gebhart/patrepeval huggingface dataset:
Identification of the 14.3.3 ζ Domains Important for Self-association and Raf Binding (1995)

The 14.3.3 zeta protein is a ubiquitous and abundant arachidonate-selective acyltransferase and putative phospholipase A2, which self-assembles into dimers and binds to c-Raf-1 and other polypeptides in vitro and in intact cells. The 14.3.3 polypeptides endogenous to Sf9 cells associate in situ with both active and inactive recombinant Raf and copurify at a fairly reproducible molar ratio that is probably 1. Purified baculoviral recombinant Raf, despite its preassociated 14.3.3 polypeptide, binds additional recombinant 14.3.3 zeta polypeptide in vitro, in a saturable and specific reaction, forming a complex that is resistant to 1 M LiCl. A two-hybrid analysis indicates that 14.3.3 zeta binds primarily to Raf noncatalytic sequences distinct from those that bind Ras-GTP, and in vitro 14.3.3 zeta binds to Raf without inhibiting the Ras-Raf association or Raf-catalyzed MEK phosphorylation. Deletion analysis of 14.3.3 zeta (1-245) indicates that the 14.3.3 domain responsible for binding to Raf extends over the carboxyl-terminal 100 amino acids, whereas 14.3.3 dimerization is mediated by amino-terminal sequences. As with Ras, the 14.3.3 zeta polypeptide does not activate purified Raf directly in vitro. Moreover, expression of recombinant 14.3.3 zeta in COS cells beyond the substantial level of endogenous 14.3.3 protein does not alter endogenous Raf kinase, as judged by the activity of a cotransfected Erk-1 reporter. Coexpression of recombinant 14.3.3 with recombinant Myc-tagged Raf in COS cells does increase substantially the Myc-Raf kinase activity achieved during transient expression, which is attributable primarily to an increased level of Myc-Raf polypeptide, without alteration of Myc-Raf specific activity or the activation that occurs in response to epidermal growth factor or 12-O-tetradecanoylphorbol-13-acetate. Nevertheless, evidence that 14.3.3 actively participates in Raf activation in situ is provided by the finding that although full-length 14.3.3 zeta binds active Raf in situ, truncated versions of 14.3.3, some of which bind Raf polypeptide in situ nearly as well as full-length 14.3.3 zeta, are recovered in association only with inactive Raf polypeptides. Thus, 14.3.3 polypeptides bind tightly to one or more sites on c-Raf. Overexpression of 14.3.3 zeta enhances the expression of recombinant Raf, perhaps by stabilizing the Raf polypeptide. In addition, Raf polypeptides bound to truncated 14.3.3 polypeptides are unable to undergo activation in situ, indicating that 14.3.3 participates in the process of Raf activation by mechanisms that remain to be elucidated.
The effect of iron on <i>in vitro</i> decalcification of human tooth enamel (1985)

The effect of iron chloride on an in vitro acid attack of human enamel was studied. Slices of teeth were covered with varnish except for a window left on one of the enamel surfaces for exposure. The iron salt was used as a supplement to acid gel, or as pretreatment of the enamel surfaces before exposure to the pure gel. Differences in light transmission of the experimental and control specimen from the radiographs taken before and after immersion in the decalcifying media were assessed quantitatively. The increase in radio-opacity of the enamel sections incubated in the iron-containing acid media was attributed to a lower degree of enamel decalcification.
New microbial fuel cell power system for efficiency improvement (2011)

This paper presents a power management system for energy harvesting with multiple microbial fuel cells (MFCs), devices that can generate electricity in water environments using electro-chemical reactions caused by bacteria. The system first connects a capacitor to each MFC in parallel so that the capacitors are charged by the MFCs. Then the system disconnects the capacitors from the MFCs, connects all the capacitors in series, and connects all the series-connected capacitors to a boost converter. As a result, the boost converter receives sufficient voltage and energy from the capacitors and starts up, providing high enough voltage and current to the load. The system allows low voltage low current MFCs to be used to power high voltage high current electronic devices deployed in the water. The system was tested in the lab.
Modes and models of GABA<sub>A</sub>receptor gating (2006)

