gebhart/patrepeval huggingface dataset:
Complement Inhibitor of C5 Activation from the Soft Tick <i>Ornithodoros moubata</i> (2005)

Blood-feeding ticks must control C activation or be damaged by the host inflammatory response. We report the characterization and expression of a novel, relatively small, broad-acting C inhibitory protein (termed OmCI) from the soft tick Ornithodoros moubata. The native 17-kDa nonglycosylated protein inhibits both human and guinea pig classical and alternative C activation pathways. The IC50 values for each pathway were 12 and 27 nM, respectively, in hemolytic assays using human serum diluted 40-fold. The cDNA encodes a protein of 168 aa, including an 18-aa secretion signal sequence that is absent in the mature form. The inhibitor has 46% amino acid identity with moubatin, a platelet aggregation inhibitor also from O. moubata that is an outlying member of the lipocalin family. Native OmCI had no inhibitory effect on the addition of C8 and C9 to preformed C5b-C7 and C5b-C8 to form the membrane attack complex and no effect on the rate of C3a production by the C3 convertase enzymes C4bC2a, C3(H2O)Bb, or C3bBb. Both recombinant and native OmCI abolish production of C5a by human classical (C4bC3bC2a) and alternative (C3bC3bBb) C5 convertases. Addition of excess C5 but not C3 competes away the inhibitory activity of OmCI, indicating that OmCI targets C5 itself rather than inhibiting the C5 convertase C4bC3bC2a itself. Direct binding of OmCI to C5 was demonstrated by Western blotting and gel filtration chromatography using 125I-labeled proteins. OmCI is the first lipocalin family member shown to inhibit C and also the first natural inhibitor that specifically targets the C5 activation step.
Oxidation of iron in iron/gold core/shell nanoparticles (2002)

Recently, reverse micelles were used to produce core/shell nanoparticles of iron and gold of highly uniform size distribution and reported to contain metallic iron. A composite structure of this sort is attractive in biosensor and bioactuator applications; the metallic iron core provides high magnetic sensitivity and the gold coating is easily functionalized. With iron/gold nanoparticles prepared by this method, we directly measure the chemical state of the iron component using x-ray absorption spectroscopy (XAS) and interpret our results along with the measured magnetization of the particles. In earlier reports, metallicity of the iron core was inferred from magnetization measurements rather than directly measured. In contrast, XAS directly measures the structural environment of the iron atoms. Because XAS interpretation is independent of symmetry or periodicity, it is an ideal tool for characterizing nanoparticles. Using XAS, we demonstrate that the iron component of the iron/gold nanoparticles is fully oxidized. We suggest that oxidation is a persistent problem in core/shell nanoparticles of this variety and recommend that characterization by XAS be a standard part of nanoparticle preparation.
Murine models for evaluating antiretroviral therapy. (1990)

The pandemic of the acquired immunodeficiency syndrome (AIDS), caused by the human immunodeficiency virus type 1 (HIV-1), requires rapid development of effective therapy and prevention. Analysis of candidate anti-HIV-1 drugs in animals is problematic since no ideal animal model for HIV-1 infection and disease exists. For many reasons, including small size, availability of inbred strains, immunological reagents, and lymphokines, murine systems have been used for in vivo analysis of antiretroviral agents. Here we review currently available murine models involving HIV-1 in transgenic mice and in chimeric mice reconstituted with human cells, as well as murine systems using retroviruses of the subfamily Oncovirinae rather than Lentivirinae. We report our results on various antiretroviral treatment strategies, including chemoprophylaxis after acute retroviral exposure, therapy of chronic viremia, quantitative analysis of combination therapy, and therapy during pregnancy and in the neonatal period aimed at preventing viremia in the offspring. Due to our highly effective postexposure treatment protocols with 3'-azido-3'-deoxythymidine (zidovudine) combined with recombinant human interferon-alpha A/D, retrovirus-inoculated mice developed immunity to the virus to which they were exposed, which will allow us to determine the nature of protective antiretroviral immunity in inbred mice.
Arene–Ruthenium Chemistry and Brønsted Acid Catalysis of a Chiral Phosphane-Hydroxyl Ligand (2014)

