gebhart/patrepeval huggingface dataset:
A Cyclic AMP Receptor Protein-Regulated Cell-Cell Communication System Mediates Expression of a FecA Homologue in <i>Stenotrophomonas maltophilia</i> (2007)

Stenotrophomonas maltophilia WR-C possesses an rpf/diffusible signal factor (DSF) cell-cell communication system. It produces cis-Delta2-11-methyl-dodecenoic acid, a DSF, and seven structural derivatives, which require rpfF and rpfB for synthesis. Acquisition of iron from the environment is important for bacterial growth as well as the expression of virulence genes. We identified a gene homologous to fecA, which encodes a ferric citrate receptor that transports exogenous siderophore ferric citrate from the environment into the bacterial periplasm. Western blot analysis with anti-FecA-His(6) antibody showed that the FecA homologue was induced in the iron-depleted medium supplemented with a low concentration of ferric citrate. Deletion of rpfF or rpfB resulted in reduced FecA expression compared to the wild type. Synthetic DSF restored FecA expression by the DeltarpfF mutant to the wild-type level. Reverse transcription-PCR showed that the fecA transcript was decreased in the DeltarpfF mutant compared to the wild type. These data suggest that DSF affected the level of fecA mRNA. Transposon inactivation of crp, which encodes cyclic AMP (cAMP) receptor protein (CRP) resulted in reduced FecA expression and rpfF transcript level. Putative CRP binding sites were located upstream of the rpfF promoter, indicating that the effect of CRP on FecA is through the rpf/DSF pathway and by directly controlling rpfF. We propose that CRP may serve as a checkpoint for iron uptake, protease activity, and hemolysis in response to environmental changes such as changes in concentrations of glucose, cAMP, iron, or DSF.
Peptidomimetics as receptors agonists or peptidase inhibitors: A structural approach in the field of enkephalins, ANP and CCK (1992)

Stabilization of biologically active conformations of native peptides by cyclization or introduction of hindering residues led to peptidominetics endowed with high affinity and selectivity for one class of receptors and able to cross the blood brain barrier. This is the case of BUBU, Tyr-D-Ser(OtBu)-Gly-Phe-Leu-Thr(OtBu) and BUBUC, Tyr-D-Cys-(OtBu)-Gly-Phe-Leu-Thr(OtBu) for the opioid delta receptors and of BC 254, Boc-gamma-D-Glu-Tyr(SO3H)-Nle-D-Lys-Trp-Nle-Asp-PheNH2 and of BC 264, Boc-Tyr(SO3H)gNle-mGly-Trp-MeNle-Asp-PheNH2 for central CCK-B receptors. Inhibition of metabolizing peptidases such as aminopeptidase N and endopeptidase 24.11 (NEP) for enkephalins and of NEP and ACE for atrial natriuretic peptide and angiotensin I by mixed inhibitors such as kelatorphan and RB 101 or ES14, rationally designed by taking into account the structural differences in the active site of these zinc-metallopeptidases, led to potent analgesics devoid of the major morphine side effects or to new antihypertensives.
Risk factors of young‐onset dementia: a UK Biobank study (2023)

