gebhart/patrepeval huggingface dataset:
Embryonic stem cells differentiate in vitro to endothelial cells through successive maturation steps (1996)

The mechanisms involved in the regulation of vasculogenesis still remain unclear in mammals. Totipotent embryonic stem (ES) cells may represent a suitable in vitro model to study molecular events involved in vascular development. In this study, we followed the expression kinetics of a relatively large set of endothelial-specific markers in ES-derived embryoid bodies (EBs). Results of both reverse transcription-polymerase chain reaction and/or immunofluorescence analysis show that a spontaneous endothelial differentiation occurs during EBs development. ES-derived endothelial cells express a full range of cell lineage-specific markers: platelet endothelial cell adhesion molecule (PECAM), Flk-1, tie-1, tie-2, vascular endothelial (VE) cadherin, MECA-32, and MEC-14.7. Analysis of the kinetics of endothelial marker expression allows the distinction of successive maturation steps. Flk-1 was the first to be detected; its mRNA is apparent from day 3 of differentiation. PECAM and tie-2 mRNAs were found to be expressed only from day 4, whereas VE-cadherin and tie-1 mRNAs cannot be detected before day 5. Immunofluorescence stainings of EBs with antibodies directed against Flk-1, PECAM, VE-cadherin, MECA-32, and MEC-14.7 confirmed that the expression of these antigens occurs at different steps of endothelial cell differentiation. The addition of an angiogenic growth factor mixture including erythropoietin, interleukin-6, fibroblast growth factor 2, and vascular endothelial growth factor in the EB culture medium significantly increased the development of primitive vascular-like structures within EBs. These results indicate that this in vitro system contains a large part of the endothelial cell differentiation program and constitutes a suitable model to study the molecular mechanisms involved in vasculogenesis.
Recent advances in plant tissue culture of the halophyte Leymus chinensis T. (Poaceae) (2011)

Halophyte Leymus chinensis (Trin.), a perennial grass in the Poaceae family, is widely distributed in Northern China, Mongolia and Siberia. Due to its intrinsic stress adaptation and agronomic properties, this grass has been used in artificial grassland construction, ecological environment improvement, grazing, and forage production. However, low fecundity and seed-set are huge problem facing this species, so that physiological trait improvement becomes more indispensable and vital. Plant tissue culture is a rapid way of achieving plant genetic breeding; whereas an efficient tissue culture and in-vitro plant regeneration system is the precondition. The goal of this review is to summarize the influence of some factors affecting callus induction, optimization of callus status and plant regeneration to improve in-vitro plant regeneration conditions of L. chinensis. This report would help optimize callus induction and plant regeneration conditions and provide the basis for genetic improvement of traits in this grass.

	 

	Key words: Leymus chinensis, plant tissue culture, halophyte, genotype, explants type, medium composition.
Formation Mechanism of Amorphous TiO2 Spheres in Organic Solvents. 1. Roles of Ammonia (2008)

The roles of ammonia in the formation of monodisperse amorphous TiO2 spheres through hydrolysis of titanium butoxide in its homogeneous solution of a mixed solvent of butanol/acetonitrile with ammonia have been investigated. The hydrolysis of titanium butoxide was originally so fast as to finish almost instantly within a few seconds even in the absence of ammonia that the effect of ammonia as an accelerator of the hydrolysis of titanium butoxide was not observed. Instead, ammonia was found to play key roles as an accelerator of the precipitation of the hydrolysis product, as an inhibitor of the coagulation of the growing hydroxide particles, and as a promoter for production of highly spherical particles. All of these effects are deemed to be mainly due to the reduced affinity between butanol and the hydroxide monomer joined with ammonia through hydrogen bonding. In addition, ammonia was revealed to work as a powerful accelerator of the condensation of the hydroxide monomer, which proceeds not in the solution phase but only in the individual particles during aging after precipitation. The accelerated condensation by ammonia was explained in terms of the promoted release of hydroxide ion of the monomer in each particle by the nucleophilic coordination of ammonia to its titanium ion. These mechanisms widely applicable to other sol−gel systems of transition metal oxides as well have been discussed in comparison with silica particle systems.
Quantitative Estimation about the Influence of Various Factors on the Smelting Reduction Rate of Cr-ore by Top-and-bottom Blowing Converter (1988)

