gebhart/patrepeval huggingface dataset:
AtGA3ox2, a Key Gene Responsible for Bioactive Gibberellin Biosynthesis, Is Regulated during Embryogenesis by LEAFY COTYLEDON2 and FUSCA3 in Arabidopsis (2004)

Embryonic regulators LEC2 (LEAFY COTYLEDON2) and FUS3 (FUSCA3) are involved in multiple aspects of Arabidopsis (Arabidopsis thaliana) seed development, including repression of leaf traits and premature germination and activation of seed storage protein genes. In this study, we show that gibberellin (GA) hormone biosynthesis is regulated by LEC2 and FUS3 pathways. The level of bioactive GAs is increased in immature seeds of lec2 and fus3 mutants relative to wild-type level. In addition, we show that the formation of ectopic trichome cells on lec2 and fus3 embryos is a GA-dependent process as in true leaves, suggesting that the GA pathway is misactivated in embryonic mutants. We next demonstrate that the GA-biosynthesis gene AtGA3ox2, which encodes the key enzyme AtGA3ox2 that catalyzes the conversion of inactive to bioactive GAs, is ectopically activated in embryos of the two mutants. Interestingly, both beta-glucuronidase reporter gene expression and in situ hybridization indicate that FUS3 represses AtGA3ox2 expression mainly in epidermal cells of embryo axis, which is distinct from AtGA3ox2 pattern at germination. Finally, we show that the FUS3 protein physically interacts with two RY elements (CATGCATG) present in the AtGA3ox2 promoter. This work suggests that GA biosynthesis is directly controlled by embryonic regulators during Arabidopsis embryonic development.
Purification and properties of an iron‐sulfur and FAD‐containing 4‐hydroxybutyryl‐CoA dehydratase/vinylacetyl‐CoA3‐2‐isomerase from Clostridium aminobutyricum (1993)

4-Hydroxybutyryl-CoA dehydratase, the key enzyme in the metabolism of gamma-aminobutyrate in Clostridium aminobutyricum, represents approximately 15-25% of the soluble protein. The enzyme was purified to homogeneity under anaerobic conditions to a specific activity of 209 nkat mg-1. The dehydratase catalyses the reversible conversion of 4-hydroxybutyryl-CoA (Km = 50 microM) to crotonyl-CoA and possesses a probably intrinsic vinylacetyl-CoA delta 3-delta 2-isomerase with a specific activity of 223 nkat mg-1. The equilibrium of the reversible dehydration was determined from both sides as K = [crotonyl-CoA]/[4-hydroxybutyryl-CoA] = 4.2 +/- 0.3. Cyclopropylcarboxyl-CoA was not converted to crotonyl-CoA. The native enzyme has an apparent molecular mass of 232 kDa and is composed of four apparently identical subunits (molecular mass = 56 kDa), indicating a homotetrameric structure. Under anaerobic conditions the active enzyme revealed a brown colour and contained 2 +/- 0.2 mol FAD (64 +/- 5% oxidized), 16 +/- 0.8 mol Fe and 14.4 +/- 1.2 mol inorganic sulfur, which probably form iron-sulfur clusters. Exposure to air resulted initially in a slight activation followed by irreversible inactivation. Concomitantly the vinylacetyl-CoA delta-isomerase activity was lost and the colour of the enzyme changed to yellow. Reduction by sodium dithionite yielded inactive enzyme which could be completely reactivated by oxidation with potassium hexacyanoferrate(III). The data indicate that the active enzyme contains oxidized FAD despite its sensitivity towards oxygen. During the dehydration a non activated C-H bond at C-3 of 4-hydroxybutyryl-CoA has to be cleaved. A putative mechanism for 4-hydroxybutyryl-CoA dehydratase is proposed in which this cleavage is achieved by a FAD-dependent oxidation of 4-hydroxybutyryl-CoA to 4-hydroxycrotonyl-CoA. In a second step the hydroxyl group is substituted by a hydride derived from the now reduced FAD in an SN2' reaction leading to vinylacetyl-CoA. Finally isomerisation yields crotonyl-CoA. 4-Hydroxybutyryl-CoA dehydratase is quite distinct from 3-hydroxyacyl-CoA dehydratase (crotonase) and 2-hydroxyacyl-CoA dehydratases. Contrary to the latter enzyme [e.g. (R)-lactyl-CoA dehydratase and (R)-2-hydroxyglutaryl-CoA dehydratase] which are composed of three different subunits and similarly catalyse the cleavage of a non activated C-H bond at C-3, 4-hydroxybutyryl-CoA dehydratase does not require ATP, MgCl2 and Ti(III)citrate for activity. Furthermore 4-hydroxybutyryl-CoA dehydratase is not inactivated by oxidants such as 5 mM 4-nitrophenol, 5 mM chloramphenicol and 5 mM hydroxylamine.
Non-invasive measurements of arterial structure and function: repeatability, interrelationships and trial sample size (1998)

