gebhart/patrepeval huggingface dataset:
JPEG ringing artifact visibility evaluation (2014)

To achieve high perceptual quality of compressed images, many objective image quality metrics for compression artifacts evaluation and reduction have been developed based on characterization of local image features. However, it is the end user who is judging the image quality in various applications, so the validation of how well these metrics predict human perception is important and necessary. In this paper, we present a preliminary psychophysics experiment method to capture human perception of local ringing artifacts in JPEG images with different severity levels. Observers are asked to annotate the compressed image where they perceive artifacts along the edges, directly on the screen using an interactive tablet display. They are asked to catalog the severity of artifacts into one of the three levels: Strong, Medium, and Light. We process the hand-marked data into a ringing visibility edge map showing a ringing severity mean opinion score (MOS) at every edge pixel. The perceptual information captured in this experiment, enables us to study the correlation between human perception and local image features, which is an important step towards the goal of developing a non-reference (NR) objective metric to predict the visibility of JPEG ringing artifacts in alignment with the assessments of human observers.
Combined Ionic and Hydrogen Bonding in Polymer Multilayer Thin Film for High Gas Barrier and Stretchiness (2015)

A unique polymer multilayer thin film with high gas barrier at high strain (>10%) was achieved with a combination of ionic and hydrogen bonding. Layer-by-layer assembly was used to deposit quadlayers (QL) of polyethylenimine (PEI), poly(acrylic acid) (PAA), poly(ethylene oxide) (PEO), and PAA. Altering the deposition pH of the various layers resulted in different physical and mechanical properties. PEI/PAA/PEO/PAA quadlayers assembled at pH 10/4/2.5/2.5 grow much thicker than the same film with all components deposited at pH 3, which is due to a porosity transition during assembly and in-and-out diffusion of the partially charged polyelectrolytes with high chain mobility (PEI at pH 10 and PAA at pH 4). The change in pH during the film assembly induces a porous structure in the 10/4/2.5/2.5 film that results in poor gas barrier. Films deposited on 1 mm thick polyurethane rubber at pH 3 have a densely packed structure with no pores. A 20 QL film (∼1 μm thick) achieves an oxygen transmission rate 15 times lower than uncoated rubber due to the synergistic effect of the interdigitated layers of ionic and hydrogen bonding. When stretched 10%, the barrier improves by a factor of 28 relative to uncoated polyurethane. This combination of stretchability and high gas barrier is unprecedented and offers the opportunity to produce relatively high barrier elastomers.
Pegylation of a chlorin(e6) polymer conjugate increases tumor targeting of photosensitizer. (2001)

Photodynamic therapy is emerging as a viable modality for the treatment of many cancers. A limiting factor in its use against intracavity tumors such as disseminated ovarian cancer is insufficient selectivity of the photosensitizer for tumor compared with normal tissue. We report on an approach to improve tumor targeting by exploiting differences between cell types and by chemical modification of a photosensitizer conjugate. Attachment of polyethylene glycol (pegylation) to a polyacetylated conjugate between poly-l-lysine and chlorin(e6) increased the relative phototoxicity in vitro toward an ovarian cancer cell line (OVCAR-5) while reducing it toward a macrophage cell line (J774), compared with the nonpegylated conjugate. Surprisingly, the increased phototoxicity of the pegylated conjugate correlated with reduced oxygen consumption. Pegylation also reduced the tendency of the conjugate to aggregate and reduced the consumption of oxygen when the conjugates were illuminated in solution in serum containing medium, suggesting a switch in photochemical mechanism from type II (singlet oxygen) to type I (radicals or electron transfer). Pegylation led to more mitochondrial localization as shown by confocal fluorescence microscopy in OVCAR-5 cells, and, on illumination, produced a switch in cell death mechanism toward apoptosis not seen with J774 cells. Conjugates were injected i.p. into nude mice bearing i.p. OVCAR-5 tumors, and the pegylated conjugate gave higher amounts of photosensitizer in tumor and higher tumor:normal tissue ratios and increased the depth to which the chlorin(e6) penetrated into the peritoneal wall. Taken together, these results suggest that pegylation of a polymer-photosensitizer conjugate improves tumor-targeting and may increase the efficacy of photodynamic therapy for ovarian cancer.
A TRAMP‐derived orthotopic prostate syngeneic (TOPS) cancer model for investigating anti‐tumor treatments (2018)

