gebhart/patrepeval huggingface dataset:
Processing of the <i>Drosophila</i> Sog protein creates a novel BMP inhibitory activity (2000)

Structurally unrelated neural inducers in vertebrate and invertebrate embryos have been proposed to function by binding to BMP4 or Dpp, respectively, and preventing these homologous signals from activating their receptor(s). In this study, we investigate the functions of various forms of the Drosophila Sog protein using the discriminating assay of Drosophila wing development. We find that misexpression of Drosophila Sog, or its vertebrate counterpart Chordin, generates a very limited vein-loss phenotype. This sog misexpression phenotype is very similar to that of viable mutants of glass-bottom boat (gbb), which encodes a BMP family member. Consistent with Sog selectively interfering with Gbb signaling, Sog can block the effect of misexpressing Gbb, but not Dpp in the wing. In contrast to the limited BMP inhibitory activity of Sog, we have identified carboxy-truncated forms of Sog, referred to as Supersog, which when misexpressed cause a broad range of dpp(-) mutant phenotypes. In line with its phenotypic effects, Supersog can block the effects of both misexpressing Dpp and Gbb in the wing. Vertebrate Noggin, on the other hand, acts as a general inhibitor of Dpp signaling, which can interfere with the effect of overexpressing Dpp, but not Gbb. We present evidence that Sog processing occurs in vivo and is biologically relevant. Overexpression of intact Sog in embryos and adult wing primordia leads to the developmentally regulated processing of Sog. This in vivo processing of Sog can be duplicated in vitro by treating Sog with a combination of the metalloprotease Tolloid (Tld) plus Twisted Gastrulation (Tsg), another extracellular factor involved in Dpp signaling. In accord with this result, coexpression of intact Sog and Tsg in developing wings generates a phenotype very similar to that of Supersog. Finally, we provide evidence that tsg functions in the embryo to generate a Supersog-like activity, since Supersog can partially rescue tsg(-) mutants. Consistent with this finding, sog(- )and tsg(-) mutants exhibit similar dorsal patterning defects during early gastrulation. These results indicate that differential processing of Sog generates a novel BMP inhibitory activity during development and, more generally, that BMP antagonists play distinct roles in regulating the quality as well as the magnitude of BMP signaling.
Typical sequences and all that: entropy, pattern matching, and data compression (2002)

The author applies pattern matching results to three problems in information theory. The characterisation of a probability law is also discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Rubisco activity and regulation as targets for crop improvement (2012)

Rubisco (ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase) enables net carbon fixation through the carboxylation of RuBP. However, some characteristics of Rubisco make it surprisingly inefficient and compromise photosynthetic productivity. For example, Rubisco catalyses a wasteful reaction with oxygen that leads to the release of previously fixed CO(2) and NH(3) and the consumption of energy during photorespiration. Furthermore, Rubisco is slow and large amounts are needed to support adequate photosynthetic rates. Consequently, Rubisco has been studied intensively as a prime target for manipulations to 'supercharge' photosynthesis and improve both productivity and resource use efficiency. The catalytic properties of Rubiscos from diverse sources vary considerably, suggesting that changes in turnover rate, affinity, or specificity for CO(2) can be introduced to improve Rubisco performance in specific crops and environments. While attempts to manipulate plant Rubisco by nuclear transformation have had limited success, modifying its catalysis by targeted changes to its catalytic large subunit via chloroplast transformation have been much more successful. However, this technique is still in need of development for most major food crops including maize, wheat, and rice. Other bioengineering approaches for improving Rubisco performance include improving the activity of its ancillary protein, Rubisco activase, in addition to modulating the synthesis and degradation of Rubisco's inhibitory sugar phosphate ligands. As the rate-limiting step in carbon assimilation, even modest improvements in the overall performance of Rubisco pose a viable pathway for obtaining significant gains in plant yield, particularly under stressful environmental conditions.
Comparative studies on the degradability of poly(ester amide)s derived fromL- andL,D-alanine (1999)

