gebhart/patrepeval huggingface dataset:
Localization and Regulation of Pregnancy-Associated Plasma Protein A Expression in Healing Human Skin (2003)

Pregnancy-associated plasma protein A (PAPP-A) is an IGF-binding protein-4 (IGFBP-4) metalloproteinase that cleaves inhibitory IGFBP-4 to amplify local IGF-I bioavailability in vitro. Thus it has functional implications in injury/repair responses. In this study we determined PAPP-A expression in healing human skin. Wounds were induced with a scalpel on the forearms of three normal subjects and were allowed to heal by first intention. Biopsies obtained on d 0, 2, 8, and 14 were processed for immunohistochemical detection of PAPP-A, IGF-I, and IGFBP-4. In uninjured skin (d 0), strong staining for PAPP-A was present in the epidermis, sweat and sebaceous gland epithelial cells, hair follicles, and blood vessels; no PAPP-A was detected in dermal fibroblasts or with mature collagen bundles. IGF-I localized strongly to epithelial cells of skin glands was weak to moderate in epidermis and blood vessels, and was absent in dermal cells. Weak focal staining for IGFBP-4 was found within uninjured epidermis. During wound healing, PAPP-A expression was induced in dermal granulation tissue within and adjacent to the injury. PAPP-A was present in dermis on d 2 and was increased in intensity and extent on d 8 and 14. PAPP-A expression also increased in the epidermis. PAPP-A expression in cells of granulation tissue colocalized with alpha-smooth actin staining of myofibroblasts and new blood vessels as well as with CD68 staining of macrophages and was associated with the compact, newly synthesized collagen of the healing wound. IGF-I staining was enhanced in the epidermis localized to the area of the incision and in granulation tissue associated with lymphoid cells. IGFBP-4 staining of the epidermis remained unchanged during wound healing, but was induced in the fibroblastic cells of granulation tissue over time. These data demonstrate localized and regulated expression of PAPP-A in human skin and suggest that PAPP-A may play an important role in an integrated IGF system in wound healing and tissue remodeling in vivo.
Accurate <i>in vitro</i> transcription from circularized plasmid templates by plant whole cell extracts (1995)

A convenient in vitro transcription system using monocot and dicot whole cell extracts and circular DNA templates has been developed. The system consists of incubating template and whole cell extract to generate initiation complexes, followed by addition of nucleotide triphosphates to support elongation, and primer extension assay to detect authentic transcripts. This in vitro transcription system required circularized templates and was essentially inactive with linearized templates. Accurate in vitro transcription of a rice phenylalanine ammonia-lyase (PAL) promoter-beta-glucuronidase (GUS) gene fusion and a tobacco sesquiterpene cyclase promoter-GUS gene fusion was examined in their homologous whole cell extracts, and the optimal concentrations for several reaction components, including DNA template, whole cell extract, monovalent and divalent cations, were determined for specific initiation from the in vivo start site. Transcription was inhibited by low concentrations of alpha-amanitin, demonstrating that the reaction was mediated by RNA polymerase II. Accurate transcription initiation was dependent on the TATA-box motif within the respective promoters. Based on the effect of delayed addition of sarkosyl at a concentration sufficient to inhibit transcription initiation but not elongation, three to four rounds of transcription were initiated in standard assays.
Effect of pad surface micro-texture on dishing and erosion during shallow trench isolation chemical mechanical planarization (2014)

The effect of pad surface micro-texture on dishing and erosion during shallow trench isolation (STI) chemical mechanical planarization was investigated. To generate different pad surface micro-textures, a 3M A2810 disc (3M) and a Mitsubishi Materials Corporation disc (MMC) were used to condition a Dow® IC1000™ K-groove pad. For each disc, 200-mm blanket TEOS wafers and SKW3-2 STI wafers were polished. Results showed that the two discs generated similar blanket wafer removal rates, while the MMC disc generated significantly higher dishing and erosion compared to the 3M disc during patterned wafer polishing. Pad surface topography was analyzed using laser confocal microscopy after patterned wafer polishing. Results showed that the MMC disc generated a pad surface with significantly higher mean pad summit curvatures than the 3M disc. As the MMC disc generated more and sharper pad asperities, it resulted in higher dishing and erosion as these sharp asperities make greater direct contact with the "down" features.
pH-Triggered Disassembly in a Caged Protein Complex (2009)

