transcranial Colour-Coded Duplex Ultrasonic Imaging (2002)

SonoVue at a single dose of 1.2 or 2.4 ml is effective in increasing the detection of normal or pathological flow in the intracerebral arteries in patients who do not have a fully diagnostic unenhanced TCCS examination.
Lithium Redistribution in Lithium-Metal Batteries (2012)

A model of a lithium-metal battery with a CoO2 positive electrode has been modeled in order to predict the movement of lithium in the negative electrode along the negative electrode/separator interface during cell cycling. A finite-element approach was used to incorporate an intercalation positive electrode using superposition, electrode tabbing, transport using concentrated solution theory, as well as the net movement of the lithium electrode during cycling. From this model, it has been found that movement of lithium along the negative electrode/separator interface does occur during cycling and is affected by three factors: the cell geometry, the slope of the open-circuit-potential function of the positive electrode, and concentration gradients in both the solid and liquid phases in the cell.
Crack-resistant Al2O3–SiO2 glasses (2016)

Obtaining "hard" and "crack-resistant" glasses have always been of great important in glass science and glass technology. However, in most commercial glasses both properties are not compatible. In this work, colorless and transparent xAl2O3-(100-x)SiO2 glasses (30 ≤ x ≤ 60) were fabricated by the aerodynamic levitation technique. The elastic moduli and Vickers hardness monotonically increased with an increase in the atomic packing density as the Al2O3 content increased. Although a higher atomic packing density generally enhances crack formation in conventional oxide glasses, the indentation cracking resistance increased by approximately seven times with an increase in atomic packing density in binary Al2O3-SiO2 glasses. In particular, the composition of 60Al2O3 • 40SiO2 glass, which is identical to that of mullite, has extraordinary high cracking resistance with high elastic moduli and Vickers hardness. The results indicate that there exist aluminosilicate compositions that can produce hard and damage-tolerant glasses.
Liposomes and hyperthermia in mice: increased tumor uptake and therapeutic efficacy of doxorubicin in sterically stabilized liposomes. (1994)

We have shown that sterically stabilized (Stealth) liposomes (SL), can accumulate in the extracellular space within tumors, and may improve pharmacokinetics and therapeutic efficacy of encapsulated doxorubicin (SL-DOX). When SL-DOX were incubated in vitro at different temperatures with 50% bovine serum, approximately 20% of the encapsulated DOX was released at 42 degrees C within 1 min, compared with less than 1% DOX released at 37 degrees C. In vivo, mice were implanted s.c. with C-26 colon carcinoma in both flanks to produce matched tumors 6-10 mm in diameter. Topical hyperthermia treatment consisting of 42 degrees C minimum tumor temperature for 30 min was applied with a microwave device to the tumor on one side only at 1 h after i.v. injection of SL-DOX or free DOX. Tumor DOX concentration in the group which was given injections of SL-DOX and sacrificed 2 h after drug injection was 1.5-fold higher compared with the nonheated tumor in mice given injections of SL-DOX. At 24 h after injection the thermal enhancement ratio for DOX accumulation in tumor remained at 1.5. In addition, there was a 15-fold higher concentration of DOX in tumor from the group given injections of SL-DOX compared to mice given injections of free doxorubicin. To assess therapeutic efficacy, we treated mice with hyperthermia for 15 min either at 1, or at 24 h or at both time points after injection of SL-DOX. We have found that the life span of the group of mice treated with SL-DOX and two 15-min hyperthermia treatments increased 51% compared with control groups receiving the same dosage of SL-DOX but without hyperthermia, and 59% compared to those receiving two hyperthermia treatments but with free DOX. A single hyperthermia treatment either at 1 or 24 h was less effective in increasing life span compared with two treatments, but all groups treated with SL-DOX and single hyperthermia were still superior to the control groups, showing a 27-38% increase in life span.
Antiplatelet and Anticoagulation Therapy for Acute Coronary Syndromes (2014)

The past 2 decades have witnessed the introduction and demise of several different antithrombotic medications for acute coronary syndromes. Part of the assessment of these compounds has been their effect on thrombotic events relative to the degree of increase in bleeding events. This review will outline the data supporting various antiplatelet and anticoagulant therapies and their combinations in patients with acute coronary syndromes and related disorders in both the acute and chronic phases of therapy.
YdiV: a dual function protein that targets FlhDC for ClpXP‐dependent degradation by promoting release of DNA‐bound FlhDC complex (2012)

YdiV is an EAL-like protein that acts as a post-transcriptional, negative regulator of the flagellar master transcriptional activator complex, FlhD(4)C(2), in Salmonella enterica to couple flagellar gene expression to nutrient availability. Mutants defective in ClpXP protease no longer exhibit YdiV-dependent inhibition of FlhD(4)C(2)-dependent transcription under moderate YdiV expression conditions. ClpXP protease degrades FlhD(4)C(2), and this degradation is accelerated in the presence of YdiV. YdiV complexed with both free and DNA-bound FlhD(4)C(2); and stripped FlhD(4)C(2) from DNA. A L22H substitution in FlhD was isolated as insensitive to YdiV inhibition. The FlhD L22H substitution prevented the interaction of YdiV with free FlhD(4)C(2) and the ability of YdiV to release FlhD(4)C(2) bound to DNA. These results demonstrate that YdiV prevents FlhD(4)C(2)-dependent flagellar gene transcription and acts as a putative adaptor to target FlhD(4)C(2) for ClpXP-dependent proteolysis. Our results suggest that YdiV is an EAL-like protein that has evolved from a dicyclic-GMP phosphodiesterase into a dual-function regulatory protein that connects flagellar gene expression to nutrient starvation.
Multigene Families in Trypanosoma cruzi and Their Role in Infectivity (2012)

The Trypanosoma cruzi genome contains the most widely expanded content (∼12,000 genes) of the trypanosomatids sequenced to date. This expansion is reflected in the high number of repetitive sequences and particularly in the large quantity of genes that make up its multigene families. Recently it was discovered that the contents of these families vary between phylogenetically unrelated strains. We review the basic characteristics of trans-sialidases and mucins as part of the mechanisms of immune evasion of T. cruzi and as ligands and factors involved in the cross talk between the host cell and the parasite. We also show recently published data describing two new multigene families, DGF-1 and MASP, that form an important part of the scenario representing the complex biology of T. cruzi.
Fabrication and characterization of high-quality-factor silicon nitride nanobeam cavities (2011)

We present the fabrication and characterization of high-quality-factor (Q) Si3N4 photonic crystal nanobeam cavities at visible wavelengths for coupling to nitrogen-vacancy centers in a cavity QED system. Confocal microphotoluminescence analysis of the nanobeam cavities demonstrates quality factors up to Q ~ 55,000, which are limited by the resolution of our grating spectrometer. This is a 1-order-of-magnitude improvement over previous SiNx cavities at this important wavelength range. We also demonstrate coarse tuning of cavity resonances across 600-700 nm by lithographically scaling the size of fabricated devices.