gebhart/patrepeval huggingface dataset:
Nitrogen stress response and stringent response are coupled in Escherichia coli (2014)

Assimilation of nitrogen is an essential process in bacteria. The nitrogen regulation stress response is an adaptive mechanism used by nitrogen-starved Escherichia coli to scavenge for alternative nitrogen sources and requires the global transcriptional regulator NtrC. In addition, nitrogen-starved E. coli cells synthesize a signal molecule, guanosine tetraphosphate (ppGpp), which serves as an effector molecule of many processes including transcription to initiate global physiological changes, collectively termed the stringent response. The regulatory mechanisms leading to elevated ppGpp levels during nutritional stresses remain elusive. Here, we show that transcription of relA, a key gene responsible for the synthesis of ppGpp, is activated by NtrC during nitrogen starvation. The results reveal that NtrC couples these two major bacterial stress responses to manage conditions of nitrogen limitation, and provide novel mechanistic insights into how a specific nutritional stress leads to elevating ppGpp levels in bacteria.
The Role of Excitonic Light Collection, Exciton Diffusion to Interfaces, Internal Fields for Charge Separation, and High Charge Carrier Mobilities (1994)

Abstract Organic photovoltaic thin film structures made by vacuum vapor deposition have been studied. From the spectral response as a function of the absorption coefficient we conclude that electron — hole generation takes place at the interface between the organic thin film and one or both of the semitransparent cover electrodes. The observed short circuit currents, however, are too large to be explained on the basis of a direct light-induced charge transfer at the organic thin film/electrode interface. Rather, a contribution of the bulk-absorbed photons is necessary to account for the observed quantum yield. Transfer of the energy to the interface sites can be explained by diffusional migration of excitons. The efficiency of charge separation can be improved by combining donor and acceptor type partners in organic double layers. The efficiency of power conversion, however, not only depends on a suitable choice of the absorption spectra and of the ionic energy levels of the materials employed, but also on the internal cell resistance, a fact that calls for high charge carrier mobilities, and hence for using materials with crystal structures that allow strong π-electron interactions, and for deposition in high chemical purity and structural perfection.
Molecular characterization of commercial porcine factor VIII concentrate (1988)

Commercial porcine factor VIII concentrate (Hyate:C) is effective in treatment of patients with hemophilia A who have circulating antibodies to factor VIII. The molecular forms of factor VIII in the concentrate were identified and evaluated in light of the known properties of porcine and human factor VIII. The factor VIII in the concentrate was isolated by tandem chromatography on gelatin-Sepharose and monoclonal anti-factor VIII-Sepharose. The factor VIII was 1% of the protein mass of the concentrate when calculated by either quantity of protein recovered or by radioimmunoassay. Both functional assay and Western blotting of the crude concentrate indicated that maximum coagulant function was achieved by proteolytic activation of procofactor forms of factor VIII. The factor VIII can be fractionated by cation-exchange high-performance liquid chromatography (HPLC) into two or three species of heterodimers depending on the lot. The specific activity of the purified porcine factor VIII was 550 U/mg using pooled porcine plasma at 1 U/mL as a standard. From this value, a factor VIII concentration in normal pig plasma of 2 micrograms/mL was calculated. This agreed well with a value of 3 micrograms/mL obtained by radioimmunoassay (RIA) of factor VIII in porcine plasma. In contrast, reported values for human factor VIII average 5800 U/mg, resulting in a calculated concentration in plasma of 0.2 microgram/mL. The finding that porcine plasma contains a significantly higher circulating mass of factor VIII than human plasma appears to explain previous difficulties in comparing porcine and human factor VIII in standard assays.
Mapping the Gnutella network (2002)

We studied the topology and protocols of the public Gnutella network. Its substantial user base and open architecture make it a good large-scale, if uncontrolled, testbed. We captured the network's topology, generated traffic, and dynamic behavior to determine its connectivity structure and how well (if at all) Gnutella's overlay network topology maps to the physical Internet infrastructure. Our analysis of the network allowed us to evaluate costs and benefits of the peer-to-peer (P2P) approach and to investigate possible improvements that would allow better scaling and increased reliability in Gnutella and similar networks. A mismatch between Gnutella's overlay network topology and the Internet infrastructure has critical performance implications.
IP routers: new tool for gigabit networking (1998)

