gebhart/patrepeval huggingface dataset:
Two‐dimensional liquid chromatography‐capillary zone electrophoresis‐sheathless electrospray ionization‐mass spectrometry: Evaluation for peptide analysis and protein identification (2004)

A peptide separation strategy that combines two-dimensional (2-D) liquid chromatography (LC)-capillary zone electrophoresis (CZE) with tandem mass spectrometry (MS/MS) is described for the identification of proteins in complex mixtures. To test the effectiveness of this strategy, a serum sample was depleted of the high-abundance proteins by methanol precipitation, digested with trypsin to generate a complex peptide mixture, and separated into 96 fractions by reversed-phase (RP)-LC. Compared to ion-exchange LC separations, RPLC provides much higher resolution and peak capacity. Fractions were collected off-line from the RPLC separation, and subjected to short 20 min CZE separations. The separated zones were introduced to the mass spectrometer through a sheathless electrospray ionization interface that is integrated on the separation capillary. The ease of fabrication of the interface and its durability allowed for the analysis of all fractions on a single capillary in a relatively short analysis time. A stable electrospray was produced at nanoliter flowrates by augmenting analyte electrophoretic and electroosmotic mobilities with pressure-assisted flow. Unlike first-dimensional ion-exchange LC fractionation, where there is a large degree of overlap, the CZE-MS results show less than 15% overlap between neighboring RPLC fractions.
fAR-PLAY: A framework to develop Augmented/Alternate Reality Games (2011)

Augmented/Alternate Reality Games are a relatively new, yet increasingly interesting, class of social applications. These games are fundamentally intertwined with the players' real life, in that the players' everyday activities generate events that advance the game logic. At the same time, they augment the players' “regular” activities with game-related tasks and challenges and with rich digital content that is communicated to the players through a variety of devices, usually augmenting their mobile-device views. In our work, we have been developing a software framework, fAR-Play, to support the development of educational AARG games, in the treasure-hunt style, using space as the context for communicating information. Our toolkit extends the stereotypical notion of AARGs to include a virtual world in which the players can also interact and play. Our toolkit has been evaluated through (and has evolved based on our experience with) the development of several specific games.
Tumor Necrosis Factor-α-converting Enzyme Is Required for Cleavage of erbB4/HER4 (2000)

HER4 is a member of the epidermal growth factor receptor family and has an essential function in heart and neural development. Identification of two HER4 isoforms, HER4 JM-a and JM-b, which differ in their extracellular juxtamembrane region and in their susceptibility to cleavage after phorbol ester stimulation, showed that the juxtamembrane region of the receptor is critical for proteolysis. We now demonstrate that phorbol ester and pervanadate are effective stimuli for HER4 JM-a processing and that the HER4 JM-b isoform does not undergo cleavage in response to any of the stimuli studied. We also show that HER4 JM-a is not cleaved in cells lacking the metalloprotease tumor necrosis factor-alpha-converting enzyme (TACE) and that reexpression of TACE in these cells restores constitutive and regulated processing of HER4 JM-a. Moreover, we show that the sequence specific to the HER4 JM-a juxtamembrane region is sufficient to confer susceptibility to phorbol 12-myristate 13-acetate-induced cleavage of the HER2 receptor. In conclusion, we provide evidence that TACE is essential for the regulated shedding of the HER4 JM-a receptor.
Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information (1996)

Artificial neural networks have been combined with a rule based system to predict intron splice sites in the dicot plant Arabidopsis thaliana. A two step prediction scheme, where a global prediction of the coding potential regulates a cutoff level for a local prediction of splice sites, is refined by rules based on splice site confidence values, prediction scores, coding context and distances between potential splice sites. In this approach, the prediction of splice sites mutually affect each other in a non-local manner. The combined approach drastically reduces the large amount of false positive splice sites normally haunting splice site prediction. An analysis of the errors made by the networks in the first step of the method revealed a previously unknown feature, a frequent T-tract prolongation containing cryptic acceptor sites in the 5' end of exons. The method presented here has been compared with three other approaches, GeneFinder, Gene-Mark and Grail. Overall the method presented here is an order of magnitude better. We show that the new method is able to find a donor site in the coding sequence for the jelly fish Green Fluorescent Protein, exactly at the position that was experimentally observed in A.thaliana transformants. Predictions for alternatively spliced genes are also presented, together with examples of genes from other dicots, monocots and algae. The method has been made available through electronic mail (NetPlantGene@cbs.dtu.dk), or the WWW at http://www.cbs.dtu.dk/NetPlantGene.html
Lithography-based methods to manufacture biomaterials at small scales (2016)

