gebhart/patrepeval huggingface dataset:
Structure-function studies of human granulocyte-macrophage colony-stimulating factor. Identification of residues required for activity. (1988)

Human granulocyte-macrophage colony stimulating factor (hGM CSF), a protein containing 127 amino acids, was chemically synthesized by using automated stepwise solid-phase methods. The unpurified synthetic hGM-CSF had the same range of actions on hemopoietic cells as the purified recombinant protein. The structural requirements for the activities of synthetic hGM-CSF were examined by the design and synthesis of fragments and analogs. The synthetic fragment, hGM-CSF (54-127), containing all four of the cysteine residues found in the intact protein, lacked detectable activity. Assays of fragments shortened at the N terminus showed that the residues 1-13 were not required for activity, but that the integrity of residues 14-25, particularly residues 16, 17, and 18, was critical for biologic activity. The 14-25 region is predicted to form the first alpha-helix in hGM-CSF. Synthetic peptides within the N-terminal 53 residue region lacked detectable activity. The synthetic analog hGM-CSF (1-121), which lacks the C-terminal 6 residues, had similar activity to hGM-CSF (1-127) indicating that residues 122-127 are not required for activity. An analog, [Ala88] hGM-CSF (14-96), which lacks the hydrophobic C-terminal region and 2 cysteine residues, had low but readily detectable activity suggesting that residues 14-96 are sufficient for detectable synthetic hGM-CSF activity, although the presence of residues 97-121 are required for full activity. No dissociation of the multiple biological activities of hGM-CSF was detected.
Enhanced Cellular Uptake of Short Polyarginine Peptides through Fatty Acylation and Cyclization (2014)

Many of the reported arginine-rich cell-penetrating peptides (CPPs) for the enhanced delivery of drugs are linear peptides composed of more than seven arginine residues to retain the cell penetration properties. Herein, we synthesized a class of nine polyarginine peptides containing 5 and 6 arginines, namely, R5 and R6. We further explored the effect of acylation with long chain fatty acids (i.e., octanoic acid, dodecanoic acid, and hexadecanoic acid) and cyclization on the cell penetrating properties of the peptides. The fluorescence-labeled acylated cyclic peptide dodecanoyl-[R5] and linear peptide dodecanoyl-(R5) showed approximately 13.7- and 10.2-fold higher cellular uptake than that of control 5,6-carboxyfluorescein, respectively. The mechanism of the peptide internalization into cells was found to be energy-dependent endocytosis. Dodecanoyl-[R5] and dodecanoyl-[R6] enhanced the intracellular uptake of a fluorescence-labeled cell-impermeable negatively charged phosphopeptide (F'-GpYEEI) in human ovarian cancer cells (SK-OV-3) by 3.4-fold and 5.5-fold, respectively, as shown by flow cytometry. The cellular uptake of F'-GpYEEI in the presence of hexadecanoyl-[R5] was 9.3- and 6.0-fold higher than that in the presence of octanoyl-[R5] and dodecanoyl-[R5], respectively. Dodecanoyl-[R5] enhanced the cellular uptake of the phosphopeptide by 1.4-2.5-fold higher than the corresponding linear peptide dodecanoyl-(R5) and those of representative CPPs, such as hepta-arginine (CR7) and TAT peptide. These results showed that a combination of acylation by long chain fatty acids and cyclization on short arginine-containing peptides can improve their cell-penetrating property, possibly through efficient interaction of rigid positively charged R and hydrophobic dodecanoyl moiety with the corresponding residues in the cell membrane phospholipids.
General Electric ATS Program technical review Phase 2 activities (1995)

In response to the industrial and utility objectives specified for the ATS, the GE Power Generation ATS Phase 2 Program consisted of a dual approach. These were (1) development of an Industrial ATS (aircraft engine based) led by GE Aircraft Engines, and (2) development of a Utility ATS which was already underway at GEPG. Both programs required the identification and resolution of critical technical issues. Both systems were studied in Tasks 3-7, and both have resulted in designs that meet all ATS goals. The Industrial ATS as defined (130 MW) did not meet projected market power size requirements, and emphasis has remained on the Utility ATS development. The design and testing effort has been focused on the MS7001H combined cycle gas turbine, as the next product evolution in GE Power Generation`s product line. Common technology derived from the ATS Program is also being incorporated into the 50 Hz version of the ATS utility machine designated as the MS9001H.
Automated lip‐sync: Background and techniques (1991)