Self-assembling protein cage structures have many potential applications in nanotechnology, one of which is therapeutic delivery. For intracellular targeting, pH-controlled disassembly of virus-like particles and release of their molecular cargo is particularly strategic. We investigated the potential of using histidines for introducing pH-dependent disassembly in the E2 subunit of pyruvate dehydrogenase. Two subunit interfaces likely to disrupt stability, an intratrimer interface (the N-terminus) and an intertrimer interface (methionine-425), were redesigned. Our results show that changing the identity of the putative anchor site 425 to histidine does not decrease stability. In contrast, engineering non-native pH-dependent behavior and modulating the transition pH at which disassembly occurs can be accomplished by mutagenesis of the N-terminus and by ionic strength changes. The observed pH-triggered disassembly is due to electrostatic repulsions generated by histidine protonation. These results suggest that altering the degree of electrostatic repulsion at subunit interfaces could be a generally applicable strategy for designing pH-triggered assembly in protein macromolecular structures.
Decision theoretic search for small objects through integrating far and near cues (2015)

In an object search scenario with several small objects spread over a large indoor environment, the robot cannot infer about all of them at once. Pruning the search space is highly desirable in such a case. It has to actively select a course of actions to closely examine a selected set of objects. Here, we model the inferences about far away objects and their viewpoint priors into a decision analytic abstraction to prioritize the waypoints. By selecting objects of interest, a potential field is built over the environment by using Composite Viewpoint Object Potential (CVOP) maps. A CVOP is built using VOP, a framework to identify discriminative viewpoints to recognize small objects having distinctive features only in specific views. Also, a CVOP helps to clearly disambiguate objects which look similar from far away. We formulate a Decision Analysis Graph (DAG) over the above information, to assist the robot in actively navigating and maximize the reward earned. This optimal strategy increases search reliability, even in the presence of similar looking small objects which induce confusion into the agent and simultaneously reduces both time taken and distance travelled. To the best of our knowledge, there is no current unified formulation which addresses indoor object search scenarios in this manner. We evaluate our system over ROS using a TurtleBot mounted with a Kinect.
Purification and Characterization of Two Novel Halotolerant Extracellular Proteases from<i>Bacillus subtilis</i>Strain FP-133 (2006)

Bacillus subtilis strain FP-133, isolated from a fermented fish paste, synthesized two novel halotolerant extracellular proteases (expro-I and expro-II), showing activity and stability at concentrations of 0-20% (w/v) NaCl. Each protease was purified to homogeneity and characterized. The purified expro-I was a non-alkaline serine protease with an optimum pH of 7.5, although most serine proteases from Bacillus strains act at the alkaline side. The molecular mass of expro-I was 29 kDa. The purified expro-II was a metalloprotease with a molecular mass of 34 kDa. It was activated by Fe(2+), which has never been reported as a bacterial protease activator. At a concentration of 7.5% (w/v) NaCl, both proteases preferred animal proteins to vegetable proteins as natural substrates. In addition, under saline conditions, expro-I and II showed high catalytic activity toward gelatin and casein respectively.
Universal dependence of hydrogen oxidation and evolution reaction activity of platinum-group metals on pH and hydrogen binding energy (2016)

Understanding how pH affects the activity of hydrogen oxidation reaction (HOR) and hydrogen evolution reaction (HER) is key to developing active, stable, and affordable HOR/HER catalysts for hydroxide exchange membrane fuel cells and electrolyzers. A common linear correlation between hydrogen binding energy (HBE) and pH is observed for four supported platinum-group metal catalysts (Pt/C, Ir/C, Pd/C, and Rh/C) over a broad pH range (0 to 13), suggesting that the pH dependence of HBE is metal-independent. A universal correlation between exchange current density and HBE is also observed on the four metals, indicating that they may share the same elementary steps and rate-determining steps and that the HBE is the dominant descriptor for HOR/HER activities. The onset potential of CO stripping on the four metals decreases with pH, indicating a stronger OH adsorption, which provides evidence against the promoting effect of adsorbed OH on HOR/HER.
Making Data Secure (2000)

