gebhart/patrepeval huggingface dataset:
Evidence for a New Type of Outer Membrane Lipid in Oral Spirochete Treponema denticola (1998)

A new class of outer membrane lipid (OML) was isolated from the oral spirochete Treponema denticola strain ATCC 33521 using a phenol/chloroform/light petroleum procedure normally applied for lipopolysaccharide extraction. In addition to chemical analysis, Fourier transform infrared (FTIR) spectroscopy was applied to compare the biophysical properties of OML with lipopolysaccharides (LPS) and lipoteichoic acids (LTA). Isolated OML fractions represent 1.4% of the total dry cell weight, are about 4 kDa in size, and contain 6% amino sugars, 8% neutral sugars, 14% phosphate, 35% carbazol-positive compounds, and 11% fatty acids (containing iso- and anteiso-fatty acyl chains). Rare for outer membrane lipids, OML contains no significant amount of 3-deoxy-D-manno-octulosonic acids, heptoses, and beta-hydroxy fatty acids. The fatty acyl chain composition, being similar to that of the cytoplasmic membrane, is quite heterogeneous with anteiso-pentadecanoic acid (12%), palmitic acid (51%), and iso-palmitic acid (19%) as the predominant fatty acids present. Findings of a glycerol-hexose unit and two glycerol-hexadecanoic acid fragments indicate a glycolipid membrane anchor typically found in LTA. There was also no evidence for the presence of a sphingosine-based lipid structure. The results of FTIR measurements strongly suggest that the reconstituted lipid forms normal bilayer structures (vesicles) expressing a high membrane state of order with a distinct phase transition as typical for isolated LPS. However, in contrast to LPS, OML of T. denticola has a lower Tm near 22 degreesC and a lower cooperativity of the phase transition. The results suggest a different kind of permeation barrier that is built up by this particular OML of T. denticola, which is quite different from LPS normally essential for Gram-negative bacteria.
PROPANESULTONE (1964)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPROPANESULTONER. F. FischerCite this: Ind. Eng. Chem. 1964, 56, 3, 41–45Publication Date (Print):March 1, 1964Publication History Published online1 May 2002Published inissue 1 March 1964https://pubs.acs.org/doi/10.1021/ie50651a008https://doi.org/10.1021/ie50651a008research-articleACS PublicationsRequest reuse permissionsArticle Views606Altmetric-Citations46LEARN 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 options Get e-Alerts
Phase Differential Angular Rate Sensor—Concept and Analysis (2004)

This paper proposes and analyzes a new differential phase angular rate (AR) sensor employing a vibrating beam mass structure that traces an elliptical path when subject to rotation due to Coriolis force. Two sensing elements are strategically located to sense a combination of drive and Coriolis vibration to create a phase differential representative of the input rotation rate. A general model is developed, describing the device operation. The main advantages of the phase detection scheme are explored, including removing the need to maintain constant drive amplitude, independence of sensing element gain factor, and advantageous response shapes. A ratio of device parameters is defined and shown to dictate the device response shape. This ratio can be varied to give an optimally linear phase difference output over a set input range, a high sensitivity around zero input rate, or a response shape not seen before, that can give maximum sensitivity around an offset from the zero-rate input. This may be exploited in an array configuration for a highly accurate device over a wide input range. A worked example shows how the developed equations can be used as design tools to achieve a desired response with low sensitivity to variation in device parameters.
Photo-EPR studies of electron and hole trapping by [Fe(CN)<sub>6</sub>]<sup>4-</sup>complexes in silver chloride (1995)

Abstract [Fe(CN)6]4- was incorporated into silver chloride powders precipitated from aqueous solution with all six cyanide ligands intact. The most notable feature of this dopant was its amphoteric behavior, acting as either a deep hole trap or a shallow electron trap. The filled t2g orbital manifold of this complex lies below the Fermi level, which places the vacant eg levels well above the conduction band minimum. The trapping behavior of [Fe(CN)6]4- was determined by whether or not it was closely associated with a charge-compensating silver ion vacancy.
Surface-active compounds and their role in the access to hydrocarbons in Gordonia strains (2008)

