gebhart/patrepeval huggingface dataset:
Direct Mass Spectrometric Analysis of in Situ Thermally Hydrolyzed and Methylated Lipids from Whole Bacterial Cells (1998)

Fatty acid methyl esters (FAMEs) were generated in situ, during pyrolysis, from whole-cell bacterial samples and analyzed by mass spectrometry (MS). The FAME profiles obtained by an in situ thermal hydrolysis methylation (THM) step were compared with gas chromatography (GC) and MS analyses of the chemically extracted and methylated fatty acids. This correlation was based on the ability of each technique to differentiate a representative group of 15 bacteria at the species level as predicted by principal component analysis. All three analyses, GC/FAME, pyrolysis-MS/FAME, and in situ THM-MS/FAME differentiated the studied bacterial sample set into three discrete clusters. The bacteria comprising each cluster were the same for all three analyses, showing that taxonomic information of the lipid profiles was preserved in the Py-MS/FAME and in situ THM-MS/FAME analyses of whole cells. Contributions from saturated, unsaturated, cyclopropyl, and branched bacterial fatty acids to the differentiation of microorganisms were identified for all three analyses. The in situ THM-MS/FAME approach is simple, requires small samples (approximately 2 x 10(6) cells/profile), and is rapid, with a total analysis time under 5 min/sample.
Molecular basis of cytokine receptor activation (2010)

Cytokines are secreted soluble peptides that precisely regulate multiple cellular functions. Amongst these the GM-CSF/IL-3/IL-5 family of cytokines controls whether hematopoietic cells will survive or apoptose, proliferate, differentiate, migrate, or perform effector functions such as phagocytosis or reactive oxygen species release. Their potent and pleiotropic activities are mediated through binding to high affinity membrane receptors at surprisingly low numbers per cell. Receptor binding triggers a cascade of intracellular signaling events, including reversible phosphorylation of receptor subunits and associated signaling molecules, leading to multiple biological responses, with the prevention of apoptosis or "cell survival" being a key cellular function that underpins all others. Many chronic inflammatory diseases and a number of haematological malignancies are driven by deregulated GM-CSF, IL-3, or IL-5 cytokine receptor signaling, highlighting their importance in disease. A major step in understanding how these cytokine receptors function is to elucidate their three dimensional structure and to relate this to the many signaling pathways emanating from their receptors. We have recently solved the structure of the human GM-CSF receptor complexed to GM-CSF which revealed distinct forms of receptor assembly: a hexamer that comprises two molecules each of GM-CSF, GM-CSF receptor alpha chain and GM-CSF receptor beta chain; and an unexpected dodecamer in which two hexameric complexes associate through a novel site 4. This latter form is necessary to bring JAK2 molecules sufficiently close together to enable full receptor activation. In this review we focus on the most recent insights in cytokine receptor signaling, and in receptor assembly. The stage is now set to link distinct forms of cytokine receptor assembled structures to specific forms of cytokine receptor signaling and function. Armed with this knowledge it may be possible to map distinct cytokine receptor signaling pathways from the cell surface to the cell nucleus which may themselves become new therapeutic targets.
Flow Batteries for Microfluidic Networks: Configuring An Electroosmotic Pump for Nonterminal Positions (2011)

A micropump provides flow and pressure for a lab-on-chip device, just as a battery supplies current and voltage for an electronic system. Numerous micropumps have been developed, but none is as versatile as a battery. One cannot easily insert a micropump into a nonterminal position of a fluidic line without affecting the rest of the fluidic system, and one cannot simply connect several micropumps in series to enhance the pressure output, etc. In this work we develop a flow battery (or pressure power supply) to address this issue. A flow battery consists of a +EOP (in which the liquid flows in the same direction as the field gradient) and a -EOP (in which the liquid flows opposite to the electric field gradient), and the outlet of the +EOP is directly connected to the inlet of the -EOP. An external high voltage is applied to this outlet-inlet joint via a short gel-filled capillary that allows ions but not bulk liquid flow, while the +EOP's inlet and the -EOP's outlet (the flow battery's inlet and outlet) are grounded. This flow battery can be deployed anywhere in a fluidic network without electrically affecting the rest of the system. Several flow batteries can be connected in series to enhance the pressure output to drive HPLC separations. In a fluidic system powered by flow batteries, a hydraulic equivalent of Ohm's law can be applied to analyze system pressures and flow rates.
<i>In vitro</i> and <i>in vivo</i> biosynthesis of wax diesters by an unspecific bifunctional wax ester synthase/acyl‐CoA:diacylglycerol acyltransferase from <i>Acinetobacter calcoaceticus</i> ADP1 (2003)

