gebhart/patrepeval huggingface dataset:
Phosphorylation of p27 on Serine 10 Is Required for Its Binding to CRM1 and Nuclear Export (2002)

Phosphorylation of the cyclin-dependent kinase inhibitor p27(Kip1) has been thought to regulate its stability. Ser(10) is the major phosphorylation site of p27(Kip1), and phosphorylation of this residue affects protein stability. Phosphorylation of p27(Kip1) on Ser(10) has now been shown to be required for the binding of CRM1, a carrier protein for nuclear export. The p27(Kip1) protein was translocated from the nucleus to the cytoplasm at the G(0)-G(1) transition of the cell cycle, and this export was inhibited by leptomycin B, a specific inhibitor of CRM1-dependent nuclear export. The nuclear export and subsequent degradation of p27(Kip1) at the G(0)-G(1) transition were observed in cells lacking Skp2, the F-box protein component of an SCF ubiquitin ligase complex, indicating that these early events are independent of Skp2-mediated proteolysis. Substitution of Ser(10) with Ala (S10A) markedly reduced the extent of p27(Kip1) export, whereas substitution of Ser(10) with Asp (S10D) or Glu (S10E) promoted export. Co-immunoprecipitation analysis showed that CRM1 preferentially interacted with S10D and S10E but not with S10A, suggesting that the phosphorylation of p27(Kip1) on Ser(10) is required for its binding to CRM1 and for its subsequent nuclear export.
Genotypic and phenotypic analyses of HIV-1 in antiretroviral-experienced patients treated with tenofovir DF (2002)

Adding tenofovir DF 300 mg to an existing regimen in patients with ongoing viral replication and a wide range of genotypic resistance patterns resulted in significant and durable HIV-1 RNA reductions. In addition, there was a low incidence of genotypic or phenotypic resistance to tenofovir DF arising during 48 weeks of therapy.
The Super Elongation Complex (SEC) in Development and Disease (2013)

Chromosomal translocations involving the <i>mixed lineage leukemia (MLL)</i> gene are associated with infant acute leukemia. There are a large number of translocation partners of MLL that share very little sequence similarities, yet their translocations into MLL result in the pathogenesis of leukemia. To define the molecular reason why these translocations result in leukemogenesis, I purified several of the commonly occurring MLL chimeras and identified a novel Super Elongation Complex (SEC) associated with all chimeras purified. SEC consists of the RNA Pol II elongation factors ELL1-3, P-TEFb, and several frequent MLL-translocation partners. SEC is one of the most active P-TEFb complexes and is required for the proper expression of MLL chimera target genes and the oncogene, <i>MYC</i>, suggesting that the regulation of transcription elongation checkpoint control (TECC) by SEC could play essential roles in leukemia. <br><br>Paused Pol II has been proposed to be associated with loci that respond rapidly to environmental stimuli. My studies in mouse ES cells demonstrated that SEC is required for rapid transcriptional activation of genes, many of which contain paused Pol II. However, SEC is also required for the activation of the <i>Cyp26al</i> gene, which does not contain detectable Pol II, yet responds much more rapidly to retinoic acid than those paused genes, suggesting that paused Pol II is not a prerequisite for rapid gene activation. Furthermore, Ell3, a member of the ELL family of proteins, predominately occupies poised, active, and inactive enhancers of many developmental genes in ES cells. Ell3’s association with enhancers is required for setting up proper Pol II occupancy at the promoter-proximal regions of neighboring genes, providing a yet to be discovered mechanism for the transition from Ell3’s presence at poised enhancers in ES cells to Ell2’s role in the release of paused Pol II during gene activation.
Predicting Native Language from Gaze (2017)

A fundamental question in language learning concerns the role of a speaker's first language in second language acquisition. We present a novel methodology for studying this question: analysis of eye-movement patterns in second language reading of free-form text. Using this methodology, we demonstrate for the first time that the native language of English learners can be predicted from their gaze fixations when reading English. We provide analysis of classifier uncertainty and learned features, which indicates that differences in English reading are likely to be rooted in linguistic divergences across native languages. The presented framework complements production studies and offers new ground for advancing research on multilingualism. 1
Multiaddressable Self-Assembling Organogelators Based on 2H-Chromene and N-Acyl-1,ω-amino Acid Units (2002)

