gebhart/patrepeval huggingface dataset:
Preclinical assessment of anti-cancer drugs by using RP215 monoclonal antibody (2009)

RP215 monoclonal antibody was originally generated against OC-3-VGH ovarian cancer cells. It was shown to recognize specifically a carbohydrate-associated epitope(s) of cancer cell-expressed immunoglobulin heavy chains designated as CA215. Previous studies suggest that CA215 is expressed by all human cancer cell lines and tissues in both membrane bound and secreted forms. It may be an ideal target for therapeutic treatments of human cancers with humanized RP215-related antibodies. Based on the results of large scale immunohistochemical studies (50-100 cases each), the following types of cancers revealed high percentage(s) of positive staining with RP215: esophagus (76%), stomach (50%), colon (44%), ovary (64%), breast (32%), lung (31%), cervix (84%) and endometrium (78%). Nude mouse experiments were performed to determine if RP215 has any inhibitory effect on the growth of cancer cells in vivo. Following injections of a single dose (10 mg/kg) of I(131)-labeled RP215 (specific activity, 12.5 muCi/mg), the tumor size (OC-3-VGH ovarian cancer cells) was reduced to 30% of the untreated control within two weeks. By injecting the same dose, the unlabeled RP215 also reduced the tumor size to 50% of the control during the same period. The antibody treatments were found to have little effect on the body weight as well as apparent toxicity of these animals. To proceed with clinical trial studies of RP215-based anti-cancer drugs, chimeric form of this monoclonal antibody was generated and characterized. Through our effort, the "proof of concept" of anti-cancer drugs development was clearly established for the next stages of clinical trial studies.
Deposition of Dense Siloxane Monolayers from Water and Trimethoxyorganosilane Vapor (2011)

A convenient, laboratory-scale method for the vapor deposition of dense siloxane monolayers onto oxide substrates was demonstrated. This method was studied and optimized at 110 °C under reduced pressure with the vapor of tetradecyltris(deuteromethoxy)silane, (CD(3)O)(3)Si(CH(2))(13)CH(3), and water from the dehydration of MgSO(4)·7H(2)O. Ellipsometric thicknesses, water contact angles, Fourier transform infrared (FTIR) spectroscopy, and electrochemical capacitance measurements were used to probe monolayer densification. The CD(3) stretching mode in the FTIR spectrum was monitored as a function of the deposition time and amounts of silane and water reactants. This method probed the unhydrolyzed methoxy groups on adsorbed silanes. Excess silane and water were necessary to achieve dense, completely hydrolyzed monolayers. In the presence of sufficient silane, an excess of water above the calculated stoichiometric amount was necessary to hydrolyze all methoxy groups and achieve dense monolayers. The excess water was partially attributed to the reversibility of the hydrolysis of the methoxy groups.
Methyl-β-cyclodextrin restores impaired autophagy flux in Niemann-Pick C1-deficient cells through activation of AMPK (2017)

The drug 2-hydroxypropyl-β-cyclodextrin (HPβCD) reduces lysosomal cholesterol accumulation in Niemann-Pick disease, type C (NPC) and has been advanced to human clinical trials. However, its mechanism of action for reducing cholesterol accumulation in NPC cells is uncertain and its molecular target is unknown. We found that methyl-β-cyclodextrin (MβCD), a potent analog of HPβCD, restored impaired macroautophagy/autophagy flux in Niemann-Pick disease, type C1 (NPC1) cells. This effect was mediated by a direct activation of AMP-activated protein kinase (AMPK), an upstream kinase in the autophagy pathway, through MβCD binding to its β-subunits. Knockdown of PRKAB1 or PRKAB2 (encoding the AMPK β1 or β2 subunit) expression and an AMPK inhibitor abolished MβCD-mediated reduction of cholesterol storage in NPC1 cells. The results demonstrate that AMPK is the molecular target of MβCD and its activation enhances autophagy flux, thereby mitigating cholesterol accumulation in NPC1 cells. The results identify AMPK as an attractive target for drug development to treat NPC.
The Tissue-Specific Self-Pathogen Is the Protective Self-Antigen: The Case of Uveitis (2002)

