gebhart/patrepeval huggingface dataset:
Data from MYC-Driven Tumorigenesis Is Inhibited by WRN Syndrome Gene Deficiency (2023)

&lt;div&gt;Abstract&lt;p&gt;MYC-induced DNA damage is exacerbated in WRN-deficient cells, leading to replication stress and accelerated cellular senescence. To determine whether WRN deficiency impairs MYC-driven tumor development, we used both xenograft and autochthonous tumor models. Conditional silencing of WRN expression in c-MYC overexpressing non–small cell lung cancer xenografts impaired both tumor establishment and tumor growth. This inhibitory effect of WRN knockdown was accompanied by increased DNA damage, decreased proliferation, and tumor necrosis. In the Eμ-Myc mouse model of B-cell lymphoma, a germline mutation in the helicase domain of Wrn (Wrn&lt;sup&gt;Δhel/Δhel&lt;/sup&gt;) resulted in a significant delay in emergence of lethal lymphomas, extending tumor-free survival by more than 30%. Analysis of preneoplastic B cells from Eμ-Myc Wrn mutant mice revealed increased DNA damage, elevation of senescence markers, and decreased proliferation in comparison with cells from age-matched Eμ-Myc mice. Immunohistochemical and global gene expression analysis of overt Eμ-Myc Wrn&lt;sup&gt;Δhel/Δhel&lt;/sup&gt; lymphomas showed a marked increase in expression of the CDK inhibitor, p16&lt;sup&gt;Ink4a&lt;/sup&gt;, as well as elevation of TAp63, a known mediator of senescence. Collectively, these studies show that in the context of Myc-associated tumorigenesis, loss of Wrn amplifies the DNA damage response, both in preneoplastic and neoplastic tissue, engaging activation of tumor suppressor pathways. This leads to inhibition of tumor growth and prolonged tumor-free survival. Targeting WRN or its enzymatic function could prove to be an effective strategy in the treatment of MYC-associated cancers. &lt;i&gt;Mol Cancer Res; 10(4); 535–45. ©2012 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Sequential Knowledge Transfer in Teacher-Student Framework Using Densely Distilled Flow-Based Information (2018)

This paper proposes an iterative sequential knowledge transfer (KT) technique suitable for teacher-student framework (TSF)-based image classification when a state-of-the-art residual network (ResNet) is used for the TSF. To this end, we first extracted densely distilled knowledge in terms of the flow between the layers in the teacher ResNet. Subsequently, we iteratively and sequentially trained the student ResNet using the densely extracted flow-based teacher information. When using the proposed method, the trained student ResNet exhibited better performance in terms of classification accuracy and fast learning than the existing TSF-based KT methods considered in this study.
Direct Quantification of Serum Protein Interactions with PEGylated Micelle Nanocarriers (2023)

A large repertoire of nanocarrier (NC) technologies exists, each with highly specified advantages in terms of targetability, stability, and immunological inertness. The characterization of such NC properties within physiological conditions is essential for the development of optimized drug delivery systems. One method that is well established for reducing premature elimination by avoiding protein adsorption on NCs is surface functionalization with poly(ethylene glycol) (PEG), aptly called PEGylation. However, recent studies revealed that some PEGylated NCs have a delayed immune response, indicating the occurrence of protein-NC interactions. Obvious protein-NC interactions, especially in micellar systems, may have been overlooked as many early studies relied on techniques less sensitive to molecular level interactions. More sensitive techniques have been developed, but a major challenge is the direct measurement of interactions, which must be done in situ, as micelle assemblies are dynamic. Here, we report the use of pulsed-interleaved excitation fluorescence cross-correlation spectroscopy (PIE-FCCS) to interrogate the interactions between two PEG-based micelle models and serum albumin protein to compare protein adsorption differences based on linear or cyclic PEG architectures. First, by measuring micelle diffusion in isolated and mixed solutions, we confirmed the thermal stability of diblock and triblock copolymer micelle assemblies. Further, we measured the co-diffusion of micelles and serum proteins, the magnitudes of which increased with concentration and continued incubation. The results demonstrate that PIE-FCCS is capable of measuring direct interactions between fluorescently labeled NC and serum proteins, even at concentrations 500 times lower than those observed physiologically. This capability showcases the potential utility of PIE-FCCS in the characterization of drug delivery systems in biomimetic conditions.
Complexation of dextran and glucose with thiolate boronic acid capped on nanoparticle (2004)

