gebhart/patrepeval huggingface dataset:
Processing Map and Essential Cleavage Sites of the Nonstructural Polyprotein Encoded by ORF1 of the Feline Calicivirus Genome (2002)

Feline calicivirus (FCV) nonstructural proteins are translated as part of a large polyprotein that undergoes autocatalytic processing by the virus-encoded 3C-like proteinase. In this study, we mapped three new cleavage sites (E(46)/A(47), E(331)/D(332), and E(685)/N(686)) recognized by the virus proteinase in the N-terminal part of the open reading frame 1 (ORF1) polyprotein to complete the processing map. Taken together with two sites we identified previously (E(960)/A(961) and E(1071)/S(1072)), the FCV ORF1 polyprotein contains five cleavage sites that define the borders of six proteins with calculated molecular masses of 5.6, 32, 38.9, 30.1, 12.7, and 75.7 kDa, which we designated p5.6, p32, p39 (NTPase), p30, p13 (VPg), and p76 (Pro-Pol), respectively. Mutagenesis of the E to A in each of these cleavage sites in an infectious FCV cDNA clone was lethal for the virus, indicating that these cleavages are essential in a productive virus infection. Mutagenesis of two cleavage sites (E(1345)/T(1346) and E(1419)/G(1420)) within the 75.7-kDa Pro-Pol protein previously mapped in bacterial expression studies was not lethal.
Response of White Blood Cells to Iodipamide Ethyl Ester Particles (1986)

The effect of intravenously injected iodipamide ethyl ester (IDE) particles (150 mgl/kg) on white blood cells was studied by light and electron microscopy. The clearance of IDE from rat plasma also was determined by analyzing free IDE particles in a counting chamber. The total white blood cell count remained essentially unchanged up to 40 minutes after the IDE injection, but the polymorphonuclear (PMN) neutrophil count decreased significantly. At 5 minutes postinjection, occasional PMNs contained ingested IDE particles, but by 40 minutes no intracellular particles could be found in the peripheral circulation. In vitro incubation experiments confirmed that human PMNs ingest IDE particles. In electron microscopy, the cells and particles seemed to be morphologically intact. Of the IDE particles counted at 5 minutes postinjection, only 4% remained in plasma at 30 minutes and none at 40 minutes. The decrease in PMN count apparently reflects sequestration of phagocytic cells from the circulation.
Fabrication of Nanowire Electronics on Nonconventional Substrates by Water-Assisted Transfer Printing Method (2011)

We report a simple, versatile, and wafer-scale water-assisted transfer printing method (WTP) that enables the transfer of nanowire devices onto diverse nonconventional substrates that were not easily accessible before, such as paper, plastics, tapes, glass, polydimethylsiloxane (PDMS), aluminum foil, and ultrathin polymer substrates. The WTP method relies on the phenomenon of water penetrating into the interface between Ni and SiO(2). The transfer yield is nearly 100%, and the transferred devices, including NW resistors, diodes, and field effect transistors, maintain their original geometries and electronic properties with high fidelity.
.DELTA.1-1,2-Diazetines (1969)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT.DELTA.1-1,2-DiazetinesNorbert Rieber, James Alberts, James A. Lipsky, and David M. LemalCite this: J. Am. Chem. Soc. 1969, 91, 20, 5668–5669Publication Date (Print):September 1, 1969Publication History Published online1 May 2002Published inissue 1 September 1969https://pubs.acs.org/doi/10.1021/ja01048a056https://doi.org/10.1021/ja01048a056research-articleACS PublicationsRequest reuse permissionsArticle Views419Altmetric-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-Alertsclose Get e-Alerts
Intron–Exon Organization and Phylogeny in a Large Superfamily, the Paralogous Cytochrome P450 Genes of <i>Arabidopsis thaliana</i> (2000)

