gebhart/patrepeval huggingface dataset:
Characterizing the DNA binding modes of a topoisomerase I-poisoning terbenzimidazole: evidence for both intercalative and minor groove binding properties. (1996)

We have used a broad range of spectroscopic and viscometric techniques to demonstrate that the complexation of a cytotoxic, topoisomerase I-poisoning terbenzimidazole (5PTB) with the poly(dA).poly(dT) duplex exhibits properties characteristic of both intercalation and minor groove binding. Our results reveal the following features: (i) Optical melting profiles reveal that 5PTB binding enhances the thermal stability of the poly(dA).poly(dT) duplex; (ii) Fluorescence-detected 5PTB binding to the poly(dA).poly(dT) duplex reveals four apparent "site sizes," ranging from 1 to 13 base pairs (bp) per bound drug; (iii) Flow linear dichroism data suggest conformational heterogeneity among the poly(dA).poly(dT)-bound 5PTB molecules, with substantial contributions from drug molecules bound in the minor groove; (iv) Fluorescence resonance energy transfer data reveal properties characteristic of a significant contribution from an intercalative mode of binding; (v) Viscometric, fluorescence quenching, and netropsin competition data are consistent with 5PTB binding to poly(dA).poly(dT) by "mixed" modes, which are operationally defined as single or multiple binding populations that individually and/or collectively express both intercalative and minor groove binding properties. We comment on a potential correlation between drugs that exhibit such "mixed" mode binding motifs and those that express antineoplastic activity through inhibition of topoisomerase I.
Correction: In Vivo E2F Reporting Reveals Efficacious Schedules of MEK1/2–CDK4/6 Targeting and mTOR–S6 Resistance Mechanisms (2018)

In the original version of this article (1), an error in Fig. 6C was introduced by the compositor during the production of the paper. Specifically, the Raptor Western blot was improperly shifted. The figure has been corrected in the latest online HTML and PDF versions of the article. The publisher regrets the error.
Thiobarbituric acid test for detecting lipid peroxides (1979)

Abstract The thiobarbituric acid (TBA) test has been used in the field of medical science in recent years to detect lipid peroxides. In this case, it is necessary for hydroperoxides to be decomposed to secondary products during the reaction. When purified methyl linoleate and methyl linolenate monohydro‐peroxides were used as the sample for the TBA test, they did not decompose entirely to secondary products, but did so completely when an iron catalyst (ferrous sulfate) was added. However, the iron catalyst also accelerated the autoxidation of coexisting unsaturated fatty acids. Therefore, the addition of antioxidants was required. Fifteen min of heating was sufficient to complete the reaction. With additions of catalyst and antioxidant to the TBA test, it may be possible to make useful distinctions between hydroperoxides and secondary products of lipid oxidation.
Mechanism of quasilinear temperature dependence of the surface magnetization in a semi-infinite ferromagnet (1989)

A semiclassical method involving surface spin waves is used to calculate the spontaneous magnetization M near the surface of a semi-infinite ferromagnet. The magnitude of the surface anisotropy constant ${K}_{s}$ introduced by N\'eel is assumed to be negligible compared to the magnitude of the surface anisotropy constant ${K}_{\mathrm{ss}}$ introduced by the present author. It is shown that under these conditions any positive value of ${K}_{\mathrm{ss}}$ causes the dependence of M on the temperature T to be quasilinear rather than proportional to ${T}^{3/2}$ and the dependence of M on position to be exponential. This surface-anisotropy-based mechanism contains a weakened-surface-exchange model as a special case. The theoretical predictions are found to provide a possible interpretation of recent experimental results on ${\mathrm{MnF}}_{2}$-covered Fe(110).
Segregation Distortion of T-DNA Markers Linked to the Self-Incompatibility (S) Locus in Petunia hybrida (2000)

