gebhart/patrepeval huggingface dataset:
Substrate Selectivity of YgfU, a Uric Acid Transporter from Escherichia coli (2012)

The ubiquitous nucleobase-ascorbate transporter (NAT/NCS2) family includes more than 2,000 members, but only 15 have been characterized experimentally. Escherichia coli has 10 members, of which the uracil permease UraA and the xanthine permeases XanQ and XanP are functionally known. Of the remaining members, YgfU is closely related in sequence and genomic locus with XanQ. We analyzed YgfU and showed that it is a proton-gradient dependent, low-affinity (K(m) 0.5 mM), and high-capacity transporter for uric acid. It also shows a low capacity for transport of xanthine at 37 °C but not at 25 °C. Based on the set of positions delineated as important from our previous Cys-scanning analysis of permease XanQ, we subjected YgfU to rationally designed site-directed mutagenesis. The results show that the conserved His-37 (TM1), Glu-270 (TM8), Asp-298 (TM9), and Gln-318 and Asn-319 (TM10) are functionally irreplaceable, and Thr-100 (TM3) is essential for the uric acid selectivity because its replacement with Ala allows efficient uptake of xanthine. The key role of these residues is corroborated by the conservation pattern and homology modeling on the recently described x-ray structure of permease UraA. In addition, site-specific replacements at TM8 (S271A, M274D, V282S) impair expression in the membrane, and V320N (TM10) inactivates the permease, whereas R327G (TM10) or S426N (TM14) reduces the affinity for uric acid (4-fold increased K(m)). Our study shows that comprehensive analysis of structure-function relationships in a newly characterized transporter can be accomplished with relatively few site-directed replacements, based on the knowledge available from Cys-scanning mutagenesis of a prototypic homolog.
Random nanowires of nickel doped TiO2with high surface area and electron mobility for high efficiency dye-sensitized solar cells (2012)

Mesoporous TiO(2) with a large specific surface area (~150 m(2) g(-1)) is the most successful material in dye-sensitized solar cells so far; however, its inferior charge mobility is a major efficiency limiter. This paper demonstrates that random nanowires of Ni-doped TiO(2) (Ni:TiO(2)) have a dramatic influence on the particulate and charge transport properties. Nanowires (dia ~60 nm) of Ni:TiO(2) with a specific surface area of ~80 m(2) g(-1) were developed by an electrospinning technique. The band gap of the Ni:TiO(2) shifted to the visible region upon doping of 5 at% Ni atoms. The Mott-Schottky analysis shows that the flat band potential of Ni:TiO(2) shifts to a more negative value than the undoped samples. The electrochemical impedance spectroscopic measurements showed that the Ni:TiO(2) offer lower charge transport resistance, higher charge recombination resistance, and enhanced electron lifetime compared to the undoped samples. The dye-sensitized solar cells fabricated using the Ni:TiO(2) nanowires showed an enhanced photoconversion efficiency and short-circuit current density compared to the undoped analogue. The transient photocurrent measurements showed that the Ni:TiO(2) has improved charge mobility compared with TiO(2) and is several orders of magnitude higher compared to the P25 particles.
Electron paramagnetic resonance studies of carbon monoxide absorbed on thorium oxide (1971)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTElectron paramagnetic resonance studies of carbon monoxide absorbed on thorium oxideWallace S. Brey Jr., R. B. Gammage, and Y. P. VirmaniCite this: J. Phys. Chem. 1971, 75, 7, 895–901Publication Date (Print):April 1, 1971Publication History Published online1 May 2002Published inissue 1 April 1971https://pubs.acs.org/doi/10.1021/j100677a009https://doi.org/10.1021/j100677a009research-articleACS PublicationsRequest reuse permissionsArticle Views34Altmetric-Citations9LEARN 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
Programming pervasive and mobile computing applications (2009)