Abstract Acinetobacter calcoaceticus ADP1 possesses a bifunctional wax ester synthase/acyl‐CoA:diacylglycerol acyltransferase (WS/DGAT) catalyzing the biosynthesis of wax esters and triacylglycerols. The unspecificity of WS/DGAT was used for in vitro and in vivo biosynthesis of wax diesters consisting of 1, 16‐hexadecanediol esterified with longchain fatty acids. An in vitro assay employing the membrane fraction of recombinant Escherichia coli XL1‐Blue expressing wax/dgat coding for WS/DGAT and using 1, 16‐hexadecanediol and 1 ‐14 C‐palmitoyl‐CoA as substrates resulted in the production of 2 radiolabeled substances as revealed by autoradiography suggesting the acylation of one or both hydroxy groups of 1, 16‐hexadecanediol by WS/DGAT. For in vivo biosynthesis of wax diesters, the knock‐out mutant A. calcoaceticus ADP1 acr1 | Km was generated by disruption of acr1 coding for acyl‐CoA reductase which caused the inability to synthesize fatty alcohols and, thus in consequence, wax esters. Co‐cultivation of A. calcoaceticus ADP1 acr1 | Km on gluconate and 1, 16‐hexadecanediol in nitrogen‐limited mineral salts medium resulted in the accumulation of a mixture of wax diesters of 1, 16‐hexadecanediol esterified with palmitic and oleic acid as revealed by electron impact ionization mass spectrometry. 1‐Monopalmitoylglycerol could also be utilized as an alternative acyl acceptor by the unspecific WS/DGAT in vitro resulting in the synthesis of 1, 2‐ and 1, 3‐dipalmitoylglycerol, whereas 1‐oleoylglycerol‐3‐phosphate (lysophosphatidic acid) was not accepted.
Enhancing security of Docker using Linux hardening techniques (2016)

Docker which is a lightweight containerization tool has enabled DevOps to build and run applications in distributed environment effectively. Docker has generated a significant momentum by bringing together a standardized containing method which is easy to use by enabling the users to use Linux containers to its full capacity. Docker currently supports the Linux hardening capabilities and Linux Security Modules (LSM) with AppArmor and SELinux for host system hardening. Docker interacts with the kernel security systems and LSMs. In this research work, the security depth of a popular open source model based on containers and study on other security features and techniques to enhance the security of Docker is performed. Integrating virtualization, automated testing, Deployment tools and security configurations management will enhance the security capability of Docker on premise.
Interactive assembly planning in virtual environments (2002)

This paper investigates assembly planning in virtual environments. It introduces a virtual teaching pendant and develops an interactive planning algorithm. This algorithm is capable of extracting human expertise of mechanical assembly from human-computer interaction and then using it for the automatic generation and interactive evaluation of assembly sequences. Analysis shows that the proposed interactive approach has a low complexity and hence offers a valid alternative to the usual autonomous approaches of assembly planning.
The Reactions of Peroxides with Lignin and Lignin Model Compounds (2001)

