gebhart/patrepeval huggingface dataset:
BUILDING AN ORGAN-SPECIFIC CARCINOGENIC DATABASE FOR SAR ANALYSES (2004)

FDA reviewers need a means to rapidly predict organ-specific carcinogenicity to aid in evaluating new chemicals submitted for approval. This research addressed the building of a database to use in developing a predictive model for such an application based on structure-activity relationships (SAR). The Internet availability of the Carcinogenic Potency Database (CPDB) provided a solid foundation on which to base such a model. The addition of molecular structures to the CPDB provided the extra ingredient necessary for SAR analyses. However, the CPDB had to be compressed from a multirecord to a single record per chemical database; multiple records representing each gender, species, route of administration, and organ-specific toxicity had to be summarized into a single record for each study. Multiple studies on a single chemical had to be further reduced based on a hierarchical scheme. Structural cleanup involved removal of all chemicals that would impede the accurate generation of SAR type descriptors from commercial software programs; that is, inorganic chemicals, mixtures, and organometallics were removed. Counterions such as Na, K, sulfates, hydrates, and salts were also removed for structural consistency. Structural modification sometimes resulted in duplicate records that also had to be reduced to a single record based on the hierarchical scheme. The modified database containing 999 chemicals was evaluated for liver-specific carcinogenicity using a variety of analysis techniques. These preliminary analyses all yielded approximately the same results with an overall predictability of about 63%, which was comprised of a sensitivity of about 30% and a specificity of about 77%.
Structural development during nonlinear free-radical polymerizations (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStructural development during nonlinear free-radical polymerizationsNeil A. Dotson, Rafael Galvan, and Christopher W. MacoskoCite this: Macromolecules 1988, 21, 8, 2560–2568Publication Date (Print):August 1, 1988Publication History Published online1 May 2002Published inissue 1 August 1988https://pubs.acs.org/doi/10.1021/ma00186a041https://doi.org/10.1021/ma00186a041research-articleACS PublicationsRequest reuse permissionsArticle Views116Altmetric-Citations37LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
The effect of cationic salt addition on the settling and dewatering properties of an industrial activated sludge (1998)

Cations have been found to influence the settling and dewatering properties of activated sludge, especially for industrial wastewaters in which very high concentrations of monovalent cations are often found. Because the cation content of wastewaters is often influenced by upstream processes, an understanding of the influence of various cations can be an important consideration in pinpointing operational problems in wastewater treatment plants. An industrial activated‐sludge treatment plant was studied to determine whether variations in settling and dewatering properties of the mixed liquor and waste solids could be caused by changes in the cation content of the wastewater. Laboratory reactors received both return activated sludge and wastewater from the industrial treatment plant, and the feed was supplemented with either sodium (Na + ), potassium (K + ), or magnesium (Mg + ). It was found that when the monovalent‐to‐divalent (M:D) cation ratio on a milliequivalent basis was increased to greater than approximately 2:1 by either Na + or K + addition, dewatering properties became poorer and polymer conditioning requirements increased. The soluble protein content also increased as the mixed liquor M:D ratio increased, indicating release of biopolymer from the flocs. Magnesium addition at low doses caused a decrease in the dewatering rate, but at higher doses both the settling and dewatering properties of waste solids improved substantially. Conversely, when Na + and K + concentrations in the raw wastewater decreased significantly to less than 10 and 0.1 milliequivalents (meq), respectively, settling and dewatering properties improved substantially and addition of Mg 2+ did not improve conditions beyond those of the unamended control. Each of the cations studied caused unique changes in the properties of activated‐sludge solids that could not be correlated with the M:D ratio, suggesting that some of the effects are not simply physical/chemical but may be physiological as well.
Vision Zero: on a Provable Method for Eliminating Roadway Accidents\n without Compromising Traffic Throughput (2018)

We propose an economical, viable, approach to eliminate almost all car\naccidents. Our method relies on a mathematical model of safety and can be\napplied to all modern cars at a mild cost.\n
Thiazepine photochemistry. Ready 1,3-hydrogen shifts from a side-chain amide (1971)

