gebhart/patrepeval huggingface dataset:
The Hotdog Thioesterase EntH (YbdB) Plays a Role In Vivo in Optimal Enterobactin Biosynthesis by Interacting with the ArCP Domain of EntB (2007)

In response to iron limitation, the siderophore enterobactin is synthesized and secreted by Escherichia coli. Its biosynthesis is performed by a series of enzymes encoded by the Ent gene cluster. Among the genes of this cluster, ybdB has not been implicated in enterobactin production to date. We demonstrate here an in vivo role for the hotdog protein EntH (YbdB) in the optimal production of enterobactin. Indeed, we showed that EntH is a thioesterase specifically produced under iron limitation conditions. Furthermore, EntH interacts specifically with the aryl carrier protein (ArCP) domain of EntB, a crucial bifunctional enzyme of the enterobactin biosynthesis pathway and a potential target of EntH thioesterase activity. A strain devoid of EntH is impaired for growth under iron limitation associated with the presence of the salicylate inhibitor, correlating with the diminution of enterobactin production under these conditions. Normal growth and enterobactin production are restored upon expression of entH in trans. Inversely, unnecessary overproduction of EntH provokes a fall of the quantity of siderophore produced under iron starvation conditions. Our findings point to a proofreading role for EntH during biosynthesis of enterobactin in vivo. EntH thioesterase activity could be required for cleaving wrongly charged molecules on the carrier protein EntB. This is the first description of such a role in the optimization of a nonribosomal biosynthesis pathway for a protein of the hotdog superfamily.
Primer-design for multiplexed genotyping (2003)

Single-nucleotide polymorphism (SNP) analysis is a powerful tool for mapping and diagnosing disease-related alleles. Mutation analysis by polymerase-mediated single-base primer extension (minisequencing) can be massively parallelized using DNA microchips or flow cytometry with microspheres as solid support. By adding a unique oligonucleotide tag to the 5' end of the minisequencing primer and attaching the complementary antitag to the array or bead surface, the assay can be 'demultiplexed'. Such high-throughput scoring of SNPs requires a high level of primer multiplexing in order to analyze multiple loci in one assay, thus enabling inexpensive and fast polymorphism scoring. We present a computer program to automate the design process for the assay. Oligonucleotide primers for the reaction are automatically selected by the software, a unique DNA tag/antitag system is generated, and the pairing of primers and DNA tags is automatically done in a way to avoid any crossreactivity. We report results on a 45-plex genotyping assay, indicating that minisequencing can be adapted to be a powerful tool for high-throughput, massively parallel genotyping. The software is available to academic users on request.
Retinal Vascular Layers Imaged by Fluorescein Angiography and Optical Coherence Tomography Angiography (2014)

Fluorescein angiography does not image the radial peripapillary or the deep capillary networks well. However, OCT angiography can image all layers of the retinal vasculature without dye injection. Therefore, OCT angiography, and the findings generated, have the potential to affect clinical evaluation of the retina in healthy patients and patients with disease.
Ibuprofen and Alzheimer's disease. (2004)

There is epidemiological observation that long-term treatment of patients suffering from rheumatoid arthritis with ibuprofen results in reduced risk and delayed onset of Alzheimer's disease (AD). Chronic central nervous system inflammation in AD brain is implicated in the pathology, but how ibuprofen impacts the pathogenic AD pathways is unclear. Ibuprofen, a commonly used over-the-counter nonsteroidal anti-inflammatory drug (NSAID) that is a cyclooxygenase (COX)-1 and COX-2 inhibitor as well as a peroxisome proliferator-activated receptor (PPAR) agonist, decreases the production of nitric oxide (NO), protects neurons against glutamate toxicity and decreases the production of proinflammatory cytokines. Ibuprofen crosses the blood brain barrier and suppresses neuritic plaque pathology and inflammation in AD brain. Furthermore, ibuprofen is a potent free radical scavenger, and it could reduce lipid peroxidation and free radical generation. Because of neuroprotective activity, relative safety, and its long history of use, ibuprofen is currently being developed for clinical use in AD. Ibuprofen may be a promising new therapeutic avenue for the treatment of neurodegenerative diseases such as AD.
Inter simple sequence repeats separate efficiently hemp from marijuana (Cannabis sativa L.) (2007)