Pervasive and mobile computing call for suitable middleware and programming models to support the activities of complex software systems in dynamic network environments. In this article we present TOTA (“Tuples On The Air”), a novel middleware and programming approach for supporting adaptive context-aware activities in pervasive and mobile computing scenarios. The key idea in TOTA is to rely on spatially distributed tuples, adaptively propagated across a network on the basis of application-specific rules, for both representing contextual information and supporting uncoupled interactions between application components. TOTA promotes a simple way of programming that facilitates access to distributed information, navigation in complex environments, and the achievement of complex coordination tasks in a fully distributed and adaptive way, mostly freeing programmers and system managers from the need to take care of low-level issues related to network dynamics. This article includes both application examples to clarify concepts and performance figures to show the feasibility of the approach
Vertical profiles of environmental parameters measured on discrete water samples collected with Niskin bottles at station TARA_009 during the Tara Oceans expedition 2009-2013 (2014)

The Tara Oceans Expedition (2009-2013) was a global survey of ocean ecosystems aboard the Sailing Vessel Tara. It carried out extensive measurements of evironmental conditions and collected plankton (viruses, bacteria, protists and metazoans) for later analysis using modern sequencing and state-of-the-art imaging technologies. Tara Oceans Data are particularly suited to study the genetic, morphological and functional diversity of plankton. The present data set includes properties of seawater, particulate matter and dissolved matter that were measured from discrete water samples collected with Niskin bottles during the 2009-2013 Tara Oceans expedition. Properties include pigment concentrations from HPLC analysis (10 depths per vertical profile, 25 pigments per depth), the carbonate system (Surface and 400m; pH (total scale), CO2, pCO2, fCO2, HCO3, CO3, Total alkalinity, Total carbon, OmegaAragonite, OmegaCalcite, and dosage Flags), nutrients (10 depths per vertical profile; NO2, PO4, N02/NO3, SI, quality Flags), DOC, CDOM, and dissolved oxygen isotopes. The Service National d'Analyse des Paramètres Océaniques du CO2, at the Université Pierre et Marie Curie, determined CT and AT potentiometrically. More than 200 vertical profiles of these properties were made across the world ocean. DOC, CDOM and dissolved oxygen isotopes are available only for the Arctic Ocean and Arctic Seas (2013).
Sepsis: molecular mechanisms underlying lipopolysaccharide recognition (2004)

Sepsis is an often-fatal response of the immune system against microbial pathogens. The molecular mechanisms that have been designed to protect the host from invading pathogens are responsible for the damage and injury. It is now widely known that this crucial response of the immune system is mediated by innate immunity, which employs a plethora of pattern recognition receptors that recognise motifs expressed by pathogens. A lack of knowledge of the mediators involved in innate recognition has led to unsuccessful attempts at designing effective therapeutic interventions for sepsis. However, in recent years, great leaps forward have been achieved in our knowledge of these mediators. In this review we attempt to unravel the molecular mechanisms underlying bacterial recognition, particularly recognition of bacterial lipopolysaccharide, and we propose future potential therapeutic targets for septic shock.
Acoustic methods for the remote probing of the lower atmosphere (1969)

The potential usefulness of acoustic methods for the remote probing of the lower atmosphere is reviewed. Starting with a comparison of the effects of temperature, wind, and humidity fluctuations upon the refractive index of air to electromagnetic and acoustic waves, it is shown that the fluctuations in acoustic refractive index may be expected to be about 1000 times stronger than in the radio case. The opportunities for passive and for line-of-sight remote acoustical sensing of the troposphere offered by this relatively strong interaction are briefly identified. Since the scattered power is proportional to the square of the refractive index fluctuations, the scatter of acoustic waves may be expected to be roughly one million times stronger than for radio waves. Based on the theoretical work of Kallistratova (but including the effects of atmospheric absorption), the system parameters required for effective acoustic echo-sounding of the lower atmosphere are deduced. It is concluded that the acoustic sounding technique could be developed to monitor, to heights of at least 1500 meters, 1) the vertical profile of wind speed and direction, 2) the vertical profile of humidity, 3) the location and intensity of temperature inversions, 4) the three-dimensional spectrum of mechanical turbulence, and 5) the three-dimensional spectrum of temperature inhomogeneity (i.e., of optical refractive index fluctuation). Typical time and height resolutions for the proposed acoustic echo-sounders could be of the order 10 seconds and 10 meters; the spatial wave number explored could range from about 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-2</sup> m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> to about 400 m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-1</sup> .
Applications Of Geophysical Logging For Dilution Control In Mining (1996)

