gebhart/patrepeval huggingface dataset:
Comparison of X‐ray and NMR structures: Is there a systematic difference in residue contacts between X‐ray‐ and NMR‐resolved protein structures? (2005)

We have compared structures of 78 proteins determined by both NMR and X-ray methods. It is shown that X-ray and NMR structures of the same protein have more differences than various X-ray structures obtained for the protein, and even more than various NMR structures of the protein. X-ray and NMR structures of 18 of these 78 proteins have obvious large-scale structural differences that seem to reflect a difference of crystal and solution structures. The other 60 pairs of structures have only small-scale differences comparable with differences between various X-ray or various NMR structures of a protein; we have analyzed these structures more attentively. One of the main differences between NMR and X-ray structures concerns the number of contacts per residue: (1) NMR structures presented in PDB have more contacts than X-ray structures at distances below 3.0 A and 4.5-6.5 A, and fewer contacts at distances of 3.0-4.5 A and 6.5-8.0 A; (2) this difference in the number of contacts is greater for internal residues than for external ones, and it is larger for beta-containing proteins than for all-alpha proteins. Another significant difference is that the main-chain hydrogen bonds identified in X-ray and NMR structures often differ. Their correlation is 69% only. However, analogous difference is found for refined and rerefined NMR structures, allowing us to suggest that the observed difference in interresidue contacts of X-ray and NMR structures of the same proteins is due mainly to a difference in mathematical treatment of experimental results.
An evaporation-based microfluidic sample concentration method (2002)

We present a method for sample concentration within microfluidic devices using evaporation-induced flow. Evaporation-induced flow is easy to incorporate into microfluidic designs and can be used to concentrate a wide variety of molecules. The practicality of this method was demonstrated with 0.2 microm fluorescent spheres and FITC-labeled BSA. Thirty two percent of the 0.6 microL fluorescent sphere suspension was concentrated into a well within a microfluidic device. In the same amount of time, 93% of the 0.6 microL FITC-labeled BSA solution was concentrated.
Different Toll-like receptor agonists induce distinct macrophage responses (2001)

We previously reported that gram-negative bacterial lipopolysaccharide (LPS) activates cells via Toll-like receptor (TLR) 4, whereas the mycobacterial cell wall glycolipid lipoarabinomannan (LAM) activates cells via TLR2. We also identified a secreted TLR2 agonist activity in short-term culture filtrates of Mycobacterium tuberculosis bacilli, termed soluble tuberculosis factor (STF). Here we show that STF contains mannosylated phosphatidylinositol (PIM) and that purified PIM possesses TLR2 agonist activity. Stimulation of RAW 264.7 macrophages by LPS, LAM, STF, and PIM rapidly activated nuclear factor (NF)-kappaB, activator protein-1 (AP-1), and mitogen-activated protein (MAP) kinases. These TLR agonists induced similar levels of NF-kappaB and AP-1 DNA-binding activity, as well as trans-activation function. Unexpectedly, these TLR agonists induced tumor necrosis factor alpha secretion, whereas only LPS was capable of inducing interleukin-1beta and nitric oxide secretion. Thus, different TLR proteins are still capable of activating distinct cellular responses, in spite of their shared capacities to activate NF-kappaB, AP-1, and MAP kinases.
Role of extracellular subdomains of p185 c-neu and the epidermal growth factor receptor in ligand-independent association and transactivation (2003)