Abstract The problem of creating mouth animation synchronized to recorded speech is discussed. Review of a model of speech sound generation indicates that the automatic derivation of mouth movement from a speech soundtrack is a tractable problem. Several automatic lip‐sync techniques are compared, and one method is described in detail. In this method a common speech synthesis method, linear prediction, is adapted to provide simple and accurate phoneme recognition. The recognized phonemes are associated with mouth positions to provide keyframes for computer animation of speech. Experience with this technique indicates that automatic lip‐sync can produce useful results.
Database integration with the Web for biologists to share data and information (2002)

The Internet has fundamentally changed the way we conduct our business. Even 10 years ago or so, it was not possible to order a book or access a sequence database in another continent using the computer in our office. All these become possible due to the progress in information technology. It is especially important for biologists to realise that information technology has brought us enormous opportunities in sharing our data. In this paper, authors review and introduce the technologies relating to biological data, database, dynamic integration of databases with the World Wide Web (Web hereafter), and data standardisation.
The N-Ethylmaleimide-sensitive Fusion Protein and α-SNAP Induce a Conformational Change in Syntaxin (1995)

The N-ethylmaleimide-sensitive fusion protein (NSF) plays an essential role in intracellular membrane fusion events and has been implicated in the exocytosis of synaptic vesicles. NSF binds through soluble NSF attachment proteins (SNAPs) to a complex of neuronal membrane proteins comprised of synaptobrevin, syntaxin, and SNAP-25. Disassembly of this complex by NSF is thought to be a critical step in the molecular events which lead to vesicle fusion with the plasma membrane. Here we have studied the interaction of alpha-SNAP and NSF with individual components of this complex and have identified syntaxin as a primary substrate for NSF/alpha-SNAP. We find that alpha-SNAP binds directly to syntaxin 1A as well as weakly to SNAP-25, while it does not bind to synaptobrevin II. NSF binds to syntaxin through alpha-SNAP and in the presence of ATP catalyzes a conformational rearrangement which abolishes binding of itself and alpha-SNAP. This reaction leads to the previously described disassembly of the fusion complex, since synaptobrevin binding to syntaxin is also reduced. alpha-SNAP binds to a carboxyl-terminal syntaxin fragment (residues 194-288) that also binds synaptobrevin and SNAP-25. However, NSF action on this syntaxin fragment has no effect on the binding of alpha-SNAP or synaptobrevin. This suggests that the conformational change normally induced by NSF in syntaxin depends on an interaction between carboxyl- and amino-terminal domains of syntaxin.
Preparation and characterization of trans-bis(.alpha.-dioximato)ruthenium complexes (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticlePreparation and characterization of trans-bis(.alpha.-dioximato)ruthenium complexesJames G. Muller and Kenneth J. TakeuchiCite this: Inorg. Chem. 1990, 29, 11, 2185–2188Publication Date (Print):May 1, 1990Publication History Published online1 May 2002Published inissue 1 May 1990https://pubs.acs.org/doi/10.1021/ic00336a032https://doi.org/10.1021/ic00336a032research-articleACS PublicationsRequest reuse permissionsArticle Views225Altmetric-Citations26LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Nitrone dipolar cycloaddition routes to piperidines and indolizidines. Part 9.Part 8. See Ref. 22. Formal synthesis of (–)-pinidine and total synthesis of (–)-histrionicotoxin, (+)-histrionicotoxin and (–)-histrionicotoxin 235AThis manuscript is dedicated to the sixtieth birthday of Professor L. Tietze. (2002)

