gebhart/patrepeval huggingface dataset:
Conformational studies of anionic melittin analogues: Effect of peptide concentration, pH, ionic strength, and temperature—models for protein folding and halophilic proteins (1992)

Melittin (MLT), a 26-residue cationic (net charge +5 at pH 7.2) peptide from bee venom, is well known to be a monomeric, approximately random coil; but when its charges are reduced by titration, by acetylation (net charge +2) or succinylation (net charge -2), or by screening by salt, it goes over to tetrameric alpha-helix. The conversion is promoted by raising the peptide concentration. The tetramer is held together by hydrophobic forces. We have changed the net charge to -6 by acylation with acetylcitric anhydride (a new acylating agent); this anionic derivative forms tetrameric helix at neutral pH, without salt, and at relatively low concentration, conditions under which the cationic MLT does not become helical. Thus, a high net charge is not sufficient to prevent association and helix formation. We have synthesized an anionic melittin analogue of MLT (E-MLT; net charge -4) in which all five lysine and arginine residues are replaced with glutamate, and acetyl and succinyl derivatives of E-MLT (net charges -5 and -6). All three of these are resistant to helix formation. They require much higher NaCl or NaClO4 concentration for helix formation than does MLT. Even CaCl2, MgCl2, and spermine.4HCl are less effective in helicizing E-MLT than MLT. MLT, at pH 7.2, shows increasing helix as the peptide concentration increases (8-120 microM), but E-MLT and its acyl derivatives do not. MLT and acylated MLTs in the helical tetramer show both cold- and heat-induced unfolding, with maximum stability near room temperature. At high temperature, a significant amount of residual structure remains. Heating (to 100 degrees C) monomeric MLT (i.e., MLT at low concentration) or E-MLT results in a monotonic increase in negative ellipticity. In 1.0 M NaCl, E-MLT (at sufficiently high concentration) also shows cold and hot unfolding. The results are discussed in respect to charge-charge and charge-dipole interactions, and hydrophobic effects. E-MLT is also discussed in relation to proteins of halophilic bacteria, which have higher proportions of anionic residues than do corresponding proteins of nonhalophiles.
A genetic map of the mouse suitable for typing intraspecific crosses. (1992)

We report the construction of a genetic linkage map of the mouse, consisting entirely of genetic markers that can be rapidly typed by polymerase chain reaction and that show a high degree of polymorphism among inbred laboratory strains. Specifically, the map contains 317 simple sequence length polymorphisms at an average spacing of 4.3 cM and is detectably linked to approximately 99% of the mouse genome. In typical crosses between inbred laboratory strains, about 50% of the markers are polymorphic, making it straightforward to follow inheritance in almost any cross.
Expression of the coxsackie and adenovirus receptor in human astrocytic tumors and xenografts (2002)

The sensitivity of human tissues and tumors to infection with type C adenoviruses correlates with the expression of the human coxsackie B- and adenovirus receptor, hCAR. HCAR is heterogeneously expressed in various tissues and types of human cancer cells, which has implications for the use of adenoviruses as vectors in cancer gene therapy. Using immunoblotting, real-time PCR, FACS-analysis and sensitivity to infection with adenovirus-lacZ, we analyzed the expression level of hCAR in glioma Grade IV cell lines. With real-time PCR, we also analyzed hCAR expression in primary human astrocytomas of different malignancy grades, as well as in their xenograft derivatives. Analysis of a set of 10 cell lines showed great variation in hCAR expression. Susceptibility to Ad5lacZ correlated well with hCAR expression, whereas no correlation was observed with the expression of alphavbeta3/alphavbeta5 integrins, proposed to function as co-receptors for adenoviruses. A great variation of CAR expression was also observed in primary astrocytomas of different malignancy grades. The mean value of CAR expression was significantly lower in 22 Grade IV tumors as compared to the values for 6 Grade II (p = 0.01) and 6 Grade III (p = 0.01) tumors. When the hCAR expression in 11 xenografts derived from Grade IV gliomas were compared to the levels detected in the original parental tumors, a mean 12-fold higher expression was seen in the xenografts (P = 0.01). Two xenografts with low hCAR expression grew considerably faster than the hCAR-expressing cells. Our results have relevance for the use of adenoviruses in gene therapy against astrocytomas.
p-Benzyne. Generation as an intermediate in a thermal isomerization reaction and trapping evidence for the 1,4-benzenediyl structure (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTp-Benzyne. Generation as an intermediate in a thermal isomerization reaction and trapping evidence for the 1,4-benzenediyl structureRichard R. Jones and Robert G. BergmanCite this: J. Am. Chem. Soc. 1972, 94, 2, 660–661Publication Date (Print):January 1, 1972Publication History Published online1 May 2002Published inissue 1 January 1972https://pubs.acs.org/doi/10.1021/ja00757a071https://doi.org/10.1021/ja00757a071research-articleACS PublicationsRequest reuse permissionsArticle Views3174Altmetric-Citations605LEARN 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
Small microstrip patch antenna (1995)

