gebhart/patrepeval huggingface dataset:
RhoGDI-3 Is a New GDP Dissociation Inhibitor (GDI) (1996)

RhoB is a small GTP-binding protein highly homologous to the RhoA protein. While RhoA is known to regulate the assembly of focal adhesions and stress fibers in response to growth factors, the function of RhoB remains unknown. We have reported that the transient expression of the endogenous RhoB protein is regulated during the cell cycle, contrasting with the permanent RhoA protein expression (). Using the yeast two-hybrid system to characterize proteins interacting with RhoB, we identified a new mouse Rho GDP dissociation inhibitor, referenced as RhoGDI-3. The NH2-terminal alpha helix of RhoGDI-3 is strongly amphipatic and differs thus from that found in previously described bovine, human, and yeast RhoGDI proteins and mouse and human D4/Ly-GDIs. Contrary to the cytosolic localization of all known GDI proteins, acting on Rab or Rho, RhoGDI-3 is associated to a Triton X-100-insoluble membranous or cytoskeletal subcellular fraction. In the two-hybrid system, RhoGDI-3 interacts specifically with GDP- and GTP-bound forms of post-translationally processed RhoB and RhoG proteins, both of which show a growth-regulated expression in mammalian cells. No interaction is found with RhoA, RhoC, or Rac1 proteins. We show that GDI-3 is able to inhibit GDP/GTP exchange of RhoB and to release GDP-bound but not GTP-bound RhoB from cell membranes.
Essential Mechanisms in the Catalysis of Peptide Bond Formation on the Ribosome (2005)

Peptide bond formation is the main catalytic function of the ribosome. The mechanism of catalysis is presumed to be highly conserved in all organisms. We tested the conservation by comparing mechanistic features of the peptidyl transfer reaction on ribosomes from Escherichia coli and the Gram-positive bacterium Mycobacterium smegmatis. In both cases, the major contribution to catalysis was the lowering of the activation entropy. The rate of peptide bond formation was pH independent with the natural substrate, amino-acyl-tRNA, but was slowed down 200-fold with decreasing pH when puromycin was used as a substrate analog. Mutation of the conserved base A2451 of 23 S rRNA to U did not abolish the pH dependence of the reaction with puromycin in M. smegmatis, suggesting that A2451 did not confer the pH dependence. However, the A2451U mutation alters the structure of the peptidyl transferase center and changes the pattern of pH-dependent rearrangements, as probed by chemical modification of 23 S rRNA. A2451 seems to function as a pivot point in ordering the structure of the peptidyl transferase center rather than taking part in chemical catalysis.
Unusual Allylpalladium Carboxylate Complexes: Identification of the Resting State of Catalytic Enantioselective Decarboxylative Allylic Alkylation Reactions of Ketones (2009)

Prickelnd! Die enantioselektive palladiumkatalysierte decarboxylierende Alkylierung von Ketonenolaten verläuft über η1-σ-Allylpalladium-Carboxylat-Komplexe wie 1 (Pd gelb, O rot, N blau, P violett) durch langsamen CO2-Verlust. An Brausepulver erinnert das Verhalten unreiner Proben von 1, die im festen Zustand ein Gas (vermutlich CO2) ausstoßen und in Lösung aufschäumen. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
The syntheses and <i>in vitro</i> biotransformation studies of [<sup>14</sup>C]apixaban, a highly potent, selective, efficacious and orally bioavailable inhibitor of blood coagulation Factor Xa (2011)

Abstract Apixaban is a potent inhibitor of blood coagulation Factor Xa in the late stages of development. [ 14 C]apixaban was synthesized with the 14C label in the two different lactam ring systems within the molecule for various in vitro and in vivo metabolism studies. A nine‐step synthesis of [ 14 C]apixaban, 10 , with the label in the central lactam ring was completed in 14% overall yield. A second synthesis of [ 14 C]apixaban, 14 , with the 14C label in the outer lactam ring was completed in three steps in a 14% overall yield. No significant differences were observed between the metabolite profiles of 10 and 14 , [ 14 C]apixaban, from both rat and human hepatocyte or microsomal incubations. Copyright © 2011 John Wiley & Sons, Ltd.
Epstein-Barr Virus Nuclear Antigen 3C Regulates Cyclin A/p27 Complexes and Enhances Cyclin A-Dependent Kinase Activity (2004)