An intramolecular hydroxylamine-alkyne cyclisation is used for the enantioselective synthesis of the cyclic nitrones 36 and 44. We have demonstrated the use of a novel nitrone protection strategy by cycloaddition of styrene to the cyclic nitrone 44 in the synthesis of the spirocyclic core of the histrionicotoxin family of alkaloids. Deprotection by dipolar cycloreversion of the styrene adduct (the bicyclic isoxazolidine 39) and in situ intramolecular dipolar cycloaddition of a pendant (Z)-α,β-unsaturated nitrile to the intermediate nitrone 50 gave the isoxazolidine 51 in high yield with a surprising degree of regioselectivity compared with the corresponding (Z)-enyne 36. The method is amenable to the synthesis of both enantiomers 51 and 62 of the tricyclic core structure which can be converted by way of the common intermediates (e.g.53 and ent-53) respectively into the natural configuration of alkaloids (−)-histrionicotoxin 1 and (−)-histrionicotoxin 235A 65 as well as the unnatural (+)-histrionicotoxin 63.
CSR1 Inducing Cell Death Through Inactivation Of CPSF3 (2008)

CSR1, a newly characterized tumor suppressor gene located in the 8p21 region, undergoes hypermethylation of its promoter and exon 1 regions in over 30% of prostate cancers. Re‐expression of CSR1 inhibits cell growth and induces cell death, but the mechanisms of CSR1‐mediated tumor suppressor activity are not clear. In this study, a Yeast‐two hybrid screening identified proteins interacting with the C‐terminus of CSR1. The cleavage and poly‐adenylation specific factor 3 (CPSF3), an essential component for converting hnRNA to mRNA, bound with CSR1 C‐terminus with high affinity. Analysis of a series of GST‐CSR1 mutants found the binding motifs for CPSF3 located at sequence between amino acids 440–513. The interaction between CSR1 and CPSF3 induced CPSF3 translocation from nucleus to cytoplasm, resulting in nuclear inhibition of the polyadenylation activity both in vitro and in vivo. Down‐regulation of CPSF3 using siRNA induced cell death in a manner similar to those induced by CSR1 expression. CSR1 mutant unable to bind to CPSF3 did not alter CPSF3 subcellular distribution, and did not inhibit its polyadenylation activity nor induce cell death. In summary, CSR1 appears to induce cell death through a novel mechanism by hijacking a critical RNA processing enzyme.
Regulation of the B Cell Receptor Repertoire and Self-Reactivity by BAFF (2010)

The TNF-family cytokine BAFF (BLyS) promotes B lymphocyte survival and is overexpressed in individuals with systemic lupus erythematosus and Sjögren's Syndrome. BAFF can rescue anergic autoreactive B cells from death, but only when competition from nonautoreactive B cells is lacking. Yet, high BAFF levels promote autoantibody formation in individuals possessing diverse B cells. To better understand how excess BAFF promotes autoimmunity in a polyclonal immune system, Ig L chain usage was analyzed in 3H9 site-directed IgH chain transgenic mice, whose B cells recognize DNA and chromatin when they express certain endogenous L chains. BAFF levels were manipulated in 3H9 mice by introducing transgenes expressing either BAFF or its natural inhibitor ΔBAFF. B cells in BAFF/3H9 mice were elevated in number, used a broad L chain repertoire, including L chains generating high-affinity autoreactivity, and produced abundant autoantibodies. Comparison of spleen and lymph node B cells suggested that highly autoreactive B cells were expanded. By contrast, ΔBAFF/3H9 mice had reduced B cell numbers with a repertoire similar to that of 3H9 mice, but lacking usage of a subset of Vκ genes. The results show that limiting BAFF signaling only slightly selects against higher affinity autoreactive B cells, whereas its overexpression leads to broad tolerance escape and positive selection of autoreactive cells. The results have positive implications for the clinical use of BAFF-depleting therapy.
Seamless data-rate change using punctured convolutional codes for time-varying signal-to-noise ratio (2002)

In a time-varying signal-to-noise ratio (SNR) environment, the symbol rate is often changed to maximize the data return. However, the symbol-rate change has some undesirable effects such as changing the transmission bandwidth and perhaps causing the receiver symbol loop to lose lock temporarily, thus losing some data. We propose an alternate way of varying the data rate without changing the symbol rate and therefore the transmission bandwidth. The data rate change is achieved in a seamless fashion by puncturing the convolutionally encoded symbol stream to adapt to the changing SNR environment. We have also derived an exact expression to enumerate the number of distinct puncturing patterns. To demonstrate this seamless rate-change capability, we searched for good puncturing patterns for the Galileo mission (14,1/4) convolutional code and changed the data rates by using the punctured codes to match the Galileo SNR profile of November 9, 1997. We show that this scheme reduces the symbol-rate changes from 8 to 2 and provides a comparable data return and a higher symbol SNR in a day.
Cell proliferation kinetics of normal and tumour tissue in vitro: quiescent reproductive cells and the cycling reproductive fraction (1995)