The reactions of peroxides with lignin and lignin model compounds have been extensively investigated. It is generally accepted that peroxides react via two reaction mechanisms depending on the structure of the peroxide and the reaction conditions employed. In alkaline conditions peroxides react nucleophilically with electron deficient carbonyl and conjugated carbonyl structures. In neutral to acidic media, most peroxides react with electron rich aromatic and olefinic structures via electrophilic pathways. In this paper, the reactions of peroxides with lignocellulosic materials, concentrating on lignin and lignin model compounds are reviewed. Emphasis is placed on the reactions of hydrogen peroxide and peroxy acids. However, owing to their chemical structures, and susceptibility to thermal and transition metal catalyzed decomposition, the reactions of hydroxyl, HO· and superoxide ·O2- radicals with lignin model compounds will also be discussed.
Creatine Ethyl Ether (1955)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCreatine Ethyl EtherJames D. Mold, Robert C. Gore, Joseph M. Lynch, and E. J. SchantzCite this: J. Am. Chem. Soc. 1955, 77, 1, 178–180Publication Date (Print):January 1, 1955Publication History Published online1 May 2002Published inissue 1 January 1955https://pubs.acs.org/doi/10.1021/ja01606a060https://doi.org/10.1021/ja01606a060research-articleACS PublicationsRequest reuse permissionsArticle Views199Altmetric-Citations6LEARN 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
Reg4 <sup>+</sup> deep crypt secretory cells function as epithelial niche for Lgr5 <sup>+</sup> stem cells in colon (2016)

Leucine-rich repeat-containing G-protein coupled receptor 5-positive (Lgr5(+)) stem cells reside at crypt bottoms of the small and large intestine. Small intestinal Paneth cells supply Wnt3, EGF, and Notch signals to neighboring Lgr5(+) stem cells. Whereas the colon lacks Paneth cells, deep crypt secretory (DCS) cells are intermingled with Lgr5(+) stem cells at crypt bottoms. Here, we report regenerating islet-derived family member 4 (Reg4) as a marker of DCS cells. To investigate a niche function, we eliminated DCS cells by using the diphtheria-toxin receptor gene knocked into the murine Reg4 locus. Ablation of DCS cells results in loss of stem cells from colonic crypts and disrupts gut homeostasis and colon organoid growth. In agreement, sorted Reg4(+) DCS cells promote organoid formation of single Lgr5(+) colon stem cells. DCS cells can be massively produced from Lgr5(+) colon stem cells in vitro by combined Notch inhibition and Wnt activation. We conclude that Reg4(+) DCS cells serve as Paneth cell equivalents in the colon crypt niche.
Ets1 and Elk1 transcription factors regulate<i>cancerous inhibitor of protein phosphatase 2A</i>expression in cervical and endometrial carcinoma cells (2012)

Cancerous inhibitor of protein phosphatase 2A (CIP2A) has been identified as a proto-oncogene that is overexpressed in various types of human cancers. CIP2A acts by inhibiting protein phosphatase 2A-dependent destabilization of c-Myc, resulting in increased cell proliferation. Here, we have characterized the proximal promoter region of the human CIP2A gene in cervical, endometrial and liver carcinoma cells. The 5' flanking minimal proximal promoter of the CIP2A gene consists of putative binding sites for Ets1 and Elk1 in forward and reverse orientations. Here, we show that Ets1 and Elk1 binding is essential for CIP2A basal expression in several urogenital cancer cell lines. Interestingly, both Ets1 and Elk1 are required together for CIP2A expression, as siRNA knockdown of Ets1 and Elk1 together decreased CIP2A gene transcription, whereas knockdown of Ets1 or Elk1 alone had no effect. Moreover, ectopic expression of Ets1 and Elk1 together increased CIP2A expression. To gain physiological significance of the Ets1 and Elk1 regulation we observed, a panel of matched human cervical carcinoma samples was analyzed for the expression of CIP2A and Ets1 and/or Elk1. We found a direct correlation between the levels of CIP2A and the levels of Ets1 and Elk1. Our results suggest that the binding of Ets1 and Elk1 together to the proximal CIP2A promoter is absolutely required for CIP2A expression in cervical, endometrial and liver carcinoma cell lines. Thus, different factors regulate CIP2A expression in a cell-type specific manner. As previous work has shown a requirement for only Ets1 in prostate and gastric carcinomas, our results now indicate that CIP2A regulation is more complex than previously determined.
Trigger Management Mechanisms (2007)

