gebhart/patrepeval huggingface dataset:
neXtProt: Organizing Protein Knowledge in the Context of Human Proteome Projects (2012)

About 5000 (25%) of the ~20400 human protein-coding genes currently lack any experimental evidence at the protein level. For many others, there is only little information relative to their abundance, distribution, subcellular localization, interactions, or cellular functions. The aim of the HUPO Human Proteome Project (HPP, www.thehpp.org ) is to collect this information for every human protein. HPP is based on three major pillars: mass spectrometry (MS), antibody/affinity capture reagents (Ab), and bioinformatics-driven knowledge base (KB). To meet this objective, the Chromosome-Centric Human Proteome Project (C-HPP) proposes to build this catalog chromosome-by-chromosome ( www.c-hpp.org ) by focusing primarily on proteins that currently lack MS evidence or Ab detection. These are termed "missing proteins" by the HPP consortium. The lack of observation of a protein can be due to various factors including incorrect and incomplete gene annotation, low or restricted expression, or instability. neXtProt ( www.nextprot.org ) is a new web-based knowledge platform specific for human proteins that aims to complement UniProtKB/Swiss-Prot ( www.uniprot.org ) with detailed information obtained from carefully selected high-throughput experiments on genomic variation, post-translational modifications, as well as protein expression in tissues and cells. This article describes how neXtProt contributes to prioritize C-HPP efforts and integrates C-HPP results with other research efforts to create a complete human proteome catalog.
Perspectives in Pancreatic Pain (1997)

This review describes some of the mechanisms which are thought to be important in the causation of pain in chronic pancreatitis. Both medical and surgical techniques for treating this pain are described.
Emotion to emotion speech conversion in phoneme level (2004)

Having an ability to synthesize emotional speech can make human–machine interaction more natural in spoken dialogue management. This study investigates the effectiveness of prosodic and spectral modification in phoneme level on emotion-to-emotion speech conversion. The prosody modification is performed with the TD-PSOLA algorithm (Moulines and Charpentier, 1990). We also transform the spectral envelopes of source phonemes to match those of target phonemes using LPC-based spectral transformation approach (Kain, 2001). Prosodic speech parameters (F0, duration, and energy) for target phonemes are estimated from the statistics obtained from the analysis of an emotional speech database of happy, angry, sad, and neutral utterances collected from actors. Listening experiments conducted with native American English speakers indicate that the modification of prosody only or spectrum only is not sufficient to elicit targeted emotions. The simultaneous modification of both prosody and spectrum results in higher acceptance rates of target emotions, suggesting that not only modeling speech prosody but also modeling spectral patterns that reflect underlying speech articulations are equally important to synthesize emotional speech with good quality. We are investigating suprasegmental level modifications for further improvement in speech quality and expressiveness.
GBAS ionospheric threat analysis using DLRs hardware signal simulator (2010)

Ionospheric fronts pose a significant threat to single frequency ground based augmentation systems (GBAS) for airplane precision approach. Here, we show our implementation of two ionospheric threat models in the DLR MASTER GNSS Simulator, a modified Spirent GSS7780/779. These threat models include the standard GBAS ”front” threat model as required for CAT-1 certification and a simplified plasma bubble model intended to represent equatorial conditions. These models can now easily be simulated at the German Aerospace Center's facilities. As an example, we simulate a GBAS ground facility (with a code carrier divergence monitor) affected by both a plasma bubble with a constant differential delay of -2 m and fronts of various gradients and speeds. Results confirm that a plasma bubble can lead to worst case position biases that may cause misleading and hazardously misleading information to be used by an approaching aircraft. Moreover, we confirm that ionospheric fronts at a speeds close to the airplane approach speed and propagating into the approach direction cause the most severe range biases. These, mapped to the position domain, can also cause hazardously misleading information.
Crystallization and preliminary X-ray crystallographic study of alanyl-tRNA synthetase from the archaeon<i>Archaeoglobus fulgidus</i> (2007)

In order to analyze the alanyl-tRNA synthetase from the archaeon Archaeoglobus fulgidus, the N-terminal fragment lacking the dimerization domain and the C-terminal dimerization-domain fragment were each overexpressed in Escherichia coli, purified and crystallized. A 3.7 A resolution data set was collected for the N-terminal fragment. The crystal belongs to the tetragonal space group P4(1) or P4(3), with unit-cell parameters a = b = 101.15, c = 124.24 A. For the C-terminal fragment, a SeMet MAD data set was collected to 3.2 A resolution. The crystal belongs to the orthorhombic space group P222(1), with unit-cell parameters a = 124.15, b = 131.91, c = 138.68 A.
ChemInform Abstract: COUPLING REACTIONS OF THE TETRANUCLEAR RECTANGULAR CLUSTERS MO4CL8(PR3)4. PHOSPHINE LIGAND ABSTRACTION AND FORMATION OF THE CONDENSATION PRODUCTS (MO4CL8(PR3)2)X (1985)

