gebhart/patrepeval huggingface dataset:
Hormonal regulation and identification of chicken progesterone receptor phosphorylation sites. (1990)

The present studies examine the effects of in vivo and in situ progesterone treatment in the regulation of site-specific phosphorylation of the chicken oviduct progesterone receptor (PR). By gas-phase protein sequencing we have identified three hormonally regulated phosphorylation sites: Ser-211, Ser-260, and Ser-530. We determined phosphorylation stoichiometries by analyzing the amounts of phosphorylated and dephosphorylated serine at each site. Stoichiometries of sites 211 and 260 were about 20% under basal conditions and increased 1.5-2-fold by in situ progesterone treatment. Site 530 was virtually absent under basal conditions and induced to greater than 33% by in situ progesterone treatment. We tested several protein kinases for phosphorylation of the PR in vitro on these sites or peptides containing these sites. We found that the catalytic subunit of cAMP-dependent protein kinase mimicked the in vivo, hormone-induced altered mobility of PRs in sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Both the in vivo and in vitro alterations were reversed by alkaline phosphatase. Finally, we showed that cAMP-dependent protein kinase phosphorylated Ser-528.
Hydrogel Nanoparticle Dispersions with Inverse Thermoreversible Gelation (2004)

A novel aqueous solution of hydrogel nanoparticles with interpenetrating polymer networks of poly(isopropylacrylamide) and poly(acrylic acid) has been synthesized. This hydrogel can form a physically bonded nanoparticle network above a certain gelation temperature. The system exhibits a very rich phase behavior, including a colloidal crystalline phase, in which the system displays iridescent colors (for examples, see Figure).
Protein p<i>I</i> Shifts due to Posttranslational Modifications in the Separation and Characterization of Proteins (2005)

Proteins from breast cancer cell lines are characterized using a 2-D liquid separation technique in which protein pI is used as the first-dimension separation parameter. To effect this protein pI separation, chromatofocusing(CF) is employed whereby a pH gradient is generated on-column using a weak anion exchange medium with the intact proteins fractionated and collected every 0.2 pH unit. It is demonstrated that the pI for expressed intact proteins as generated by CF is an important parameter for identification and characterization of the actual protein modifications occurring in the cancer cell. For most proteins, the experimentally determined pI is very close to that predicted by the databases. In other cases, however, where the pI is observed to be shifted from the expected value, it is shown that this shift is often correlated to protein modifications. The modifications that cause such shifts include truncations and deletions often observed in cancer cells or phosphorylations that can shift the pI by several pH units. It is also shown that the effects of phosphorylation on the observed shift can vary depending upon the protein and the amount of phosphorylation. Moreover, large changes in the pI are often observed for proteins with a pI above 7.0 upon phosphorylation, whereas little change is observed for proteins with a pI of approximately 5.0. The expressed protein's pI value thus becomes an important parameter together with the intact MW value, peptide map, and MS/MS results for identification of the presence and type of posttranslational modifications occurring in the cancer cell.
Semiconductor digital optical switches and arrays (1994)

With the increasing number of services, leading to a rapid capacity increase and, in parallel, the need for more reliable and flexible networks, photonic routing is becoming more and more attractive. A number of recent network architectures take advantage of optics by exploiting their full potential and thus wavelength and space switching are considered. Wavelength switching requires elements such as tunable emitters, tunable filters, and wavelength translators. As far as space switches are concerned, most of the recent progress has been in guided- wave switching matrices, using either LiNbO3 or III–V semi- conductor materials. Although the latter have greater potential, their performances to date have been below those of LiNbO3 devices. This paper reviews the digital optical switch (DOS), initially demonstrated on LiNbO3 but now successfully implemented on InP. Compared to other guided-wave switching elements, the DOS has the advantage of combining in a single device polarization independence, large optical bandwidth, and low driving power. The design optimization of the structure and the technological steps needed for the device fabrication will be presented.
Template‐Assisted Self‐Assembly: Alignment, Placement, and Arrangement of Two‐Dimensional Mesostructured DNA–Silica Platelets (2013)