Tiopronin-monolayer protected silver nanoparticles (<i>average</i> diameter = 5 nm) were partially replaced by thiolate boronic acid via ligand exchange. The uncapped boronic acids could be coupled with both a polysaccharide (Dextran) and a monoaccharide (glucose). Boronic acids capped on the particle were coupled selectively only by Dextran. With the decrease of charge on particle surface at pH = 5, boronic acids capped on the particle could be coupled with glucose. The particles were observed to aggregate along the Dextran chain, resulting in an absorbance decrease of the transverse plasmon at 397 nm and simultaneous rising of longitudinal plasmon at 640 nm. The aggregation increased with the concentration of Dextran. Luminescence intensity of phenyl boronic acid was enhanced by an upward deviation from a line with the concentration of Dextran in solution but the decay time was decreased, principally by the aggregation of the metallic cores.
Protein structure-based drug design: applications, limitations and future developments (2008)

DOAJ is a unique and extensive index of diverse open access journals from around the world, driven by a growing community, committed to ensuring quality content is freely available online for everyone.
Temperature-Sensitive Mutants of Influenza Virus. III. Further Characterization of the ts-1[E] Influenza A Recombinant (H3N2) Virus in Man (1973)

The potential of live, attenuated influenza A virus vaccine strain (ts-1[E]) to safely evoke immunity in man was studied. Virus grown in eggs, like virus grown in bovine kidney culture, exhibited an acceptable balance between attenuation and immunogenicity. The attenuation of this virus was evident by its large 50% infectious dose for man (105tcid50) and by the failure of a large quantity of virus (107tcid50) to cause influenzal illness. The ts-1[E] virus replicated well in the nasopharynx and was genetically stable in man. Moderate levels of neutralizing antibodies were induced in serum and nasal wash, and there was a suggestion that the latter antibody was associated with resistance to wild-type influenza A virus. However, the ts-1[E] virus was a poor stimulator of antibody to neuraminidase. Overall the pattern of infection produced by the ts-1[E] recombinant virus was comparable to that seen with wild-type virus but was of shorter duration and lesser magnitude. These features make the ts-1[E] virus suitable for use as a live influenza A vaccine in man.
Biofuel and chemical production by recombinant microorganisms via fermentation of proteinaceous biomass (2023)

Provided herein are metabolically modified microorganisms characterized by having an increased keto-acid flux when compared with the wild-type organism and comprising at least one polynucleotide encoding an enzyme that when expressed results in the production of a greater quantity of a chemical product when compared with the wild-type organism. The recombinant microorganisms are useful for producing a large number of chemical compositions from various nitrogen containing biomass compositions and other carbon sources. More specifically, provided herein are methods of producing alcohols, acetaldehyde, acetate, isobutyraldehyde, isobutyric acid, n-butyraldehyde, n-butyric acid, 2-methyl-1-butyraldehyde, 2-methyl-1-butyric acid, 3-methyl-1-butyraldehyde, 3-methyl-1-butyric acid, ammonia, ammonium, amino acids, 2,3-butanediol, 1,4-butanediol, 2-methyl-1,4-butanediol, 2-methyl-1,4-butanediamine, isobutene, itaconate, acetoin, acetone, isobutene, 1,5-diaminopentane, L-lactic acid, D-lactic acid, shikimic acid, mevalonate, polyhydroxybutyrate (PHB), isoprenoids, fatty acids, homoalanine, 4-aminobutyric acid (GABA), succinic acid, malic acid, citric acid, adipic acid, p-hydroxy-cinnamic acid, tetrahydrofuran, 3-methyl-tetrahydrofuran, gamma-butyrolactone, pyrrolidinone, n-methylpyrrolidone, aspartic acid, lysine, cadeverine, 2-ketoadipic acid, and/or S-adenosyl-methionine (SAM) from a suitable nitrogen rich biomass.
Calibration of High-Speed Time-Interleaving DAC (2023)

Distortion in high-speed time-interleaving DAC caused by the mismatch among sub- DACs is experimentally calibrated by the enhanced error backpropagation scheme. Undesired spur is reduced by 20 dB, and the ENOB is improved by 0.72 bit.
Anomalous Resistance Hysteresis in Oxide ReRAM: Oxygen Evolution and Reincorporation Revealed by In Situ TEM (2017)

