gebhart/patrepeval huggingface dataset:
A test of the linear extrapolation of unfolding free energy changes over an extended denaturant concentration range (1992)

Guanidine hydrochloride (GdnHCl) and thermally induced unfolding measurements on the oxidized form of Escherichia coli thioredoxin at pH 7 were combined for the purpose of assessing the functional dependence of unfolding free energy changes on denaturant concentration over an extended GdnHCl concentration range. Conventional analysis of GdnHCl unfolding exhibits a linear plot of unfolding delta G vs [GdnHCl] in the transition zone. In order to extend unfolding delta G measurements outside of that narrow concentration range, thermal unfolding measurements were performed using differential scanning calorimetry (DSC) in the presence of low to moderate concentrations of GdnHCl. The unfolding delta G values from the DSC measurements were corrected to 25 degrees C using the Gibbs-Helmholtz equation and mapped onto the delta G vs [GdnHCl] plot. The dependence of unfolding delta G on [GdnHCl] was found to be linear over the full denaturant concentration range, provided that the chloride ion concentration was kept at a threshold of greater than or equal to 1.5 M. In the DSC experiments performed in the presence of GdnHCl, chloride concentrations were maintained at 1.5 M by addition of appropriate amounts of NaCl. The linear extrapolation method (LEM) gives an unfolding free energy change in the absence of denaturant (delta G degrees N-U) in excellent agreement with the delta G determined by DSC measurement in 1.5 M NaCl. The various methods give a consensus unfolding delta G value of 8.0 kcal/mol at 25 degrees C in the absence of denaturant.(ABSTRACT TRUNCATED AT 250 WORDS)
State-of-the-Art Revascularization Therapy: Peripheral Artery Disease (2009)

Recently, options for the endovascular treatment of peripheral vascular disease—including carotid artery disease, renal artery disease, and peripheral artery disease of the legs—have expanded dramatically. In general, physicians tend to use endovascular techniques for first-line therapy and reserve surgery for more complex cases. This article discusses the benefits and drawbacks of optimal medical therapy compared with endovascular or surgical approaches to vascular disease.
Effects of 2164U90 on ileal bile acid absorption and serum cholesterol in rats and mice. (1995)

2164U90, [(3R,5R)-trans-3-butyl-3-ethyl-2,3,4,5-tetrahydro-5-phenyl-1,4- benzothiazepine 1,1-dioxide], was found to be a potent inhibitor of the ileal bile acid active transport system. In vitro, 2164U90 decreased uptake and active transport of taurocholic acid by rat everted ileal sacs with IC50s of 4.0 microM and 1.5 microM, respectively. In vivo, 2164U90 produced dose-dependent increases in 23,25-75Se-labeled homocholic acid taurine (SeHCAT) fecal excretion in rats and mice at doses of 3-30 mg/kg and 1-10 mg/kg, respectively. In rats, 30 mg/kg 2164U90 was equivalent to 500 mg/kg cholestyramine. Two days oral administration of 10 mg/kg 2164U90 to rats decreased the bile concentrations of total bile acids 42%, orally administered [3H]taurocholic acid ([3H]TC) 82%, and cholesterol 35%. Cholestyramine (500 mg/kg) had effects similar to 2164U90 on total bile acid and orally administered [3H]TC concentrations but had no effect on biliary cholesterol. The hypocholesterolemic activity of 2164U90 was determined in cholesterol-cholic acid-fed rats and cholesterol-cholic acid-coconut oil-fed mice. 2164U90 inhibited the dietary-induced increase in dextran sulfate-precipitable lipoprotein cholesterol (VLDL+LDL) at doses comparable to doses needed to increase the fecal excretion of bile acids. These data indicate that 2164U90 decreases bile acid absorption by inhibiting the ileal bile acid active transport system, resulting in hypocholesterolemic activity.
Recovery phase of the murine rod photoresponse reconstructed from electroretinographic recordings (1996)

