gebhart/patrepeval huggingface dataset:
Reduction-Reoxidation Cycles Contribute to Catalysis of disulfide Isomerization by Protein-disulfide Isomerase (2003)

Protein-disulfide isomerase (PDI) catalyzes the formation and isomerization of disulfides during oxidative protein folding. This process can be error-prone in its early stages, and any incorrect disulfides that form must be rearranged to their native configuration. When the second cysteine (CGHC) in the PDI active site is mutated to Ser, the isomerase activity drops by 7-8-fold, and a covalent intermediate with the substrate accumulates. This led to the proposal that the second active site cysteine provides an escape mechanism, preventing PDI from becoming trapped with substrates that isomerize slowly (Walker, K. W., and Gilbert, H. F. (1997) J. Biol. Chem. 272, 8845-8848). Escape also reduces the substrate, and if it is invoked frequently, disulfide isomerization will involve cycles of reduction and reoxidation in preference to intramolecular isomerization of the PDI-bound substrate. Using a gel-shift assay that adds a polyethylene glycol-conjugated maleimide of 5 kDa for each sulfhydryl group, we find that PDI reduction and oxidation are kinetically competent and essential for isomerization. Oxidants inhibit isomerization and oxidize PDI when a redox buffer is not present to maintain the PDI redox state. Reductants also inhibit isomerization as they deplete oxidized PDI. These rapid cycles of PDI oxidation and reduction suggest that PDI catalyzes isomerization by trial and error, reducing disulfides and oxidizing them in a different configuration. Disulfide reduction-reoxidation may set up critical folding intermediates for intramolecular isomerization, or it may serve as the only isomerization mechanism. In the absence of a redox buffer, these steady-state reduction-oxidation cycles can balance the redox state of PDI and support effective catalysis of disulfide isomerization.
Historical document digitization through layout analysis and deep content classification (2016)

Document layout segmentation and recognition is an important task in the creation of digitized documents collections, especially when dealing with historical documents. This paper presents an hybrid approach to layout segmentation as well as a strategy to classify document regions, which is applied to the process of digitization of an historical encyclopedia. Our layout analysis method merges a classic top-down approach and a bottom-up classification process based on local geometrical features, while regions are classified by means of features extracted from a Convolutional Neural Network merged in a Random Forest classifier. Experiments are conducted on the first volume of the “Enciclopedia Treccani”, a large dataset containing 999 manually annotated pages from the historical Italian encyclopedia.
A Preliminary Investigation into Sentiment Analysis of Informal Political Discourse. (2006)

With the rise of weblogs and the increasing tendency of online publications to turn to message-board style reader feedback venues, informal political discourse is becoming an important feature of the intellectual landscape of the Internet, creating a challenging and worthwhile area for experimentation in techniques for sentiment analysis. We describe preliminary statistical tests on a new dataset of political discussion group postings which indicate that posts made in direct response to other posts in a thread have a strong tendency to represent an opposing political viewpoint to the original post. We conclude that traditional text classification methods will be inadequate to the task of sentiment analysis in this domain, and that progress is to be made by exploiting information about how posters interact with each other.
TURTLE-ASSOCIATED SALMONELLOSIS (1972)

