gebhart/patrepeval huggingface dataset:
Structural Evidence for a [4Fe‐5S] Intermediate in the Non‐Redox Desulfuration of Thiouracil (2020)

We recently discovered a [Fe-S]-containing protein with in vivo thiouracil desulfidase activity, dubbed TudS. The crystal structure of TudS refined at 1.5 Å resolution is reported; it harbors a [4Fe-4S] cluster bound by three cysteines only. Incubation of TudS crystals with 4-thiouracil trapped the cluster with a hydrosulfide ligand bound to the fourth non-protein-bonded iron, as established by the sulfur anomalous signal. This indicates that a [4Fe-5S] state of the cluster is a catalytic intermediate in the desulfuration reaction. Structural data and site-directed mutagenesis indicate that a water molecule is located next to the hydrosulfide ligand and to two catalytically important residues, Ser101 and Glu45. This information, together with modeling studies allow us to propose a mechanism for the unprecedented non-redox enzymatic desulfuration of thiouracil, in which a [4Fe-4S] cluster binds and activates the sulfur atom of the substrate.
The Titan haze simulation experiment: Investigating Titan’s low-temperature atmospheric chemistry in a pulsed plasma jet expansion (2019)

Abstract The Titan Haze Simulation (THS) experiment is a unique experimental platform that allows to simulate Titan’s complex atmospheric chemistry at low Titan-like temperature by generating a plasma discharge in the stream of a plasma jet expansion. Both gas and solid phase products are generated and can be analyzed using different in-situ and ex-situ diagnostics. Here, we present an overall description of the work accomplished with the THS in the last 10 years, our current research efforts, and the important implications for the analysis of Cassini’s returned data and preparation for future Titan missions.
Energy Efficiency of the IEEE 802.15.4 Standard in Dense Wireless Microsensor Networks: Modeling and Improvement Perspectives (2005)

Wireless microsensor networks, which have been the topic of intensive research in recent years, are now emerging in industrial applications. An important milestone in this transition has been the release of the IEEE 802.15.4 standard that specifies interoperable wireless physical and medium access control layers targeted to sensor node radios. In this paper, we evaluate the potential of an 802.15.4 radio for use in an ultra low power sensor node operating in a dense network. Starting from measurements carried out on the off-the-shelf radio, effective radio activation and link adaptation policies are derived. It is shown that, in a typical sensor network scenario, the average power per node can be reduced down to 211 /spl mu/W. Next, the energy consumption breakdown between the different phases of a packet transmission is presented, indicating which part of the transceiver architecture can most effectively be optimized in order to further reduce the radio power, enabling self-powered wireless microsensor networks.
Measurement of the inclusive cross-section for the production of jets in association with a Z boson in proton–proton collisions at 8 TeV using the ATLAS detector (2019)

Abstract The inclusive cross-section for jet production in association with a Z boson decaying into an electron–positron pair is measured as a function of the transverse momentum and the absolute rapidity of jets using 19.9 fb $$^{-1}$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msup> <mml:mrow/> <mml:mrow> <mml:mo>-</mml:mo> <mml:mn>1</mml:mn> </mml:mrow> </mml:msup> </mml:math> of $$\sqrt{s}=8$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:msqrt> <mml:mi>s</mml:mi> </mml:msqrt> <mml:mo>=</mml:mo> <mml:mn>8</mml:mn> </mml:mrow> </mml:math> TeV proton–proton collision data collected with the ATLAS detector at the Large Hadron Collider. The measured $$Z\text { + jets}$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mrow> <mml:mi>Z</mml:mi> <mml:mspace/> <mml:mtext>+ jets</mml:mtext> </mml:mrow> </mml:math> cross-section is unfolded to the particle level. The cross-section is compared with state-of-the-art Standard Model calculations, including the next-to-leading-order and next-to-next-to-leading-order perturbative QCD calculations, corrected for non-perturbative and QED radiation effects. The results of the measurements cover final-state jets with transverse momenta up to 1 TeV, and show good agreement with fixed-order calculations.
Measurement of 1.3 and 1.55 μm gain-switched semiconductor laser pulses with a picosecond IR streak camera and a high-speed InGaAs PIN photodiode (1985)