Current protocol stacks can handle only a handful of events that may trigger actions for mobility management, such as signal strength indicators and cell load. We argue for new mechanisms that can deal with a greater variety of triggering events, which may originate from any component of the node's protocol stack as well as mobility management entities within the network. We present the main concepts that govern our trigger management mechanisms (TMM), which aim at operating in a richer mobility management framework, and enable the deployment of new applications and services. After summarizing the architectural requirements with respect to trigger collection, processing, storage, and dissemination, we introduce a real implementation of TMM on commodity mobile devices. We briefly review our testbed environment and present experimental results using TMM to drive a lossless streaming video session handover between a laptop and a PDA. We position the current TMM design and implementation within the ambient networks architecture, centering in particular on the use of policies to steer TMM operation, and the role that TMM can play in an information service infrastructure. Finally, we outline current and future work items
[Effect of overexpression of malate dehydrogenase on succinic acid production in Escherichia coli NZN111]. (2011)

Escherichia coli NZN111 is a double mutant with lactate dehydrogenase (ldhA) and pyruvate formate-lyase (pflB) inactivated. Under anaerobic conditions, disequilibrium of coenzyme NADH and NAD+ causes Escherichia coli NZN111 losing the glucose utilizing capability. In this study, we constructed a recombinant strain E. coli NZN111/pTrc99a-mdh and overexpressed the mdh gene with 0.3 mmol/L of IPTG under anaerobic fermentation condition in sealed bottles. The specific malate dehydrogenase (MDH) activity in the recombinant strain was 14.8-fold higher than that in E. coli NZN111. The NADH/ NAD+ ratio decreased from 0.64 to 0.26 and the concentration of NAD+ and NADH increased 1.5-fold and 0.2-fold respectively. Under anaerobic conditions, the recombinant strain possessed the capability of growth and glucose absorption. We took dual-phase fermentation for succinate production. After the dry cell weight (DCW) reached 6.4 g/L under aerobic conditions, the cell culture was changed to anaerobic conditions. After 15 h, 14.75 g/L glucose was consumed and succinic acid reached 15.18 g/L. The yield of succinic acid was 1.03 g/g Glu and the productivity of succinic acid was 1.012 g/(L x h).
Influence of Sodium Borohydride on Kraft Pulping of European Black Pine as a Digester Additive (2011)

In this study, the effects of sodium borohydride (NaBH4) on properties of kraft pulp and paper obtained from European black pine (Pinus nigra Arn.) were investigated. Kraft−NaBH4 cookings were done under fixed cooking conditions by adding NaBH4 in the amounts of 0.5%, 1%, 1.5%, and 2% (oven-dried wood) to the cooking liquor. NaBH4-free kraft cooking was carried out as control. The results indicated that addition of NaBH4 to cooking liquor increased the pulp yield. However, the kappa number of pulp and beating time decreased. The brightness of kraft−NaBH4 papers was found to be higher than that of control papers. Addition of NaBH4 significantly decreased pulp viscosity and slightly decreased strength properties of papers.
Imaging multi-energy gamma-ray fields with a Compton scatter camera (1994)

Multi-energy gamma-ray fields have been imaged with a ring Compton scatter camera (RCC). The RCC is intended for industrial applications, where there is a need to image multiple gamma-ray lines from spatially extended sources. To our knowledge, the ability of a Compton scatter camera to perform this task had not previously been demonstrated. Gamma rays with different incident energies are distinguished based on the total energy deposited in the camera elements. For multiple gamma-ray lines, separate images are generated for each line energy. Random coincidences and other interfering interactions have been investigated. Camera response has been characterized for energies from 0.511 to 2.75 MeV. Different gamma-ray lines from extended sources have been measured and images reconstructed using both direct and iterative algorithms.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
High efficiency ring-lens supercritical angle fluorescence (SAF) detection for optimum bioassay performance (2013)

We present a polymer biochip with embedded optics which allows the detection of supercritical angle fluorescence (SAF) without losses due to total internal reflection within the substrate. The chip design comprises structured spherical and aspherical optical elements on the bottom, while the top is chemically functionalized for direct binding of biomolecules. Furthermore, this design facilitates integration in lab-on-a-chip systems with appropriate microfluidics. In the confocal optical setup an ellipsoidal mirror is used for collection of SAF light above the critical angle of the water-polymer interface, which is detected by a photon-counting detector. The work presented here represents a proof of concept for performing sensitive and rapid point-of-care testing, using this low-cost, robust and disposable optical biochip platform. The performance of the platform was validated using direct binding DNA and human IgG assays which yielded low limits of detection 10 pM for DNA and 10 pg/ml for human IgG.
Effects of surface oxide formation on germanium nanowire band-edge photoluminescence (2013)