Epstein-Barr virus (EBV) nuclear antigen 3C (EBNA3C) is essential for primary B-cell transformation. In this report we show that cyclin A, an activator of S phase progression, bound tightly to EBNA3C. EBNA3C interacted with cyclin A in vitro and associated with cyclin A complexes in EBV-transformed lymphoblastoid cell lines. Importantly, EBNA3C stimulated cyclin A-dependent kinase activity and rescued p27-mediated inhibition of cyclin A/Cdk2 kinase activity by decreasing the molecular association between cyclin A and p27 in cells. Additionally, phosphorylation of the retinoblastoma protein, a major regulator of cell cycle progression, was enhanced both in vitro and in vivo in the presence of EBNA3C. Cyclin A interacted with a region of the carboxy terminus of EBNA3C, shown to be important both for stimulation of cyclin A-dependent kinase activity and for cell cycle progression. This provides the first evidence of an essential EBV latent antigen's directly targeting a cell cycle regulatory protein and suggests a novel mechanism by which EBV deregulates the mammalian cell cycle, which is of critical importance in B-cell transformation.
Decreased expression of p38 MAPK mediates protective effects of hydrogen sulfide on hepatic fibrosis. (2013)

Exogenous H2S inhibits activated HSC-T6 cells and induces cell cycle arrest and apoptosis. Decreased Phospho-p38 and increased Phospho-Akt expressions may mediate the anti-fibrosis effect by exogenous H2S.
Thermal Cook-Off Experiments of the HMX Based High Explosive LX-04 to Characterize Violence with Varying Confinement (2006)

Thermal cook‐off experiments were carried out using LX‐04 explosive (85% HMX and 15% Viton by weight) with different levels of confinement to characterize the effect of confinement on the reaction violence. These experiments involved heating a porous LX‐04 sample in a stainless steel container with varying container end plate thickness and assembly bolt diameter to control overall confinement. As expected, detonation did not occur and reducing the overall confinement lowered the reaction violence. This is consistent with modeling results that predict that a lower confinement will act to lower the cook‐off pressure and thus the overall burn rate which lowers the overall violence. These results suggest that controlling the overall system confinement can modify the relative safety in a given scenario.
The Selectivity for K<sup>+</sup> versus Na<sup>+</sup> in DNA Quadruplexes Is Dominated by Relative Free Energies of Hydration:  A Thermodynamic Analysis by <sup>1</sup>H NMR (1996)

We have studied the competition between Na+ and K+ for coordination by G quartets using the oligonucleotide d(G3T4G3) as a model system. d(G3T4G3) forms a dimeric foldback structure containing three G quartets in the presence of either NaCl or KCl. Proton chemical shifts, which are particular to the species of coordinated ion, have been used to monitor the conversion between the sodium and potassium forms under equilibrium conditions. Analysis of titration experiments indicates that at least two K+ are coordinated by the three quartets of the dimeric molecule, and perfect fits of the data are obtained for two Na+ being displaced by two K+. Our results also indicate that the conversion of [d(G3T4G3)]2 from the sodium to the potassium form is associated with a net free energy change (delta G degrees) of -1.7 +/- 0.15 kcal/mol. It has long been suggested that the greater thermal stability of DNA quadruplex structures in the presence of K+ is primarily a result of the optimal fit of this ion in the coordination sites formed by G quartets. However, a consideration of the relatively small change in free energy associated with the conversion from the sodium to the potassium form and the relatively large difference between the free energy of hydration for Na+ and K+ indicates that this cannot be correct. Rather, the preferred coordination of K+ over Na+ is actually driven by the greater energetic cost of Na+ dehydration with respect to K+ dehydration.
Privacy-preservation for gradient descent methods (2007)