We have developed a powerful animal model to advance the current selection of effective treatments for patients with advanced prostate cancer.
A photoactivatable drug–caged fluorophore conjugate allows direct quantification of intracellular drug transport (2013)

We report here a method that utilizes a photoactivatable drug-caged fluorophore conjugate to quantify intracellular drug trafficking processes at single cell resolution. Photoactivation is performed in labeled cellular compartments to visualize intracellular drug exchange under physiological conditions, without the need for washing, facilitating its translation into in vivo cancer models.
Self-aligned mechanical attachment of carbon nanotubes to silicon dioxide structures by selective silicon dioxide chemical-vapor deposition (2003)

A self-aligned thin-film deposition technique was developed to mechanically attach carbon nanotubes to surfaces for the fabrication of structurally robust nanotube-based nanomechanical devices. Single-walled carbon nanotubes were grown by thermal chemical-vapor deposition (CVD) across 150-nm-wide SiO2 trenches. The nanotubes were mechanically attached to the trench tops by selective silicon tetraacetate-based SiO2 CVD. No film was deposited on the nanotubes where they were suspended across the trenches.
CD5 Negative B-cell Chronic Lymphocytic Leukemia: Clinical and Biological Features of 42 cases (1998)

Chronic lymphocytic leukemia cell (CLL) usually (95%) express B-phenotype and the CD5 antigen which is usually present on the surface of normal T cells. However, among B CLL, 7 to 20% do not express CD5. The significance of the lack of CD5 expression remains unclear. We reviewed 42 consecutive CD5- B CLL seen in three French medical centers from 1985 to 1991 and compared them with 79 CD5+ B CLL. Immunophenotype studies were performed using indirect immunofluorescence under light microscopy as well as flow cytometry after 1988. B CLL was considered to be CD5 negative when less than 5% of mononuclear cells expressed CD5 after subtraction of the number of T-cells. Cases with CD5- B CLL had isolated splenomegaly more frequently (p = 2.10(-7)). They frequently expressed a higher level of surface immunoglobulin (S-Ig) or the switch mu/delta phenotype (p = 4.7 10(-2)). The median survival time was not reached but no significant difference between CD5 negative and positive B CLL was observed at the time of our data analysis (p = 0.97). Clinical presentation of CD5- B CLL seems to be different from other forms of B CLL. Although, no conclusion can be reached in terms of prognosis, CLL with low expression of CD5 should be regarded as a subtype of CLL with a different clinical presentation than CD5+ CLL.
Coarse grained model for calculating the ion mobility of hydrocarbons (2016)

Hydrocarbons are widely used as insulating compounds. However, their fundamental characteristics in conduction phenomena are not completely understood. A great deal of effort is required to determine reasonable ionic behavior from experiments because of their complicated procedures and tight controls of the temperature and the purity of the liquids. In order to understand the conduction phenomena, we have theoretically calculated the ion mobilities of hydrocarbons and investigated their characteristics using the coarse grained model in molecular dynamics simulations. We assumed a molecule of hydrocarbons to be a bead and simulated its dependence on the viscosity, electric field, and temperature. Furthermore, we verified the suitability of the conformation, scale size, and long-range interactions for the ion mobility. The results of the simulations show that the ion mobility values agree reasonably well with the values from Walden’s rule and depend on the viscosity but not on the electric field. The ion mobility and self-diffusion coefficient exponentially increase with increasing temperature, while the activation energy decreases with increasing molecular size. These values and characteristics of the ion mobility are in reasonable agreement with experimental results. In the future, we can understand not only the ion mobilies of hydrocarbons in conduction, but also we can predict general phenomena in electrochemistry with molecular dynamics simulations.
Van der Waals nanomesh electronics on arbitrary surfaces (2023)