Current methods for measuring the cell kinetics of human tumours are made and interpreted within the context of a simplistic two compartment model for cell proliferation, consisting of cells that are cycling and those that are not. It is now recognized that the non-cycling compartment of many tumours is heterogeneous, composed of non-reproductive end-stage cells and reproductive cells that are dormant/quiescent. We have developed an in vitro analysis that distinguishes for the first time quiescent reproductive cells from non-reproductive end-stage cells and have integrated this analysis with monolayer clonogenic and suicide assays to simultaneously quantitate the duration of the cell cycle and reproductive cells that are: cycling, quiescent, clonogenic, and non-reproductive end-stage cells. We have defined a new parameter, the Cycling Reproductive Fraction (CRF), which is the cycling cell population referenced specifically to the reproductive cell population. Measurements of CRF from 72 tumour biopsies and from 5 normal foreskins showed that CRF approached 100% in some tumours; however, CRF showed near normal values (< 1%) in others suggesting that cell cycle control may be maintained in some tumours. Because of CRF's improved specificity, we believe that CRF may enhance classification, prognostication, and the optimization and prediction of response to chemotherapy.
SiGe relaxation on silicon-on-insulator substrates: An experimental and modeling study (2003)

The strain relaxation behavior of Si0.82Ge0.18 films on silicon-on-insulator (SOI) substrates was investigated for films grown beyond the critical thickness and strain-relaxed during growth and metastable films, grown beyond the critical thickness, which relaxed during subsequent thermal annealing. The thickness of the top silicon layer of the SOI substrate was varied over a range from 40 nm to 10 μm. In all cases, the SiGe film relaxation occurred via the nucleation and propagation of dislocations with the same onset of film relaxation and same relaxation rate for both SOI and bulk Si substrates. The SOI substrate does not serve as a compliant substrate but does alter the dislocation structure and motion. The buried amorphous oxide layer in the SOI substrate leads to the relaxation of the dislocation strain field through the removal of the dislocation line tension. This removal of the dislocation line tension drives dislocation motion and leads to the development of strain in the thin Si layer of the SOI substrate. Models of this dislocation behavior for SiGe growth on the SOI substrate are presented and calculation of the equilibrium strain of the thin Si substrate layer closely fits the measured strain of several SOI substrates. The article addresses the implications of the modified dislocation structure and kinetics for film relaxation on SOI substrates.
Developments in Nanostructured Cathode Materials for High‐Performance Lithium‐Ion Batteries (2008)

Abstract Nanostructured materials lie at the heart of fundamental advances in efficient energy storage and/or conversion, in which surface processes and transport kinetics play determining roles. This Review describes some recent developments in the synthesis and characterization of nanostructured cathode materials, including lithium transition metal oxides, vanadium oxides, manganese oxides, lithium phosphates, and various nanostructured composites. The major goal of this Review is to highlight some new progress in using these nanostructured materials as cathodes to develop lithium batteries with high energy density, high rate capability, and excellent cycling stability resulting from their huge surface area, short distance for mass and charge transport, and freedom for volume change in nanostructured materials.
Total GaN solution to electrical power conversion (2011)

We present the first 600V-class, total GaN solution for electrical power conversion applications. A 220V-400V boost converter using a GaN transistor and a GaN diode with fast & clean hard-switched waveforms has been demonstrated. The conversion efficiency was >;99.1% at 100 kHz and >;98.2% at 800 kHz.
Intratumoral injection of taxol in vivo suppresses A549 tumor showing cytoplasmic vacuolization (2011)