In plants with a gametophytic self-incompatibility system the specificity of the pollen is determined by the haploid genotype at the self-incompatibility (S) locus. In certain crosses this can lead to the exclusion of half the gametes from the male parent carrying a particular S-allele. This leads to pronounced segregation distortion for any genetic markers that are linked to the S-locus. We have used this approach to identify T-DNA insertions carrying a maize transposable element that are linked to the S-locus of Petunia hybrida. A total of 83 T-DNA insertions were tested for segregation distortion of the selectable marker used during transformation with Agrobacterium. Segregation distortion was observed for 12 T-DNA insertions and at least 8 of these were shown to be in the same linkage group by intercrossing. This indicates that differential transmission of a single locus (S) is probably responsible for all of these examples of T-DNA segregation distortion. The identification of selectable markers in coupling with a functional S-allele will allow the preselection of recombination events around the S-locus in petunia. Our approach provides a general method for identifying transgenes that are linked to gametophytic self-incompatibility loci and provides an opportunity for transposon tagging of the petunia S-locus.
Polymer-Supported Quinuclidinyl Catalysts for Synthesis of Cyclopolymerizable Monomers via the Aldehyde−Acrylate Coupling Reaction (1997)

With an appropriate amine catalyst, formaldehyde addition to acrylates results in α-hydroxymethyl acrylate intermediates that undergo a further condensation reaction to provide ether-linked 1,6-diene monomers capable of efficient cyclopolymerization. While 1,4-diazabicyclo[2.2.2]octane (DABCO) is an effective catalyst in the synthesis of these cyclopolymerizable monomers, a series of polymer-supported amine catalysts were prepared and evaluated in an effort to further simplify this process. 3-Quinuclidinol was reacted with methacrylic anhydride to give the functionalized methacrylate monomer, which was copolymerized with methyl methacrylate and triethylene glycol dimethacrylate. Various polymerization techniques (bulk, solution, and suspension) were used to produce the cross-linked polymeric catalysts. Supports with mole fractions of catalyst ranging from 20% to 98% were examined. In reactions with ethyl acrylate and paraformaldehyde, certain polymer-supported catalysts gave near quantitative conversion to products. The rate of reaction with the polymeric catalysts was less than that of reactions with DABCO or other nonpolymeric model catalysts; however, after reaction times of 20 h, product yields and distributions were quite similar. With the polymeric catalysts, product isolation required only simple filtration or a solvent wash rather than an aqueous extraction step. This technique was also applied to the preparation of cyclopolymerizable resins containing multifunctional oligomers.
Information Issues in Model Specification (1991)

This paper explores the tradeoffs and information issues in model specification, i.e., choosing the appropriate level of detail and precision of decision support models. For many real-time and distributed decision problems, decision-makers face a wide spectrum of information gathering choices that vary in the amount and quality of information as well as their associated costs and delays. Modeling these problems raises several operational and strategic questions including: • how much and what type of information to acquire before making a decision. • what protocol to use for exchanging information among multiple decision-makers. • what organization and information structure (e.g., centralized, coordinated, distributed) to use for effective information sharing and decision-making. We highlight the modeling issues and tradeoffs using examples from production planning, distributed processing, and network routing, and draw upon research in diverse fields, including information economics and game theory, knowledge logic in computer science, and distributed computation, to obtain model specification insights. Our discussions emphasize and illustrate two main model specification themes. First, acquiring additional information often has diminishing returns (in terms of the quality of decisions suggested by the model); therefore, an imprecise model based on partial information might be more appropriate than using a detailed and accurate model that identifies ‘optimal’ decisions. Concepts from information economics and team theory provide a framework for analyzing this tradeoff. We also briefly discuss some heuristic methods to identify effective information gathering strategies. Our second theme applies to systems consisting of several decision-makers who make interdependent decisions. In this context, the decision model for each agent must be based on an understanding of what information to exchange, how frequently, and what protocol to use for exchanging information. We illustrate how complete information sharing among distributed decision-makers might even be impossible because of a possible dead-lock in decision-making. This game-theoretic phenomenon has implications for designing the organization structure, information systems, and communication protocols to support multi-agent decision-making.
Up-regulation of plasma membrane-associated ganglioside sialidase (Neu3) in human colon cancer and its involvement in apoptosis suppression (2002)

