gebhart/patrepeval huggingface dataset:
Insertion of a Yop translocation pore into the macrophage plasma membrane by <i>Yersinia enterocolitica</i>: requirement for translocators YopB and YopD, but not LcrG (1999)

The Yersinia survival strategy is based on its ability to inject effector Yops into the cytosol of host cells. Translocation of these effectors across the eukaryotic cell membrane requires YopB, YopD and LcrG, but the mechanism is unclear. An effector polymutant of Y. pseudotuberculosis has a YopB-dependent contact haemolytic activity, indicating that YopB participates in the formation of a pore in the cell membrane. Here, we have investigated the formation of such a pore in the plasma membrane of macrophages. Infection of PU5-1.8 macrophages with an effector polymutant Y. enterocolitica led to complete flattening of the cells, similar to treatment with the pore-forming streptolysin O from Streptococcus pyogenes. Upon infection, cells released the low-molecular-weight marker BCECF (623 Da) but not the high-molecular-weight lactate dehydrogenase, indicating that there was no membrane lysis but, rather, insertion of a pore of small size into the macrophage plasma membrane. Permeation to lucifer yellow CH (443 Da) but not to Texas red-X phalloidin (1490 Da) supported this hypothesis. All these events were found to be dependent not only on translocator YopB as expected but also on YopD, which was required equally. In contrast, LcrG was not necessary. Consistently, lysis of sheep erythrocytes was also dependent on YopB and YopD, but not on LcrG.
Examining correlates of treatment satisfaction for injectable insulin in type 2 diabetes: lessons learned from a clinical trial comparing biphasic and basal analogues (2007)

By examining predictors independently, significant relationships were identified. However, not all findings remained significant when examined in combination with each other. Thus, to more accurately characterize the impact of factors on treatment satisfaction, a more comprehensive approach may be necessary. By improving patient treatment satisfaction, the efficacy of treatments, as well as critical treatment outcomes such as compliance and cost of care should be improved.
Biometry and intraocular lens power calculation (2007)

Postoperative refractive results depend on the precision of multiple factors and measurements. The element with the highest variability and inaccuracy is, ultimately, going to determine the outcome. By understanding the advantages and limitations of the current technology, it is possible to consistently achieve highly accurate results.
Synthesis and reactivity of a ferrocene-derived PCP-pincer ligand (2002)

The 1,3-bis(diphosphinomethyl)ferrocene 3 readily reacts with [(C2H4)2RhCl]2 to form an equilibrating pair of diastereomers 8a and 8b by C-H insertion into the ferrocene.
Morphology and growth, tumorigenicity, and cytogenetics of human neuroblastoma cells in continuous culture. (1973)

Summary Continuous cell lines, SK-N-SH and SK-N-MC, were established in cell culture from human metastatic neuroblastoma tissue and maintained in vitro for 1 to 2 years. SK-N-SH comprises two morphologically distinctive cell types, a small spiny cell and a large epithelioid cell. SK-N-MC is composed of small fibroblast-like cells with scant cytoplasm. In monolayer culture both cell lines form disoriented growth patterns and reach high saturation densities. Population-doubling times were 44 and 32 hr for SK-N-SH and SK-N-MC, respectively. Inoculum levels of 10 7 cells of both lines produced tumors confirmed by histopathological examination, at frequencies of 30 to 40% in cheek pouches of conditioned Syrian hamsters. SK-N-SH cells are characterized by high dopamine-β-hydroxylase activity while SK-N-MC cells have no detectable activity. However, for SK-N-MC but not SK-N-SH, the presence of intracellular catecholamine was indicated by formaldehyde-induced fluorescence. The lines are near-diploid with several chromosomal markers; SK-N-MC cells contain double- minute chromosomes. Growth, biochemical, and cytogenetic properties confirmed that the lines comprise malignant cells of neurogenic origin.
Hydrogen in amorphous and microcrystalline silicon films prepared by hydrogen dilution (1996)