This article explains how smart cards can be used to not only meet the requirements of the new Data Protection Act but also to make life that much easier for the average user drowning in multiple usernames and passwords.
Experimental determination of the rate constants for spin exchange between optically pumped K, Rb, and Cs atoms and<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:mmultiscripts><mml:mrow><mml:mi mathvariant="normal">Xe</mml:mi></mml:mrow><mml:mprescripts/><mml:mrow/><mml:mrow><mml:mn>129</mml:mn></mml:mrow><mml:mrow/><mml:mrow/></mml:mmultiscripts></mml:mrow></mml:math>nuclei in alkali-metal<i>–</i>noble-gas van der Waals molecules (1985)

By analyzing the measured spin-relaxation transients of $^{129}\mathrm{Xe}$ nuclear spins and alkali-metal-atomic spins in mixtures of alkali-metal-atom vapors, Xe gas, and larger amounts of ${\mathrm{N}}_{2}$ gas, we have determined the three-body formation rates and the spin-transfer probabilities for alkali- metal--noble-gas van der Waals molecules. Three parameters, in addition to the spin quantum numbers of the alkali-metal and noble-gas nuclei, are needed to predict the spin-transfer rates. These parameters, which we have determined from experimental measurements, are x=\ensuremath{\gamma}N/\ensuremath{\alpha}, the ratio of the spin-rotation interaction \ensuremath{\gamma}N to the spin-exchange interaction \ensuremath{\alpha}; ${p}_{0}$, the third-body pressure for which the molecular breakup rate ${\ensuremath{\tau}}^{\mathrm{\ensuremath{-}}1}$ is equal to the spin-rotation frequency \ensuremath{\gamma}N/h; and Z, the three-body rate constant for forming van der Waals molecules.
Classification of Kinase Inhibitors Using a Bayesian Model (2004)

The use of Bayesian statistics to model both general (multifamily) and specific (single-target) kinase inhibitors is investigated. The approach demonstrates an alternative to current computational methods applied to heterogeneous structure/activity data sets. This approach operates rapidly and is readily modifiable as required. A generalized model generated using inhibitor data from multiple kinase classes shows meaningful enrichment for several specific kinase targets. Such an approach can be used to prioritize compounds for screening or to optimally select compounds from third-party data collections. The observed benefit of the approach is finding compounds that are not structurally related to known actives, or novel targets for which there is not enough information to build a specific kinase model. The general kinase model described was built from a basis of mostly tyrosine kinase inhibitors, with some serine/threonine inhibitors; all the test cases used in prediction were also on tyrosine kinase targets. Confirming the applicability of this technique to other kinase families will be determined once those biological assays become available.
Bridged aminotetralins. 4. Resolution of potent analgesics of the bridged aminotetralin type (1976)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTBridged aminotetralins. 4. Resolution of potent analgesics of the bridged aminotetralin typeMeier E. Freed, John R. Potoski, George L. Conklin, and Stanley C. BellCite this: J. Med. Chem. 1976, 19, 4, 560–562Publication Date (Print):April 1, 1976Publication History Published online1 May 2002Published inissue 1 April 1976https://doi.org/10.1021/jm00226a026RIGHTS & PERMISSIONSArticle Views120Altmetric-Citations13LEARN 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 InReddit PDF (421 KB) Get e-Alerts Get e-Alerts
Conformational restraints revealing bioactive β‐bend structures for hα CGRP<sub>8–37</sub> at the CGRP<sub>2</sub> receptor of the rat prostatic vas deferens (1999)