The cytochrome P450 gene superfamily is represented by 80 genes in animal genomes and perhaps more than 300 genes in plant genomes. We analyzed about half of all Arabidopsis P450 genes, a very large dataset of truly paralogous genes. Sequence alignments were used to draw phylogenetic trees, and this information was compared with the intron-exon organization of each P450 gene. We found 60 unique intron positions, of which 37 were phase 0 introns. Our results confirm the polyphyletic origin of plant P450 genes. One group of these genes, the A-type P450s, are plant specific and characterized by a simple organization, with one highly conserved intron. Closely related A-type P450 genes are often clustered in the genome with as many as a dozen genes (e.g., of the CYP71 subfamily) on a short stretch of chromosome. The other P450 genes (non-A-type) form several distinct clades and are characterized by numerous introns. One such clade contains the two CYP51 genes, which are thought to encode obtusifoliol 14a demethylase. The two CYP51 genes have a single intron that is not shared with CYP51 genes from vertebrates or fungi, or with any other Arabidopsis P450 gene. Only a few of the Arabidopsis P450 genes are intronless (e.g., the CYP710A and CYP96A subfamilies). There was a relatively good correlation between intron conservation and phylogenetic relationships between members of the P450 subfamilies. Gene organization appears to be a useful tool in establishing the evolutionary relatedness of P450 genes, which may help in predictions of P450 function.
Anti‐(Arg‐Gly‐Asp‐Ser) antibody and its interaction with fibronectin, fibrinogen and platelets (1988)

An antibody population recognizing the sequence Arg-Gly-Asp-Ser (RGDS) in fibronectin, anti-(RGDS)N, was isolated by immunoadsorption. Between 2.5% and 4.9% of antibodies were obtained from two different anti-fibronectin sera indicating that this region represents an antigenic epitope in native fibronectin. Complete inhibition of binding of 125I-fibronectin to anti-(RGDS)N was produced only by nonreduced and reduced fibronectin. Fibrinogen and synthetic RGDS tetrapeptide, each at concentration of 10 microM, showed only a slight inhibition of 22% and 17%, respectively. Measurements of the conformational constant, the equilibrium constant for the interconversion of the non-native and native conformations of this epitope, showed that less than 0.0001% of the RGDS molecules adopt the native conformation in aqueous solutions. It indicates that long-range interactions in fibronectin and fibrinogen result in different conformations of the RGDS sequence in both proteins. Anti-(RGDS)N antibodies purified from anti-fibronectin serum had a strong inhibitory effect on thrombin-stimulated platelet aggregation. They also inhibited binding of fibronectin and fibrinogen to thrombin-stimulated platelets, supporting the primary role of the RGDS sequence in the direct interaction of these proteins with platelet membrane receptors.
Playing Tricks with Designer "Atoms" (2002)

Macromolecules or colloids in solution can serve as large-scale models for atoms and simple molecules. But as Frenkel explains in his Perspective, this is not all. Colloidal suspensions can also form new states of matter. He highlights the reports by Velikov et al. and Pham et al., who demonstrate how the properties of such suspensions can be tuned in unprecedented ways.
Control of nephrotoxicity in the rat during repeated <i>cis</i>‐platinum treatments (1989)

The nephrotoxicity of cis-platinum (CDDP) in the rat can be controlled throughout a series of weekly administrations of CDDP (each of 5 mg kg-1, i.v.) for at least three weeks by a combination of protective measures involving pretreatment with dithiocarbamates and diuretics and the administration of appropriate dithiocarbamates given 1 h after the CDDP. The use of dithiocarbamates with polar substitutents is effective in removing both renal and hepatic deposits of platinum from rats subsequent to its administration and in this respect these compounds are significantly superior to meso-2,3-dimercaptosuccinic acid (DMSA) in the rate at which platinum is removed and in the amounts removed. The most effective of the dithiocarbamates remove ca. 70% of the platinum from the kidneys and the liver; the least effective remove ca. 50% of the platinum from these organs when given at a level of 1.57 mmol kg-1 i.p. for 6 days subsequent to the administration of CDDP. Acetazolamide was shown to be much less effective in preventing renal damage than the dithiocarbamates and was not effective in reducing renal or hepatic levels of platinum. Pretreatment with sodium diethyldithiocarbamate 12 h prior to the administration of the CDDP was more effective in preventing renal damage than the administration of this compound 30 min before the cis-platinum. Several dithiocarbamates are found to be superior to sodium diethyldithiocarbamate in reducing renal platinum burdens of rats given CDDP at the level of 6 mg kg-1, and dose-response curves for the removal of renal and hepatic platinum were determined for sodium N-methyl-D-glucamine dithiocarbamate (NaG).(ABSTRACT TRUNCATED AT 250 WORDS)
Chapter VI: Darwin (1980)