IP routing continues to receive much attention from the research and vendor communities. Its primary function-forwarding packets between networks-must keep pace with the demands of the exponentially growing end user population. It must accommodate attachment of gigabit data link technologies such as ATM, packet Sonet, Gigabit Ethernet, and dense wave division multiplexing, and fill those links at full capacity. As network providers introduce new services supporting multicast, QoS, voice, and security, IP routing-and more specifically the IP forwarding function-will be called upon to analyze additional packet information at gigabit rates to determine how each packet should be handled. Performing these new functions while maintaining parity with the advances in available bandwidth will present an interesting challenge for the forwarding capabilities of IP routers. Indeed, for the Internet to scale, we must scale all dimensions of the IP routing process.
Magnetic domain structures of focused ion beam-patterned cobalt films using scanning ion microscopy with polarization analysis (2004)

Studies of magnetic domain distributions in patterned magnetic materials are of pivotal importance in the areas of ultrahigh density magnetic recording, MRAM design, and miniaturized magnetic sensor arrays. Scanning ion microscopy with polarization analysis (SIMPA) is used to perform in situ topographic and magnetic domain imaging and focused ion beam (FIB) patterning. For FIB-patterned 30 nm thick Co films, it is found that rectangular Co bars of sizes between 10–30 μm exhibit S type, whereas circular shaped magnetic elements show C type micromagnetic magnetization patterns. It is shown that SIMPA provides a simple way to directly identify different micromagnetic domain patterns.
Fludarabine induces apoptosis, activation, and allogenicity in human endothelial and epithelial cells: protective effect of defibrotide (2002)

Fludarabine is a nonmyeloablative immunosuppressant increasingly used as a component of alternative conditioning regimens before allogeneic bone marrow transplantation. It is expected to reduce conditioning-related toxicity and proinflammatory activation of the host tissues. However, in our in vitro study, we provide evidence that 2-fluoroadenine 9-beta-D-arabinofuranoside (F-Ara) as the active metabolized form of fludarabine damages human microvascular endothelial cells (HMECs) and dermal and alveolar epithelial cell lines after 48 hours of culture when it is used in pharmacologically relevant concentrations (range, 10 microg/mL-1 microg/mL). In addition, flow cytometric analyses revealed a significant up-regulation of intercellular adhesion molecule 1 and major histocompatibility complex (MHC) class I molecules by F-Ara, suggesting a proinflammatory activation of HMECs. Cytotoxicity assays demonstrated that target HMECs pretreated with F-Ara (10 microg/mL) showed increased lysis by allogeneic MHC class I-restricted cytotoxic T lymphocytes from healthy human donors. We conclude that, beside its immunosuppressive activities, F-Ara can be harmful for target tissues of transplantation-related complications and can even stimulate allogeneic immune responses. We identified the pharmaceutical compound defibrotide as protective against F-Ara- induced apoptosis and alloactivation, importantly, without affecting the antileukemic effect of F-Ara. This observation argues for a potential clinical usage of defibrotide in pretransplantation conditioning.
Anti–Interleukin-17 Monoclonal Antibody Ixekizumab in Chronic Plaque Psoriasis (2012)

Use of a humanized anti-interleukin-17 monoclonal antibody, ixekizumab, improved the clinical symptoms of psoriasis. Further studies are needed to establish its long-term safety and efficacy in patients with psoriasis. (Funded by Eli Lilly; ClinicalTrials.gov number, NCT01107457.).
The decoration of carbon nanotubes by metal nanoparticles (1996)

Acid-treated carbon nanotubes have been decorated with nanoscale Au, Pt and Ag clusters by employing several procedures. The nature and extent of metal coverage can be varied by changing the concentration of the metal compound or by mild sonication (treatment with ultrasound). The metal clusters seem to get deposited on the acidic surface sites of the nanotubes.
Structure-activity studies of the hepatocarcinogenicities of alkenylbenzene derivatives related to estragole and safrole on administration to preweanling male C57BL/6J x C3H/HeJ F1 mice. (1987)

