gebhart/patrepeval huggingface dataset:
Discovery, Biosynthesis, and Engineering of Lantipeptides (2012)

Aided by genome-mining strategies, knowledge of the prevalence and diversity of ribosomally synthesized natural products (RNPs) is rapidly increasing. Among these are the lantipeptides, posttranslationally modified peptides containing characteristic thioether cross-links imperative for bioactivity and stability. Though this family was once thought to be a limited class of antimicrobial compounds produced by gram-positive bacteria, new insights have revealed a much larger diversity of activity, structure, biosynthetic machinery, and producing organisms than previously appreciated. Detailed investigation of the enzymes responsible for installing the posttranslational modifications has resulted in improved in vivo and in vitro engineering systems focusing on enhancement of the therapeutic potential of these compounds. Although dozens of new lantipeptides have been isolated in recent years, bioinformatic analyses indicate that many hundreds more await discovery owing to the widespread frequency of lantipeptide biosynthetic machinery in bacterial genomes.
THE NATURE OF FATTY ACIDS AND CAPSANTHIN ESTERS IN PAPRIKA (1971)

SUMMARY– The triglycerides present in whole ground paprika and paprika pods were extracted and hydrolyzed. The fatty acids were methylated, separated by gas chromatography and identified by mass spectrometry. The whole paprika and pods, respectively, contained approximately 66 and 45% linoleic acid, 14 and 19% palmitic acid, 12 and 14% oleic acid and 5 and 17% linolenic acid. Small quantities of myristic and lauric acids and traces of capric, stearic and palmitoleic acids also were present. Capsanthin, which amounted to 35% of the total carotenoids, occurred as the dilaurate ester. It was isolated from paprika by thin‐layer chromatography after interesterification of the triglycerides. Capsanthin dilaurate, synthesized in the laboratory, gave identical R f value and infrared and visible spectra to those of the naturally occurring compounds.
&lt;title&gt;Color correction using principle components&lt;/title&gt; (1991)

White point mapping color correction is compared to a method which performs color correction using knowledge of the spectral reflectance distribution in the image. The methods are compared using chromaticity plots and the CIE L*a*b* (Delta) E measurement.
Larval zebrafish as a model for glucose metabolism: expression of phosphoenolpyruvate carboxykinase as a marker for exposure to anti-diabetic compounds (2007)

The zebrafish model system is one of the most widely used animal models for developmental research and it is now becoming an attractive model for drug discovery and toxicological screening. The completion of sequencing the zebrafish genome and the availability of full-length cDNAs and DNA microarrays for expression analysis, in addition to techniques for generating transgenic lines and targeted mutations, have made the zebrafish model even more attractive to researchers. Recent data indicate that the regulation of glucose metabolism in zebrafish, through the production of insulin, is similar to mammalian models, and many of the genes involved in regulating blood glucose levels have been identified in zebrafish. The data presented here show that adult zebrafish respond to anti-diabetic drugs similarly to mammalian models, by reducing blood glucose levels. Furthermore, we show that the expression of phosphoenolpyruvate carboxykinase (PEPCK), which catalyzes a rate-limiting step in gluconeogenesis and is transcriptionally regulated by glucagon and insulin, is regulated in larval zebrafish similarly to that seen in mammalian systems, and changes in PEPCK expression can be obtained through real-time PCR analysis of whole larval RNA. Taken together, these data suggest that larval zebrafish may be an appropriate model for the examination of glucose metabolism, using PEPCK as an indicator of blood glucose levels.
Negative Regulation of Transactivation Function but Not DNA Binding of NF-κB and AP-1 by IκBβ1 in Breast Cancer Cells (1999)