The phosphane-hydroxyl ligand (SC1,RC2)-Ph2PC(Ph)HC(OH)HCH2OMe (POH) displays κ1P, κ2P,O, κ3P,O,O′, and anionic deprotonated κ3P,O,O′ coordination modes toward the metallic (η6-p-MeC6H4iPr)Ru moiety. The hydroxyl group in [(η6-p-MeC6H4iPr)Ru(κ3P,O,O′-POH)][SbF6]2 (3) has strong acidic properties. This complex catalyzes the Diels–Alder reaction between cyclopentadiene and trans-β-nitrostyrene or methacrolein as well as the Friedel–Crafts reaction between indole and methyl 3,3,3,-trifluoropyruvate or trans-β-nitrostyrene. Solution studies strongly indicate that complex 3 acts as a metallic Lewis acid assisted Brønsted-acid catalyst.
Indoor experiments on real-time multiuser MIMO transmission in wireless LAN systems (2012)

This paper presents indoor experimental results on an implemented real-time downlink multiuser multiple-input multiple-output (DL-MU-MIMO) transceiver for next generation wireless LAN systems. In the transceiver, channel state information (CSI) is estimated at each station (STA) and fed back to an access point (AP) on a real-time basis. At the AP, transmit beamforming weight for DL-MU-MIMO transmission is calculated by using the estimated CSI. This paper also proposes a fast computation scheme for computing transmit weight in real time. Indoor experiments with the DL-MU-MIMO transceiver demonstrate its feasibility. The experimental results clarify that DL-MU-MIMO transmission can achieve system throughput of greater than 500 Mbit/s with simple digital signal processing of single-antenna STAs in an indoor environment.
Interaction Models for Multi-Display Slideshows (2007)

We present an investigation of interaction models for slideshow applications in a multi-display environment. Three models are examined: Direct Manipulation, Billiard Ball, and Flow. These concepts can be demonstrated by the ModSlideShow prototype, which is designed as a configurable modular display system where each display unit communicates with its neighbors and fundamental operations that act locally can be composed to support the higher level interaction models. We also describe the gesture input scheme, animation feedback, and other enhancements.
The<i>Arabidopsis</i>ATNRT2.7 Nitrate Transporter Controls Nitrate Content in Seeds (2007)

In higher plants, nitrate is taken up by root cells where Arabidopsis thaliana NITRATE TRANSPORTER2.1 (ATNRT2.1) chiefly acts as the high-affinity nitrate uptake system. Nitrate taken up by the roots can then be translocated from the root to the leaves and the seeds. In this work, the function of the ATNRT2.7 gene, one of the seven members of the NRT2 family in Arabidopsis, was investigated. High expression of the gene was detected in reproductive organs and peaked in dry seeds. beta-Glucuronidase or green fluorescent protein reporter gene expression driven by the ATNRT2.7 promoter confirmed this organ specificity. We assessed the capacity of ATNRT2.7 to transport nitrate in Xenopus laevis oocytes or when it is expressed ectopically in mutant plants deficient in nitrate transport. We measured the impact of an ATNRT2.7 mutation and found no difference from the wild type during vegetative development. By contrast, seed nitrate content was affected by overexpression of ATNRT2.7 or a mutation in the gene. Finally, we showed that this nitrate transporter protein was localized to the vacuolar membrane. Our results demonstrate that ATNRT2.7 plays a specific role in nitrate accumulation in the seed.
Improved depth resolution with one-dimensional coded aperture imaging (1979)

The method of coded aperture imaging with a one-dimensional aperture coding mask is applied to the problem of imaging a two-dimensional axial slice through a three-dimensional source distribution. A rigorous expression for the point spread function associated with the combined encoding-decoding process is derived. A least-squares procedure is then used to determine the decoding function which, for a given aperture code, minimises the mean square magnitude of the sidelobes of the point spread function. Replacement of the initial decoding function by its optimised counterpart is seen, by means of an example, to produce a point spread function which not only oscillates rapidly in sign (thus minimising the build-up of background), but also has substantially smaller mean square sidelobe magnitudes. Finally, the analysis is extended to the case of imaging with multiple views. An example demonstrates that the use of multiple views can further improve the suppression of sidelobes in the point spread function. Computer-generated plots of point spread functions accompany the analysis.
A Review and a Suggested Classification System for Myopia on the Basis of Age-Related Prevalence and Age of Onset (1987)