A novel small microstrip patch antenna is presented. The probe-fed circular microstrip patch incorporates a single shorting post which significantly reduces the overall size of the antenna. Experimental and theoretical impedance behaviour and radiation characteristics of the modified patch are given. Very good agreement between experiment and theory was achieved.
Phase Behavior of Block Copolymers in a Neutral Solvent (2003)

The phase behavior of eight poly(styrene-b-isoprene) diblock copolymers in the neutral solvent dioctyl phthalate (DOP) has been examined over the full concentration (φ) range and from room temperature up to 250 °C. The copolymer compositions (f) ranged from 0.15 to 0.76, and molecular weights were chosen to make the melt order−disorder transition (ODT) accessible, or nearly so. Definitive phase assignments were made on the basis of small-angle X-ray scattering (SAXS). Individual order−order transitions (OOTs) and ODTs were located by a combination of rheology, static birefringence, and SAXS; all three techniques gave equivalent results. The transition temperatures were converted to values of the effective interaction parameter, χ, using an established relation for this system. For all compositions, χODT scales as φ-α, with α varying from 1.3 to 1.6. These results are in conflict with the mean-field dilution approximation (α = 1.0), as was previously demonstrated for lamellae-forming samples. This result is attributed to the additional fluctuation stabilization of the disordered state in two-component solutions. Three of the samples displayed OOTs: cylinder to sphere (f = 0.15), gyroid to cylinder (f = 0.31), and lamellae to gyroid (f = 0.33). In each case, χOOT scaled as φ-1.0, in agreement with the dilution approximation. This result underscores the reliability of mean-field theory for computing relative free energies of the various ordered phases. The domain spacing, d, scales approximately as φ 0.33 and χ0.25, independent of morphology, in good agreement with both mean-field theory and previous experiments.
Interactive Cost Configuration Over Decision Diagrams (2010)

In many AI domains such as product configuration, a user should interactively specify a solution that must satisfy a set of constraints. In such scenarios, offline compilation of feasible solutions into a tractable representation is an important approach to delivering efficient backtrack-free user interaction online. In particular,binary decision diagrams (BDDs) have been successfully used as a compilation target for product and service configuration. In this paper we discuss how to extend BDD-based configuration to scenarios involving cost functions which express user preferences. We first show that an efficient, robust and easy to implement extension is possible if the cost function is additive, and feasible solutions are represented using multi-valued decision diagrams (MDDs). We also discuss the effect on MDD size if the cost function is non-additive or if it is encoded explicitly into MDD. We then discuss interactive configuration in the presence of multiple cost functions. We prove that even in its simplest form, multiple-cost configuration is NP-hard in the input MDD. However, for solving two-cost configuration we develop a pseudo-polynomial scheme and a fully polynomial approximation scheme. The applicability of our approach is demonstrated through experiments over real-world configuration models and product-catalogue datasets. Response times are generally within a fraction of a second even for very large instances.
Cell proliferation and natural killer cell activity by polyherbal formulation, Immu-21 in mice. (2002)