The transcription factor NF-kappaB regulates the expression of genes involved in cancer cell invasion, metastasis, angiogenesis, and resistance to chemotherapy. In normal cells NF-kappaB is maintained in the cytoplasm by protein-protein interaction with inhibitor IkappaBs. In contrast, in cancer cells a substantial amount of NF-kappaB is in the nucleus and constitutively activates target genes. To understand the mechanisms of constitutive NF-kappaB activation, we have analyzed the function of IkappaBalpha and IkappaBbeta in breast cancer cells. In most cases, constitutive NF-kappaB DNA binding correlated with reduced levels of either IkappaBalpha or IkappaBbeta isoforms. Overexpression of IkappaBalpha but not IkappaBbeta1 resulted in reduced constitutive DNA binding of NF-kappaB in MDA-MB-231 cells. Unexpectedly, IkappaBbeta1 overexpression moderately increased 12-O-tetradecanoylphorbol-13-acetate- and interleukin-1-inducible NF-kappaB DNA binding. 12-O-Tetradecanoylphorbol-13-acetate- and interleukin-1-induced transactivation by NF-kappaB, however, was lower in IkappaBbeta1-overexpressing cells. Mutants of IkappaBbeta1 lacking the C-terminal casein kinase II phosphorylation sites, which form a stable complex with DNA bound NF-kappaB without inhibiting its transactivation in other cell types, repressed the transactivation by NF-kappaB in MDA-MB-231 cells. Consistent with the results of transient transfections, the expression of urokinase plasminogen activator, an NF-kappaB target gene, was reduced in IkappaBbeta1-overexpressing cells. These results suggest that depending on the cell type, IkappaBbeta1 represses the expression of NF-kappaB-regulated genes by inhibiting either DNA binding or transactivation function of NF-kappaB.
Atom optics with microfabricated optical elements (2001)

We introduce a new direction in the field of atom optics, atom interferometry, and neutral-atom quantum information processing. It is based on the use of microfabricated optical elements. With these elements versatile and integrated atom optical devices can be created in a compact fashion. This approach opens the possibility to scale, parallelize, and miniaturize atom optics for new investigations in fundamental research and application. It will lead to new, compact sources of ultracold atoms, compact sensors based on matter wave interference and new approaches towards quantum computing with neutral atoms. The exploitation of the unique features of the quantum mechanical behavior of matter waves and the capabilities of powerful state-of-the-art micro- and nanofabrication techniques lend this approach a special attraction.
Ghrelin elicits a marked stimulatory effect on GH secretion in freely-moving rats (2000)

Ghrelin is a growth hormone-releasing acylated peptide from stomach. The purified peptide consist of 28 amino acids in which the serine 3 residue is n-octanoylated. Ghrelin has been reported to increase in vitro GH secretion as well as in vivo plasma GH levels in pentobarbital anaesthetized rats. The aim of this work was to characterize the stimulatory effect of Ghrelin on in vivo GH secretion in freely-moving rats. Furthermore, we compare the effect of Ghrelin with GHRH. In addition to vehicle, we administered different doses of Ghrelin (3 nmol/Kg, 12 nmol/Kg and 60 nmol/Kg); GHRH (3 nmol/Kg and 12 nmol/kg). Plasma GH levels were measured in blood samples taken at 5, 10, 15, 20, 30 and 45 min after their administration as an i.v. bolus at 0 min. Administration of Ghrelin led to an increase in plasma GH levels at all time-points tested (5, 10, 15, 20 and 30 min, P<0.01; and 45 min, P<0.05) in comparison to control untreated rats. A maximal stimulatory effect on plasma GH was observed following administration of 12 nmol/Kg of Ghrelin, the effect being similar to the one obtained with 60 nmol/Kg in terms of both AUC and mean peak GH levels. At the dose of 3 nmol/Kg GHRH and Ghrelin exhibited a similar stimulatory effect in term of both, AUC and mean peak GH levels. However following administration of a dose of 12 nmol/Kg, the effect of Ghrelin was much greater than the same dose of GHRH in terms of both AUC and mean peak GH levels. In summary, this study provides the first evidences that Ghrelin exert a marked stimulatory effect in plasma GH levels in freely-moving rats and provides further evidences that Ghrelin may play an important role in the physiological control of GH secretion.
Scanning Mutagenesis Identifies Amino Acid Residues Essential for the <i>in Vivo</i> Activity of the <i>Escherichia coli</i> DnaJ (Hsp40) J-Domain (2002)

