gebhart/patrepeval huggingface dataset:
Cell Membranes Under Hydrostatic Pressure Subjected to Micro-Injection (2011)

The work is concerned with the determination of the mechanical behaviour of cell membranes under uniform hydrostatic pressure subject to micro‐injections. For that purpose, assuming that the shape of the deformed cell membrane is axisymmetric a variational statement of the problem is developed on the ground of the so‐called spontaneous curvature model. In this setting, the cell membrane is regarded as an axisymmetric surface in the three‐dimensional Euclidean space providing a stationary value of the shape energy functional under the constraint of fixed total area and fixed enclosed volume. The corresponding Euler‐Lagrange equations and natural boundary conditions are derived, analyzed and used to express the forces and moments in the membrane. Several examples of such surfaces representing possible shapes of cell membranes under pressure subjected to micro injection are determined numerically.
A Shared PMD and Chromatic Dispersion Monitor Based on a Coherent Receiver (2010)

We demonstrate a shared optical performance monitor utilizing a dual-polarization quadrature-phase-shift-keyed coherent single-ended receiver, with no optical filtering. The channel to be monitored is selected by tuning the local oscillator. The chromatic dispersion and instantaneous differential group delay of a channel can be read while 80 channels are simultaneously impinging upon the detector.
Insights into the molecular determinants of EF-G catalyzed translocation (2011)

Translocation, the directional movement of transfer RNA (tRNA) and messenger RNA (mRNA) substrates on the ribosome during protein synthesis, is regulated by dynamic processes intrinsic to the translating particle. Using single-molecule fluorescence resonance energy transfer (smFRET) imaging, in combination with site-directed mutagenesis of the ribosome and tRNA substrates, we show that peptidyl-tRNA within the aminoacyl site of the bacterial pretranslocation complex can adopt distinct hybrid tRNA configurations resulting from uncoupled motions of the 3'-CCA terminus and the tRNA body. As expected for an on-path translocation intermediate, the hybrid configuration where both the 3'-CCA end and body of peptidyl-tRNA have moved in the direction of translocation exhibits dramatically enhanced puromycin reactivity, an increase in the rate at which EF-G engages the ribosome, and accelerated rates of translocation. These findings provide compelling evidence that the substrate for EF-G catalyzed translocation is an intermediate wherein the bodies of both tRNA substrates adopt hybrid positions within the translating ribosome.
CATHODIC PROTECTION OF CONCRETE BRIDGES: A MANUAL OF PRACTICE (1993)

This document provides explanation, guidance, and direction concerning cathodic protection of concrete bridge elements to the highway engineer who wants to incorporate cathodic protection in a bridge project. The manual which provides background information on corrosion fundamentals, is divided into 3 parts: design, construction, and operation and maintenance. An appendix provides standard specifications for cathodic protection systems for both decks and substructures. These specifications are modeled after those currently being developed under the American Association of State Highway and Transportation Officials, Associated General Contractors, and the American Road and Transportation Builders' Association Task Force 29. The document is intended to be a useful reference for engineers who design and prepare specifications or who oversee turnkey operations.
Fine Tuning Inflammation at the Front Door: Macrophage Complement Receptor 3-mediates Phagocytosis and Immune Suppression for Francisella tularensis (2013)