Human plasma membrane-associated sialidase (Neu3) is unique in specifically hydrolyzing gangliosides, thought to participate in cell differentiation and transmembrane signaling, thereby playing crucial roles in the regulation of cell surface functions. We have discovered levels of mRNA for this sialidase to be increased in restricted cases of human colon cancer by 3- to 100-fold compared with adjacent nontumor mucosa (n = 32), associated with significant elevation in sialidase activity in tumors (n = 50). In situ hybridization showed the sialidase expression in epithelial elements of adenocarcinomas. In cultured human colon cancer cells, the sialidase level was down-regulated in the process of differentiation and apoptosis induced by sodium butyrate, whereas lysosomal sialidase (Neu1) was up-regulated. Transfection of the sialidase gene into colon cancer cells inhibited apoptosis and was accompanied by increased Bcl-2 and decreased caspase expression. Colon cancer exhibited a marked accumulation of lactosylceramide, a possible sialidase product, and addition of the glycolipid to the culture reduced apoptotic cells during sodium butyrate treatment. These results indicate that high expression of the sialidase in cancer cells leads to protection against programmed cell death, probably modulation of gangliosides. This finding provides a possible sialidase target for diagnosis and therapy of colon cancer.
Characteristics of Radiating Variable Resonant Frequency Crystal Systems (1954)

Calculations based on the usual one-dimensional theory of piezoelectric crystal systems have been carried out for several particular variable resonant frequency crystal systems radiating into water. Curves are presented showing the (1) power output as a function of frequency for operation both on and off resonance, (2) resonant frequency shift as a function of backing length, and (3) relative band width as a function of frequency. The validity of certain approximations is checked so that the operating characteristics of systems made up of different materials can be quickly estimated. The curves indicate that a variable resonant frequency system of crystals all of equal free-free resonant frequency operating with an allowable power variation for fixed applied field strength of 2:1 can have a continuous variation of resonant frequency of about 2.3:1. A system half the crystals of which have twice the free-free resonant frequency of the others for the same allowable field strength variation can operate over a frequency range of about 5.3:1.
<p>In-vitro blood-brain barrier models for drug screening and permeation studies: an overview</p> (2019)

The blood-brain barrier (BBB) is comprised of brain microvascular endothelial central nervous system (CNS) cells, which communicate with other CNS cells (astrocytes, pericytes) and behave according to the state of the CNS, by responding against pathological environments and modulating disease progression. The BBB plays a crucial role in maintaining homeostasis in the CNS by maintaining restricted transport of toxic or harmful molecules, transport of nutrients, and removal of metabolites from the brain. Neurological disorders, such as NeuroHIV, cerebral stroke, brain tumors, and other neurodegenerative diseases increase the permeability of the BBB. While on the other hand, semipermeable nature of BBB restricts the movement of bigger molecules i.e. drugs or proteins (>500 kDa) across it, leading to minimal bioavailability of drugs in the CNS. This poses the most significant shortcoming in the development of therapeutics for CNS neurodegenerative disorders. Although the complexity of the BBB (dynamic and adaptable barrier) affects approaches of CNS drug delivery and promotes disease progression, understanding the composition and functions of BBB provides a platform for novel innovative approaches towards drug delivery to CNS. The methodical and scientific interests in the physiology and pathology of the BBB led to the development and the advancement of numerous in vitro models of the BBB. This review discusses the fundamentals of BBB structure, permeation mechanisms, an overview of all the different in-vitro BBB models with their advantages and disadvantages, and rationale of selecting penetration prediction methods towards the critical role in the development of the CNS therapeutics.
Photosensitisation (2016)