Multiaddressable organogelators are 3,3-diphenyl-3H-naphtho[2,1-b]pyrans covalently linked to sodium N-acyl-11-aminoundecanoate. These molecules have been designed to respond to changes to their environment. They are shown to act as efficient gelators for polar organic fluids, and obviously they exhibit a thermosensitive answer as low molecular mass organogelators. In these fluids, the aggregative properties are totally suppressed upon conversion to neutral carboxylic species. The gels of these carboxylate sodium salts are shown to be markedly affected by light irradiation. Supramolecular gelating assemblies can be disrupted by the photoinduced ring opening of the chromene subunit, so that the macroscopic flowing property is recovered. Upon a further thermal treatment, the system is reversibly converted back to the supramolecular network. Controlled gelation could be achieved using temperature, light, or acidity as external stimuli.
Dendritic cells can present antigen in vivo in a tolerogenic or immunogenic fashion (1996)

Dendritic cells (DC) are unmatched among APCs in their ability to bind, process, and present Ag. Presentation by such potent APCs, if always immunogenic and never tolerogenic, might stimulate pathogenic autoimmune responses. To determine whether Ag presentation by DC can induce tolerance, mice were injected with a rat IgG2b anti-splenic DC mAb, 33D1, and challenged 13 to 28 days later with a stimulatory rat IgG2b mAb. Injection of mice with 1 ng/100 micrograms of 33D1 rarely induced an anti-rat IgG2b Ab response and, in most mice, induced rat IgG2b-specific T cell and B cell tolerance. Tolerant mice had decreased ability to secrete Ab and make both type 1 and type 2 cytokine mRNA and protein in response to immunization with rat IgG2b. 33D1 was 100- to 1000-fold more potent as a tolerogen than an isotype-matched control rat IgG2b mAb. Injecting mice with aggregated 33D1, 33D1 plus anti-IgD mAb, or 33D1 plus IL-1 induced an IgG1 anti-rat IgG2b Ab response rather than tolerance. IL-1 injected 3 days after 33D1 still induced an Ab response rather than tolerance. Not all anti-DC mAbs are tolerogenic. Injection of a DC-specific hamster anti-CD11c mAb (N418) stimulates an IgG anti-hamster response, and injection of 33D1 plus N418 stimulates both anti-hamster and anti-rat IgG2b responses. These observations indicate that DCs can present Ag in either a tolerogenic or stimulatory manner and suggest that inflammatory stimuli can convert an otherwise tolerogenic signal to a stimulatory signal.
MMseqs software suite for fast and deep clustering and searching of large protein sequence sets (2016)

Supplementary data are available at Bioinformatics online.
Publishing Bibliographic Data On Optical Disks: A Prototypical Application And Its Implications (1985)

Bibliographic databases are quite large and relatively static, making them ideally suited for storage on optical media now becoming available. Consequently, libraries and publishing houses are pioneering certain applications of optical disks. The high storage density and the economy of optical disks make them attractive media for large databases. However, two factors create problems in the design of sophisticated retrieval software: certain device characteristics (e.g., slow access time compared to magnetic media), and the user interface requirements for bibliographic data. We discuss a prototypical application of optical disks to the publishing of the Library of Congress&apos;s machine-readable collection (the MARC and REMARC databases). The prototype disk is manufactured from pre-mastered videotape and is controlled by an IBM PC microcomputer. The prototype represents a significant effort in system integration, requiring development of hardware interface, error correction, low-level access software, high-level language interface, and user-friendly front-end applications. To prepare the data for indexing and display, mainframe software was developed. Based on our experience with the prototype, we discuss a number of issues common to the publication of such databases: data structures, search strategies, precomputation of retrieval results (a powerful technique well-suited to optical disk applications), and issues pertaining to standardization and publication formats.
Selection In Vitro<I> </I>of Allosteric Ribozymes (2004)