In mining, waste rock dilution occurs when uneconomic rock is mined and processed with economic mineralized&lt;br&gt;ore. A survey of selected stopes from various Noranda Group mines estimated that aggregate dilution and oreloss&lt;br&gt;stood at 20% and 8% respectively in 1994. Various technologies are being investigated by Noranda Group mines&lt;br&gt;in an ongoing effort to minimize dilution and oreloss. The following three potential applications of geophysical&lt;br&gt;logging have been identified for dilution and oreloss reduction through improved orebody delineation.
New insights into the thermally activated defects in n-type float-zone silicon (2019)

Float-zone silicon has been long assumed to be bulk defect free and stable. Nevertheless, recently it was found that upon annealing between 450 °C to 700 °C detrimental defects can be activated in this material. Previous studies via deep level transient spectroscopy have identified several defect levels. However, it is still not clear which of these levels have a substantial impact on the minority carrier lifetime. In this study, we determine the recombination parameters of the dominant defect level using a combination of deep level transient spectroscopy and temperature and injection dependent lifetime spectroscopy. Additionally, we investigated the effect of hydrogenation on the thermally activated defects in n- type float-zone silicon.
Supplementary Data from Intercohort Gene Expression Co-Analysis Reveals Chemokine Receptors as Prognostic Indicators in Ewing's Sarcoma (2023)

Supplementary Data from Intercohort Gene Expression Co-Analysis Reveals Chemokine Receptors as Prognostic Indicators in Ewing's Sarcoma
Initiation Behavior of Crack Originated from Non-Metallic Inclusion in Rolling Contact Fatigue (2010)

Abstract Recently, it has been generally accepted that flaking life is dependent on the size of non-metallic inclusion under proper condition in bearing use. Statistics of extreme values to predict the maximum non-metallic inclusion size and ultrasonic test to assess large non-metallic inclusions in a large volume are widely used as practical methods for the evaluation of bearing steel cleanliness. Murakami’s formula is well known, which describes the relationship between non-metallic inclusion size and fatigue strength. However, the formula cannot be directly applied to rolling contact fatigue because of the difference in applied stress mode. While the equation was invented to predict the fatigue limit in principal stress mode, rolling contact fatigue is mainly caused by shear stress. It is expected that the condition of bearing use will be more critical due to the downsizing tendency in various industrial or automotive machine units. Thus the research on the flaking mechanism becomes more important from the viewpoint of global ecology because that is beneficial to the improvement in bearing life and methods for cleanliness evaluation. Due to the difficulty in experimental observation, however, the details of the flaking mechanism in rolling contact fatigue caused by non-metallic inclusion has not yet been clarified. Focusing on the relationship between non-metallic inclusion and initiation of the crack, the flaking mechanism is proposed in this paper.
Immediate Effects of Functional Electrical Stimulation on Kinematic and Kinetic Variables and Oxygenation in Medial Sensorimotor Cortices during Gait in Patients with Acute Cerebral Infarction (2015)