Further information on the structure-activity relationships among the synthetic and naturally occurring alkenylbenzene derivatives was obtained by examining their hepatocarcinogenicities for mice following administration of one or a few doses prior to weaning. Under these conditions preweanling male C3H/HeJ mice were more susceptible than male C57BL/6J mice or females of either strain to liver tumor induction by 1'-hydroxyestragole (1'-hydroxy-1-allyl-4-methoxybenzene) and 1'-hydroxysafrole (1'-hydroxy-1-allyl-3,4-methylenedioxybenzene). Male C57BL/6J X C3H/HeJ F1 mice given a single dose of 1'-hydroxyestragole at 12 days of age developed approximately twice as many hepatomas per liver as did those given the same dose per g of body weight at 1 day of age. The acetylenic compounds 1'-hydroxy-2',3'-dehydroestragole and 1'-hydroxy-2',3'-dehydrosafrole were the most potent derivatives studied; they were 5- and 10-fold more potent (based on the average numbers of hepatomas per liver) than the corresponding allylic benzene derivatives. 1'-Acetoxyestragole and 1'-acetoxysafrole had activities similar to those of their respective 1'-hydroxy derivatives; estragole derivatives were consistently 2- to 3-fold more potent than the related safrole derivatives. 1'-Hydroxyelemicin (1'-hydroxy-1-allyl-3,4,5-trimethoxybenzene), its acetic acid ester 1'-oxoestragole, and 3'-bromo-trans-anethole (3'-bromo-1-trans-propenyl-4-methoxybenzene) each had very weak, but statistically significant, hepatocarcinogenic activity. The propenylic derivatives cis-anethole, trans-isosafrole, 1:1 cis,trans-isosafrole, 3'-hydroxy-trans-anethole, piperine, and trans-cinnamaldehyde showed no hepatocarcinogenic activity at the levels examined. In contrast, the propenylic derivatives cis- and trans-asarone (1-propenyl-2,4,5-trimethoxybenzene) were each active; the hepatocarcinogenicities of the asarones were not inhibited by prior administration of pentachlorophenol, a sulfotransferase inhibitor that abolished the hepatocarcinogenicity of estragole under the same conditions. Furthermore, precocene II (6,7-dimethoxy-2,2-dimethyl-2H-1-benzopyran), a cyclic propenylic plant metabolite and asarone analogue, showed strong hepatocarcinogenic activity similar to that of 1'-hydroxy-2',3'-dehydroestragole and 1'-hydroxy-2',3'-dehydrosafrole; precocene I (the 7-methoxy analogue of precocene II) was less active than precocene II but more active than cis-asarone.
Baclofen treatment in a patient with tardive dystonia. (1986)

The use of baclofen, a structural analog of gamma-aminobutyric acid (GABA), is described in the treatment of a patient with tardive dystonia. The patient, a woman with a clinical diagnosis of Alzheimer's disease, developed tardive dystonia after 8 weeks of haloperidol therapy and experienced complete remission of her dystonia while taking baclofen 60 mg/day. This case suggests that baclofen may facilitate remission of tardive dystonia in some cases and provides a basis for further investigation.
Novel Approach to Inhibit Asthma-Mediated Lung Inflammation Using Anti-CD147 Intervention (2006)

Extracellular cyclophilins have been well described as chemotactic factors for various leukocyte subsets. This chemotactic capacity is dependent upon interaction of cyclophilins with the cell surface signaling receptor CD147. Elevated levels of extracellular cyclophilins have been documented in several inflammatory diseases. We propose that extracellular cyclophilins, via interaction with CD147, may contribute to the recruitment of leukocytes from the periphery into tissues during inflammatory responses. In this study, we examined whether extracellular cyclophilin-CD147 interactions might influence leukocyte recruitment in the inflammatory disease allergic asthma. Using a mouse model of asthmatic inflammation, we show that 1) extracellular cyclophilins are elevated in the airways of asthmatic mice; 2) mouse eosinophils and CD4+ T cells express CD147, which is up-regulated on CD4+ T cells upon activation; 3) cyclophilins induce CD147-dependent chemotaxis of activated CD4+ T cells in vitro; 4) in vivo treatment with anti-CD147 mAb significantly reduces (by up to 50%) the accumulation of eosinophils and effector/memory CD4+ T lymphocytes, as well as Ag-specific Th2 cytokine secretion, in lung tissues; and 5) anti-CD147 treatment significantly reduces airway epithelial mucin production and bronchial hyperreactivity to methacholine challenge. These findings provide a novel mechanism whereby asthmatic lung inflammation may be reduced by targeting cyclophilin-CD147 interactions.
[INVITED] Tilted fiber grating mechanical and biochemical sensors (2015)