The DnaJ (Hsp40) cochaperone regulates the DnaK (Hsp70) chaperone by accelerating ATP hydrolysis in a cycle closely linked to substrate binding and release. The J-domain, the signature motif of the Hsp40 family, orchestrates interaction with the DnaK ATPase domain. We studied the J-domain by creating 42 mutant E. coli DnaJ variants and examining their phenotypes in various separate in vivo assays, namely, bacterial growth at low and high temperatures, motility, and propagation of bacteriophage lambda. Most mutants studied behaved like wild type in all assays. In addition to the (33)HisProAsp(35) (HPD) tripeptide found in all known functional J-domains, our study uncovered three new single substitution mutations (Y25A, K26A, and F47A) that totally abolish J-domain function. Furthermore, two glycine substitution mutants in an exposed flexible loop (R36G, N37G) showed partial loss of J-domain function alone and complete loss of function as a triple (RNQ-GGG) mutant coupled with the phenotypically silent Q38G. Interestingly, all the essential residues map to a small region on the same solvent-exposed face of the J-domain. Engineered mutations in the corresponding residues of the human Hdj1 J-domain grafted in E. coli DnaJ also resulted in loss of function, suggesting an evolutionarily conserved interaction surface. We propose that these clustered residues impart critical sequence determinants necessary for J-domain catalytic activity and reversible contact interface with the DnaK ATPase domain.
A charge pump with reduced current variation and mismatch in low-voltage low-power PLLs (2013)

A charge pump with excellent current matching and negligible current variation characteristics over wide output voltage dynamic range is proposed, which is simulated in the 0.18µm standard CMOS process with the power supply 1.8V. The proposed charge pump circuit improves current matching by applying a high gain operational trans-conductance amplifier. Negligible current variation is achieved by inducing a negative feedback loop to suppress the channel modulation effect. Compared with conventional charge pump circuit, the current mismatch of the proposed charge pump circuit is less than 0.5% within the output voltage dynamic range from 0.2V to 1.7V, and the current variation is reduced to 0.8% over the output voltage dynamic range from 0.32V to 1.7V. Besides, the average power consumption of the proposed charge pump circuit is about 0.48mW making it suitable for low voltage and low power PLLs.
Catalytic Intermolecular Ortho-Arylation of Phenols (2003)

The use of rhodium catalysts such as [RhCl(PPh3)3] or [[RhCl(COD)]2] with PiPr2(OAr) or P(NMe2)3 co-catalysts allows the ortho-selective intermolecular arylation of phenols. The reaction proceeds via orthometalation of P-OAr groups and then transesterification liberates the product phenol. When 2-substituted phenols are used as substrates, [RhCl(PPh3)3]/iPr2(OAr) mixtures are typically the catalysts of choice, whereas for substrates without 2-substitution [[RhCl(COD)]2]/P(NMe2)3 mixtures tend to give better results.
Ignition of aluminum droplets behind shock waves in water (1994)

Gram quantities of molten aluminum droplets at temperatures up to 1973 K are forced to interact with water under sustained pressure pulses of up to 40.8 MPa in a hydrodynamic shock tube. Conditions are identified under which the thermal interaction (physical regime) develops into chemical ignition and total combustion events. This, and the absence of catastrophic breakup in the physical regime, raises some very interesting questions with regard to the sequence of events during large-scale aluminum–water explosions.
Isolation of a cDNA clone and localization of the human glutathione S‐transferase 3 genes to chromosome bands 11q13 and 12q13‐14 (1989)