The capacities of RNA for both catalysis and molecular recognition have been appreciated for some time. Recently, a number of studies have shown that these distinct functional classes may be combined to generate multipartite ribozymes in which the catalytic and ligand-binding elements act coordinately. In this chapter, we describe a procedure known as allosteric selection, in which an RNA catalyst in conjunction with a random sequence domain is subjected to iterative in vitro selection in order selectively to recover ligand-dependent ribozymes.
Active site-directed double mutants of dihydrofolate reductase. (1996)

Variants of dihydrofolate reductase (DHFR), which confer resistance to antifolates, are used as dominant selectable markers in vitro and in vivo and may be useful in the context of gene therapy. To identify improved mutant human DHFRs with increased catalytic efficiency and decreased binding to methotrexate, we constructed by site-directed mutagenesis four variants with substitutions at both Leu22 and Phe31 (i.e., Phe22-Ser31, Tyr22-Ser31, Phe22-Gly31, and Tyr22-Gly31). Antifolate resistance has been observed previously when individual changes are made at these active-site residues. Substrate and antifolate binding properties of these "double" mutants revealed that each have greatly diminished affinity for antifolates (> 10,000-fold) yet only slightly reduced substrate affinity. Comparison of in vitro measured properties with those of single-residue variants indicates that double mutants are indeed significantly superior. This was verified for one of the double mutants that provided high-level methotrexate resistance following retrovirus-mediated gene transfer in NIH3T3 cells.
Synthesis of (+)-CP-263,114 (2000)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTSynthesis of (+)-CP-263,114Chuo Chen, Mark E. Layton, Scott M. Sheehan, and Matthew D. ShairView Author Information Department of Chemistry and Chemical Biology Harvard University, Cambridge, Massachusetts 02138 Cite this: J. Am. Chem. Soc. 2000, 122, 30, 7424–7425Publication Date (Web):July 18, 2000Publication History Received2 June 2000Published online18 July 2000Published inissue 1 August 2000https://pubs.acs.org/doi/10.1021/ja001958xhttps://doi.org/10.1021/ja001958xrapid-communicationACS PublicationsCopyright © 2000 American Chemical SocietyRequest reuse permissionsArticle Views5117Altmetric-Citations74LEARN 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 SUBJECTS:Carbon,Catalysts,Cyclization,Organic compounds,Rearrangement Get e-Alerts
Guided-wave planar optical interconnects using highly multiplexed polymer waveguide holograms (1992)

An intraplanar interconnection scheme using substrate guided modes in conjunction with a highly multiplexed waveguide volume hologram is proposed. Acoustooptically addressed 1-to-50 passive and 1-to-2-to-100 reconfigurable interconnections with a fan-out diffraction efficiency of 55% at 514-nm wavelength are demonstrated. A coordinate transformation converts the 3-D diffraction problem into a 2-D one, which significantly simplifies the theoretical calculation. Intraplane massive fan-out optical interconnection using substrate guided mode provides both collinear and coplanar fan-out capability for data and clock signals. Colinearity of signal distribution allows the 2-D input signal array to be processes. The laminated waveguide device containing a highly multiplexed dichromated gelatin (DCG) hologram has been evaluated.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
FUNCTION AND STRUCTURE RELATIONSHIPS IN DNA POLYMERASES (1994)

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
Optimal insertion of pilot symbols for transmissions over time-varying flat fading channels (2004)

Two major training techniques for wireless channels are time-division multiplexed (TDM) training and superimposed training. For the TDM schemes with regular periodic placements (RPPs), the closed-form expression for the steady-state minimum mean square error (MMSE) of the channel estimate is obtained as a function of placement for Gauss-Markov flat fading channels. We then show that among all periodic placements, the single pilot RPP scheme (RPP-1) minimizes the maximum steady-state channel MMSE. For binary phase-shift keying (BPSK) and quadrature phase-shift keying (QPSK) signaling, we further show that the optimal placement that minimizes the maximum uncoded bit error rate (BER) is also RPP-1. We next compare the MMSE and BER performance under the superimposed training scheme with those under the optimal TDM scheme. It is shown that while the RPP-1 scheme performs better at high SNR and for slowly varying channels, the superimposed scheme outperforms RPP-1 in the other regimes. This demonstrates the potential for using superimposed training in relatively fast time-varying environments.
Diversity of Human Vaginal Bacterial Communities and Associations with Clinically Defined Bacterial Vaginosis (2008)