Abstract Background While age is the main risk factor for developing dementia, in young‐onset dementia (YOD) symptoms can already start before the age of 65 years. Genetic factors figure more prominent in the onset of YOD than late‐onset dementia but still only account for 5‐10% of the clinical YOD cases. It is therefore important to understand how modifiable risk factors, such as lifestyle or cardiovascular factors, and their interactions with genetic factors are associated with risk for YOD. The aim of this study was to examine a comprehensive set of factors and their association with the incidence of YOD. Method We used data from individuals aged under 65 years (n = 356,052) in the UK Biobank, a prospective population‐based cohort, to investigate risk factors related to YOD. Incidence of dementia was determined from hospital and death records. Potential risk factors were identified from systematic reviews on late‐onset dementia and YOD, including socio‐demographic, genetic, lifestyle, environmental, blood markers, cardiometabolic, psychiatric and other factors. These were analyzed in multivariable Cox proportional hazards regression. Result During 2,891,409 person‐years of follow‐up, 485 cases of YOD were reported. Incidence rates for women increased from 1.88/100,000 person‐years in age 40‐44 to 53.38/100,000 person‐years in age 60‐64. In men incidence rates increased from 5.41/100,000 person‐years in age 45‐49, to 79.54/100,000 person‐years in age 60‐64. A total of 38 variables were analyzed. In univariable analyses, 30 factors were associated with YOD, of which 15 were significantly associated with the incidence of YOD in multivariable analyses. These variables included lower formal education, lower socioeconomic status, carrying the apolipoprotein ε4 allele, no alcohol use, alcohol intoxication, social isolation, vitamin D deficiency, high c‐reactive protein levels, lower handgrip strength (i.e., higher physical frailty), hearing impairment, orthostatic hypotension, stroke, diabetes, heart disease and depression. Conclusion This study found potentially modifiable risk factors for YOD. While further exploration of these risk factors is necessary to validate our findings and identify potential underlying mechanisms, addressing these modifiable factors may prove effective in mitigating the risk of developing YOD.
The Cleavage of t-Butyldimethylsilyl Ethers with Boron Trifluoride Etherate (1979)

Abstract The t-butyldimethylsilyl protecting group for alcohols was introduced by Corey in 19722. Since then it has proved a popular choice in many syntheses.
Trends in rig-floor technology (1981)

A discussion is presented of the four basic motivating factors influencing changes: safety, force, crew size, and efficiency.
Laser Ablation Mass Spectrometry of Pyrolyzed Koppers Coal-Tar Pitch:  A Precursor for Fullerenes and Metallofullerenes (1999)

Pyrolyzed Koppers coal-tar pitch samples consisting mainly of polycyclic aromatic hydrocarbons were studied by direct laser vaporization Fourier transform ion cyclotron resonance and time-of-flight mass spectrometry. Fullerene cations were readily formed from these carbonaceous precursors over a wide range of low-laser ablation power densities. The laser-desorption ionization of the pyrolyzed coal-tar pitches shows the presence of a range of polyaromatic hydrocarbons some containing as many as 70 carbon atoms, which should require only small amounts of laser energy to convert them into fullerenes. Metallofullerene formation also occurs with low power laser ablation of pyrolyzed mixtures of metal oxides, metal sulfides, or metal carbonates and the Koppers coal-tar pitch. Ablation with two different laser pulse widths of 230 μs and 8 ns, at a laser wavelength of 1064 nm, shows that only the long-pulse low-power (200−2000 kW cm-2) laser radiation produces metallofullerene ions. The short-pulse high-power (1−2300 MW cm-2) laser ablation results only in the formation of small metal carbide cluster and fullerene ions. Collision-induced dissociation experiments were used to study the structures of the small metal carbide clusters and the endohedral metallofullerene ion, La@C60+.
Inhibition of coagulation factors by recombinant barley serpin BSZx (1996)

Barley serpin BSZx is a potent inhibitor of trypsin and chymotrypsin at overlapping reactive sites (Dahl, S.W., Rasmussen, S.K. and Hejgaard, J. (1996) J. Biol. Chem., in press). We have now investigated the interactions of BSZx with a range of serine proteinases from human plasma, pancreas and leukocytes, a fungal trypsin and three subtilisins. Thrombin, plasma kallikrein, factor VIIa/tissue factor and factor Xa were inhibited by BSZx at heparin independent association rates (k(ass)) of 4.5 X 10(3)-1.3 x 10(5) M(-1) s(-1) at 22 degrees C. Only factor Xa turned a significant fraction of BSZx over as substrate. Complexes of these proteinase with BSZx resisted boiling in SDS, and amino acid sequencing showed that cleavage in the reactive center loop only occurred after P1 Arg. Activated protein C and leukocyte elastase were slowly inhibited by BSZx (k(ass)=1-2 x 10(2) M(-1) s(-1)) whereas factor XIIa, urokinase and tissue type plasminogen activator, plasmin and pancreas kallikrein and elastase were not or only weakly affected. The inhibition pattern with mammalian proteinases reveal a specificity of BSZx similar to that of antithrombin III. Trypsin from Fusarium was not inhibited while interaction with subtilisin Carlsberg and Novo was rapid but most BSZx was cleaved as a substrate. Identification of a monoclonal antibody specific for native BSZx indicate that complex formation and loop cleavage result in similar conformational changes.
Noncoding RNA and Polycomb recruitment (2013)