In the same direction: Two-dimensional mesostructured DNA–silica platelets were horizontally or vertically aligned on unpatterned substrate surfaces using “bottom-up” self-assembly. Through template-assisted self-assembly, vertically aligned DNA–silica platelets were selectively placed in the grooves and on the protuberances and with a parallel arrangement near the edges on patterned surfaces. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to 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.
Robust predictive cruise control for commercial vehicles (2013)

Abstract In this paper we explore learning-based predictive cruise control and the impact of this technology on increasing fuel efficiency for commercial trucks. Traditional cruise control is wasteful when maintaining a constant velocity over rolling hills. Predictive cruise control (PCC) is able to look ahead at future road conditions and solve for a cost-effective course of action. Model- based controllers have been implemented in this field but cannot accommodate many complexities of a dynamic environment which includes changing road and vehicle conditions. In this work, we focus on incorporating a learner into an already successful model- based predictive cruise controller in order to improve its performance. We explore back propagating neural networks to predict future errors then take actions to prevent said errors from occurring. The results show that this approach improves the model based PCC by up to 60% under certain conditions. In addition, we explore the benefits of classifier ensembles to further improve the gains due to intelligent cruise control.
Optimization of Carrot Juice Color and Cloud Stability (1993)

ABSTRACT Investigations were conducted on the effects of heating, acidification, and enzyme treatment on carrot juice color and cloud stability. Heating whole carrots to 93°C prior to milling and pressing improved juice color, but reduced juice yield compared to heating milled carrots to 93°C. Juice color was improved by acidification of milled carrots to pH 5 or 4 with citric acid prior to pressing. Juice from carrots heated before milling clarified quickly if not acidified before pressing. Acidification after juice extraction did not stabilize cloud. A commercial pectinase/hemicellulase preparation improved juice color, but not juice yield. Only 20% of potential β‐carotene was extracted from carrots during pressing, and β‐carotene was extracted to a greater extent than α‐carotene.
Colorimetric control of photographic prints: the problem of fluorescence (2002)

The colorimetric control of photographic prints is an important issue of color reproduction quality. Concentration series of the three photographic dyes Yellow, Magenta and Cyan on photographic paper are very often measured without considering the optical quality of the substrate. However, this substrate, the photographic paper, produces problems for colorimetry because it emits luminenscent light from optical brighteners. Many instruments used in colorimetry are not adapted to measure such an output correctly. Here, an experimental investigation is presented which quantifies systematic shifts of spectral curves and colorimetric values of photographic paper and dyes for various measuring parameters. Several spectrophotometers equipped with different sources for irradiation such as Tungsten halogen lamp, Xenon flash lamp, D65 simulator, and two Xenon lamps with adjustable UV-filter were referenced against the results of two-monochromator spectrophotometer. In the photographic paper the largest color-difference extended to approximately 10 CIELAB-units between irradiation by a Tungsten halogen and a Xenon lamp. These differences diminished with increasing concentration of the photographic dyes, however, did not die away at the highest concentration of the dyes used. The correct colorimetric values for D65 irradiation were halfway between those for the two former lamps and near to measures received from Xenon lamp irraditoin with adjustable UV-filter. Therefore, such spectrophotometers may be used for colorimetric control of photographic prints to attain an accuracy below 3 CIELAB units, or else, two measurements with a Tungsten halogen and a Xenon lamp should be averaged.
<title>Architectural considerations in the design of WDM-based optical access networks</title> (1998)

We describe a WDM-based optical access network architecture for providing broadband Internet services. The architecture uses a passive collection and distribution network and a configurable Feeder network. Unlike earlier papers that concentrate on the physical layer design of the network, we focus on higher layer architectural considerations. In particular we discuss the joint design of the electronic and optical layers including: WDM Medium Access Control protocols; the choice of electronic multiplexing and switching between the IP and WDM layers: joint optical and electronic protection mechanisms; network reconfiguration algorithms that alter the logical topology of the network in response to changes in traffic; and traffic grooming algorithms to minimize the cost of electronic multiplexing.
KCNQ1 and KCNE1 K<sup>&plus;</sup> Channel Components are Involved in Early Left-Right Patterning in <i>Xenopus laevis</i> Embryos (2008)

