gebhart/patrepeval huggingface dataset:
Bryostatin Enhancement of Memory inHermissenda (2006)

Bryostatin, a potent agonist of protein kinase C (PKC), when administered to Hermissenda was found to affect acquisition of an associative learning paradigm. Low bryostatin concentrations (0.1 to 0.5 ng/ml) enhanced memory acquisition, while concentrations higher than 1.0 ng/ml down-regulated the pathway and no recall of the associative training was exhibited. The extent of enhancement depended upon the conditioning regime used and the memory stage normally fostered by that regime. The effects of two training events (TEs) with paired conditioned and unconditioned stimuli, which standardly evoked only short-term memory (STM) lasting 7 min, were--when bryostatin was added concurrently--enhanced to a long-term memory (LTM) that lasted about 20 h. The effects of both 4- and 6-paired TEs (which by themselves did not generate LTM), were also enhanced by bryostatin to induce a consolidated memory (CM) that lasted at least 5 days. The standard positive 9-TE regime typically produced a CM lasting at least 6 days. Low concentrations of bryostatin (<0.5 ng/ml) elicited no demonstrable enhancement of CM from 9-TEs. However, animals exposed to bryostatin concentrations higher than 1.0 ng/ml exhibited no behavioral learning. Sharp-electrode intracellular recordings of type-B photoreceptors in the eyes from animals conditioned in vivo with bryostatin revealed changes in input resistance and an enhanced long-lasting depolarization (LLD) in response to light. Likewise, quantitative immunocytochemical measurements using an antibody specific for the PKC-activated Ca2+/GTP-binding protein calexcitin showed enhanced antibody labeling with bryostatin. Animals exposed to the PKC inhibitor bisindolylmaleimide-XI (Ro-32-0432) administered by immersion prior to 9-TE conditioning showed no training-induced changes with or without bryostatin exposure. However, if animals received bryostatin before Ro-32, the enhanced acquisition and demonstrated recall still occurred. Therefore, pathways responsible for the enhancement effects induced by bryostatin were putatively mediated by PKC. Overall, the data indicated that PKC activation occurred and calexcitin levels were raised during the acquisition phases of associative conditioning and memory initiation, and subsequently returned to baseline levels within 24 and 48 h, respectively. Therefore, the protracted recall measured by the testing regime used was probably due to bryostatin-induced changes during the acquisition and facilitated storage of memory, and not necessarily to enhanced recall of the stored memory when tested many days after training.
VECS. Interactively Correcting .STL Files in a Virtual Environment (2018)

Free Form Fabrication (FFF) machines transform objects merely existing as Os or&#13;\n1s in a computer into a tangible object. FFF machines shift the paradigm of standard 2&#13;\nDimensional printers/paper printouts to 3 Dimensional printers/volumetric printouts (or 3D&#13;\nhardcopies). Currently, this technology is weakened by the link between computers and FFF&#13;\nmachines: the .STL file, which contains a series oftriangles representing the skin ofthe object&#13;\nto be prototyped. A prototype, reflecting precisely the evolution of a concept within a design&#13;\ncycle and allowing a systematic inspection/verification, is essential. A system responding to&#13;\nthis need was designed at Clemson University for the inspection and the correction ofsuch a&#13;\nfile. IVECS, the Interactive Virtual Environment for the Correction of.STL files, is a tool that&#13;\nallows minute surgery to be performed on faulty tessellated models. IVECS allows STL files&#13;\nto be imported, tessellation errors to be detected and automatically or manually fixed. This&#13;\npaper expands on the use of IVECS for the inspection and the correction of .STL files. It&#13;\nextends the usefulness of the STL format by allowing designers to virtually prototype before&#13;\nactually building a physical model, thus contributing to a shorter design cycle.
Intra-tRNA distance measurements for nucleocapsid proteindependent tRNA unwinding during priming of HIV reverse transcription (1999)

