gebhart/patrepeval huggingface dataset:
P‐175: High Triplet Energy Exciplex Forming Hole Type Host for High Performance in Deep‐blue Phosphorescent Organic Light‐emitting Diodes (2018)

We designed and synthesized hole type host, N,N‐bis(4‐(tert‐butyl)phenyl)‐3,5‐bis(3,6‐di‐tert‐butyl‐9H‐carbazol‐9‐yl)aniline (t‐DCDPA) to use as an exciplex host with 2,8‐bis(4,6‐diphenyl‐1,3,5‐triazin‐2‐yl)dibenzo[b,d]furan (DBFTrz) electron type host material in deep‐blue phosphorescent organic light‐emitting diodes (PhOLEDs). To evaluate ability of t‐DCDPA, other hole type host materials were used as reference materials, which are tris(4‐(9H‐carbazol‐9‐yl)phenyl)amine (TCTA) and 3,5‐di(9H‐carbazol‐9‐yl)‐N,N‐diphenylaniline (DCDPA). Three pairs showed red‐shifted emission compared to that of each host emission, which means that they formed exciplex. t‐DCDPA:DBFTrz pair showed triplet energy of 2.94 eV, which is similar to that of DCDPA:DBFTrz pair (2.95 eV) and higher than TCTA:DBFTrz (2.83 eV). In deep‐blue PhOLEDs, t‐DCDPA:DBFTrz host pair showed the highest performance among three pairs, which proved that the newly synthesized host is efficient in deep‐blue PhOLEDs.
Synthesis of chitosan-sugar hybrid and evaluation of its bioactivity (1999)

Various chitosan–sugar hybrids were synthesized. The influence of the hybrids on the active oxygen generation of canine polymorphonuclear leukocyte (PMN) cells was investigated by measurement of the chemiluminescence (CL) response. The CL responses depended on the degree of substitution (DS) and water solubility of the hybrids. Water-insoluble hybrids stimulated the PMN cells directly by phagocytosis and the water-soluble ones would sensitize the PMN cells by a priming effect. Copyright © 1999 John Wiley & Sons, Ltd.
Model Predictive Controller with Average Emissions Constraints for Diesel Airpath (2018)

Diesel airpath controllers are required to deliver good tracking performance whilst satisfying operational constraints and physical limitations of the actuators. Due to explicit constraint handling capabilities, model predictive controllers (MPC) have been successfully deployed in diesel airpath applications. Previous MPC implementations have considered instantaneous constraints on engine-out emissions in order to meet legislated emissions regulations. However, the emissions standards are specified over a drive cycle, and hence, can be satisfied on average rather than just instantaneously, potentially allowing the controller to exploit the trade-off between emissions and fuel economy. In this work, an MPC is formulated to maximise the fuel efficiency whilst tracking boost pressure and exhaust gas recirculation (EGR) rate references, and in the face of uncertainties, adhering to the input, safety constraints and constraints on emissions averaged over some finite time period. The tracking performance and satisfaction of average emissions constraints using the proposed controller are demonstrated through an experimental study considering the new European drive cycle.
Custom-made holey graphene via scanning probe block co-polymer lithography (2022)

Oxidative chemical etching of metal nanoparticles (NPs) to produce holey graphene (hG) suffers from the presence of aggregated NPs on the graphene surface triggering heterogeneous etching rates and thereby producing irregular sized holes. To encounter such a challenge, we investigated the use of scanning probe block co-polymer lithography (SPBCL) to fabricate precisely positioned silver nanoparticles (AgNPs) on graphene surfaces with exquisite control over the NP size to prevent their aggregation and consequently produce uniformly distributed holes after oxidative chemical etching. SPBCL experiments were carried out <i>via</i> printing an ink suspension consisting of poly(ethylene oxide-<i>b</i>-2-vinylpyridine) and silver nitrate on a graphene surface in a selected pattern under controlled environmental and instrumental parameters followed by thermal annealing in a gaseous environment to fabricate AgNPs. Scanning electron microscopy revealed the uniform size distribution of AgNPs on the graphene surface with minimal to no aggregation. Four main sizes of AgNPs were obtained (37 ± 3, 45 ± 3, 54 ± 2, and 64 ± 3 nm) <i>via</i> controlling the printing force, <i>z</i>-piezo extension, and dwell time. Energy dispersive X-ray spectroscopy analysis validated the existence of elemental Ag on the graphene surface. Subsequent chemical etching of AgNPs using nitric acid (HNO<sub>3</sub>) with the aid of sonication and mechanical agitation produced holes of uniform size distribution generating hG. The obtained <i>I</i> <sub>D</sub>/<i>I</i> <sub>G</sub> ratios ≤ 0.96 measured by Raman spectroscopy were lower than those commonly reported for GO (<i>I</i> <sub>D</sub>/<i>I</i> <sub>G</sub> > 1), indicating the removal of more defective C atoms during the etching process to produce hG while preserving the remaining C atoms in ordered or crystalline structures. Indeed, SPBCL could be utilized to fabricate uniformly distributed AgNPs of controlled sizes on graphene surfaces to ultimately produce hG of uniform hole size distribution.
Allosteric activation dictates PRC2 activity independent of its recruitment to chromatin (2017)