Lamm, S. H., A. Taylor, Jr., E. J. Gangarosa (CDC, Atlanta, Georgia 30333), H. W. Anderson, W. Young, M. H. Clark and A. R. Bruce. Turtle-associated salmonellosis. I. An estimation of the magnitude of the problem in the U.S., 1970–71. Am J Epidemiol 95: 511–517, 1972.—To determine the magnitude of turtle-associated salmonellosis, surveys were conducted in 5 areas. Of cases of salmonellosis in Connecticut, 24% were turtle-associated compared with an association of 2% in the control group. Uncontrolled studies in Utah, in Atlanta, Georgia, in Santa Clara County, California, and in the Seattle area of Washington showed an association of 16, 9.2, 18, and 11.5%, respectively. A previously reported uncontrolled study in Minneapolis-St. Paul showed an association of 25% and a recently completed, well controlled study in New Jersey indicated that 22.6% of salmonellosis cases in children were turtle-associated compared with 5.7% in the control group. Based on these data, we estimate approximately 280,000 cases of turtle-associated salmonellosis occurred in the U.S. in 1970 and 1971 with related medical expenses amounting to millions of dollars. A decrease in the incidence of salmonellosis in the age groups most at risk and a marked decrease in turtle-associated cases of salmonellosis ensued following a regulation in 1968 by the State of Washington controlling the sale of turtles. Based on the magnitude of the problem and the apparent effectiveness of the Washington regulation, it is recommended that all political jurisdictions take appropriate regulatory action to prevent the sale of salmonella-contaminated turtles within their borders.
Relative Rates and Isomer Distributions in the Halogenation of t-Butylbenzene and Some of Its Derivatives. Partial Rate Factors for Non-catalytic Bromination and Chlorination in Acetic Acid<sup>1-3</sup> (1959)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRelative Rates and Isomer Distributions in the Halogenation of t-Butylbenzene and Some of Its Derivatives. Partial Rate Factors for Non-catalytic Bromination and Chlorination in Acetic Acid1-3Leon M. Stock and Herbert C. BrownCite this: J. Am. Chem. Soc. 1959, 81, 21, 5615–5620Publication Date (Print):November 1, 1959Publication History Published online1 May 2002Published inissue 1 November 1959https://pubs.acs.org/doi/10.1021/ja01530a024https://doi.org/10.1021/ja01530a024research-articleACS PublicationsRequest reuse permissionsArticle Views299Altmetric-Citations24LEARN 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 optionsGet e-Alertsclose Get e-Alerts
A versatile approach to grafting biofouling resistant coatings from polymeric membrane surfaces using an adhesive macroinitiator (2015)

The use of a polydopamine-based macroinitiator provides a flexible attachment method that is virtually independent of membrane substrate. The subsequent ARGET-ATRP controllably grafts the stable biofouling resistant polyzwitterion coating.
Suppression of elastic scattering loss for slowly colliding Bose-Einstein condensates (2001)

Superfluid suppression of the elastic scattering loss in atomic Bose condensed systems can be significant when the ratio of the relative velocity of the wave packets to the critical velocity is $\ensuremath{\sim}1.$ We show how to incorporate the effect of such losses and their suppression into the time-dependent dynamics of two colliding condensate wave packets. We illustrate the magnitude of the effect through three-dimensional simulations of the collision dynamics of an $|F=2,{M}_{F}=2〉$ with an $|F=2,{M}_{F}=1〉{}^{87}\mathrm{Rb}$ condensate in a harmonic trap, as studied in a recent experiment [Maddaloni et al., Phys. Rev. Lett. 85, 2413 (2000)]. These calculations show that the effect of elastic scattering and its suppression should be seen in the oscillatory center-of-mass amplitude of the ${M}_{F}=1$ wave packet for suitable experimental conditions.
The structure and resonance Raman spectra – structure correlations for methyloxycarbonyl-<scp>L</scp>-phenylalanyl-<scp>L</scp>-alanine ethyl dithioester (1986)

The structure of methyloxycarbonyl-L-phenylalanyl-L-alanine ethyl dithioester has been determined by X-ray crystallographic analysis. The N—C—C—S(thiol) and C—N—C—C(S) torsional angles are 141(1)° and −69(2)°, respectively. Consequently, the N and thiono (C=S) sulfur atoms are in close contact and the [Formula: see text](thiono) distance is 3.078(5) Å. The structure is a perturbed A conformer, which we designate A′, by analogy to a previously characterised A conformer (Huber etal., Biochemistry, 21 3109 (1982)). The [Formula: see text] angles for the Phe residue are −87(2) and 151(2)°, respectively. A Raman spectroscopic study of a single crystal of the LL form and a resonance Raman (RR) spectroscopic study of powdered methyloxycarbonyl-L-phenylalanyl-DL-alanine ethyl dithioester establish the RR signature of the dithio moiety for the compound in the A′ form. The RR spectrum of the dithioester in CCl 4 defines the RR signature for the C 5 form in solution, while the RR spectrum from a solution in H 2 O/CH 3 CN provides information on the signatures of the A and B conformers. As for the case of N-benzoyl-DL-alanine dithioester, the A and C 5 signatures of the title compound closely resemble those for glycine-based dithioesters but the key marker bands for the B conformer are shifted by ≈30 cm −1 to lower frequency compared to those for a glycine dithioester.
Application of Transition Metal Nanoparticles in the Streams Production of Heavy Crude Oil Treatment: H2S Mitigation (2017)