A partial cDNA clone of the glutathione S-transferase 3 gene (GST3) was obtained by screening a lambda gt11 human lung cDNA library with antiserum to human lung GST3. The sequence of this cDNA showed two base differences from the coding sequence of a GST3 cDNA isolated from a human placental cDNA library. Hybridization of the cloned GST3 cDNA to human chromosomes resulted in a primary peak of grains over band 11q13, a localization predicted by prior experiments. An unexpected strong secondary peak of grains was obtained over bands 12q13 and 12q14, indicating that there is a GST3-like gene on the long arm of chromosome 12 in man.
Electrified droplet fission and the Rayleigh limit (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTElectrified droplet fission and the Rayleigh limitDaniel C. Taflin, Timothy L. Ward, and E. James DavisCite this: Langmuir 1989, 5, 2, 376–384Publication Date (Print):March 1, 1989Publication History Published online1 May 2002Published inissue 1 March 1989https://pubs.acs.org/doi/10.1021/la00086a016https://doi.org/10.1021/la00086a016research-articleACS PublicationsRequest reuse permissionsArticle Views3713Altmetric-Citations204LEARN 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
Enzyme immunoassay for simultaneous measurement of autoantibodies against thyroglobulin and thyroid microsome in serum. (1987)

A combined enzyme immunoassay (micro-ELISA) technique was established for measuring autoantibodies against thyroglobulin and thyroid microsome, involving the immuno-dot blot technique. Thyroglobulin and thyroid microsome antigens (1 g/L each) prepared from normal thyroids were spotted separately onto nitrocellulose membrane filter discs. Results by this method and those by immunofluorescence correlated well. The percentages of confirmed positives were 30% and 48% and the negatives were 58% and 46% (n = 50) for thyroglobulin and microsome, respectively. Testing these samples by gelatin agglutination gave a high percentage of false positives (up to 20%, n = 128) and hemagglutination testing yielded a high percentage of false negatives (up to 20%, n = 45). The titer of autoantibodies by the micro-ELISA technique was greater than by agglutination. This technique is highly specific and sensitive.
Architecting a distributed bioinformatics platform with iRODS and iPlant Agave API (2015)

Abstract Over the past few years, cloud-based platforms have been proposed to address storage, management, and computation of large-scale data, especially in the field of genomics. However, for collaboration efforts involving multiple institutes, data transfer and management, interoperability and standardization among different platforms have imposed new challenges. This paper proposes a distributed bioinformatics platform that can leverage local clusters with remote computational clusters for genomic analysis using the unified bioinformatics workflow. The platform is built with a data server configured with iRODS, a computation cluster authenticated with iPlant Agave system, and web server to interact with the platform. A Genome-Wide Association Study workflow is integrated to validate the feasibility of the proposed approach.
Digital breast tomosynthesis using an amorphous selenium flat panel detector (2005)

A prototype breast tomosynthesis system has been developed, allowing a total angular view of ±25&deg;. The detector used in this system is an amorphous selenium direct-conversion digital flat-panel detector suitable for digital tomosynthesis. The system is equipped with various readout sequences to allow the investigation of different tomosynthetic data acquisition modes. In this paper, we will present basic physical properties -- such as MTF, NPS, and DQE -- measured for the full resolution mode and a binned readout mode of the detector. From the measured projections, slices are reconstructed employing a special version of filtered backprojection algorithm. In a phantom study, we compare binned and full resolution acquisition modes with respect to image quality. Under the condition of same dose, we investigate the impact of the number of views on artifacts. Finally, we show tomosynthesis images reconstructed from first clinical data.
Analog signal processing and instrumentation (1980)

Integrated circuits have revolutionised design electronics. This new paperback edition of Professor Arbel's text for electronic systems designers treats integrated circuits as black boxes whose properties are specified by the manufacturer and shows bow to design circuits that make the best use of them. This approach enables the designer to concentrate on the best way of using the circuit modules. A most valuable feature of the book is the presence of many practical problems together with their solutions. There is also a bibliography.
Privileged Traders and Asset Market Efficiency: A Laboratory Study (1993)

The 39 experiments reported here examine the impact on trading profits and on market performance of awarding special trading privileges to some traders and not others. In call market experiments, the last-mover and orderflow access privileges are both modestly profitable and neither impairs market performance. In continuous market experiments, quicker access to orderflow information is quite profitable and more detailed access is possibly profitable; both privileges seem to enhance market performance slightly. By contrast, privileged marketmaking is extremely profitable and greatly impairs market performance.
Learning with synthesized speech for automatic emotion recognition (2010)