In this year falls the fiftieth anniversary of the death of Charles Darwin—one of those rare individuals who have altered the main trend of thought and inaugurated a new attitude and a new outlook in human affairs.—J ULIAN H UXLEY , Contemporary Review , October 1932. Language has justly been considered as one of the chief distinctions between man and the lower animals. But man, as a highly competent judge, Archbishop Whately, remarks, ‘is not the only animal that can make use of language to express what is passing in his mind, and can understand, more or less, what is so expressed by another.’—D ARWIN , Descent of Man , Chap. III. The investigation of language, as pointed out in the last chapter, had been carried on for a hundred years in the belief that language was a unique characteristic of man, and did not extend to the animal world beneath him. But with the publication of the Descent of Man in 1871 the whole problem of language was suddenly expanded into a much wider region. Darwin, in that book, distinctly challenged the human boundaries that had been set to language as being artificial and arbitrary, and extended the problem over into the animal world, maintaining that the difference between the language of man and the cries of animals was not a difference in kind, as had been formerly thought, but a difference in degree only, a difference in definiteness of connotation and distinctness of articulation. This difference in language followed naturally, he maintained, upon the difference in degree of their mental development.
Targeting GLP-1 receptor trafficking to improve agonist efficacy (2018)

Glucagon-like peptide-1 receptor (GLP-1R) activation promotes insulin secretion from pancreatic beta cells, causes weight loss, and is an important pharmacological target in type 2 diabetes (T2D). Like other G protein-coupled receptors, the GLP-1R undergoes agonist-mediated endocytosis, but the functional and therapeutic consequences of modulating GLP-1R endocytic trafficking have not been clearly defined. Here, we investigate a series of biased GLP-1R agonists with variable propensities for GLP-1R internalization and recycling. Compared to a panel of FDA-approved GLP-1 mimetics, compounds that retain GLP-1R at the plasma membrane produce greater long-term insulin release, which is dependent on a reduction in β-arrestin recruitment and faster agonist dissociation rates. Such molecules elicit glycemic benefits in mice without concomitant increases in signs of nausea, a common side effect of GLP-1 therapies. Our study identifies a set of agents with specific GLP-1R trafficking profiles and the potential for greater efficacy and tolerability as T2D treatments.
A Single Factor Underlies the Metabolic Syndrome (2006)

OBJECTIVE—Confirmatory factor analysis (CFA) was used to test the hypothesis that the components of the metabolic syndrome are manifestations of a single common factor. RESEARCH DESIGN AND METHODS—Three different datasets were used to test and validate the model. The Spanish and Mauritian studies included 207 men and 203 women and 1,411 men and 1,650 women, respectively. A third analytical dataset including 847 men was obtained from a previously published CFA of a U.S. population. The one-factor model included the metabolic syndrome core components (central obesity, insulin resistance, blood pressure, and lipid measurements). We also tested an expanded one-factor model that included uric acid and leptin levels. Finally, we used CFA to compare the goodness of fit of one-factor models with the fit of two previously published four-factor models. RESULTS—The simplest one-factor model showed the best goodness-of-fit indexes (comparative fit index 1, root mean-square error of approximation 0.00). Comparisons of one-factor with four-factor models in the three datasets favored the one-factor model structure. The selection of variables to represent the different metabolic syndrome components and model specification explained why previous exploratory and confirmatory factor analysis, respectively, failed to identify a single factor for the metabolic syndrome. CONCLUSIONS—These analyses support the current clinical definition of the metabolic syndrome, as well as the existence of a single factor that links all of the core components.
Nanofibril Formation of Electrospun TiO<sub>2</sub>Fibers and its Application to Dye‐Sensitized Solar Cells (2005)