Abstract The in-line scavenging of hydrogen sulfide is the preferred method for minimizing the corrosion and operational risks in oil production (Rajagopal et al. 2009). On the other hand, it is known that Nanoparticles by their small size and high dispersion increase the probability of collision between molecules and minimize the diffusion problems. Additionally, oxides of iron, manganese, zinc, magnesium and copper are considered suitable sorbents for gas desulfurization at temperatures in excess of 300°C (Husein et al. 2010). The experiments were designed to apply nanoparticles for the streams treatment during enhanced heavy oil recovery (steam injection). Sorption of the H2S present in oil phases finds application for mitigating H2S forming during this process. In this study, our heavy crude oil whose viscosity is 10500 mPa.s, was obtained from a reservoir block of the Faja Petrolífera del Orinoco Hugo Chávez (FPOHC, Venezuela), with temperature about 80°C, and when the steam is injected temperature reach up to 260°C. Three types of nanoparticles were used to treat the heavy crude oil (H2S scavengers and reduce viscosity). The organic matrix was high vacuum gas oil (HVGO) which serves as the carrier of dispersed particles, to reduce both H2S production and viscosity, and the nanoparticles, based on transition metals that serve as H2S scavengers centers are, respectively, FexOy, CuxOy and NixOy. In these experiments, before reaction, the sand and the gaseous products were separated to remove any catalytic effect from the minerals and H2S present. Experiments were carried out in an autoclave reactor simulating steam injection condition (~600 psi and ~260°C). Appropriate quantities of heavy crude oil and water, and 500 ppm of dispersed nanoparticles were placed in the reactor; methane was used as reservoir gas. Results indicate the reduction of H2S production from 1500 ppm in the experiment without nanoparticles up to 100 ppm, 250 ppm and traces to FexOy, NixOy and CuxOy, respectively. Also, reductions of viscosity were obtained for all tests, from 15 to 26%.
CT appearances of the normal tentorial hiatus and expanding lesions of the incisura. (1978)

The electronic relaxation processes of a photoexcited linear perylenediimide-perylenemonoimide (PDI-PMI) acceptor-donor dyad were studied. PDI-PMI serves as a model compound for donor-acceptor systems in photovoltaic devices and has been designed to have a high-energy PDI--PMI + charge transfer (CT) state. Our study focuses on the minimal Gibbs free energy (AGET) required to achieve quantitative CT and on establishing the role of charge recombination to a triplet state. We used time-resolved photoluminescence and picosecond photoinduced absorption (PIA) to investigate excited singlet (S1) and CT states and complemented these experiments with singlet oxygen (1?g) luminescence and PIA measurements on longer timescales to study the population of triplet excited states (Ti). In an apolar solvent like cyclohexene (CHX), photoinduced electron transfer does not occur, but in more polar solvents such as toluene (TOL) and chlorobenzene (CB), photoexcitation is followed by a fast electron transfer, populating the PDI--PMI+ CT state. We extract rate constants for electron transfer (ET; S1?CT), back electron transfer (BET; S1?CT), and charge recombination (CR) to lower-energy states (CT?S0 and CT?T1). Temperature-dependent measurements yield the barriers for the transfer reactions. For ET and BET, these correspond to predictions from Marcus-Jortner theory and show that efficient, near quantitative electron transfer (k ET/kBET ? 100) can be obtained when ?G ET ? -120 meV. With respect to triplet state formation, we find a relatively low triplet quantum yield (? &lt;25%) in CHX but much higher values (?T = 30-98%) in TOL and CB. We identify the PDI --PMI+ state as a precursor to the T1 state. Recombination to T1, rather than to the ground-state S0, is required to rationalize the experimental barrier for CR. Finally, we discuss the relevance of these results for electron donor-acceptor films in photovoltaic devices. © 2008 American Chemical Society
First-aid sensor system: New methods for single-point detection and analysis of vital parameters such as pulse and respiration (2007)

