gebhart/patrepeval huggingface dataset:
Identification of functional domains in the formyl peptide receptor‐like 1 for agonist‐induced cell chemotaxis (2005)

Formyl peptide receptor-like 1 (FPRL1) is a seven transmembrane domain, G protein-coupled receptor that interacts with a variety of exogenous and host-derived agonists. In order to identify domains crucial for ligand recognition by FPRL1, we used chimeric receptors with segments in FPRL1 replaced by corresponding amino acid sequences derived from the prototype formyl peptide receptor FPR. The chimeric receptors were stably transfected into human embryonic kidney epithelial cells and the capacity of the cells to migrate in response to formyl peptide receptor agonists was evaluated. Our results showed that multiple domains in FPRL1 are involved in the receptor response to chemotactic agonists with the sixth transmembrane domain and the third extracellular loop playing a prominent role. Interestingly, the N-terminus and a segment between the fourth transmembrane domain and the third intracellular loop of FPRL1 are important for receptor interaction with a 42 amino acid amyloid beta peptide (Abeta42), an Alzheimer's disease-associated FPRL1 agonist, but not with MMK-1, a synthetic FPRL1 agonist, suggesting that diverse agonists may use different domains in FPRL1. Considering the potential importance of FPRL1 in inflammation and neurodegenerative diseases, the identification of functional domains in this receptor will provide valuable information for the design of specific receptor antagonists.
Decreased Expression of BNC1 and BNC2 Is Associated with Genetic or Epigenetic Regulation in Hepatocellular Carcinoma (2016)

The aberrant expression of transcription factor Basonuclin (BNC) had been reported in different kinds of tumors. Here, we investigated the expression and methylation status of two Basonuclin homologs, BNC1 and BNC2 in hepatocellular carcinoma (HCC). We found that the expression levels of both BNC1 and BNC2 were down-regulated in HCC cell lines and primary HCC tissues. The frequency and intensity of BNC1 promoter hypermethylation in tumor tissues was significantly higher than that in adjacent non-tumor tissues. 5-Aza-2'-Deoxycytidine treatment could significantly increase the BNC1 expression in the methylated HCC cell lines, which implicated that epigenetic modification contributed to the down-regulation of BNC1. In addition, BNC1 hypermethylation in tumor tissues was more likely to happen in female patients. No methylation of the BNC2 promoter was found in HCC tumor tissues. However, a frequent deletion of the BNC2 gene was observed, which indicated that the chromosomal loss of the BNC2 gene might be one important reason for its lower expression level in HCC. Our results suggested that BNC1 and BNC2 were down-regulated in HCC which may provide new insight into the tumorigenesis of HCC.
DNA Sequence and Mutational Analysis of Rhizobitoxine Biosynthesis Genes in Bradyrhizobium elkanii (2001)

We cloned and sequenced a cluster of genes involved in the biosynthesis of rhizobitoxine, a nodulation enhancer produced by Bradyrhizobium elkanii. The nucleotide sequence of the cloned 28.4-kb DNA region encompassing rtxA showed that several open reading frames (ORFs) were located downstream of rtxA. A large-deletion mutant of B. elkanii, USDA94 Delta rtx::Omega 1, which lacks rtxA, ORF1 (rtxC), ORF2, and ORF3, did not produce rhizobitoxine, dihydrorhizobitoxine, or serinol. The broad-host-range cosmid pLAFR1, which contains rtxA and these ORFs, complemented rhizobitoxine production in USDA94 Delta rtx::Omega 1. Further complementation experiments involving cosmid derivatives obtained by random mutagenesis with a kanamycin cassette revealed that at least rtxA and rtxC are necessary for rhizobitoxine production. Insertional mutagenesis of the N-terminal and C-terminal regions of rtxA indicated that rtxA is responsible for two crucial steps, serinol formation and dihydrorhizobitoxine biosynthesis. An insertional mutant of rtxC produced serinol and dihydrorhizobitoxine but no rhizobitoxine. Moreover, the rtxC product was highly homologous to the fatty acid desaturase of Pseudomonas syringae and included the copper-binding signature and eight histidine residues conserved in membrane-bound desaturase. This result suggested that rtxC encodes dihydrorhizobitoxine desaturase for the final step of rhizobitoxine production. In light of results from DNA sequence comparison, gene disruption experiments, and dihydrorhizobitoxine production from various substrates, we discuss the biosynthetic pathway of rhizobitoxine and its evolutionary significance in bradyrhizobia.
Software-improved hardware lock elision (2014)