Vaccination with peptides derived from interphotoreceptor retinoid-binding protein (a self-Ag that can cause experimental autoimmune uveoretinitis) resulted in protection of retinal ganglion cells from glutamate-induced death or death as a consequence of optic nerve injury. In the case of glutamate insult, no such protection was obtained by vaccination with myelin Ags (self-Ags associated with an autoimmune disease in the brain and spinal cord that evokes a protective immune response against consequences of injury to myelinated axons). We suggest that protective autoimmunity is the body's defense mechanism against destructive self-compounds, and an autoimmune disease is the outcome of a failure to properly control such a response. Accordingly, the specific self-Ag (although not necessarily its particular epitopes) used by the body for protection against potentially harmful self-compounds (e.g., glutamate) can be inferred from the specificity of the autoimmune disease associated with the site at which the stress occurs (irrespectively of the type of stress) and is in need of help.
JOHN DEWEY'NİN EĞİTİME BAKIŞI ÜZERİNE YENİ BİR YORUM (2005)

Bu calismada, unlu pedagog John Dewey’nin egitim anlayisi, Turk egitim sistemi ile iliskilendirilerek degerlendirilmektedir. Dewey pragmatist felsefeyi egitime uygulamistir. Ona gore; egitim, yasam boyu suren bir eylemdir. Bu yuzden en etkili ogrenme, yaparak ve yasarak edinilir. Cocugun dogal yapisi, bireysel farkliliklari dikkate alinmali ve egitimin merkezi cocuk olmali, dersler de onun ilgi ve yeteneklerine gore duzenlenmelidir. Cocuk edilgen, ezberci bir egitime asla zorlanmamali, kurama degil uygulamaya agirlik verilmelidir. Bilgiler hicbir zaman hazir sunulmamali, cocugun kesfetmesine ve dusunmesine olanak taninmalidir. Sonuc olarak, Dewey’nin gorusleri, egitim alaninda onemli yaklasimlar one surmus, ardindan baska fikirlerin gelisimine yol acmistir. Onun gorusleri uzerine yeniden dusunmemiz ise, egitim sistemimize yonelik elestirel bir degerlendirme firsati sunmasi bakimindan onem tasimaktadir
'Fine-to-Coarse' Route Planning and Navigation in Regionalized Environments (2003)

Environments that are divided into regions lead to hierarchical encoding of space. Such memory structures are known to systematically distort estimates of distance and direction and affect spatial priming and memory recall. Here we present two navigation experiments in virtual environments that reveal an influence of environmental regions on human route planning and navigation behaviour. Following the hierarchical theories of spatial representations, it is argued that environmental regions are explicitly represented in spatial memory and that human route planning takes into account region-connectivity and is not based on place-connectivity alone. We also propose a fine-to-coarse planning heuristic that could account for the empirical data by planning in a representation that uses fine-space information for close locations and coarse-space information for distant locations simultaneously.
Dispersion of a non-uniform slug in time-dependent flow (1971)

Abstract Dispersion of a non-uniform slug in time variable fully developed laminar flow is studied by an exact method which in principle is valid for all values of time. A generalized dispersion model, which involves an infinite set of time-dependent coefficients Ki(T), arises naturally as a consequence of the analysis. Expressions are obtained from first principles for the convective coefficient K1(T), the apparent diffusion coefficient K2(T), and the rest of the coefficients Ki(T). The convective coefficient K1(T) is a new quantity which is time dependent, even if the velocity field is steady, because the initial distribution of solute is non-uniform. The general method of analysis proposed is applied to the particular case of a slug of material of length xs and radius aR which is initially symmetrically located in a tube of radius R, and then is dispersed in steady laminar flow. Breakthrough curves for various downstream positions show that the mean velocity of the material in the slug is greater than the average velocity of flow for small residence times and, as one would expect intuitively, approaches this value as the distance between the injection and observation points increases. It also is shown that for T ≲ 0.5, K2, the axial dispersion coefficient, decreases as the initial slug radius decreases. However, for all values of 'a', both K1 and K2 approach the asymptotic values of —½ and (Pe)-2 + 1/192 respectively for values of dimensionless time T ≳ 0.5. Since the initial concentration distribution of solute in the slug affects the time of arrival of the peak mean concentration at a downstream location, this may cause errors in the estimation of mean flow rates by tracer techniques. For example, if one injects a quantity of material into a stream and assumes it is uniformly distributed across the tube, when in reality it occupies only a part of the tube, this leads to overestimating the average flow velocity. This may be of practical importance in a variety of applications.
.pi.-Groups in ion pair bonding. Fluorenyllithium bisquinuclidine (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT.pi.-Groups in ion pair bonding. Fluorenyllithium bisquinuclidineJ. J. Brooks, Wendell Rhine, and G. D. StuckyCite this: J. Am. Chem. Soc. 1972, 94, 21, 7339–7346Publication Date (Print):October 1, 1972Publication History Published online1 May 2002Published inissue 1 October 1972https://pubs.acs.org/doi/10.1021/ja00776a013https://doi.org/10.1021/ja00776a013research-articleACS PublicationsRequest reuse permissionsArticle Views139Altmetric-Citations94LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Estimation of Electron Transfer Distances from AM1 Calculations (2000)