We report here the direct measurement of intra-tRNA distances during annealing of the tRNA primer to the HIV RNA genome. This key step in the initiation of retroviral reverse transcription involves hybridization of one strand of the acceptor arm of a specific lysine tRNA to the primer binding site on the RNA genome. Although the mechanism of tRNA unwinding and annealing is not known, previous studies have shown that HIV nucleocapsid protein (NC) greatly accelerates primer/template binary complex formation in vitro. An open question is whether NC alone unwinds the primer or whether unwinding by NC requires the RNA genome. We monitored the annealing process in solution by using fluorescence resonance energy transfer (FRET). Distance measurements demonstrate unequivocally that the tRNA acceptor stem is not substantially unwound by NC in the absence of the RNA genome, that is, unwinding is not separable from hybridization. Moreover, FRET measurements show that both heat- and NC-mediated annealing result in an approximately 40-A increase in the separation of the two ends of the tRNA acceptor arm on binding to the template. This large increase in separation of the two ends suggests a complete displacement of the nonhybridized strand of the acceptor stem in the initiation complex.
Laser-Assisted Formation of Porous Si in Diverse Fluoride Solutions:  Reaction Kinetics and Mechanistic Implications (2001)

The formation rate of porous silicon by photoelectrochemical etching of n-type silicon is measured in situ by a novel technique. The reflection of the laser beam used to drive the reaction contains circular patterns, the outer radius of which bears a linear relationship to the depth of etching. The use of the radius to measure etch rate and the absolute depth of etching is described and justified. The rates are analyzed in terms of the calculated activities of the different species in solution. A rate equation, which is first order in HF and is deduced and rate coefficients calculated. It is concluded that the etching mechanism includes two parallel rate-determining steps involving HF and and that the channel is roughly 20 times faster than the HF channel. In light of our data, previously proposed mechanisms of Si dissolution in fluoride solutions should be reevaluated.
Lightweight security primitives for E-Commerce (1997)

Emerging applications in electronic commerce often involve very low-cost transactions, which execute in the context of ongoing, extended clientserver relationships. For example, consider a website (server) which offers repeated authenticated personalized stock quotes to each of its subscribers (clients). The value of a single transaction (e.g., delivery of a web-page with a customized set of quotes) does not warrant the cost of executing a handshake and key distribution protocol. Also, a client might not always use the same machine during such an extended relationship (e.g., a PC at home, a laptop on a trip). Typical transport/session-layer security mechanisms such as SSL and S-HTTP either require handshake/key distribution for each transaction or do not support client mobility. We propose a new security framework for extended relationships between clients and servers, based on persistent shared keys. We argue that this is a preferred model for inexpensive transactions executing withi...
Equation of State Modeling of Phase Equilibrium in the Low-Density Polyethylene Process:  The Sanchez−Lacombe, Statistical Associating Fluid Theory, and Polymer-Soave−Redlich−Kwong Equations of State (1998)

Applicability of the equation of state models for modeling and simulation of phase equilibrium in polymer production processes is investigated. The flash separation of unreacted ethylene from polyethylene is used as a prototype for simulation. First, three equation of state models (statistical associating fluid theory, Sanchez−Lacombe, and an augmented Soave−Redlich−Kwong cubic equation of state) are comparatively used to correlate pure component volumetric, calorimetric, and phase equilibrium properties for ethylene and polyethylene. Next, they are tested for correlation of vapor−liquid equilibrium of ethylene + low-density polyethylene mixtures. Finally, a two-stage flash problem that mimics the separation process in the low-density polyethylene production is simulated using the three models. Each equation of state model has some unique characteristics that affect the outcome of modeling pure component as well as mixture behavior. The advantages and disadvantages of each model are discussed.
Investigations of the in Vitro Transport of Human Milk Oligosaccharides by a Caco-2 Monolayer Using a Novel High Performance Liquid Chromatography-Mass Spectrometry Technique (2001)