1. The main aim of this study was to identify putative beta-bends and the role of the N- and C-terminus in the CGRP receptor antagonist halpha CGRP8-37, which was measured against halpha CGRP inhibition of twitch responses in the rat prostatic vas deferens. 2. With a bend-biasing residue (proline) at position 16 in halpha CGRP8-37 (10(-5) M) an inactive compound was produced, while alanine at the same position retained antagonist activity (apparent pKB 5.6+/-0.1 at 10(-5) M). Proline at position 19 within halpha CGRP8-37 (10(-5) M) was an antagonist (apparent pKB 5.8+/-0.1). 3. Incorporation of a bend-forcing structure (beta-turn dipeptide or BTD) at either positions 19,20 or 33,34 in halpha CGRP8-37 (10(-5) M) antagonized halpha CGRP responses (apparent pKB 6.0+/-0.1 and 6.1+/-0.1, respectively). Replacement by BTD at both positions 19,20 and 33,34 within halpha CGRP8-37 competitively antagonized responses to halpha CGRP (pA2 6.2; Schild plot slope 1.0+/-0.1). 4. Halpha CGRP8-37 analogues (10(-5) M), substituted at the N-terminus by either glycine8, or des-NH2 valine8 or proline8 were all antagonists against halpha CGRP (apparent pKB 6.1+/-0.1, 6.5+/-0.1 and 6.1+/-0.1, respectively), while halpha CGRP8-37 (10(-5) M) substituted in three places by proline8 and glutamic acid10,14 was inactive. 5. Replacement of the C-terminus by alanine amide37 in halpha CGRP8-37 (10(-5) M) failed to antagonize halpha CGRP responses. 6. Peptidase inhibitors did not alter either the agonist potency of halpha CGRP or the antagonist affinities of halpha CGRP8-37 BTD19,20 and 33,34 and halpha CGRP8-37 Gly8 (against halpha CGRP responses). 7. In conclusion, two beta-bends at positions 18-21 and 32-35 are compatible with high affinity by BTD and is the first approach of modelling the bioactive structure of halpha CGRP8-37. Further, the N-terminus of halpha CGRP8-37 is not essential for antagonism, while the C-terminus interacts directly with CGRP receptor binding sites of the rat vas deferens.
Allosteric sites of the large subunit of the spinach leaf ADPglucose pyrophosphorylase. (1994)

Pyridoxal-P, an analog of 3-phosphoglycerate, activates spinach leaf ADPglucose pyrophosphorylase. Reductive phosphopyridoxylation of the enzyme yields enzyme less dependent on the presence of activator for activity. Labeled pyridoxal-P is incorporated into both the 51- and 54-kDa subunits of the enzyme. The sequence of the single tryptic labeled peptide of the small subunit has been reported (Morell, M., Bloom, M., and Preiss, J. (1988) J. Biol. Chem. 263, 633-637). Three distinct labeled peptides are isolated from the tryptic digest of the large subunit. 3-Phosphoglycerate inhibits incorporation of pyridoxal-P by 80% into all three large subunit tryptic peptides, whereas inorganic phosphate, the allosteric inhibitor, inhibits incorporation into only one of those peptides. Comparison of the sequences of the labeled tryptic peptides with those of large and small subunits of the enzyme from other species indicate their positions in the primary structure of the spinach enzyme large subunit. The conservation in the amino acid sequences surrounding the lysyl residue in the small subunit and of the lysyl residue in the large subunit in higher plant and in cyanobacterial ADPglucose pyrophosphorylases, which are protected from phosphopyridoxylation by both allosteric effectors, suggests that these lysyl residues are involved in activator binding.
Layer sequence and silicide formation of a Co/(refractory metal) bilayer on (100)Si substrate (1995)

The solid state reactions of bilayer systems, such as Co/Cr and Co/V, with a silicon substrate have been investigated. The layer sequence could be explained in terms of competitive relations between the diffusion of cobalt atoms toward the substrate and the surface reaction (i.e., silicide formation at the silicon substrate). It was also found that the intermixing between the cobalt and the refractory beneath it is related to the solid solubility between them, and the layer reversal phenomenon critically depends on the silicide formation temperature of the interlayer refractory metal. For example, in the Co/Cr bilayer, where the silicide formation temperature of the chromium is not higher than that of the cobalt, only a partial layer reversal occurs. However, in the Co/V bilayer, where vanadium has a higher silicide formation temperature than cobalt, a complete layer reversal occurs.
Learning Finite State Machines With Self-Clustering Recurrent Networks (1993)