Systems for the classification of myopia are usually based on etiological dichotomies such as hereditary vs. environmental, physiological vs. pathological, structural vs. functional, or axial vs. refractive. The purpose of this paper is to propose a system for the classification of myopia based not on assumed etiological factors but on readily available and easily verifiable information, including age-related prevalence and age of onset. The proposed system classifies myopia into four categories: congenital, youth-onset, early adult-onset, and late adult-onset. Paradoxically, such a classification, being devoid of etiological assumptions, may help to make possible a better understanding of the etiology of the various categories of myopia.
Security Analysis of Mobile Payment Systems (2015)

Mobile payments have evolved from mobile banking to contactless payment which uses radio communication technology. NFC has enabled mobile devices to emulate contactless cards either by using hardware-based Secure Element (SE) or software-based i.e. Host Card Emulation (HCE). We provide a detailed comparison between the different forms of SE. We provide an analysis of HCE and a security mechanism implemented in Android 4.4 and above, which turns o�ff the NFC controller and application controller when the device display screen is disabled, to prevent device skimming. We present a flaw in the design of the implementation of this security mechanism and provide a proof-of-concept for the same. In addition, we present di�fferent attack vectors like man-in-the-middle attack and denial-of-service attack for HCE-based applications. We also provide an analysis of the Vodafone NFC SIM card payment solution and describe di�fferent components involved. We also present diff�erent attack vectors like spoofi�ng and relay attack on the Vodafone NFC SIM card payment solution. We also propose two countermeasures for relay attacks which are based on challenge response protocol.
<i>Editorial</i> (2009)

Publiée sans interruption depuis 1979, The Tocqueville Review / La Revue Tocqueville a accompagné la résurgence du « tocquevillisme » dans le champ intellectuel français et américain. Toutefois, elle l'a fait selon des modalités particulières qui dessinent une identité savante et des exigences qu'il nous faut poursuivre : insistance sur l'importance de la perspective comparatiste chez Tocqueville et intérêt pour les enjeux de la traduction (d'où la proximité avec de grands traducteurs comme Arthur Goldhammer), historicisation des multiples usages et de la réception de l'œuvre des deux côtés de l'Atlantique (manifeste dès l'article inaugural de Raymond Aron « Tocqueville retrouvé»), et surtout, défense d'une certaine érudition qui puisse faire pièce aux idéologues trop pressés d'instrumentaliser leur « grand homme », pluralisme idéologique et priorité intellectuelle à la complexité, aux ambivalences et aux aspects les plus déroutants de la pensée de Tocqueville. The Tocqueville Review/La Revue Tocqueville n'est pas la revue de la « vulgate tocquevillienne ».
Numerical modeling of the Lower Mississippi River-influence of forcings on flow distribution and impact of sea level rise on the system (2009)

The Mississippi River, with one of the world's largest watersheds draining 41% of the continental U.S., is the seventh largest river in the world. The lower Mississippi River delta system along the northern Gulf of Mexico coast experiences annual coastal marsh losses between 25 and 35 square miles. The lower River is a highly complex system impacted by multiple forcings. An understanding of the hydrodynamics in this system will be important for understanding the potential outcomes of coastal restoration projects such as large-scale River diversions and for future management decisions. This study describes the development and application of a hydrodynamic model of a reach of the Lower Mississippi River from Carrolton (New Orleans) at RM 103 down to the Gulf of Mexico. The USACE Adaptive Hydraulics Model (ADH), an unstructured finite element model, is used to model the hydrodynamics. An unstructured mesh was developed for the study area, which includes detailed bathymetry and topography from the most recent available survey data. The mesh is fine enough to capture the changes in bathymetry and relies upon automated mesh refinement to capture flow details. Mississippi River stage data collected from thirteen stations between Carrolton and Port Eads for the water years between 1987 and 2008 is used in the model calibration. In addition, discharge data collected in various Lower River passes is used to examine the ability of the hydrodynamic model to properly simulate the flow distribution through different reaches and lower River passes. Steady state solutions for water surface elevations at gage locations match well with observational data and the distribution of river flow among the different sections of river channel and passes are consistent with the limited field data available. The effect of the sea level rise is most significant in the lower 20 miles of the river and it loses its effect with increasing flow rates
Disruption of the murine MRP (multidrug resistance protein) gene leads to increased sensitivity to etoposide (VP-16) and increased levels of glutathione. (1997)