The hydrolytic degradation of two poly(ester amide)s derived from sebacic acid, dodecanediol, and alanine in both the quiral L configuration and the racemic L,D mixture has been studied. The degradation was monitored by following the changes in intrinsic viscosity, mass loss, chemical constitution, and mechanical properties. The results show that these poly(ester amide)s degrade slowly at 37°C through the ester linkage. Little changes in the Young's modulus of both samples were found at the beginning of the degradation process. Biodegradation has also been studied by using different enzymes. Papain was the most effective one, although the degradation rate was dependent on the stereochemical composition of the polymer. © 1999 John Wiley & Sons, Inc. J Appl Polym Sci 74: 2312–2320, 1999
Monitoring the excitability of neocortical efferent neurons to direct activation by extracellular current pulses (1992)

1. Extracellular action potentials were recorded from antidromically activated efferent neurons in visual, somatosensory, and motor cortex of the awake rabbit using low-impedance metal microelectrodes. Efferent neurons were also activated by current pulses delivered near the soma [juxtasomal current pulses (JSCPs)] through the recording microelectrode. Action potentials generated by JSCPs were not directly observed (because of the stimulus artifact), but were inferred with the use of a collision paradigm. Efferent populations studied include callosal neurons [CC (n = 80)], ipsilateral corticocortical neurons [C-IC (n = 21)], corticothalamic neurons of layer 6 [CF-6 (n = 57)], and descending corticofugal neurons of layer 5 [CF-5, corticotectal neurons of the visual cortex (n = 48)]. 2. Most CC neurons (45/46) and all C-IC (8/8) and CF-6 neurons (39/39) were directly activated by JSCPs at near-threshold intensities. Some CF-5 neurons (9/38), however, showed evidence of indirect activation. All efferent classes had similar current thresholds (means 1.85-2.10 microA) to direct activation by JSCPs, and thresholds were inversely related to extracellular spike amplitude. For each neuron, the range of JSCP intensities that generated response probabilities of between 0.2 and 0.8 was measured, and this "range of uncertainty" was significantly greater in CF-5 neurons (mean 32.7% of threshold) than in CC (mean 19.0%) or CF-6 (mean 20.4%) neurons. 3. Several factors indicate that the threshold of efferent neurons to JSCPs is very sensitive to excitatory and inhibitory synaptic inputs. Iontophoretic applications of gamma-aminobutyric acid (GABA) increased the threshold to JSCPs, and glutamate reduced the threshold. Electrical stimulation of afferent pathways at intensities just below threshold for eliciting action potentials resulted in a dramatic decrease in JSCP threshold. This initial short-latency threshold decrease was specific to stimulation of particular afferent pathways and is thought to reflect excitability changes associated with EPSPs. Examination of such subliminal responses revealed subthreshold synaptic inputs that were not revealed by examination of all-or-none action potentials. In contrast to the specificity of the short-latency threshold decrease, a long-lasting increase in JSCP threshold was seen in virtually all neurons after stimulation of each of the afferent pathways tested. This increase in threshold usually began 20-40 ms after stimulation, lasted for 100-200 ms, and is thought to reflect excitability changes associated with a long-lasting inhibitory postsynaptic potential (IPSP) seen in many cortical neurons. 4. Many neurons in primary somatosensory cortex of rat, cat, and rabbit have no demonstrable receptive fields.(ABSTRACT TRUNCATED AT 400 WORDS)
A novel carrier recovery technique for orthogonal multicarrier systems (1996)