Upon activation by agonist, the type A gamma-aminobutyric acid receptor (GABAR) 'gates', allowing chloride ions to permeate membranes and produce fast inhibition of neurons. There is no consensus kinetic model for the GABAR gating mechanism. We expressed human alpha(1)beta(1)gamma(2S) GABARs in HEK 293 cells and recorded single channel currents in the cell-attached configuration using various GABA concentrations (50-5000 microm). Closed and open events occurred individually and in clusters that had at least three different modes that were distinguishable by open probability (P(O)): High (P(O)= 0.73), Mid (P(O)= 0.50), and Low (P(O)= 0.21). We used a critical time to isolate shorter bursts of openings and to thus eliminate long-lived, desensitized events. Bursts from all three modes contained three closed and three open components. We employed maximum likelihood fitting, autocorrelation analysis and macroscopic current simulation to distinguish kinetic schemes. The 'core' gating scheme for most models contained two closed states that preceded an open state (C(1) C(2) O(1)). The two best-fitting models had a third closed state connected to C(1) and a second open state (O(2)) connected to C(2). The third open state, whose occupancy varied greatly between modes, could be connected either to O(2) or C(2). We estimated rate constants for two identical, independent GABA binding steps by globally fitting data across GABA concentrations ranging from 50 to 1000 microm. For the most highly ranked model the binding rate constants were: k(+)= 3 microm(-1) s(-1) and k(-)= 272 s(-1) (K(D)= 91 microm).
Effects of Inlet Distortion on the Stability of an Advanced Military Swept Fan Stage With Casing Treatment (2005)

It is possible to improve the stability of a fan in both clean and distorted inlet flow through the use of forward sweep and/or rotor casing treatment. However, for a practical design, there is the need to know whether sweep, casing treatment or a combination of both is most effective for enhancing stability. A further complication is that both these measures can have implications on downstream blade rows. There is therefore a requirement to be able to analyse 3D blade designs with casing treatments within a multi-stage environment. This paper presents both experimental and numerical studies of an advanced low hub-tip-ratio military fan stage of pressure ratio 2.2 subjected to an undistorted and tip-low radial distorted inlet total pressure profile. The case discussed is the second build of this research stage and features a rotor which has been successfully re-designed with forward sweep to improve stability. The stage was tested with and without casing treatment. The intention of this paper is therefore to outline an efficient method whereby a rotor casing treatment can be modelled unsteadily as part of the full compressor or fan stage. To the authors knowledge, all previously published unsteady numerical simulations of slotted casing treatments have been confined to rotor only calculations. Numerical studies of the stage use a mixed approach to speed convergence, employing a fully unsteady simulation of a single rotor passage with casing treatment coupled via a mixing plane to a steady simulation of the downstream stator vane. These studies, supported by test results, indicate that the swept blade in undistorted flow does not stall at the rotor tip and interacts significantly towards stall with the downstream stator vane. However, with the introduction of tip-low inlet distortion the swept rotor can be made to stall at the tip. Both experimental and numerical studies show that in the case of tip-low radial distortion the stability line can be successfully extended by employing rotor casing treatment.
Circular Base Plates with Large Eccentric Loads (2004)

Circular base plates are commonly used for pipe columns, such as pylons in cable-stayed bridges, lighting poles, and electric power line posts. Although the explicit solutions for rectangular base plates can be found in many textbooks and AISC design procedures for base plates, a design procedure for circular base plates has not been documented. In this paper, two equilibrium equations are presented for circular base plates with large eccentric loads. Since these two equations cannot be solved explicitly, an iteration approach is used to solve them.
A New Feature Extraction Method Based on Instantaneous Phase for Clamp Looseness on Pipes (2018)