With hardware transactional memory (HTM) becoming available in mainstream processors, lock-based critical sections may now initiate a hardware transaction instead of taking the lock, enabling their concurrent execution unless a real data conflict occurs. However, just a few transactional aborts can cause the lock to be acquired non-transactionally resulting in the serialization of all the threads, severely degrading the amount of speedup obtained. In this paper we provide two software extension mechanisms that considerably improve the concurrency and speedup levels attained by lock based programs using HTM-based lock elision. The first sacrifices opacity to achieve higher levels of concurrency, and the second retains opacity while reaching slightly lower levels of concurrency.
Photoconduction in Polydiacetylene Multilayer Structures and Single Crystals. Evidence for Band‐to‐Band Excitation (1978)

Abstract Steady state photoconduction action spectra for polydiacetylene multilayer structures and single crystals (TCDU) are reported. Interpretation is given in terms of a valence‐to‐conduction band transition which is buried under the vibronic sidebands of the dominant exciton transition. The associated absorption coefficient follows a (α b ħω) ˜ (ħω − E g ) 2 law which indicates either an indirect transition or a direct transition between non‐parabolic bands. The general validity of this relationship is supported by literature data for PTS, DCHD, and polyethylene. Gap energies are (2.5 ± 0.1) eV and (2.6 ± 0.1) eV for two different multilayer forms, (2.6 ± 0.1) eV for TCDU, (2.1 ± 0.1) eV for PTS, and (2.30 ± 0.05) eV for DCHD. The transition is three‐dimensional indicating finite valence and conduction band dispersion perpendicular to the polymer chain direction.
An Efficient High-Frequency Drive Circuit for GaN Power HFETs (2009)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> The requirements for driving gallium nitride (GaN) heterostructure field-effect transistors (HFETs) and the design of a resonant drive circuit for GaN power HFET switches are discussed in this paper. The use of wideband III-nitride (such as GaN) devices today is limited to telecom and low-power applications. The current lack of high-frequency high-power drivers prevents their application in power converters. The proposed circuit is based upon resonant switching transition techniques, by means of an <formula formulatype="inline"><tex Notation="TeX">$LC$</tex></formula> tag, to recover part of the power back into the voltage source in order to reduce the power loss. This circuit also uses level shifters to generate the zero and negative gate–source voltages required to turn the GaN HFET on and off, and it is highly tolerant to input-signal timing variances. The circuit reduces the overall power consumed in the driver and thus reduces the power loss. This is particularly important for high-frequency driver operation to take full advantage, in terms of efficiency, of the superior switching speed of GaN devices. In this paper, the topology of the low-power-loss high-speed drive circuit is introduced. Some simulation results and preliminary experimental measurements are discussed. </para>
WATER CHANNELS AND UREA TRANSPORTERS (1997)