Abstract Die l:l‐molare Umsetzung der tetrameren Cluster (I) mit Mohexacarbonyl in siedendem Chorbenzol führt unter Phosphin‐Abstraktion zu den Titelkondensationsprodukten (III).
Folding Cooperativity in RNA and DNA Is Dependent on Position in the Helix (2007)

Secondary structural motifs play essential roles in the folding and function of RNA and DNA molecules. Previous work from our lab compared the folding of small DNA and RNA hairpin loops containing a sheared GA pair [Moody, E. M., Feerar, J. C., and Bevilacqua, P. C. (2004) Biochemistry 43, 7992-7998]. We found that the small DNA hairpins fold in a highly cooperative manner with indirect coupling, while their RNA counterparts fold in a much less cooperative fashion and display direct coupling. Herein, we extend this study to the double-stranded helix. We carried out double mutant cycles on base pairs having identical nearest-neighbor contexts but located in either external or internal helical registers. In the external register, both RNA and DNA exhibit extensive folding cooperativity between the penultimate and terminal base pair, which is independent of mismatch identity. In contrast, DNA exhibits virtually no folding cooperativity in the center of the helix, while RNA maintains substantial coupling, which is dependent on mismatch identity. Two models account for these non-nearest-neighbor effects: one involves the unfavorable entropy of helix initiation common to DNA and RNA, and the other involves steric and electrostatic strain peculiar to RNA. These data show that RNA can display cooperativity less than, greater than, or equal to that of DNA depending on context and position.
Binding site number variation and high-affinity binding consensus of Myb-SANT-like transcription factor Adf-1 in Drosophilidae (2010)

There is a growing interest in the evolution of transcription factor binding sites and corresponding functional change of transcriptional regulation. In this context, we have examined the structural changes of the ADF-1 binding sites at the Adh promoters of Drosophila funebris and D. virilis. We detected an expanded footprinted region in D. funebris that contains various adjacent binding sites with different binding affinities. ADF-1 was described to direct sequence-specific DNA binding to sites consisting of the multiple trinucleotide repeat . The ADF-1 recognition sites with high binding affinity differ from this trinucleotide repeat consensus sequence and a new consensus sequence is proposed for the high-affinity ADF-1 binding sites. In vitro transcription experiments with the D. funebris and D. virilis ADF-1 binding regions revealed that stronger ADF-1 binding to the expanded D. funebris ADF-1 binding region only moderately lead to increased transcriptional activity of the Adh gene. The potential of this regional expansion is discussed in the context of different ADF-1 cellular concentrations and maintenance of the ADF-1 stimulus. Altogether, evolutionary change of ADF-1 binding regions involves both, rearrangements of complex binding site cluster and also nucleotide substitutions within sites that lead to different binding affinities.
The Influence of Increased Plasma Protein Binding on the Disposition of Quinidine in Turpentine-Treated Rats. (1993)

The effect of the increased plasma protein binding of quinidine on its disposition was investigated in turpentine-treated rats, since turpentine treatment is known to increase the plasma concentration of alpha 1-acid glycoprotein which preferentially binds basic drugs. The plasma free fraction of quinidine 16 and 48 h after turpentine treatment was decreased by 30 and 76%, respectively, compared to the control value. The treatment did not cause liver injury nor alter the hepatic blood flow. The disappearance of quinidine in plasma after an intravenous injection (3.0, 7.0, 12.5 mg/kg) was analyzed by a two-compartment open model in both control and turpentine-treated rats. The blood total body clearance (CLb) of quinidine at 48 h after the treatment was decreased by 30 to 65% in a dose-dependent manner, compared to that in control rats. The distribution volume (Vdss) of quinidine (12.5 mg/kg) at 16 and 48 h after turpentine treatment was decreased by 30 and 79%, respectively. Hepatic extraction ratio (HER) of quinidine, which was determined at steady state blood concentrations from 0.5 to 2.3 micrograms/ml, was decreased from 0.8 to 0.35 with an increase in the quinidine concentration in control rats. The HER value 48 h after turpentine treatment was consistently reduced by 15 to 40% in a concentration-dependent manner compared to the corresponding control value. These findings indicate that the increased plasma binding of quinidine caused a reduction of HER of the drug, and the reduced HER resulted in the decrease in CLb in turpentine-treated rats.(ABSTRACT TRUNCATED AT 250 WORDS)
An energy efficient Clique-based CDS discovery protocol for wireless sensor networks (2010)