An unusual, thermally reversible, 1,3-hydrogen shift occurs during irradiation of 6-benzyloxycarbonyl-amino-2,3-dihydro-1,4-thiazepines (2, 3, and the corresponding sulphoxide and sulphone of 3b); this is a special case of imine-enamine tautomerism, arising from the singlet excited state.
ChemInform Abstract: Nonneurotoxic Tetralin and Indan Analogues of 3,4‐(Methylenedioxy)amphetamine (MDA). (1990)

Abstract Nitrosation of the indanones (I), followed by reduction, yields the aminoindans (III).
Improved sensitivity in blue-membrane bacteriorhodopsin films (1999)

We show that D85N/V49A, a mutant bacteriorhodopsin in which two residues, aspartate (D) at position 85 and valine (V) at position 49, have been replaced with asparagine (N) and alanine (A), respectively, has significantly improved optical properties compared with other forms of blue-membrane Bacteriorhodopsin. Absorption studies of the mutant in gels show that it forms the P(490) state at light levels that are comparable with M-state formation in wild-type films. Theoretical calculations based on Kramers-Kronig transformation of light-induced absorption data predict that the refractive index is three times larger than that of mutant D85N. Holographic measurements performed on gelatin-based films confirm that the sensitivity is improved by a factor of 50 over that of D85N.
Abstract IA27: MYC drives molecular and therapeutically distinct subtype of SCLC (2018)

Abstract Small cell lung cancer (SCLC) has largely been treated in the clinic as a homogeneous disease for the last 40 years. However, it is become increasingly appreciated that SCLC exhibits both intra- and intertumoral heterogeneity. Genetic loss of the tumor suppressors RB1 and TP53 is nearly universal in SCLC, while amplifications in MYC family members including C-, L-, and N-MYC are mutually exclusive. Using genetically engineered mouse models (GEMMs), we show that MycT58A expression cooperates with Rb1 and Trp53 loss in the mouse lung to promote aggressive, highly metastatic tumors that are initially sensitive to chemotherapy followed by relapse, similar to human SCLC. Importantly, MYC drives a neuroendocrine-low ‘‘variant’’ subset of SCLC with low ASCL1 and high NEUROD1 expression corresponding to transcriptional profiles of human SCLC. The MYC-driven subset of SCLC is also low for other clinically relevant biomarkers such as TTF1/NKX2.1 and DLL3. Targeted drug screening reveals that SCLC with high MYC expression is vulnerable to Aurora kinase inhibition, which, combined with chemotherapy, strongly suppresses tumor progression and increases survival. These findings are consistent with the results of recent clinical trials in patients with relapsed SCLC who received paclitaxel with or without the AURKA inhibitor alisertib. Furthermore, recent preclinical studies demonstrate that the MYC-driven subset of SCLC is preferentially sensitive to CHK1 inhibition and other metabolic targets compared to MYCL-driven SCLC. These data identify molecular features for patient stratification and uncover potential targeted treatment approaches for MYC-driven SCLC. Citation Format: Gurkan Mollaoglu, Matthew R. Guthrie, Stefanie Bohm, Johannes Bragelmann, Milind D. Chalishazar, Abbie S. Ireland, Fang Huang, Zeping Hu, Robert J. Cardnell, Triparna Sen, Jason Gertz, Jane E. Johnson, Adi F. Gazdar, Lauren A. Byers, Ralph J. DeBerardinis, Robert J. Wechsler-Reya, Martin Sos, Trudy G. Oliver. MYC drives molecular and therapeutically distinct subtype of SCLC [abstract]. In: Proceedings of the Fifth AACR-IASLC International Joint Conference: Lung Cancer Translational Science from the Bench to the Clinic; Jan 8-11, 2018; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2018;24(17_Suppl):Abstract nr IA27.
Perturbation of near-field scan from connected cables (2012)

The perturbation of near-fields scan from connected cables are investigated and how to handle the cables is discussed. A connected cable induced small but theoretical detectable changes in the near-field. This change can be seen in Huygens' box simulations (equivalent source currents on a box) at the cable resonance frequencies while there is no change away from the resonance frequencies.
The Enzymatic Phosphorylation of Nucleic Acids and Its Application to End-Group Analysis (1966)

