gebhart/patrepeval huggingface dataset:
Family pairwise search with embedded motif models. (1999)

Abstract MOTIVATION: Statistical models of protein families, such as position-specific scoring matrices, profiles and hidden Markov models, have been used effectively to find remote homologs when given a set of known protein family members. Unfortunately, training these models typically requires a relatively large set of training sequences. Recent work (Grundy, J. Comput. Biol., 5,&amp;lt;479-492, 1998) has shown that, when only a few family members are known, several theoretically justified statistical modeling techniques fail to provide homology detection performance on a par with Family Pairwise Search (FPS), an algorithm that combines scores from a pairwise sequence similarity algorithm such as BLAST. RESULTS: The present paper provides a model-based algorithm that improves FPS by incorporating hybrid motif-based models of the form generated by Cobbler (Henikoff and Henikoff, Protein Sci., 6, 698-705, 1997). For the 73 protein families investigated here, this cobbled FPS algorithm provides better homology detection performance than either Cobbler or FPS alone. This improvement is maintained when BLAST is replaced with the full Smith-Waterman algorithm. AVAILABILITY: http://fps.sdsc.edu
Synthesis and antiviral activity of monofluoro and difluoro analogs of pyrimidine deoxyribonucleosides against human immunodeficiency virus (HIV-1) (1990)

A range of 2'-fluoro and 2',3'-difluoro analogues of pyrimidine deoxyribonucleosides have been synthesized and evaluated against human immunodeficiency virus (HIV-1) in a human lymphoblastoid cell line. Among these compounds, 1-(2,3-dideoxy-2-fluoro-beta-D-threopentofuranosyl)cytosine (12), 2',3'-didehydro-2',3'-dideoxy-2'-fluorocytidine (35), 1-(2,3-dideoxy-2,3-difluoro-beta-D-arabinofuranosyl)cytosine (41), and 3'-deoxy-2',3'-didehydro-2'-fluorothymidine (45) were found to have significant antiviral activity, with IC50 values of 0.65, 10, 10, and 100 microM, respectively. The structure-activity relationships are discussed.
<title>Self-assembled flexible electrodes on electroactive polymer actuators</title> (1999)

Thin film metal/polymer composite electrodes with electrical conductivities on the order of those of bulk metals have been formed on electroactive polymer actuator elements using a novel self-assembly technique. The electrodes exhibit good flexibility and mechanical performance.
Sol-gel Encapsulation of Biomolecules and Cells for Medicinal Applications (2015)

The sol-gel process provides a robust and versatile technology for the immobilization of biologicals. A wide range of inorganic, composites and hybrid materials can be prepared to encapsulate molecular drugs, proteins, antibodies/antigens, enzymes, nucleic acids, prokaryotic and eukaryotic cells into bulk gels, particles and films. This review describes the applications of sol-gel encapsulation relevant to medicinal chemistry focusing on the recent development of biosensors as well as systems for production, screening and delivery of bioactive compounds and biomaterials.
Toll-like receptor family and signalling pathway (2000)

Toll is a Drosophila gene essential for ontogenesis and anti-microbial resistance. Several orthologues of Toll have been identified and cloned in vertebrates, namely Toll-like receptors (TLRs). Human TLRs are a growing family of molecules involved in innate immunity. TLRs are characterized structurally by a cytoplasmic Toll/interleukin-1 receptor (TIR) domain and by extracellular leucine-rich repeats. TLRs characterized so far activate the MyD88/interleukin-1 receptor-associated kinase (IRAK) signalling pathway. Genetic, gene-transfer and dominant-negative approaches have involved TLR family members (TLR2 and TLR4) in Gram-positive and Gram-negative bacteria recognition and signalling. Accumulating evidence suggests that TLR2 is also involved in signalling-receptor complexes that recognize components of yeast and mycobacteria. However, the definitive roles of other TLRs are still lacking. A systematic approach has been used to determine whether different human leucocyte populations selectively or specifically express TLR mRNA. Based on expression pattern, TLR can be classified as ubiquitous (TLR1), restricted (TLR2, TLR4 and TLR5) and specific (TLR3). Expression and regulation of distinct but overlapping ligand-recognition patterns may underlie the existence of a large, seemingly redundant TLR family. Alternatively, the expression of a TLR in a single cell type may indicate a specific role for this molecule in a restricted setting.
Reduction of adjusting weights space dimension in feedforward artificial neural networks training (2003)