Complex lactose-derived oligosaccharides belong to the main components of human milk and are believed to exert multiple functions in the breast-fed infant. Therefore, we investigated the transepithelial transport of human milk oligosaccharides over Caco-2 monolayers. Main human milk oligosaccharides (HMOs) in the apical, basolateral, or intracellular compartment were separated by high performance liquid chromatography using a Hypercarb(TM) column and analyzed on line by mass spectrometry. This method allowed the identification and quantification of these components in intra- and extracellular fractions without prior purification. Using this technique we were able to show that acidic and neutral HMOs cross the epithelial barrier. The transepithelial flux of neutral, but not acidic, oligosaccharides was temperature-sensitive and partly inhibited by brefeldin A and bafilomycin A. Furthermore, net flux from the apical to the basolateral compartment was only observed for the neutral components. Similarly, apical cellular uptake was only found for neutral components but not for acidic oligosaccharides. Intracellular concentrations of neutral HMOs were significantly increased by inhibitors of transcytosis such as brefeldin A, N-ethylmaleimide, or bafilomycin A. The cellular uptake was saturable, and an apparent K(m) for lacto-N-fucopentaose I of 1.7 +/- 0.1 mmol/liter and for lacto-N-tetraose of 1.8 +/- 0.4 mmol/liter was determined. Furthermore, the uptake of lacto-N-fucopentaose I could be inhibited by the addition of the stereoisomer lacto-N-fucopentaose II but not by lacto-N-tetraose. These findings suggest that neutral HMOs are transported across the intestinal epithelium by receptor-mediated transcytosis as well as via paracellular pathways, whereas translocation of acidic HMOs solely represents paracellular flux.
Stereochemical assignment, antiinflammatory properties, and receptor for the omega-3 lipid mediator resolvin E1 (2005)

The essential fatty acid eicosapentaenoic acid (EPA) present in fish oils displays beneficial effects in a range of human disorders associated with inflammation including cardiovascular disease. Resolvin E1 (RvE1), a new bioactive oxygenated product of EPA, was identified in human plasma and prepared by total organic synthesis. Results of bioaction and physical matching studies indicate that the complete structure of RvE1 is 5S,12R,18R-trihydroxy-6Z,8E,10E,14Z,16E-EPA. At nanomolar levels, RvE1 dramatically reduced dermal inflammation, peritonitis, dendritic cell (DC) migration, and interleukin (IL) 12 production. We screened receptors and identified one, denoted earlier as ChemR23, that mediates RvE1 signal to attenuate nuclear factor-kappaB. Specific binding of RvE1 to this receptor was confirmed using synthetic [(3)H]-labeled RvE1. Treatment of DCs with small interference RNA specific for ChemR23 sharply reduced RvE1 regulation of IL-12. These results demonstrate novel counterregulatory responses in inflammation initiated via RvE1 receptor activation that provide the first evidence for EPA-derived potent endogenous agonists of antiinflammation.
Clinical response and pharmacokinetics from a phase 1 study of an active dosing schedule of flavopiridol in relapsed chronic lymphocytic leukemia (2008)

We previously reported interim results of a phase 1 trial in patients with chronic lymphocytic leukemia (CLL) whereby flavopiridol was administered intravenously as a 30-minute bolus followed by 4-hour infusion. We now report full pharmacokinetic (PK) data, correlations of PK with clinical outcomes, and final response and progression-free survival (PFS). Twenty-one (40%) of 52 patients with relapsed CLL achieved a partial response (PR) with a median PFS of 12 months. Responders included 17 (40%) of 43 fludarabine refractory patients, 7 (39%) of 18 patients with del(17p13), and 14 (74%) of 19 patients with del(11q22). Six responders received repeat therapy at relapse, and 5 responded again with a second median PFS of 10 months. Noncompartmental analysis and nonlinear mixed effects modeling was used to estimate PK parameters and evaluate covariates. Two-compartment population parameter estimates were 31.4 L/h, 65.8 L, 8.49 L/h, and 157 L for CL, V1, Q, and V2, respectively. Flavopiridol area under the plasma concentration-time curve (AUC) correlated with clinical response and cytokine release syndrome, and glucuronide metabolite AUC correlated with tumor lysis syndrome. These composite results confirm high activity of this pharmacokinetically derived schedule in relapsed, genetically high-risk CLL. Furthermore, PK describes some, but not all, variability in response and toxicity.
Pharmacokinetics and immune response of 131I-chimeric mouse/human B72.3 (human gamma 4) monoclonal antibody in humans. (1991)