1. It now appears that when water crosses an endothelium which is not fenestrated, or an epithelium with tight junctions, it does so rapidly, and with low energy cost, only if the cell membrane contains an adequate number of specific water channels, encoded by one of at least six different genes. 2. The water channel genes so far cloned encode a series of integral membrane proteins called aquaporins, all of approximately 30 kDa (265-282 amino acids), in the unglycosylated state. All but one (AQP3) are specific water channels and all but one (AQP4) are inactivated by mercurial compounds. 3. Aquaporin 0 is the major (60%) intrinsic protein (MIP) of lens fibre cells of the eye. Mutations in this gene are associated with cataract formation in mice. 4. Aquaporin 1, also called CHIP-28, exists in the membrane as a homotetramer, and is present in red blood cells, the choroid plexus, the proximal tubule and descending limb of the loop of Henle in the kidney as well as in many other sites. Surprisingly, no pathological consequence is known in patients lacking a functional AQP1 gene. 5. Aquaporin 2, also called WCH-CD, is the water channel of the principal cell of the cortical and medullary collecting duct, and is located in cytoplasmic vesicles unless arginine vasopressin is acting, when it is translocated to the apical membrane by synaptobrevins or vesicle associated membrane protein 2 (VAMP2). Lack of a functional AQP2 gene leads to a rare form of nephrogenic diabetes insipidus. 6. Aquaporins 3, 4, and 5 are located in many tissues-AQP3 and AQP4 being in the basolateral membrane of the renal cortical and medullary principal cell, as well as in the gastrointestinal tract (AQP3) and the brain (AQP4). 7. Four sequences are known for urea transporters HUT11-the urea transporter of the human red cell membrane, and HUT2, rUT2, rbUT2-the arginine vasopressin inducible urea transporters of the human, rat and rabbit kidney. They are specifically permeable to urea, not to water, and are claimed to be inhibited by phloretin. 8. The water channel proteins contain six membrane-spanning regions, whilst the urea transporters are thought to contain at least 10 membrane spanning segments. 9. Very little work has examined the ontogeny of these proteins, except in the rat, and virtually nothing is known of the expression of these genes in pregnancy or in any disorder of fluid balance in the mother or foetus.
83. Experiments on the preparation of indolocarbazoles. Part VI. Compounds from two of the amino-1-phenylbenzotriazoles (1953)

A. R. Katritzky and S. G. P. Plant, J. Chem. Soc., 1953, 412 DOI: 10.1039/JR9530000412
Basal ganglia precursors found in aggregates following embryonic transplantation adopt a striatal phenotype in heterotopic locations (1998)

Transplantation of immature CNS-derived cells into the developing brain is a powerful approach to investigate the factors that regulate neuronal position and phenotype. CNS progenitor cells dissociated from the embryonic striatum and implanted into the brain of embryos of the same species generate cells that reaggregate to form easily recognizable structures that we previously called clusters and cells that disperse and integrate as single cells into the host brain. We sought to determine if the neurons in the clusters differentiate according to their final location or acquire a striatal phenotype in heterotopic positions. We transplanted dissociated cells from the E14 rat medial and lateral ganglionic eminences, either combined or in isolation, into the E16 embryonic rat brain. At all time points, we found clusters of BrdU- and DiI-labelled donor cells located in the forebrain and hindbrain, without any apparent preference for striatum. Immunocytochemical analyses revealed that cells in the clusters expressed DARPP-32 and ARPP-21, two antigens typically co-expressed in striatal medium-sized spiny neurons. In agreement with observations previously noted by several groups, isolated cells integrated into heterologous host areas do not express basal ganglia phenotypes. These data imply that immature striatal neuronal progenitors exert a community effect on each other that is permissive and/or instructive for development of a striatal phenotype in heterotopic locations.
Mouse p170 Is a Novel Phosphatidylinositol 3-Kinase Containing a C2 Domain (1996)

Phosphatidylinositol (PI) 3-kinases catalyze the formation of 3'-phosphoinositides, which appear to promote cellular responses to growth factors and such membrane trafficking events as insulin-stimulated translocation of intracellular glucose transporters. We report here the cloning of a novel PI 3-kinase, p170, from cDNA of insulin-sensitive mouse 3T3-L1 adipocytes. Mouse p170 utilizes PI and to a limited extent PI 4-P as substrates, in contrast to the PI-specific yeast VPS34 homolog PtdIns 3-kinase and the p110 PI 3-kinases, which phosphorylate PI, PI 4-P, and PI 4,5-P2. Mouse p170 is also distinct from PtdIns 3-kinase or the p110 PI 3-kinases in exhibiting a 10-fold lower sensitivity to wortmannin. Unique structural elements of p170 include C-terminal sequences strikingly similar to the phosphoinositide-binding C2 domain of protein kinase C isoforms, synaptotagmins, and other proteins. These features of mouse p170 are shared with a recently cloned Drosophila PI 3-kinase, DmPI3K_68D. Together, these proteins define a new class of PI 3-kinase likely influenced by cellular regulators distinct from those acting upon p110- or VPS34-like PI 3-kinases.
Doxorubicin prodrugs with reduced cytotoxicity suited for tumour-specific activation. (1998)