The activation and recovery phases of the murine rod photo-response were determined from corneal electroretinograms (ERGs) obtained in response to pairs of full-field flashes producing 50-10(5) photoisomerized rhodopsins (R*) per rod. The a-wave component of the ERG in response to the initial flash provided a well established measure of the activation phase of the rod response. The amplitude of the a-wave response to an intense second flash (45,000 R*) delivered 0.2-5 seconds (s) after the first flash was used to reconstruct the recovery phase of the response. For 160-3000 R* rod-1, recovery curves were isomorphic, translating on the time axis such that each e-fold increase in R* produced an incremental recovery delay of tau c = 210 +/- 50 ms (mean +/- SD). For initial flashes producing > 3000 R*, recovery curves lost their initial isomorphism and half-times had intensity dependence exceeding 1 s per e-fold increase in R*. We conclude that for flashes producing < 3000 R*, the effective lifetime of these R* is not > 210 ms. Two extant and non-mutually exclusive hypotheses are discussed that can account for the sharp increase in recovery times from flashes producing > 3000 R*. They are as follows: (1) approximately 0.03% of R* have a lifetime exceeding 1 s; and (2) the gamma subunit of phosphodiesterase (PDE gamma) serves as a GTPase-activating factor, and 3000 R* produce sufficient activated G-protein (G*) to exceed the total quantity of PDE gamma subunits such that excess G* must wait for unoccupied PDE gamma to inactivate via GTP hydrolysis.
Wafer-Level Packaged Accelerometer With Solderable SMT Terminals (2006)

Miniaturization of devices is driving replacement of electronic components with surface mount technology (SMT) equivalent parts, including any embedded sensing devices. In many cases the size of the sensor is restricted by the minimum size of the package rather than by the die. Other solutions to preserve real-estate involve manual mounting of the die onto substrates that have gone through an SMT assembly process. The +/-2g accelerometer presented here is wafer-level packaged and has solderable terminals allowing the silicon die to be mounted directly onto a substrate in a standard SMT process and without the need for stress-isolating interposers. With its small footprint and ceiling requirements (2.1times .9 times 0.8 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sup> ), and robustness and high performance it is the smallest commercially-available wafer-level packaged accelerometer suitable for medical applications where these characteristics are critical. Device performance is unaffected by the SMT assembly process. Preliminary results show that the solder mounted device is also able to withstand thermal cycling over a wide temperature range (-55 to 125degC).
Can the Human Lumbar Posterior Columns Be Stimulated by Transcutaneous Spinal Cord Stimulation? A Modeling Study (2011)

Stimulation of different spinal cord segments in humans is a widely developed clinical practice for modification of pain, altered sensation, and movement. The human lumbar cord has become a target for modification of motor control by epidural and, more recently, by transcutaneous spinal cord stimulation. Posterior columns of the lumbar spinal cord represent a vertical system of axons and when activated can add other inputs to the motor control of the spinal cord than stimulated posterior roots. We used a detailed three-dimensional volume conductor model of the torso and the McIntyre-Richard-Grill axon model to calculate the thresholds of axons within the posterior columns in response to transcutaneous lumbar spinal cord stimulation. Superficially located large-diameter posterior column fibers with multiple collaterals have a threshold of 45.4 V, three times higher than posterior root fibers (14.1 V). With the stimulation strength needed to activate posterior column axons, posterior root fibers of large and small diameters as well as anterior root fibers are coactivated. The reported results inform on these threshold differences, when stimulation is applied to the posterior structures of the lumbar cord at intensities above the threshold of large-diameter posterior root fibers.
Mechanism-Based Inactivation of Cytochrome P450 3A4 by 4-Ipomeanol (2004)

Earlier phase I and II clinical studies showed that 4-ipomeanol produced selective hepatotoxicity. To investigate the mechanism of bioactivation of 4-ipomeanol, we thoroughly studied the interaction of 4-ipomeanol with human cytochrome P450 3A4 (EC 1.14.14.1). 4-Ipomeanol produced a time- and concentration-dependent inactivation of P450 3A4. More than 80% of the P450 3A4 activity was lost after its incubation with 4-ipomeanol at the concentration of 75 microM in 12 min. The inactivation was characterized by a rate of inactivation (kinact) of 0.15 min(-1) and by an inactivation potency (KI) of 20 microM. In addition, the inhibition of P450 3A4 by 4-ipomeanol was NADPH-dependent and irreversible. Glutathione, catalase, and superoxide dismutase failed to protect P450 3A4 from inactivation by 4-ipomeanol. The presence of testosterone, a substrate of P450 3A4, protected the enzyme from inactivation. The estimated partition ratio of the inactivation was approximately 257. Covalent binding studies demonstrated that reactive metabolites of 4-ipomeanol modified P450 3A4 but not P450 reductase (EC 1.6.2.4). The stoichiometry of binding between reactive metabolites of radiolabeled 4-ipomeanol and P450 3A4 was approximately 1.5:1. In addition to P450 3A4, reactive metabolites of 4-ipomeanol were found to covalently bind to other proteins. 4-Ipomeanol failed to inactivate P450 1A2 in human liver microsomes. In conclusion, 4-ipomeanol irreversibly inhibited P450 3A4, and it was characterized as a mechanism-based inactivator of P450 3A4. This finding facilitates the understanding of the mechanism of bioactivation of 4-ipomeanol by human hepatic enzymes.
Fault Tolerance Management in Cloud Computing: A System-Level Perspective (2012)