This report provides an approach to the reduction of the adjusting weights space dimension in two-layer multioutput feedforward artificial neural networks training. Our approach is based on linear-nonlinear network structure with respect to weights. Two training algorithms based on the Newton and Gauss method with pseudo-inversion for optimization were deduced. Training algorithms are extended to multilayer networks. The report carries the information about the analysis of the proposed training algorithms. Results of numerical experiments are also included.
Selective Detection of Ethylene Gas Using Carbon Nanotube‐based Devices: Utility in Determination of Fruit Ripeness (2012)

Comparing apples and oranges: A chemoresistive sensor for ethylene can be obtained simply by mixing copper complex 1 with single-walled carbon nanotubes. The resulting devices show sub-ppm sensitivity and high selectivity towards ethylene. The utility of the sensor was demonstrated by following ripening stages in different fruits. 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.
Phase watermarking of digital images (2002)

A watermark is an invisible mark placed on an image that can be detected when the image is compared with the original. This mark is designed to identify both the source of an image as well as its intended recipient. The mark should be tolerant to reasonable quality lossy compression of the image using transform coding or vector quantization. Standard image processing operations such as low pass filtering, cropping, translation and rescaling should not remove the mark. Spread spectrum communication techniques and matrix transformations can be used together to design watermarks that are robust to tampering and are visually imperceptible. This paper discusses techniques for embedding such marks in grey scale digital images. It also proposes a novel phase based method of conveying the watermark information. In addition, the use of optimal detectors for watermark identification is also proposed.
Reaction of substituted 2-carbethoxyacetylaminopyridines and similar compounds with triethyl orthoformate and zinc chloride (1970)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTReaction of substituted 2-carbethoxyacetylaminopyridines and similar compounds with triethyl orthoformate and zinc chlorideMichael C. Seidel, Glenn C. Van Tuyle, and W. David WeirCite this: J. Org. Chem. 1970, 35, 5, 1662–1664Publication Date (Print):May 1, 1970Publication History Published online1 May 2002Published inissue 1 May 1970https://pubs.acs.org/doi/10.1021/jo00830a086https://doi.org/10.1021/jo00830a086research-articleACS PublicationsRequest reuse permissionsArticle Views221Altmetric-Citations8LEARN 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
Receiver Operating Characteristics Curves (2005)

Abstract The receiver operating characteristic (ROC) curve is the principal graphical device for signal detection theory (SDT). It is generally used when there is a right or a wrong answer and participants provide some measure of confidence in their responses. The ROC is a scatterplot between the hit rate and the false alarm rate. Exploring this space allows the researcher to consider the differential value of hits and correct rejections (or of misses and false alarms). This is where ROCs have a big advantage over the alternatives. The main alternative, logistic regression , is based on similar mathematics. Historically, SDT/ROCs assumed normal distributions, but this is very similar to the logistic distributions, and most statistical packages allow either. The choice of approach rests largely on the form of graphical communication the researcher wants to use. While logistic regression focuses on discrimination, in SDT the researcher explicitly differentiates two types of accuracy: sensitivity and specificity. The ROC curve is an excellent tool for comparing these.
Sustained Hemodynamic Efficacy of Therapy Tailored to Reduce Filling Pressures in Survivors With Advanced Heart Failure (1997)