The paper describes a first aid medical sensor system that is able to detect pulse and respiration. According to an opinion poll 79% of unexperienced first aiders were looking forward to use a system that supports them in first aid situations. Such a device has to be reliable and available in everyday use (e.g. as a keychain or in a first-aid kit). Therefore we investigated a single point sensor that is able to detect both respiration and blood flow at the same point of the body, for instance on the neck. Compared to ECG-derived methods absent pulse due to pulseless electrical activity (PEA) will be recognized as such. Tests have shown that the sensor can also be used to detect deglutition and other body motion sequences.
Effects of carthamus tinctorius on gene expression of interstitial collagenase and type I collagen in HSC-T6 cells (2013)

Objective To investigate the effects of carthamus tinctorius on gene expression of interstitial collagenase and type Ⅰ collagen in HSC-T6 cells.Methods Hepatic stellate cells (HSC-T) were cultured in medium containing different concentrations of carthamus tinctorius (1.0,and 0.5 g/L) and harvested after incubation for 48 h.Total RNA of HSCs was isolated and gene expression levels of interstitial collagenase (MMP13) and type Ⅰ collagen were detected by using reverse transcription polymerase chain reaction.Results MMP13 gene expression levels in different groups of carthamus tinctorius (1.0,and 0.5 g/L) were 0.63 ±0.10 and 0.40 ±0.07 respectively,and that in control group was 0.26 ±0.04.Type Ⅰ collagen gene expression levds in different groups of carthamus tinctorius (1.0,and 0.5 g/L)were 1.30 ±0.20 and 1.97 ±0.36 respectively,and that in control group was 3.12 ±0.46.Conclusion Carthamus tinctorius may significantly enhance MMP13 gene expression in HSC-T6 ceils,but inhibit type Ⅰ collagen gene expression remarkably in a dose-dependent manner.

Key words: 
Carthamus tinctorius;  Hepatic stellate cells;  Interstitial collagenase;  Type Ⅰ collagen;  Gene expression
Highly Efficient G-Quadruplex Recognition by Bisquinolinium Compounds (2007)

Syntheses and telomeric G-quadruplex−DNA binding properties of novel bisquinolinium compounds are reported. This series exhibits remarkable efficiency both in terms of stabilization and selectivity, thus combining the performances of the most potent quadruplex binders reported so far. These bisquinolinium compounds then represent an ideal tradeoff between rapid synthetic access and efficient target recognition. The study also highlights important structural parameters that lead to the design of highly selective G-quadruplex binders.
Effects of Transforming Growth Factors and Inhibin-Related Proteins on Rat Preovulatory Graafian Follicles<i>in vitro</i>* (1989)

In view of recent reports on ovarian production and action of transforming growth factors (TGFs) and inhibin-related proteins (inhibin, activin, and follistatin), we have examined the effects of these hormones on the function of preovulatory follicles in vitro. Individual preovulatory follicles were obtained from PMSG-treated rats and incubated with these hormones in the absence or presence of LH. Oocyte maturation and progesterone production were monitored. Treatment with TGF alpha alone, but not with TGF beta or inhibin-related proteins, mimicked the action of LH on oocyte maturation by inducing the resumption of meiosis in follicle-enclosed oocytes (56.6% and 80.6% oocytes resumed meiosis in the presence of 0.5 and 1.0 microgram/ml TGF alpha, respectively). In follicle cultures treated with LH to induce oocyte maturation, cotreatment with inhibin and TGF beta (30-50 ng/ml), but not other related hormones, partially inhibited LH-induced meiosis in follicle-enclosed oocytes (from 82% mature ova in the presence of LH to 51% and 55% mature ova with TGF beta and inhibin, respectively). In contrast to follicle cultures, none of the hormones tested significantly affected the spontaneous maturation of rat oocytes explanted from their follicles and cultured within their cumulus mass for 4 h. Treatment with TGF alpha, but not with TGF beta, inhibin, activin, or follistatin, stimulated progesterone production. The present study demonstrated that TGF alpha, like LH, induces oocyte maturation and progesterone production in preovulatory rat follicles. Furthermore, inhibin and TGF beta suppressed LH-induced resumption of meiosis in follicle-enclosed oocytes. Because these growth factors and inhibin-related proteins are synthesized by follicle cells, they may play important roles in regulating follicular development and activity.
Detecting Novel Sequence Signals in Targeting Peptides Using Deep Learning (2019)