SUMMARY PRC2 is a therapeutic target for several types of cancers currently undergoing clinical trials. Its activity is regulated by a positive feedback loop whereby its terminal enzymatic product, H3K27me3, is specifically recognized and bound by an aromatic cage present in its EED subunit. The ensuing allosteric activation of the complex stimulates H3K27me3 deposition on chromatin. Here, we report a step-wise feedback mechanism entailing key residues within distinctive interfacing motifs of EZH2 or EED that are found mutated in cancers and/or Weaver syndrome. PRC2 harboring these EZH2 or EED mutants manifest little activity in vivo but, unexpectedly, exhibited similar chromatin association as wild-type PRC2, indicating an uncoupling of PRC2 activity and recruitment. With genetic and chemical tools, we further demonstrated that targeting allosteric activation overrode the gain-of-function effect of EZH2 Y646X oncogenic mutations. These results revealed critical implications to the regulation and biology of PRC2 and a novel vulnerability in tackling PRC2-addicted cancers.
(Invited) Metal-Organic Framework-Derived Electrocatalysts for Li‒O2 Batteries (2017)

Recently, metal-organic framework (MOF) materials have been studied as cathode materials for Li‒O 2 batteries due to their high catalytic activity, uniform structure, and simple preparation process. However, further optimization of materials and structures should be undertaken to improve their electrochemical performance for the practical application. 1-3 Here we report a uniform MOF-derived multiple-capsule heterostructure, nitrogen-doped cobalt@graphene, as the cathode catalysts for Li‒O 2 cells. This N-Co@graphene multiple-nanocapsule structure improves the electrical properties and makes the high/uniform electroactive zones possible. In addition, the rational design of flexible foam-based electrodes possessing colander-like porous structures facilitates the oxygen diffusion, catalytic reaction, and deposition of discharge products. The electrode thus exhibits much improved electrochemical performance associated with unique morphologies of electrochemically grown lithium peroxides. Figs. 1a-c display the microstructure and morphology of N-Co@graphene nanocomposite. The composite has a lotus shower-like shape, where the crystalline Co nanoparticles, sized of 10‒20 nm, display highly ordered lattice fringes, being wrapped by few-layer graphenes, thus forming core-shell nanostructures. Note that there are few layers of specific lattice fringes with 0.25 nm lattice spacing existing on the surface of Co particles, which are indexed to be cobalt nitride that are generated from the nitrogen dopant into surficial lattices of Co crystalline. Fig. 1d show its EELS profile, which confirms the presence of C, N, and Co elements in the composite. Figs. 1e, f show its electrochemical performance in Li‒O 2 cells. The composite electrodes exhibit reduced charge-discharge overpotential and good cycling stability. This finding is mainly attributed to the improved electrical properties, electrocatalytic activity, and structural stability of N-Co@graphene nanostructures. Fig. 1 Structural and electrochemical characterization of MOF-derived N-Co@graphene catalysts. (a-c) TEM images, and (d) EELS profile of N-Co@graphene nanocomposite. (e,f) Voltage profiles versus selected cycles of N-Co@graphene composite based on carbon fiber (e) and nickel foam (f) electrodes. References 1. Li, Q.; Xu, P.; Gao, W.; Ma, S.; Zhang, G.; Cao, R.; Cho, J.; Wang, H. L.; Wu, G. Adv. Mater. 2014 , 26 , 1378-1386. 2. Wu, D.; Guo, Z.; Yin, X.; Pang, Q.; Tu, B.; Zhang, L.; Wang, Y. G.; Li, Q. Adv. Mater. 2014 , 26 , 3258-3262. 3. Tan, G.; Chong, L.; Amine, R.; Lu, J.; Liu, C.; Yuan, Y.; Wen, J.; He, K.; Bi, X.; Guo, Y.; Wang, H.-H.; Shahbazian-Yassar, R.; Hallaj, S. A.; Miller, D. J.; Liu, D; Amine, K. Nano Lett . 2017 , DOI: 10.1021/acs.nanolett.7b00207. Figure 1
Physical modeling of low-frequency sound propagation through human thoracic tissue (2010)