Abstract This paper deals with the carrier frequency synchronization of orthogonal multicarrier systems, which are an effective transmission technique for coping with the typical channel impairments present in mobile reception. A new carrier frequency detector is introduced and its performance thoroughly analyzed in the presence of a multipath channel. In particular we have analytically derived the frequency detector characteristic curve and its noise power spectral density. We have compared the new algorithm with other known algorithms and we have shown that it permits a considerable improvement in the noise level to be achieved. Therefore the proposed algorithm seems to be a valid candidate for carrier frequency recovery in applications employing multicarrier transmission.
Activated Carbon for Sugar Decolorization (1941)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTActivated Carbon for Sugar DecolorizationE. S. Hertzog and S. J. BroderickCite this: Ind. Eng. Chem. 1941, 33, 9, 1192–1198Publication Date (Print):September 1, 1941Publication History Published online1 May 2002Published inissue 1 September 1941https://pubs.acs.org/doi/10.1021/ie50381a024https://doi.org/10.1021/ie50381a024research-articleACS PublicationsRequest reuse permissionsArticle Views629Altmetric-Citations3LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
An Adaptive-Duration Version of the PVT Accurately Tracks Changes in Psychomotor Vigilance Induced by Sleep Restriction (2012)

We developed and validated a highly accurate, sensitive, and specific adaptive-duration version of the 10-minute PVT. Test duration of the adaptive PVT averaged less than 6.5 minutes, with 60 tests (4.3%) terminating after less than 2 minutes, increasing the practicability of the test in operational and clinical settings. The adaptive-duration strategy may be superior to a simple reduction of PVT duration in which the fixed test duration may be too short to identify subjects with moderate impairment (showing deficits only later during the test) but unnecessarily long for those who are either fully alert or severely impaired.
Expression and localization of pannexin‐1 hemichannels in human colon in health and disease (2013)

The presence of Panx1 in the colon and changes to its distribution in disease suggests that Panx1 channels may play an important role in mediating gut function and in IBD pathophysiology.
Theoretical and numerical study of the interaction of a nanosecond laser pulse with a copper target for laser-induced breakdown spectroscopy applications (2013)

This work is a presentation of a modeling approach aimed at describing laser–matter interaction under laser-induced breakdown spectroscopy operating conditions. In order to set up a simple numerical tool to compute our model, only the most relevant processes appearing during the interaction were considered. This allowed us to develop a quick and rather accurate idea about how some physical parameters evolve during the interaction, so that the optimization of the laser beam parameters for better analytical results would be possible. For a basic understanding we used for our numerical computation a nanosecond laser pulse with an ideal Gaussian temporal profile and a pure Cu target. In order to optimize the interaction parameters, this study was focused on the effect of some of the laser parameters such as the wavelength (UV, Vis, IR), the pulse duration, and the irradiation on the results of the interaction. An investigation of the influence of some processes such as the vaporization effects and the plasma shielding was also included. The processes occuring on the material surface were closely examined as well. A comparison between the use of temperature-dependent and temperature-independent optical parameters was conducted, and their influence on the results was investigated. The use of variable optical parameters is revealed to be a means to correct the values of the temperature distribution inside the material and convert them into more realistic ones. Our code was first validated when operating under the same conditions used by other authors, and then it was used to present our proper contributions, as previously stated.
Cystic fibrosis gene repair: correction of ΔF508 using ZFN and CRISPR/Cas9 guide RNA gene editing tools (2013)

Cystic Fibrosis (CF) is an autosomal recessive monogenic disorder caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene with the ΔF508 mutation accounting for approximately 70% of all CF cases worldwide. This thesis investigates whether existing zinc finger nucleases designed in this lab and CRISPR/gRNAs designed in this thesis can mediate efficient homology-directed repair (HDR) with appropriate donor repair plasmids to correct CF-causing mutations in a CF cell line. Firstly, the most common mutation, ΔF508, was corrected using a pair of existing ZFNs, which cleave in intron 9, and the donor repair plasmid pITR-donor-XC, which contains the correct CTT sequence and two unique restriction sites. HDR was initially determined to be <1% but further analysis by next generation sequencing (NGS) revealed HDR occurred at a level of 2%. This relatively low level of repair was determined to be a consequence of distance from the cut site to the mutation and so rather than designing a new pair of ZFNs, the position of the existing intron 9 ZFNs was exploited and attempts made to correct >80% of CF-causing mutations. The ZFN cut site was used as the site for HDR of a mini-gene construct comprising exons 10-24 from CFTR cDNA (with appropriate splice acceptor and poly A sites) to allow production of full length corrected CFTR mRNA. Finally, the ability to cleave closer to the mutation and mediate repair of CFTR using the latest gene editing tool CRISPR/Cas9 was explored. Two CRISPR gRNAs were tested; CRISPR ex10 was shown to cleave at an efficiency of 15% and CRISPR in9 cleaved at 3%. Both CRISPR gRNAs mediated HDR with appropriate donor plasmids at a rate of ~1% as determined by NGS. This is the first evidence of CRISPR induced HDR in CF cell lines.
Tensile Strength of Plastics above the Glass Temperature (1955)