The tilted fiber Bragg grating (TFBG) is a new kind of fiber-optic sensor that possesses all the advantages of well-established Bragg grating technology in addition to being able to excite cladding modes resonantly. This device opens up a multitude of opportunities for single-point sensing in hard-to-reach spaces with very controllable cross-sensitivities, absolute and relative measurements of various parameters, and an extreme sensitivity to materials external to the fiber without requiring the fiber to be etched or tapered. Over the past five years, our research group has been developing multimodal fiber-optic sensors based on TFBG in various shapes and forms, always keeping the device itself simple to fabricate and compatible with low-cost manufacturing. This paper presents a brief review of the principle, fabrication, characterization, and implementation of TFBGs, followed by our progress in TFBG sensors for mechanical and biochemical applications, including one-dimensional TFBG vibroscopes, accelerometers and micro-displacement sensors; two-dimensional TFBG vector vibroscopes and vector rotation sensors; reflective TFBG refractometers with in-fiber and fiber-to-fiber configurations; polarimetric and plasmonic TFBG biochemical sensors for in-situ detection of cell, protein and glucose.
Systematic Enantiomeric Separation of [60]Fullerene Bisadducts Possessing an Inherent Chiral Addition Pattern (2003)

The optical resolution of trans-2 and trans-3 [60]fullerene bisadducts with an inherent chiral addition pattern, modified by Bingel reaction, cycloaddition by benzyne, Prato reaction, and cycloaddition by o-quinodimethane, was systematically investigated by using chiral HPLC columns (Chiralcel OD and Chiralpak AD). The chiroptical properties of enantiomers separated were also examined.
Vinylogous Urethane Vitrimers (2015)

Vitrimers are a new class of polymeric materials with very attractive properties, since they can be reworked to any shape while being at the same time permanently cross‐linked. As an alternative to the use of transesterification chemistry, we explore catalyst‐free transamination of vinylogous urethanes as an exchange reaction for vitrimers. First, a kinetic study on model compounds reveals the occurrence of transamination of vinylogous urethanes in a good temperature window without side reactions. Next, poly(vinylogous urethane) networks with a storage modulus of ≈2.4 GPa and a glass transition temperature above 80 °C are prepared by bulk polymerization of cyclohexane dimethanol bisacetoacetate, m ‐xylylene diamine, and tris(2‐aminoethyl)amine. The vitrimer nature of these networks is examined by solubility, stress‐relaxation, and creep experiments. Relaxation times as short as 85 s at 170 °C are observed without making use of any catalyst. In addition, the networks are recyclable up to four times by consecutive grinding/compression molding cycles without significant mechanical or chemical degradation.
Poly(isothianaphthene) (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPoly(isothianaphthene)Fred Wudl, M. Kobayashi, and A. J. HeegerCite this: J. Org. Chem. 1984, 49, 18, 3382–3384Publication Date (Print):September 1, 1984Publication History Published online1 May 2002Published inissue 1 September 1984https://pubs.acs.org/doi/10.1021/jo00192a027https://doi.org/10.1021/jo00192a027research-articleACS PublicationsRequest reuse permissionsArticle Views2356Altmetric-Citations507LEARN 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
Chemical Genetics Define the Roles of p38α and p38β in Acute and Chronic Inflammation (2007)