Along with the search for new therapeutic agents, advanced formulation and fabrication of drug carriers are required for better targeting, sensing, and responding to environmental stimuli as well as maximizing treatment efficiency. The emergence of intelligent therapeutics involves the use of functional biomaterials to mimic biological system for prolonged circulation and to work harmoniously with the body. One of the main concerns lies in the feasibility of creating systems with well-defined architectures including size, shape, components, and functionality. This review provides an overview regarding current challenges and potential of manufacturing and fabrication of biomaterials at small scales for various biomedical applications. Accordingly, novel lithography-based fabrication approaches are introduced together with their remarkable applications. Besides being popular in microelectronics, lithography techniques have demonstrated a great potential use for drug delivery, tissue engineering, and diagnostic tools.
Synthesis of Coumarin-Appended Pyridyl Tricarbonylrhenium(I) 2,2′-Bipyridyl Complexes with Oligoether Spacer and Their Fluorescence Resonance Energy Transfer Studies (2009)

A series of rhenium(I) complexes with appended coumarin ligand has been synthesized and characterized, and their fluorescence resonance energy transfer (FRET) properties have been studied. The interaction of the complexes with metal ions was investigated by UV−vis, luminescence, and NMR spectroscopic methods. The binding of various metal ions of different sizes would cause the changes in the conformation of the molecule, leading to a change in the donor−acceptor distance and FRET efficiency.
Reserve carbohydrates metabolism in the yeastSaccharomyces cerevisiae (2001)

Glycogen and trehalose are the two glucose stores of yeast cells. The large variations in the cell content of these two compounds in response to different environmental changes indicate that their metabolism is controlled by complex regulatory systems. In this review we present information on the regulation of the activity of the enzymes implicated in the pathways of synthesis and degradation of glycogen and trehalose as well as on the transcriptional control of the genes encoding them. cAMP and the protein kinases Snf1 and Pho85 appear as major actors in this regulation. From a metabolic point of view, glucose-6-phosphate seems the major effector in the net synthesis of glycogen and trehalose. We discuss also the implication of the recently elucidated TOR-dependent nutrient signalling pathway in the control of the yeast glucose stores and its integration in growth and cell division. The unexpected roles of glycogen and trehalose found in the control of glycolytic flux, stress responses and energy stores for the budding process, demonstrate that their presence confers survival and reproductive advantages to the cell. The findings discussed provide for the first time a teleonomic value for the presence of two different glucose stores in the yeast cell.
Does Somatostatin Analogue Prevent Experimental Acute Pancreatitis? (1990)

• Because somatostatin is a potent inhibitor of pancreatic secretion, we hypothesized that pretreatment with somatostatin analogue octreotide (SMS 201-995) might prevent cerulein-induced edematous pancreatitis. We studied 18 rats prepared with jugular vein catheters. The following agents were administered intravenously to groups of four rats for 6 hours: 1 mL/h (control) crystalloid solution; 1-μg/kg bolus then 1 μg/kg per hour of octreotide; and 5 μg/kg per hour of cerulein; also, in a fourth group of six rats, octreotide and cerulein were administered simultaneously. At the end of experiments, blood was drawn for plasma amylase determinations; rats were killed and pancreata were examined. Supramaximal cerulein administration to conscious rats induced hyperamylasemia and edematous pancreatitis, confirming previous observations; in both groups of rats receiving cerulein, there was prominent interstitial edema, acinar vacuolization, and mild-to-moderate acute inflammation. While octreotide pretreatment of rats with cerulein-induced acute pancreatitis was associated with a lesser increase of wet pancreas weight and plasma amylase concentration, there was little overall benefit of octreotide pretreatment in this form of experimental acute pancreatitis. (<i>Arch Surg</i>. 1990;125:1570-1572)
ASSEMBLY OF ASPARAGINE-LINKED OLIGOSACCHARIDES (1985)

The Hippo pathway was initially discovered in Drosophila melanogaster as a key regulator of tissue growth. It is an evolutionarily conserved signaling cascade regulating numerous biological processes, including cell growth and fate decision, organ size ...Read More
General strategy for the systematic synthesis of oligosiloxanes. Silicone dendrimers (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTGeneral strategy for the systematic synthesis of oligosiloxanes. Silicone dendrimersHiroaki Uchida, Yoshio Kabe, Koji Yoshino, Akira Kawamata, Takeshi Tsumuraya, and Satoru MasamuneCite this: J. Am. Chem. Soc. 1990, 112, 19, 7077–7079Publication Date (Print):September 1, 1990Publication History Published online1 May 2002Published inissue 1 September 1990https://pubs.acs.org/doi/10.1021/ja00175a062https://doi.org/10.1021/ja00175a062research-articleACS PublicationsRequest reuse permissionsArticle Views784Altmetric-Citations167LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Fast Electrically Switchable Capillary Effects (1998)