A theory is presented for the tensile strength of rubbery plastics under dynamic test conditions. It is found that a nearly universal curve may be plotted relating the tensile strength of rubbers to the time of application of the load in a simple creep test or to the shear rate in a conventional type tensile test. The dependence on chain length, degree of cross linking, and temperature is also predicted. Experimental results for the tensile strength of poly butyl methacrylate in the range 30–95°C are presented. These are shown to agree with the theory within the experimental error. The experimental testing scale extends over a range of eight decades when use is made of a temperature—time superposition principle predicted by the theory. By comparing the tensile creep and tensile strength curves for poly butyl methacrylate, it is possible to find the size of a segment as defined in the theory of viscoelasticity. One segment is found to contain about six monomer units.
DRC-1339 AND DRC-2698 RESIDUES IN STARLINGS: PRELIMINARY EVALUATION OF THEIR EFFECTS ON SECONDARY HAZARD POTENTIAL (1979)

DRC-1339 (3-chloro-4-methylbenzenamine HCI) is the active ingredient in Starlicide Complete, a commercial bait used to control starlings (Sturnus vulgaris) at animal feedlots throughout the U.S. Because of the recent widespread use of this product, par- ticularly within the wintering range of many raptors, they and other avian or mammalian scavenger or predator species may be exposed to large numbers of dead or dying star- lings and blackbirds (Icteridae) throughout the winter roosting season (November-March). Acute toxicity data are available for five species of raptors and a number of mammals indicating that DRC-1339 or its primary toxic metabolite DRC-2698 (N-(3-chloro-4-methylphenyl) acetamide, CAT), a potential roost toxicant, are only moderately toxic (100-300 mg/kg) to these animals. However, there are some avian and mammalian scavengers or predators to which these compounds are considerably more toxic (i.e., cats, owls, magpies). Secondary hazards have not been observed when DRC-1339 killed starlings were fed to three raptor species for as long as 141 days and to domestic cats for seven days (DeCino, Cunningham and Schafer 1966; Holler et al. 1979, unpubl, manuscript); however, the direct long-term effects of both chemicals have not been determined on raptors or other predatory or scavenger species. In order to decide if long-term studies are needed on predator or scavenger species, it is necessary to estimate accurately the degree of expected exposure to DRC-1339 and DRC-2698under actual use conditions. Since exposure will depend primarily upon the amount of these chemicals that remains in bird carcasses from bait ingestion until death, the metabolic or excretion rate of DRC-1339 and DRC-2698 must be known in target and at-risk, nontarget bird species. Although considerable data are available to determine the metabolic or excretion rate of DRC-1339 in target birds, some of these data are conflicting. We are therefore presenting the preliminary results of some of our current research with DRC-1339 and DRC-2698.
$A^{4}NT$: Author Attribute Anonymity by Adversarial Training of Neural Machine Translation (2017)