Gradient descent is a widely used paradigm for solving many optimization problems. Stochastic gradient descent performs a series of iterations to minimize a target function in order to reach a local minimum. In machine learning or data mining, this function corresponds to a decision model that is to be discovered. The gradient descent paradigm underlies many commonly used techniques in data mining and machine learning, such as neural networks, Bayesian networks, genetic algorithms, and simulated annealing. To the best of our knowledge, there has not been any work that extends the notion of privacy preservation or secure multi-party computation to gradient-descent-based techniques. In this paper, we propose a preliminary approach to enable privacy preservation in gradient descent methods in general and demonstrate its feasibility in specific gradient descent methods.
EFFECTS OF NITROGEN FERTIGATION ON RESERVE NITROGEN AND CARBOHYDRATE STATUS AND REGROWTH PERFORMANCE OF PEAR NURSERY PLANTS (2001)

ISHS IV International Symposium on Mineral Nutrition of Deciduous Fruit Crops EFFECTS OF NITROGEN FERTIGATION ON RESERVE NITROGEN AND CARBOHYDRATE STATUS AND REGROWTH PERFORMANCE OF PEAR NURSERY PLANTS
Efficient Synthesis of 2-(Trifluoromethyl)nicotinic Acid Derivatives from Simple Fluorinated Precursors (2008)

Novel routes to 2-trifluoromethyl-nicotinic acid derivatives have been developed involving synthesis of the pyridine ring. These pyridyl compounds serve as key intermediates in the manufacture of the recently discovered COMT inhibitor, 3-(5-(3,4-dihydroxy-5-nitrophenyl)-1,2,4-oxadiazol-3-yl)-2-(trifluoromethyl)pyridine 1-oxide.
Implementing feature variability for models and code with projectional language workbenches (2010)

Product line engineering deals with managing and implementing the variability among a set of related products. We distinguish between two kinds of variability: configuration and customization. Customization variability can be described using programming language code or creative construction DSLs, whereas configuration variability is described using configuration based approaches, such as feature models. Many product lines have both kinds of variability, and they need to be integrated efficiently. This paper describes an approach for product line engineering using projectional language workbenches. These represent code and models with the same fundamental technology, enabling the mixing of models and code. They make the tight integration between several domain-specific languages possible and simple. Since they can store arbitrary information in models, it is possible to overlay configuration variability over customization variability (i.e. apply feature model-based configuration to code and models). Because of the projectional approach to editing, programs can be shown with or without the dependencies on feature models, they can even be rendered (and edited) for a specific variant. This approach leads to highly integrated and productive tools for product line development. The paper explains the approach, outlines the implementation of a prototype tool based on Jetbrains MPS and illustrates the benefits using a small product line for embedded systems.
EEG Slow (∼1 Hz) Waves Are Associated With Nonstationarity of Thalamo-Cortical Sensory Processing in the Sleeping Human (2003)

Intracellular studies reveal that, during slow wave sleep (SWS), the entire cortical network can swing rhythmically between extremely different microstates, ranging from wakefulness-like network activation to functional disconnection in the space of a few hundred milliseconds. This alternation of states also involves the thalamic neurons and is reflected in the EEG by a slow (<1 Hz) oscillation. These rhythmic changes, occurring in the thalamo-cortical circuits during SWS, may have relevant, phasic effects on the transmission and processing of sensory information. However, brain reactivity to sensory stimuli, during SWS, has traditionally been studied by means of sequential averaging, a procedure that necessarily masks any short-term fluctuation of responsiveness. The aim of this study was to provide a dynamic evaluation of brain reactivity to sensory stimuli in naturally sleeping humans. To this aim, single-trial somatosensory evoked potentials (SEPs) were grouped and averaged as a function of the phase of the ongoing sleep slow (<1 Hz) oscillation. This procedure revealed a dynamic profile of responsiveness, which was conditioned by the phase of the spontaneous sleep EEG. Overall, the amplitude of the evoked potential changed sistematically, increasing and approaching wakefulness levels along the negative slope of the EEG oscillation and decaying below SWS average levels along the positive drift. These marked and fast changes of stimulus-correlated electrical activity involved both short (N20) and long latency (P60 and P100) components of SEPs. In addition, the observed short-term response variability appeared to be centrally generated and specifically related to the evolution of the spontaneous oscillatory pattern. The present findings demonstrate that thalamo-cortical processing of sensory information is not stationary in the very short period (approximately 500 ms) during natural SWS.
Prolonged Hot Electron Dynamics in Plasmonic‐Metal/Semiconductor Heterostructures with Implications for Solar Photocatalysis (2014)