F388 extraction is a key step in mechanical fault diagnosis and the phase is a significant parameter that is more sensitive to the regularity of signals than amplitude. This work proposed a new method to extract feature of complexity from the phase of signals, which is the auto-correlation scatterplot of instantaneous phase (ASIP). Moreover, the high diversity of ASIP represents that the signal has complex components. According to the simulation analysis, the ASIP is a more sensitive way to represent the appearance of random component in signals, so that the diversity of ASIP is a good feature for regularity detection. And in the experimental analysis on detection of clamp looseness on pipes, it demonstrates that the looseness of the clamp would affect the strain of pipe on its upstream side, and the distribution of the ASIP could visually reflect the complexity of the signal collected by fiber Bragg grating sensors placed on the pipe. Therefore, ASIP is an effective method to describe the regularity of a complex signal.
Development and Validation of an Ultrasensitive Procalcitonin Sandwich Immunoassay (2017)

Procalcitonin (PCT) is well established as a highly specific biomarker for the detection of bacterial infections and sepsis. However, the currently available diagnostic tests are not able to detect very low or very early increases of PCT or even baseline levels in healthy individuals or patients with non-bacterial infections. In order to be able to detect these very low concentrations of PCT, a sandwich immunoassay was developed using high sensitivity Single Molecule Array technology (Simoa). The assay was thoroughly validated and applied to analyze human cerebrospinal fluid (CSF) and serum samples from patients with bacterial or viral meningitis as well as CSF, serum, and K2 EDTA plasma from healthy control subjects. A 50-fold increase in sensitivity compared to the current gold standard assays was achieved, which was sensitive enough for the detection of baseline PCT levels. Both serum and CSF showed significantly elevated PCT levels in patients with bacterial meningitis compared to patients with viral meningitis and the healthy control group. Procalcitonin concentration levels for patients with viral meningitis and the control group could be measured, but were not significantly different. The determination of PCT in the low pg·mL<sup>-1</sup> range could help to improve the monitoring of bacterial infectious diseases, as PCT level changes could be detected earlier.
Achieving oblivious transfer using weakened security assumptions (1988)

The authors present some general techniques for establishing the cryptographic strength of a wide variety of games. As case studies, they analyze some weakened versions of the standard forms of oblivious transfer. They also consider variants of oblivious transfer that are motivated by coding theory and physics. Among their results, they show that a noisy telephone line is in fact a very sophisticated cryptographic device. They also present an application to quantum cryptography.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Wellbore-to-Fracture Communication Problems Pose Challenges in California Diatomite Horizontal Wells (1997)

Abstract In an increasing number of hydraulic fracturing environments, the petroleum industry has aimed for greater cost-effectiveness through the use of horizontal wells instead of conventional vertical wells. Several recent examples where this strategy has been evaluated include the giant Belridge oilfield where three horizontal wells have been drilled with an oblique orientation of roughly 700 to the preferred fracture orientation (determined by the existing well pattern), and completed with multiple propped fracture stages. In the past, industry has focused much attention on the connection between transverse hydraulic fractures and horizontal wellbores, primarily to avoid bridging screen-outs in the near-wellbore tortuous region. It was assumed that if the proppant could be placed successfully, then the fracture stimulation would be successful. However, in the soft diatomite rocks in the San Joaquin Valley, a different problem has emerged. While premature screen-outs have not been a problem, the complex character of hydraulic fracture initiation in this rock has impeded the creation of a sufficiently conductive connection between the wellbore and the primary propped fracture(s). Integration of several diagnostic techniques (such as net fracture pressure analysis, tiltmeter fracture mapping, Hydraulic Impedance Testing (HIT), post-fracture production logging and video logging) reveals that the poor wellbore-to-fracture connection is due to the complex initiation of multiple hydraulic fractures along the horizontal wellbore, many of which are not effectively connected to the perforations. Despite appropriate far-field propped fracture penetration in the reservoir zones of interest, connection between the reservoir and wellbore is compromised because the main propped transverse fracture can be displaced 10 – 100 ft along the wellbore away from the perforated interval, This breakdown in wellbore-to-reservoir connection can severely damage well productivity, in extreme cases reducing individual stage contributions to zero. Figure 1 shows a conceptual sketch of what the actual fracture geometry induced from a single stage may look like. Note the small longitudinal fracture that runs along the wellbore and the many transverse fractures that leave the wellbore away from the perforated interval. As petroleum production from transversely fractured horizontal wells has been successful in other environments, it is believed that the severity of the problems encountered with these wells was due the specific environment conditions (3D-stress state, rock properties, poor cement quality, etc.). However, these same problems are likely to occur, perhaps to a lesser degree, in many environments. P. 635^
Calcium release microdomains and mitochondria (2013)