Based on our recent in vitro studies, this report was designed to explore the mechanism by which high concentration of taxol (70 µM) induced paraptosis-like cell death in human lung carcinoma (A549) cells, and to evaluate the therapeutic efficacy of taxol using A549 tumor-bearing mice in vivo. Exposure of cells to taxol induced time-dependent cytotoxicity and cytoplasmic vacuolization without the involvement of Bax, Bak, Mcl-1, Bcl-XL, and caspase-3. Although taxol treatment induced activating transcription factor 6 (ATF6) cleavage indicative of endoplasmic reticulum (ER) stress, silencing ATF6 by shATF6 did not prevent taxol-induced both cytotoxcity and cytoplasmic vacuolization, suggesting that taxol-induced cytoplasmic vacuolization and cell death were not due to ER stress. Moreover, taxol-treated cells did not show DNA fragmentation and loss of mitochondrial membrane potential, the typical characteristics of apoptosis. In addition, taxol-induced cytoplasmic vacuolization did not show the cellular lysis, the characteristics of oncosis, and positive of β-galactosidase, the characteristic of senescence, indicating that taxol induced paraptosis-like cell death is neither oncosis nor senescence. Moreover, our in vivo data showed that intratumoral injection of taxol (50 mg/kg) in A549 tumor xenograft mice on day 1 and day 19 potently suppressed tumor growth showing significant ER vacuolization without toxicity. In conclusion, high concentration of taxol exhibits a significant anticancer activity by inducing paraptosis-like cell death in vitro and in vivo, without significant toxicity, suggesting a promising therapeutic strategy for apoptosis-resistance cancer by inducing ER vacuolization.
Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium (2011)

The goal of the Gene Ontology (GO) project is to provide a uniform way to describe the functions of gene products from organisms across all kingdoms of life and thereby enable analysis of genomic data. Protein annotations are either based on experiments or predicted from protein sequences. Since most sequences have not been experimentally characterized, most available annotations need to be based on predictions. To make as accurate inferences as possible, the GO Consortium's Reference Genome Project is using an explicit evolutionary framework to infer annotations of proteins from a broad set of genomes from experimental annotations in a semi-automated manner. Most components in the pipeline, such as selection of sequences, building multiple sequence alignments and phylogenetic trees, retrieving experimental annotations and depositing inferred annotations, are fully automated. However, the most crucial step in our pipeline relies on software-assisted curation by an expert biologist. This curation tool, Phylogenetic Annotation and INference Tool (PAINT) helps curators to infer annotations among members of a protein family. PAINT allows curators to make precise assertions as to when functions were gained and lost during evolution and record the evidence (e.g. experimentally supported GO annotations and phylogenetic information including orthology) for those assertions. In this article, we describe how we use PAINT to infer protein function in a phylogenetic context with emphasis on its strengths, limitations and guidelines. We also discuss specific examples showing how PAINT annotations compare with those generated by other highly used homology-based methods.
Cloning, expression and chromosomal localization of a novel gene for protein tyrosine phosphatase (PTP-U2) induced by various differentiation-inducing agents. (1995)

Previously, we cloned two gene fragments encoding novel protein tyrosine phosphatases, termed PTP-U1 and PTP-U2. Here, we report the full-length sequence, expression, and chromosomal localization of the PTP-U2 gene. The cDNA for PTP-U2, which was obtained from a human normal kidney library, predicts a protein of 1216 amino acids, -140 kDa, that contains a single transmembrane domain and a single intracellular catalytic domain. The extracellular domain of PTP-U2 contains 14 putative N-glycosylation sites and eight repeats of fibronectin type III-like motif. These data suggest that PTP-U2 is structurally similar to HPTP beta and DPTP10D, which have been reported previously. Northern blot analysis revealed that there were two different transcripts for PTP-U2. In kidney and brain, gene expression of PTP-U2 was detected as a 5.4 kb mRNA and in lung and placenta as 3.5 kb. The 3.5 kb transcript was also detected in human leukemia cell lines (eg., U937). Interestingly, its gene expression was enhanced by various differentiation-inducing agents, such as phorbol ester, dihydroxy vitamin D3, retinoic acid, and dimethyl sulfoxide. The bacterially expressed PTP-U2 fusion protein exhibited intrinsic tyrosine phosphatase activity. The PTP-U2 gene was assigned to chromosome 12p13.2-p13.3.