Hydrogen incorporation in silicon layers prepared by plasma-enhanced chemical-vapor deposition using silane dilution by hydrogen has been studied by infrared spectroscopy (IR) and elastic recoil detection analysis (ERDA). The large range of silane dilution investigated can be divided into an amorphous and a microcrystalline zone. These two zones are separated by a narrow transition zone at a dilution level of 7.5%; here, the structure of the material cannot be clearly identified. The films in/near the amorphous/microcrystalline transition zone show a considerably enhanced hydrogen incorporation. Moreover, comparison of IR and ERDA and film stress measurements suggests that these layers contain a substantial amount of molecular hydrogen probably trapped in microvoids. In this particular case the determination of the total H content by IR spectroscopy leads to substantial errors. At silane concentrations below 6%, the hydrogen content decreases sharply and the material becomes progressively microcrystalline. The features observed in the IR-absorption modes can be clearly assigned to mono- and/or dihydride bonds on (100) and (111) surfaces in silicon crystallites. The measurements presented here constitute a further indication for the validity of the proportionality constant of Shanks et al. [Phys. Status Solidi B 110, 43 (1980)], generally used to estimate the hydrogen content in ‘‘conventional’’ amorphous silicon films from IR spectroscopy; additionally, they indicate that this proportionality constant is also valid for the microcrystalline samples.
Association of Type 2 Diabetes With Cyclooxygenase-Mediated Inflammation and Oxidative Stress in an Elderly Population (2004)

This is the first study to show that type 2 diabetes in elderly men is related to COX-mediated inflammation, reflected by enhanced prostaglandin formation. The high levels of cytokine-mediated acute-phase proteins observed in men with diabetes appear to be related to obesity and increased fasting insulin. The results further suggest that the appearance of chronic inflammation is an early process in the pathogenesis of diabetes, whereas oxidative injury may be a later process, possibly related to inflammation.
Prevention of infection in xenotransplantation: Designated pathogen‐free swine in the safety equation (2020)

Post-transplantation infections are common. In immunosuppressed human xenograft recipients, infection is most likely to be due to the same pathogens seen in human allotransplantation. However, organisms derived from swine and transmitted with xenografts have the potential to cause novel infections in xenograft recipients. The specific organisms likely to cause infection or "xenosis" are unknown but are postulated to be like those causing infection in allograft recipients. On this basis, theoretical exclusion criteria have been developed to guide the development of source animal herds. Herds developed based on the exclusion of potential human pathogens have been termed "designated pathogen-free" (DPF). Lists of potential pathogens will require revision with changing epidemiology of infection in swine worldwide and clinical experience. Development of new microbiological assays is required both for animal screening and in clinical diagnosis should infections occur. Genetic modifications of swine have the potential to eliminate certain infectious agents such as the porcine endogenous retrovirus; infectious complications of such modifications have not been observed. Unexpected, off target effects of genetic modifications require further study. Monitoring for infection in asymptomatic recipients is important to define infectious risks which are unknown in the absence of clinical trials data. Advanced microbiological techniques may be applied to diagnose and prevent infection in xenograft recipients.
Development and application of physics-based compact models for high-impedance electromagnetic surfaces integrated in a power plane configuration (2004)

Physics-based compact models for the unit cell of power planes with integrated high-impedance electromagnetic surfaces are developed and cascaded in a two-dimensional array to build full models for large and multi-layer power planes. The compact model offers a significant advantage to the FEM-based electromagnetic simulation as it reduces the analysis time of a typical 10 cm/spl times/10 cm power plane from 40 hours to less than 10 seconds. The proposed compact model is also used to explore the noise mitigation at different locations of the power plane and in combination with RC decoupling for broadband noise mitigation.
The insulated gate tunnel junction triode (1965)

The gate modulated voltage breakdown of the drain diode in the MOS transistor is considered and shown to be direct electric field control of a reverse biased surface <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">p+-n</tex> junction. A structure designed to isolate this effect has been suggested by Atalla and experimentally evaluated by Nathanson, et al., and by the authors. The mechanism of operation discussed involves the application of an external electric field normal to the surface of the highly doped side of the junction to produce direct field emission of carriers. The reverse biased low doped side of the junction then acts as a collector of the field-emitted carriers resulting in a net current flow across the junction. Using the Atalla structure, a model is presented and a quantitative theory is developed to explain and predict the device performance. It is found that the actual device may be represented as an MOS transistor in series with an "ideal" field-controlled tunnel junction, and that the performance of the actual device can never be better than that of the limiting MOS transistor. The theoretical characteristics of the ideal field-controlled tunnel junction are derived and found to agree closely with the experimental results. It is shown that, at the present time, the device is limited by the "ideal" tunnel junction region and not by the series MOS transistor.
Ultraviolet–ultraviolet dual‐cure process based on acrylate oxetane monomers (2002)