We investigated the assembly and activation of the epidermal growth factor receptor (EGFR)-p185c-neu heterodimer by using a sequential immunoprecipitation methodology. Using this approach we detected heterodimers and also higher-ordered oligomeric complexes. Phosphorylated EGFR-p185c-neu heterodimeric forms were detected in the absence of EGF, but the species became highly phosphorylated after EGF stimulation. To evaluate heterodimer formation and additional transactivation by EGF, we investigated the roles of the four extracellular subdomains of p185c-neu and the EGFR. Subdomains I-IV of the EGFR dimerized with subdomains I-IV of p185c-neu, respectively, in a parallel manner. In addition, subdomains I-IV of the EGFR also associated with p185c-neu subdomains III, IV, I, and II, respectively. A lack of one of the p185c-neu cysteine-rich domains (subdomains II or IV) resulted in a loss of EGF-induced transactivation. These data suggest that two cysteine-rich domains play defining roles in ligand-dependent transactivation and that both of these cysteine-rich extracellular subdomains as well as non-cysteine-rich extracellular subdomains are involved in ligand-independent interactions with the EGFR. Our studies provide biochemical evidence of the role of the cysteine-rich domains of p185c-neu in assembly and transactivation of erbB complexes and also indicate that these subdomains might be useful clinical targets.
Changes in coagulation and permeability properties of human endothelial cells in vitro induced by TNF-alpha or 5,6 MeXAA. (1996)

5,6 dimethyl xanthenone acetic acid (5,6 MeXAA), an analogue of flavone acetic acid (FAA), has been shown to be more active against murine tumours than FAA. As both drugs have a vascular component in their mechanism of action similar to that observed for TNF-alpha, we have studied the effects of 5,6 MeXAA alone and in combination with TNF-alpha on endothelial function in vitro. The changes induced by the drugs on procoagulant activity and permeability were determined under tumour-simulated conditions of low oxygen tension and the presence of tumour-secreted factors. Procoagulant activity was assayed by measuring the time taken for human umbilical vein endothelial cells (HUVECs) to clot normal human plasma, increased activity resulting in reduced clotting times. HUVECs incubated under aerobic conditions were more sensitive to TNF-alpha than cells incubated at < or = 0.2% oxygen. Culture medium conditioned by the human breast adenocarcinoma cell line MDA-MB-231 strongly upregulated procoagulant activity under both aerobic and hypoxic conditions; clotting times were further reduced by TNF-alpha. Both 5,6 MeXAA and FAA potentiated the effect of TNF-alpha on normal hypoxic endothelial cells; however, under all other conditions, neither drug in combination with TNF-alpha upregulated clotting activity. The presence of tumour-secreted factors had a far greater effect on upregulating procoagulant activity than did oxygen tension. In contrast to procoagulant activity, permeability was insensitive to TNF-alpha and low concentrations of 5,6 MeXAA also caused no change in permeability.
A magnetically driven PDMS micropump with ball check-valves (2005)

In this paper, we present a low-cost, PDMS-membrane micropump with two one-way ball check-valves for lab-on-a-chip and microfluidic applications. The micropump consists of two functional PDMS layers, one holding the ball check-valves and an actuating chamber, and the other covering the chamber and holding a miniature permanent magnet on top for actuation. An additional PDMS layer is used to cover the top magnet, and thereby encapsulate the entire device. A simple approach was used to assemble a high-performance ball check-valve using a micropipette and heat shrink tubing. The micropump can be driven by an external magnetic force provided by another permanent magnet or an integrated coil. In the first driving scheme, a small dc motor (6 mm in diameter and 15 mm in length) with a neodymium–iron–boron permanent magnet embedded in its shaft was used to actuate the membrane-mounted magnet. This driving method yielded a large pumping rate with very low power consumption. A maximum pumping rate of 774 µL min−1 for deionized water was achieved at the input power of 13 mW, the highest pumping rate reported in the literature for micropumps at such power consumptions. Alternatively, we actuated the micropump with a 10-turn planar coil fabricated on a PC board. This method resulted in a higher pumping rate of 1 mL min−1 for deionized water. Although more integratable and compact, the planar microcoil driving technique has a much higher power consumption.
Automated analysis of nursing home observations (2004)

Pervasive activity monitoring in a skilled-nursing facility helps capture a continuous audio and video record. The CareMedia project analyzes this video information by automatically tracking people, helping to efficiently label individuals, and characterizing selected activities and actions.
A Sulfur Cathode with Pomegranate‐Like Cluster Structure (2015)

