gebhart/patrepeval huggingface dataset:
An outer envelope membrane component of the plastid protein import apparatus plays an essential role in Arabidopsis (2004)

Translocon at the outer envelope membrane of chloroplasts, 34 kDa (Toc34) is a GTP-binding component of the protein import apparatus within the outer envelope membrane of plastids. The Arabidopsis genome encodes two homologues of Toc34, designated atToc33 and atToc34. In this report, we describe the identification and characterization of two atToc34 knockout mutants, plastid protein import 3-1 (ppi3-1) and ppi3-2. Aerial tissues of the ppi3 mutants appeared similar to the wild type throughout development, and contained structurally normal chloroplasts that were able to efficiently import the Rubisco small subunit precursor (prSS) in vitro. The absence of an obvious ppi3 phenotype in green tissues presumably reflects the ability of atToc33 to substitute for atToc34 in the mutant, and the relatively high level of expression of the atTOC33 gene in these tissues. In the roots, where atTOC33 is expressed at a much lower level, significant growth defects were observed in both mutants: ppi3 roots were approximately 20-30% shorter than wild-type roots. Attempts to identify a double homozygote lacking atToc34 and atToc33 (by crossing the ppi3 mutants with ppi1, an atToc33 knockout mutant) were unsuccessful, indicating that the function provided by atToc33/atToc34 is essential during early development. Plants that were homozygous for ppi1 and heterozygous for ppi3 displayed a chlorotic phenotype much more severe than that of the ppi1 single mutant. Furthermore, the siliques of these plants contained approximately 25% aborted seeds, indicating that the double homozygous mutation is embryo lethal. The data demonstrate that atToc33/atToc34 performs a central and essential role during plastid protein import, and indicate that the atToc34 isoform is relatively more important for plastid biogenesis in roots.
Dynamic Adaptive Video Streaming: Towards a Systematic Comparison of ICN and TCP/IP (2017)

Streaming of video content over the Internet is experiencing an unprecedented growth. While video permeates every application, it also puts tremendous pressure in the network-to support users having heterogeneous accesses and expecting a high quality of experience, in a furthermore cost-effective manner. In this context, future internet paradigms, such as information centric networking (ICN), are particularly well suited to not only enhance video delivery at the client (as in the dynamic adaptive streaming over HTTP (DASH) approach), but to also naturally and seamlessly extend video support deeper in the network functions. In this paper, we contrast ICN and transmission control protocol/internet protocol (TCP/IP) with an experimental approach, where we employ several state-of-the-art DASH controllers (PANDA, AdapTech, and BOLA) on an ICN versus TCP/IP network stack. Our campaign, based on tools that we developed and made available as open-source software, includes multiple clients (homogeneous vesrus heterogeneous mixture and synchronous vesrus asynchronous arrivals), videos (up to 4k resolution), channels (e.g., DASH profiles, emulated WiFi and LTE, and real 3G/4G traces), and levels of integration with an ICN network (i.e., vanilla named data networking (NDN), wireless loss detection and recovery at the access point, and load balancing). Our results clearly illustrate, as well as quantitatively assess, the benefits of ICN-based streaming, warning about potential pitfalls that are however easy to avoid.
CD271 as a marker to identify mesenchymal stem cells fromdiverse sources before culture (2015)

Mesenchymal stem cells, due to their characteristicsare ideal candidates for cellular therapy. Currently,in culture these cells are defined by their adherenceto plastic, specific surface antigen expression andmultipotent differentiation potential. However, thein vivo identification of mesenchymal stem cells,before culture, is not so well established. Pre-cultureidentification markers would ensure higher purity thanthat obtained with selection based on adherence toplastic. Up until now, CD271 has been described asthe most specific marker for the characterization andpurification of human bone marrow mesenchymal stemcells. This marker has been shown to be specificallyexpressed by these cells. Thus, CD271 has beenproposed as a versatile marker to selectively isolatedand expand multipotent mesenchymal stem cells withboth immunosuppressive and lymphohematopoieticengraftment-promoting properties. This reviewfocuses on this marker, specifically on identificationof mesenchymal stem cells from different tissues.Literature revision suggests that CD271 should not bedefined as a universal marker to identify mesenchymalstem cells before culture from different sources. In thecase of bone marrow or adipose tissue, CD271 couldbe considered a quite suitable marker; however thismarker seems to be inadequate for the isolation ofmesenchymal stem cells from other tissues such asumbilical cord blood or wharton＇s jelly among others.
Localized Surface Plasmon Resonance Spectroscopy and Sensing (2006)