Three new bacterial strains (M22, BS25 and BS29) belonging to the Gordonia genus were isolated from a site chronically contaminated by diesel. Those Gordonia strains were able to grow using a wide range of straight and branched aliphatic hydrocarbons as carbon and energy sources and to produce at least two classes of surface-active compounds. Emulsifying agents were released in the culture medium when bacteria grew both on hydrocarbons and water-soluble substrates. Cell-bound biosurfactants, which reduce the surface tension, were produced on hydrocarbons; however, their production was significantly lower on water soluble substrates. The relationship of growth phase, surface-active compound production and cell-surface properties was analyzed in kinetic experiments on hydrocarbons. Gordonia sp. BS29 synthesized, and released extracellularly, bioemulsans during the exponential phase with n-hexadecane as carbon and energy source. The production of biosurfactants started in the exponential phase and their concentration increased during the following linear growth. Furthermore, the adhesion of bacterial cells to hydrocarbons decreased during growth. Our results led us to hypothesize a change in the mode by which Gordonia cells access the substrate during growth on hydrocarbons.
Arrhythmia Mechanisms Revealed by Ripple Mapping (2018)

Ripple mapping is a novel method of 3D intracardiac electrogram visualisation that allows activation of the myocardium to be tracked visually without prior assignment of local activation times and without interpolation into unmapped regions. It assists in the identification of tachycardia mechanism and optimal ablation site, without the need for an experienced computer-operating assistant. This expert opinion presents evidence demonstrating the benefit of Ripple Mapping, compared with traditional electroanatomic mapping techniques, for the diagnosis and management of atrial and ventricular tachyarrhythmias during electrophysiological procedures.
Elucidation and Structural Modeling of CD71 as a Molecular Target for Cell-Specific Aptamer Binding (2019)

Pancreatic cancer is a highly lethal malignancy associated with tissues of the pancreas. Early diagnosis and effective treatment are crucial to improving the survival rate of patients with pancreatic cancer. In a previous study, we employed the cell-SELEX strategy to obtain an ssDNA aptamer termed XQ-2d with high binding affinity for pancreatic cancer. Here, we first identify CD71 as the XQ-2d-binding target. We found that knockdown of CD71 abolished the binding of XQ-2d and that the binding affinity of XQ-2d is associated with membrane-bound CD71, rather than total CD71 levels. Competitive analysis revealed that XQ-2d shares the same binding site on CD71 with transferrin (Tf), but not anti-CD71 antibody. We then used a surface energy transfer (SET) nanoruler to measure the distance between the binding sites of XQ-2d and anti-CD71 antibody, and it was about 15 nm. Furthermore, we did molecular dynamics simulation to clarify that the spatial structure of XQ-2d and Tf competitively binding to CD71. We also engineered XQ-2d-mediated targeted therapy for pancreatic cancer, using an XQ-2d-based complex for loading doxorubicin (Dox). Because CD71 is overexpressed not only in pancreatic cancer but also in a variety of tumors, our work provides a systematic novel way of studying a potential biomarker and also promising tools for cancer diagnosis and therapy, opening new doors for effective cancer theranostics.
Cell culture-derived influenza vaccines from Vero cells: a new horizon for vaccine production (2012)

In the 20th century, three influenza pandemics killed approximately 100 million people. The traditional method of influenza vaccine manufacturing is based on using chicken eggs. However, the necessity of the availability of millions of fertile eggs in the event of a pandemic has led research to focus on the development of cell culture-derived vaccines, which offer shorter lead-in times and greater flexibility of production. So far, the cell substrates being evaluated and in use include Vero, Madin-Darby canine kidney, PER.C6 and insect cells. However, Vero cells are the most widely accepted among others. This review introduces briefly the concepts of advanced cell culture-derived influenza vaccine production and highlights the advantages of these vaccines in terms of efficiency, speed and immunogenicity based on the clinical data obtained from different studies.
The 62- and 80-kDa subunits of transcription factor IIH mediate the interaction with Epstein-Barr virus nuclear protein 2. (1995)