Polynucleotide kinase catalyzes the transfer of a phosphate group from ATP to the 5'-hydroxyl termini of polynucleotides. Selective labeling of the 5'-hydroxyl termini of DNA with polynucleotide kinase has been used to study the number and the identity of the 5'-terminal residues of bacteriophage DNA's, and to examine the nature of the phosphodiester bond cleavages produced by endonucleases and by sonic irradiation. The intact strands of T7 DNA bear 5'-phosphoryl end-groups; only deoxyadenylate and deoxythymidylate are present as 5'-terminal residues. The intact strands of native lambda-DNA bear 5'-hydroxyl end-groups. M13 DNA, a circular molecule, cannot be phosphorylated. End-group labeling of DNA provides a method for determination of molecular weight; calibration against other DNA preparations is not required. The molecular weight of a single strand of T7 DNA, determined by end-group labeling, is 13.1 x 10(6); the molecular weight of a single strand of lambda-DNA is 16.0 x 10(6). These values are in agreement with molecular weight estimates by sedimentation analysis and electron microscopy. Sonic irradiation of DNA has been shown to favor the production of polynucleotides terminated by 5'-phosphomonoester groups. All four deoxyribonucleotides are present as 5'-terminal residues of sonicated DNA.
Heuristic algorithms to solve combinatorial problems with photonics (2021)

Combinatorial problems, such as the Ising problem, are hard to solve with conventional electronics. Photonic systems have recently been proposed as an efficient platform to solve these problems faster and more efficiently, thus calling for the development of featured algorithms to run on photonic machines. A few recent findings, including the Photonic Recurrent Ising Sampler, a photonic machine that recurrently solves arbitrary Ising problems, will be presented in this talk, along with their experimental realizations in various platforms.
Porphyrin- or phthalocyanine-bridged silsesquioxane nanoparticles for two-photon photodynamic therapy or photoacoustic imaging (2017)

Porphyrin- or phthalocyanine-bridged silsesquioxane nanoparticles (BSPOR and BSPHT) were prepared. Their endocytosis in MCF-7 cancer cells was shown with two-photon excited fluorescence (TPEF) imaging. With two-photon excited photodynamic therapy (TPE-PDT), BSPOR was more phototoxic than BSPHT, which in contrast displayed a very high signal for photoacoustic imaging in mice.
193 nm Immersion Lithography-Taking the Plunge (2004)

This paper reviews the current status and future outlook of materials for 193 nm immersion lithography, with special focus on top barrier layers, photoresists, bottom antireflective coatings for numerical apertures exceeding unity, and future challenges for imaging materials along the Roadmap.
Supplementary Figures and Legends from Cancer-Associated Fibroblasts Promote Immunosuppression by Inducing ROS-Generating Monocytic MDSCs in Lung Squamous Cell Carcinoma (2023)

&lt;p&gt;Supplementary Figures 1-11&lt;/p&gt;
Oats (2019)

Originally seen as a weed, oats have become an international food staple and the usefulness of oats has steadily increased. Oats contain macronutrients such as protein, fat, and dietary fiber and micronutrients, such as phenolic acids, vitamins, and minerals. Deficiencies of micronutrients, required by organisms throughout life in small quantities, are often known as "hidden hunger," since they are less visible than deficiencies of macronutrients such as protein. The micronutrients in oats include not only trace minerals but also vitamins, as well as phytochemicals such as carotenoids, phenolic acids, flavonoids, avenanthramides, and saponins. Oats are nutrient dense and have a healthy composition of macromolecules; the high protein content of oats sets it apart from other commonly eaten cereals. Whole oats contain many nutrients and bioactive phytochemicals, and oat consumption is demonstrated to reduce the risk of several diseases, including cardiovascular disease, diabetes, and possibly certain types of cancer.
Melatonin exists in porcine follicular fluid and improves in vitro maturation and parthenogenetic development of porcine oocytes (2009)