Localized surface plasmon resonance (LSPR) spectroscopy of metallic nanoparticles is a powerful technique for chemical and biological sensing experiments. Moreover, the LSPR is responsible for the electromagnetic-field enhancement that leads to surface-enhanced Raman scattering (SERS) and other surface-enhanced spectroscopic processes. This review describes recent fundamental spectroscopic studies that reveal key relationships governing the LSPR spectral location and its sensitivity to the local environment, including nanoparticle shape and size. We also describe studies on the distance dependence of the enhanced electromagnetic field and the relationship between the plasmon resonance and the Raman excitation energy. Lastly, we introduce a new form of LSPR spectroscopy, involving the coupling between nanoparticle plasmon resonances and adsorbate molecular resonances. The results from these fundamental studies guide the design of new sensing experiments, illustrated through applications in which researchers use both LSPR wavelength-shift sensing and SERS to detect molecules of chemical and biological relevance.
Microbial Community Profiling of Human Saliva Using Shotgun Metagenomic Sequencing (2014)

Human saliva is clinically informative of both oral and general health. Since next generation shotgun sequencing (NGS) is now widely used to identify and quantify bacteria, we investigated the bacterial flora of saliva microbiomes of two healthy volunteers and five datasets from the Human Microbiome Project, along with a control dataset containing short NGS reads from bacterial species representative of the bacterial flora of human saliva. GENIUS, a system designed to identify and quantify bacterial species using unassembled short NGS reads was used to identify the bacterial species comprising the microbiomes of the saliva samples and datasets. Results, achieved within minutes and at greater than 90% accuracy, showed more than 175 bacterial species comprised the bacterial flora of human saliva, including bacteria known to be commensal human flora but also Haemophilus influenzae, Neisseria meningitidis, Streptococcus pneumoniae, and Gamma proteobacteria. Basic Local Alignment Search Tool (BLASTn) analysis in parallel, reported ca. five times more species than those actually comprising the in silico sample. Both GENIUS and BLAST analyses of saliva samples identified major genera comprising the bacterial flora of saliva, but GENIUS provided a more precise description of species composition, identifying to strain in most cases and delivered results at least 10,000 times faster. Therefore, GENIUS offers a facile and accurate system for identification and quantification of bacterial species and/or strains in metagenomic samples.
Unifying user-based and item-based collaborative filtering approaches by similarity fusion (2006)

Memory-based methods for collaborative filtering predict new ratings by averaging (weighted) ratings between, respectively, pairs of similar users or items. In practice, a large number of ratings from similar users or similar items are not available, due to the sparsity inherent to rating data. Consequently, prediction quality can be poor. This paper re-formulates the memory-based collaborative filtering problem in a generative probabilistic framework, treating individual user-item ratings as predictors of missing ratings. The final rating is estimated by fusing predictions from three sources: predictions based on ratings of the same item by other users, predictions based on different item ratings made by the same user, and, third, ratings predicted based on data from other but similar users rating other but similar items. Existing user-based and item-based approaches correspond to the two simple cases of our framework. The complete model is however more robust to data sparsity, because the different types of ratings are used in concert, while additional ratings from similar users towards similar items are employed as a background model to smooth the predictions. Experiments demonstrate that the proposed methods are indeed more robust against data sparsity and give better recommendations.
Abstract 2614: Anti-tumor efficacy and pharmacokinetics of the novel aptamer AS1411 in a continuous infusion nude rat xenograft model (2010)