This work aims at modeling, in the presence of simplifying physical and geometrical assumptions, acoustic wave propagation through human thoracic tissue. Presented here are preliminary modeling results that are indicative of dominant lung resonances at specific frequencies. These resonant modes strongly impact pressure distribution in the tissue as well as the pressure and acceleration at the tissue-air interface. Under the modeling conditions, the effect of these lung resonant modes outweighs that of bones on acoustic waves at these frequencies.
Mobile link memory: daisy-chain memory with variable-latency control mode for future mobile systems (2009)

A link (MLM hereafter) for future mobile systems has been developed. In the MLM, for improving data transfer rate, the CPU, DRAM, NOR-type flash memory, and NAND-type flash memory are linked with point-to-point connections on a daisy chain. A low latency control technology is also key importance for future mobile systems. To reduce the latency of the MLM, a variable-latency control mode, a new latency-control technique, has also been developed. An analysis using application programs shows the MLM improves data-transfer rate by 18% on average compared to that by a conventional memory with a traditional parallel bus topology. A prototype MLM was developed and tested. The test results demonstrate that the latency varies within a narrow range of eight clock cycles with a high data-transfer rate of 344 MB/s under the variable-latency control mode.
Sulphatide binds to human and animal influenza A viruses, and inhibits the viral infection (1996)

We found, by using a virus overlay assay, that influenza A virus isolates bind to sulphatide (HSO3-Gal beta 1-->1'Cer), which has no sialic acid residue, and that the infection of Madin-Darby canine kidney cells with the human influenza virus A/Memphis/1/71 (H3N2) is inhibited by sulphatide. A/Memphis/1/71 (H3N2) causes obvious haemagglutination and low-pH haemolysis of asialoerythrocytes reconstituted with sulphatide. All influenza A virus isolates from the species of animals so far tested bound to sulphatide. The sulphatide-binding specificity of the isolates was different from the viral sialyl-linkage specificity. Influenza A virus isolates also bound to galactosyl ceramide (GalCer; Gal beta 1-->1'Cer), as well as sulphatide, in the virus overlay assays. In contrast, the influenza virus did not bind to N-deacyl, a derivative of sulphatide, glucosyl ceramide or the other neutral glycolipids tested. These results indicate that the linkage of galactose, or sulphated galactose, to ceramide is important for viral binding.
Inhibition of FGF receptor blocks adaptive resistance to RET inhibition in CCDC6-RET –rearranged thyroid cancer (2022)

Genetic alterations in RET lead to activation of ERK and AKT signaling and are associated with hereditary and sporadic thyroid cancer and lung cancer. Highly selective RET inhibitors have recently entered clinical use after demonstrating efficacy in treating patients with diverse tumor types harboring RET gene rearrangements or activating mutations. In order to understand resistance mechanisms arising after treatment with RET inhibitors, we performed a comprehensive molecular and genomic analysis of a patient with RET-rearranged thyroid cancer. Using a combination of drug screening and proteomic and biochemical profiling, we identified an adaptive resistance to RET inhibitors that reactivates ERK signaling within hours of drug exposure. We found that activation of FGFR signaling is a mechanism of adaptive resistance to RET inhibitors that activates ERK signaling. Combined inhibition of FGFR and RET prevented the development of adaptive resistance to RET inhibitors, reduced cell viability, and decreased tumor growth in cellular and animal models of CCDC6-RET-rearranged thyroid cancer.
Acute and Subchronic Oral Toxicity of Oil Palm Puree in Sprague–Dawley Rats (2020)