Several ion transporters have been implicated in left-right (LR) patterning. Here, we characterize a new component of the early bioelectrical circuit: the potassium channel KCNQ1 and its accessory subunit KCNE1. Having cloned the native Xenopus versions of both genes, we show that both are asymmetrically localized as maternal proteins during the first few cleavages of frog embryo development in a process dependent on microtubule and actin organization. Molecular loss-of-function using dominant negative constructs demonstrates that both gene products are required for normal LR asymmetry. We propose a model whereby these channels provide an exit path for K(+) ions brought in by the H(+),K(+)-ATPase. This physiological module thus allows the obligate but electroneutral H(+),K(+)-ATPase to generate an asymmetric voltage gradient on the left and right sides. Our data reveal a new, bioelectrical component of the mechanisms patterning a large-scale axis in vertebrate embryogenesis.
Beneficial behavioural and neurogenic effects of agomelatine in a model of depression/anxiety (2011)

Agomelatine (S20098) is a novel antidepressant drug with melatonergic agonist and 5-HT2C receptor antagonist properties, displaying antidepressant/anxiolytic-like properties in animal models and in humans. In a depression/anxiety-like mouse model in which the response of the HPA axis is blunted, we investigated whether agomelatine could reverse behavioural deficits related to depression/anxiety compared to the classical selective serotonin reuptake inhibitor, fluoxetine. Adult mice were treated for 8 wk with either vehicle or corticosterone (35 μg/ml.d) via drinking water. During the final 4 wk, animals were treated with vehicle, agomelatine (10 or 40 mg/kg i.p.) or fluoxetine (18 mg/kg i.p.) and tested in several behavioural paradigms and also evaluated for home-cage activity. Our results showed that the depressive/anxiety-like phenotype induced by corticosterone treatment is reversed by either chronic agomelatine or fluoxetine treatment. Moreover, agomelatine increased the dark/light ratio of home-cage activity in vehicle-treated mice and reversed the alterations in this ratio induced by chronic corticosterone, suggesting a normalization of disturbed circadian rhythms. Finally, we investigated the effects of this new antidepressant on neurogenesis. Agomelatine reversed the decreased cell proliferation in the whole hippocampus in corticosterone-treated mice and increased maturation of newborn neurons in both vehicle- and corticosterone-treated mice. Overall, the present study suggests that agomelatine, with its distinct mechanism of action based on the synergy between the melatonergic agonist and 5-HT2C antagonist properties, provides a distinct antidepressant/anxiolytic spectrum including circadian rhythm normalization.
Measurement of free water in foods by secondary derivative thermogravimetry (2018)

The thermogravimetry (TGA) and derivative thermogravimetry (DTG) methods have been used to measure the free water in low-moisture foods. In this study, the 2nd derivative thermogravimetry (2nd DTG) method distinguished the free and bound water based on the speed of moisture evaporation, which could be used for both low-moisture and high-moisture foods. First, the key factors related to moisture evaporation were optimized. Isothermal temperature of 30 ~ 50°C, dynamic temperature of 0.033 ~ 0.133°C/min, and flow rate of nitrogen of 20 ~ 40 mL/min were the optimal parameters for the 2nd DTG method. Under these conditions, the repeatability and reproducibility of the 2nd DTG method were enhanced, its applicability was expanded to high-moisture foods, and the accuracy was ± 4.0% of the nuclear magnetic resonance results. Hence, the 2nd DTG method is better suited for the measurement of free water in foods.
19F Relaxation Rate Enhancement and Frequency Shift with Gd-DTPA (1989)

RATNER, ADAM V. MD; QUAY, STEVEN MD, PhD; MULLER, HOLDE H. MS; SIMPSON, BEVERLY BRADLEY BS; HURD, RALPH PhD; YOUNG, STUART W. MD Author Information
Approaches to on-chip testing of mixed signal macros in ASICs (1996)