Abstract AS1411 is a novel DNA aptamer that binds to the multi-functional protein nucleolin and induces cell death. AS1411 has shown activity at two different doses in combination with cytarabine in a phase II study of patients with AML. We have previously shown that AS1411 has activity against a range of solid and hematological cancer cell lines, with IC50 values between 1 and 10 μM, when cells are exposed to AS1411 continuously for more than 3 days. We have also demonstrated efficacy in vivo in both lung (A549) and renal (A498) mouse xenografts. However, it has been challenging to provide optimal continuous dosing of AS1411 in mice; use of osmotic pumps or intraperitoneal bolus injection have been associated with low drug exposure. In the current study, we optimized the continuous infusion model by using nude, athymic rats with a surgically implanted catheter in a two-cycle xenograft study. Plasma and tumor samples were collected for PK determination, allowing a correlation of PK with efficacy. The colorectal cell line HT29, which is sensitive to AS1411 in vitro, was used in this study. Cells (5×106) were implanted subcutaneously in the flank of female nude rats and tumors were allowed to grow to approximately 200 − 300 mm3 before surgical cannulation of the femoral vein. Following recovery, animals received AS1411 at 40, 80 or 180 mg/kg/day for two 7 day cycles of continuous infusion, 7 days apart. A vehicle control group received saline. Animals in the 80 and 180 mg/kg/day groups exhibited a significant (p&amp;lt;0.01) reduction in tumor volume compared to control animals at day 33 and at day 22 (interim analysis); this was not observed for animals in the 40mg/kg/day group (40mg kg/day in this model does not directly correlate to the clinical dose of the same name). AS1411 was well-tolerated by all animals in all dose groups. Plasma levels of AS1411 were measured at the three dose levels after one cycle of treatment. Mean AS1411 plasma concentrations were 0.7, 2.5 and 5.0 μM, for rats treated at 40, 80 and 180 mg/kg/day, respectively. The plasma concentrations in the two higher dose groups are within the range of the in vitro IC50 concentrations of a panel of cell lines. We conclude that AS1411 shows activity in vivo in the HT29 nude rat xenograft model. Doses associated with significant reductions in tumor volume were those that produced plasma concentrations close to the IC50 level for AS1411. This correlation has been used in planning further clinical development of AS1411, including a phase IIb study of patients with AML. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 2614.
Integrated dynamic body contact for H-gate PD-SOI MOSFETs for high performance/low power (2005)

This paper discusses on the integrated dynamic body contact for H-gate PD-SOI MOSFETs for high performance/low power. PD-SOI circuit designers often must explicitly account for the MOSFET body voltage. Here, a dynamic body bias is implemented with a compact layout style to achieve improved performance and reduced power consumption.
Matrix‐assisted laser desorption/ionization mass spectrometry of carbohydrates (1999)

This review describes the application of matrix-assisted laser desorption/ionization (MALDI) mass spectrometry to carbohydrate analysis and covers the period 1991–1998. The technique is particularly valuable for carbohydrates because it enables underivatised, as well as derivatised compounds to be examined. The various MALDI matrices that have been used for carbohydrate analysis are described, and the use of derivatization for improving mass spectral detection limits is also discussed. Methods for sample preparation and for extracting carbohydrates from biological media prior to mass spectrometric analysis are compared with emphasis on highly sensitive mass spectrometric methods. Quantitative aspects of MALDI are covered with respect to the relationship between signal strength and both mass and compound structure. The value of mass measurements by MALDI to provide a carbohydrate composition is stressed, together with the ability of the technique to provide fragmentation spectra. The use of in-source and post-source decay and collision-induced fragmentation in this context is described with emphasis on ions that provide information on the linkage and branching patterns of carbohydrates. The use of MALDI mass spectrometry, linked with exoglycosidase sequencing, is described for N-linked glycans derived from glycoproteins, and methods for the analysis of O-linked glycans are also covered. The review ends with a description of various applications of the technique to carbohydrates found as constituents of glycoproteins, bacterial glycolipids, sphingolipids, and glycolipid anchors. © 1999 John Wiley & Sons, Inc., Mass Spec Rev 18: 349–451, 1999
Coastal Orographic Rainfall Processes Observed by Radar during the California Land-Falling Jets Experiment (2003)