Chimeric B72.3, composed of the V-regions of murine B72.3 and the constant regions of human immunoglobulin G4 heavy and kappa light chain, was administered as a 131I-labeled conjugate to 12 patients with metastatic colon cancer. Seven of these patients had an antibody response after initial infusion, and the immune response was primarily directed to the murine V-region, although a small proportion of the antibody response was directed to topographical epitopes requiring the presence of both murine V-region and human CH-1 and kappa constant regions (neo-epitopes). The pharmacokinetics included a plasma disappearance curve best fit by a two-compartmental model with an alpha t 1/2 of 18 +/- 7 h and a beta t 1/2 of 224 +/- 66 h. A second infusion of the same dose of 131I-chimeric B72.3 was administered to four of these patients 8 wk after the first infusion. Two patients who had a high antibody response to initial infusion had an anamnestic antibody response, and the infused ch-B72.3 rapidly disappeared from the circulation with associated immune complexes and free 131I in the plasma. One patient with no initial antibody response had no antibody response and identical pharmacokinetics on second infusion. One patient with a modest transient antibody response to initial infusion had no antibody response on second infusion and a modest shortening of plasma circulation. Thus, the human immunoglobulin G4 isotype chimeric B72.3 monoclonal antibody has a plasma half-life 6 to 8 times as long as murine B72.3 and retains considerable immunogenicity in some patients which can adversely affect repetitive infusions.
Activating Phosphorylation of the Kin28p Subunit of Yeast TFIIH by Cak1p (1999)

Cyclin-dependent kinase (CDK)-activating kinases (CAKs) carry out essential activating phosphorylations of CDKs such as Cdc2 and Cdk2. The catalytic subunit of mammalian CAK, MO15/Cdk7, also functions as a subunit of the general transcription factor TFIIH. However, these functions are split in budding yeast, where Kin28p functions as the kinase subunit of TFIIH and Cak1p functions as a CAK. We show that Kin28p, which is itself a CDK, also contains a site of activating phosphorylation on Thr-162. The kinase activity of a T162A mutant of Kin28p is reduced by approximately 75 to 80% compared to that of wild-type Kin28p. Moreover, cells containing kin28(T162A) and a conditional allele of TFB3 (the ortholog of the mammalian MAT1 protein, an assembly factor for MO15 and cyclin H) are severely compromised and display a significant further reduction in Kin28p activity. This finding provides in vivo support for the previous biochemical observation that MO15-cyclin H complexes can be activated either by activating phosphorylation of MO15 or by binding to MAT1. Finally, we show that Kin28p is no longer phosphorylated on Thr-162 following inactivation of Cak1p in vivo, that Cak1p can phosphorylate Kin28p on Thr-162 in vitro, and that this phosphorylation stimulates the CTD kinase activity of Kin28p. Thus, Kin28p joins Cdc28p, the major cell cycle Cdk in budding yeast, as a physiological Cak1p substrate. These findings indicate that although MO15 and Cak1p constitute different forms of CAK, both control the cell cycle and the phosphorylation of the C-terminal domain of the large subunit of RNA polymerase II by TFIIH.
Spontaneous emission control of colloidal nanocrystals using nanoimprinted photonic crystals (2007)

The authors report on the fabrication and optical characterizations of two-dimensional photonic crystals fabricated by nanoimprint lithography in a nanocomposite polymer incorporating highly luminescent and red emitting (CdSe)ZnS core-shell colloidal nanocrystals. Photonic crystal structures enhance the light emitted from the quantum sized nanoparticles in the composite layer by slowing the propagation speed of the photons, thus increasing the coupling to the out-of-plane radiative modes. A 200% enhancement of the light collection is achieved compared to an unpatterned sample.
IBM System Storage Tape Library Guide for Open Systems (2011)