During chronic therapy tailored to early hemodynamic response in advanced heart failure, acute vasodilator response persists, and near-normal filling pressures can be maintained in patients who survive without transplantation. Stroke volumes at low filling pressures increase further over time. Chronic hemodynamic improvement was accompanied by symptomatic improvement, but the contributions of the monitored hemodynamic approach, increased vasodilator doses, and comprehensive outpatient management have not yet been established.
Correction: Structure, function, self-assembly, and applications of bottlebrush copolymers (2015)

Correction for 'Structure, function, self-assembly, and applications of bottlebrush copolymers' by Rafael Verduzco et al., Chem. Soc. Rev., 2015, 44, 2405-2420.
Receptor-mediated endothelial cell dysfunction in diabetic vasculopathy. Soluble receptor for advanced glycation end products blocks hyperpermeability in diabetic rats. (1996)

Dysfunctional endothelium is associated with and, likely, predates clinical complications of diabetes mellitus, by promoting increased vascular permeability and thrombogenicity. Irreversible advanced glycation end products (AGEs), resulting from nonenzymatic glycation and oxidation of proteins or lipids, are found in plasma, vessel wall, and tissues and have been linked to the development of diabetic complications. The principal means through which AGEs exert their cellular effects is via specific cellular receptors, one of which, receptor for AGE (RAGE), is expressed by endothelium. We report that blockade of RAGE inhibits AGE-induced impairment of endothelial barrier function, and reverse, in large part, the early vascular hyperpermeability observed in diabetic rats. Inhibition of AGE- and diabetes-mediated hyperpermeability by antioxidants, both in vitro and in vivo, suggested the central role of AGE-RAGE-induced oxidant stress in the development of hyperpermeability. Taken together, these data support the concept that ligation of AGEs by endothelial RAGE induces cellular dysfunction, at least in part by an oxidant-sensitive mechanism, contributing to vascular hyperpermeability in diabetes, and that RAGE is central to this pathologic process.
Distinguishing beauty, creating distinctions: the politics and poetics of dress among young Black women (2011)

NTHABISENG MOTSEMME discusses emerging styles of dress among young Black women. She argues that while these sartorical practices seek to liberate black female bodies from their histories of oppression, they also create new separations and distinctions among them
Intelligent transportation system Mayday becomes a reality (2002)

The Intelligent Transportation System (ITS) is envisioned as linking existing and emerging technologies of computers, wireless radio communications systems, and various sophisticated sensors to be used in cars and highways to create an integrated system that has the potential to change the way millions of American. In Colorado, a large scale operational test of an ITS Mayday emergency dispatch system has been launched. This Mayday operational test in Colorado is evaluating the use of GPS location technology and cellular phone two-way communications to provide assistance to travelers in an emergency dispatch area of more than 12,000 square miles in central Colorado. The test implements 2,000 in-vehicle units using a low cost GPS location device called the TIDGET, developed by NAVSYS Corporation. The major objectives of the Colorado test are: to evaluate the impact of the system and response network on emergency response activities, time, and public safety; to evaluate a low cost system that allows user to request roadside assistance; and to identify the necessary structure, responsibilities, and service levels of a Travel Assistance Center for commercial operation of the system. The results of this emergency location project are anticipated to make a significant contribution to increased highway traveler safety and reduced emergency response time. This NAVSYS Mayday system is an example of the rapid progress by which the ITS vision is becoming a reality in today's travel technology.
Purification, Properties and Structural Aspects of a Thermoacidophilic α‐Amylase from Alicyclobacillus Acidocaldarius Atcc 27009 (1994)