Power- and location-unaware topology control protocols for wireless sensor networks (WSNs) generally conserve energy by forming node clusters using the connected dominating set (CDS) principle. CDS-based clustering allows nodes lying outside the CDS to enter the sleep mode thereby extending node and network lifetimes. In this paper, we introduce a simple, distributed and efficient graph-theoretic topology construction protocol that uses sensor cliques to discover a CDS in an energy efficient manner. Our simulation results show that the proposed protocol consistently outperforms existing solutions (Rule K, EECDS and A3) in terms of energy efficiency, message complexity and residual energy present in the CDS.
Effects of Fractionated Abdominal Irradiation on Small Intestinal Motility<i>Studies in a Novel In Vitro Animal Model</i> (1997)

Disordered small intestinal motility occurs frequently during acute radiation enteritis. However, the characteristics and time course of the motor dysfunction are poorly defined. These parameters were assessed in a novel animal model of radiation enteritis. Ileal pressures were recorded in vitro with perfused micromanometric catheter using an arterially perfused ileal loop in 22 ferrets following fractionated abdominal irradiation (9 doses 2.50 Gy thrice weekly for 3 weeks). Tissue damage was graded histologically. Studies were performed 3 to 29 days after irradiation. Tissue from 7 control animals was also studied. All treated animals developed diarrhoea. Histology showed changes consistent with mild to moderate radiation enteritis. Following irradiation, there was an initial increase in frequency followed by a non-significant reduction in the frequency, but not the amplitude of ileal pressure waves. The frequency of pressure waves showed an inverse relationship with time after radiation (r = -0.634, p < 0.002). There was no relationship between motility and histology. We conclude that abdominal irradiation is associated with a time-dependent reduction in ileal motility which does not correlate with light microscopic changes.
Chemical modification of yeast alanine transfer ribonucleic acid with a radioactive carbodiimide (1970)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTChemical modification of yeast alanine transfer ribonucleic acid with a radioactive carbodiimideSteven W. Brostoff and Vernon M. IngramCite this: Biochemistry 1970, 9, 11, 2372–2376Publication Date (Print):May 26, 1970Publication History Published online1 May 2002Published inissue 26 May 1970https://pubs.acs.org/doi/10.1021/bi00813a023https://doi.org/10.1021/bi00813a023research-articleACS PublicationsRequest reuse permissionsArticle Views70Altmetric-Citations11LEARN 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
The role of tissue plasminogen activator in methamphetamine‐related reward and sensitization (2005)

In the central nervous system, tissue plasminogen activator (tPA) plays a role in synaptic plasticity and remodeling. Our recent study has suggested that tPA participates in the rewarding effects of morphine by regulating dopamine release. In this study, we investigated the role of tPA in methamphetamine (METH)-related reward and sensitization. Repeated METH treatment dose-dependently induced tPA mRNA expression in the frontal cortex, nucleus accumbens, striatum and hippocampus, whereas single METH treatment did not affect tPA mRNA expression in these brain areas. The METH-induced increase in tPA mRNA expression in the nucleus accumbens was completely inhibited by pre-treatment with R(+)-SCH23390 and raclopride, dopamine D1 and D2 receptor antagonists, respectively. In addition, repeated METH treatment increased tPA activity in the nucleus accumbens. There was no difference in METH-induced hyperlocomotion between wild-type and tPA-deficient (tPA-/-) mice. On the other hand, METH-induced conditioned place preference and behavioral sensitization after repeated METH treatment were significantly reduced in tPA-/- mice compared with wild-type mice. The defect of behavioral sensitization in tPA-/- mice was reversed by microinjections of exogenous tPA into the nucleus accumbens. Our findings suggest that tPA is involved in the rewarding effects as well as the sensitization of the locomotor-stimulating effect of METH.
Hoch enantioselektive Synthese von α‐Aminosäurederivaten durch NHC‐katalysierte intermolekulare Stetter‐Reaktion (2011)

PROTONtyp! Eine NHC-katalysierte (NHC=N-heterocyclisches Carben), hoch enantioselektive intermolekulare Stetter-Reaktion mit einer stereoselektiven intramolekularen Protonierung im entscheidenden Schritt liefert auf effiziente und atomökonomische Weise Aminosäurederivate (siehe Schema). Erstmals wurde ein in β-Position nicht substituierter Michael-Akzeptor in einer solchen Reaktion eingesetzt, und zwar mit einer großen Substratbreite an Aldehyden. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by 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.
Activated adsorption of hydrogen on nickel catalysts (1951)