Purpose: The aim of this study was to determine the immediate effects of functional electrical stimulation (FES) on kinematic and kinetic gait variables and oxygenation in medial sensorimotor cortices (mSMC). Methods: We performed gait analysis using Vicon motion capture system and brain oxygenation in mSMC using near-infrared spectroscopy (NIRS) in eight subjects with acute cerebral infarction. FES was performed during walking on the tibialis anterior muscles and gastrocnemius of the paretic limb during the swing and terminal stance phases, respectively. Results: Gait velocity, paretic hip flexion, knee extension, and ankle plantar flexion moments in the stance phase significantly increased when FES was performed during walking compared with those with walking before FES. Moreover, these improvements of gait quality were carried over after performing FES. Oxygenated hemoglobin levels in unaffected mSMC were significantly lower during walking with FES than that during walking without FES. Conclusion: FES can improve weight shifting to the paretic limb during the stance phase and improve propulsion as a roll-off function in the late stance. Furthermore, FES may inhibit cortical excitability in unaffected mSMC.
Plasma, tissue, and urine carnitine concentrations in healthy adult cats and kittens (1990)

Mean carnitine concentrations [( carnitine]) were higher (P less than 0.05) in adult cats than in kittens for skeletal muscle (total and free carnitine), myocardium (free carnitine), and urine (total and free carnitine). The free/total carnitine ratio was lower (P less than 0.05) in kittens than in adults for liver, myocardium, and urine. Carnitine concentrations were similar between genders in kittens, but in adult cats, [carnitine] in plasma (total, free, and esterified carnitine) and liver (total and free carnitine) were higher (P less than 0.05) in female than in male cats. Total and free plasma [carnitine] were correlated to total and free liver [carnitine], respectively. Skeletal muscle [carnitine] was not correlated to plasma [carnitine]. Correlations in [carnitine] between plasma and myocardium, kidney, or urine were inconsistent.
Miniaturization of Magnetically Levitated Motor for Pediatric Ventricular Assist Device (2020)

A miniaturized magnetically levitated motor which has high durability and excellent blood compatibility to realize a pediatric ventricular assist device (VAD). The developed motor consists of a top stator, a bottom stator and a levitated impeller which is controlled with 5-degrees of freedom control. This motor is an axial self-bearing motor with double stator mechanism. In this study, A motor miniaturization design was performed using theoretical calculation of magnetic circuit and three-dimensional magnetic field analysis of finite element method. The improved motor Reduced volume from 13cc to 11cc and indicates the acceleration coefficient can be generated 4.84 G/A. It was also confirmed that it could resist acceleration disturbances near to 5 G/A, which is the target performance.
Acousto-optic devices: principles, design, and applications (1992)

Crystal Optics and Acoustics Acousto-Optic Interaction The Piezoelectric Effect and Piezoelectric Transducers Thin-Film Acousto-Optic Devices Multifrequency Acousto-Optic Diffraction Deflectors and Bragg Cells Modulators and Tunable Filters Transducers and Thin-Film Devices Applications of Acousto-Optic Devices Acousto-Optic Signal Processing Appendices Index.
Precision GMTI tracking using road constraints with visibility information and a refined sensor model (2008)

For detecting targets moving on ground, airborne ground moving target indicator (GMTI) radar is well-suited due to its wide-area, all-weather, day/night, and real time capabilities. The generation of GMTI tracks from these data is the backbone for target identification, ground surveillance as well as traffic flow analysis. The generation of precise and continuous tracks from GMTI radar plots often is a demanding task due to terrain and technical obscuration and clutter. The exploitation of non-standard background information such as road maps and terrain information is therefore highly desirable for the enhancement of track quality and track continuity. The present paper presents a Bayesian tracking scheme that incorporates digital road-map information and a model for the clutter notch of the GMTI sensor. The significant gain in track quality and track continuity is demonstrated in a number of simulation scenarios involving Doppler blindness and terrain obscuration.
Effect of selective media on loss of congo red binding inShigella flexneri (1990)