A plethora of noncoding (nc) RNAs has been revealed through the application of high-throughput analysis of the transcriptome, and this has led to an intensive search for possible biological functions attributable to these transcripts. A major category of functional ncRNAs that has emerged is for those that are implicated in coordinate gene silencing, either in cis or in trans. The archetype for this class is the well-studied long ncRNA Xist which functions in cis to bring about transcriptional silencing of an entire X chromosome in female mammals. An important step in X chromosome inactivation is the recruitment of the Polycomb repressive complex PRC2 that mediates histone H3 lysine 27 methylation, a hallmark of the inactive X chromosome, and recent studies have suggested that this occurs as a consequence of PRC2 interacting directly with Xist RNA. Accordingly, other ncRNAs have been linked to PRC2 targeting either in cis or in trans, and here also the mechanism has been proposed to involve direct interaction between PRC2 proteins and the different ncRNAs. In this review, I discuss the evidence for and against this hypothesis, in the process highlighting alternative models and discussing experiments that, in the future, will help to resolve existing discrepancies.
Progeria - A Brief Review (2010)

Progeria or Hutchinson‐Gilford progeria syndrome is a rare genetic disorder characterized by dramatic premature aging and accelerated cardiovascular dise ase. It is almost never passed on from parent to child. Progeria is almost always caused by de novo point mutation in the laminA gene that activates a cryptic splice donor site, producing a truncated mu tant protein termed ‘‘progerin.’’ Progeria shows characteristic facial appearance including prominen t eyes, thin nose with a beaked tip, thin lips, a s mall chin, and protruding ears, severe hardening of the arteries beginning in childhood. In the past, docto rs had to base a diagnosis of progeria solely on physi cal symptoms but progeria research foundation establishes the Progeria cell and tissue bank to as sist in further research and diagnostic process. As pirin may help prevent atherothrombotic events, stroke an d heart attacks by hindering platelet aggregation. Vitamin supplementation, Fluoride supplements are recommended. A Study of Zoledronic acid, Pravastatin, and Lonafarnib for Patients with Proge ria is ongoing, it is under phase II.
Continuous word embeddings for detecting local text reuses at the semantic level (2014)

Text reuse is a common phenomenon in a variety of user-generated content. Along with the quick expansion of social media, reuses of local text are occurring much more frequently than ever before. The task of detecting these local reuses serves as an essential step for many applications. It has attracted extensive attention in recent years. However, semantic level similarities have not received consideration in most previous works. In this paper, we introduce a novel method to efficiently detect local reuses at the semantic level for large scale problems. We propose to use continuous vector representations of words to capture the semantic level similarities between short text segments. In order to handle tens of billions of documents, methods based on information geometry and hashing methods are introduced to aggregate and map text segments presented by word embeddings to binary hash codes. Experimental results demonstrate that the proposed methods achieve significantly better performance than state-of-the-art approaches in all six document collections belonging to four different categories. At some recall levels, the precisions of the proposed method are even 10 times higher than previous methods. Moreover, the efficiency of the proposed method is comparable to or better than that of some other hashing methods.
Editable graphical histories (2003)

The authors have designed a testbed system that creates a series of automatically generated panels that depict in chronological order the important events in the history of a users session with Chimera, a graphical editor. The authors' system heuristically determines the contents of each panel and the actions that it illustrates. The user can scroll through the sequence of panels, reviewing actions at different levels of detail, and selectively undoing, modifying, and redoing previous actions.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
The Emerging Understanding of Myeloid Cells as Partners and Targets in Tumor Rejection (2015)