Complement receptor 3 (CR3, CD11b/CD18) is a major macrophage phagocytic receptor. The biochemical pathways through which CR3 regulates immunologic responses have not been fully characterized. Francisella tularensis is a remarkably infectious, facultative intracellular pathogen of macrophages that causes tularemia. Early evasion of the host immune response contributes to the virulence of F. tularensis and CR3 is an important receptor for its phagocytosis. Here we confirm that efficient attachment and uptake of the highly virulent Type A F. tularensis spp. tularensis strain Schu S4 by human monocyte-derived macrophages (hMDMs) requires complement C3 opsonization and CR3. However, despite a>40-fold increase in uptake following C3 opsonization, Schu S4 induces limited pro-inflammatory cytokine production compared with non-opsonized Schu S4 and the low virulent F. novicida. This suggests that engagement of CR3 by opsonized Schu S4 contributes specifically to the immune suppression during and shortly following phagocytosis which we demonstrate by CD11b siRNA knockdown in hMDMs. This immune suppression is concomitant with early inhibition of ERK1/2, p38 MAPK and NF-κB activation. Furthermore, TLR2 siRNA knockdown shows that pro-inflammatory cytokine production and MAPK activation in response to non-opsonized Schu S4 depends on TLR2 signaling providing evidence that CR3-TLR2 crosstalk mediates immune suppression for opsonized Schu S4. Deletion of the CD11b cytoplasmic tail reverses the CR3-mediated decrease in ERK and p38 activation during opsonized Schu-S4 infection. The CR3-mediated signaling pathway involved in this immune suppression includes Lyn kinase and Akt activation, and increased MKP-1, which limits TLR2-mediated pro-inflammatory responses. These data indicate that while the highly virulent F. tularensis uses CR3 for efficient uptake, optimal engagement of this receptor down-regulates TLR2-dependent pro-inflammatory responses by inhibiting MAPK activation through outside-in signaling. CR3-linked immune suppression is an important mechanism involved in the pathogenesis of F. tularensis infection.
COMP - Comparing Ontology Matching Plug-in (2009)

Improving the ontology integration seems to be an important thing for maintenance of cooperation among various directions of ontology engineering (semantic web services, social networks, etc.). While particular ontologies cover a view at one specific domain of interest, many applications require much more general approach to describe their data. On this account it approaches to a promising solution to the semantic heterogeneity, ontology matching. Matching can be improved in various ways, such as improving matching strategies, tools and systems, basic techniques and methods or by explaining, representing and further processing and evaluating matching results. This paper describe a matching plug-in into the open-source ontology editor, Prote¿ge¿. The plug-in is called COMP and it is a tool for comparing and evaluating various matching techniques and strategies.
4G Test-bed trial: Building wireless research &#x201C;HEART&#x201D; &#x2014; CoMP probes the first step (2010)

Along with LTE-Advanced system and standardization investigation progress, the requirement for verifying relevant key technologies become more and more urgent. This article summarizes the progress of Huawei 4G Test-bed “HEART” (Huawei Experimental Advanced Radio Test-bed). CoMP technology is considered as a launch point to build up this test-bed competence. Some initial analysis and results are addressed in this article. The future work has been identified as well in the last section.
Treatment of genitourinary tract infections with fluoroquinolones: clinical efficacy in genital infections and adverse effects (1989)

Role of fluoroquinolones in the treatment of genital infections: Gonorrhea, Chlamydia trachomatis infections, norgonococcal urethritis caused by other agents, pelvic inflammatory disease, chancroid, syphilis, bacterial vaginosis, miscellaneous genital infections. Adverse effects of these agents when used for the treatment of genitourinary tract infections
Reactions of 2-azidopyridine and 1-pyridinio ylides with transition-metal complexes (1978)

The reactions of 2-azidopyridine (L1) and 1-pyridinio ylides C5H5N–NR [R = O2SC6H4Me-p(L2) or OCC6H4Me-p(L3)] with metal(II) halogeno-complexes give derivatives of formula [MnL12Cl2], [FeL13Cl2], [CoL1Cl2], [CuL1Cl2], [ZnL12Cl2], [(NiL1Cl2)n], [NiL12Br2], [(NiL2Cl2)n], [NiL22Br2], [PdL12Cl2], [PdL22Cl2], [PdL32Cl2], [Ru(PPh3)2-L12X2], and [Ru(SbPh3)2L12Cl2](X = Cl or Br). The complexes [M(CO)5L1](M = W or Cr) have been obtained from [M(CO)5(thf)](thf = tetrahydrofuran) and tetrazolopyridine. In these complexes L1 is present in its tetrazole form. From [Pt(SMe2)2Cl2] and L1, [Pt(SMe2)L1Cl2] has been isolated, while L3 gives a derivative in which the aryl group is metallated in the position ortho to the carbonyl group and the ylide is bidentate. The complex [Ru(PPh3)2L12Cl2] reacts with carbon monoxide to give [Ru(PPh3)2(CO)L1Cl2]. 2-Azido-5-nitropyridine (RN3) reacts in its azide form with the hydride [Pt(PEt3)2H(Cl)] to give the amido-complex [Pt(PEt3)2(NHR)Cl] and with [Pt(PPh3)2(C2H4)] to give a complex of composition [Pt(PPh3)2(N3)(N2R)]. The spectroscopic properties of the new complexes are reported and their structures discussed.
Three Methods for Generating Monotonic OWA Operator Weights with Given Orness Level (2004)