Radar and rain gauge observations collected in coastal mountains during the California Land-Falling Jets Experiment (CALJET) are used to diagnose the bulk physical properties of rainfall during a wet winter season (January–March 1998). Three rainfall types were clearly distinguishable by differences in their vertical profiles of radar reflectivity and Doppler vertical velocity: nonbright band, bright band, and hybrid (seeder–feeder). The contribution of each rainfall type to the total rainfall observed at the radar site (1841 mm) was determined by a new, objective algorithm. While hybrid rain occurred most often, nonbrightband rain (NBB rain) contributed significantly (28%) to the total. This paper focuses on characterizing NBB rain because of the need to document this key physical process and because of its impact on Weather Surveillance Radar-1988 Doppler (WSR-88D) precipitation surveillance capabilities. NBB rain is a quasi-steady, shallow rain process that does not exhibit a radar bright band, that occurs largely beneath the melting level, and that can produce rain rates exceeding 20 mm h−1. Composite vertical profiles were produced for NBB rain using 1417 samples and brightband rain using 5061 samples. Although the mean rain rate for each composite was 3.95 mm h−1, at all altitudes NBB rain had systematically weaker equivalent radar reflectivity (e.g., 20.5 dBZe vs 28.5 dBZe at 263 m above ground level) and much smaller Doppler vertical fall velocities (e.g., 2.25 m s−1 vs 6.25 m s−1 at 263 m) than did brightband rain. The reflectivity–rain-rate (Z–R) relationship for NBB rain (Z = 1.2R1.8) differs significantly from that of brightband/hybrid rain (Z = 207R1.1). The meteorological context in which NBB rain occurred is described through case studies and seasonal statistics. NBB rain occurred in a wide variety of positions relative to frontal zones within land-falling storms, but three-quarters of it fell when the layer-mean, profiler-observed wind direction at 1250 m MSL (the altitude of the composite low-level jet) was between 190° and 220°. The importance of orographic forcing during NBB rain, relative to all rain events, was indicated by a stronger correlation between upslope wind speed and coastal rain rates at 1250 m MSL (r = 0.74 vs r = 0.54), stronger low-level wind speeds, and wind directions more orthogonal to the mean terrain orientation.
Cardioprotective effects of lixisenatide in rat myocardial ischemia-reperfusion injury studies (2013)

(ELIXA, ClinicalTrials.gov Identifier: NCT01147250).
Interaction of the cellular prion protein with raft-like lipid membranes (2007)

Conversion of the cellular isoform of the prion protein (PrP(C)) into the disease-associated isoform (PrP(Sc)) plays a key role in the development of prion diseases. Within its cellular pathway, PrP(C) undergoes several posttranslational modifications, i.e., the attachment of two N-linked glycans and a glycosyl phosphatidyl inositol (GPI) anchor, by which it is linked to the plasma membrane on the exterior cell surface. To study the interaction of PrP(C) with model membranes, we purified posttranslationally modified PrP(C) from transgenic Chinese hamster ovary (CHO) cells. The mono-, di- and oligomeric states of PrP(C) free in solution were analyzed by analytical ultracentrifugation. The interaction of PrP(C) with model membranes was studied using both lipid vesicles in solution and lipid bilayers bound to a chip surface. The equilibrium and mechanism of PrP(C) association with the model membranes were analyzed by surface plasmon resonance. Depending on the degree of saturation of binding sites, the concentration of PrP(C) released from the membrane into aqueous solution was estimated at between 10(-9) and 10(-7) M. This corresponds to a free energy of the insertion reaction of -48 kJ/mol. Consequences for the conversion of PrP(C) to PrP(Sc) are discussed.
Ribose-Modified Nucleosides as Ligands for Adenosine Receptors:  Synthesis, Conformational Analysis, and Biological Evaluation of 1‘-C-Methyl Adenosine Analogues (2002)