The effect of intentional surface oxide formation on band-edge photoluminescence (PL) of Ge nanowires was investigated. Thermal oxidation in molecular O2 was used to produce a surface oxide layer on assemblies of single crystal nanowires grown by the vapor-liquid-solid method. With increasing oxidation of the wires, the band-edge PL associated with the indirect gap transition becomes more intense. X-ray photoelectron spectroscopy confirms the formation of an increasingly GeO2-like surface oxide under annealing conditions that enhance the indirect-gap PL, consistent with surface oxide passivation of nonradiative recombination centers initially present on the nanowire surface.
Interferon-γ Axis in Graft Arteriosclerosis (2007)

Cardiac transplantation is the most effective treatment for advanced heart failure. Despite improvements in immunosuppression therapy that prevent acute rejection, cardiac allografts fail at rates of 3% to 5% per posttransplant year. The hallmark morphological lesion of chronically failing cardiac allografts, also seen in chronic renal and liver graft failure, is luminal stenosis of blood vessels, especially of conduit arteries. Late graft failure results from widespread secondary ischemic injury to the graft parenchyma rather than direct immune-mediated damage. Although this process affects the entire graft vasculature, graft arteriosclerosis is a suitable term to describe the problem because it applies to different types of failing organs and because it emphasizes the central feature, namely an accelerated form of arterial injury and remodeling. The precise pathogenesis of graft arteriosclerosis is unknown. In this review, we make the case that the signature T-helper type 1 cytokine, interferon (IFN)-gamma, is a key effector in graft arteriosclerosis, which, together with the IFN-gamma-inducing cytokine interleukin-12 and IFN-gamma-inducible chemokines such as CXCR3 ligands, constitute a positive feedback loop for T-cell activation, differentiation, and recruitment that we refer to as the IFN-gamma axis. We evaluate the evidence to support this hypothesis in clinical observational and experimental animal studies. Additionally, we examine the regulation of IFN-gamma production within the artery wall, the effects of IFN-gamma on vessel wall cells, and the outcome of therapeutic agents on IFN-gamma production and signaling. These observations lead us to suggest that new therapies for graft arteriosclerosis should be optimized which focus on reducing IFN-gamma synthesis or actions.
Electroforming and resistance-switching mechanism in a magnetite thin film (2007)

The electroforming and the resistance-switching behaviors in magnetite, Fe3O4, by the application of an appropriate electric field are demonstrated on a lateral device with multiple electrodes. By means of this device, both the location and the nature of the change in Fe3O4 are specified from the electrical measurements and Raman spectroscopy. The switching phenomenon is caused in maghemite, γ-Fe2O3, which is formed by oxidation of Fe3O4, near an interface of an anode. The authors argue that the switching motion is originated in a redox reaction between the Fe3O4 and γ-Fe2O3.
Integration of microstructures onto negative electron affinity cathodes: Fabrication and operation of an addressable negative electron affinity cathode (1993)

A new cathode technology which integrates isolated multilayer structures onto negative electron affinity (NEA) cathodes has been developed. The process is designed to have the emission areas protected throughout the processing steps. With this process, a three-metal layer structure has been integrated onto a GaAs chip to fabricate an addressable-array NEA cathode. The metal layers are sputter-deposited TiW, the topmost layer is SiN. The addressable-array NEA cathodes were tested in an ultrahigh vacuum chamber, where they were coated with cesium and oxygen to achieve the NEA condition on the lithographically selected areas. Electron emission from the addressable cathodes has been projected onto a phosphorous screen. The photocurrent was modulated by applying a voltage to each control electrode. Pictures demonstrating the addressing capability are presented. The addressable-array NEA cathode technology offers the possibility of new projection electron-beam architectures for high throughput electron-beam lithography.