We examine a simple approximate method for calculating the electron transfer (ET) distance suitable for extracting the off-diagonal electronic coupling element (Hab) of Marcus−Hush theory from the optical spectrum of nitrogen-centered organic intervalence radical cations. A very simple estimate of the ET distance on the adiabatic ground-state surface (d12(dm)) is employed. AM1-UHF calculation of the dipole moment component in the long axis direction (μ1) for the radical cation using the center of mass as the origin gives the estimated d12(dm) (Å) = 2μ1(Debye)/4.8023 (eq 7). Cave and Newton's Generalized Mulliken−Hush theory equation allows calculation of the diabatic counterpart (dab) in terms of d12 and the transition dipole moment (μ12), obtained from the experimental intervalence optical band. These calculations indicate that dab is significantly smaller than the distance between the nominal sites or charge localization, ratio 0.82−0.85 for the aromatic-bridged bis(hydrazines), 0.76−0.87 for the unsaturated-bridged bis(triarylamines), 0.74−0.79 for the saturated-bridged bis(diazenes), and 0.71−0.85 for the saturated-bridged bis(hydrazines) examined here. Furthermore, dab is not very different for diastereomers that differ in relative orientation of the oxidized and reduced charge-bearing units for the aromatic-bridged compounds; experimental data corresponds to a superposition of the spectra of such isomers. There appears to be a problem with the trend of calculated ET distances as methyl groups are substituted on a benzene-1,4-diyl bridge. The d12(dm) calculated is smaller for the compound with the tetramethyl-substituted bridge (DU) than that with the dimethyl-substituted bridge (XY), in contrast to the general trend in d12 as twisting increases, and to the dipolar splitting constant for the triplet form of the dication oxidation states of these compounds.
Spectrometer manager: A versatile control software for pulse EPR spectrometers (2005)

A versatile control software for pulse EPR spectrometers is introduced. Common and task-specific problems are discussed and their solutions are described. The software provides the full spectrum of possibilities needed to perform arbitrary multidimensional pulse experiments. It allows for an easy interfacing of commonly used hardware components and enables straightforward modifications of the spectrometer. Good performance, configurability, and a number of unique features turn this software into an excellent tool for the operation of modern EPR spectrometers and upgrading old ones. © 2005 Wiley Periodicals, Inc. Concepts Magn Reson Part B (Magn Reson Engineering) 26B: 36–45, 2005
Novel adhesion promoters based on hyper-branched polymers (2004)