The control and rational design of redox-based memristive devices, which are highly attractive candidates for next-generation nonvolatile memory and logic applications, is complicated by competing and poorly understood switching mechanisms, which can result in two coexisting resistance hystereses that have opposite voltage polarity. These competing processes can be defined as regular and anomalous resistive switching. Despite significant characterization efforts, the complex nanoscale redox processes that drive anomalous resistive switching and their implications for current transport remain poorly understood. Here, lateral and vertical mapping of O vacancy concentrations is used during the operation of such devices in situ in an aberration corrected transmission electron microscope to explain the anomalous switching mechanism. It is found that an increase (decrease) in the overall O vacancy concentration within the device after positive (negative) biasing of the Schottky-type electrode is associated with the electrocatalytic release and reincorporation of oxygen at the electrode/oxide interface and is responsible for the resistance change. This fundamental insight presents a novel perspective on resistive switching processes and opens up new technological opportunities for the implementation of memristive devices, as anomalous switching can now be suppressed selectively or used deliberately to achieve the desirable so-called deep Reset.
Insert‐molded poly(ether imide)/carbon fiber poly(ether ether ketone) bimaterial composites: Fracture and interfacial analysis (2006)

Abstract Bimaterial composites were constructed by injecting carbon‐fiber‐filled poly(etheretherketone) (CF PEEK) into a mold containing one‐half of a poly(etherimide) (PEI) tensile specimen. Specimens were notched at the interface and tested in tension. Using fracture mechanics, the adhesion strength of the interface (a fracture energy with units of energy per area) was calculated from notch size and stress–strain behavior of the notched specimens. Fracture energies (with units of energy per area) of the PEI/CF PEEK bimaterial composites were slightly less than those measured from the monolithic materials of construction. Variations in test speed (below the glass transition temperature of the two components) had little effect on stiffness or fracture energy. However, fracture energies decreased slightly as temperature increased. Composites fractured through the CF PEEK near the PEI/CF PEEK interface. Consequently, the fracture surface of the PEI portion had a thin layer of CF PEEK (a qualitative indicator of good adhesion). Microscopy and X‐ray photoelectron spectroscopy confirmed the presence of a thin layer of CF PEEK on the PEI. It appears that the miscibility of PEI and PEEK contributed to the strength of the PEI/CF PEEK thermophysical bond. The strength of the thermophysical bond of the PEI/CF PEEK bimaterial composites was greater than the cohesive strength of amorphous commodity polymers such as polystyrene and should be more than adequate for most microelectronics device handling applications. © 2006 Wiley Periodicals, Inc. J Appl Polym Sci 102:2362–2371, 2006
Tortuosity Measurement and the Effects of Finite Pulse Widths on Xenon\n Gas Diffusion NMR Studies of Porous Media (2002)

We have extended the utility of NMR as a technique to probe porous media\nstructure over length scales of ~ 100 - 2000 micron by using the spin 1/2 noble\ngas 129Xe imbibed into the system's pore space. Such length scales are much\ngreater than can be probed with NMR diffusion studies of water-saturated porous\nmedia. We utilized Pulsed Gradient Spin Echo NMR measurements of the\ntime-dependent diffusion coefficient, D(t) of the xenon gas filling the pore\nspace to study further the measurements of both the surface area-pore volume\nratio, S/Vp, and the tortuosity (pore connectivity) of the medium. In\nuniform-size glass bead packs, we observed D(t) decreasing with increasing t,\nreaching an observed asymptote of ~ 0.62 - 0.65D0, that could be measured over\ndiffusion distances extending over multiple bead diameters. Measurements of\nD(t)/D0 at differing gas pressures showed this tortuosity limit was not\naffected by changing the characteristic diffusion length of the spins during\nthe diffusion encoding gradient pulse. This was not the case at the short time\nlimit, where D(t)/D0 was noticeably affected by the gas pressure in the sample.\nIncreasing the gas pressure, and hence reducing D0 and the diffusion during the\ngradient pulse served to reduce the previously observed deviation of D(t)/D0\nfrom the S/Vp relation. The Pade approximation is used to interpolate between\nthe long and short time limits in D(t). While the short time D(t) point lay\nabove the interpolation line in the case of small beads, due to diffusion\nduring the gradient pulse on the order of the pore size, it was also noted that\nthe experimental D(t) data fell below the Pade line in the case of large beads,\nmost likely due to finite size effects.\n
Fibroblast growth factor 23 correlates with volume status in haemodialysis patients and is not reduced by haemodialysis (2015)