The effect of growth of Shigella flexneri on various selective media on retention of congo red (CR) binding ability was determined to evaluate the effectiveness of isolation techniques regarding maintenance of the virulence plasmid. When S.flexneri was surface-plated onto selective agars dnd the resulting colonies replica plated onto CR plates, no white colonies indicative of loss of virulence were found despite repeated trials. However, when S. flexneri was grown in liquid media (agar was removed from agar-containing media by centrifugation), white colonies were found upon plating onto CR plates. Most common selective media for shigellae produced fewer than 5-10 white colonies/1000 red colonies. However, growth in broth prepared from violet red bile agar, desoxycholate citrate agar, and SS agar gave more than 100 white colonies/1000 red colonies. Loss of CR binding was demonstrated when S.flexneri was grown in broth containing tergitol 7, sodium dodecyl sulfate, bile salts # 3, crystal violet, eosin y, or methylene blue. However, concentrations of selective agents that led to loss of CR binding were much higher than those used in selective media. Results indicate that under usual conditions of isolation of S.flexneri from food and clinical specimens, CR binding appears to be a relatively stable character with most selective media; however, use of violet red bile agar, desoxycholate citrate agar, and SS agar may lead to substantial loss.of congo red binding indicating that the isolates may not be virulent.
Neuraminidase Inhibitor-Rimantadine Combinations Exert Additive and Synergistic Anti-Influenza Virus Effects in MDCK Cells (2004)

There is insufficient information about combination therapy with approved anti-influenza agents. We tested combinations that paired a neuraminidase (NA) inhibitor (zanamivir, oseltamivir carboxylate, or peramivir) with rimantadine against infection of MDCK cells with H1N1 and H3N2 subtypes of influenza A virus and characterized their mode of interaction. When reduction of extracellular virus was analyzed by individual regression models and three-dimensional representations of the data, all three combinations showed additive and synergistic effects with no cytotoxicity. Maximum synergy against A/New Caledonia/20/99 (H1N1) virus infection was observed with <2.5 microM rimantadine paired with low concentrations of NA inhibitors. All combinations reduced the extracellular yield of A/Panama/2007/99 (H3N2) influenza virus synergistically. However, our findings were different for the cell-associated virus yield. At some drug concentrations, the yield of cell-associated virus was inhibited antagonistically. Therefore, the method of analysis can be a crucial factor in evaluating the interactions of drugs with different mechanisms. We hypothesize that assays based on cell-associated virus yield may underestimate the efficacies of drug combinations that include an NA inhibitor. Taken together, our results suggest that regimens that combine NA inhibitors and rimantadine exert synergistic anti-influenza effects in vitro. These findings provide baseline information for therapeutic testing of the drug combinations in vivo.
Rickettsia parkeri with a Genetically Disrupted Phage Integrase Gene Exhibits Attenuated Virulence and Induces Protective Immunity against Fatal Rickettsioses in Mice (2021)

Although rickettsiae can cause life-threatening infections in humans worldwide, no licensed vaccine is currently available. To evaluate the suitability of live-attenuated vaccine candidates against rickettsioses, we generated a <i>Rickettsia parkeri</i> mutant RPATATE_0245::pLoxHimar (named 3A2) by insertion of a modified pLoxHimar transposon into the gene encoding a phage integrase protein. For visualization and selection, <i>R. parkeri</i> 3A2 expressed mCherry fluorescence and resistance to spectinomycin. Compared to the parent wild type (WT) <i>R. parkeri</i>, the virulence of <i>R. parkeri</i> 3A2 was significantly attenuated as demonstrated by significantly smaller size of plaque, failure to grow in human macrophage-like cells, rapid elimination of <i>Rickettsia</i> and ameliorated histopathological changes in tissues in intravenously infected mice. A single dose intradermal (i.d.) immunization of <i>R. parkeri</i> 3A2 conferred complete protection against both fatal <i>R. parkeri</i> and <i>R. conorii</i> rickettsioses in mice, in association with a robust and durable rickettsiae-specific IgG antibody response. In summary, the disruption of RPATATE_0245 in <i>R. parkeri</i> resulted in a mutant with a significantly attenuated phenotype, potent immunogenicity and protective efficacy against two spotted fever group rickettsioses. Overall, this proof-of-concept study highlights the potential of <i>R. parkeri</i> mutants as a live-attenuated and multivalent vaccine platform in response to emergence of life-threatening spotted fever rickettsioses.