This study focused on the effect of melatonin on in vitro maturation of porcine oocytes and their parthenogenetic embryonic development. Melatonin was measured in porcine follicular fluid of follicles of different sizes in the same ovary. Melatonin exists in follicular fluid, and the concentration is approximately 10(-11) m. Its concentration decreased as the diameter of follicle increased, which suggests an effect of melatonin on oocyte maturation. Therefore, immature oocytes were cultured in vitro in maturation medium supplemented with melatonin (10(-11), 10(-9), 10(-7), 10(-5) and 10(-3) m) or without melatonin. The oocytes at maturation stage were collected and activated. The parthenogenetic embryos were cultured and observed in medium supplemented with or without melatonin. Fresh immature oocytes without melatonin treatment were used as control. When only maturation medium was supplemented with 10(-9) m melatonin, the cleavage rate, blastocyst rate and the cell number of blastocyst (70 +/- 4.5%, 28 +/- 2.4% and 50 +/- 6.5%) were significantly higher (P < 0.05) than that of controls; when only culture medium was supplemented with melatonin, the highest cleavage rate, blastocyst rate and the cell number of blastocyst was observed at 10(-7) m melatonin, which were significantly higher than that of controls (P < 0.05). The best results (cleavage rates 79 +/- 8.4%, blastocyst rates 35 +/- 6.7%) were obtained when both the maturation and culture medium were supplemented with 10(-9) m melatonin respectively (P < 0.05). In conclusion, exogenous melatonin at the proper concentration may improve the in vitro maturation of porcine oocytes and their parthenogenetic embryonic development. Further research is needed to identify the effect of melatonin on in vitro and in vivo oocyte maturation and embryo development in porcine.
Crenotalea thermophila gen. nov., sp. nov., a member of the family Chitinophagaceae isolated from a hot spring (2014)

A thermophilic aerobic bacterium designated strain STH-1-Y1(T) was isolated from sulfur-turf in a Japanese hot spring (Okuhodaka hot spring, Gifu Pref.). Colonies of strain STH-1-Y1(T) were yellow and low convex morphology with a slightly irregular fringe. Cells were slender long rods, 0.4-0.6 µm wide and 1.2-3.0 µm long. The isolate was an obligate aerophilic organism, and could not grow by fermentation or nitrate respiration. The isolate had a thermophilic trait, and could grow at 35-60 °C and pH 5.5-7.5; maximum growth occurred at 55 °C and pH 7.0 with a doubling time of 1.9 h. The Biolog and API tests suggested that strain STH-1-Y1(T) was able to use various sugars such as glucose, lactose, mannose, maltose, trehalose, cellobiose and sucrose, but could not use sugar alcohols other than glycerol, i.e. adonitol, arabitol, erythritol, inositol, mannitol, sorbitol and xylitol. Lactate and glutamate could be used, but other fatty acids, i.e. acetate, citrate, propionate and succinate could not. Gelatin, casein, starch and glycogen were hydrolysed, but neither chitin nor agar was degraded. Cells lacked flexirubin and showed oxidase and catalase activities. The major respiratory quinone was menaquinone-7 (MK-7), and major cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH, iso-C17 : 0 and anteiso-C15 : 0. No unsaturated fatty acids were detected. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain STH-1-Y1(T) was closely related to the family Chitinophagaceae within the phylum Bacteroidetes. However, the isolate was evenly distant from all members in this family with sequence similarities of 87-89 %. These significantly low sequence similarities strongly suggested that strain STH-1-Y1(T) represents a novel species in a new genus of the family Chitinophagaceae within the phylum Bacteroidetes. Based on phenotypic and phylogenetic characteristics, the name Crenotalea thermophila gen. nov., sp. nov. is proposed. The type strain of the type species is STH-1-Y1(T) ( = JCM 11541(T) = DSM 14807(T)).
Abstract A46: Identification of ALDH1A3 as an important biomarker and therapeutic target for non-small cell lung cancer (NSCLC) cancer stem cells (CSCs) (2012)