Electrospun TiO2 nanofibers were employed to the quasi‐solid state dye‐sensitized solar cells with porous electrodes, which enhanced the penetration of viscous polymer gel electrolytes. The morphology of electrospun TiO2 fibers was affected by the electrospinning parameters such as the types of polymers, the concentration of polymer and titanium(IV) propoxide (TiP), the ratio of TiP/PVAc. The TiO2 fibers electrospun from poly(vinyl acetate) matrix formed the one‐dimensionally aligned fibrillar morphology as an islands‐in‐a‐sea structure. The new TiO2 electrodes demonstrated that the photocurrent generation with polymer gel electrolytes was over 90% of the performance in a dye‐sensitized solar cell with liquid electrolytes.
Management of Liver Trauma In 811 Consecutive Patients (1974)

University of Texas, Southwestern Medical Center, Dallas, Texas *Department of Surgery, San Francisco General Hospital, San Francisco, California 94110.
Stem Cells and Regenerative Medicine on the Asian Horizon: An Economic, Industry and Social Perspective (2009)

For the past decade, forays into stem cell research and regenerative medicine by institutes and companies based in the Asia-Pacific region have attracted global attention at levels unprecedented in the life sciences. The unique combination of economic pressures, competitiveness and opportunism, laissez-faire regulation, burgeoning investment in the life sciences and rapidly growing markets, coupled with its great diversity, have propelled the region to surge forward in some areas, but to stumble in others. This article provides a historical and scientific context to the state of stem cell research and clinical applications in the region, and highlights trends and new possibilities to watch for on the Asian horizon.
Noise parameters and light sensitivity of low-noise high-electron-mobility transistors at 300 and 12.5 K (1986)

The four noise parameters of cryogenically cooled HEMT's have been investigated. Two different HEMT structures, with and without spacer layer were tested. The noise parameters of both structures were similar at the room temperature, while they were dramatically different at cryogenic temperatures. The minimum noise temperatures measured at 8.4 GHz were 75 ± 5 K at the room temperature and 8.5 ± 1.5 K at the temperature of 12.5 K. The cryogenic performance is the best ever observed for field-effect transistors.
Dynamic Non-Parametric Mixture Models and The Recurrent Chinese Restaurant Process: with Applications to Evolutionary Clustering (2008)

Clustering is an important data mining task for exploration and visualization of different data types like news stories, scientific publications, weblogs, etc. Due to the evolving nature of these data, evolutionary clustering, also known as dynamic clustering, has recently emerged to cope with the challenges of mining temporally smooth clusters over time. A good evolutionary clustering algorithm should be able to fit the data well at each time epoch, and at the same time results in a smooth cluster evolution that provides the data analyst with a coherent and easily interpretable model. In this paper we introduce the temporal Dirichlet process mixture model (TDPM) as a framework for evolutionary clustering. TDPM is a generalization of the DPM framework for clustering that automatically grows the number of clusters with the data. In our framework, the data is divided into epochs; all data points inside the same epoch are assumed to be fully exchangeable, whereas the temporal order is maintained across epochs. Moreover, The number of clusters in each epoch is unbounded: the clusters can retain, die out or emerge over time, and the actual parameterization of each cluster can also evolve over time in a Markovian fashion. We give a detailed and intuitive construction of this framework using the recurrent Chinese restaurant process (RCRP) metaphor, as well as a Gibbs sampling algorithm to carry out posterior inference in order to determine the optimal cluster evolution. We demonstrate our model over simulated data by using it to build an infinite dynamic mixture of Gaussian factors, and over real dataset by using it to build a simple non-parametric dynamic clustering-topic model and apply it to analyze the NIPS12 document collection.
Variable Range Hopping Conduction in Semiconductor Nanocrystal Solids (2004)

The temperature and electrical field dependent conductivity of n-type CdSe nanocrystal thin films is investigated. In the low electrical field regime, the conductivity follows sigma approximately exp([-(T(*)/T)(1/2)] in the temperature range 10<T<120 K. At high electrical field, the conductivity is strongly field dependent. At 4 K, the conductance increases by 8 orders of magnitude over one decade of bias. At a very high field, conductivity is temperature independent with sigma approximately exp([-(E(*)/E)(1/2)]. The complete behavior is very well described by variable range hopping with a Coulomb gap.
Pigment Formation for Differentiating <i>Cryptococcus neoformans</i> from <i>Candida albicans</i> (1971)