1. Repeatability of measurements of arterial compliance and flow-mediated dilation of the brachial artery has been infrequently reported, despite increasing use in interventional and risk-factor modification studies. Furthermore, little is known about the interrelationships of the various indices. The purposes of this study were to determine the repeatability and interrelationships of a range of arterial indices.2. Fifty healthy volunteers, 20 men and 30 women, aged 20-70 (mean 46.5) years, were studied on two occasions, using an identical protocol, at a mean interval of 2.5 weeks. Tonometry, ultrasound and Doppler technique were used to measure the following: carotid wall intima-media thickness (IMT), total systemic artery compliance (SAC), arterial pulse wave velocity [PWV aorto-femoral (A-F), and femoral-dorsalis pedis (F-D)], carotid distensibility coefficient (DC) and carotid augmentation index (AI). Brachial flow-mediated dilation was measured in 30 subjects with analysis of diameter change for 4 min post ischaemia.3. There were no systematic differences over the observed range of measurements for any of the reported parameters. Coefficients of variation were as follows: IMT 2.8%, SAC 9.2%, PWV(A-F) 3.2%, PWV(F-D) 5.0%, DC 10.0%, AI 1.3%. Brachial flow-mediated dilation curves were not different between visits; changes were maximum 60-s post ischaemia. All indices of arterial compliance were significantly correlated with age. The three different indices of central arterial compliance [SAC, PWV(A-F) and AI] were significantly correlated with carotid intima-media thickness.4. Under controlled experimental conditions there was good repeatability of measurements of indices between sessions of both intrinsic and functional arterial mechanical properties (central and carotid arterial compliance, intima-media thickness and brachial flow-mediated dilation). Sample size tables for clinical trials using these indices are presented.
Novel technique for mode selection in a multimode fiber laser (2011)

A simple technique for transverse mode selection in a large-mode-area (multimode) fiber laser is described. The technique exploits the different spectral responses of feedback elements based on a fiber Bragg grating and a volume Bragg grating to achieve wavelength-dependent mode filtering. This approach has been applied to a cladding-pumped thulium-doped fiber laser with a multimode core to achieve a single-spatial-mode output beam with a beam propagation factor (M2) of 1.05 at 1923 nm. Without mode selection the free-running fiber laser has a multimode output beam with an M2 parameter of 3.3. Selective excitation of higher order modes is also possible via the technique and preliminary results for laser oscillation on the LP11 mode are also discussed along with the prospects for scaling to higher power levels.
Robust vehicle localization in urban environments using probabilistic maps (2010)

Autonomous vehicle navigation in dynamic urban environments requires localization accuracy exceeding that available from GPS-based inertial guidance systems. We have shown previously that GPS, IMU, and LIDAR data can be used to generate a high-resolution infrared remittance ground map that can be subsequently used for localization. We now propose an extension to this approach that yields substantial improvements over previous work in vehicle localization, including higher precision, the ability to learn and improve maps over time, and increased robustness to environment changes and dynamic obstacles. Specifically, we model the environment, instead of as a spatial grid of fixed infrared remittance values, as a probabilistic grid whereby every cell is represented as its own gaussian distribution over remittance values. Subsequently, Bayesian inference is able to preferentially weight parts of the map most likely to be stationary and of consistent angular reflectivity, thereby reducing uncertainty and catastrophic errors. Furthermore, by using offline SLAM to align multiple passes of the same environment, possibly separated in time by days or even months, it is possible to build an increasingly robust understanding of the world that can be then exploited for localization. We validate the effectiveness of our approach by using these algorithms to localize our vehicle against probabilistic maps in various dynamic environments, achieving RMS accuracy in the 10cm-range and thus outperforming previous work. Importantly, this approach has enabled us to autonomously drive our vehicle for hundreds of miles in dense traffic on narrow urban roads which were formerly unnavigable with previous localization methods.
Localization of Cellulase Components in Pseudomonas fluorescens var. cellulosa* (1971)