The alpha-amylase from the thermoacidophilic eubacterium Alicyclobacillus (Bacillus) acidocaldarius strain ATCC 27009 was studied as an example of an acidophilic protein. The enzyme was purified from the culture fluid. On an SDS/polyacrylamide gel, the protein an apparent molecular mass of 160 kDa, which is approximately 15% higher than that predicted from the nucleotide sequence. The difference is due to the enzyme being a glycoprotein. Deglycosylation or synthesis of the enzyme in Escherichia coli gave a product with the mass expected for the mature protein. The amylase hydrolyzed starch at random and from the inside, and its main hydrolysis products were maltotriose and maltose. It also formed glucose from starch (by hydrolysing the intermediate product maltotetraose to glucose and maltotriose) and exhibited some pullulanase activity. the pH and temperature optima were pH3 and 75 degrees C, respectively, characterizing the enzyme as being thermoacidophilic. Alignment of the sequence of the enzyme with that of its closest neutrophilic relatives and with that of alpha-1,4 or alpha-1,6 glycosidic-bond hydrolyzing enzymes of known three-dimensional structure showed that the acidophilic alpha-amylase contains approximately 30% less charged residues than do its closest relatives, that these residues are replaced by neutral polar residues, and that hot spots for these exchanges are likely to be located at the surface of the protein. Literature data show that similar effects are observed in three other acidophilic proteins. It is proposed that these proteins have adapted to the acidic environment by reducing the density of both positive and negative charges at their surface, that this effect circumvents electrostatic repulsion of charged groups at low pH, and thereby contributes to the acidostability of these proteins.
Determination of Ni by ICP-MS: Correction of Calcium Oxide and Hydroxide Interferences Using Principal Components Analysis (1990)

Determination of Ni by ICP-MS is hampered by the overlap of Ca oxides and hydroxides with each of the major isotopes of Ni. This is problematic in biological fluids with high Ca:Ni ratios, such as urine, and is worsened by other interferents such as NaK that arise from a urine matrix. These problems have been overcome by using principal components analysis to separate Ni information. This approach allows determination of Ni in Ca solutions and urine. In addition the method can be used to separate Ni information from two distinct sources (for example, naturally abundant and isotopically enriched Ni) in the presence of Ca. Limits of detection of approximately 1 ng/mL for naturally abundant Ni and for a 62 Ni enriched source were determined in a matrix of 40% urine.
Role of domain II of Pseudomonas exotoxin in the secretion of proteins into the periplasm and medium by Escherichia coli. (1988)

Pseudomonas exotoxin (PE) is composed of structural domains I, II, and III; when interacting with mammalian cells the function of domain I is cell recognition, the function of domain II is membrane translocation, and domain III functions in ADP ribosylation. PE is secreted by Pseudomonas aeruginosa into its growth medium. The domain responsible for secretion has been examined by expressing modified PE genes in Escherichia coli under the control of a T7 promoter. Without a signal sequence, PE accumulates within the cell, but PE is secreted into the periplasm when part or all of domain I is removed. PE appears in the periplasm and medium when domain I and part of domain II are removed. Domain II alone is secreted into the periplasm, whereas domain III alone remains within the cell. Addition of an OmpA signal sequence results in secretion of mature PE into the periplasm and secretion of domains II-III into the medium. A protein composed of transforming growth factor alpha fused to the amino terminus of domains II-III is secreted into the periplasm without a signal sequence and into the medium with a signal sequence. A protein composed of domain(s) II or II-III fused to the amino terminus of alkaline phosphatase is secreted into the periplasm and the medium with or without a signal sequence. We conclude that domain II contains important information for protein secretion.
Cellular and biochemical characterization of thioxanthenes for reversal of multidrug resistance in human and murine cell lines. (1990)