The p38 MAP kinase signal transduction pathway is an important regulator of proinflammatory cytokine production and inflammation. Defining the roles of the various p38 family members, specifically p38alpha and p38beta, in these processes has been difficult. Here we use a chemical genetics approach using knock-in mice in which either p38alpha or p38beta kinase has been rendered resistant to the effects of specific inhibitors along with p38beta knock-out mice to dissect the biological function of these specific kinase isoforms. Mice harboring a T106M mutation in p38alpha are resistant to pharmacological inhibition of LPS-induced TNF production and collagen antibody-induced arthritis, indicating that p38beta activity is not required for acute or chronic inflammatory responses. LPS-induced TNF production, however, is still completely sensitive to p38 inhibitors in mice with a T106M point mutation in p38beta. Similarly, p38beta knock-out mice respond normally to inflammatory stimuli. These results demonstrate conclusively that specific inhibition of the p38alpha isoform is necessary and sufficient for anti-inflammatory efficacy in vivo.
Identification of a Functional Peroxisome Proliferator-responsive Element in the Murine Fatty Acid Transport Protein Gene (1999)

Fatty acid transport protein (FATP), a plasma membrane protein implicated in controlling adipocyte transmembrane fatty acid flux, is up-regulated as a consequence of adipocyte differentiation and down-regulated by insulin. Based upon the sequence of the FATP gene upstream region (Hui, T. Y., Frohnert, B. I., Smith, A. J., Schaffer, J. A., and Bernlohr, D. A. (1998) J. Biol. Chem. 273, 27420-27429) a putative peroxisome proliferator-activated receptor response element (PPRE) is present from -458 to -474. To determine whether the FATP PPRE was functional, and responded to lipid activators, transient transfection of FATP-luciferase reporter constructs into CV-1 and 3T3-L1 cells was carried out. In CV-1 cells, FATP-luciferase activity was up-regulated 4- and 5.5-fold, respectively, by PPARalpha and PPARgamma in the presence of their respective activators in a PPRE-dependent mechanism. PPARdelta, however, was unable to mediate transcriptional activation under any condition. In 3T3-L1 cells, the PPRE conferred a small but significant increase in expression in preadipocytes, as well as a more robust up-regulation of FATP expression in adipocytes. Furthermore, the PPRE conferred the ability for luciferase expression to be up-regulated by activators of both PPARgamma and retinoid X receptor alpha (RXRalpha) in a synergistic manner. PPARalpha and PPARdelta activators did not up-regulate FATP expression in 3T3-L1 adipocytes, however, suggesting that these two subtypes do not play a significant role in differentiation-dependent activation in fat cells. Electromobility shift assays showed that all three PPAR subtypes were able to bind specifically to the PPRE as heterodimers with RXRalpha. Nuclear extracts from 3T3-L1 adipocytes also showed a specific gel-shift complex with the FATP PPRE. To correlate the expression of FATP to its physiological function, treatment of 3T3-L1 adipocytes with PPARgamma and RXRalpha activators resulted in an increased uptake of oleate. Moreover, linoleic acid, a physiological ligand, up-regulated FATP expression 2-fold in a PPRE-dependent manner. These results demonstrate that the FATP gene possesses a functional PPRE and is up-regulated by activators of PPARalpha and PPARgamma, thereby linking the activity of the protein to the expression of its gene. Moreover, these results have implications for the mechanism by which certain PPARgamma activators such as the antidiabetic thiazolidinedione drugs affect adipose lipid metabolism.
E1A-dependent trans-activation of the human MYC promoter is mediated by the E2F factor. (1989)

E2F is a cellular transcription factor that binds to two sites in the adenovirus E2 promoter. Previous experiments have implicated E2F in the E1A-dependent transactivation of the E2 gene since levels of active E2F increase markedly during adenovirus infection in parallel with the increase in E2 transcription, and an E2F binding site can confer E1A inducibility to a heterologous promoter. Here we show that E2F binds to two sequence elements within the P2 promoter of the human MYC gene which are within a region that is critical for promoter activity. The MYC promoter can be trans-activated in an E1A-dependent manner and site-directed mutagenesis demonstrates that these E2F elements are essential for trans-activation. Finally, we also find that adenovirus infection of quiescent cells results in a stimulation of the endogenous MYC gene. We conclude that the activation of the E2F factor, which is likely responsible for the activation of viral E2 transcription, is also responsible for the E1A-dependent induction of MYC transcription.