Cannabis sativa L. is a multiple-use plant that provides raw material for the production of seed oil, natural fiber for textiles, automotive and pulp industries. It has also been used in insulating boards, ropes, varnishes, animal feed, and as medicinal agents. Cannabis has potential to be used for phytoremediation: however, its cultivation is strictly controlled due to its psychoactive nature and usage in producing drugs such as marijuana, and hashish. In this study, psychoactive type Cannabis samples, which were seized from 23 different locations of Turkey, and nine hemp type Cannabis accessions, as well as an unknown accession were used. Our interest was to identify the genetic relatedness of the seized samples and to separate drug and hemp type plants. Inter Simple Sequence Repeats (ISSRs) were employed for analysis based on single plant material (SET1) and bulked samples of them (SET2). Data was analysed via cluster analysis and principal coordinate analysis (PCoA). PCoA analyses, by using SET1 and SET2, were able to efficiently discriminate the seized samples from the fiber type accessions. However, separation of the plants was not clear via unweighted pair-group method using arithmetic average (UPGMA) dendogram in SET1, while they were clearly separated in SET2. Hemp type accessions showed high levels of variation compared to drug type Cannabis both in SET1 and SET2.
The AES-CBC Cipher Algorithm and Its Use with IPsec (2003)

This document describes the use of the Advanced Encryption Standard (AES) Cipher Algorithm in Cipher Block Chaining (CBC) Mode, with an explicit Initialization Vector (IV), as a confidentiality mechanism within the context of the IPsec Encapsulating Security Payload (ESP).
Recent advances in the physiology of eating (2002)

Since the discovery of the protein product of the ob/ob gene, leptin, knowledge of the neurochemical pathways involved in the regulation of feeding has increased enormously. Our understanding of the mechanisms regulating food intake in man has also progressed greatly over a similar time span. Previous research into the regulation of food intake has largely proceeded through a reductionist approach, defining ever-smaller components of these mechanisms. This research strategy has been very productive and instructive, and has yielded a great deal of information on the specific putative components linking energy status and food intake. However, to fully understand the regulation of feeding it is important that these components are systematically reconstructed to investigate relevant interactions. In the present review recent data relating to interactions between systems proposed to be involved in feeding regulation will be highlighted. The review will be directed predominantly (but not exclusively) towards the regulation of human feeding.
Overview: Fundamentals of Controlled/Living Radical Polymerization (1998)

The fundamentals of controlled/"living" polymerization are discussed and the effects of slow initiation, transfer, termination and slow exchange on rates, molecular weights, polydispersities and end-functionalities are described. Some special features of and requirements for controlled radical polymerization are presented. Historical evolution of concepts leading to controlled radical polymerization is reviewed. Developments of several basic concepts in this field are summarized. Potential prospects for controlled radical reactions are evaluated.
Use of Carbonyl Group Addition−Elimination Reactions for Synthesis of Nucleic Acid Conjugates (2005)

This review outlines the synthesis of covalent conjugates of oligonucleotides and their analogues that are obtained by reactions of carbonyl compounds with various nucleophiles such as primary amines, N-alkoxyamines, hydrazines, and hydrazides. The products linked by imino, oxime, hydrazone, or thiazolidine groups are shown to be useful intermediates for a wide range of chemical biology applications. Methods for their preparation, isolation, purification, and analysis are highlighted, and the comparative stabilities of the respective linkages are evaluated. The relative merits of incorporation of a carbonyl group, particularly an aldehyde group, into either the oligonucleotide or the ligand parts are considered. Examples of harnessing of aldehyde-nucleophile coupling for the labeling of nucleic acids are given, as well as their conjugation to various biomolecules (e.g. peptides and small molecule ligands), site-specific cross-linking of oligonucleotides to nucleic acid-binding proteins, assembly of multibranched supramolecular structures, and immobilization on functionalized surfaces. Future perspectives of bioconjugation and complex molecular engineering via carbonyl group addition-elimination reactions in nucleic acids chemistry are discussed.
NOTES ON CELLULOSE ESTERS. (1909)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNOTES ON CELLULOSE ESTERS.R. G. Woodbridge Jr.Cite this: J. Am. Chem. Soc. 1909, 31, 9, 1067–1071Publication Date (Print):September 1, 1909Publication History Published online1 May 2002Published inissue 1 September 1909https://pubs.acs.org/doi/10.1021/ja01939a016https://doi.org/10.1021/ja01939a016research-articleACS PublicationsRequest reuse permissionsArticle Views70Altmetric-Citations4LEARN 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
Enteropathogenic Escherichia coli decreases the transepithelial electrical resistance of polarized epithelial monolayers (1993)