We have previously shown that phenothiazines sensitize multidrug resistant (MDR) cells to chemotherapeutic drugs in a manner related to specific structural features, and have identified structurally related thioxanthenes with increased anti-MDR activity. We have now studied the structure-activity relationships of 16 thioxanthenes in the human breast cancer line MCF-7 AdrR. trans-Thioxanthene stereoisomers were 2- to 7-fold more potent than cis-thioxanthenes for antagonizing MDR. The most potent thioxanthenes possessed a halogenated tricyclic ring connected by a 3-carbon alkyl bridge to a piperazinyl or piperadinyl side group. The chemosensitizing effects of the lead compound, trans-flupenthixol, its stereoisomer cis-flupenthixol, its phenothiazine homologue fluphenazine, and the calcium channel blocker verapamil, were further studied in a series of sensitive and MDR cell lines. trans-Flupenthixol caused a greater reversal of cellular resistance to doxorubicin, vinblastine, vincristine, and colchicine in MCF-7 AdrR, KB-V1, and P388/DOX MDR cells than the other chemosensitizers. In particular, trans-flupenthixol was 2- to 3-fold more potent for reversing MDR than equimolar concentrations of verapamil. Furthermore, trans-flupenthixol fully reversed resistance to doxorubicin, vincristine, and colchicine in MDR MCF-7 and NIH 3T3 cells transfected with the mdr1 gene. None of these agents altered MDR in a non-P-glycoprotein expressing MCF-7 cell line selected with mitoxantrone, nor in any of the parental cell lines. The stereoselective antagonism of the flupenthixol isomers on several putative cellular targets was studied to explore the mechanism of their chemosensitizing activity. cis- and trans-flupenthixol were equally active inhibitors of protein kinase C and calmodulin. Both cis- and trans-flupenthixol were also potent inhibitors of [3H]azidopine binding to P-glycoprotein. The apparent lack of clinical toxicity of trans-flupenthixol makes it an attractive drug for possible use in the modulation of tumor resistance in vivo if appropriate tissue concentrations can be achieved.
Improved Conditions for the Formation of Tetrazoles (1987)

Tetrazoles can be prepared from nitriles and sodium azide in improved yield over shorter reaction time using triethylammonium chloride as the catalyst and 1-methyl-2-pyrrolidinone as the solvent.
Different binding specificities and transactivation of variant CRE's by CREB complexes (1994)

The DNA binding specificities of CREB1 and CREB2 homodimers and the CREB2/cJun heterodimer were analyzed with a CASTing technique. All but one of the selected sequences varied from the consensus CRE (TGACGTCA) by three nucleotides or less. The profile of variations selected and the binding affinity for these sequences were unique for each CREB complex. The affinities were not effected by the palindromic nature of the sequences, but were strongly effected by flanking sequences. The strength of DNA binding in vitro correlated with the degree of transactivation observed in JEG-3 cells transfected with reporter plasmids harboring CRE variants, when hybrid CREB proteins fused to the VP16 activation domain were expressed. When native CREB proteins were expressed, the correlation was attenuated by the nature of the variant sequence. A CRE variant (TGACATCA) found in several natural promoters, exhibited the lowest basal transcription rate of the variants and a lower level of induction than expected when compared with the in vitro binding data. These results indicate that transactivation of DNA sequence elements is strongly effected by the strength of transcription factor binding, and that individual sequences can attenuate the level of induction.
Virological and immunological bases for HIV-1 vaccine design (2007)

A logical approach for prophylactic HIV-1 vaccine development begins by recognition that the regimen needs to contain viruses which are not cleared by primary host immune responses and develop persistent infection. Hence the required strategy is different from the one against self-remitting acute infections which aims at eliciting robust host immune responses in advance by infection mimicry. Host adaptive immune responses do play a central role in primary resolution from acute HIV-1 and simian immunodeficiency virus (SIV) infection, but as observed in the non-remitting disease course, their function is not fully exerted, leading to failure in viral containment. Either overcoming the limitations of antiviral immunity in natural infection or augmenting the effectors potentially capable of controlling virus replication would be essential for development of an effective HIV-1 vaccine. This approach is hand-in-hand with understanding of the reversibility of various steps leading to establishment of persistent HIV-1 infection. This article reviews the interplay between HIV-1/SIV and the infected host, mainly focusing on macaque models of SIV infection and characterization of the two major wings of adaptive immunity, cytotoxic T lymphocytes (CTLs) and neutralizing antibodies. Discussed in parallel are the up-to-date topics of HIV-1 vaccine development including our recent progress.