Chemical bonds, including covalent and ionic bonds, endow semiconductors with stable electronic configurations but also impose constraints on their synthesis and lattice-mismatched heteroepitaxy. Here, the unique multi-scale van der Waals (vdWs) interactions are explored in one-dimensional tellurium (Te) systems to overcome these restrictions, enabled by the vdWs bonds between Te atomic chains and the spontaneous misfit relaxation at quasi-vdWs interfaces. Wafer-scale Te vdWs nanomeshes composed of self-welding Te nanowires are laterally vapor grown on arbitrary surfaces at a low temperature of 100 °C, bringing greater integration freedoms for enhanced device functionality and broad applicability. The prepared Te vdWs nanomeshes can be patterned at the microscale and exhibit high field-effect hole mobility of 145 cm<sup>2</sup>/Vs, ultrafast photoresponse below 3 μs in paper-based infrared photodetectors, as well as controllable electronic structure in mixed-dimensional heterojunctions. All these device metrics of Te vdWs nanomesh electronics are promising to meet emerging technological demands.
A graph neural network approach for molecule carcinogenicity prediction (2022)

The code and data underlying this article are available on github at https://github.com/bowang-lab/CONCERTO.
Nitric oxide inhibits lipopolysaccharide-induced apoptosis in pulmonary artery endothelial cells (1998)

Our group recently reported that cultured sheep pulmonary artery endothelial cells (SPAECs) became resistant to lipopolysaccharide (LPS)-induced apoptosis several days after constitutive synthesis of nitric oxide (NO) after adenoviral (Ad) transfer of inducible NO synthase (iNOS) or exposure to the NO donor S-nitroso-N-acetylpenicillamine (SNAP) (E. Tzeng, Y.-M. Kim, B. R. Pitt, A. Lizonova, I. Kovesdi, and T. R. Billiar. Surgery 122: 255-263, 1997). In the present study, we confirmed this observation by establishing stable transfectants after retroviral gene transfer [replication-deficient retrovirus (DFG)] of human iNOS (DFG-iNOS) SPAECs and then used all three approaches (Ad, DFG, and SNAP) to determine underlying mechanisms of this phenomenon. Continuous endogenous production of NO in itself did not cause apoptosis as assessed by phase-contrast microscopy, nuclear morphology, and internucleosomal DNA fragmentation. Prolonged (72-96 h) synthesis of NO, however, after DFG- or replication-deficient adenovirus (Ad. CMV)-iNOS or SNAP (100 microM, 96 h) inhibited LPS-induced apoptosis. The kinetics of such protection suggested that NO may be inducing other gene products. Ad-mediated transfer of manganese superoxide dismutase (MnSOD) decreased the sensitivity of wild-type SPAECs to LPS-induced apoptosis. MnSOD, however, was not induced in an NG-monomethyl-L-arginine (L-NMMA)-sensitive time-dependent fashion after Ad.CMV-iNOS. Other inducible genes that may be affected by NO and that may protect against potential oxidant-mediated LPS-induced apoptosis including 70-kDa heat shock protein, heme oxygenase-1, metallothionein, and Bcl-2 also were not elevated in an L-NMMA-sensitive, time-dependent fashion. Although the candidate gene product underlying NO-induced protection remains unclear, we did note that prolonged synthesis of NO inhibited LPS-induced activation of an interleukin-1beta-converting enzyme-like cysteine protease (cysteine protease protein-32-like) in a dithiothreitol-sensitive fashion, suggesting that S-nitrosylation of an important downstream target of convergence of apoptotic signals may contribute to the sensitivity of SPAECs to LPS.
Three-dimensional genomic mapping of human pancreatic tissue reveals striking multifocality and genetic heterogeneity in precancerous lesions (2023)

Pancreatic intraepithelial neoplasia (PanIN) is a precursor to pancreatic cancer and represents a critical opportunity for cancer interception. However, the number, size, shape, and connectivity of PanINs in human pancreatic tissue samples are largely unknown. In this study, we quantitatively assessed human PanINs using CODA, a novel machine-learning pipeline for 3D image analysis that generates quantifiable models of large pieces of human pancreas with single-cell resolution. Using a cohort of 38 large slabs of grossly normal human pancreas from surgical resection specimens, we identified striking multifocality of PanINs, with a mean burden of 13 spatially separate PanINs per cm<sup>3</sup> of sampled tissue. Extrapolating this burden to the entire pancreas suggested a median of approximately 1000 PanINs in an entire pancreas. In order to better understand the clonal relationships within and between PanINs, we developed a pipeline for CODA-guided multi-region genomic analysis of PanINs, including targeted and whole exome sequencing. Multi-region assessment of 37 PanINs from eight additional human pancreatic tissue slabs revealed that almost all PanINs contained hotspot mutations in the oncogene <i>KRAS</i>, but no gene other than <i>KRAS</i> was altered in more than 20% of the analyzed PanINs. PanINs contained a mean of 13 somatic mutations per region when analyzed by whole exome sequencing. The majority of analyzed PanINs originated from independent clonal events, with distinct somatic mutation profiles between PanINs in the same tissue slab. A subset of the analyzed PanINs contained multiple <i>KRAS</i> mutations, suggesting a polyclonal origin even in PanINs that are contiguous by rigorous 3D assessment. This study leverages a novel 3D genomic mapping approach to describe, for the first time, the spatial and genetic multifocality of human PanINs, providing important insights into the initiation and progression of pancreatic neoplasia.
Flow Behavior in Thin-Gapped Diamond-Shaped Channels With Pins (1993)