Text-based analysis methods allow to reveal privacy relevant author attributes such as gender, age and identify of the text's author. Such methods can compromise the privacy of an anonymous author even when the author tries to remove privacy sensitive content. In this paper, we propose an automatic method, called Adversarial Author Attribute Anonymity Neural Translation ($A^4NT$), to combat such text-based adversaries. We combine sequence-to-sequence language models used in machine translation and generative adversarial networks to obfuscate author attributes. Unlike machine translation techniques which need paired data, our method can be trained on unpaired corpora of text containing different authors. Importantly, we propose and evaluate techniques to impose constraints on our $A^4NT$ to preserve the semantics of the input text. $A^4NT$ learns to make minimal changes to the input text to successfully fool author attribute classifiers, while aiming to maintain the meaning of the input. We show through experiments on two different datasets and three settings that our proposed method is effective in fooling the author attribute classifiers and thereby improving the anonymity of authors.
Withaferin A Effectively Targets Soluble Vimentin in the Glaucoma Filtration Surgical Model of Fibrosis (2013)

Withaferin A (WFA) is a natural product that binds to soluble forms of the type III intermediate filament (IF) vimentin. Currently, it is unknown under what pathophysiological contexts vimentin is druggable, as cytoskeltal vimentin-IFs are abundantly expressed. To investigate druggability of vimentin, we exploited rabbit Tenon's capsule fibroblast (RbTCF) cell cultures and the rabbit glaucoma filtration surgical (GFS) model of fibrosis. WFA potently caused G₀/G₁ cell cycle inhibition (IC₅₀ 25 nM) in RbTCFs, downregulating ubiquitin E3 ligase skp2 and inducing p27(Kip1) expression. Transforming growth factor (TGF)-ß-induced myofibroblast transformation caused development of cell spheroids with numerous elongated invadopodia, which WFA blocked potently by downregulating soluble vimentin and α-smooth muscle actin (SMA) expression. In the pilot proof-of-concept study using the GFS model, subconjunctival injections of a low WFA dose reduced skp2 expression in Tenon's capsule and increased p27(Kip1) expression without significant alteration to vimentin-IFs. This treatment maintains significant nanomolar WFA concentrations in anterior segment tissues that correspond to WFA's cell cycle targeting activity. A ten-fold higher WFA dose caused potent downregulation of soluble vimentin and skp2 expression, but as found in cell cultures, no further increase in p27(Kip1) expression was observed. Instead, this high WFA dose potently induced vimentin-IF disruption and downregulated α-SMA expression that mimicked WFA activity in TGF-ß-treated RbTCFs that blocked cell contractile activity at submicromolar concentrations. These findings illuminate that localized WFA injection to ocular tissues exerts pharmacological control over the skp2-p27(Kip1) pathway by targeting of soluble vimentin in a model of surgical fibrosis.
Total Synthesis of (+)-Geldanamycin and (−)-<i>o</i>-Quinogeldanamycin with Use of Asymmetric <i>Anti- </i>and <i>Syn</i>-Glycolate Aldol Reactions (2002)

Geldanamycin (GA), an antitumor Hsp90 inhibitor, was made for the first time by using an oxidative demethylation reaction as the final step. A biaryldioxanone auxiliary set the anti C11-12 hydroxy-methoxy functionality and a methylglycolate auxiliary based on norephedrine was used for the syn C6-7 methoxy-urethane. p-Quinone-forming oxidants, CAN and AgO, produced an unusual aza-quinone product. Nitric acid gave GA from a trimethoxy precursor in 55% yield as a 1:10 mixture with nonnatural o-quino-GA. [structure: see text]
Quantitative velocity images from thick slab 2D phase contrast (1993)

Abstract Thick slab two‐dimensional phase contrast (2D PC) angiography provides a large amount of anatomical information in a short acquisition time. Quantitative velocity information is, however, destroyed by the necessary projection dephasing gradient. We present a 2D PC acquisition scheme which retains quantitative velocity information in a thick slab acquisition. A thick slab acquisition produces an image which is a projection through an entire vessel. Accurate velocity measurements must take into account the intravoxel phase cancellation caused by a distribution of velocities within the vessel. In addition to the description of the data acquisition scheme, we outline a method for determining the mean velocity within a vessel having a laminar flow distribution. It is shown that without the consideration for intravoxel phase cancellation, the mean velocity measurement from thick slab images overestimates the true mean velocity by 10%.