Smelting reduction rate of Cr-ore in top-and-bottom blowing converter was quantitatively estimated by 600 kg scale fundamental experiment and 100 t scale industrial furnace (LD-OB). The change of Cr oxide in slag with time showed zero-order reaction kinetics and the following points were clarified on the reduction rate. 1) The rate was in propotion to ε0.5 and L1.0, where ε was stirring energy, L was diameter of furnace. 2) The activation energy was about 210 kJ/mol. 3) The rate were not cleary affected by the kind of Cr-sources, namely, pellets, briquettes of powder ore, carbon containing briquettes and lump ore. 4) The rate increased with the increase in amount of carbon for reduction and the decrease of [%Cr]. According to these results, it was posturated that the transfer of Cr oxide in molten slag phase to the carbon-slag and the metal-slag interfaces was the rate controlling step. The reduction rate was formulated as a function of ε., L, [%Cr], temperature and the containing ratio of carbon for reduction in slag. The results of calculation showed fairly good agreement with the observed values.
A Semi-high-throughput Imaging Method and Data Visualization Toolkit to Analyze <em>C. elegans</em> Embryonic Development (2019)

C. elegans is the premier system for the systematic analysis of cell fate specification and morphogenetic events during embryonic development. One challenge is that embryogenesis dynamically unfolds over a period of about 13 h; this half day-long timescale has constrained the scope of experiments by limiting the number of embryos that can be imaged. Here, we describe a semi-high-throughput protocol that allows for the simultaneous 3D time-lapse imaging of development in 80–100 embryos at moderate time resolution, from up to 14 different conditions, in a single overnight run. The protocol is straightforward and can be implemented by any laboratory with access to a microscope with point visiting capacity. The utility of this protocol is demonstrated by using it to image two custom-built strains expressing fluorescent markers optimized to visualize key aspects of germ-layer specification and morphogenesis. To analyze the data, a custom program that crops individual embryos out of a broader field of view in all channels, z-steps, and timepoints and saves the sequences for each embryo into a separate tiff stack was built. The program, which includes a user-friendly graphical user interface (GUI), streamlines data processing by isolating, pre-processing, and uniformly orienting individual embryos in preparation for visualization or automated analysis. Also supplied is an ImageJ macro that compiles individual embryo data into a multi-panel file that displays maximum intensity fluorescence projection and brightfield images for each embryo at each time point. The protocols and tools described herein were validated by using them to characterize embryonic development following knock-down of 40 previously described developmental genes; this analysis visualized previously annotated developmental phenotypes and revealed new ones. In summary, this work details a semi-high-throughput imaging method coupled with a cropping program and ImageJ visualization tool that, when combined with strains expressing informative fluorescent markers, greatly accelerates experiments to analyze embryonic development.
Iron regulatory protein 1 as a sensor of reactive oxygen species (2005)

Iron regulatory proteins (IRP1 and 2) function as translational regulators that coordinate the cellular iron metabolism of eukaryotes by binding to the mRNA of target genes such as the transferrin receptor or ferritin. In addition to IRP2, IRP1 serves as sensor of reactive oxygen species (ROS). As iron and oxygen are essential but potentially toxic constituents of most organisms, ROS-mediated modulation of IRP1 activity may be an important regulatory element in dissecting iron homeostasis and oxidative stress. The responses of IRP1 towards reactive oxygen species are compartment-specific and rather complex: H2O2 activates IRP1 via a signaling cascade that leads to upregulation of the transferrin receptor and cellular iron accumulation. Contrary, superoxide inactivates IRP1 by a direct chemical attack being limited to the intracellular compartment. In particular, activation of IRP1 by H2O2 has established a new regulatory link between inflammation and iron metabolism with new clinical implications. This mechanism seems to contribute to the anemia of chronic disease and inflammation-mediated iron accumulation in tissues. In addition, the cytotoxic side effects of redox-cycling anticancer drugs such as doxorubicin may involve H2O2-mediated IRP1 activation. These molecular insights open up new therapeutic strategies for the clinical management of chronic inflammation and drug-mediated cardiotoxicity.
Image-based end-to-end EO system performance modeling as a design and optimization tool (2018)