Myeloid cells are the most prominent among cells capable of presenting tumor-derived antigens to T cells and thereby maintaining the latter in an activated state. Myeloid populations of the tumor microenvironment prominently include monocytes and neutrophils (sometimes loosely grouped as myeloid-derived suppressor cells), macrophages, and dendritic cells. Although intratumoral myeloid populations, as a whole, have long been considered nonstimulatory or suppressive, it has only recently been appreciated that not all tumor-infiltrating myeloid cells are made equal. Because of advances in high-dimensional flow cytometry as well as more robust transcriptional profiling, we now also understand that the subsets of the tumor-myeloid compartment are far more diverse and notably even contain a rare population of stimulatory dendritic cells. As all of these myeloid populations represent major T-cell-interacting partners for incoming tumor-reactive cytotoxic T lymphocytes, understanding the distinctions in their lineage and function reveals and guides numerous therapeutic avenues targeting these antigen-presenting cells. In this Cancer Immunology at the Crossroads overview, we review the recent progress in this rapidly evolving field and advance the hypothesis that the antigen-presenting compartment within tumor microenvironments may contain significant numbers of potent allies to be leveraged for immune-based tumor clearance.
Large polycyclic aromatic hydrocarbons: Synthesis and discotic organization (2009)

Abstract Polycyclic aromatic hydrocarbons (PAHs) have attracted enormous interest due to their unique electronic and optoelectronic properties as well as the potential applications in organic electronics. This article reviews the progress in the modern synthesis of large PAHs with different sizes, shapes, edge structures, and substituents. Due to their outstanding self-organization characteristics, the discotic liquid-crystalline properties, self-assembled nanostructures on the surfaces, as well as the application in electronic devices will be discussed.
Optimization of extraction and purification of active fractions from<i> Schisandra chinensis</i> (Turcz.) and its osteoblastic proliferation stimulating activity (2008)

Extraction and purification conditions of lignans from the fruits and seeds of Schisandra chinensis (Turcz.) were investigated through an orthogonal design of L(9)(3(4)) assay and macroporous resin technology. The extraction was optimized using 95% ethanol. For purification, the extract was dissolved in 30% ethanol, then adsorbed on a AB-8 macroporous resin and eluted with 30% ethanol and 70% ethanol successively, the latter resulting in a residue containing 65.2% of lignans. By HPLC analysis schisandrin, deoxyschisandrin and gamma-schisandrin were quantitatively determined. UMR 106 cells were used to examine the stimulatory activity of the lignans on osteoblasts in vitro. The lignans stimulated the proliferation of and the activity of alkaline phosphatase in the osteoblasts indicating their potential activity against osteoporosis.
A hybrid solar cell based on silicon nanowire and organic thin film (2014)

In this work, a hybrid solar cell based on Si nanowires (NWs) coated with a polymer (PCBM) is presented. Vertically well-aligned Si NWs were successfully synthesized by a Ag-assisted electroless etching technique with etching depth of ∼3 µm uniformly distributed over the surface of p-type Si wafer. Three-dimensional (p-Si NW)/PCBM ([6,6]-phenyl C61-butyric acid methyl ester) hybrid solar cell was fabricated by encapsulation of Si NW arrays by a thin layer of PCBM deposited by spin-coating process. The characteristics of the hybrid cell was studied with current–voltage and capacitance–voltage measurements by which the barrier height and ideality factor were found to be 0.85 V and 2.2, respectively. From a partially illuminated area of the Al/p-Si NW/PCBM/ITO structured hybrid solar cell, the open circuit voltage, short-circuit current density, fill factor, and power conversion efficiency were calculated as 0.19 V, 8.1 mA cm−2, 27 and 0.41%, respectively.
Structural Considerations of NK109, an Antitumor Benzo[<i>c</i>]phenanthridine Alkaloid (1999)

The antitumor activities of a synthetic benzo[c]phenanthridine, NK109 (7-hydroxy-2, 3-methylenedioxy-5-methyl-8-methoxybenzo[c]phenanthridinium hydrogensulfate dihydrate), and of natural benzo[c]phenanthridines were tested in vitro and in vivo. NK109 (3) had the highest activity among them. NK109 is similar in structure to fagaronine and fagaridine; however, it has a phenolic-OH at C-7. NK109 exists as a resonance hybrid, the keto-amine and zwitterionic forms in neutral media. The resonance hybrid is cationic and has molecular planarity; these have been considered to be essential for the antitumor activity of the benzo[c]phenanthridinium salts. On the other hand, the structurally similar benzo[c]phenthridine alkaloids, chelerythrine and sanguinarine, exist as pseudobases under the same conditions. The latter do not exhibit antitumor activity in vivo, probably because they lose both the immonium region and molecular planarity. Thus, 3 may be considered to be novel category of benzo[c]phenanthridinium salt from the viewpoint of its structure under biological conditions.
Pea Xyloglucan and Cellulose (1984)