The present experimental study investigates the nature of the fluid flow in various modified version of a high heat-flux, multi-cell, very compact heat exchanger. The basic transport concept has previously been applied to the cooling of high power laser mirrors, for which it has been shown to achieve extremely high rates of heat transfer in single-phase liquid flow. The original device was patented by Schmidt (1975). It is composed of multiple square cells machined in a honeycomb arrangement into the backside of a silicon mirror blank. Each cell contains a circular pin at its center which spans the narrow gap between the mirror substrate on one side of the flow channel and the coolant header plate on the other. A schematic diagram of one of the cells with one pin at the center of the cell is shown. The header design for delivering and returning the liquid flow is quite novel. Four diamond-shaped cells receive coolant from a single inlet and four cells exhaust coolant into a single outlet. The flow enters a cell at a corner and exits at the opposite corner. Hence, in each of the small cells in the honeycomb array, the coolant flows across the pinmore » in the diamond direction.« less
Chemoselective Multicomponent Synthesis of α,β‐Unsaturated Esters and Lactones and of Their Diels‐Alder Adducts (1985)

The “one-pot reaction” of alcohols 1 (also chiral), aldehydes 2, and ketenylidenetriphenylphosphorane 3 yields α,β-unsaturated esters 4. With γ-hydroxyaldehydes the reaction leads to formation of macrocyclic α,β-unsaturated lactones. Four-component reactions between 1, 2, 3, and a diene lead immediately to Diels-Alder adducts of 4.
Cutting to measure the elasticity and fracture of soft gels (2020)

The fracture properties of very soft and/or brittle materials are challenging to measure directly due to the limitations of existing fracture testing methods. To address this issue, we introduce a razorblade-initiated fracture test (RIFT) to measure the mechanical properties related to fracture for soft polymeric gels. We use RIFT to quantify the elasticity, crack initiation energy, and the fracture energy of gellan hydrogels as a function of gellan concentration. Additionally, we use RIFT to study the role of friction in quantifying the fracture properties for poly(styrene-b-ethylene butadiene-b-styrene) gels as a function of test velocity. This new method provides a simple and efficient means to quantify the fracture properties of soft materials.
Perkin 1 Abstracts: Natural Product Synthesis (2002)

A. Gunn, S. McAteer, J. E. Milne and M. de Puit, J. Chem. Soc., Perkin Trans. 1, 2002, 17-vii DOI: 10.1039/B207912G
Subnanosecond Thomson scattering on a vacuum arc discharge in tin vapor (2005)

In a previous series of Thomson scattering (TS) experiments on an extreme ultraviolet producing vacuum arc discharge in tin vapor, background radiation emitted by the plasma was found to make measurements impossible for all parts of the discharge except the prepinch phase. To reduce the level of recorded background radiation, we have built a setup for time and space resolved subnanosecond TS. Results obtained with this new setup are presented for experiments on previously inaccessible parts of the discharge--the ignition phase, pinch phase, and decay phase. For the first two, measurements have been performed at different heights in the plasma. Electron densities for the pinch phase have been derived. For the decay phase, the electron densities confirm previous Stark broadening data. From the overall results, a more complete picture of the plasma evolution can be formed.
Semi-quantitative Measurement of a Specific Glycoform Using a DNA-tagged Antibody and Lectin Affinity Chromatography for Glyco-biomarker Development * (2014)