Abstract A dual‐cure process consisting of two subsequent ultraviolet‐initiated radical and cationic polymerizations was investigated. The process was studied with two acrylate oxetane monomers, one of them having a spacer between the two polymerizable moieties. It was shown by Fourier transform infrared (FTIR) that the first (radical) step was performed successfully for both systems. As for the second (cationic) step, only the monomer with the spacer was able to polymerize, allowing the crosslinking of the polyacrylic chains generated by the first step. The efficiency of the process was confirmed by differential scanning calorimetry because the glass‐transition temperatures of the cured films were −16 and + 34 °C after the first and second steps, respectively. The dual cure of this system was further analyzed by real‐time FTIR, which showed that 86% of the acrylate and 80% of the oxetane moieties were converted after 20 and 50 s of light exposure, respectively. © 2002 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 41: 469–475, 2003
The Use of Fractal Analysis and Photometry to Estimate the Accuracy of Bulbar Redness Grading Scales (2008)

Despite the generally strong linear associations between the physical characteristics of reference images in each scale, the scales themselves are not inherently accurate and are too different to allow for cross-calibration.
Genome Studies on Nematophagous and Entomogenous Fungi in China (2016)

The nematophagous and entomogenous fungi are natural enemies of nematodes and insects and have been utilized by humans to control agricultural and forestry pests. Some of these fungi have been or are being developed as biological control agents in China and worldwide. Several important nematophagous and entomogenous fungi, including nematode-trapping fungi (<i>Arthrobotrys oligospora</i> and <i>Drechslerella stenobrocha</i>), nematode endoparasite (<i>Hirsutella minnesotensis</i>), insect pathogens (<i>Beauveria bassiana</i> and <i>Metarhizium</i> spp.) and Chinese medicinal fungi (<i>Ophiocordyceps sinensis</i> and <i>Cordyceps militaris</i>), have been genome sequenced and extensively analyzed in China. The biology, evolution, and pharmaceutical application of these fungi and their interacting with host nematodes and insects revealed by genomes, comparing genomes coupled with transcriptomes are summarized and reviewed in this paper.
Recombinant Factor VIIa for Refractory Bleeding After Cardiac Surgery Secondary to Anticoagulation with the Direct Thrombin Inhibitor Lepirudin (2006)

A 56-year-old man with heparin-induced thrombocytopenia with thrombosis syndrome (HITTS) received anticoagulation with recombinant hirudin (lepirudin) for emergency coronary artery bypass graft (CABG) surgery and aortic valve replacement. The patient experienced life-threatening refractory bleeding that was successfully treated with recombinant factor VIIa. He had a history of infective endocarditis that resulted in severe aortic insufficiency, three-vessel coronary artery disease, and acute renal failure requiring hemodialysis. The patient was transferred from another hospital for the emergency surgery, but before his transfer, he developed HITTS secondary to therapeutic heparin for a deep vein thrombosis of the lower extremity. The presence of HITTS, the urgent nature of the case, and the availability of the direct thrombin inhibitor led the surgical team to select lepirudin for anticoagulation to facilitate cardiopulmonary bypass. After separation from cardiopulmonary bypass, the patient was in a coagulopathic state due to the inability to reverse the lepirudin and the slowed elimination of the drug secondary to inadequate renal function. As a result, the patient experienced excessive generalized oozing that was unresponsive to traditional therapies and blood product transfusions. Recombinant factor VIIa 35 microg/kg was given as rescue therapy. The bleeding slowed, which allowed placement of chest tubes and closing of the sternum. The patient was transferred to the intensive care unit in stable condition with no evidence of thrombosis in the freshly placed bypass grafts or on the bioprosthetic valve. Recombinant factor VIIa appears to be a suitable option as salvage therapy in patients with refractory bleeding secondary to anticoagulation with a direct thrombin inhibitor during cardiac surgery.
Megabase Chromatin Domains Involved in DNA Double-Strand Breaks in Vivo (1999)