Abstract The chemisorption of hydrogen on a Ni‐catalyst obtained by coprecipitation from Ni(NO 3 ) 2 , Na 2 CO 3 ‐ and Na silicate solutions at 80° C and containing Ni and SiO 2 in the ratio 3 Ni‐1 SiO 2 was investigated. In agreement with other investigations it was found that the adsorption consists of a very rapid process followed by a much slower one, the latter increasing in velocity with increasing temperature. The transition between the two is not sharp but gradual. However, some distinction may be made by observing the amounts of hydrogen adsorbed at liquid nitrogen temperatures and very low pressure (type I) and the amounts which can be adsorbed in excess of this quantity (type II). It was found that a more thorough reduction of the catalyst resulted in an increase of the type I adsorption at the cost of type II. Adsorption of oxygen on a well‐reduced catalyst on the contrary decreased the type I and increased the type II adsorption, the change being linear with the amount of oxygen adsorbed. Oxygen adsorption can occur in two different manners. It is assumed that depending on the conditons one adsorption site can be occupied by either an oxygen atom or an oxygen molecule. Heating of a reduced catalyst in an inert atmosphere or under vacuum tends to eliminate the type I adsorption while also the total adsorption diminishes. It is suggested here that a reoxidation of the surface occurs (combined with some sintering). Two causes for this reoxydation are considered: diffusion of oxygen in the interior of the metal—metaloxide structure to the surface liberation of water vapour by the silica carrier followed by the reaction Ni + H 2 O → NiO + H 2 .
1-Formylpiperazine and Related Compounds (1955)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT1-Formylpiperazine and Related CompoundsBruce W. Horrom, Morris Freifelder, and George R. StoneCite this: J. Am. Chem. Soc. 1955, 77, 3, 753–754Publication Date (Print):February 1, 1955Publication History Published online1 May 2002Published inissue 1 February 1955https://pubs.acs.org/doi/10.1021/ja01608a061https://doi.org/10.1021/ja01608a061research-articleACS PublicationsRequest reuse permissionsArticle Views256Altmetric-Citations10LEARN 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
REMARKABLE INHIBITION OF OXYGEN QUENCHING OF PHOSPHORESCENCE BY COMPLEXATION WITH CYCLODEXTRINS (1983)

Abstract The phosphorescence of the 4‐bromo‐l‐naphthoyl group is readily quenched by molecular oxygen in homogeneous solvents. However, when this lumophore is complexed with γ‐cyclodextrin in aqueous solution at room temperature, its phosphorescence is observed even under 1 atm of oxygen! Phosphorescence decay data indicated that two types of probe/cyclodcxtrin complexes are formed with lifetimes of 600 u,s and 3.5 ms. Oxygen completely quenches the fast decay, but only partially quenches the slow decay.
THE RELATIONSHIP BETWEEN METEOROLOGICAL FACTORS AND PAVEMENT TEMPERATURE (1973)

The boundary condition for calculation of frost penetration is discussed. The heat flow in and out of a pavement subgrade can be calculated in 2 ways: the heat flow through the surface of a pavement can be calculated by studying the total heat balance at the surface; if the surface temperature is known, the temperature gradient for the materials beneath the surface can be studied. Thus the heat flow into and out of the surface can be calculated on the basis of the thermal conductivity, the thermal capacity and the temperature gradient. The analysis of the heat balance at the pavement surface is considered in detail. The different factors involved in the heat balance are illustrated in a figure. Radiation is the most importance factor. The calculation is described of the heat flow in and out of a pavement surface. At the test road considered here, the pavement surface temperature was calculated on the basis of recorded temperatures very close to the surface. This temperature is an important controlling factor for the conduction of heat into and out of the pavement structure and its subgrade. A graph illustrates a method of correcting recorded air temperatures for use in estimating surface pavement temperature for years with cold winters. A multiple regression analysis is used to find a correlation between the pavement temperature and standard meteorological observations. Regression coefficients are tabulated which were evaluated for the test road (which had no special insulating layers and had a bituminous concrete surfacing). This could lead to a reliable basis for the calculation of the depth of freezing.
Photographic Essays (2006)

Herein a clinical case of an unusual metastasis from breast cancer to the retina and vitreous confirmed by diagnostic vitrectomy is described. Further investigation also demonstrated the central nervous system metastasis.
Site of binding of mouse IgG2b to the Fc receptor on mouse macrophages. (1979)

Three mouse immunoglobulins with altered heavy chains have been used to study the specificity of the mouse IgG2b Fc receptor on mouse macrophages. These immunoglobulins were synthesized by variant clones derived from the MPC 11, IgG2b-producing mouse myeloma cell line. One variant, whose Fc receptor. A second variant, which makes a short heavy chain lacking the CH3 domain, binds specifically to the IgG2b Fc receptor. The third variant makes a hybrid IgG2b-IgG2a heavy chain whose CH3 domain is enterely IgG2a-like and binds to both IgG2a and IgG2b Fc receptors. These data suggest that the binding of mouse IgG2b immunoglobulins to the mouse macrophage Fc receptor involves a site within the CH2 domain and indicate that immunoglobulins with altered heavy chains are a useful tool to probe Fc receptors.