A novel sulfur cathode with pomegranate-like cluster structure is developed for high-energy lithium–sulfur batteries. It has stable cycling stability, high volumetric energy density, and excellent rate capability.
A comprehensive association study for genes in inflammation pathway provides support for their roles in prostate cancer risk in the CAPS study (2006)

Our study provides the first objective support for an association between prostate cancer and multiple modest-effect genes in inflammatory pathways.
Total synthesis of dehydrogliotoxin (1973)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTotal synthesis of dehydrogliotoxinYoshito. Kishi, Tohru. Fukuyama, and Shinichi. NakatsukaCite this: J. Am. Chem. Soc. 1973, 95, 19, 6492–6493Publication Date (Print):September 1, 1973Publication History Published online1 May 2002Published inissue 1 September 1973https://pubs.acs.org/doi/10.1021/ja00800a078https://doi.org/10.1021/ja00800a078research-articleACS PublicationsRequest reuse permissionsArticle Views748Altmetric-Citations59LEARN 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
Bandpass Sampling Digital Frontend Architecture for Multi-Band Access Cognitive Radio (2009)

Bandpass sampling (BPS) theory enables the conversion of RF frequency directly down to baseband, which is a significant technique in cognitive radio (CR) systems because they require flexibility in RF frontend. Based on this concept, second-order BPS frontends for CR systems are designed and verified by using a hardware platform. The methods adopted to manipulate spectrums to remove aliasing and images are described, and the equations employed to design interpolants are provided. The results of experiment indicate that the proposed second-order BPS frontends can realize universal access and environment sensing functionalities in CR systems.
Thyroid Status is a Key Modulator of Tumor Oxygenation: Implication for Radiation Therapy (2007)

In normal tissues, thyroid hormones play a major role in the metabolic activity and oxygen consumption of cells. Because the rate of oxygen consumption is a key factor in the response of tumors to radiation, we hypothesized that thyroid hormones may affect the metabolic activity of tumor cells and hence modulate the response to cytotoxic treatments. We measured the influence of thyroid status on the tumor microenvironment in experimental tumors. Hypothyroidism and hyperthyroidism were generated in mice by chronic treatment with propyl thiouracil and l-thyroxine. Thyroid status significantly modified tumor pO(2) as measured with EPR oximetry. Mechanistically, this was the result of the profound changes in oxygen consumption rates. Thyroid status was associated with a significant change in tumor radiosensitivity since the regrowth delay was increased in hypothyroid mice compared to euthyroid mice, an effect that was abolished when temporarily clamped tumors were irradiated. This study provides unique insights into the impact of modulating tumor oxygen consumption and could have implications in the management of cancer patients with thyroid disorders.
The cell surface leucine-rich repeat receptor for At Pep1, an endogenous peptide elicitor in Arabidopsis , is functional in transgenic tobacco cells (2006)

AtPep1 is a 23-aa endogenous peptide elicitor from Arabidopsis leaves that signals the activation of components of the innate immune response against pathogens. Here, we report the isolation of an AtPep1 receptor from the surface of Arabidopsis suspension-cultured cells. An (125)I-labeled AtPep1 analog interacted with suspension-cultured Arabidopsis with a K(d) of 0.25 nM, and an (125)I-labeled azido-Cys-AtPep1 photoaffinity analog specifically labeled a membrane-associated protein of approximately 170 kDa. The labeled protein was purified to homogeneity, and its tryptic peptides were identified as gene At1g73080, which encodes a leucine-rich repeat receptor kinase, here called PEPR1. Verification of the binding protein as the receptor for AtPep1 was established by demonstrating the loss of function of microsomal membranes of two SALK insertional mutants and by a gain in function of the alkalinization response to AtPep1 by tobacco suspension-cultured cells expressing the At1g73080 transgene. Synthetic homologs of AtPep1, deduced from the C termini of six known paralogs of PROPEP1, were biologically active and were competitors of the interaction of an AtPep1 radiolabeled analog with the receptor. The data are consistent with a role for PEPR1 as the receptor for AtPep1 to amplify innate immunity in response to pathogen attacks.
The mycosubtilin synthetase of Bacillus subtilis ATCC6633: A multifunctional hybrid between a peptide synthetase, an amino transferase, and a fatty acid synthase (1999)