Palm puree is rich in antioxidants and is produced via blending various proportions of mesocarp fibre and crude palm oil. The aim of this study was to assess the acute and subchronic toxicity of palm puree in male and female Sprague-Dawley rats. For the acute toxicity study, animals administered single palm-puree doses (2000 mg kg<sup>-1</sup>) by gavage were observed daily for 14 d. For the subchronic toxicity study, the rats were administered 500, 1000, or 2000 mg kg<sup>-1</sup> palm puree daily for 28 d. We evaluated body and organ weights; performed haematological, biochemical, and histopathological analyses of blood and organ samples during and after treatment; and calculated the oral no-observed-adverse-effect level (NOAEL). The toxicity studies showed no signs of toxicity or mortality. The haematological, biochemical, and histopathological analyses and body and organ weights indicated no evidence of substantial toxicity at any dose of palm puree. The oral lethal dose and NOAEL for the palm puree were greater than 2000 mg kg<sup>-1</sup> d<sup>-1</sup> over 28 d. To the best of our knowledge, the present study is the first to confirm the safety of palm puree as a novel functional food. These encouraging results warrant further studies to elucidate its potential for pharmaceutical formulations.
Importance of metallothioneins in the cadmium detoxification process in Daphnia magna (2006)

Good knowledge of the relationship between toxic metals and biological systems, particularly the sub-cellular fraction, could be a suitable early indicator of toxic effects. These effects and the sub-cellular behaviour of cadmium were studied with a widely used species in freshwater toxicity bioassays, Daphnia magna. In spite of this very commonplace usage in ecotoxicological studies, very few data are available on its toxicant metabolism and in particular metal homeostasis. Combining multi-tools analysis, a soluble protein was found: it is heat-stable, rich in sulfhydryl groups (differential pulse polarography), characterised by a molecular mass of approximately 6.5 kDa, with a G-75 chromatographic profile corresponding to the rabbit metallothioneins monomer, with few if any aromatic-containing amino acids, it binds metals (e.g. Cd, Cu), and its concentration increases with Cd exposure. This evidence led us to hypothesise that metallothioneins (MTs) are present in D. magna. Up to 75% of the Cd body burden with Cd exposure is bound to the MTs fraction. The increase in the Cd concentration in the surrounding medium and concomitantly in daphnids induces sub-cellular reorganisation of essential metals such as Cu and Zn. The rate of metals in the soluble cellular fraction and associated with MTs increases with the Cd body burden. Monitoring sub-cellular distribution of metals after exposure in the natural environment could be very useful for ecotoxicological assessment.
Reinspection of a Clinical Proteomics Tumor Analysis Consortium (CPTAC) Dataset with Cloud Computing Reveals Abundant Post-Translational Modifications and Protein Sequence Variants (2021)

The Clinical Proteomic Tumor Analysis Consortium (CPTAC) has provided some of the most in-depth analyses of the phenotypes of human tumors ever constructed. Today, the majority of proteomic data analysis is still performed using software housed on desktop computers which limits the number of sequence variants and post-translational modifications that can be considered. The original CPTAC studies limited the search for PTMs to only samples that were chemically enriched for those modified peptides. Similarly, the only sequence variants considered were those with strong evidence at the exon or transcript level. In this multi-institutional collaborative reanalysis, we utilized unbiased protein databases containing millions of human sequence variants in conjunction with hundreds of common post-translational modifications. Using these tools, we identified tens of thousands of high-confidence PTMs and sequence variants. We identified 4132 phosphorylated peptides in nonenriched samples, 93% of which were confirmed in the samples which were chemically enriched for phosphopeptides. In addition, our results also cover 90% of the high-confidence variants reported by the original proteogenomics study, without the need for sample specific next-generation sequencing. Finally, we report fivefold more somatic and germline variants that have an independent evidence at the peptide level, including mutations in ERRB2 and BCAS1. In this reanalysis of CPTAC proteomic data with cloud computing, we present an openly available and searchable web resource of the highest-coverage proteomic profiling of human tumors described to date.
Theoretical Study on the Mechanism of the Hydride Transfer Reaction between Alkanes and Alkylcarbenium Ions (1997)