Abstract A considerable amount of evidence reveals the important roles of cancer stem cells (CSCs, also called “cancer initiating cells”) in tumor growth, metastasis, relapse and drug resistance. Our group has identified lung CSCs in both lung cancer cell lines and patient tumor samples by their elevated Aldehyde Dehydrogenase (ALDH) activity and demonstrated that NSCLC patients whose tumors are enriched in ALDH+ cells have inferior survival, and that the ALDH+ subpopulations (ranging from 0.5 to 30% of tumor cells) are self renewing, and significnatly more clonogenic and tumorigencic (in xenograft models) than the ALDH− population. To further define the molecular profile of lung CSCs and to identify key pathways involved in lung CSC function we performed genome wide microarray expression profiling of isolated ALDH+ and ALDH− cell populations from 8 non-small cell lung cancer (NSCLC) lines representing a variety of oncogenotypes to determine genes that are differentially expressed in these two populations. Strikingly we found that different lung cancers exhibited different ALDH+ cell population expression profiles but that the ALDH1A3 isozyme was one of the few commonly genes whose expression was elevated. (Previously our group and other investigators in lung and other cancers had found the ALDH1A1 and not ALDH1A3 isozyme to be a marker of the ALDH+ population). ALDH1A3 differential expression was confirmed by q RT PCR and elevated ALDH1A3 protein levels which in turn was correlated with the % of ALDH+ tumor cells in each tumor. ALDH1A3 mRNA levels in (N = 182) resected lung adenocarcinoma samples showe that the highest levels of ALDH1A3 were associated with inferior survival. Of great importance, shRNA mediated knockdown of ALDH1A3 dramatically reduced both NSCLC cell colony formation in vitro and tumor growth in vivo demonstrating the functional importance of ALDH1A3 expression in NSCLCs. However, ectopic expression of ALDH1A3 in NSCLC cells did not enhance lung cancer cell growth and tumor formation, suggesting that ALDH1A3 alone is not sufficient to promote lung cancer progression. We conclude that ALDH1A3 is the predominant ALDH isozyme responsible for ALDH activity in NSCLCs of many oncogenotypes, is of potential prognostic importance, and a new therapeutic target for eliminating NSCLC stem cells.
Toward a Force Spectroscopy of Polymer Surfaces (1998)

The adhesional forces between a series of polymer film surfaces and chemically well-defined atomic force microscopy tips have been measured and found to depend strongly on the chemical nature of both probe and sample surfaces. For a given series of polymers, the ranking in adhesion strength was markedly different for polar and nonpolar probes, irrespective of the precise chemical composition of those probes. In the case of nonpolar polymers, a correlation of adhesion force with calculations based on the Lifshitz theory of Van der Waals interactions was found. In the case of polar polymers, a reasonable correlation with water-contact angle was observed. The adhesional differences between different probe tips translate into reversals of chemical contrast in high-spatial-resolution lateral force images, when examining polymer blends using chemically different tips, demonstrating the potential of this approach for the nanometer-scale, friction-mediated surface-chemical imaging of polymers. Central to these experiments has been the use of perfluorodecalin as a medium for measuring interactions. Employment of this liquid greatly facilitates measurement of the forces between the probe tip and the polymer surface.
Photosensitized release of von Willebrand factor from cultured human endothelial cells. (1991)

Cultured endothelial cells from the human umbilical vein were incubated with low concentrations (1 microgram/ml) of the photosensitizer Photofrin II. Following a sublethal light exposure, a light dose-dependent release of von Willebrand factor (vWf) into the culture medium was observed. Analysis of the multimeric composition of the released protein indicated that it originated from the intracellular pool of large vWf multimers stored in the Weibel-Palade bodies. This release was detected as early as 1 h postirradiation. Release was inhibited at low temperature and was dependent upon the presence of extracellular calcium. Photosensitization resulted in an influx of calcium whose time course paralleled vWf release from the cells. Since vWf mediates platelet adhesion to the vascular subendothelium, it is possible that its photochemically stimulated release in vivo could contribute to platelet thrombus formation observed in tissue following photodynamic therapy.