The increasing popularity of Cloud computing as an attractive alternative to classic information processing systems has increased the importance of its correct and continuous operation even in the presence of faulty components. In this paper, we introduce an innovative, system-level, modular perspective on creating and managing fault tolerance in Clouds. We propose a comprehensive high-level approach to shading the implementation details of the fault tolerance techniques to application developers and users by means of a dedicated service layer. In particular, the service layer allows the user to specify and apply the desired level of fault tolerance, and does not require knowledge about the fault tolerance techniques that are available in the envisioned Cloud and their implementations.
Design at Work (2020)

Contents: J. Greenbaum, M. Kyng, Preface: Memories of the Past. J. Greenbaum, M. Kyng, Introduction: Situated Design. Part I:Reflecting on Work Practice. L. Bannon, From Human Factors to Human Actors: The Role of Psychology and Human-Computer Interaction Studies in System Design. E. Wynn, Taking Practice Seriously. L.A. Suchman, R.H. Trigg, Understanding Practice: Video as a Medium for Reflection and Design. P.B. Andersen, B. Holmqvist, Language, Perspectives, and Design. K. Bodker, J.S. Pedersen, Workplace Cultures: Looking at Artifacts, Symbols, and Practices. Part II:Designing for Work Practice. S. Bodker, J. Greenbaum, M. Kyng, Setting the Stage for Design as Action. F. Kensing, K.H. Madsen, Generating Visions: Future Workshops and Metaphorical Design. P. Ehn, M. Kyng, Cardboard Computers: Mocking-it-up or Hands-on the Future. S. Bodker, K. Gronboek, Design in Action: From Prototyping by Demonstration to Cooperative Prototyping. A. Henderson, M. Kyng, There's No Place Like Home: Continuing Design in Use. P. Ehn, D. Sjogren, From System Descriptions to Scripts for Action. J. Greenbaum, M. Kyng, Epilogue: Design by Doing.
A study of the Reformatsky reaction on formylcoumarins (1995)

The reactions of bromozinc enolate reagents on formylcoumarins (1, 2) afforded spiro-γ-lactones (15–18), furan derivatives (13, 14), and coumarinylcarbinols (3, 4) as highly unusual products along with the expected β-hydroxyesters (5–12). Stereochemical features of some of these products turned out to be highly informative and were unambiguously corroborated. Keywords: formylcoumarins, unusual Reformatsky products, stereochemistry.
An Adenoviral Vaccine Encoding Full-Length Inactivated Human Her2 Exhibits Potent Immunogenicty and Enhanced Therapeutic Efficacy without Oncogenicity (2010)

Vaccination with mutationally inactivated, nononcogenic Ad-HER2-ki results in robust polyclonal immune responses to HER2 in tolerant models, which translates into strong and effective antitumor responses in vivo. Ad-HER2-ki is thus a safe and promising vaccine for evaluation in clinical trials.
B cell receptor-mediated uptake of CD1d-restricted antigen augments antibody responses by recruiting invariant NKT cell help in vivo (2008)