This paper initially researches the use of available low-cost analogue CMOS macros to perform simple on-chip tests on the Analogue to Digital Converter macro. The results are evaluated for these tests and then further fuller tests are undertaken. The technique of transient response testing is then applied to three CMOS analogue and mixed submacros to provide more comprehensive test results.
Background elimination using the SNIP algorithm for Bragg reflections from a protein crystal measured by a TOF single-crystal neutron diffractometer (2015)

In white neutron diffraction studies, the energy, intensity, and number of resolved Bragg peaks depend on detector resolution and background from physics processes. The statistics-sensitive non-linear iterative peak-clipping (SNIP) algorithm is widely used for subtracting the background under a peak. This paper reports the validation procedures and availability of the SNIP algorithm for time-of-flight (TOF) Bragg reflections observed with a TOF single-protein-crystal neutron diffractometer.
Multiprocessor cache synchronization: issues, innovations, evolution (1986)

Many options are possible in a cache synchronization (or consistency) scheme for a broadcast system. We clarify basic concepts, analyze the handling of shared data, and then describe a protocol that we are currently exploring. Finally, we analyze the evolution of options that have been proposed under write-in (or write-back) policy. We show how our protocol extends this evolution with new methods for efficient busy-wait locking, waiting, and unlocking. The lock scheme allows locking and unlocking to occur in zero time, eliminating the need for test-and-set. The scheme also integrates processor atomic read-modify-write instructions and programmer/compiler busy-wait-synchronized operations under the same mechanism. The wait scheme eliminates all unsuccessful retries from the bus, and allows a process to work while waiting.
Kinase inhibitors in the treatment of immune-mediated disease (2012)

Protein kinases are fundamental components of diverse signaling pathways, including immune cells. Their essential functions have made them effective therapeutic targets. Initially, the expectation was that a high degree of selectivity would be critical; however, with time, the use of "multikinase" inhibitors has expanded. Moreover, the spectrum of diseases in which kinase inhibitors are used has also expanded to include not only malignancies but also immune-mediated diseases. At present, thirteen kinase inhibitors have been approved in the United States, all for oncologic indications. However, there are a growing number of molecules, including several Janus kinase inhibitors, that are being tested in clinical trials for autoimmune diseases such as rheumatoid arthritis, psoriasis and inflammatory bowel diseases. It appears likely that this new class of immunomodulatory drugs will have a major impact on the treatment of immune-mediated diseases in the near future.
Regional Dynamic Tensile Properties of the TMJ Disc (2008)

Although the TMJ disc has been well-characterized under tension and compression, dynamic viscoelastic regional and directional variations have heretofore not been investigated. We hypothesized that the intermediate zone under mediolateral tension would exhibit lower dynamic moduli compared with the other regions of the disc under either mediolateral or anteroposterior tension. Specimens were prepared from porcine discs (3 regions/direction), and dynamic tensile sweeps were performed at 1% strain over a frequency range of 0.1 to 100 rad/sec. Generally, the intermediate zone possessed the lowest storage and loss moduli, and the highest loss tangent. This study further accentuates the known distinct character of the intermediate zone by showing for the first time that these differences also extend to dynamic behavior, perhaps implicating the TMJ disc as a structure primarily exposed to predominantly anteroposterior tension via anterior and posterior attachments, with a need for great distension mediolaterally across the intermediate zone.
Preparation and characterisation of noble metal solid sols in poly(methyl methacrylate) (1993)

Y. Nakao, J. Chem. Soc., Chem. Commun., 1993, 826 DOI: 10.1039/C39930000826
Edlib: a C/C ++ library for fast, exact sequence alignment using edit distance (2016)

Supplementary data are available at Bioinformatics online.
O2-DN: An Overlay-based Distributed Rate Limit Framework to Defeat DDoS Attacks (2006)