Based on the properties of ordered weighted averaging (OWA) operator and regular increasing monotone (RIM) quantifier, three methods for generating monotonic OWA operator weights are proposed. They are geometric OWA operator weights, equidifferent OWA operator weights and the modified RIM quantifier OWA weights. Compared with most of the common OWA methods for generating weights, the methods proposed in this paper are more intuitive and efficient in computation. And as there are more than one solution in most cases, the decision maker can set some initial condition and chooses the appropriate solution in the real decision process, which increases the flexibility of decision making to some extent. All these three OWA methods for generating weights are illustrated by numerical examples.
Association and interaction analyses of genetic variants in ADIPOQ, ENPP1, GHSR, PPAR  and TCF7L2 genes for diabetic nephropathy in a Taiwanese population with type 2 diabetes (2009)

The results suggest that the SNPs from the T2D-related genes may contribute to the risk of DN in T2D independently and/or in an interactive manner in Taiwanese T2D patients.
CDSE Quantum Dots and Luminescent/ Magnetic Particles for Biological Applications (2005)

CdSe semiconductor nanocrystals (quantum dots--QDs) with diameters ranging between 1.5 and 8 nm exhibit strong, tunable luminescence [1-5]. They have been widely investigated for their size-dependent optoelectronic properties [6], and for their potential use in optical devices [7], biological labels [8] and sensors [9]. Luminescent quantum dots (QDs) show higher photostability and narrower emission peaks compared to organic fluorophores [8]. The objective of my project was to apply QDs magnetic/luminescent nanoparticle as biological labels in cells. Luminescent CdSe QDs emit bright visible light with high quantum yield and sharp emission peak. The CdSe QDs were capped with a ZnS layer. This increased their emission efficiency and photostability due to the larger band gap of ZnS. The QDs were transferred from organic solvent (e.g. chloroform, hexane) to water by exchanging the capping group (Trioctylphosphine Oxide—TOPO) with mercaptoacetic acid. To develop a separation and detection tool for cells, we combined γ-Fe2O3 magnetic particles with CdSe/ZnS QDs in core-shell composite. The composite nanoparticles showed strong fluorescence emission and high water solubility. Different antibodies were attached to the particles through EDAC coupling. The antibody-coated particles were used to successfully separate and detect breast cancer cells in blood cells.
A Convenient and General Iron‐Catalyzed Reduction of Amides to Amines (2009)

While the iron is hot: The first general and efficient iron-catalyzed reduction of secondary and tertiary amides into amines using polymethylhydrosiloxane (PMHS) has been developed (see scheme). Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Stabilization of Polymersome Vesicles by an Interpenetrating Polymer Network (2006)

Vesicles from Pluronic L121 (PEO5-PPO68-PEO5) triblock copolymers were stabilized by an interpenetrating polymer network from pentaerythritol tetraacrylate by UV or thermal initiator induced radical polymerization. Fluorescence labeling, atomic force microscopy, and electron microscopy studies were used to study the morphology of the particles and showed that stable vesicles are formed. The block copolymers are noncovalently trapped in the interpenetrating polyacrylate network. The stabilized vesicles retain their size for more than 1 month at room temperature. Upon cooling, the vesicles reversibly lose block copolymer
1393. A Phase 1, Randomized, Open-Label, Crossover Study in Healthy Subjects Under Fasting Conditions of Orally Administered Sulopenem Etzadroxil Alone or with Probenecid to Determine the Pharmacokinetics of Sulopenem (2018)