Of the cellulase [EC 3. 2. 1. 4] components A, B and C produced by Pseudomonas fluorescens var. cellulosa, the last one was usually localized in ‘intrawall’ or periplasmic fraction of the cell which was solubilized by spheroplasting with a combined action of lysozyme [EC 3. 2. 1. 17] and EDTA. In contrast, cellulases A and B occurred mainly in extracellular fraction or culture medium. In the cytoplasmic fraction, only a very small amount of cellulase was found to be present, and its properties could not be examined in this work. On the basis of the localities of these cellulase components in the cell and their particular substrate specificities, their physiological significance was discussed.
Solute Coupled Diffusion in Osmotically Driven Membrane Processes (2009)

Forward osmosis (FO) is an emerging water treatment technology with potential applications in desalination and wastewater reclamation. In FO, water is extracted from a feed solution using the high osmotic pressure of a hypertonic solution that flows on the opposite side of a semipermeable membrane; however, solutes diffuse simultaneously through the membrane in both directions and may jeopardize the process. In this study, we have comprehensively explored the effects of different operating conditions on the forward diffusion of solutes commonly found in brackish water and seawater, and reverse diffusion of common draw solution solutes. Results show that reverse transport of solutes through commercially available FO membranes range between 80 mg to nearly 3,000 mg per liter of water produced. Divalent feed solutes have low permeation rates (less than 1 mmol/m2-hr) while monovalent ions and uncharged solutes exhibit higher permeation. Findings have significant implications on the performance and sustainability of the FO process.
Widespread recombinase expression using FLPeR (Flipper) mice (2000)

As conditional genetic strategies advance, the need for multiple site-specific recombinase systems has emerged. To meet this need in part, we have targeted the constitutive ROSA26 locus to create a mouse strain with generalized expression of the enhanced version of the site-specific recombinase FLP (FLPe). This strain is designated FLPeR ("flipper"). Using this strain, extensive target gene recombination can be achieved in most tissue types, including cells of the developing germ line. FLPeR mice therefore serve two important functions: as a source of many different FLPe-expressing primary cell lines and as a deleter strain. Moreover, because the FLPeR mouse is a 129-derived strain, a 129 genetic background can be preserved when crossed to most ES cell-derived mice. This enables conditional genetic alterations to be maintained on a standard background, a feature important for obtaining reproducible results and genetically defined controls.
Ribonucleotide reductase M1 subunit in cellular proliferation, quiescence, and differentiation. (1988)

Ribonucleotide reductase catalyzes the first unique, rate-limiting step in DNA synthesis; both its large (M1) and small (M2) subunits are necessary for activity. While direct studies of M2 expression have previously shown a tight correlation with S phase, the kinetic features of M1-expressing cells have remained ill defined. Therefore we have, using immunofluorescence flow cytometry, analyzed changes in whole cell M1 levels and DNA content during various cell cycle and differentiation events. In asynchronous cultures M1 levels are sustained throughout the cell cycle, including G1 phase when M2 levels and ribonucleotide reductase catalytic activity are known to be very low. In contrast M1 is virtually absent from quiescent lymphocytes but is expressed following mitogen stimulation, shortly before S phase cells appear. M1 declines to low levels in "plateau phase" cultures, the major reduction occurring in cells with 2n (G0/G1) DNA content. HL-60 promyelocytic leukemia cells, induced into either myeloid or monocyte-macrophage differentiation, show a similar marked decrease in M1 levels concomitant with the cessation of cell division. We conclude that the M1 subunit of ribonucleotide reductase is constitutively expressed by cycling cells. It is acquired during stimulated transition from G0 to G1 and is lost during exit to G0 or terminal differentiation. This pattern of expression suggests that determination of cellular M1 content may be useful in distinguishing proliferating (including G1) and quiescent (including G0) cells in vivo.
7,12-dimethylbenz[a]anthracene induces oxidative DNA modification in vivo (1995)