Several density functional theory based methods and the ab initio MP2 method were used to investigate the mechanism of secondary−secondary, tertiary−tertiary, and secondary−tertiary hydride-transfer reactions between alkanes and alkylcarbenium ions. All these reactions were found to proceed through a mechanism consisting of two steps: formation of a stable tight intermediate complex and decomposition of the complex to the products without activation energy. The optimized geometry of all the intermediate complexes is linear, with an open three-center two-electron C−H−C bond that is more or less symmetrical depending on the nature of the involved carbon atoms. By comparison of the results obtained at different levels of theory, it was shown that DFT-based methods provide optimized geometries in very good agreement with those obtained at the MP2 level, but the former fail in describing the energetics of the complex formation reactions studied. While DFT underestimates in some cases the stability of the intermediate complexes, the MP2 results are in very good agreement with the experimental data, indicating the adequacy of this method for studying this type of reaction mechanism. It was also shown that when large systems are involved and geometry optimization and characterization of the stationary points at the MP2 level become computationally too expensive, MP2 single-point calculations on DFT-optimized geometries yield results of comparable quality. Finally, energy profiles along the reaction coordinate were calculated for the three types of hydride-transfer processes considered, and neither a loose complex nor an internal potential barrier was found for any of them.
Effect of Glu-143 and His-231 substitutions on the catalytic activity and secretion of Bacillus subtilis neutral protease (1989)

On the basis of the homology with the Bacillus thermoproteolyticus zinc endopeptidase thermolysin, we hypothesized that Glu-143 and His-231 are the key residues for the catalytic activity of the Bacillus subtilis neutral protease. To test this possibility by site-directed mutagenesis, we substituted these two residues with Ala, Ser, Trp and Arg, and Leu, Val and Cys respectively. All these substitutions dramatically affected the amount of secreted mutant proteins, as determined by immunological methods, and their catalytic activities. No appreciable secretion was observed with the three Glu mutants Trp, Ser and Arg, whereas the Glu----Ala mutant enzyme was secreted at a level of a few hundred micrograms per litre of culture. The His mutants were all secreted at higher levels (in the order of a few milligrams per litre) and their residual catalytic activity could be determined using Z-Ala-Leu-Ala as substrate. Our results confirm the key role played by Glu-143 and His-231 in catalysis and moreover suggest the existence of a relationship between the catalytic activity of the enzyme and the extent of its secretion. In this context, we present data suggesting an autoproteolytic mechanism of cleavage of the precursor form of the enzyme, analogous to the one previously reported for the B. subtilis subtilisin.
Sequence and distribution of pro-opiomelanocortin in the pituitary and the brain of the chicken (Gallus gallus) (2000)

Although pro-opiomelanocortin (POMC) is a well-known hormone precursor in many species, molecular information about avian POMCs is still relatively scarce. In a former study (Berghman et al., [1998] Mol Cell Endocrinol. 142:119-130) the nucleotide and amino acid sequence of N-terminal POMC in the chicken were reported. To complete the nucleotide sequence of the precursor, rapid amplification of 3' and 5' cDNA end reactions were performed and the polymerase chain reaction (PCR) products were cloned and sequenced. The chicken POMC coding region appears to consist of 678 base pairs in the pituitary and also in the hypothalamus, as assessed by reverse transcriptase PCR. Overall nucleotide sequence homology with other species ranges from 41% (in bovine) to 57% (in rat). The distribution of the POMC mRNA in pituitary and brain was analyzed by in situ hybridization by using 33P-labelled oligonucleotides. Expression of POMC mRNA in the pituitary was restricted to the cephalic lobe, whereas in the brain, the signal was limited to the hypothalamic region. As assessed by Northern blot analysis, the length of the POMC mRNA in both the pituitary and the hypothalamus was approximately 1,200 nucleotides. By using antisera to N-terminal POMC, alpha-melanotropin and beta-endorphin, POMC-containing cells were observed in the cephalic lobe of the pituitary and immunopositive perikarya were localized in the infundibular nucleus and median eminence of the hypothalamus. Immunoreactive fibers were found in the preoptic area and in the medial basal hypothalamus surrounding the third ventricle and more dorsally in the thalamus. Double-staining experiments in the pituitary clearly indicated a complete overlap of the signals generated by these antisera.