Abstract In bioinformatics, machine learning methods have been used to predict features embedded in the sequences. In contrast to what is generally assumed, machine learning approaches can also provide new insights into the underlying biology. Here, we demonstrate this by presenting TargetP 2.0, a novel state of art method to identify N-terminal sorting signals, which direct proteins to the secretory pathway, mitochondria and chloroplasts or other plastids. By examining the strongest signals from the attention layer in the network, we find that the second residue in the protein, i.e. the one following the initial methionine, has a strong influence on the classification. When subsequently examining all targeting peptides, we observe that two-thirds of chloroplast and thylakoid transit peptides have an alanine in position two, but only 20% of other plant proteins. Further highlighting the importance of the second residue, we also note that in fungi and single-celled eukaryotes, less than 30% of the targeting peptides have an amino acid that allows the removal of the N-terminal methionine compared with 60% for the proteins without targeting peptide. TargetP 2.0 is available at http://www.cbs.dtu.dk/services/TargetP-2.0/index.php
Folates in foods: reactivity, stability during processing, and nutritional implications. (1989)

Nutritional deficiencies are eminent at all socioeconomic levels of the world population and have created a critical need for a reevaluation of the nutritional quality of the food supply. A particular group of vitamers, collectively referred to as folates, has received a great deal of attention due to their significance in human metabolism, their prevalent deficiency worldwide, as well as their complexity of analysis. Severe folate deficiency may result in megaloblastic anemia and is generally attributed to low dietary intake, although it may also result from malabsorption. Such concerns have instigated increased interest in food-fortification programs. In order to ensure appropriate levels of nutrient fortification and optimization of food processes for maximum folate retention, it is of great importance to have a basic understanding of the kinetic behavior of individual vitamers with respect to processing parameters and various environmental conditions. This article reviews kinetic stability of folates as affected by processing conditions, discusses problems associated with current methodology for folate analyses, and integrates this information with the nutritional aspects of folates.
Synthesis and metal ion complexation of synthetic ionophores (1985)

The use of synthetic ionophores in both academic and industrial settings continues to increase. Growth in this field of chemistry has created a need for ionophores with pendant groups which allow for further chemical elaboration. This dissertation treats the synthesis of such ionophores.\n\nCrown ethers (macrocyclic polyethers) and cryptands (macrobicyclic polyethers) which bear hydroxymethyl functions are prepared from benzyl-protected and allyl-protected precursors, respectively. Crown ethers containing ionizable chromogenic subunits are synthesized from benzocrown ether and hydroxymethylcrown ether starting materials in high yields. Neutral fluorogenic crown ethers are obtained in two steps from commercially-available starting materials. A series of novel bis-crown ethers results from condensation of diacid chlorides with hydroxy-16-crown-5 compounds.\n\nSeveral bis-crown ethers are tested for their ability to complex the alkali metal cations by the picrate extraction method. Results indicate that the formation of 2:1 (crown:cation) complexes with potassium ion may be promoted by linking two oxymethyl-15-crown-5 units ortho on an aryl ring. A broad spectrum of small-ring four-oxygen crown ethers are tested by the same method for their ability to extract lithium ion. Results indicate that the 14-crown-4 ring size is the best suited in extraction capacity and selectivity for the complexation of lithium. Chloroform solutions of the ionizable chromogenic crown ethers are tested for their response upon contact with aqueous solutions of the alkali metal hydroxides. It is determined that the l-amino-2,4-dinitro-6-trifluoromethylbenzene chromophore is the best suited for incorporation into chromogenic crown ethers because of its acidity, high extinction coefficient and well-resolved spectral shift upon ionization.
On-line Computation of MTIE using Binary Decomposition and Direct Search with Sequential Data Reducing (2007)

In this paper the methods enabling assessment of maximum time interval error (MTIE) in the real-time are presented and compared. The idea of real-time quasi-parallel computation of MTIE is described first. Then two different methods enabling real-time MTIE calculation are described. The results of experimental tests performed for different data sequences and using different computers are presented and discussed.