Gain-switched semiconductor laser pulses at 1.3 and 1.55 μm were measured both with a high-speed InGaAs PIN photodiode and an IR synchroscan streak camera. Gain-switching characteristics and their bias dependence observed with both detection schemes are consistent with each other. Laser pulses of 24–30 ps duration are observed. Picosecond pulses from a gain-switched 1.55 μm DFB laser are found to be chirped but not transform-limited.
Effects of CT-Xp Gene Knock down in Melanoma Cell Lines (2013)

Cancer/testis (CT) genes are encoded by genes that are normally expressed only in the human germ line but which are activated in various malignancies. CT proteins are frequently immunogenic in cancer patients and their expression is highly restricted to tumors. They are thus important targets for anticancer immunotherapy. In several different tumor types, the expression of CT-X genes is associated with advanced disease and poor outcome, indicating that their expression might contribute to tumorigenesis. CT-X genes encoding members of the MAGE protein family on Xq28 have been shown to potentially influence the tumorigenic phenotype. We used small interfering RNA (siRNA) to investigate whether CT-X mapping to the short arm of the X-chromosome might also have tumorigenic properties and therefore be potentially targeted by functional inhibitors in a therapeutic setting. siRNAs specific to GAGE, SSX and XAGE1 were used in cell proliferation, migration and cell survival assays using cell lines derived from melanoma, a tumor type known to present high frequencies of expression of CT antigens. We found that of these, those specific to GAGE and XAGE1 most significantly impeded melanoma cell migration and invasion and those specific to SSX4 and XAGE1 decreased the clonogenic survival of melanoma cells. Our results suggest that GAGE, XAGE1 and SSX4 might each have a role in tumor progression and are possible therapeutic targets for the treatment of melanoma and other malignancies.
Microfluidic tapered aspirators for mechanical characterization of microgel beads (2023)

In this study, we report a microfluidic approach for the measurement of mechanical properties of spherical microgel beads. This technique is analogous to tapered micropipette aspiration, while harnessing the benefits of microfluidics. We fabricate alginate-based microbeads and determine their mechanical properties using the microfluidic tapered aspirators. Individual microgel beads are aspirated and trapped in tapered channels, the deformed equilibrium shape is measured, and a stress balance is used to determine the Young's modulus. We investigate the effect of surface coating, taper angle, and bead diameter and find that the measured modulus is largely insensitive to these parameters. We show that the bead modulus increases with alginate concentration and follows a trend similar to that of the modulus measured using standard uniaxial compression. The critical pressure to squeeze out the beads from the tapered aspirators was found to depend on both the modulus and the bead diameter. Finally, we demonstrate how temporal changes in bead moduli due to enzymatic degradation of the hydrogel could be quantitatively determined. The results from this study highlight that the microfluidic tapered aspirators are a useful tool to measure hydrogel bead mechanics and have the potential to characterize dynamic changes in mechanical properties.
S‐Sulfonation: a Reversible Chemical Modification of Human Immunoglobulins Permitting Intravenous Application (1983)

S-sulfonation represents a reversible chemical modification of disulfide bonds by which under the special conditions chosen only about 2.2 cystine units per IgG molecule are cleaved. Physicochemical and functional evidence for reconstitution is presented. Molecules reconstituted in vitro or in vivo regain, within a few hours, a reactivity (antigen binding, immunoprecipitation, Clq-mediated cross-linking of immune complexes) comparable to equimolar control preparations.
Splattering During Turbulent Liquid Jet Impingement on Solid Targets (1994)