FGF-23 was associated with volume status in haemodialysis patients. The strong association with UFV suggests that optimization of volume status, for example by more intensive haemodialysis regimens, may also benefit mineral homeostasis. A single dialysis session did not lower FGF-23 levels.
Inpainting of surfaces and Images (2018)

Inpainting of images, represented on surfaces, was previously considered successfully by the application of a two-dimensional Laplacian operator, including in the context of the discrete representation on surfaces. Considering the shortcoming of errors and computational complexity of the strictly-two-dimensional approaches, we propose a one-dimensional-based multi-line approach, wherein the set of lines cover the region of inpainting and its boundaries. The multi-line framework is implemented on smooth and non-smooth surfaces and on images and the results are found to be superior to the previously published results. Additional possible one-dimensional representations are discussed.
Multimodality imaging in the diagnosis of a large accessory papillary muscle. (2017)

An accessory papillary muscle is an uncommon congenital anomaly usually found incidentally on routine cardiac imaging. While frequently asymptomatic, it is occasionally associated with mitral regurgitation, left ventricular dynamic outflow obstruction and hypertrophic cardiomyopathy1 and it is important to differentiate it from other pathological processes including papillary fibroelastoma, left ventricle thrombus, hemangioma, a single papillary muscle with a parachute mitral valve and a left ventricle false tendon. The clinical implication of these findings varies according to the degree of left ventricular out flow obstruction, location and pathology. We report a case that underscores the importance of multimodality imaging in the diagnosis and differentiation of an accessory papillary muscle from other intracardiac masses. [Full article available at http://rimed.org/rimedicaljournal-2017-09.asp].
Thalamic structural connectivity in medial temporal lobe epilepsy (2014)

Summary The thalamus has been implicated in various stages of medial temporal lobe epilepsy ( MTLE) seizure evolution. The relative density and functional significance (in epileptogenesis) of thalamic projections to MTL subregions, however, remains to be determined. This study used structural and diffusion magnetic resonance imaging ( MRI) to evaluate thalamic connection density with distinct MTL subregions in terms of location and volume. Nineteen MTLE patients with unilateral hippocampal sclerosis ( HS; 12 right; 10 female) were compared to 19 age‐matched controls. Five regions of interest ( ROI s) per hemisphere were created in native space: thalamus, amygdala, entorhinal cortex, hippocampus, and parahippocampus. Separate probabilistic tractography analyses were performed between the thalamus and each ipsilateral MTL subregion (four per hemisphere). Individual connectivity profiles and regional volumes were assessed. The medial pulvinar consistently showed the highest connection density with the hippocampus in healthy controls and in MTLE patients. Decreased thalamic connected volume was observed for thalamohippocampal pathways in patients with MTLE , and indicates pathway‐specific deafferentation. Regional hippocampal and thalamic atrophy was also observed, indicating gray and white matter loss in the thalamohippocampal pathway. Consistent localization of dense medial pulvinar (PuM) connectivity with the hippocampus suggests chronic PuM stimulation could modulate the MTLE seizure network. Decreased thalamic connected volume is a promising biomarker for epileptogenesis that merits longitudinal validation. A PowerPoint slide summarizing this article is available for download in the Supporting Information section here .
Enhancing the Lithium Ion Conductivity in Lithium Superionic Conductor (LISICON) Solid Electrolytes through a Mixed Polyanion Effect (2017)

Lithium superionic conductor (LISICON)-related compositions Li<sub>4±x</sub>Si<sub>1-x</sub>X<sub>x</sub>O<sub>4</sub> (X = P, Al, or Ge) are important materials that have been identified as potential solid electrolytes for all solid state batteries. Here, we show that the room temperature lithium ion conductivity can be improved by several orders of magnitude through substitution on Si sites. We apply a combined computer simulation and experimental approach to a wide range of compositions (Li<sub>4</sub>SiO<sub>4</sub>, Li<sub>3.75</sub>Si<sub>0.75</sub>P<sub>0.25</sub>O<sub>4</sub>, Li<sub>4.25</sub>Si<sub>0.75</sub>Al<sub>0.25</sub>O<sub>4</sub>, Li<sub>4</sub>Al<sub>0.33</sub>Si<sub>0.33</sub>P<sub>0.33</sub>O<sub>4</sub>, and Li<sub>4</sub>Al<sub>1/3</sub>Si<sub>1/6</sub>Ge<sub>1/6</sub>P<sub>1/3</sub>O<sub>4</sub>) which include new doped materials. Depending on the temperature, three different Li<sup>+</sup> ion diffusion mechanisms are observed. The polyanion mixing introduced by substitution lowers the temperature at which the transition to a superionic state with high Li<sup>+</sup> ion conductivity occurs. These insights help to rationalize the mechanism of the lithium ion conductivity enhancement and provide strategies for designing materials with promising transport properties.
Regenerative Medicine for the Cornea (2013)