The three new hydrophilic prodrugs 2, 3 and 4 have been prepared from methyl (4-hydroxymethyl-2-nitrophenyl 2,3,4-tri-O-acetyl-beta-D-glucopyranosid)uronate (5) and doxorubicin. Their low cytotoxicity, efficient release of doxorubicin after hydrolysis by beta-D-glucuronidase, and in the cases of 2 and 3 stability at pH 7.2 fulfil the preliminary requirement for their use in antibody-directed enzyme prodrug therapy or prodrug monotherapy.
Epidermal Growth Factor Receptor Inhibitors in Development for the Treatment of Non–Small Cell Lung Cancer (2006)

The epidermal growth factor receptor (EGFR) inhibitors erlotinib, gefitinib, and cetuximab have undergone extensive clinical testing and have established clinical activity in non-small cell lung cancer and other types of solid tumors. A number of newer inhibitors are currently in clinical development with different spectra of activity or mechanisms of receptor inhibition. These include monoclonal antibodies, such as panitumumab and matuzumab; dual inhibitors of EGFR and vascular endothelial growth factor receptor, such as ZD6474 and AEE788; inhibitors of multiple EGFR family members, such as lapatinib; and irreversible inhibitors, such as canertinib and HKI272. Preclinical studies suggest that several of these agents may have activity in tumors refractory to erlotinib or gefitinib. Among these agents, ZD6474 has undergone the most extensive clinical testing. The antitumor activity of ZD6474 in these two randomized phase II clinical trials in patients with non-small cell lung cancer was felt to be sufficiently promising to warrant phase III clinical testing. Several of the other EGFR inhibitors are also undergoing advanced clinical testing, either alone or in combination with other agents. EGFR has now been validated as a clinically relevant target, and several different types of agents inhibiting this receptor are currently in development. Future research will be needed to elucidate the role of these agents in patients with EGFR inhibitor-naive and EGFR inhibitor-refractory disease, to define the molecular characteristics that predict response, and to determine whether these drugs should be used in combination with other targeted agents or chemotherapy.
Selective Modification of Variable Loops Alters Tropism and Enhances Immunogenicity of Human Immunodeficiency Virus Type 1 Envelope (2004)

Although the B clade of human immunodeficiency virus type 1 (HIV-1) envelopes (Env) includes five highly variable regions, each of these domains contains a subset of sequences that remain conserved. The V3 loop has been much studied for its ability to elicit neutralizing antibodies, which are often restricted to a limited number of closely related strains, likely because a large number of antigenic structures are generated from the diverse amino acid sequences in this region. Despite these strain-specific determinants, subregions of V3 are highly conserved, and the effects of different portions of the V3 loop on Env tropism and immunogenicity have not been well delineated. For this report, selective deletions in V3 were introduced by shortening of the stem of the V3 loop. These mutations were explored in combination with deletions of selected V regions. Progressive shortening of the stem of V3 abolished the immunogenicity as well as the functional activity of HIV Env; however, two small deletions on both arms of the V3 stem altered the tropism of the dualtropic 89.6P viral strain so that it infected only CXCR4(+) cells. When this smaller deletion was combined with removal of the V1 and V2 loops and used as an immunogen in guinea pigs, the antisera were able to neutralize multiple independent clade B isolates with a higher potency. These findings suggest that highly conserved subregions within V3 may be relevant targets for eliciting neutralizing antibody responses, affecting HIV tropism, and increasing the immunogenicity of AIDS vaccines.
Horizontal drilling is becoming commonplace (1989)