Immunomodulatory activity of an Ayurvedic polyherbal formulation, Immu-21 containing extracts of Ocimum sanctum, Withania somnifera, Emblica officinalis and Tinospora cordifolia was studied on proliferative response of splenic leukocytes to T cell mitogens, concanavalin (Con)-A and phytohemagglutinin (PHA) and B cell mitogen, lipopolysaccharide (LPS) in vitro by [3H]-thymidine uptake assay in mice. The cytotoxic activity of Immu-21 was tested by measuring the splenic leukocyte natural killer (NK) cell activity against K 562 cells. Intraperitoneal (i.p.) treatment with Immu-21 (30 mg/kg) once a day for 14 and 21 days did not cause change in body weight and spleen weight, where as splenocytes/spleen count was increased. Treatment of Immu-21 (30 mg/kg, i.p.) for 14 days and 1 mg/kg for 21 days significantly increased LPS induced leukocyte proliferation. NK cell activity was significantly increased when mice were pretreated with Immu-21 (10 and 30 mg/kg, i.p.) once a day for 7 days. The results indicate that pretreatment with Immu-21 selectively increased the proliferation of splenic leukocyte to B cell mitogen, LPS and cytotoxic activity against K 562 cells in mice.
Imprint Lithography with 25-Nanometer Resolution (1996)

A high-throughput lithographic method with 25-nanometer resolution and smooth vertical sidewalls is proposed and demonstrated. The technique uses compression molding to create a thickness contrast pattern in a thin resist film carried on a substrate, followed by anisotropic etching to transfer the pattern through the entire resist thickness. Metal patterns with a feature size of 25 nanometers and a period of 70 nanometers were fabricated with the use of resist templates created by imprint lithography in combination with a lift-off process. With further development, imprint lithography should allow fabrication of sub-10-nanometer structures and may become a commercially viable technique for manufacturing integrated circuits and other nanodevices.
Design of Pulse Oximeters (1997)

Normal oxygen transport (S A Clark). Motivation of pulse oximetry (D J Sebald). Blood oxygen measurement (J Farmer). Light absorbance in pulse oximetry (O Wieben). Light-emitting diodes and their control (B W J Bourgeois). Photodetectors and amplifiers (J S Schowalter). Probes (M V S Reddy). Electronic instrument control (K S Paranjape). Signal processing algorithms (S Palreddy). Calibration (J S Schowalter). Accuracy and errors (S Tungjitkusolmun). User interface for a pulse oximeter (A Lozano-Nieto). Applications of pulse oximetry (J B Ruchala). Glossary. Index.
Stoichiometry of the Interaction between the Major Histocompatibility Complex-Related Fc Receptor and Its Fc Ligand (1999)

The neonatal Fc receptor (FcRn) transports immunoglobulin G (IgG) across epithelia, providing passive immunity and protecting serum IgG from degradation. For both functions, FcRn binds to IgG at the acidic pH of intracellular vesicles (pH </= 6.5) and releases IgG at the basic pH of the bloodstream (pH approximately 7.4). Crystallographic studies show that rat FcRn can interact with the Fc portion of IgG in a repeating array in which FcRn dimers are bridged by Fc fragments to create an "oligomeric ribbon" with a 2n:n stoichiometry. The stoichiometry of the interaction between soluble FcRn and Fc has been reported as either 2:1 for rat FcRn [Huber et al. (1993) J. Mol. Biol. 230, 1077-1083] or 1:1 for mouse FcRn [Popov et al. (1996) Mol. Immunol. 33, 521-530]. To ascertain the reasons for this difference, we analyzed complexes formed in solution between soluble rat or mouse FcRn and Fc. Using a gel-filtration assay under nonequilibrium conditions, we find that both forms of FcRn produce 2:1 receptor-ligand complexes, but that alterations of the carbohydrate moieties on mouse FcRn can result in an apparent stoichiometry of 1:1. However, under equilibrium conditions, all forms of FcRn make complexes with a 2:1 stoichiometry. We conclude that rat and mouse FcRn share the same general ligand binding properties but that small differences in affinities can produce apparent differences under nonequilibrium conditions.
Graph coloring register allocation for processors with multi-register operands (1990)

Though graph coloring algorithms have been shown to work well when applied to register allocation problems, the technique has not been generalized for processor architectures in which some instructions refer to individual operands that are comprised of multiple registers. This paper presents a suitable generalization.
PI3K-Related Kinases (2000)