Through the application of a potential between a water droplet on a hydrophobic coating and the underlying conductive substrate, we have shown control over the contact angle of the droplet. The same phenomenon can be used to control capillary rise of a liquid in a coated capillary over several centimeters in a short time. Interesting applications such as a temporary improvement of adhesion (drying of paint), electrical control of liquid lenses, and patternwise and dynamic filling of a capillary array are in sight.
A 19-kDa C-terminal tryptic fragment of the alpha chain of Na/K-ATPase is essential for occlusion and transport of cations. (1990)

Tryptic digestion of pig renal Na/K-ATPase in the presence of Rb and absence of Ca ions removes about half of the protein but leaves a stable 19-kDa membrane-embedded fragment derived from the alpha chain, a largely intact beta chain, and essentially normal Rb- and Na-occlusion capacity. Subsequent digestion with trypsin in the presence of Ca or absence of Rb ions leads to rapid loss of the 19-kDa fragment and a parallel loss of Rb occlusion, demonstrating that the fragment is essential for occlusion. The N-terminal sequence of the 19-kDa fragment is Asn-Pro-Lys-Thr-Asp-Lys-Leu-Val-Asn-Glu-Arg-Leu-Ile-Ser-Met-Ala, beginning at residue 830 and extending toward the C terminus. Membranes containing the 19-kDa fragment have the following functional properties. (i) ATP-dependent functions are absent. (ii) The apparent affinity for occluding Rb is unchanged, the affinity for Na is lower than in the control enzyme, and activation is now strongly sigmoidal rather than hyperbolic. (iii) Membranes containing the 19-kDa fragment can be reconstituted into phospholipid vesicles and sustain slow Rb-Rb exchange. Thus the transport pathway is retained. We conclude that cation occlusion sites and the transport pathway within transmembrane segments are quite separate from the ATP binding site, located on the cytoplasmic domain of the alpha chain. Interactions between cation and ATP sites, the heart of active transport, must be indirect--mediated, presumably, by conformational changes of the protein.
The dietary-regulated biosynthesis of high-sulphur wool proteins (1966)

1. When the diet of sheep is supplemented by the abomasal infusion of sulphur-containing amino acids or casein, a special group of proteins, with a very high content of sulphur (about 8.3%), is incorporated into the high-sulphur proteins of wool. These special proteins cannot be detected in control wool from the same sheep. 2. This is a naturally occurring process, as these special proteins are found in wool from sheep on a high level of nutrition under ordinary conditions of feeding, and in wool of an inherently high sulphur content. 3. This represents a control mechanism in protein synthesis that has not previously been observed, and may be further evidence that the high-sulphur proteins of wool are produced by an unusual synthetic route.
Preparation and antibacterial activities of new 1,2,3-diazaborine derivatives and analogs (1984)

1,2-Dihydro-1-hydroxy-2-(organosulfonyl)areno[d] [1,2,3]diazaborines 2 (arene = benzene, naphthalene, thiophene, furan, pyrrole) were synthesized by reaction of (organosulfonyl)hydrazones of arene aldehydes or ketones with tribromoborane in the presence of ferric chloride. The activities of 2 against bacteria in vitro and in vivo (Escherichia coli) were determined and structure-activity relationships are discussed. Included in this study are 2,3-dihydro-1-hydroxy-2-(p-tolylsulfonyl)-1H-2,1-benzazaborole+ ++ (3) and 1-hydroxy-1,2,3,4-tetrahydro-2-(p-tolylsulfonyl)-2,1-benzazabor ine (4) as well as the carbacyclic benzodiazaborine analogue 4-hydroxy-3-(p-tolylsulfonyl)isoquinoline (7). The nature of the active species is briefly discussed.
Applications of Combinatorial Technologies to Drug Discovery. 2. Combinatorial Organic Synthesis, Library Screening Strategies, and Future Directions (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTApplications of Combinatorial Technologies to Drug Discovery. 2. Combinatorial Organic Synthesis, Library Screening Strategies, and Future DirectionsEric M. Gordon, Ronald W. Barrett, William J. Dower, Stephen P. A. Fodor, and Mark A. GallopCite this: J. Med. Chem. 1994, 37, 10, 1385–1401Publication Date (Print):May 1, 1994Publication History Published online1 May 2002Published inissue 1 May 1994https://pubs.acs.org/doi/10.1021/jm00036a001https://doi.org/10.1021/jm00036a001research-articleACS PublicationsRequest reuse permissionsArticle Views3199Altmetric-Citations953LEARN 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 Chemical Probe for the ATAD2 Bromodomain (2016)

ATAD2 is a cancer-associated protein whose bromodomain has been described as among the least druggable of that target class. Starting from a potent lead, permeability and selectivity were improved through a dual approach: 1) using CF2 as a sulfone bio-isostere to exploit the unique properties of fluorine, and 2) using 1,3-interactions to control the conformation of a piperidine ring. This resulted in the first reported low-nanomolar, selective and cell permeable chemical probe for ATAD2.
Global and local document degradation models (2002)