Bacillus subtilis strain ATCC6633 has been identified as a producer of mycosubtilin, a potent antifungal peptide antibiotic. Mycosubtilin, which belongs to the iturin family of lipopeptide antibiotics, is characterized by a beta-amino fatty acid moiety linked to the circular heptapeptide Asn-Tyr-Asn-Gln-Pro-Ser-Asn, with the second, third, and sixth position present in the D-configuration. The gene cluster from B. subtilis ATCC6633 specifying the biosynthesis of mycosubtilin was identified. The putative operon spans 38 kb and consists of four ORFs, designated fenF, mycA, mycB, and mycC, with strong homologies to the family of peptide synthetases. Biochemical characterization showed that MycB specifically adenylates tyrosine, as expected for mycosubtilin synthetase, and insertional mutagenesis of the operon resulted in a mycosubtilin-negative phenotype. The mycosubtilin synthetase reveals features unique for peptide synthetases as well as for fatty acid synthases: (i) The mycosubtilin synthase subunit A (MycA) combines functional domains derived from peptide synthetases, amino transferases, and fatty acid synthases. MycA represents the first example of a natural hybrid between these enzyme families. (ii) The organization of the synthetase subunits deviates from that commonly found in peptide synthetases. On the basis of the described characteristics of the mycosubtilin synthetase, we present a model for the biosynthesis of iturin lipopeptide antibiotics. Comparison of the sequences flanking the mycosubtilin operon of B. subtilis ATCC6633, with the complete genome sequence of B. subtilis strain 168 indicates that the fengycin and mycosubtilin lipopeptide synthetase operons are exchanged between the two B. subtilis strains.
Concanavalin A—induced T-cell—mediated hepatic injury in mice: The role of tumor necrosis factor (1995)

Concanavalin A activates T lymphocytes in vitro and causes T-cell-dependent hepatic injury in mice. T lymphocytes were previously identified as effector cells of concanavalin A-induced liver injury. Here we report that hepatic injury is characterized by apoptotic cell death. On concanavalin A challenge, the cytokines tumor necrosis factor-α (TNF α), interleukin-2, granulocyte macrophage-colony stimulating factor, and interferon-γ were detectable in the circulation of the mice. Pretreatment of mice with anti-mouse TNF-α antiserum protected them from concanavalin A-induced liver injury. Nude mice failed to release TNF-α or interleukin-2 after concanavalin A challenge and were protected from liver injury. Lymph node cell transfer from responder mice to resistant nude mice resulted in susceptibility of the latter towards concanavalin A, i.e., to induction of cytokine release and hepatotoxicity. These experiments suggest that immunocompetent T cells play a pivotal role in concanavalin A-stimulated TNF-α release in vivo. After intravenous administration of fluorescein isothiocyanate-labeled concanavalin A to mice, the most fluorescence was found within the liver. In vitro , concanavalin A stimulation of separate cultures of mouse lymph node cells or nonparenchymal liver cells induced the release of minute amounts of TNF, whereas stimulation of cocultures of these cells resulted in production of substantial amounts of TNF-α. These findings may explain the hepatotropic effect of concanavalin A. In conclusion, T-cell-dependent concanavalin A-induced apoptotic liver injury in mice is related to immunological and cytokinemediated disorders and possibly to autoreactive hepatic processes. (Hepatology 1995;21:190-198).
Detailed characterization of the posttranscriptional gene-silencing-related small RNA in a GUS gene-silenced tobacco (2000)