In turbulent liquid jet impingement, a spray of droplets often breaks off of the liquid layer formed on the target. This splattering of liquid alters the efficiencies of jet impingement heat transfer processes and chemical containment safety devices, and leads to problems of aerosol formation in jet impingement cleaning processes. In this paper, we present a more complete study of splattering and improved correlations that extend and supersede our previous reports on this topic. We report experimental results on the amount of splattering for jets of water, isopropanol-water solutions, and soap-water mixtures. Jets were produced by straight tube nozzles of diameter 0.8–5.8 mm, with fully developed turbulent pipe-flow upstream of the nozzle exit. These experiments cover Weber numbers between 130-31,000, Reynolds numbers between 2700-98,000, and nozzle-to-target separations of 0.2 ≤ l/d ≤ 125. Splattering of up to 75 percent of the incoming jet liquid is observed. The results show that only the Weber number and l/d affect the fraction of jet liquid splattered. The presence of surfactants does not alter the splattering. A new correlation for the onset condition for splattering is given. In addition, we establish the range of applicability of the model of Lienhard et al. (1992) and we provide a more accurate set of coefficients for their correlation.
Reactive and highly submicron magnetic latex for bionanotechnology applications (2009)

International audience
Differential uptake of antisense oligonucleotides in mouse hepatocytes and macrophages revealed by simultaneous 2P-fluorescence and coherent Raman imaging (2022)

The primary goal of this study was to track PS-ASO and GalNAc-PS-ASO uptake in two cell cultures as the first step to understand the observations from the clinical studies. The multimodal imaging setup of CARS and 2PF modalities in conjunction with the image analysis pipeline made it uniquely possible to address these challenges. We report here the time-dependent uptake, internalization, and localization differences between GalNAc-PS-ASOs and PS-ASOs in liver cells. We believe our findings will help us form the basis for further investigations with more complex cellular co-cultures and with tissue and animal models.
Supplementary Fig. S4 from Quantitative live imaging of cancer and normal cells treated with Kinesin-5 inhibitors indicates significant differences in phenotypic responses and cell fate (2023)

Supplementary Fig. S4 from Quantitative live imaging of cancer and normal cells treated with Kinesin-5 inhibitors indicates significant differences in phenotypic responses and cell fate
Microseismic activity induced by hydraulic mining of steeply inclined coal seams (1984)

A microseismic monotoring facility was applied to observe rock failure associated with the hydraulic mining of steeply inclined coal seams, where seismometers were so arranged on the surface and underground that a seismic array could almost enclose the mining panels. The seismic foci distributed uniformly at one view over the mining panels, however, a considerable number of seismic events were concentrated within a few zones bounded on the pre-existing faults. The distribution of seismic foci in regard to the distance from the plane of the coal seam was approximated by the normal distribution whose mean value and standard deviation were 16 - 34 m from the seam plane and 43 - 51 m around the mean value respectively. An analysis revealed that the maximum compression axis at the seismic focus might be in good agreement with the dip direction of the coal seam, whilst the maximum tension axis was nearly allied to the normal direction of the coal seam. A comparison of microseismic activity between before and after mining of seams showed that the spatial rate of seismic energy in preceding mining was about more than 7.0 times higher than that of in successive mining.
Molecular cloning and expression during myogenesis of sequences coding for M-creatine kinase. (1982)

Sequences complementary to muscle poly(A)+RNA were cloned in the plasmid pBR322 and the resulting colonies were screened by colony hybridization with labeled cDNA derived from skeletal muscle and smooth muscle (gizzard). The skeletal muscle-specific clones were further screened by RNA blotting hybridization for a muscle mRNA having the size expected for a putative type M creatine kinase (M-CK) mRNA. The remaining clones with the expected hybridization properties were finally characterized by hybrid-selected translation, and a cloned sequence was shown to contain DNA hybridizing to mRNA that could be translated into M-CK. This plasmid, pMCK1, was further characterized by restriction mapping. Blot analysis of total cell RNA from differentiating myogenic cell cultures showed accumulation of M-CK mRNA in cultures older than 42 hr but not in young little-differentiated cultures.
NK1.1+ T cells from IL-7-deficient mice have a normal distribution and selection but exhibit impaired cytokine production (1996)