The mechanisms whereby enteropathogenic Escherichia coli (EPEC) causes diarrhea remain undefined. We found that EPEC caused a decrease in transepithelial electrical resistance across polarized monolayers of Caco-2 and MDCK epithelial cells. This occurred approximately 6 to 10 h after bacterial addition and was reversible if the monolayers were treated with tetracycline or gentamicin. Although significant alterations in host actin occurred beneath adherent EPEC, actin filaments supporting tight junctions were not noticeably affected in the epithelial cells, nor was the distribution of ZO-1, a tight junction protein. Despite the decrease in transepithelial electrical resistance, EPEC did not cause an increase in [3H]inulin penetration across MDCK monolayers. Unlike in the parental strain, mutations in any loci involved in adherence or formation of attaching and effacing lesions were unable to cause a decrease in transepithelial resistance. These data indicate that EPEC causes a decrease in transepithelial electrical resistance by disrupting a transcellular (intracellular) pathway rather than by disrupting intercellular tight junctions (paracellular) and that these disruptions occur only when attaching and effacing lesions are formed.
Adaptive system for processing of electrogastric signals (2003)

An adaptive system for the processing of electrogastric (EGG) signals that enhances the signals is proposed. The main disturbance, respiratory artifact, can be efficiently canceled and time variations of the gastric signal frequency can be monitored online. Results for four different positional EGG signals are presented and discussed. The algorithms used by the system are simple and easy to implement, and the system can be installed on a personal computer.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Expression of a functional influenza viral cap-recognizing protein by using a bovine papilloma virus vector. (1985)

The gene for the influenza viral PB2 protein, which recognizes and binds the 5'-terminal cap 1 structures (m7GpppNm) on eukaryotic mRNAs, was inserted into a bovine papilloma virus vector under the control of a mouse metallothionein I (MT-I) promoter. After transfection of this vector into mouse NIH 3T3 cells, a cell line, cPB2, was obtained that produces PB2-specific mRNA and authentic PB2 protein. Induction of the MT-I promoter with CdCl2 causes about a 10-fold increase in PB2 mRNA and protein levels. The expressed PB2 protein is functional, as it relieves the block in viral mRNA synthesis exhibited by a temperature-sensitive viral mutant containing a cap-binding defect in the PB2 protein. This demonstrates complementation of a function of a negative-strand RNA virus by a gene product expressed in a cell line from recombinant DNA.
Nanofiltration Membranes Based on Rigid Star Amphiphiles (2007)

Rigid star amphiphiles (RSAs) of nanoscale dimension were synthesized and used to fabricate a new generation of nanofiltration (NF) membranes. NF membranes were prepared by direct percolation of methanol solutions of the RSAs through an asymmetric polyethersulfone (PES) support film that had been previously conditioned with methanol and cross-linked polyvinyl alcohol (PES-MeOH-PVA support). The resulting RSA membranes (RSAMs) have been shown to exhibit significantly enhanced water permeability while maintaining high rejection of water contaminants compared to commercial NF membranes. The RSAMs were characterized with the goal of elucidating the structural changes brought about by deposition of RSA. Characterization techniques used included attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectrometry, field emission scanning electron microscopy (FE-SEM), atomic force microscopy (AFM), X-ray photoelectron spectroscopy (XPS), confocal microscopy, Rutherford backscattering spectrometry (RBS), and gas adsorption/desorption analyses. Results suggest that the RSAs produce a uniform, ultrathin active layer atop the PES-MeOH-PVA support after lining its nanopores with sizes similar to those of the RSAs. Such active layer constitution was found crucial for rejecting organic contaminants and achieving high water flux. These findings encourage further exploration of NF membrane preparation by molecular deposition as an attractive approach for constructing ultrathin membrane active layers to remove challenging contaminants with high water permeability.
Role of dendritic cells in the induction and maintenance of autoimmune diseases (1999)

Autoimmune diseases are characterised by the loss of tolerance against self-determinants, activation of autoreactive lymphocytes and pathological damage to single or multiple organs. The mechanisms by which autoimmune responses are triggered and activation of autoreactive lymphocytes is initiated and maintained are not yet fully understood. Translocation of previously immunologically ignored antigens from the periphery to secondary lymphoid organs is probably a key step in the initiation of autoimmunity. Antigen transport and primary sensitisation of T lymphocytes is mainly mediated by dendritic cells which reside in peripheral non-lymphoid tissues and maintain a continuous gradient of antigens towards secondary lymphoid tissues. In the transgenic rat insulin promoter-glycoprotein model of autoimmune diabetes, dendritic cell (DC)-mediated antigen transport initiates an autoimmune response against a pancreatic neoself-antigen. Dose and timing of antigen delivery by DC and turnover of antigenic peptides presented by DC are the main parameters regulating the outcome of autoimmune diabetes in this model system. An important sequel of continued antigenic stimulation via DC is the formation of lymphoid structures in the pancreas. Thus, appropriate and repeated activation of cytotoxic T lymphocytes by DC, in concert with local inflammatory processes leading to formation of organised lymphoid tissue in the target organ, is likely to be crucial in the development of destructive autoimmunity. Therapeutic intervention to selectively manipulate antigen transport by dendritic cells or to influence antigen presentation may prove beneficial for the treatment of autoimmune diseases. Furthermore, the capacity of DC to induce potent antiself responses might have implications for the use of DC presenting self-antigens in treatment of established tumours.
Storing red blood cells with vitamin C and N-acetylcysteine prevents oxidative stress-related lesions: a metabolomics overview. (2014)