Two auxin-induced endo-1,4-beta-glucanases (EC 3.2.1.4) were purified from pea (Pisum sativum L. var. Alaska) epicotyls and used to degrade purified pea xyloglucan. Hydrolysis yielded nonasaccharide (glucose/xylose/galactose/fucose, 4:3:1:1) and heptasaccharide (glucose/xylose, 4:3) as the products. The progress of hydrolysis, as monitored viscometrically (with amyloid xyloglucan) and by determination of residual xyloglucan-iodine complex (pea) confirmed that both pea glucanases acted as endohydrolases versus xyloglucan. K(m) values for amyloid and pea xyloglucans were approximately the same as those for cellulose derivatives, but V(max) values were lower for the xyloglucans. Auxin treatment of epicotyls in vivo resulted in increases in net deposits of xyloglucan and cellulose in spite of a great increase (induction) of endogenous 1,4-beta-glucanase activity. However, the average degree of polymerization of the resulting xyloglucan was much lower than in controls, and the amount of soluble xyloglucan increased. When macromolecular complexes of xyloglucan and cellulose (cell wall ghosts) were treated in vitro with pea 1,4-beta-glucanase, the xyloglucan component was preferentially hydrolyzed and solubilized. It is concluded that xyloglucan is the main cell wall substrate for pea endo-1,4-beta-glucanase in growing tissue.
Combinatorial Chemistry and Mass Spectrometry in the 21st Century Drug Discovery Laboratory (2001)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCombinatorial Chemistry and Mass Spectrometry in the 21st Century Drug Discovery LaboratoryD. B. KasselView Author Information DuPont Pharmaceuticals Research Laboratories, 4570 Executive Drive, Suite 400, San Diego, California 92121 Cite this: Chem. Rev. 2001, 101, 2, 255–268Publication Date (Web):January 19, 2001Publication History Received24 July 2000Published online19 January 2001Published inissue 1 February 2001https://pubs.acs.org/doi/10.1021/cr990085qhttps://doi.org/10.1021/cr990085qresearch-articleACS PublicationsCopyright © 2001 American Chemical SocietyRequest reuse permissionsArticle Views1317Altmetric-Citations108LEARN 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 SUBJECTS:Chemical synthesis,Combinatorial libraries,Mass spectrometry,Peptides and proteins,Purification Get e-Alerts
Infrared Transmission Properties of Sapphire, Spinel, and Yttria as a Function of Temperature (1986)

The characterization of the bulk absorption and scattering properties of sapphire, spinel, and yttria, as a function of temperature, is accomplished using a Bomem DA3.02 Fourier transform spectrometer and a heated cell. The measurements are performed between 2 μm and 20 μm and from room temperatures to 775 K. The ratio of the spectra of two samples of different thicknesses is taken to eliminate mutual surface effects and to provide a direct measure of the bulk extinction coefficient. The absorption coefficient data are used to determine parameters in a mulitphoton absorption model. The model has proven valid up to the melting temperature of the material. Therefore, an accurate means of interpolating and extrapolating the data is obtained. A comprehensive characterization of the material's absorption properties with frequency and temperature is realized.
Skeletal Structures for Modeling Generalized Chamfers and Fillets in the Presence of Complex Miters (2018)

Computer-Aided Design and Applications is an international journal on the applications of CAD and CAM. It publishes papers in the general domain of CAD plus in emerging fields like bio-CAD, nano-CAD, soft-CAD, garment-CAD, PLM, PDM, CAD data mining, CAD and the internet, CAD education, genetic algorithms and CAD engines. The journal is aimed at all developers and users of CAD technology to ptovide CAD solutions for various stages of design and manufacturing. The journal publishes all about Computer-Aided Design and Computer-Aided technologies.