In the not too distant past, the very large and still growing family of signaling kinases could be neatly subdivided into two broad classes, those that phosphorylated lipids and those that used proteins as substrates. Investigators who focused on protein kinases rarely crossed ideological paths with researchers involved in lipid kinase research. However, as is often the case in modern-day cell biology, the conceptual division of ATP-binding phosphotransferases into lipid kinases and protein kinases has proved an oversimplification of the chaotic reality that typifies the process of intracellular signaling. First, we were surprised to learn that certain bona fide lipid kinases, specifically the phosphoinositide 3-kinases (PI3Ks), were quite capable of phosphorylating a limited spectrum of protein substrates, at least when pressed to do so under in vitro conditions. Then, during the mid-1990s, the molecular cloning efforts of several laboratories further confused the picture with the identification of a novel family of high molecular mass kinases whose catalytic domains bore a clear resemblance to those of PI3Ks. Based on this primary sequence homology, the newly identified kinases were named PI3Krelated kinases (PIKKs). The expectation at the time was that the PIKK family members would relay signals, at least in part, through the phosphorylation of inositol phospholipids. Instead, it now appears that evolution has brought us full circle—in spite of the lipid kinase-like catalytic domain, the PIKKs apparently have dedicated themselves fully to the phosphorylation of protein substrates.
Ionizing radiation mediates expression of cell adhesion molecules in distinct histological patterns within the lung. (1997)

Inflammatory cell infiltration of the lung is a predominant histopathological change that occurs during radiation pneumonitis. Emigration of inflammatory cells from the circulation requires the interaction between cell adhesion molecules on the vascular endothelium and molecules on the surface of leukocytes. We studied the immunohistochemical pattern of expression of cell adhesion molecules in lungs from mice treated with thoracic irradiation. After X-irradiation, the endothelial leukocyte adhesion molecule 1 (ELAM-1; E-selectin) was primarily expressed in the pulmonary endothelium of larger vessels and minimally in the microvascular endothelium. Conversely, the intercellular adhesion molecule 1 (ICAM-1; CD54) was expressed in the pulmonary capillary endothelium and minimally in the endothelium of larger vessels. Radiation-mediated E-selectin expression was first observed at 6 h, whereas ICAM-1 expression initially increased at 24 h after irradiation. ICAM-1 and E-selectin expression persisted for several days. P-selectin is constitutively expressed in Weibel-Palade bodies in the endothelium, which moved to the vascular lumen within 30 min after irradiation. P-selectin was not detected in the pulmonary endothelium at 6 h after irradiation. The radiation dose required for increased cell adhesion molecule expression within the pulmonary vascular endothelium was 2 Gy, and expression increased in a dose-dependent manner. These data demonstrate that ICAM-1 and E-selectin expression is increased in the pulmonary endothelium following thoracic irradiation. The pattern of expression of E-selectin, P-selectin, and ICAM-1 is distinct from one another.
Finite state machine has unlimited concurrency (1991)

General methods for introducing concurrency, by which the throughput of finite-state machines (FSM) can be improved at the expense of latency, are described. The methods are applicable to software and hardware implementation using parallelism or pipelining and demonstrate that there is no theoretical limit to concurrency in a discrete-time finite-state machine. The methods can arbitrarily improve the iteration bound of discrete-time FSMs with low hardware overhead. They are efficient when the state size is finite and moderate, as in controllers, encoders, source decoders, etc. When the state size is large and the recurrence is not a closed-form function of specific classes, the methods cannot be applied directly. Another limitation is the latency induced by the block methods. In most cases, this is not a problem because the overall cost and throughput rather than latency are at stake.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Redox-Conjugated Reversible Isomerization of Ferrocenylazobenzene with a Single Green Light (2002)