Abstract With the emergence of experimental and commercial highly branched polymers (HBPs) having two or three dimensional morphologies with high peripheral functionality, new opportunities have been created for formulating and tailoring new architectures for thermoset adhesives and related adhesion promoters. The authors studied a few adhesive systems previously, where the crosslinking agents had been either totally or partially replaced by the HBPs. In epoxy and polyurethane systems addition of poly-amido-amines (PAMAMs) HBPs, improved the mechanical and thermal properties of the adhesives due to increase of crosslinking density and formation of modified multiphase morphologies having high-energy absorption network. In the present study the objective was to investigate the effects of HBP PAMAM primers on interfacial characteristics of epoxy and polyurethane bonded joints, using various substrates (Aluminum, Magnesium, plastics and fibers) prior and after exposure to a combination of heat and humidity. It was shown that the interfacial adhesion and the durability increase significantly (100–250%) in all the studied joints where PAMAMs were used for surface treatment. Keywords: ADHESION PROMOTERHYPER-BRANCHDENDRIMERSHEAR STRENGTHDURABILITY
Fuzzy handling of uncertainty in industrial recycling (2002)

During the latest years recycling has become more and more important. When the products have reached their end of life they need to be classified for repair or disassembly. The products classified for repair are then manually repaired. For those products classified for disassembly this can be performed either manually or automatically. In order to perform automatic disassembly we need to make measurements, sometimes complex, on the product. To this end, a complex sensor system with flexible sensor signal fusion is required. The fusion algorithm must be fast, flexible, robust, able to handle all kinds of sensors and achieve a high degree of transparency. It is not easy to fulfil all these requirements, which are central to automatized disassembly. Fuzzy logic, however, holds promise to this end. However, there are problems even with fuzzy logic. The theory concerning fuzzy logic deals only with uncertainty for control actions or for measured values but not for the combination of both. When we measure for automatic disassembly there are many sources of uncertainty and concurrently uncertainty in the control actions. Hence a technique for fuzzy handling of uncertainty for the combination is needed. A solution to this problem is proposed in this paper. The proposed method deals with uncertainty in the measured values as well as in the membership functions.
Processes driving nocturnal transpiration and implications for estimating land evapotranspiration (2015)

Evapotranspiration is a major component of the water cycle, yet only daytime transpiration is currently considered in Earth system and agricultural sciences. This contrasts with physiological studies where 25% or more of water losses have been reported to occur occurring overnight at leaf and plant scales. This gap probably arose from limitations in techniques to measure nocturnal water fluxes at ecosystem scales, a gap we bridge here by using lysimeters under controlled environmental conditions. The magnitude of the nocturnal water losses (12-23% of daytime water losses) in row-crop monocultures of bean (annual herb) and cotton (woody shrub) would be globally an order of magnitude higher than documented responses of global evapotranspiration to climate change (51-98 vs. 7-8 mm yr(-1)). Contrary to daytime responses and to conventional wisdom, nocturnal transpiration was not affected by previous radiation loads or carbon uptake, and showed a temporal pattern independent of vapour pressure deficit or temperature, because of endogenous controls on stomatal conductance via circadian regulation. Our results have important implications from large-scale ecosystem modelling to crop production: homeostatic water losses justify simple empirical predictive functions, and circadian controls show a fine-tune control that minimizes water loss while potentially increasing posterior carbon uptake.
Encephalopathy and bilateral cataract in a boy with an interstitial deletion of Xp22 comprising the CDKL5 and NHS genes (2007)

We describe a male patient with a deletion at Xp22, detected by high resolution X-array CGH. The clinical phenotype present in this infant boy, consists of severe encephalopathy, congenital cataracts and tetralogy of Fallot and can be attributed to the deletion of the genes within the interval. Among these deleted genes are the gene for Nance-Horan syndrome and the cyclin-dependent kinase-like 5 gene (CDKL5), responsible for the early seizure variant of Rett syndrome. This is the first description of a male patient with a deletion of these genes, showing the involvement of CDKL5 in severe epileptic encephalopathy in males. Moreover it illustrates the added value of high resolution array-CGH in molecular diagnosis of mental retardation-multiple congenital anomaly cases.
Predictive maintenance decision using statistical linear regression and kernel methods (2014)