Image-based Electro-Optical system simulation including an end-to-end performance test is a powerful tool to characterize a camera system before it has been built. In particular, it can be used in the design phase to make an optimal trade-off between performance on the one hand and SWaPC (Size, Weight, Power and Cost) criteria on the other. During the design process, all components can be simulated in detail, including optics, sensor array properties, chromatic and geometrical lens corrections, signal processing, and compression. Finally, the overall effect on the outcome can be visualized, evaluated and can be optimized. In this study, we developed a detailed model of the CMOS camera system imaging chain (including scene, image processing and display). The model simulation was evaluated by comparing simulated (display) imagery with recorded image using both physical (SNR) and psychophysical measures (acuity and contrast thresholds using the TOD-methodology with a human observer) for a range of conditions: different light levels, moving stimuli with different speeds, movies and single frames. The performance analysis show that the model simulations are largely in line with the recorded sensor images with some minor deviations. The result of the study is a detailed, validated and powerful sensor performance prediction model. This project has received funding from the Electronic Component Systems for European Leadership Joint Undertaking.
Molecular Cloning of Mouse Type 2 and Type 3 Inositol 1,4,5-Trisphosphate Receptors and Identification of a Novel Type 2 Receptor Splice Variant (2005)

We isolated cDNAs encoding type 2 and type 3 inositol 1,4,5-trisphosphate (IP(3)) receptors (IP(3)R2 and IP(3)R3, respectively) from mouse lung and found a novel alternative splicing segment, SI(m2), at 176-208 of IP(3)R2. The long form (IP(3)R2 SI(m2)(+)) was dominant, but the short form (IP(3)R2 SI(m2)(-)) was detected in all tissues examined. IP(3)R2 SI(m2)(-) has neither IP(3) binding activity nor Ca(2+) releasing activity. In addition to its reticular distribution, IP(3)R2 SI(m2)(+) is present in the form of clusters in the endoplasmic reticulum of resting COS-7 cells, and after ATP or Ca(2+) ionophore stimulation, most of the IP(3)R2 SI(m2)(+) is in clusters. IP(3)R3 is localized uniformly on the endoplasmic reticulum of resting cells and forms clusters after ATP or Ca(2+) ionophore stimulation. IP(3)R2 SI(m2)(-) does not form clusters in either resting or stimulated cells. IP(3) binding-deficient site-directed mutants of IP(3)R2 SI(m2)(+) and IP(3)R3 fail to form clusters, indicating that IP(3) binding is involved in the cluster formation by these isoforms. Coexpression of IP(3)R2 SI(m2)(-) prevents stimulus-induced IP(3)R clustering, suggesting that IP(3)R2 SI(m2)(-) functions as a negative coordinator of stimulus-induced IP(3)R clustering. Expression of IP(3)R2 SI(m2)(-) in CHO-K1 cells significantly reduced ATP-induced Ca(2+) entry, but not Ca(2+) release, suggesting that the novel splice variant of IP(3)R2 specifically influences the dynamics of the sustained phase of Ca(2+) signals.
Microstructural Effects on Thermal Conductivity of Uranium Oxide: A 3D Multi-Physics Simulation (2013)

Transport mechanisms, such as mass and heat transfer, are critical to the efficiency and the reliability of nuclear fuels such as uranium oxide. These properties can be significantly affected by the microstructure of the material. This paper looks into the effects of grain boundary (GB) Kapitza resistance on the overall heat conductivity of UO2 using a 3-D finite element model with microstructurally explicit information. The model developed is created with a 3-D reconstruction of the microstructure of depleted uranium samples performed using serial sectioning techniques with Focused Ion Beam (FIB) and Electron Backscattering Diffraction (EBSD). The model treats grain bulks, GBs and triple junctions using elements of different dimensionalities, and it is thus capable of incorporating information of all three entities in one model while keeping a manageable computational cost. Furthermore, the properties of these microstructural entities are characterized by misorientation angles and Coincident Site Lattice (CSL) models, which provide a framework to assign spatially dependent thermal and mass transfer properties based on the location and connectivity of these entities in actual microstructures. Coupling between heat transfer and mass transfer of fission products is also taken into account in the study, to make it a multi-physics model capable of following the evolution of thermal performance as fission products are produced. These simulations can provide input and insight into the fuel pellet behaviors at the initial stage of power generation when burnups are low.
Putting Recommendations on the Map -- Visualizing Clusters and Relations (2009)