Aberrant glycosylation-targeted disease biomarker development is based on cumulative evidence that certain glycoforms are mass-produced in a disease-specific manner. However, the development process has been hampered by the absence of an efficient validation method based on a sensitive and multiplexed platform. In particular, ELISA-based analytical tools are not adequate for this purpose, mainly because of the presence of a pair of N-glycans of IgG-type antibodies. To overcome the associated hurdles in this study, antibodies were tagged with oligonucleotides with T7 promoter and then allowed to form a complex with corresponding antigens. An antibody-bound specific glycoform was isolated by lectin chromatography and quantitatively measured on a DNA microarray chip following production of fluorescent RNA by T7-trascription. This tool ensured measurement of targeted glycoforms of multiple biomarkers with high sensitivity and multiplexity. This analytical method was applied to an in vitro diagnostic multivariate index assay where a panel of hepatocellular carcinoma (HCC) biomarkers comprising alpha-fetoprotein, hemopexin, and alpha-2-macroglobulin (A2M) was examined in terms of the serum level and their fuco-fractions. The results indicated that the tests using the multiplexed fuco-biomarkers provided improved discriminatory power between non- hepatocellular carcinoma and hepatocellular carcinoma subjects compared with the alpha-fetoprotein level or fuco-alpha-fetoprotein test alone. The developed method is expected to facilitate the validation of disease-specific glycan biomarker candidates.
Targeting SRC Family Kinases and HSP90 in Lung Cancer (2015)

Abstract : Lung cancer has the highest mortality rate of all cancers in the United States and has adversely affected the lives of many Americans. Typically, only 16 of patients survive 5 years beyond initial diagnosis. The goal of this proposal is to try to improve application of a drug, dasatinib, which has some promise for lung cancer treatment. Dasatinib is a targeted drug, with action that involves blocking the function of a group of proteins (defined as the Src group) whose action is important in lung cancer metastasis. In our study, we have been testing whether the action of dasatinib in lung cancer is enhanced by combining it with a second agent, ganetespib, that targets Src and other pro-cancerous proteins by an alternative mechanism. We have also been evaluating whether cellular status of a protein, NEDD9, that we have shown to bind directly to Src, influences the activity of dasatinib. Using in vivo analysis, experiments in progress are indicating that mice lacking NEDD9 are greatly sensitized to dasatinib but not ganetespib, and that mice lacking NEDD9 develop more aggressive lung cancers than those with intact NEDD9;while the dasatinib/ganetespib combination does not improve the efficacy of dasatinib.
Towards 20.5% efficiency PERC Cells by improved understanding through simulation (2011)

This paper investigates by means of finite-elements and SPICE simulation the further improvement of solar cell performance of PERC-type cells by introduction of industry-compatible solutions, such as a 120 sq. phosphorous emitter with a lower surface concentration than that of current 60 sq. standard emitters and the replacement of the silver screen-printed front-side metallization by narrow, dense electro-plated copper lines on lowly resistive Ti or NiSi contacts.
Microstructure and properties of highly oriented PZT thin films on epitaxial ceramic electrodes prepared by CSD (1999)

Abstract Epitaxial thin films of Lag0.7Sr0.3MnO3 and Lag0.5Sr0.5CoO3 were deposited by chemical solution deposition on single-crystal LaAlO3. These single-crystal layers served as bottom electrodes for the growth of ferroelectric PZT thin films. By XRD analysis, influences of processing on crystallographic properties were found. The thin film properties were influenced by the thickness of the crystallizing amorphous layer and also by the heating rate. Hysteresis measurements were performed on selected samples, showing a dependence of the remanent polarization on the crystallographic properties.
SPIN TRANSFER TORQUE SWITCHING AND PERPENDICULAR MAGNETIC ANISOTROPY IN FULL HEUSLER ALLOYCo2FeAl-BASED TUNNEL JUNCTIONS (2014)

Some of Co -based full Heusler alloys have remarkable properties in spintronics, that is, high spin polarization of conduction electrons and low magnetic damping. Owing to these properties, magnetic tunnel junctions (MTJs) using Co -based full Heusler alloys are potentially of particular importance for spintronic application such as magnetoresistive random access memories (MRAMs). Recently, we have first demonstrated spin transfer torque (STT) switching and perpendicular magnetic anisotropy (PMA), which are required for developing high-density MRAMs, in full-Heusler Co 2 FeAl alloy-based MTJs. In this review, the main results of the experimental demonstrations are shown with referring to related issues, and the prospect of MTJs using Heusler alloys is also discussed.