Initiation and promotion are major stages in the multistage carcinogenesis process. Formation of initiating carcinogen-DNA base adducts leads to heritable genetic changes, but the tumor-promoting events induced by complete carcinogens have not, as yet, been elucidated. Oxidant production and oxidative DNA damage induced by phorbol esters (i.e., 12-O-tetradecanoyl-phorbol-13-acetate) are associated with tumor promotion, while antioxidants and inhibitors of oxidative DNA damage suppress promotion and carcinogenesis. Our goal was to establish whether a carcinogen that requires oxidative metabolism for its activity can also induce oxidant production and DNA base oxidation. We found that topical treatment of SENCAR mice with 7,12-dimethylbenz[a]anthracene, which induces tumors in 40-50% of the mice, also causes hydrogen peroxide production and formation of oxidized bases (i.e., 8-hydroxyl-2'-deoxyguanosine and 5-hydroxymethyl-2'-deoxyuridine) in epidermal DNA. The levels of oxidized bases were of comparable magnitude to those mediated by the potent tumor promoter 12-O-tetradecanoyl-phorbol-13-acetate. The oxidized bases persisted over several weeks in epidermal DNA. These oxidative events appear to be temporally associated with inflammatory responses that include edema and polymorphonuclear leukocyte infiltration, which remained elevated over longer periods of time and at higher levels than those induced by phorbol ester. Because these processes are usually associated with tumor promotion, our results support the conjecture that oxidative events may be involved in what is operationally referred to as the tumor promotion process by 7,12-dimethylbenz[a]anthracene.
Tissue Engineering: Current Strategies and Future Directions (2011)

Novel therapies resulting from regenerative medicine and tissue engineering technology may offer new hope for patients with injuries, end-stage organ failure, or other clinical issues. Currently, patients with diseased and injured organs are often treated with transplanted organs. However, there is a shortage of donor organs that is worsening yearly as the population ages and as the number of new cases of organ failure increases. Scientists in the field of regenerative medicine and tissue engineering are now applying the principles of cell transplantation, material science, and bioengineering to construct biological substitutes that can restore and maintain normal function in diseased and injured tissues. In addition, the stem cell field is a rapidly advancing part of regenerative medicine, and new discoveries in this field create new options for this type of therapy. For example, new types of stem cells, such as amniotic fluid and placental stem cells that can circumvent the ethical issues associated with embryonic stem cells, have been discovered. The process of therapeutic cloning and the creation of induced pluripotent cells provide still other potential sources of stem cells for cell-based tissue engineering applications. Although stem cells are still in the research phase, some therapies arising from tissue engineering endeavors that make use of autologous, adult cells have already entered the clinical setting, indicating that regenerative medicine holds much promise for the future.
WarningBird: Detecting Suspicious URLs in Twitter Stream. (2012)

Twitter can suffer from malicious tweets containing suspicious URLs for spam, phishing, and malware distribution. Previous Twitter spam detection schemes have used account features such as the ratio of tweets containing URLs and the account creation date, or relation features in the Twitter graph. Malicious users, however, can easily fabricate account features. Moreover, extracting relation features from the Twitter graph is time and resource consuming. Previous suspicious URL detection schemes have classified URLs using several features including lexical features of URLs, URL redirection, HTML content, and dynamic behavior. However, evading techniques exist, such as time-based evasion and crawler evasion. In this paper, we propose WARNINGBIRD, a suspicious URL detection system for Twitter. Instead of focusing on the landing pages of individual URLs in each tweet, we consider correlated redirect chains of URLs in a number of tweets. Because attackers have limited resources and thus have to reuse them, a portion of their redirect chains will be shared. We focus on these shared resources to detect suspicious URLs. We have collected a large number of tweets from the Twitter public timeline and trained a statistical classifier with features derived from correlated URLs and tweet context information. Our classifier has high accuracy and low false-positive and falsenegative rates. We also present WARNINGBIRD as a realtime system for classifying suspicious URLs in the Twitter stream. ∗This research was supported by the MKE (The Ministry of Knowledge Economy), Korea, under the ITRC (Information Technology Research Center) support program supervised by the NIPA (National IT Industry Promotion Agency) (NIPA-2011-C1090-1131-0009) and World Class University program funded by the Ministry of Education, Science and Technology through the National Research Foundation of Korea(R31-10100).
Costimulating aberrant T cell responses by B7-H1 autoantibodies in rheumatoid arthritis (2003)