Daily low dose rhuIL-2 adjunctive treatment stimulates immune activation and may enhance the antimicrobial response in MDR-TB.
Isolation of cDNA clones encoding the 80-kd subunit protein of the human autoantigen Ku (p70/p80) by antisera raised against ciliary processes of human eye donors. (1994)

The ocular ciliary epithelium induces a species-specific immune response in xenogenic animals. In particular, the human ciliary epithelium elicits a strong immune recognition of the 80-kd subunit protein of the human autoantigen Ku (p70/p80) in ODM-2 cells.
Error-Correction in Flash Memories via Codes in the Ulam Metric (2013)

<?Pub Dtl=""?> We consider rank modulation codes for flash memories that allow for handling arbitrary charge-drop errors. Unlike classical rank modulation codes used for correcting errors that manifest themselves as swaps of two adjacently ranked elements, the proposed translocation rank codes account for more general forms of errors that arise in storage systems. Translocations represent a natural extension of the notion of adjacent transpositions and as such may be analyzed using related concepts in combinatorics and rank modulation coding. Our results include derivation of the asymptotic capacity of translocation rank codes, construction techniques for asymptotically good codes, as well as simple decoding methods for one class of constructed codes. As part of our exposition, we also highlight the close connections between the new code family and permutations with short common subsequences, deletion and insertion error-correcting codes for permutations, and permutation codes in the Hamming distance.
Flame-Retardants for Fabrics. Function of Boron-Containing Additives (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFlame-Retardants for Fabrics. Function of Boron-Containing AdditivesM. A. Kasem and H. R. RichardsCite this: Ind. Eng. Chem. Prod. Res. Dev. 1972, 11, 2, 114–133Publication Date (Print):June 1, 1972Publication History Published online1 May 2002Published inissue 1 June 1972https://pubs.acs.org/doi/10.1021/i360042a002https://doi.org/10.1021/i360042a002research-articleACS PublicationsRequest reuse permissionsArticle Views277Altmetric-Citations10LEARN 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 options Get e-Alerts
Synthesis of 5‐(4‐substituted benzyl)‐2,4‐diaminoquinazolines as inhibitors of candida albicans dihydrofolate reductase (1995)

Abstract Several 5‐(4‐substituted benzyl)‐2,4‐diaminoquinazolines were prepared as potentially selective inhibitors of Candida albicans dihydrofolate reductase. These compounds were synthesized by a novel route, which included as a key step the displacement of a fluoro group in 2,6‐difluorobenzonitrile by the anions of ethyl or methyl 4‐substituted phenylacetates. The resultant diarylacetates were saponified and decarboxylated to the 2‐fluoro‐6‐(4‐substituted phenyl)benzonitriles. Ring closure of these benzonitriles with guanidine carbonate gave the 5‐(4‐substituted benzyl)‐2,4‐diaminoquinazolines.
An overview of the Amber biomolecular simulation package (2012)

Abstract Molecular dynamics (MD) allows the study of biological and chemical systems at the atomistic level on timescales from femtoseconds to milliseconds. It complements experiment while also offering a way to follow processes difficult to discern with experimental techniques. Numerous software packages exist for conducting MD simulations of which one of the widest used is termed Amber. Here, we outline the most recent developments, since version 9 was released in April 2006, of the Amber and AmberTools MD software packages, referred to here as simply the Amber package. The latest release represents six years of continued development, since version 9, by multiple research groups and the culmination of over 33 years of work beginning with the first version in 1979. The latest release of the Amber package, version 12 released in April 2012, includes a substantial number of important developments in both the scientific and computer science arenas. We present here a condensed vision of what Amber currently supports and where things are likely to head over the coming years. Figure 1 shows the performance in ns/day of the Amber package version 12 on a single‐core AMD FX‐8120 8‐Core 3.6GHz CPU, the Cray XT5 system, and a single GPU GTX680. © 2012 John Wiley &amp; Sons, Ltd. This article is categorized under: Software &gt; Molecular Modeling