Distributed denial-of-service attack has become one of the major threats to Internet today. And the distributed nature of DDoS problem needs a distributed solution. In this paper, we propose using a hierarchical domain-aware overlay to construct a built-in distributed rate limit framework throughout the Internet. And we leverage the IP traceback technique to avoid collateral damage on legitimate traffic and mitigate DDoS effect near attack sources as possible as we can. This defense framework is a serviceoriented economic model that not only motivates ISPs to deploy it, but also benefits all participants.
Carbonic Anhydrase Inhibitors. Inhibition of Mitochondrial Isozyme V with Aromatic and Heterocyclic Sulfonamides (2004)

The first inhibition study of the mitochondrial isozyme carbonic anhydrase (CA) V (of murine origin) with a series of aromatic and heterocyclic sulfonamides is reported. Inhibition data of the cytosolic isozymes CA I and CA II and the membrane-bound isozyme CA IV with these inhibitors are also provided for comparison. Several low nanomolar CA V inhibitors were detected (KI values in the range of 4−15 nM), most of them belonging to the acylated sulfanilamide, ureido-benzenesulfonamide, 1,3,4-thiadiazole-2-sulfonamide, and aminobenzolamide type of compounds. The clinically used inhibitors acetazolamide, methazolamide, ethoxzolamide, dorzolamide, brinzolamide, and topiramate on the other hand were less effective CA V inhibitors, showing inhibition constants in the range of 47−63 nM. Some of the investigated sulfonamides, such as the ureido-benzenesulfonamides and the acylated sulfanilamides showed higher affinity for CA V than for the other isozymes, CA II included, which is a remarkable result, since most compounds investigated up to now inhibited the cytosolic isozyme CA II better. These results prompt us to hypothesize that the selective inhibition of CA V, or the dual inhibition of CA II and CA V, may lead to the development of novel pharmacological applications for such sulfonamides, for example in the treatment or prevention of obesity, by inhibiting CA-mediated lipogenetic processes.
The distribution of pageRank follows a power-law only for particular values of the damping factor (2006)

We show that the empirical distribution of the PageRank values in a large set of Web pages does not follow a power-law except for some particular choices of the damping factor. We argue that for a graph with an in-degree distribution following a power-law with exponent between 2.1 and 2.2, choosing a damping factor around 0.85 for PageRank yields a power-law distribution of its values. We suggest that power-law distributions of PageRank in Web graphs have been observed because the typical damping factor used in practice is between 0.85 and 0.90.
Multimode Control of a DFIG-Based Wind-Power Unit for Remote Applications (2009)

This paper proposes a multimode control strategy for a doubly fed induction generator-based wind-power unit, which enables operation in the islanded (autonomous) mode as well as the grid-connected mode. The configuration can be an option for electricity generation in remote communities with favorable wind conditions, but limited or unreliable connection to the grid. In the grid-connected mode, the proposed control enables the wind power unit to operate with or without battery energy storage, as desired. In case that the wind-power unit is augmented with battery energy storage, in the islanded mode, the proposed control strategy enables voltage and frequency regulation for the network, and parallel operation with constant-speed wind-power units, induction motor loads, and passive loads. The proposed control strategy employs a unified controller for all of the foregoing modes of operation and, therefore, relieves the need for switching between different controllers or reconfiguration of the hardware. The effectiveness and robustness of the proposed control strategy are demonstrated for faulted as well as normal operating conditions through simulation studies carried out on a detailed switched model of the system in the PSCAD/EMTDC software environment.
Occurrence of the Oil-Forming Alga Botryococcus in Lignites and Other Tertiary Sediments (1955)

Certain Paleozoic oil-bearing rocks-boghead coals or torbanites, and others-derive their oil con- tent from the hydrocarbon-producing alga Botryococcus. The same genus produces fatty sediments in modern brackish and fresh-water lakes. It has seemed likely that the organism was important in the Cenozoic also. The appearance is noted here of a number of recently reported Tertiary records of Botryococcus in India and Australia, and the first American Tertiary record, in the organic silt overlying the Brandon lignite, Vermont, is described. Botryococcus microfossils from the Warlands Creek locality, Australia, are very closely comparable