A pathogenic hallmark of rheumatoid arthritis (RA) is persistent activation of self-reactive CD4(+) T cells. The cause of this aberrant activity remains elusive. We report here detection of autoantibodies against B7-H1, a recently described member of the B7 family, in 29% of patients with RA versus 4% of healthy donors. High-level expression of cell surface B7-H1 are found on activated human CD4(+), CD8(+), and CD45RO(+) T cells. Immobilized autoantibodies to B7-H1 are capable of costimulating the proliferation of CD4(+) T cells in vitro, and the presence of these autoantibodies correlates with active disease status. Using immobilized B7-H1 mAb's and programmed death 1Ig, we demonstrate that engagement of B7-H1 on CD4(+) T cells costimulates proliferation and secretion of IL-10, and subsequently leads to programmed cell death, accompanied with upregulated expression of TNF-related apoptosis-inducing ligand and activation of caspase-3. Taken together with our previous findings, these data indicate a bidirectional signaling role of B7-H1 in T cell costimulation and apoptosis and implicate B7-H1 autoantibodies as contributing to the progression of RA by inducing aberrant T cell responses.
Synthesis and preliminary evaluation of a carbon‐11‐labelled agonist of the α7 nicotinic acetylcholine receptor (2001)

Abstract The lead compound of a new series of azabicyclic carbamates described by Astra Laboratories as ligands for the α 7 nicotinic acetylcholine receptor subtype, namely N ‐(4‐bromophenyl)carbamic acid quinuclidin‐3‐yl ester, has been labelled with carbon‐11 using no‐carrier‐added [ 11 C]phosgene and the isocyanate pathway. Typically, 25–35 mCi (0.92–1.29 GBq) of the tracer was obtained within 30 min of radiosynthesis (HPLC purification included) with specific radioactivities ranging from 500 to 800 mCi/µmol (18.5–29.6 GBq/µmol). Biodistribution studies demonstrated a relatively good brain uptake of the compound (0.8–1.2% I.D./g tissue in various brain regions), but without preferential concentration in brain regions rich in α 7‐subtype nicotinic receptor (e.g. hippocampus, pons and colliculi). No specific binding could be demonstrated in pre‐saturation studies performed with both the cold compound and nicotine. Therefore, this ligand is not suitable for further exploration in PET imaging. Copyright © 2001 John Wiley &amp; Sons, Ltd.
Typing Problems (2002)

Guided by the work of William Alston, Jonathan Adler and Michael Levin propose a solution to the generality problem for reliabilism. In some respects their proposal improves on those we have discussed. We argue that the problem remains unsolved.
A placebo‐controlled pilot study of the novel opioid receptor antagonist ALKS‐33 in binge eating disorder (2013)

In this preliminary proof-of-concept study in BED, ALKS-33 did not separate from placebo. Although a failed trial cannot be excluded, the finding is consistent with earlier observations in bulimia nervosa with other opioid antagonists and suggests ALKS-33, at least when administered daily for 6 weeks, may not be efficacious for BED.
Using “Click‐e‐Bricks” to Make 3D Elastomeric Structures (2014)

Soft, 3D elastomeric structures and composite structures are easy to fabricate using click-e-bricks, and the internal architecture of these structures together with the capabilities built into the bricks themselves provide mechanical, optical, electrical, and fluidic functions.
Narrowband perceptual audio coding: enhancements for speech (2001)

This paper presents a bi-modal coding paradigm to compress narrowband audio signals at 8 kbit/s.In the general mode, the Enhanced Narrowband Audio Coder (ENPAC) exploits the characteristics of the human hearing system to adaptively code the perceptually important spectral components of the input audio.The other mode is employed to handle audio inputs with a strong harmonic structure.In that mode, the input block is represented by its audible harmonics.The spectral magnitude is modeled by the linear prediction analysis in the time domain.The phase of each harmonic is predicted and the phase residues are quantized using an adaptive bit allocation algorithm.This paper introduces a perceptually-based upper bound for phase errors of spectral components.The ENPAC encoder delivers good quality for narrowband speech and non-speech inputs.