Particular subsets of T cells expressing the NK1.1 antigen have been proposed to play an immune regulatory role by their fast and strong production of cytokines, in particular IL-4. We sought to determine factors driving the functional differentiation of NK1.1+ T cells. Since NK1.1+ T cells are exquisitely sensitive to IL-7 stimulation, we analyzed the development, selection and IL-4 production of NK1.1+ T cells in IL-7-deficient mice (IL-7-/-m mice). Besides a sharp reduction of all T cell subsets, NK1.1+ T cells develop at normal relative frequencies in IL-7-/- mice. They also undergo a normal selection process, as revealed by the biased V beta TCR repertoire identical to the one in IL-7+/+ mice. However, NK1.1+ T cells from IL-7-/- mice were found to be impaired in IL-4 and IFN-gamma production in in vitro and in vivo models. In addition, IL-7 was able to restore IL-4 production by NK1.1+ thymocytes from IL-7-/- mice. Finally, IL-7 but not IL-2 or IL-4 was able to maintain and increase IL-4 production by NK1.1+ thymocytes from normal mice. These data suggest that the functional maturation of NK1.1+ T cells requires a cytokine-driven differentiation process, in which IL-7 plays a major role.
Pushing Atoms with Darkness: Adiabatic Momentum Transfer (1994)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text J. Lawall, M. Prentiss, L. S. Goldner, C. Gerz, R. J. C. Spreeuw, S. L. Rolston, C. I. West-brook, W. D. Phillips, P. Marte, and P. Zoller, "Pushing Atoms with Darkness: Adiabatic Momentum Transfer," Optics & Photonics News 5(12), 28-28 (1994) Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
TSG-6 Inhibits Neutrophil Migration via Direct Interaction with the Chemokine CXCL8 (2014)

TNF-stimulated gene/protein-6 (TSG-6) is expressed by many different cell types in response to proinflammatory cytokines and plays an important role in the protection of tissues from the damaging consequences of acute inflammation. Recently, TSG-6 was identified as being largely responsible for the beneficial effects of multipotent mesenchymal stem cells, for example in the treatment of animal models of myocardial infarction and corneal injury/allogenic transplant. The protective effect of TSG-6 is due in part to its inhibition of neutrophil migration, but the mechanisms underlying this activity remain unknown. In this study, we have shown that TSG-6 inhibits chemokine-stimulated transendothelial migration of neutrophils via a direct interaction (KD, ∼ 25 nM) between TSG-6 and the glycosaminoglycan binding site of CXCL8, which antagonizes the association of CXCL8 with heparin. Furthermore, we found that TSG-6 impairs the binding of CXCL8 to cell surface glycosaminoglycans and the transport of CXCL8 across an endothelial cell monolayer. In vivo this could limit the formation of haptotactic gradients on endothelial heparan sulfate proteoglycans and, hence, integrin-mediated tight adhesion and migration. We further observed that TSG-6 suppresses CXCL8-mediated chemotaxis of neutrophils; this lower potency effect might be important at sites where there is high local expression of TSG-6. Thus, we have identified TSG-6 as a CXCL8-binding protein, making it, to our knowledge, the first soluble mammalian chemokine-binding protein to be described to date. We have also revealed a potential mechanism whereby TSG-6 mediates its anti-inflammatory and protective effects. This could inform the development of new treatments for inflammation in the context of disease or following transplantation.
A novel cell encapsulation mode for delivery of therapeutic antibodies against West Nile Virus infections that maintains steady plasma antibody levels throughout therapy (2010)