Bacterial vaginosis (BV) is a common syndrome associated with numerous adverse health outcomes in women. Despite its medical importance, the etiology and microbial ecology of BV remain poorly understood. We used broad-range PCR to census the community structure of the healthy and BV-affected vaginal microbial ecosystems and synthesized current publicly available bacterial 16S rRNA gene sequence data from this environment. The community of vaginal bacteria detected in subjects with BV was much more taxon rich and diverse than in subjects without BV. At a 97% sequence similarity cutoff, the number of operational taxonomic units (OTUs) per patient in 28 subjects with BV was nearly three times greater than in 13 subjects without BV: 14.8 +/- 0.7 versus 5.2 +/- 0.75 (mean +/- standard error). OTU-based analyses revealed previously hidden diversity for many vaginal bacteria that are currently poorly represented in GenBank. Our sequencing efforts yielded many novel phylotypes (123 of our sequences represented 38 OTUs not previously found in the vaginal ecosystem), including several novel BV-associated OTUs, such as those belonging to the Prevotella species complex, which remain severely underrepresented in the current NCBI database. Community composition was highly variable among subjects at a fine taxonomic scale, but at the phylum level, Actinobacteria and Bacteroidetes were strongly associated with BV. Our data describe a previously unrecognized extent of bacterial diversity in the vaginal ecosystem. The human vagina hosts many bacteria that are only distantly related to known species, and subjects with BV harbor particularly taxon-rich and diverse bacterial communities.
Screening and Selection Methods for Large-Scale Analysis of Protein Function (2002)

High-throughput assays hold tremendous promise for protein engineering and proteomics. With powerful assays it should be possible to evolve, for example, a stereoselective esterase for the chemical synthesis or a site-specific endonuclease for biomedical research. Entire cDNA libraries, which encode all of the proteins expressed in a given organism or cell line, should simply be passed through a battery of biochemical assays to determine the function of each individual protein. Herein we look at the types of assays that have been developed and how close we are to our goals of engineering proteins with new activities as well as rapidly assigning function to the thousands of proteins that make up each genome.
Donor−Acceptor Polymer Electrochromes with Tunable Colors and Performance (2010)

To demonstrate the effect of donor (D) and acceptor (A) units on the structure−property relationships of electrochromic polymers, design, synthesis, characterization and polymerization of a series of D−A type systems, 1−5, based on thiophene, 3,4-ethylenedioxythiophene, and 3,3-didecyl-3,4-dihydro-2H-thieno[3,4-b][1,4]dioxepine as D units and 2,1,3-benzoselenadiazole, 2,1,3-benzothiadiazole and 2-decyl-2H-benzo[d][1,2,3]triazole as A units are highlighted. It is found that these units play key roles on the redox behavior, band gap, neutral state color, and the electrochromic performance (stability, optical contrast, coloration efficiency, and switching time) of the system. It is noted that electropolymerization of these D−A systems provides processable low band gap electrochromes, P1-P5, exhibiting high redox stability, coloration efficiency, transmittance and/or contrast ratio and low response time. Furthermore, P1-P5 reflect various hues of blue and green pallets of the RGB color-space in the neutral state. In particular, it is noteworthy that P5 is an excellent blue-to-colorless polymeric electrochrome, which, to our best knowledge, exhibits the highest optical contrast and coloration efficiency among the D−A type systems. The panoramic breadth of the neutral state colors and intriguing features of these polymeric materials further confirm that D−A approach allows engineering tunable electrochromes, which hold promise for commercialization of polymeric RGB electrochromics.
Purification and characterization of glucose dehydrogenase from the thermoacidophilic archaebacterium Thermoplasma acidophilum (1989)