For users, recommendations can sometimes seem odd or counterintuitive. Visualizing recommendations can remove some of this mystery, showing how a recommendation is grouped with other choices. A drawing can also lead a user's eye to other options. Traditional 2D-embeddings of points can be used to create a basic layout, but these methods, by themselves, do not illustrate clusters and neighborhoods very well. In this paper, we propose the use of geographic maps to enhance the definition of clusters and neighborhoods, and consider the effectiveness of this approach in visualizing similarities and recommendations arising from TV shows and music selections. All the maps referenced in this paper can be found in http://www.research.att.com/~volinsky/maps
A CSRR Loaded MIMO Antenna System for ISM Band Operation (2013)

A 2 × 2 (four-element) multiple-input multiple-output (MIMO) patch antenna system is designed and fabricated for a 2.45-GHz ISM band operation. It uses complementary split-ring resonator (CSRR) loading on its ground plane for antenna miniaturization. This reduces the single-element antenna size by 76%. The total board size of the proposed MIMO antenna system, including the GND plane is 100 × 50 × 0.8 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> , while the single-patch antenna element has a size of 14 × 18 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . The antenna is fabricated and tested. Measured results are in good agreement with simulations. A minimum measured isolation of 10 dB is obtained given the close interelement spacing of 0.17λ. The maximum measured gain for a single operating element is -0.8 dBi.
Combined Disruptions of the Ribosomal Protein s19 and Pim1 Kinase Genes Are Associated with Increased Myeloid/Erythroid Cellularity and Reduced Apoptosis (2008)

Abstract Diamond Blackfan anemia (DBA) is characterized by reduced proliferation and increased apoptosis of erythroid progenitors. Approximately 25% of patients are heterozygous for mutations in the gene encoding ribosomal protein S19 (RPS19). The molecular mechanisms behind DBA remain unclear and RPS19 was recently shown to interact with PIM1 kinase. To elucidate the phenotypic and cellular effects of this interaction we generated mice strains with the genotypes Rps19 +/− Pim1 +/+; Rps19 +/+ Pim1 −/− and Rps19 +/− Pim1 −/−. We analyzed the mice for peripheral blood and bone marrow parameters as well as apoptotic markers in primary bone marrow cells. The double mutant mice (Rps19 +/− Pim1 −/−) show normal growth and life span with increased white and red blood cell counts when compared to wild type, Rps19 heterozygous, and Pim1 null mice, respectively. Analysis of proteins in bone marrow cells shows that the combination of Rps19 insufficiency and Pim1 deficiency is associated with increased levels of Stat5 as well as the anti-apoptotic markers Mcl-1, Bcl-2 and Bcl-XL. The pro-apoptotic markers Bak, Caspase-3 and p21 show decreased levels whereas p53 remains unchanged. These findings suggest a co-operative effect of Rps19 insufficiency and Pim1 deficiency on cell proliferation in murine hematopoiesis.
Acoustic streaming of microparticles using graphene-based interdigital transducers (2021)

Surface acoustic wave (SAW) devices offer many benefits in chemistry and biomedicine, enabling precise manipulation of micro-droplets, mixing of liquids by acoustic streaming and pumping of liquids in enclosed channels, while presenting a cost-effective and easy fabrication and integration with electronic devices. In this work, we present microfluidic devices which use graphene-based interdigital transducers (IDTs) to generate SAWs with a frequency of 100 MHz and an amplitude of up to 200 pm, which allow us to manipulate microparticle solutions by acoustic streaming. Due to the negligible mass loading of the piezoelectric surface by graphene, the SAWs generated by these devices have no frequency shift, typically observed when metal IDTs are used.
Phonemic Information Transmitted by a Multichannel Electrotactile Speech Processor (1988)