Background: West Nile virus (WNV) is currently endemic in various parts of all five continents in the world. Being a member of the Japanese encephalitis virus subgenus, WNV can cause potentially fatal neuro-invasive diseases such as encephalitis and meningitis. Unfortunately, to date, no vaccine or antiviral therapy has yet been approved. One antiviral strategy in development involves the passive administration of neutralizing antibodies. As with most immuno-therapies, plasma antibody levels diminish between treatments. This is especially detrimental in flavivirus immuno-therapies as sub-neutralizing concentrations of antibodies can instead enhance infection. Here, we report a proof-of-concept for a novel mode of delivery using encapsulation of hybridoma cells producing therapeutic antibodies which enables the maintenance of a steady level of antibody in the plasma, thus preventing any possible antibody-dependent enhancement (ADE). Methods: Recombinant domain III of the envelope glycoprotein (rE-DIII) of WNV was cloned, expressed in bacteria, and purified. It was then inoculated into balb/c female mice and splenocytes harvested to generate hybridomas. Limiting dilution was subsequently performed and producers of antibody specific to WNV were selected. Following which, the selected hybridomas were encapsulated in polymers of sodium cellulose sulfate. Viability of the encapsulated hybridoma clones, their ability to continuously secrete antibodies, and most importantly, whether antibodies can be released from the capsules were then characterized. Results: Pilot batches of hybridomas remained viable and divided beyond 100 days postencapsulation. Moreover, the encapsulated hybridoma cells and their progeny were able to continuously secrete WNV-specific antibodies, and the secreted antibodies could be released from the capsules. Conclusion: Our preliminary results showed that encapsulation of cells producing therapeutic antibodies can indeed be a potential solution to improving treatment outcomes for immunotherapies. This is especially essential for immunotherapies against flavivirus infections so as to minimize any potential ADE side-effect. However, the application of this technology for the treatment of infectious diseases is still at its infancy and we are currently in the midst of further optimizing and characterizing this technology. Abstracts for SupplementInternational Journal of Infectious DiseasesVol. 14Preview Full-Text PDF Open Archive
Metal acetylide CpW(CO)3C.tplbond.CPh and hydride CpW(CO)3H complexes as building blocks to prepare tungsten-ruthenium heterometallic clusters. Synthesis, characterization, and crystal structure of CpWRu3(CO)9(.mu.3-COMe)(C:CHPh), Cp2W2Ru3(CO)9[CC(Ph)C(OMe)](C:CHPh), and Cp2W2Ru3(CO)9(COMe)(C.tplbond.CPh) (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMetal acetylide CpW(CO)3C.tplbond.CPh and hydride CpW(CO)3H complexes as building blocks to prepare tungsten-ruthenium heterometallic clusters. Synthesis, characterization, and crystal structure of CpWRu3(CO)9(.mu.3-COMe)(C:CHPh), Cp2W2Ru3(CO)9[CC(Ph)C(OMe)](C:CHPh), and Cp2W2Ru3(CO)9(COMe)(C.tplbond.CPh)Yun Chi, Shiow Huey Chuang, Ling Kang Liu, and Yuh Sheng WenCite this: Organometallics 1991, 10, 7, 2485–2492Publication Date (Print):July 1, 1991Publication History Published online1 May 2002Published inissue 1 July 1991https://pubs.acs.org/doi/10.1021/om00053a061https://doi.org/10.1021/om00053a061research-articleACS PublicationsRequest reuse permissionsArticle Views79Altmetric-Citations18LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Chromogenic Carbamate and Acetal Substrates for Glycosaminidases (2011)

The enzyme Dispersin B is a medicinally relevant β-hexosaminidase with potential for use in the treatment of biofilm-related infections. Here we describe the synthesis and evaluation of a p-nitrophenyl glycosyl carbamate and a p-nitrophenyl glycosyl acetal as improved substrates of Dispersin B. The p-nitrophenyl glycosyl carbamate shows substantially improved analytical signal in continuous assays and superior kinetics (kcat/Km 6.1 mM−1 s−1) when compared to the benchmark substrate 4-nitrophenyl N-acetyl-β-D-glucosaminide (kcat/Km 0.021 mM−1 s−1) in measuring Dispersin B activity. The improvements observed are compared to the activity of jack bean β-hexosaminidase toward these substrates.