Abstract Background Antimicrobial resistance to available oral antibiotics is becoming progressively more common, precipitating the need for additional treatment options as step-down from initial intravenous (IV) therapy as well as for treatment of infections in the community. Sulopenem (CP-70,429) is a thiopenem antibiotic active against quinolone non-susceptible and ESBL-producing Enterobacteriaceae. As the key pharmacokinetic-pharmacodynamic variable correlating with efficacy for penem antibiotics is time above minimum inhibitory concentration (T &gt; MIC), we examined the utility of probenecid, an OAT-1 inhibitor of β-lactam excretion, on the pharmacokinetic (PK) parameters for the oral prodrug of sulopenem, sulopenem etzadroxil Methods Twelve healthy males and females received a single oral dose of 500 mg sulopenem etzadroxil as powder in bottle either alone or co-administered with a single oral dose of probenecid 500 mg in a crossover design with a washout period of 6 days. All doses were administered under fasting conditions. Blood samples for plasma PK analysis were collected and PK parameters for sulopenem, the parent compound of sulopenem etzadroxil, were determined. Results Treatment Conclusion Probenecid increases the AUC of sulopenem by 28% in the fasted state and extends the mean time over MIC. Disclosures M. Dunne, Iterum Therapeutics: Employee and Shareholder, Salary. S. Aronin, Iterum Therapeutics: Employee and Shareholder, Salary. E. Dunzo, Parexel: Consultant, Consulting fee. S. Puttagunta, Iterum Therapeutics: Employee and Shareholder, Salary.
Silymarin and milk thistle extract may prevent the progression of diabetic nephropathy in streptozotocin-induced diabetic rats (2010)

Milk thistle extract, to a lesser extent silymarin, can attenuate DN in rats possibly by increasing kidney CAT and GPx activity and decreasing lipid peroxidation in renal tissue.
CRISPR base editors: genome editing without double-stranded breaks (2018)

The CRISPR (clustered regularly interspaced short palindromic repeat)/Cas9 adaptive immunity system has been harnessed for genome editing applications across eukaryotic species, but major drawbacks, such as the inefficiency of precise base editing and off-target activities, remain. A catalytically inactive Cas9 variant (dead Cas9, dCas9) has been fused to diverse functional domains for targeting genetic and epigenetic modifications, including base editing, to specific DNA sequences. As base editing does not require the generation of double-strand breaks, dCas9 and Cas9 nickase have been used to target deaminase domains to edit specific loci. Adenine and cytidine deaminases convert their respective nucleotides into other DNA bases, thereby offering many possibilities for DNA editing. Such base-editing enzymes hold great promise for applications in basic biology, trait development in crops, and treatment of genetic diseases. Here, we discuss recent advances in precise gene editing using different platforms as well as their potential applications in basic biology and biotechnology.
Comparative activity of immunofluorescent antibody and complement-fixing antibody in cytomegalovirus infection (1976)

Three different tests for detection of antibodies to human cytomegalovirus (CMV), complement fixing with antigen prepared by freeze-thaw disruption (CF-FT) or with antigen prepared by extraction with alkaline glycine buffer (CF-GE) and immunofluorescent staining (FA), were compared in renal transplant recipients and their healthy donors, FA and CF-GE tests yielded positive results at an identical and significantly higher frequency than CF-FT in both donors and recipients. CF-GE and FA performed on donors and recipients predicted all virus shedding post-transplant, whereas CF-FT did not. In the individuals who developed primary infection concurrent with the transplanted kidney, FA developed earlier than other antibodies in about one-half and at the same time in the remainder. In addition, the FA test could be completed more quickly and all sera could be interpreted, which made the FA test more useful than the CF-GE, but both of these tests were clearly superior to CF-FT.
In Situ Deprotection and Assembly of <i>S</i>-Tritylalkanethiols on Gold Yields Monolayers Comparable to Those Prepared Directly from Alkanethiols (2004)