Posttranscriptional gene-silencing phenomena such as cosuppression and RNA interference are associated with the occurrence of small, about 21-23 nt short RNA species homologous to the silenced gene. We here show that the small RNA present in silenced transgenic plants can easily be detected in total RNA isolated according to standard procedures. This will allow for the development of routine and early screenings for the presence of small RNA species and, therefore, gene silencing in transgenic plants. We further demonstrate that the small RNA fraction can be visualized with the SYBR Green II RNA stain, isolated from a gel, labeled and used as a specific probe. Using these approaches, we have fine-mapped the sequences of the GUS gene that are represented in the small RNA fraction of a GUS-silenced tobacco line containing an inverted repeat of the GUS gene. In this tobacco line, the silencing-associated small RNA is a mixture of fragments that cover the 3' two-thirds of the GUS coding region. The 5' coding and the 3' noncoding ends of the GUS mRNA are not represented in the small RNA fraction. The RNA fragments are not likely to be a primary synthesis product of an RNA-dependent RNA polymerase, but rather degradation products from nuclease activity. Surprisingly, RNA isolated from wild-type, untransformed plants showed the presence of a similar-sized small RNA pool. This might indicate the existence of small RNA species from putative endogenous genes that are down regulated by a similar posttranscriptional gene-silencing mechanism. The possibility of isolating and labeling the small RNA pool from wild-type plants will provide a way to identify and study such putative genes.
Surface Initiation of Living Radical Polymerization for Growth of Tethered Chains of Low Polydispersity (1999)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTSurface Initiation of Living Radical Polymerization for Growth of Tethered Chains of Low PolydispersityX. Huang and M. J. WirthView Author Information Department of Chemistry & Biochemistry, University of Delaware, Newark, Delaware 19716 Cite this: Macromolecules 1999, 32, 5, 1694–1696Publication Date (Web):February 20, 1999Publication History Received18 August 1998Revised22 December 1998Published online20 February 1999Published inissue 1 March 1999https://pubs.acs.org/doi/10.1021/ma981304xhttps://doi.org/10.1021/ma981304xbrief-reportACS PublicationsCopyright © 1999 American Chemical SocietyRequest reuse permissionsArticle Views1571Altmetric-Citations172LEARN 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:Living polymerization,Monomers,Polymer films,Polymers,Thickness Get e-Alerts
Characterization of composite high temperature superconductors for magnetic bearing applications (1990)

A study of high temperature superconductor composites for use in magnetic bearings applications is presented. Fabrication and characterization techniques are described. Magnetometry and mechanical force measurements are correlated with a particular emphasis on the role of superconductor particle size. Results are discussed in terms of fundamental limits of Meissner effect levitation. 21 refs., 11 figs., 1 tab.
Compression of optical solitons by conversion of nonlinear modes (1995)

One can transform an optical pulse containing higher-order soliton modes and/or radiation modes into a compressed almost ideal single-soliton pulse by passing it through an initial adaptive fiber of suitably chosen length and dispersion. Analytical approximations, in good agreement with numerical simulations, are found for the optimal values of the length and the dispersion of the adaptive fiber. The technique is applied to the case of nonadiabatically amplified soliton pulses, for which the transformation is shown to result in efficiently compressed soliton pulses.
Deposition of Co3O4 nanoparticles onto exfoliated graphite oxide sheets (2008)

A composite of graphite oxide (GO)-supported Co3O4nanoparticles (NPs) was prepared through a facile chemical route. The lamellar GO sheets in this composite were exfoliated and decorated randomly by Co3O4 particles with an average size of 100 nm. The formation route to anchor Co3O4 NPs onto the exfoliated GO sheets was proposed as the intercalation and adsorption of cobalt ions into the layered GO sheets, followed by the nucleation and growth of Co3O4 crystals, resulting in the exfoliation of GO sheets. The nanocomposite reveals unusual catalytic effect for the decomposition of ammonium perchlorate due to the concerted effects of GO and Co3O4 NPs or their integrated properties. This methodology made the synthesis of GO-NP composites possible and may be further extended to prepare more complicated nanocomposites based on GO sheets for technological applications.