1'-C-Methyl analogues of adenosine and selective adenosine A(1) receptor agonists, such as N-[(1R)-1-methyl-2-phenylethyl]adenosine ((R)-PIA) and N(6)-cyclopentyladenosine, were synthesized to further investigate the subdomain that binds the ribose moiety. Binding affinities of these new compounds at A(1) and A(2A) receptors in rat brain membranes and at A(3) in rat testis membranes were determined and compared. It was found that the 1'-C-methyl modification in adenosine resulted in a decrease of affinity, particularly at A(1) and A(2A) receptors. When this modification was combined with N(6) substitutions with groups that induce high potency and selectivity at A(1) receptors, the high affinity was in part restored and the selectivity was increased. The most potent compound proved to be the 1'-C-methyl analogue of (R)-PIA with a K(i) of 23 nM for the displacement of [(3)H]CHA binding from rat brain A(1) receptors and a > 435-fold selectivity over A(2A) receptors. In functional assays, these compounds inhibited forskolin-stimulated adenylate cyclase with IC(50) values ranging from 0.065 to 3.4 microM, acting as full agonists. Conformational analysis based on vicinal protonminus signproton J-coupling constants and molecular mechanics calculations using the MM2 force field proved that the methyl group on C1' in adenosine has a pronounced impact on the furanose conformation by driving its conformational equilibrium toward the north, gamma+, syn form.
99mTc myocardial perfusion imaging. (1991)

For more than 15 years, 201Tl has been used for measuring myocardial perfusion and viability although its physical characteristics, which include a photon energy of 68 to 80 keV and a physical half-life of 73 hours, are far from ideal. In early 1991, 99mTc tracers from the group of compounds known as isonitriles and boronic acid adducts of technetium dioximes (BATO) compounds were made available for general use in the United States, with approval by the Food and Drug Administration in late 1990. The uptake of these agents in the myocardium is proportional to regional blood flow. Because these tracers have 99mTc as the radiolabel, they have better physical characteristics--a gamma photon energy of 140 keV and a half-life of 6 hours--than 201Tl. The isonitrile with the best properties for myocardial imaging is 99mTc-hexakis-2-methoxyisobutyl isonitrile (MIBI) (Cardiolite, DuPont, Wilmington, DE). It has transient hepatic uptake and little or no myocardial redistribution, making it an ideal single-photon emission CT tracer. The commercially developed agent of the BATO group is 99mTc-teboroxime (Cardiotec, Squibb, Princeton, NJ). Its extraction fraction by the myocardium is higher than that of 201Tl and 99mTc-MIBI but its washout is very rapid and flow related. Because of the lack of redistribution with 99mTc-MIBI and the rapid washout with 99mTc-teboroxime, two separate injections are necessary for these new tracers to enable them to distinguish ischemia from scar tissue. It is recommended to perform the rest study first, and then to do the exercise study if a 1-day protocol is being used.(ABSTRACT TRUNCATED AT 250 WORDS)
Comparative Analyses of N‐Acylated Homoserine Lactones Reveal Unique Structural Features that Dictate Their Ability to Activate or Inhibit Quorum Sensing (2008)

Bacterial quorum sensing is mediated by low molecular-weight signals and plays a critical role in both the pathogenesis of infectious disease and beneficial symbioses. There is significant interest in the development of synthetic ligands that can intercept bacterial quorum sensing signals and modulate these outcomes. Here, we report the design and comparative analysis of the effects of approximately 90 synthetic N-acylated homoserine lactones (AHLs) on quorum sensing in three Gram negative bacterial species and a critical examination of the structural features of these ligands that dictate agonistic and antagonistic activity, and selectivity for different R protein targets. These studies have revealed the most comprehensive set of structure-activity relationships to date that direct AHL-mediated quorum sensing and a new set of chemical probes with which to study this complex signaling process. Furthermore, this work provides a foundation on which to design next-generation quorum sensing modulators with improved activities and selectivities.
Plant-derived human papillomavirus 16 E7 oncoprotein induces immune response and specific tumor protection. (2002)

Vaccine strategies for treatment of human papillomavirus-induced cervical cancer are based on either the recombinant E7 fusion oncoprotein or E7 CTL peptides. The therapeutic potential of the E7-based vaccine depends on the use of different adjuvants. In this study, we describe for the first time the expression of the human papillomavirus 16 E7 protein in Nicotiana benthamiana plant using a potato virus X-derived vector. C57BL/6 mice immunized with E7-containing crude foliar extracts developed both humoral and cell-mediated immune responses and were protected from tumor development after challenge with the E7-expressing C3 tumoral cell line. Our data support the possibility of producing a cost-effective anticancer vaccine in plant with intrinsic adjuvant-like properties.