Glucose dehydrogenase was purified to homogeneity from the thermoacidophilic archaebacterium Thermoplasma acidophilum. The enzyme is a tetramer of polypeptide chain Mr 38,000 +/- 3000, it is catalytically active with both NAD+ and NADP+ cofactors, and it is thermostable and remarkably resistant to a variety of organic solvents. The amino acid composition was determined and compared with those of the glucose dehydrogenases from the archaebacterium Sulfolobus solfataricus and the eubacteria Bacillus subtilis and Bacillus megaterium. The N-terminal amino acid sequence of the Thermoplasma acidophilum enzyme was determined to be: (S/T)-E-Q-K-A-I-V-T-D-A-P-K-G-G-V-K-Y-T-T-I-D-M-P-E.
Effects of the compatibility of a polyacrylic block copolymer/tackifier blend on the phase structure and tack of a pressure‐sensitive adhesive (2011)

Abstract Adhesion and viscoelastic properties and morphology of a polyacrylic block copolymer/tackifier blend were investigated. Special rosin ester resins with different weight average molecular weights of 650, 710, 890, and 2160 were used as the tackifier and blended with a polyacrylic block copolymer consisting of poly(methyl methacrylate) and poly( n ‐butyl acrylate) blocks at tackifier content levels of 10, 30, and 50 wt %. The compatibility decreased with an increase in molecular weight. From TEM observation, the number of formed agglomerates of the tackifier with sizes on the order of several tens of nanometers increased with increasing tackifier content and molecular weight of the tackifier in the range from 650 to 890. For the tackifier with a molecular weight of 2160, micrometer‐sized agglomerates were observed. The storage modulus at low temperature and the glass transition temperature of adhesive measured by a dynamic mechanical analysis increased dependent on the number of formed nanometer sized agglomerates. Tack was measured using a rolling cylinder tack tester over wide temperature and rolling rate ranges, and master curves were prepared in accordance with the time‐temperature superposition law. Tack and peel strength were optimum at a blend combination of intermediate compatibility, i.e., the molecular weight of 890. These optimum properties were correlated to maximal values of the storage modulus at room temperature and the glass transition temperature. Therefore, it was found that these features of blend properties are strongly affected by the nanometer sized agglomerates of tackifier. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2012
Texture Feature Application in Oil Spill Detection by Satellite Data (2008)

Oil spills in the ocean are one of major environmental concerns, especially in the costal waters. Many satellite sensors, including optical sensors and microwave sensors, have been used to detect oil spills which often exhibit different feature in the satellite images compared with the surrounding waters. In this study, we used texture feature analysis to detect oil spill using MODIS and SAR images. The MODIS images of one incident were analyzed and the results proved the efficiency of algorithm. However, in very near shore regions, delineation of water and oil boundary is noisy due to a similar spectral signature across land-water boundary. The SAR image of Prestige accident was segmented with our method and result is better than the result from the single threshold method.
Topical Fluconazole Therapy of Candida Keratitis (1996)

A prospective clinical trial of topical fluconazole solution (2 mg/ml) was undertaken in six consecutive eyes of microbiologically proven Candida keratitis with abscess formation. All eyes responded well to the medical therapy. Average duration required for healing was 22.6 +/- 2.3 days. The findings of our study suggest that topical fluconazole is a safe and effective antifungal drug for the management of Candida keratitis with deep abscess.
Toward the development of vectored vaccines in compliance with evolutionary medicine (2008)

Immunity is a result of coevolution between the immune system and pathogens. Microbes have evolved multiple strategies to evade, confuse or inhibit the immune defense mechanism in order to proliferate in a biological shelter. The immune system must counter microbial invasions by eliciting protective immunity without inducing autoimmune disorders that could dampen species survival. Vaccination activates the immune system by mimicking a microbial invasion without the harmful, sometimes fatal, consequences of an infection. Vaccine design can potentially exploit pathogens’ weaknesses, thus tipping the scales of coevolution toward defeating pathogens at their own game.