This IBM Redbooks publication presents a general introduction to Linear Tape-Open (LTO) technology and the implementation of corresponding IBM products.This ninth edition of the book includes information about the latest enhancements to the IBM Ultrium family of tape drives and tape libraries. In addition, it includes a description of the IBM TS1140 Tape Drive, which can be installed in the IBM System Storage TS3500 Tape Library. This book also contains technical information about each IBM tape product for OpenSystems. It includes generalized sections about Small Computer System Interface (SCSI) and Fibre Channel connections and multipath architecture configurations.This edition includes details about the new IBM System Storage TS3500 Tape Library Connector Model SC1. The Shuttle Complex enables extreme scalability of over 300,000 LTO cartridges in a single library image by supporting transport of cartridges from one TS3500 library string to another TS3500 library string.This book also includes information about the tools and techniques for library management. The new IBM Linear Tape File System (LTFS) Library Edition extends the capability of theIBM LTFS Single Drive Edition (SDE) to the TS3500, TS3200 and TS3100. If you benefit from indexing your LTO data stored in these tape libraries for ease of use you can now do so with the IBM LTFS Library Edition.This book is intended for anyone who wants to understand more about the general LTO technology specification, how it came about, and the IBM implementation of that specification.This book is suitable for IBM clients, IBM Business Partners, IBM specialist sales representatives, and technical specialists. If you do not have a background in computer tape storage products, you might need to reference other sources of information. In the interest of being concise, topics that are generally understood are not covered in detail.
L-leucine methyl ester stimulates insulin secretion and islet glutamate dehydrogenase (1983)

Column perifusion of collagenase-isolated mouse pancreatic islets was used to study the dynamics of insulin release in experiments lasting for several hours. The methyl esters of L-leucine and L-arginine were synthesized. Whereas L-arginine methyl ester (L-arginine OMe) had no effect, L-leucine OMe stimulated the release of insulin. The effect of L-leucine OMe was maximal at 5 mmol/liter. Whereas the Km for glucose-stimulated insulin release was unaffected by 1 mmol/liter L-leucine OMe, the maximal release of D-glucose was increased by the amino acid derivative that appeared more effective than L-leucine. L-Leucine OMe was also a potent stimulus of insulin release from the perfused mouse pancreas. In the presence of 10 mmol/liter L-glutamine, 1 mmol/liter L-leucine OMe induced a 50- to 75-fold increase in insulin release. A similar stimulatory effect was also observed in column-perifused RIN 5F cells, a cloned rat islet tumor cell line. A twofold increase in islet glutamate dehydrogenase activity was induced by 5 mmol/liter L-leucine OMe, a larger effect than that of L-leucine (P less than 0.02), whereas L-arginine OMe had a small inhibitory effect. We conclude that L-leucine OMe is a potent stimulus of insulin secretion and that its effect on the beta-cells may be exerted by activating islet glutamate dehydrogenase.
Fluidic self-assembly of semiconductor devices: a promising new method of mass producing flexible circuitry (2002)

We review the basics of fluidic self-assembly, some recent processing developments, and some of the applications of this technology. In particular, we discuss the shape of the NanoBlock/sup TM/ IC devices used in FSA/sup TM/ processing, present a brief overview of the versatility of our process, and outline both a current process application and some future potential applications.
A case-control study of toenail selenium and cancer of the breast, colon, and prostate. (2000)

To study the possible role of dietary and supplementary selenium intake in the etiology of cancer, we carried out a case-control study of breast, colon, and prostate cancer in Montreal between 1989 and 1993. In this study, we were able to interview a total of 1,048 incidence cases of colon (402), breast (414) and prostate (232) cancer subjects and 688 population-based controls matched for age and gender. Of these, a total of 501 cancer cases and 202 controls produced toenail samples for their selenium concentrations, which were determined by neutron activation analysis. We found no association between toenail selenium and breast cancer (odds ratio [OR], 0.72; 95% confidence interval [CI], 0.4-1.31) or prostate cancer (OR, 1.14; 95% CI, 0.46-2.83), though we did observe a statistically significant inverse association between toenail selenium level and the risk of colon cancer for both genders combined (OR, 0.42; 95% CI, 0.19-0.93; P = .009) and for female subjects (P = .050). We also found that nonsmoker case and control subjects had higher selenium in their toenail samples. This could be due either to the nature of tobacco, which reduces selenium absorption, or to smokers' consumption of certain foods containing less selenium. Further epidemiologic studies are required to clarify the role of selenium in the etiology of certain cancers.