Highly regulated activation of B cells is required for the production of specific antibodies necessary to provide protection from pathogen infection. This process is initiated by specific recognition of antigen through the B cell receptor (BCR), leading to early intracellular signaling followed by the late recruitment of T cell help. In this study we demonstrate that specific BCR uptake of CD1d-restricted antigens represents an effective means of enhancing invariant natural killer T (iNKT)-dependent B cell responses in vivo. This mechanism is effective over a wide range of antigen affinities but depends on exceeding a tightly regulated avidity threshold necessary for BCR-mediated internalization and CD1d-dependent presentation of particulate antigenic lipid. Subsequently, iNKT cells provide the help required for stimulating B cell proliferation and differentiation. iNKT-stimulated B cells develop within extrafollicular foci and mediate the production of high titers of specific IgM and early class-switched antibodies. Thus, we have demonstrated that in response to particulate antigenic lipids iNKT cells are recruited for the assistance of B cell activation, resulting in the enhancement of specific antibody responses. We propose that such a mechanism may operate to potentiate adaptive immune responses against pathogens in vivo.
Posttransfusion non-A, non-B hepatitis in chimpanzees. Physicochemical evidence that the tubule-forming agent is a small, enveloped virus. (1985)

Posttransfusion non-A, non-B hepatitis associated with the formation of hepatocyte cytoplasmic tubules was experimentally transmitted to chimpanzees by intravenous inoculation of a proven-infectious plasma that had been pelleted and microfiltrated, or purified by a combination of pelleting and rate-zonal banding. The results of these studies indicate that a factor VIII-derived non-A, non-B tubule-forming agent will pass through an 80-nm membrane filter and that it can be recovered from infected plasma by use of a purification procedure that assumes the non-A, non-B tubule-forming agent is a small, enveloped virus. Our findings, in combination with the known sensitivity of the non-A, non-B tubule-forming agent to chloroform and its apparent lack of nucleic acid homology with hepatitis B virus, further suggest that at least one etiologic agent of human posttransfusion non-A, non-B hepatitis may be a small, enveloped RNA virus.
High transconductance enhancement-mode AlGaN/GaN HEMTs on SiC substrate (2003)

Using inductively-coupled-plasma reactive ion etching (ICP-RIE), recessed 1 µm gate-length enhancement-mode (E-mode) AlGaN/GaN high electron mobility transistors (HEMTs) were fabricated. These 1 µm gate-length devices exhibited maximum drain current density of 470 mA/mm, extrinsic transconductance of 248 mS/mm and threshold voltage of 75 mV. These characteristics are much higher than previously reported values for GaN-based E-mode HEMTs. A unity gain cutoff frequency (fT) of 8 GHz and a maximum frequency of oscillation (fmax) of 26 GHz were also measured on these devices.
bcl-x exhibits regulated expression during B cell development and activation and modulates lymphocyte survival in transgenic mice. (1996)

We have assessed during B cell development, the regulation and function of bcl-x, a member of the bcl-2 family of apoptosis regulatory genes. Here we show that Bcl-xL, a product of bcl-x, is expressed in pre-B cells but downregulated at the immature and mature stages of B cell development. Bcl-xL but not Bcl-2 is rapidly induced in peripheral B cells upon surface immunoglobulin M (IgM) cross-linking, CD40 signaling, or LPS stimulation. Transgenic mice that overexpressed Bcl-xL within the B cell lineage exhibited marked accumulation of peripheral B cells in lymphoid organs and enhanced survival of developing and mature B cells. B cell survival was further increased by simultaneous expression of bcl-xL and bcl-2 transgenes. These studies demonstrate that Bcl-2 and Bcl-xL are regulated differentially during B cell development and activation of mature B cells. Induction of Bcl-xL after signaling through surface IgM and CD40 appears to provide mature B cells with an additional protective mechanism against apoptotic signals associated with antigen-induced activation and proliferation.
Raman Spectroscopy for Protein Analysis (2014)

Proteins are essential parts of organisms and participate in virtually every process within cells. Raman spectroscopy can be a powerful tool for the characterization of modified amino acids and proteins. In addition to the potential for quantitative results, it offers the advantage of not requiring any sample preparation. This review focuses on applications for protein analysis, published in the period 2010–2014.
Reflections on 4 Years of mLearning Implementation (2007-2010) (2011)