EBNA 2 (Epstein-Barr virus nuclear antigen 2) is an acidic transactivator essential for EBV transformation of B lymphocytes. We show that EBNA 2 directly interacts with general transcription factor IIH. Glutathione S-transferase (GST)-EBNA 2 acidic domain fusion protein depleted transcription factor IIH activity from a TFIIH nuclear fraction. The p89 (ERCC3), p80 (ERCC2), and p62 subunits of TFIIH were among the proteins retained by GST-EBNA 2. Eluates from the GST-EBNA 2 beads reconstituted activity in a TFIIH-dependent in vitro transcription assay. The p62 and p80 subunits of TFIIH independently bound to GST-EBNA 2, whereas the p34 subunit of TFIIH only bound in the presence of p62. A Trp-->Thr mutation in the EBNA 2 acidic domain abolishes EBNA 2 transactivation in vivo and greatly compromised EBNA 2 association with TFIIH activity and with the p62 and p80 subunits, providing a link between EBNA 2 transactivation and these interactions. Antibodies directed against the p62 subunit of TFIIH coimmunoprecipitated EBNA 2 from EBV-transformed B lymphocytes, indicating that EBNA 2 associates with TFIIH in vivo.
Counting on jobs for physicists (2011)

I read Margaret Harris's article on graduate careers for physicists (March pp54–56) with interest as this is an area in which I am heavily involved.
Potential for Zoonotic Transmission of<i>Brachyspira pilosicoli</i> (2006)

To the Editor: Anaerobic intestinal spirochetes of the genus Brachyspira colonize the large intestine (1). Most Brachyspira species have a restricted host range, whereas Brachyspira (formerly Serpulina) pilosicoli colonizes a variety of animal and bird species and humans. B. pilosicoli is an important colonic pathogen of pigs and chickens (2). It occurs at high prevalence rates in humans in developing countries and in male homosexuals and HIV-positive persons in industrialized countries (3). Its potential as a human pathogen was emphasized after its identification in the bloodstream of a series of debilitated persons (4).
Post-Translational Phosphorylation of Serine 74 of Human Deoxycytidine Kinase Favors the Enzyme Adopting the Open Conformation Making It Competent for Nucleoside Binding and Release (2011)

Deoxycytidine kinase (dCK) uses either ATP or UTP as a phosphoryl donor to catalyze the phosphorylation of nucleoside acceptors. The kinetic properties of human dCK are modulated in vivo by phosphorylation of serine 74. This residue is a part of the insert region and is distant from the active site. Replacing the serine with a glutamic acid (S74E variant) can mimic phosphorylation of Ser74. To understand how phosphorylation affects the catalytic properties of dCK, we examined the S74E variant of dCK both structurally and kinetically. We observe that the presence of a glutamic acid at position 74 favors the adoption by the enzyme of the open conformation. Glu74 stabilizes the open conformation by directly interacting with the indole side chain of Trp58, a residue that is in the proximity of the base of the nucleoside substrate. The open dCK conformation is competent for the binding of nucleoside but not for phosphoryl transfer. In contrast, the closed conformation is competent for phosphoryl transfer but not for product release. Thus, dCK must make the transition between the open and closed states during the catalytic cycle. We propose a reaction scheme for dCK that incorporates the transition between the open and closed states, and this serves to rationalize the observed kinetic differences between wild-type dCK and the S74E variant.
Enhanced second harmonic generation in a self-similar chain of metal nanospheres (2005)

We show theoretically that an efficient nanolens (a self-similar chain of metal nanospheres) creates a nanofocus of highly enhanced (up to six orders of magnitude with respect to the flat surface) second harmonic local fields. This nanofocus is situated in the gap between the nanospheres at the surface of the smallest nanosphere on the axis of symmetry. The spectral maximum for silver nanolens in vacuum is in near-Uv at 337 nm. The generation of the second harmonic radiation in the far zone is also predicted due to the absence of the center symmetry of the nanolens considered. Perspective applications in chemical and biological sensing are discussed.
Experiments on Elastic Cloaking in Thin Plates (2012)