The loss of chromosomal integrity from DNA double-strand breaks introduced into mammalian cells by ionizing radiation results in the specific phosphorylation of histone H2AX on serine residue 139, yielding a specific modified form named gamma-H2AX. An antibody prepared to the unique region of human gamma-H2AX shows that H2AX homologues are phosphorylated not only in irradiated mammalian cells but also in irradiated cells from other species, including Xenopus laevis, Drosophila melanogaster, and Saccharomyces cerevisiae. The antibody reveals that gamma-H2AX appears as discrete nuclear foci within 1 min after exposure of cells to ionizing radiation. The numbers of these foci are comparable to the numbers of induced DNA double-strand breaks. When DNA double-strand breaks are introduced into specific partial nuclear volumes of cells by means of a pulsed microbeam laser, gamma-H2AX foci form at these sites. In mitotic cells from cultures exposed to nonlethal amounts of ionizing radiation, gamma-H2AX foci form band-like structures on chromosome arms and on the end of broken arms. These results offer direct visual confirmation that gamma-H2AX forms en masse at chromosomal sites of DNA double-strand breaks. The results further suggest the possible existence of units of higher order chromatin structure involved in monitoring DNA integrity.
Altered calcium sensitivity of isometric tension in myocyte-sized preparations of porcine postischemic stunned myocardium. (1993)

Postischemic ventricular myocardial dysfunction, termed stunning, is characterized by a persistent but ultimately reversible depression of contractile function. The present study was undertaken to investigate the possibilities that reduced contractile force in stunning is due to a decrease in maximal tension-generating capability or to a decrease in the Ca2+ sensitivity of the myofilaments. The experiments combine an in vivo open-chest porcine heart model of stunning (n = 5) with in vitro measures of myocyte myofilament calcium sensitivity from these same hearts. Regional myocardial function in the left anterior descending coronary artery (LAD) perfusion bed of porcine hearts was measured with transmural ultrasonic crystals. The protocol was 45 minutes of low-flow LAD ischemia at 40% of control flow, followed by 30 minutes of postischemic reperfusion at control aerobic flow. Percent systolic wall thickening decreased to 8 +/- 5% of control during ischemia (p < 0.05) and returned to 38 +/- 8% of control in the postischemic stunned state (p < 0.05). Serial endocardial biopsies were obtained from the preischemic and postischemic myocardium in the LAD perfusion bed and from the aerobically perfused myocardium in the circumflex bed. The biopsies were mechanically disrupted, and myocyte-sized preparations of permeabilized myocardium were attached to a force transducer and a length-changing device to allow for direct measurement of steady-state tension-pCa (i.e., -log[Ca2+]) relations. The pCa for half-maximal activation of tension, i.e., pCa50, in LAD myocardium decreased from 5.88 +/- 0.05 before ischemia to 5.69 +/- 0.03 after ischemia (p < 0.05); however, maximal Ca(2+)-activated tension and the slope of the tension-pCa relation were unaffected by the ischemic episode.(ABSTRACT TRUNCATED AT 250 WORDS)
Atomic Layer Deposition of LiCoO<sub>2</sub>Thin-Film Electrodes for All-Solid-State Li-Ion Micro-Batteries (2013)