A new reversible isomerization cycle for meta-ferrocenylazobenzene accomplished by combination of a single green light (546 nm) and redox change between Fe(II) and Fe(III) was discovered. In the Fe(II) state, trans-to-cis isomerization proceeded upon the green light irradiation exciting the metal-to-ligand charge transfer (MLCT) in a high quantum yield (Phit-->c = 0.51) which exceeds that of azobenzene (Phit-->c = 0.12 (313 nm excitation)). The cis molar ratio reached 35% in the photostationary state. The oxidation to the Fe(III) state followed by irradiation with the same green light led to the cis-to-trans back-reaction to recover almost all of the trans-form. The "on-off switching" of the MLCT character played an important role in the redox-dependent response to the green light for the isomerization. The photoisomerization behavior of ferrocenylazobenzenes was strongly dependent on the substitution position of the ferrocenyl moiety on the benzene ring. The MLCT excitation was not effective for the trans-to-cis conversion in para-ferrocenylazobenzene. Time-dependent density functional theory (TD-DFT) calculations for meta- and para-ferrcenylazobenzene showed that the origin of the visible band (MLCT band) is different. The initial orbital for the MLCT in meta-ferrocenylazobenzene is delocalized over Fe and the Cp ring, while that in para-ferrocenylazobenzene is localized on the iron.
LSD1 Substrate Binding and Gene Expression Are Affected by HDAC1-Mediated Deacetylation (2016)

Lysine Specific Demethylase 1 (LSD1) catalyzes the demethylation of histone 3 to regulate gene expression. With a fundamental role in gene regulation, LSD1 is involved in multiple cellular processes, including embryonic development, cell proliferation, and metastasis. Significantly, LSD1 is overexpressed in multiple cancers and has emerged as a potential anticancer drug target. LSD1 is typically found in association with another epigenetic enzyme, histone deacetylase (HDAC). HDAC and LSD1 inhibitor compounds have been tested as combination anticancer agents. However, the functional link between LSD1 and HDAC has yet to be understood in detail. Here, we used a substrate trapping strategy to identify cellular substrates of HDAC1. Using inactive HDAC1 mutants, we identified LSD1 as an HDAC1 substrate. HDAC1 mediated deacetylation of LSD1 at K374 in the substrate binding lobe, which affected the histone 3 binding and gene expression activity of LSD1. The mechanistic link between HDAC1 and LSD1 established here suggests that HDAC inhibitors influence LSD1 activity, which will ultimately guide drug design targeting epigenetic enzymes.
NO-mediated alterations in skeletal muscle nutritive blood flow and lactate metabolism in fibromyalgia (2005)

(1) There is reduced nutritive flow response to aerobic exercise and reduced maximal exercise time in FM that might relate to higher iNOS protein content and contribute to exertional fatigue in FM; (2) The increased dialysate lactate in FM in response to stimulation of NOS or a nitric oxide donor suggest that FM may be more sensitive than HC to the suppressive effect of nitric oxide on oxidative phosphorylation.
Human placental cytotrophoblasts produce the immunosuppressive cytokine interleukin 10. (1996)

The mechanism by which the mammalian mother accepts the implanting fetus as an allograft remains unexplained, but is likely to be the result of a combination of factors. Mononuclear cytotrophoblasts, the specialized fetal cells of the placenta that invade the uterus, play an important role. These cells express HLA-G, an unusual major histocompatibility complex class I-B molecule, and secrete cytokines and pregnancy-specific proteins that can regulate immune function. We investigated whether cytotrophoblasts secrete interleukin 10 (IL-10), a cytokine that potently inhibits alloresponses in mixed lymphocyte reactions. Cytotrophoblasts from all stages of pregnancy produced IL-10 in vitro, but neither placental fibroblasts nor choriocarcinoma (malignant trophoblast) cell lines did so. Spontaneous IL-10 production averaged 650, 853, and 992 pg/10(6) cells in the first, second, and third trimesters of pregnancy, respectively. IL-10 secretion dropped approximately 10-fold after the first 24 h of culture, and was paralleled by a decrease in messenger RNA. IL-10 messenger RNA was detected in biopsies of the placenta and the portion of the uterus that contains invasive cytotrophoblasts, suggesting that this cytokine is also produced in vivo. IL-10 secreted by cytotrophoblasts in vitro is bioactive, as determined by its ability to suppress interferon gamma production in an allogeneic mixed lymphocyte reaction. We conclude that human cytotrophoblast IL-10 may be an important factor that contributes to maternal tolerance of the allogeneic fetus.