In this paper we describe a systematic study comparing the properties of self-assembled monolayers (SAMs) formed by in situ deprotection and assembly of S-triphenylmethyl (trityl)- and thiolacetate-protected alkanethiols to those of SAMs formed from the parent alkanethiols. The two in situ deprotections were carried out in trifluoroacetic acid and THF/ammonium hydroxide, respectively. Monolayers of octadecanethiol (ODT) and the peptide-containing alkanethiol 3-mercapto-N-n-pentadecylpropionamide (1ATC15) were assembled on gold using the two in situ methods and characterized by contact angle goniometry, X-ray photoelectron spectroscopy, polarization modulation infrared reflection absorption spectroscopy, and electrochemical characterization methods to assess how the monolayer properties compare to those of monolayers prepared by traditional methods. The results for the in situ deprotection of the trityl-protected molecules demonstrate that this method can afford high-quality monolayers that are nearly indistinguishable from those prepared directly from alkanethiols. The quality of the monolayers prepared using this method is shown to depend on the solubility of the trityl-protected compound in trifluoroacetic acid. The results for the in situ deprotection of acetyl-ODT indicate this method yields low-quality monolayers that contain mixtures of adsorbates bound as thiolates and thiolacetates. In situ trityl deprotection is a useful approach for monolayer formation that greatly simplifies the purification, handling, and assembly of thiol-containing monolayer precursors.
Holographic evanescent-wave focusing with nanoparticle arrays (2008)

Three-dimensional focusing of evanescent waves by specially configured surface arrays of nanoparticles emulating near-field optical holograms of dipole sources (located close to the surface) is suggested and analyzed. The idea is to place chains of nanoparticles along bright fringes of calculated (holographic) interference patterns so that the local nanoparticle density along these chains would be proportional to the local intensity contrast in the interference patterns. Three different configurations are considered: a holographic scheme with totally internally reflected reference and reconstructing waves, a modified scheme with the reconstructing wave being represented by a suitable surface plasmon polariton (SPP) plane wave, and a SPP holographic scheme with reference and reconstructing waves both being (phase-conjugated) laterally-confined (Gaussian) SPP beams. Our numerical approach is based on the Greens function technique with the point-dipole approximation for radiation scattering by nanoparicles. We demonstrate that a nanoparticle array configured in accordance with the intensity interference pattern formed by a dipole field and a reference wave allows one to efficiently focus the (phase-conjugated) reconstructing wave (via its scattering by the nanoparticle array) at the site of the dipole. Influence of the polarization and wavelength of the reconstructing wave on the resulting intensity distribution is also considered. Fabrication of suitable nanoparticle arrays is discussed along with their potential applications.
Prognostic Role of Platelet to Lymphocyte Ratio in Solid Tumors: A Systematic Review and Meta-Analysis (2014)

PLR is a readily available and inexpensive biomarker with independent prognostic value in solid tumors.
Growth and characterization of GaN on <i>c</i>-plane (0001) sapphire substrates by plasma-enhanced molecular beam epitaxy (1993)

GaN films were grown on the c-plane of sapphire substrates by plasma-enhanced molecular beam epitaxy equipped with an electron-cyclotron resonance (ECR) source. Sapphire substrates were cleaned by a hydrogen plasma treatment, obviating the need for perilous elevated temperatures. ECR sources are plagued with high energetic ions, particularly at high microwave power levels, where they cause damage in the growing films. To circumvent this problem, we systematically optimized the growth conditions and other pertinent parameters for optimum layer quality. Among the parameters optimized were the magnetic field strength, microwave power, nitrogen over-pressure, and growth temperature. The quality of the GaN layers were evaluated by electrical and structural measurements as well as observing the surface morphology.
Development of a Mechanical Scanning-type Intravascular Ultrasound System Using a Miniature Ultrasound Motor (2007)

Intravascular ultrasound (IVUS) plays an important role for the detection of arteriosclerosis, which causes the ischemic heart disease. In mechanical scanning-type IVUS, it is necessary to rotate a transducer or a reflecting mirror. A method that involves rotating the transducer using a torque wire causes image distortion (NURD: non uniform rotation distortion). For a method that involves placing an electromagnetic motor on the tip of an IVUS probe is difficult to miniaturize the probe. Our objectives are to miniaturize the probe (1 mm in diameter, 5 mm in length) and to remove NURD. Therefore, we conducted a study to assess the feasibility of attaining these objectives by constructing a prototype IVUS system, in which an ultrasound motor using a stator in the form of a helical coil (abbreviated as CS–USM: coiled stator–ultrasonic motor) is incorporated, and to clarify problems that need to be solved in constructing the probe.