One of the remaining challenges in the field of portable electronics is the miniaturization of lithium-ion batteries. To prepare all-solidstate batteries with a sufficient high storage capacity it is vital to prepare high quality thin films for battery stacks on 3D-structured substrates. A remote plasma atomic layer deposition (ALD) process has therefore been developed for LiCoO 2 which can serve as a cathode material. A combination of CoCp 2 as cobalt precursor, LiO t Bu as lithium precursor and O 2 plasma as oxidant source was used to create super-cycles to deposit LiCoO 2 from Co 3 O 4 and Li 2 CO 3 cycles. The thin films were deposited at a temperature of 325 C and showed linear growth with a rate of 0.06 nm/cycle. After annealing the samples at 700 C for 6 minutes high temperature phase LiCoO 2 was obtained, as was demonstrated by XRD and Raman spectroscopy. A new procedure was proposed to obtain the composition of all three chemical elements in the LiCoO 2 films. Elastic Backscattering Spectroscopy (EBS) measurements turned out to be very convenient and reliable to obtain the quantities of all chemical elements, including lithium. Moreover, the ALD-deposited LiCoO 2 thin film electrodes were electrochemically characterized, revealing good electrochemical performance. To the best of our knowledge this paper provides the first evidence that electrochemically active LiCoO 2 can be deposited by ALD.
Self‐Assembly: A First Implementation of an Automated Reel‐to‐Reel Fluidic Self‐Assembly Machine (Adv. Mater. 34/2014) (2014)

On page 5942, H. O. Jacobs and co-workers develop an automated reel-to-reel assembly machine to assemble semiconductor dies on flexible substrates. The process is inspired by nature and uses a concept of directed self-assembly instead of conventional robotic pick-and-place. The machine is tailored to the fabrication of solid-state lighting panels that require the distribution and electrical connection of LEDs over large areas at low cost. At present, the process is able to assemble 15 000 chips per hour.
Human Embryonic Stem Cell–Derived Mesoderm-like Epithelium Transitions to Mesenchymal Progenitor Cells (2009)

Human embryonic stem cells (hESC) have the potential to produce all of the cells in the body. They are able to self-renew indefinitely, potentially making them a source for large-scale production of therapeutic cell lines. Here, we developed a monolayer differentiation culture that induces hESC (WA09 and BG01) to form epithelial sheets with mesodermal gene expression patterns (BMP4, RUNX1, and GATA4). These E-cadherin+ CD90low cells then undergo apparent epithelial-mesenchymal transition for the derivation of mesenchymal progenitor cells (hESC-derived mesenchymal cells [hES-MC]) that by flow cytometry are negative for hematopoietic (CD34, CD45, and CD133) and endothelial (CD31 and CD146) markers, but positive for markers associated with mesenchymal stem cells (CD73, CD90, CD105, and CD166). To determine their functionality, we tested their capacity to produce the three lineages associated with mesenchymal stem cells and found they could form osteogenic and chondrogenic, but not adipogenic lineages. The derived hES-MC were able to remodel and contract collagen I lattice constructs to an equivalent degree as keloid fibroblasts and were induced to express alpha-smooth muscle actin when exposed to transforming growth factor (TGF)-beta1, but not platelet derived growth factor-B (PDGF-B). These data suggest that the derived hES-MC are multipotent cells with potential uses in tissue engineering and regenerative medicine and for providing a highly reproducible cell source for adult-like progenitor cells.
3,5-Diaryl-4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) Dyes:  Synthesis, Spectroscopic, Electrochemical, and Structural Properties (1999)

This research was undertaken to obtain new “BODIPY” dyes that fluoresce at relatively long wavelengths. The title compounds 1a−e were prepared via a divergent route involving Suzuki couplings of arylboronic acids to N-tert-butoxycarbonyl-4-bromopyrrole 2, condensation of the products with an acid chloride, and incorporation of the boron difluoride entity. Two alkyl-substituted systems 7a and 7b were also prepared for comparison; the critical difference between structures 1 and 7 is that the former have an aryl group attached to each pyrrole nucleus whereas the latter only have alkyl substituents on that same ring. UV absorption and fluorescence emission data were compared for compounds 1 and 7. Absorption and fluorescence emission maxima for compounds 1 occur at higher wavelengths than for compounds 7, and the Stokes shifts for the aryl-substituted compounds 1 are larger than for the alkyl-substituted compounds 7. Fluorescence quantum yields measured for compounds 1 are less than for compounds 7, and possible reasons for this are outlined. Other physical data for the compounds were also collected. Oxidation and reduction potentials of the systems were obtained from cyclic voltammetry experiments, and a single-crystal X-ray structure determination was performed for the bisnaphthyl-substituted compound 1b.