Regenerative medicine for the cornea provides a novel treatment strategy for patients with corneal diseases instead of conventional keratoplasty. Limbal transplantation has been performed in patients with a limbal stem cell deficiency. This procedure requires long-term immunosuppression that involves high risks of serious eye and systemic complications, including infection, glaucoma, and liver dysfunction. To solve these problems, ocular surface reconstruction using cultured limbal or oral mucosal epithelial stem cells has been successfully applied to patients. However, cell sheets must be fabricated in a cell processing center (CPC) under good manufacturing practice conditions for clinical use, and the expenses of maintaining a CPC are too high for all hospitals to cover. Therefore, several hospitals should share one CPC to standardize and spread the application of regenerative therapy using tissue-engineered oral mucosal epithelial cell sheets. Consequently, we developed a cell transportation technique for clinical trial to bridge hospitals. This paper reviews the current status of regenerative medicine for the cornea.
Multipurpose implanter for high technology development (2009)

To provide basic operations of semiconductor and radiation materials technologies, a multipurpose implanter with intense ion beams was developed at the Institute of Nuclear Physics. The generated beamparameters are as follows: ions are H+, O+; C+; the ion energy is up to 200 keV; the beam current is up to 2 mA; and the implantation mode is continuous. The size of the target to be processed can reach 76 × 76 mm2. During the implanter operation, the target chamber vacuum reaches 10−4 Pa. The entire process of target irradiation is fully automated.
Stress relaxation in mismatched layers due to threading dislocation inclination (2003)

A recently observed mechanism of elastic stress relaxation in mismatched layers is discussed. The relaxation is achieved by the inclination of pure edge threading dislocation lines with respect to the layer surface normal. The relaxation is not assisted by dislocation glide but rather is caused by the “effective climb” of edge dislocations. The effective dislocation climb may result from the film growth and it is not necessarily related to bulk diffusion processes. The contribution of the dislocation inclination to strain relaxation has been formulated and the energy release due to the dislocation inclination in mismatched stressed layers has been determined. This mechanism explains recently observed relaxation of compressive stresses in the (0001) growth of AlxGa1−xN layers.
RrgA is a pilus‐associated adhesin in Streptococcus pneumoniae (2007)

Adherence to host cells is important in microbial colonization of a mucosal surface, and Streptococcus pneumoniae adherence was significantly enhanced by expression of an extracellular pilus composed of three subunits, RrgA, RrgB and RrgC. We sought to determine which subunit(s) confers adherence. Bacteria deficient in RrgA are significantly less adherent than wild-type organisms, while overexpression of RrgA enhances adherence. Recombinant monomeric RrgA binds to respiratory cells, as does RrgC with less affinity, and pre-incubation of epithelial cells with RrgA reduces adherence of wild-type piliated pneumococci. Non-adherent RrgA-negative, RrgB- and RrgC-positive organisms produce pili, suggesting that pilus-mediated adherence is due to expression of RrgA, rather than the pilus backbone itself. In contrast, RrgA-positive strains with disrupted rrgB and rrgC genes exhibit wild-type adherence despite failure to produce pili by Western blot or immunoelectron microscopy. The density of bacteria colonizing the upper respiratory tract of mice inoculated with piliated RrgA-negative pneumococci was significantly less compared with wild-type; in contrast, non-piliated pneumococci expressing non-polymeric RrgA had similar numbers of bacteria in the nasopharynx as piliated wild-type bacteria. These data suggest that RrgA is central in pilus-mediated adherence and disease, even in the absence of polymeric pilus production.
Phase transitions and melting in Mars (1997)

The basic thermal evolution model, described by Weizman et al. [1996], was modified to include the effect of phase transitions and the dependence of melting temperatures on pressure. The total amount of water release through Martian history was estimated from this model using the wet solidus of peridotite. Assuming a water content of 0.1% in the basalt, we find that the total amount of water released would be sufficient to cover the planet with a layer at least 3–300 m thick.