This glossary of terms covers phenomena considered under the very wide terms photocatalysis and radiation catalysis. A clear distinction is made between phenomena related to either photochemistry and photocatalysis or radiation chemistry and radiation catalysis. The term “radiation” is used here as embracing electromagnetic radiation of all wavelengths, but in general excluding fast-moving particles. Consistent definitions are given of terms in the areas mentioned above, as well as definitions of the most important parameters used for the quantitative description of the phenomena. Terms related to the up-scaling of photocatalytic processes for industrial applications have been included. This Glossary should be used together with the Glossary of terms used in photochemistry, 3rd edition, IUPAC Recommendations 2006: (doi:10.1351/pac200779030293) as well as with the IUPAC Compendium of Chemical Terminology, 2nd ed. (the “Gold Book” 2006–; doi:10.1351/goldbook), because many terms used in photocatalysis are defined in these documents.
Multiple B‐ and T‐cell epitopes on a major allergen of Kentucky Bluegrass pollen (1996)

The B- and T-cell epitopes of a recombinant grass allergen, rKBG60, were delineated using a set of overlapping synthetic peptides. Direct binding by enzyme-linked immunosorbent assay (ELISA) utilizing serum pools led to the identification of 13 murine immunoglobulin-, and nine to 13 human IgG- and five to seven human IgE-reactive overlapping peptides. Of the peptides which bound to human IgE antibodies, all but three peptides bound to human and/or murine IgG antibodies. Furthermore, eight out of 12 synthetic peptides induced antigen-specific antibodies in mice, suggesting that these peptides contained epitopes that recognized and/or induced T cells. These results, in conjunction with cross-recognition of different peptides at the C-terminus of rKBG60 by antibodies to neighbouring or non-overlapping peptides suggest that the C-terminus of this antigen represents a dominant antigenic and allergenic site. Peripheral blood mononuclear cell (PBMC) proliferation studies using these synthetic peptides for 13 grass allergic individuals indicated that seven potential human T-cell epitopes exist on this allergen. Taken together, the results demonstrate that multiple B- and T-cell epitopes exist on this major group of grass allergens, the majority of which are localized at the C-terminus of this antigen.
Optimization of the joint coding/decoding structure (2002)

This paper considers the estimation scenario where an original image has undergone blurring, noise corruption and compression. The authors consider these unwanted effects jointly in the estimation formalism they propose. The contribution of the paper aims to address the joint coding/decoding formulation, involving a priori assumptions on the solution and knowledge of the imaging systems to account for effects due to acquisition noise and compression noise. Most of the authors' construction is based on well-known techniques drawn from a variety of areas in modern signal processing, including optimization theory, wavelet decomposition, optimal bit allocation, inverse problem and bounded noise assumption.
Neither Intraocular Grafts of Retinal Cell Homogenates Nor Live Non-Retinal Neurons Produce Behavioral Recovery in Rats with Light-Damaged Retinas (1995)

Previously we have observed that fetal retinal cells grafted to the subretinal space of blind rats produced a functional recovery as determined by testing the visual inhibition of the startle response. Following those studies, we performed experiments to test whether the injection itself, cell by-products, or unrelated neural cells could also produce an effect. Visual function was tested by examining the inhibitory effect of a brief light flash (300 Ix) on the acoustic startle response to an immediately following intense noise burst in light blinded Fischer 344 rats. Animals were tested before and after grafts of fetal retinal cell homogenates, dissociated perinatal cerebellar cells, and sham injections in the subretinal space. Behavioral testing continued every 2 wk for 14 wk after the graft. In the pretests, the light flash inhibited the startle response, maximal at intervals of 40-70 ms with recovery thereafter. In contrast, after exposure for 4 wk to fluorescent light (300 lx) and a rest in a normal 12/12 h light/ dark environment the rats showed reflex facilitation to the light, maximal at an interval of 110 ms, followed by a late period of reflex inhibition. The light flash had no effect on other rats that had been blinded by bilateral enucleation. Light blinded animals receiving either cerebellar grafts or retinal cell homogenates were no different in performance from their sham injected control animals. The present data suggest that neither subretinal injections of neural cells nor nonspecific neurochemical factors are able to elicit a positive behavioral response in visually impaired animals.
The design and evaluation of an activity monitoring user interface for people with stroke (2014)