In this paper, we develop a predictive maintenance (PdM) method to determine the most effective time to apply maintenance to an equipment and study its application to a real semiconductor etching chamber. More specifically, we first apply linear regression to predict the (output) equipment health condition from the (input) operational parameters. This choice of linear model also allows us to propose an algorithm to reduce the number of operational parameters to be monitored for PdM purposes using t-statistics. Then, we follow a cross-validation based procedure to generate prediction error samples and apply a kernel method to construct the corresponding probability density function of the prediction error. Finally, the PdM decision can be made based on the likelihood of the predicted health condition exceeding a certain maintenance threshold. Our analysis using real data from a semiconductor etching chamber shows that the proposed PdM decision with the reduced dimension linear regression performs comparably to the one using full-scale linear model and can be used for better maintenance planning compared to the existing practice of fixed-schedule maintenance.
High-affinity uptake of L-kynurenine by a Na+-independent transporter of neutral amino acids in astrocytes (1989)

L-Kynurenine (KYN), an intermediary product in the kynurenine pathway of tryptophan metabolism, is the common precursor from which are formed both quinolinic acid, a potent endogenous "excitotoxin," and kynurenic acid, a nonselective antagonist of excitotoxins. The present work examines 3H-KYN transport in primary astrocyte cultures derived from the cerebra of newborn mice. Influx and efflux of 3H-KYN were attributable almost entirely to carrier-mediated transport. The tritium recovered in uptake experiments was identifiable as 3H-KYN, indicating a low rate of KYN metabolism during incubations up to 30 min. KYN uptake decreased in the presence of extracellular Na+, at least in part because KYN efflux was accelerated. Marked trans stimulation of KYN efflux by extracellular KYN provided evidence of the exchanging nature of the carrier. Saturation curves for the initial velocity of KYN uptake conformed to a 1-component saturable system with Km of 32 microM and Vmax of 2.1 nmol mg-1 protein min-1. KYN was notably concentrated by the astrocytes, with an estimated steady-state distribution ratio of 180-fold for 1 microM KYN. Analog inhibition studies showed that the KYN transporter exhibited a clear preference for large neutral amino acids; leucine, tryptophan, and phenylalanine were recognized with relatively higher affinity than KYN. In summary, KYN is concentratively transported into astrocytes by a Na+-independent exchanger with high affinity for branched-chain and aromatic neutral amino acids. The substrate specificity and high affinity of this transport system resemble the properties of neutral amino acid transport across the blood-brain barrier in the rat and human.
Nucleoside 2-Deoxyribosyltransferase (1995)

Nucleoside 2-deoxyribosyltransferase catalyzes cleavage of a 2'-deoxyribosylnucleoside (A) to a nucleobase (P) with deoxyribosylation of the enzyme. Substrates quenched the intrinsic fluorescence of native enzyme (E) and a catalytically inactive mutant enzyme (E98A enzyme). The time courses of these reactions were analyzed in terms of the following scheme where EX is the 2-deoxyribosyl ester of Glu-98. [formula: see text] The initial complexes between E and dAdo, dGuo, dIno, and dCyd or those between EX and the corresponding nucleobases were formed in a rapid equilibrium step. Native enzyme and E98A enzyme bound 2'-deoxyribosylnucleosides with similar affinities (k-1/k1). From a comparison of the time-dependent fluorescence changes associated with the reaction of native enzyme or E98A enzyme with these substrate, the kinetic step for 2-deoxyribosylation of Glu-98 was identified (k2 and k-2). dThd and dUrd quenched the fluorescence of native enzyme in a biphasic process. The late phase of this reaction was associated with 2-deoxyribosylation of Glu-98. The pre-steady-state kinetic constants calculated from fluorescence quenching data for dAdo and Cyt were consistent with the experimental values for the steady-state kinetic coefficients and the equilibrium constant of the reaction.
A LAT Mutation That Inhibits T Cell Development Yet Induces Lymphoproliferation (2002)

Mice homozygous for a single tyrosine mutation in LAT (linker for activation of T cells) exhibited an early block in T cell maturation but later developed a polyclonal lymphoproliferative disorder and signs of autoimmune disease. T cell antigen receptor (TCR)-induced activation of phospholipase C-gamma1 (PLC-gamma1) and of nuclear factor of activated T cells, calcium influx, interleukin-2 production, and cell death were reduced or abrogated in T cells from LAT mutant mice. In contrast, TCR-induced Erk activation was intact. These results identify a critical role for integrated PLC-gamma1 and Ras-Erk signaling through LAT in T cell development and homeostasis.