Following a theoretical proposal [M. Farhat et al., Phys. Rev. Lett. 103, 024301 (2009)], we design, fabricate, and characterize a cloaking structure for elastic waves in 1 mm thin structured polymer plates. The cloak consists of 20 concentric rings of 16 different metamaterials, each being a tailored composite of polyvinyl chloride and polydimethylsiloxane. By using stroboscopic imaging with a camera from the direction normal to the plate, we record movies of the elastic waves for monochromatic plane-wave excitation. We observe good cloaking behavior for carrier frequencies in the range from 200 to 400 Hz (one octave), in good agreement with a complete continuum-mechanics numerical treatment. This system is thus ideally suited for demonstration experiments conveying the ideas of transformation optics.
Using perspective guidance overlay to improve UAV manual control performance (2007)

The guidance information that is available to the UAV operator typically suffers from limitations of data update rate and system latency. Even when using a flight director command display, the manual control task is considerably more difficult compared to piloting a manned aircraft. Results from earlier research into perspective guidance displays show that these displays provide performance benefits and suggest a reduction of the negative effects of system latency. The current study has shown that in case of limitations of data update rate and system latency the use of a conformal sensor overlay showing a perspective presentation of the trajectory constraints is consistently superior to the flight director command display. The superiority becomes more pronounced with an increase in data latency and a decrease in update rate. The fact that the perspective pathway overlay as used in this study can be implemented on any graphics system that is capable of rendering a set of 2-D vectors makes it a viable candidate for upgrades to current systems.
Observation of Geometry Induced Doping in Thin Si Nano-grating Layers (2016)

We fabricate Si nano-grating layers and measure their electrical characteristics to monitor geometry induced doping. SOI device layer was thinned down by thermal oxidizing and subsequent wet etching of the oxide. Grating was fabricated using laser interference lithography (375 nm laser) followed by reactive ion etching of Si. Next, large square island (0.5x0.5 mm) was shaped in the device layer and four Si\Ti\Ag ohmic contacts were formed to measure electrical characteristics. The I-V characteristics were recorded using both 4 wire and 2 wire methods. Resistance-temperature dependences (T= 4-300 K) were recorded as well. For all 12 samples, nano-grating layers show 2-3 order reduction of resistivity. Resistivity anisotropy was in the range 0.2-1 at 300 K. Obtained geometry induced doping level corresponds to "effective impurity" concentration of 3x1018 cm-3. The dependence is in agreement with G-doping theory only below T=150K.
HIOS: A host interface I/O scheduler for Solid State Disks (2014)

Garbage collection (GC) and resource contention on I/O buses (channels) are among the critical bottlenecks in Solid State Disks (SSDs) that cannot be easily hidden. Most existing I/O scheduling algorithms in the host interface logic (HIL) of state-of-the-art SSDs are oblivious to such low-level performance bottlenecks in SSDs. As a result, SSDs may violate quality of service (QoS) requirements by not being able to meet the deadlines of I/O requests. In this paper, we propose a novel host interface I/O scheduler that is both GC-aware and QoS-aware. The proposed scheduler redistributes the GC overheads across non-critical I/O requests and reduces channel resource contention. Our experiments with workloads from various application domains reveal that the proposed scheduler reduces the standard deviation for latency over state-of-the-art I/O schedulers used in the HIL by 52.5%, and the worst-case latency by 86.6%. In addition, for I/O requests with sizes smaller than a superpage, our proposed scheduler avoids channel resource conflicts and reduces latency by 29.2% compared to the state-of-the-art.
Increased Foxp3+Helios+ Regulatory T Cells and Decreased Acute Graft-versus-Host Disease after Allogeneic Bone Marrow Transplantation in Patients Receiving Sirolimus and RGI-2001, an Activator of Invariant Natural Killer T Cells (2017)