The mrp (multidrug resistance protein) gene has been associated with the multidrug resistance of cancer cells in vitro and in vivo. To gain information on its physiological role, embryonic stem cells were used to generate mice homozygous for a disruption of the mrp gene, resulting in complete abrogation of mrp expression. No physiological abnormalities were observed, at least up to 4 months of age. Viability, fertility, and a range of histological, hematological, and serum-chemical parameters were similar in mrp(+/+) and mrp(-/-) mice. mrp(-/-) mice displayed an increased sensitivity to etoposide phosphate (2-fold) accompanied by greater bone marrow toxicity, whereas the acute toxicity of sodium arsenite was equivalent in mrp(+/+) and mrp(-/-) mice. Tissue levels of glutathione (GSH) were elevated in breast, lung, heart, kidney, muscle, colon, testes, bone marrow cells, blood mononuclear leukocytes, and blood erythrocytes of mrp(-/-) mice and were unchanged in organs known to express little if any mrp, such as the liver and small intestine. The increase in GSH was not due to an increase in the activity of gamma-glutamylcysteine synthetase, the rate-limiting enzyme for GSH synthesis. The findings demonstrate that mrp is dispensable for development and growth but exerts a role in drug detoxification and GSH metabolism.
Protein Frustratometer 2: a tool to localize energetic frustration in protein molecules, now with electrostatics (2016)

The protein frustratometer is an energy landscape theory-inspired algorithm that aims at localizing and quantifying the energetic frustration present in protein molecules. Frustration is a useful concept for analyzing proteins' biological behavior. It compares the energy distributions of the native state with respect to structural decoys. The network of minimally frustrated interactions encompasses the folding core of the molecule. Sites of high local frustration often correlate with functional regions such as binding sites and regions involved in allosteric transitions. We present here an upgraded version of a webserver that measures local frustration. The new implementation that allows the inclusion of electrostatic energy terms, important to the interactions with nucleic acids, is significantly faster than the previous version enabling the analysis of large macromolecular complexes within a user-friendly interface. The webserver is freely available at URL: http://frustratometer.qb.fcen.uba.ar.
Melatonin but not the ram-effect reactivates quiescent ovarian activity of mid-anestrous ewe. (1990)

The present study was conducted to examine how the social cue emanating from rams, the ram-effect, would influence the onset of melatonin-induced reproductive activity in anestrous ewes. Twenty non-lactating ewes were randomly allocated into 4 groups as follows based on a combination of the melatonin treatment (MEL) and the ram-effect (RAM): ewes of Groups A (MEL + RAM) and B (MEL) were subcutaneously implanted with melatonin capsules on April 18 (Day 0), which increased plasma melatonin levels by about 200 pg/ml for at least 5 months, while Groups C (RAM) and D (control) were untreated with melatonin. Rams were introduced to Groups A and C on Day 0, whereas Groups B and D were isolated from rams. Ovarian function of the ewe was assessed on June 9-21 (Days 52-64) by monitoring plasma progesterone (P) profiles. Luteal function (plasma P greater than 1 ng/ml for a week or longer) was evident in all the melatonin-treated ewes but only one in those untreated: 5/5 in Group A, 5/5 in Group B, 1/5 in Group C and 0/5 in Group D. By ultrasonography on Day 105 all the Group A ewes were diagnosed pregnant but none in the Group C despite that both the two groups had been run with rams. These results indicate that chronic melatonin treatment is capable of advancing the reproductive recrudescence in seasonally anestrous ewes, and that progonadal effects of rams are subtle, if any, during the mid-anestrous period.
Enhancement of ADPCM speech coding with backward-adaptive algorithms for postfiltering and noise feedback (1988)