A wearable electrotactile speech processor was evaluated in a study with seven normally hearing and four hearing-impaired subjects. The processor estimated the fundamental frequency, the second-formant frequency, and amplitude of the acoustic speech signal. These parameters were presented as a pattern of electrical pulses applied to eight electrodes positioned over the digital nerve bundles on one hand. The device was shown to provide useful information for the recognition of phonemes in closed sets of words using tactile information alone. The device also supplemented lipreading to improve the recognition of open-set words. The recognition of duration and first- and second-formant frequencies of vowels and the recognition of voicing and manner of consonants were improved over recognition with lipreading alone. Recognition of final consonants was improved more than recognition of initial consonants. These results indicate that the device may be useful to both severely and profoundly hearing-impaired people.
Atomic layer deposition of cobalt oxide on oxide substrates and low temperature reduction to form ultrathin cobalt metal films (2018)

The authors report the deposition of 4.5-nm-thick cobalt (II) oxide on SiO2/Si(001) and MgO(001) substrates at 180–270 °C by atomic layer deposition using bis(N-tert-butyl-N′-ethylpropionamidinato) cobalt (II) and water as coreactants. The resulting CoO film is smooth and carbon-free. CoO can be reduced to Co metal using hydrogen or deuterium gas at 400–500 °C in a vacuum furnace, but the high temperature processing causes dewetting, leading to discontinuous Co metal islands rather than continuous films. Two low temperature (∼200 °C) reduction methods are reported: deuterium atom reduction and the use of an O-scavenging Al metal film. The low temperature methods can suppress dewetting to a large extent, and the resulting metallic cobalt film is smooth and continuous.
Melting point depression study of polyacrylonitrile (1960)

Abstract Melting point depressions were determined by dilatometric and microscopic measurements for polyacrylonitrile in dimethylformamide and in γ‐butyrolactone. These data give for the glass transition and melting point of the pure polymer 104 and 317°C., respectively. Both the heat and entropy of fusion are low. This suggests that the high melting point of polyacrylonitrile is due to its extended molecular conformation rather than to strong attractions between the molecules in the crystalline state. Average crystallization rates measured dilatometrically indicate that the optimum temperature for crystallization from solutions in the concentration range 17–27% is only 21°C. above the glass transition temperature. On either side of the optimum temperature the rate decreases sharply, and although crystallization then continues for a longer time the amount of crystallinity finally developed is less. For 15–20% solutions the viscosity increases abruptly as the glass transition is approached, and decreases rapidly at about 25°C. below the true melting point. The shear dependence is large at low temperatures but appears to vanish at 25°C. below the melting point. As the temperature is raised a narrow region is observed for each concentration in which the viscosity exhibits an anomalous increase. These temperatures stand in good agreement with the optimum temperature for crystallization as determined dilatometrically. The foregoing observations suggest the presence of molecular aggregates which are held together by regions of small and imperfect crystallites. In addition to the low entropy of fusion, additional evidence for the extended shape of polyacrylonitrile molecules is provided by estimates based on dilute solution measurements. The interaction between nearest‐neighbor nitrile dipoles was investigated in an attempt to correlate large unperturbed dimensions with the molecular structure. This dipolar interaction is repulsive, and its magnitude depends upon the rotational position of the two nitrile groups. By adding a further contribution representing the steric repulsion the total rotational potential is estimated for isotactic and syndiotactic sequences. The dipolar interaction is much larger than the steric repulsion, and the rotation about successive chain bonds must be cooperative to avoid certain high energy conformations. This requirement probably explains the low flexibility and high extension of polyacrylonitrile molecules. The total rotational potential for an isotactic sequence favors the same helical conformation observed in crystalline isotactic polyolefins, while for a syndiotactic sequence some type of helical conformation appears to be preferred rather than the extended planar zigzag.