Ideal solar-to-fuel photocatalysts must effectively harvest sunlight to generate significant quantities of long-lived charge carriers necessary for chemical reactions. Here we demonstrate the merits of augmenting traditional photoelectrochemical cells with plasmonic nanoparticles to satisfy these daunting photocatalytic requirements. Electrochemical techniques were employed to elucidate the mechanics of plasmon-mediated electron transfer within Au/TiO2 heterostructures under visible-light (λ>515 nm) irradiation in solution. Significantly, we discovered that these transferred electrons displayed excited-state lifetimes two orders of magnitude longer than those of electrons photogenerated directly within TiO2 via UV excitation. These long-lived electrons further enable visible-light-driven H2 evolution from water, heralding a new photocatalytic paradigm for solar energy conversion.
<title>Microcontroller-based digital front-end for near-infrared spectroscopy</title> (2000)

Near IR Spectroscopy (NIRS) can be employed to noninvasively and continuously measure in-vivo local changes in haemodynamics and oxygenation of human tissues. Monitoring of these parameters is particularly useful both for basic research and during surgery, when a continuous and real-time measurement can help to avoid permanent damage to the tissues. We present a modular acquisition system in which each subsystem, from the case to the single acquisition front-end is designed to meet all the requirements of a research-grade instrument, dedicated to intraoperatory measurements. Part of the modules of the acquisition system has been dedicated to multipoint NIRS. A module prototype has been developed, which is able to control four LED sources and two detectors. On each front-end a RISC microcontroller performs source and detector multiplexing with a digital correlation technique. A number of such modules can be independently addressed through a bus by a PC-based workstation for data collection, processing and visualization. Preliminary test of the prototype on tourniquet-induced forearm ischemia show adequate detectivity and time response. The operating parameters derived from the prototype will be employed in the design of a high channel count module, which will exploit the capabilities of a digital signal processor, for spatially mapped brain oxygenation monitoring.
Automatic Cell-and-portal Decomposition (2003)

We present a method to automatically compute a decomposition of a polygonal scene into a simple cell-and-portal graph. The resulting cell-and-portal graph satisfies the following user-defined constraints: an upper bound on the rendering cost of each cell, and lower or upper bounds on the size of each cell. This is useful to achieve real-time rendering of large indoor models, and is especially suited to architectural walk-throughs and game engines. Our method relies on a binary space-subdivision preprocessing step, then on a portal grouping algorithm that selects or rejects portals generated by the subdivision. Finally the cell-and-portal graph (CPG) is built and post-processed to satisfy the constraints on the cells. We also propose a metrics for measuring the quality of portals, which is used to guide the post-processing. Furthermore, our simplification algorithm can be used on any CPG in order to reduce its complexity according to a user threshold. We present both a general algorithm and a complete implementation with practical details. Results show that portals created by our method have good geometrical properties (e.g. they often lie on doors and windows). The generated decomposition can be used for online occlusion culling.
Metabolism of androgens by human skin in acne (1974)

Shoulder skin from young men with and without acne was incubated in vitro in Krebs Improved Ringer I medium with 7α‐3Hdehydroepiandrosterone,7α‐3Handrostenedione and 7α‐3Htestosterone. There were no marked differences in steroid metabolism between the acne and control groups but skin from acne patients did form rather more 5α‐dihydrotestosterone from testosterone than did skin from control subjects. Skin from the shoulder (acne area) of acne and control subjects metabolized dehydroepiandrosterone more rapidly than did skin from the thigh (non‐acne area); this appeared to be due to higher activity of 3β‐hydroxysteroid dehydrogenase Δ4‐5 isomerase in shoulder than thigh skin. A comparison of steroid metabolism in skin incubated in Krebs Ringer medium with that in cryostat sections of skin incubated in a tris‐buffered medium showed that the method of incubation could affect the quantitative pattern of steroid metabolism in vitro.
Hepatic toll‐like receptor 4 expression is associated with portal inflammation and fibrosis in patients with <scp>NAFLD</scp> (2014)