Anti-oxidants improved storage quality by coping with oxidative stress at the expense of glycolytic metabolism, although reservoirs of high energy phosphate compounds were preserved by reduced cyclic AMP-mediated release of ATP.
Integration of Cell Membranes and Nanotube Transistors (2005)

We report the integration of a complex biological system and a nanoelectronic device, demonstrating that both components retain their functionality while interacting with each other. As the biological system, we use the cell membrane of Halobacterium salinarum. As the nanoelectronic device, we use a nanotube network transistor, which incorporates many individual nanotubes in such a way that entire patches of cell membrane are contacted by nanotubes. We demonstrate that the biophysical properties of the membrane are preserved, that the nanoelectronic devices still function as transistors, and that the two systems interact. Further, we use the interaction to study the charge distribution in the biological system, finding that the electric dipole of the membrane protein bacteriorhodopsin is located 2/3 of the way from the extracellular to the cytoplasmic side.
The Role of Confucian Concepts in Adolescent International Students’ Learning Motivation and Life Aspirations (2012)

The editorial board announced that this article has been retracted on July 30, 2013. If you have any further question, please contact us at: ass@ccsenet.org
Iron Porphyrin Catalyzed N−H Insertion Reactions with Ethyl Diazoacetate (2007)

A series of metalloporphyrin complexes were surveyed as catalysts for carbene insertion from ethyl diazoacetate into the N−H bonds of amines. Iron(III) tetraphenylporphyrin chloride, Fe(TPP)Cl, was found to be an efficient catalyst for N−H insertion reactions with a variety of aliphatic and aromatic amines, with yields ranging from 68 to 97%. Primary amines were able to undergo a second insertion when another equiv of EDA was added by slow addition. N-Heterocyclic compounds were poor substrates, giving low yields or no N−H insertion products. Competition reactions and linear free energy relationships provided mechanistic insights for the insertion reaction. The relative rates for N−H insertion into para-substituted aniline derivatives correlated with Hammett σ+ parameters. Electron-donating groups enhanced the reaction, as indicated by the negative value of ρ (ρ = −0.66 ± 0.05, R2 = 0.93). These results are consistent with a rate-determining nucleophilic attack of the amine on an iron carbene complex. In addition, the decomposition of EDA catalyzed by FeII(TPP) or FeIII(TPP)Cl was examined with various amounts of added pyridine. The Fe(II) catalyst is strongly inhibited by the presence of pyridine. In contrast, catalysis by the Fe(III) porphyrin is accelerated by amines. These experiments suggested that an iron(III) porphyrin carbene complex is the active catalyst.
Chemical properties of water-soluble porphyrins. 2. The reaction of iron(III) tetrakis(4-N-methylpyridyl)porphyrin with the superoxide radical dioxygen couple (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTChemical properties of water-soluble porphyrins. 2. The reaction of iron(III) tetrakis(4-N-methylpyridyl)porphyrin with the superoxide radical dioxygen coupleD. Solomon, P. Peretz, and M. FaraggiCite this: J. Phys. Chem. 1982, 86, 10, 1842–1849Publication Date (Print):May 1, 1982Publication History Published online1 May 2002Published inissue 1 May 1982https://doi.org/10.1021/j100207a021RIGHTS & PERMISSIONSArticle Views173Altmetric-Citations51LEARN 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 InReddit PDF (991 KB) Get e-Alerts
Connectionist speaker normalization and adaptation (1995)

In a speaker-independent, large-vocabulary continuous speech recognition systems, recognition accuracy varies considerably from speaker to speaker, and performance may be significantly degraded for outlier speakers such as nonnative talkers. In this paper, we explore supervised speaker adaptation and normalization in the MLP component of a hybrid hidden Markov model/ multilayer perceptron version of SRI's DECIPHERTM speech recognition system. Normalization is implemented through an additional transformation network that preprocesses the cepstral input to the MLP. Adaptation is accomplished through incremental retraining of the MLP weights on adaptation data. Our approach combines both adaptation and normalization in a single, consistent manner, works with limited adaptation data, and is text-independent. We show significant improvement in recognition accuracy.