Data sparseness is an ever dominating problem in automatic emotion recognition. Using artificially generated speech for training or adapting models could potentially ease this: though less natural than human speech, one could synthesize the exact spoken content in different emotional nuances - of many speakers and even in different languages. To investigate chances, the phonemisation components Txt2Pho and openMary are used with Emofilt and Mbrola for emotional speech synthesis. Analysis is realized with our Munich open Emotion and Affect Recognition toolkit. As test set we gently limit to the acted Berlin and eNTERFACE databases for the moment. In the result synthesized speech can indeed be used for the recognition of human emotional speech.
Phospholipid molecular species influence crystal habits and transition sequences of metastable intermediates during cholesterol crystallization from bile salt-rich model bile. (1994)

Despite its importance in cholesterol gallstone formation, crystallization of cholesterol from bile is poorly understood, especially with respect to the influences of other biliary lipids. We reported recently (Konikoff et al. J. Clin. Invest. 1992. 90: 1155-1160) that cholesterol can crystallize from model and native biles as filamentous crystals covered by a surface layer of lecithin molecules. During growth, filamentous crystals transformed via metastable intermediates into classical plate-like cholesterol monohydrate crystals. Using the same dilute (1.2 g/dl total lipid) bile salt-rich (97.5 moles %) model bile supersaturated with cholesterol, we have studied the effects of natural egg yolk, soy bean as well as single molecular species of lecithins, other phospholipids and related lipid classes on early filamentous cholesterol crystallization, as well as transformations between crystal habits and their growth to equilibrium cholesterol monohydrate plates. After extraction and derivatization, HPLC analysis revealed that the surfaces of filamentous crystals were enriched preferentially with lecithin molecular species having longer and more saturated sn-1 and sn-2 acyl chains compared to mixed lecithin species of whole bile. In contrast, the molecular species distribution of lecithins on equilibrium plate-like crystals resembled that of whole bile. After incubation of pre-formed anhydrous cholesterol and cholesterol monohydrate crystals in cholesterol-free lipid solutions, we demonstrated that surface-adsorbed lecithins were not preferentially enriched excluding nonspecific lecithin adsorption. Time-sequences and transformations between metastable crystalline intermediates were altered markedly by specific phospholipid species: model biles composed of saturated short-chain, medium-chain, and polyunsaturated long-chain lecithins induced rapid precipitation of short filamentous crystals that became plate-like slowly by an "arborization pattern." Long-chain saturated lecithins and natural sphingomyelins retarded cholesterol crystallization markedly, and filamentous as well as metastable intermediate crystals made transient appearances only after plate-like crystals had formed. These observations suggest that phospholipid molecular species and class influence the earliest events in cholesterol crystallization from bile salt-rich model bile. Furthermore, as the molecular species of lecithins adsorbed onto filamentous cholesterol crystals were more saturated than in whole bile and essentially identical to those in biliary vesicles, this finding provides chemical evidence for a vesicular origin of the critical cholesterol nucleus.(ABSTRACT TRUNCATED AT 400 WORDS)
Ensemble-based discriminant learning with boosting for face recognition (2006)

In this paper, we propose a novel ensemble-based approach to boost performance of traditional Linear Discriminant Analysis (LDA)-based methods used in face recognition. The ensemble-based approach is based on the recently emerged technique known as "boosting". However, it is generally believed that boosting-like learning rules are not suited to a strong and stable learner such as LDA. To break the limitation, a novel weakness analysis theory is developed here. The theory attempts to boost a strong learner by increasing the diversity between the classifiers created by the learner, at the expense of decreasing their margins, so as to achieve a tradeoff suggested by recent boosting studies for a low generalization error. In addition, a novel distribution accounting for the pairwise class discriminant information is introduced for effective interaction between the booster and the LDA-based learner. The integration of all these methodologies proposed here leads to the novel ensemble-based discriminant learning approach, capable of taking advantage of both the boosting and LDA techniques. Promising experimental results obtained on various difficult face recognition scenarios demonstrate the effectiveness of the proposed approach. We believe that this work is especially beneficial in extending the boosting framework to accommodate general (strong/weak) learners.