Regulatory T (Treg) cells play a central role in immune tolerance and prevention of aberrant immune responses. Several studies have suggested that the risk of graft-versus-host disease (GVHD) after allogeneic hematopoietic cell transplantation (HCT) can be ameliorated by increasing Tregs. We have developed an approach of in vivo expansion of Tregs with RGI-2001, a novel liposomal formulation of a synthetic derivative of alpha-galactosylceramide, a naturally occurring ligand that binds to CD1 and activates and expands invariant natural killer cells. In preclinical studies, a single intravenous infusion of RGI-2001 expanded Treg and could ameliorate GVHD in a mouse model of allogeneic HCT. To explore the role of RGI-2001 in clinical HCT, we initiated a phase 2A clinical trial (n = 29), testing 2 different doses of RGI-2001 administered as a single infusion on day 0 of allogeneic HCT. RGI-2001 was well tolerated and without infusion reactions or cytokine release syndrome. A subset of patients (8 of 29, 28%) responded to RGI-2001 by inducing a markedly increased number of cells with a Treg phenotype. The Treg had a high Ki-67 index and were almost exclusively Helios<sup>+</sup> and Foxp3<sup>+</sup>, indicating that their accumulation was due to expansion of natural Treg. Notably, the incidence of grade 2 to 4 GVHD in the 8 patients who responded to RGI-2001 was 12.5%, compared with 52.4% in the 21 patients who did not respond. No grade 3 or 4 GVHD was observed in the responder group, compared with a 9.5% incidence among nonresponders. Immunosuppression with sirolimus was also associated with a low incidence of GVHD, suggesting that RGI-2001 may have synergized with sirolimus to promote Treg expansion.
MetaQuery: a web server for rapid annotation and quantitative analysis of specific genes in the human gut microbiome (2015)

Abstract Summary: Microbiome researchers frequently want to know how abundant a particular microbial gene or pathway is across different human hosts, including its association with disease and its co-occurrence with other genes or microbial taxa. With thousands of publicly available metagenomes, these questions should be easy to answer. However, computational barriers prevent most researchers from conducting such analyses. We address this problem with MetaQuery, a web application for rapid and quantitative analysis of specific genes in the human gut microbiome. The user inputs one or more query genes, and our software returns the estimated abundance of these genes across 1267 publicly available fecal metagenomes from American, European and Chinese individuals. In addition, our application performs downstream statistical analyses to identify features that are associated with gene variation, including other query genes (i.e. gene co-variation), taxa, clinical variables (e.g. inflammatory bowel disease and diabetes) and average genome size. The speed and accessibility of MetaQuery are a step toward democratizing metagenomics research, which should allow many researchers to query the abundance and variation of specific genes in the human gut microbiome. Availability and implementation: http://metaquery.docpollard.org. Contact: snayfach@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online.
Discussion of millimeter wave FBAR with very thin AlN film fabricated using MOCVD method (2009)

We discuss millimeter-wave film bulk acoustic resonator (FBAR) with very thin aluminium nitride (AlN) film fabricated using metal organic chemical vapor deposition (MOCVD) method. In previous works, we have successfully grown c-axis oriented AlN film using MOCVD method on Ru/Ta/SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> /Si substrate. In this paper, we grew excellent orientation films of AlN and Ru electrodes in MOCVD, although their film thickness were very thin. Experimental results show that full width at half maximum (FWHM) is 1.3° at AlN thickness of 30 nm. In calculating analysis, when both top and bottom electrode thicknesses were 20 nm and AlN thickness was 30 nm, we obtained that resonant frequency was higher than 50 GHz. Therefore, FBAR is possible to apply to millimeter-wave bands devices, also contribute to small-size, low power consumption and low cost for millimeter-wave terminals.
Estimation of stroke volume from the pulmonary artery pressure record (1974)

This study describes the estimation of stroke volume in a series of dogs by a pulse contour method applied to the pulmonary artery pressure record. The results correlated well with measurements of stroke volume by an electromagnetic flowmeter and by indicator dilution curves when changes were produced by noradrenaline, isoproterenol, propranolol, haemorrhage, pacing, and respiratory outflow occlusion. However, when saline was rapidly infused, error increased significantly.