The processes of excitation-contraction (EC) coupling consume large amounts of energy that need to be replenished by oxidative phosphorylation in the mitochondria. Since Ca(2+) activates key enzymes of the Krebs cycle in the mitochondrial matrix, it is important to understand the mechanisms and kinetics of mitochondrial Ca(2+) uptake to delineate how in cardiac myocytes, energy supply is efficiently matched to demand. In recent years, the identification of various proteins involved in mitochondrial Ca(2+) signalling and the tethering of mitochondria to the sarcoplasmic reticulum (SR) has considerably advanced the field and supported the concept of a mitochondrial Ca(2+) microdomain, in which Ca(2+) concentrations are high enough to overcome the low Ca(2+) affinity of the principal mitochondrial Ca(2+) uptake mechanism, the Ca(2+) uniporter. Furthermore, defects in EC coupling that occur in heart failure disrupt SR-mitochondrial Ca(2+) crosstalk and may cause energetic deficit and oxidative stress, both factors that are thought to be causally involved in the initiation and progression of the disease.
<i>Foreword by</i> Andrew Fire (2005)

It has been a privilege to watch the growth of RNA interference technology over the last ten years. Starting with a mixture of curiosity and chagrin, the field has grown into a substantial enterprise which impacts (and utilizes resources from) virtually every field of biomedical research. Research in RNAi derives from a set of apparently unconnected observations: strange pigment patterns in plants, unexpected failures and successes in antisense and overexpression studies, small regulatory RNAs in bacteria. If there is an underlying and recurring scientific lesson, it has been: “Pursue the unexpected.” Basic and applied research each advance as a consequence of this pursuit; certainly this has been no better illustrated than in the last ten years of RNAi.
Effects of C1 Inhibitor on Tissue Damage in a Porcine Model of Controlled Hemorrhage (2012)

Activation of the complement system has been associated with tissue injury after hemorrhage and resuscitation in animals. We investigated whether administration of recombinant human C1-esterase inhibitor (rhC1-INH), a regulator of complement and contact activation systems, reduces tissue damage and cytokine release and improves metabolic acidosis in a porcine model of hemorrhagic shock. Male Yorkshire swine were assigned to experimental groups and subjected to controlled, isobaric hemorrhage to a target mean arterial pressure of 35 mmHg. Hypotension was maintained for 20 min followed by a bolus intravenous injection of rhC1-INH or vehicle; animals were then observed for 3 h. Blood chemistry and physiologic parameters were recorded. Lung and small intestine tissue samples were subjected to histopathologic evaluation and immunohistochemistry to determine the extent of injury and deposition of complement proteins. Cytokine levels and quantitative assessment of renal and hepatic function were measured via enzyme-linked immunosorbent assay and chemistry analyzer, respectively. Pharmacokinetics of rhC1-INH revealed dose proportionality for maximum concentration, half-life, and the time span in which the functional C1-INH level was greater than 1 IU/mL. Recombinant human C1-INH significantly reduced renal, intestinal, and lung tissue damage in a dose-dependent manner (100 and 250 IU/kg). In addition, rhC1-INH (250 IU/kg) markedly improved hemorrhage-induced metabolic acidosis and circulating tumor necrosis factor α. The tissue-protective effects of rhC1-INH appear to be related to its ability to reduce tissue complement activation and deposition. Recombinant human C1-INH decreased tissue complement activation and deposition in hemorrhaged animals, improved metabolic acidosis, reduced circulating tumor necrosis factor α, and attenuated tissue damage in this model. The observed beneficial effects of rhC1-INH treatment on tissue injury 20 min into severe hypotension present an attractive model of low-volume resuscitation, particularly in situations with a restrictive medical logistical footprint.
Functional expression of the <i>Erwinia uredovora</i> carotenoid biosynthesis gene <i>crtl</i> in transgenic plants showing an increase of β‐carotene biosynthesis activity and resistance to the bleaching herbicide norflurazon (1993)