Recent work has shown that recurrent neural networks have the ability to learn finite state automata from examples. In particular, networks using second-order units have been successful at this task. In studying the performance and learning behavior of such networks we have found that the second-order network model attempts to form clusters in activation space as its internal representation of states. However, these learned states become unstable as longer and longer test input strings are presented to the network. In essence, the network “forgets” where the individual states are in activation space. In this paper we propose a new method to force such a network to learn stable states by introducing discretization into the network and using a pseudo-gradient learning rule to perform training. The essence of the learning rule is that in doing gradient descent, it makes use of the gradient of a sigmoid function as a heuristic hint in place of that of the hard-limiting function, while still using the discretized value in the feedback update path. The new structure uses isolated points in activation space instead of vague clusters as its internal representation of states. It is shown to have similar capabilities in learning finite state automata as the original network, but without the instability problem. The proposed pseudo-gradient learning rule may also be used as a basis for training other types of networks that have hard-limiting threshold activation functions.
Type B Response Regulators of <i>Arabidopsis</i> Play Key Roles in Cytokinin Signaling and Plant Development (2008)

The type B Arabidopsis Response Regulators (ARRs) of Arabidopsis thaliana are transcription factors that act as positive regulators in the two-component cytokinin signaling pathway. We employed a mutant-based approach to perform a detailed characterization of the roles of ARR1, ARR10, and ARR12 in plant growth and development. The most pronounced phenotype was found in the arr1-3 arr10-5 arr12-1 triple loss-of-function mutant, which showed almost complete insensitivity to high levels of exogenously applied cytokinins. The triple mutant exhibited reduced stature due to decreased cell division in the shoot, enhanced seed size, increased sensitivity to light, altered chlorophyll and anthocyanin concentrations, and an aborted primary root with protoxylem but no metaxylem. Microarray analysis revealed that expression of the majority of cytokinin-regulated genes requires the function of ARR1, ARR10, and ARR12. Characterization of double mutants revealed differing contributions of the type B ARRs to mutant phenotypes. Our results support a model in which cytokinin regulates a wide array of downstream responses through the action of a multistep phosphorelay that culminates in transcriptional regulation by ARR1, ARR10, and ARR12.
Effectiveness of Topiramate in the Prevention of Childhood Headaches (2002)

Topiramate is potentially an effective prophylactic medication for children with frequent migraine.
Building a statistical machine translation system from scratch (2001)

We report on our experience with building a statistical MT system from scratch, including the creation of a small parallel Tamil-English corpus, and the results of a task-based pilot evaluation of statistical MT systems trained on sets of ca. 1300 and ca. 5000 parallel sentences of Tamil and English data. Our results show that even with apparently incomprehensible system output, humans without any knowledge of Tamil can achieve performance rates as high as 86% accuracy for topic identification, 93% recall for document retrieval, and 64% recall on question answering (plus an additional 14% partially correct answers).
Modeling of the formation and properties of nanocrystals in insulator matrices (SiO/sub 2/:Si, ZrO/sub 2/(Y):Zr) produced by ion implantation (2003)

The Si/sup +/-dose dependence of the photoluminescence (PL) intensity at /spl lambda/=800 nm for the SiO/sub 2/ with Si nanoinclusions (NI) and optical transmission for the ZrO/sub 2/(Y) with metallic Zr NIs produced by ion implantation are studied. It is shown that dose dependence of PL is defined by the increase of the NI surface density, the mean size of NIs being constant until their merging. The kinetics of NI accumulation is estimated with the Monte Carlo TRIDIN and TRIM codes and taking into account the diffusion of excess atoms and NI nucleation. The earlier revealed mechanisms of a PL enhancement at phosphorus doping are investigated. It is concluded that the PL enhancement is caused by the donor properties of phosphorus in Si NIs (quantum dots) and passivation of broken bonds (nonradiative centers).