When 2,3- or 3,4-dihydroxybenzoic acid, 3,4-dihydroxyphenylalanine, and 3,4-dihydroxycinnamic acid are added to growth media, they are converted to a characteristic brown pigment by Cryptococcus neoformans. This pigment formation has hitherto been encountered only when this microorganism was cultivated on media containing Guizotia abyssinica seed. This phenomenon can be used for differentiating Cryptococcus neoformans from Candida albicans. Possible precursors of these o-diphenols (quinic acid, aromatic monohydroxy acids, or tyrosine) do not give rise to the brown pigmentation.
Persistent human cytomegalovirus infection induces drug resistance and alteration of programmed cell death in human neuroblastoma cells. (1998)

Infection with human cytomegalovirus (HCMV) is a common and generally asymptomatic affection in childhood. Its role in neuroblastoma (NB) patients has not yet been elucidated. As evidence grows that HCMV interacts with apoptotic signaling due to the interaction of HCMV gene products with cellular proteins of apoptotic pathways, we used human NB cell line UKF-NB-2 persistently infected with HCMV strain AD169 to study the effects of long-term HCMV infection on programmed cell death of neuroectodermal tumor cells. The cells designated UKF-NB-2AD169 continued to produce infectious virus in successive subcultures over a period of more than 1 year. Up to 20% of cells expressed viral genes or produced infectious virus after initiation of infection. UKF-NB-2AD169 cells were significantly less sensitive to the cytotoxic agents cisplatinum and etoposide than parental (noninfected) UKF-NB-2 cells. These effects were associated with decreased ability of UKF-NB-2AD169 cells to undergo apoptosis and continuous viral replication. UKF-NB-2AD169 cells showed increased levels of antiapoptosis Bcl-2 protein (up to 12-fold), whereas expression of p53 and c-myc was not changed. Treatment of UKF-NB-2AD169 cells with ganciclovir, abolishing virus production, reestablished sensitivity to chemotherapy, lowered Bcl-2 expression, and facilitated inducibility of apoptosis to the level of the parental cell line. The results demonstrate that persistent HCMV infection confers resistance to cytotoxic agents on neuroectodermal tumor cells and protects from apoptosis, probably due to increased levels of Bcl-2 protein. Hence, it is conceivable that HCMV infection before or during tumorigenesis may contribute in some NB patients to failure of therapy.
Evaluation of a High Grain Protein QTL from <i>Triticum turgidum</i> L. var. <i>dicoccoides</i> in an Adapted Durum Wheat Background (2001)

Grain protein concentration (GPC) is an important component of durum wheat ( Triticum turgidum L. var. durum ) quality. The ‘Langdon’‐ Triticum turgidum L. var. dicoccoides chromosome 6B substitution line [LDN(DIC‐6B)] contains the high GPC quantitative trait locus “ QGpc.ndsu.6Bb ” We evaluated the effect of this quantitative trait locus on GPC, grain yield, and other agronomic traits in an adapted durum wheat background, verified its location on chromosome 6B and determined its relationship to the GPC locus previously identified. A recombinant inbred population consisting of 110 lines segregating for high GPC was developed from the LDN(DIC‐6B) with two doses of adapted germplasm. This population was evaluated in the field for GPC at two locations in 1995, and for GPC, grain yield, and other agronomic characteristics at three locations in 1996. Segregation analysis for GPC showed a bimodal distribution, indicating a single genetic factor or a tightly linked gene cluster controlling high GPC. This high GPC locus was insensitive to environmental conditions. Grain protein concentration was not correlated with plant height, but was loosely correlated with grain yield and heading date. Quantitative trait locus analysis using simple regression and interval mapping procedures identified a locus flanked by Xcdo365 and Xmwg79 on chromosome 6B as having a major effect on GPC. This high GPC locus, which explained up to 72% of the phenotypic variance, accounted for a 15 g kg −1 increase in average GPC. Selection for the two markers flanking the GPC QTL would be highly effective in introgressing this QTL into durum wheat breeding programs.