Two sources of document degradation are modeled: i) perspective distortion that occurs while photocopying or scanning thick, bound documents, and ii) degradation due to perturbations in the optical scanning and digitization process: speckle, blurr, jitter, thresholding. Perspective distortion is modeled by studying the underlying perspective geometry of the optical system of photocopiers and scanners. An illumination model is described to account for the nonlinear intensity change occuring across a page in a perspective-distorted document. The optical distortion process is modeled morphologically. First, a distance transform on the foreground is performed, followed by a random inversion of binary pixels where the probability of flip is a function of the distance of the pixel to the boundary of the foreground. Correlating the flipped pixels is modeled by a morphological closing operation.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Substrate and sequential site specificity of cytoplasmic histone acetyltransferases of maize and rat liver (1998)

The cytoplasmic B-type histone acetyltransferase was purified to apparent homogeneity from maize embryos. We established a novel protocol for easy large-scale preparation of acetylated core histone species, using preparative acetic acid-urea-Triton PAGE. The pure maize histone acetyltransferase B was highly specific for histone H4 under various assay conditions, modifying H4 up to the di-acetylated isoform. Only non-acetylated H4 isoform was accepted as substrate, whereas mono-acetylated H4 could not be further acetylated. The enzyme selectively acetylated lysines 12 and 5 in a sequential manner. The same results were obtained with a partially purified cytoplasmic histone acetyltransferase of rat liver. Protein sequencing results were supported by immunological characterization of acetylated H4 subspecies with site-specific H4-acetyllysine antibodies.
Further Studies on Motor and Sensory Nerve Regeneration in Mice With Delayed Wallerian Degeneration (1994)

The axons of both peripheral and central neurons in C57BL/Wlds (C57BL/Ola) mice are unique among mammals in degenerating extremely slowly after axotomy. Motor and sensory axons attempting to regenerate are thus confronted with an intact distal nerve stump rather than axon- and myelin-free Schwann cell-filled endoneurial tubes. Surprisingly, however, motor axons in the sciatic nerve innervating the soleus muscle regenerate rapidly, and there is evidence that they may use Schwann cells associated with unmyelinated fibres as a pathway. If this is so, motor axon regeneration might be impaired in C57BL/Wlds mice in the phrenic nerve, which has very few unmyelinated fibres. We found that as long as the myelinated axons in the distal stump of the phrenic nerve remained intact (up to 10 days), regeneration of motor axons did not occur, in spite of vigorous production of sprouts at the crush site. In contrast to motor axons, myelinated sensory axons regenerate very poorly in C57BL/Wlds mice, even in the presence of unmyelinated axons. We showed that this was also due to adverse local conditions confronting nerve sprouts, for the dorsal root ganglion cell bodies responded normally to injury with a rapid induction of Jun protein-like immunoreactivity and when the saphenous nerve was forced to degenerate more rapidly by multiple crush lesions sensory axons regrew much more successfully. The findings show that motor and sensory axons in C57BL/Wlds mice, although very atypical in the way that they degenerate, are able to regenerate normally but only in an appropriate environment.(ABSTRACT TRUNCATED AT 250 WORDS)
Space, Stars, C 60 , and Soot (1988)

Although carbon has been subjected to far more study than all other elements put together, the buckminsterfullerene hollow-cage structure, recently proposed to account for the exceptional stability of the C(60) cluster, has shed a totally new and revealing light on several important aspects of carbon's chemical and physical properties that were quite unsuspected and others that were not previously well understood. Most significant is the discovery that C(60) appears to form spontaneously, and this has particularly important implications for particle formation in combustion and in space as well as for the chemistry of polyaromatic compounds. The intriguing revelation that 12 pentagonal "defects" convert a planar hexagonal array of any size into a quasi-icosahedral cage explains why some intrinsically planar materials form quasi-crystalline particles, as appears to occur in the case of soot. Although the novel structural proposal has still to be unequivocally confirmed, this article pays particular attention to the way in which it provides convincing explanations of puzzling observations in several fields, so lending credence to the structure proposed for C(60).
Clinical Evaluation of the Delivery and Safety of Aerosolized Liposomal 9-Nitro-20(S)-Camptothecin in Patients with Advanced Pulmonary Malignancies (2004)

Aerosol administration of liposomal 9NC was found to be feasible and safe. 9NC delivered as an aerosol was detected in patient's plasma shortly after the start of treatment. The recommended dose for Phase II studies is 13.3 micro g/kg/day (equivalent to 0.5 mg/m(2)/day), which constitutes two consecutive 30-min nebulizations/day from a nebulizer reservoir with 4 mg of 9NC in 10 ml of sterile water, Monday to Friday for 8 weeks every 10 weeks.