It is shown that postfiltering circuits based on higher order LPC (linear predictive coding) models can provide very low distortion in terms of special tilt. Thus, they can provide better speech enhancement than circuits based on the backward-adaptive pole-zero predictor in ADPCM (adaptive digital pulse code modulation). Quantitative criteria for designing postfiltering circuits based on higher-order LPC models are discussed. These postfilters are particularly attractive for systems where high-order LPC analysis is an integral part of the coding algorithm. In a subjective test that used a computer-simulated version of these circuits, enhanced ADPCM obtained a mean opinion score of 3.6 at 16 kb/s.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Effect of Natural Fractures on Hydraulic Fracture Propagation (2005)

Abstract Various fracture interaction criteria were reviewed and a systematic study is presented to analyze the effect of natural fractures on hydraulic fracture propagation. From the literature review, the approach of Warpinski and Teufel was adopted to evaluat the fracture propagation that would occur after a hydraulic fracture intersects an existing natural fracture. The study determined the conditions of differential stress, angle of intersection, and fracture toughness for which dilation of the natural fracture would occur. Criteria for the subsequent modes of fracture propagation are then presented.
APC2 Plays an Essential Role in Axonal Projections through the Regulation of Microtubule Stability (2009)

Growth cones at the tip of growing axons are key cellular structures that detect guidance cues and mediate axonal growth. An increasing number of studies have suggested that the dynamic regulation of microtubules in the growth cone plays an essential role in growth cone steering. The dynamic properties of microtubules are considered to be regulated by variegated cellular factors but, in particular, through microtubule-interacting proteins. Here, we examined the functional role of adenomatous polyposis coli-like molecule 2 (APC2) in the development of axonal projections by using the chick retinotectal topographic projection system. APC2 is preferentially expressed in the nervous system from early developmental stages through to adulthood. Immunohistochemical analysis revealed that APC2 is distributed along microtubules in growth cones as well as axon shafts of retinal axons. Overexpression of APC2 in cultured cells induced the stabilization of microtubules, whereas the knockdown of APC2 in chick retinas with specific short hairpin RNA reduced the stability of microtubules in retinal axons. APC2 knockdown retinal axons showed abnormal growth attributable to a reduced response to ephrin-A2 in vitro. Furthermore, they showed drastic alterations in retinotectal projections without making clear target zones in the tectum in vivo. These results suggest that APC2 plays a critical role in the development of the nervous system through the regulation of microtubule stability.
Analysis of genomic differences among Clostridium botulinum type A1 strains (2010)

Abstract Background Type A1 Clostridium botulinum strains are a group of Gram-positive, spore-forming anaerobic bacteria that produce a genetically, biochemically, and biophysically indistinguishable 150 kD protein that causes botulism. The genomes of three type A1 C. botulinum strains have been sequenced and show a high degree of synteny. The purpose of this study was to characterize differences among these genomes and compare these differentiating features with two additional unsequenced strains used in previous studies. Results Several strategies were deployed in this report. First, University of Massachusetts Dartmouth laboratory Hall strain (UMASS strain) neurotoxin gene was amplified by PCR and sequenced; its sequence was aligned with the published ATCC 3502 Sanger Institute Hall strain and Allergan Hall strain neurotoxin gene regions. Sequence alignment showed that there was a synonymous single nucleotide polymorphism (SNP) in the region encoding the heavy chain between Allergan strain and ATCC 3502 and UMASS strains. Second, comparative genomic hybridization (CGH) demonstrated that the UMASS strain and a strain expected to be derived from ATCC 3502 in the Centers for Disease Control and Prevention (CDC) laboratory (ATCC 3502*) differed in gene content compared to the ATCC 3502 genome sequence published by the Sanger Institute. Third, alignment of the three sequenced C. botulinum type A1 strain genomes revealed the presence of four comparable blocks. Strains ATCC 3502 and ATCC 19397 share the same genome organization, while the organization of the blocks in strain Hall were switched. Lastly, PCR was designed to identify UMASS and ATCC 3502* strain genome organizations. The PCR results indicated that UMASS strain belonged to Hall type and ATCC 3502* strain was identical to ATCC 3502 (Sanger Institute) type. Conclusions Taken together, C. botulinum type A1 strains including Sanger Institute ATCC 3502, ATCC 3502*, ATCC 19397, Hall, Allergan, and UMASS strains demonstrate differences at the level of the neurotoxin gene sequence, in gene content, and in genome arrangement.