Usability is an important topic in the field of telerehabilitation research. Older users with disabilities in particular, present age-related and disability-related challenges that should be accommodated for in the design of a user interface for a telerehabilitation system. This paper describes the design, implementation, and assessment of a telerehabilitation system user interface that tries to maximize usability for an elderly user who has experienced a stroke. An Internet-connected Nintendo(®) Wii™ gaming system is selected as a hardware platform, and a server and website are implemented to process and display the feedback information. The usability of the interface is assessed with a trial consisting of 18 subjects: 10 healthy Doctor of Physical Therapy students and 8 people with a stroke. Results show similar levels of usability and high satisfaction with the gaming system interface from both groups of subjects.
Compact AC-AC converter using 3-in-1 IBPMs and adaptive commutation (1999)

Unavailable bi-directional switches and difficulties in high-current commutation have limited modern matrix converter development to low power range, below 2-3 HP. This paper reports a new design approach based on an integrated bidirectional power module (IBPM) concept and newly developed 3-in-1 IBPMs rated 1200 V and 100 A. A modularity design of phase-banks is conceived to reduce critical parasitic inductance, minimize the power connection terminals, and simplify AC bus structure and wiring. An adaptive phase commutation method is developed to improve commutation. Experimental results operating over 0-400 Hz verify the new concepts and design.
Stopping Pattern and Frequency Determination for a Multi-Modal Network (2018)

This paper proposes a model for simultaneously determining the stopping patterns and frequencies of public transport services. Model formulation considers the impacts of alternative network design with limited stop solutions on passenger choice of origin and destination stations, route choice and possibly unsatisfied demand. The model is tested for a large range of numerical scenarios to test its sensitivity and then applied to the Amsterdam metro and rail network to assess the potential of integrated operations.
Oxidative Stress Level in the Testes of Mice and Rats during Nickel Intoxication (2012)

The genotioxic and carcinogenic effect of nickel probably results from its capacity to produce reactive oxygen species (ROS) and disturb the redox balance. The aim of the study was to find out if rats lacking spermatic protamine 2 are less susceptible to Ni(II) than mice. Consequently, the levels of malondialdehyde + 4 hydroxynonenal (MDA+4HDA) - markers of lipid peroxidation, as well as the level of reduced glutathione (GSH) were measured within the rat and mouse testes. Our results showed that the levels of lipid peroxidation markers were elevated in testicular homogenates of intoxicated mice without any changes in rats. GSH level was lower in the group of intoxicated mice comparing to the control without statistically significant changes in rats' homogenates. Moreover, the level of GSH in the testes of intoxicated mice was lower than in rats. On the basis of our results, it appears that Ni(II) can initiate oxidative stress in the testes of mice but not of rats and can reduce GSH level. Consequently, the antioxidative defense of the testes is reduced. Ni(II) that causes oxidative stress in the testes may also contribute to infertility.
211. Expression and cellular localization of HTRA3 protease during placental development in mice (2005)

Placental development in mice involves highly regulated interactions between fetal- and maternal-derived cells. We have previously cloned a novel serine protease (HtrA3) containing an insulin-like growth factor (IGF) binding domain, which was upregulated during pregnancy, especially post-implantation in the mouse uterus.1 The present study examined HtrA3 regulation during placental development in mice, in particular, its expression in the different compartments of the placenta. Expression of mRNA was determined by Northern blot analysis in implantation units containing the decidua, placenta and fetus (day 8.5 to near-term). A specific HtrA3 antibody was generated, affinity-purified and used for Western blot analysis and immunohistochemistry. Both mRNA and protein of HtrA3 were identified specifically in the maternal decidua. In contrast, HtrA3 expression was below detection in trophoblasts, including the giant cells that are in direct contact with the decidua. This pattern persisted from the early stages of placentation to near term. The level of decidual HtrA3 mRNA and its protein gradually decreased as the placenta matured. In the decidua, only the maternal decidual cells, but not blood vessels or uterine NK cells that are present in large numbers, were positive for HtrA3. The specific localization of HtrA3, a protease possessing an IGF binding domain at the maternal–fetal interface, suggests that this protein plays an important role in mediating maternal decidual remodelling and maintenance, probably in association with the IGF system, in placental development and function. (1)Nie et al. (2003). Mol. Hum. Reprod.