TLR4 expression by regenerating and inflammatory cells at the porto-septal and interface level, favoured by increased LPS activity, is associated with activation of fibrogenic cells and the degree of fibrosis.
Flow signatures of popular applications (2011)

Network flow data is widely used to analyze the protocol mix forwarded by a router or to identify anomalies that may be caused by hardware and software failures, configuration errors, or intrusion attempts. The goal of our research is to find application signatures in network flow traces that can be used to pinpoint certain applications, such as specific web browsers, mail clients, or media-players. Our starting point is the hypothesis that popular applications generate application specific flow signatures. In order to verify our hypothesis, we recorded traffic traces of several applications and we subsequently analyzed the traces to identify flow signatures of these applications. The flow signatures were formalized as queries of a stream-based flow query language. The queries have been executed on several flow traces in order to evaluate our approach.
Brain magnetic resonance imaging findings in patients with systemic sclerosis (2009)

Asymptomatic as well as symptomatic central nervous system ischemic vasculopathy is not uncommon in systemic sclerosis patients and MRI is considered a sensitive noninvasive screening tool for early detection of CNS involvement in patients with systemic sclerosis.
Comparison of Anti-HBV Activity of β-D- and β-L-ddA-5′Monophosphate Prodrugs and Effectiveness in Combination with Lamivudine (1999)

We have investigated the effects of several beta-D-ddA 5'-monophospate (beta-D-ddAMP), and their corresponding beta-L-enantiomers prodrugs against HBV replication. All ddAMP prodrugs inhibited HBV replication in a dose-dependent manner.
Fostering Community Supported Agriculture in Utah (2017)

This curriculum contains seven modules that describe the fundamentals of CSA, CSA marketing and outreach, CSA management, CSA pricing, CSA crop planning, legal concerns for CSA operations, and additional resources.
Identification of a Δ4‐desaturase from the microalga <i>Ostreococcus lucimarinus</i> (2011)

Abstract Very long chain PUFA (VLCPUFA) like DHA are essential and health‐beneficial components of the human diet. Due to a shortfall in VLCPUFA supply, research is ongoing to establish VLCPUFA production in heterologous systems like for example oilseed plants. For this purpose it is crucial to identify the required enzymes from primary producers of VLCPUFA. Here, we describe a cDNA from the microalga Ostreococcus lucimarinus coding for a Δ4‐fatty acid desaturase. It exhibits a cytochrome b 5 domain fused to its amino terminus and three histidine boxes that are typically found in front‐end desaturases. Heterologous expression of the partly codon‐optimized version of the cDNA in yeast revealed that the encoded protein catalyzes the desaturation of ( n ‐3)‐ as well as ( n ‐6)‐substrates with a preference for VLCPUFA. In yeast it localized at the endoplasmic reticulum (ER) membrane and analysis of the product distribution into different lipid classes suggested that the enzyme most likely acts in a lipid‐dependent manner. Practical applications : The identified Δ4‐desaturase may be useful for the production of DHA in transgenic oleaginous organisms like annual oilseed crops.
Effect of<i>Andrographis paniculata</i>leaf extract on wound healing in rats (2011)

This work was carried out to study the effect of topical application of Andrographis paniculata on the rate of wound enclosure and its histological features. A wound was created in four groups of rat in posterior neck region. Blank placebo was applied topically to the wounds of Group 1. Groups 2 and 3 were dressed with placebo containing 5% and 10% extracts of A. paniculata, respectively. Intrasite gel was applied topically to the wounds of Group 4. Macroscopical examination revealed that the rate of wound healing was significantly accelerated in the wound dressed with A. paniculata extract compared to the blank placebo. The wounds dressed with 10% extract or Intrasite gel healed earlier compared to the wounds dressed with placebo containing 5% A. paniculata extract. Histologically, wounds dressed with A. paniculata extracts showed markedly less scar width and contained large amounts of fibroblast proliferation. More collagen and less angiogenesis with absence of inflammatory cells were seen for wounds dressed with 10% A. paniculata compared to the blank placebo. Conclusion, A. paniculata extracts significantly enhanced rate of wound healing in rats.