Among the enzymes involved in carotenoid biosynthesis, phytoene desaturase is considered to be a rate-limiting enzyme in this pathway and is also the target of many bleaching herbicides. This enzyme shows diversity concerning its function and amino acid homology among various organisms. The phytoene desaturase gene crtl of Erwinia uredovora was expressed, the 5'-region of which was fused to the sequence for the transit peptide of a pea Rubisco small subunit, in tobacco plants under the control of the CaMV 35S promoter. This chimeric gene product was targeted into chloroplasts and processed in the transgenic plants. The production and processing of the corresponding protein could be demonstrated by Western blotting. Immunogold localization showed that the location of the gene product Crtl was preferentially in the thylakoids. A radioactive labeling study using the leaves demonstrated enhanced activity for the synthesis of beta-carotene. In addition, the transgenic tobacco acquired elevated resistance to the bleaching herbicide norflurazon.
Improved estimates of ocean heat content from 1960 to 2015 (2017)

Earth's energy imbalance (EEI) drives the ongoing global warming and can best be assessed across the historical record (that is, since 1960) from ocean heat content (OHC) changes. An accurate assessment of OHC is a challenge, mainly because of insufficient and irregular data coverage. We provide updated OHC estimates with the goal of minimizing associated sampling error. We performed a subsample test, in which subsets of data during the data-rich Argo era are colocated with locations of earlier ocean observations, to quantify this error. Our results provide a new OHC estimate with an unbiased mean sampling error and with variability on decadal and multidecadal time scales (signal) that can be reliably distinguished from sampling error (noise) with signal-to-noise ratios higher than 3. The inferred integrated EEI is greater than that reported in previous assessments and is consistent with a reconstruction of the radiative imbalance at the top of atmosphere starting in 1985. We found that changes in OHC are relatively small before about 1980; since then, OHC has increased fairly steadily and, since 1990, has increasingly involved deeper layers of the ocean. In addition, OHC changes in six major oceans are reliable on decadal time scales. All ocean basins examined have experienced significant warming since 1998, with the greatest warming in the southern oceans, the tropical/subtropical Pacific Ocean, and the tropical/subtropical Atlantic Ocean. This new look at OHC and EEI changes over time provides greater confidence than previously possible, and the data sets produced are a valuable resource for further study.
Fecal Microbiota Transplant (2015)

Respice, Adspice, Prospice, look to the past, look to the present, look to the future, is one of life's valuable axioms; for it is only if one knows where one has been can one intelligently prepare for the future. I have used this approach here to review fecal microbiota transplant (FMT). First used in fourth-century China to treat an assortment of gastrointestinal (GI) symptoms, today FMT is primarily used for recurrent Clostridium difficile infection (RCDI). In the future, however, it is likely that microbiotic therapy will be extended beyond treatment of RCDI. Early on, fresh feces from patient-identified donors was used and administered by several routes. FMT cure rates for RCDI remain approximately 82% and 91% when fresh stool is given by the upper GI and lower GI routes, respectively, but now we are moving in the direction of using carefully vetted volunteers whose stool is processed into a variety of formulations including lyophilized material and even capsules. It is very likely that an array of products derived from feces or based on specific microbiotic profiles and commercially prepared in a controlled environment will be available to restore eubiosis to a dysbiotic intestinal microbial community, and thereby correct a variety of GI and non-GI disorders. We are witnessing a paradigm shift in therapeutics. Previously, bacteria were thought of only as potential pathogens, whereas now we appreciate that a diverse community of bacteria is crucial to the health of the host. We are now learning that to restore such diversity once it has been interrupted can result in miraculous cure. The future of microbiotic therapy is bright.