This paper provides a comparative analysis of five mlearning case studies involving 4 years of action research mlearning projects. The projects investigated the potential of mobile web 2.0 tools to facilitate social constructivist learning environments across multiple learning contexts. Highlighted are the design framework, identified critical success factors, and implementation strategy developed from the thirteen mlearning projects undertaken between 2007 and 2009, with an analysis of the eight 2009 projects and their subsequent adaptation in 2010. The projects illustrate the impact of mlearning supported by sustained interaction via communities of practice facilitating pedagogical shifts from teacher-directed to student-generated content and student-generated contexts.
Analysis of the CtrA Pathway in Magnetospirillum Reveals an Ancestral Role in Motility in Alphaproteobacteria (2012)

Developmental events across the prokaryotic life cycle are highly regulated at the transcriptional and posttranslational levels. Key elements of a few regulatory networks are conserved among phylogenetic groups of bacteria, although the features controlled by these conserved systems are as diverse as the organisms encoding them. In this work, we probed the role of the CtrA regulatory network, conserved throughout the Alphaproteobacteria, in the magnetotactic bacterium Magnetospirillum magneticum strain AMB-1, which possesses unique intracellular organization and compartmentalization. While we have shown that CtrA in AMB-1 is not essential for viability, it is required for motility, and its putative phosphorylation state dictates the ability of CtrA to activate the flagellar biosynthesis gene cascade. Gene expression analysis of strains expressing active and inactive CtrA alleles points to the composition of the extended CtrA regulon, including both direct and indirect targets. These results, combined with a bioinformatic study of the AMB-1 genome, enabled the prediction of an AMB-1-specific CtrA binding site. Further, phylogenetic studies comparing CtrA sequences from alphaproteobacteria in which the role of CtrA has been experimentally examined reveal an ancestral role of CtrA in the regulation of motility and suggest that its essential functions in other alphaproteobacteria were acquired subsequently.
Neurotrophic immunophilin ligands stimulate structural and functional recovery in neurodegenerative animal models (1997)

Although immunosuppressant immunophilin ligands promote neurite outgrowth in vitro, their neurotrophic activities are clearly independent of their immunosuppressive activity. In the present report, a novel nonimmunosuppressive immunophilin ligand, GPI-1046 (3-(3-pyridyl)-1-propyl (2S)-1-(3,3-dimethyl-1,2-dioxopentyl)-2-pyrrolidinecarboxylate+ ++) is described. In vitro, GPI-1046 bound to FK506 binding protein-12 and elicited neurite outgrowth from sensory neuronal cultures with picomolar potency with maximal effects comparable to nerve growth factor. In vivo, GPI-1046 stimulated the regeneration of lesioned sciatic nerve axons and myelin levels. In the central nervous system, GPI-1046 promoted protection and/or sprouting of serotonin-containing nerve fibers in somatosensory cortex following parachloroamphetamine treatment. GPI-1046 also induced regenerative sprouting from spared nigrostriatal dopaminergic neurons following 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine toxicity in mice or 6-hydroxydopamine (6-OHDA) toxicity in rats. The rotational abnormality in 6-OHDA treated rats was alleviated by GPI-1046. These neurotrophic actions in multiple models suggest therapeutic utility for GPI-1046 in neurodegenerative diseases.
Fiber Optic Sensor for Acoustic Detection of Partial Discharges in Oil-Paper Insulated Electrical Systems (2012)

A fiber optic interferometric sensor with an intrinsic transducer along a length of the fiber is presented for ultrasound measurements of the acoustic emission from partial discharges inside oil-filled power apparatus. The sensor is designed for high sensitivity measurements in a harsh electromagnetic field environment, with wide temperature changes and immersion in oil. It allows enough sensitivity for the application, for which the acoustic pressure is in the range of units of Pa at a frequency of 150 kHz. In addition, the accessibility to the sensing region is guaranteed by immune fiber-optic cables and the optical phase sensor output. The sensor design is a compact and rugged coil of fiber. In addition to a complete calibration, the in-situ results show that two types of partial discharges are measured through their acoustic emissions with the sensor immersed in oil.
Electrophilic substitution reactions of furo[3,2-b]pyrrole derivatives (1986)

Formylation of ethyl 4 H -furo[3,2- b ]pyrrole-5-carboxylate and its N-methyl analogue afforded the 2-formyl products Ia,b which on nitration yielded 2-nitro derivatives IIc,d . Formylation, nitration, Mannich reaction, and copulation of the starting products, having position 2 occupied by an aryl, took place at the pyrrole ring.