gebhart/patrepeval huggingface dataset:
DNA vaccines against human immunodeficiency virus type 1 (2004)

Development of a vaccine against human immunodeficiency virus type 1 (HIV-1) is the main hope for controlling the acquired immunodeficiency syndrome pandemic. An ideal HIV vaccine should induce neutralizing antibodies, CD4+ helper T cells, and CD8+ cytotoxic T cells. While the induction of broadly neutralizing antibodies remains a highly challenging goal, there are a number of technologies capable of inducing potent cell-mediated responses in animal models, which are now starting to be tested in humans. Naked DNA immunization is one of them. This review focuses on the stimulation of HIV-specific T cells and discusses in the context of the current 'state-of-art' of DNA vaccines, the areas where this technology might assist either alone or as a part of more complex vaccine formulations in the HIV vaccine development.
Glucose-Free <i>cis</i>,<i>cis</i>-Muconic Acid Production via New Metabolic Designs Corresponding to the Heterogeneity of Lignin (2017)

Lignin conversion to value-added products is one of the most attractive challenges to develop a complete system for lignocellulosic biomass utilization. The objective of this study was cis,cis-muconic acid (ccMA) production from lignin, in particular, without sugar. Here, two bacterial strains were developed that can synthesize ccMA from lignin without using glucose. One is applicable to softwood lignin (mostly guaiacyl-lignin), and the other is applicable to hardwood lignin (mostly syringyl- and guaiacyl-lignins). The engineered Pseudomonas putida KT2440-based strain produced ccMA from a mixture of vanillic acid (a guaiacyl-lignin model) and 4-hydroxybenzoic acid (a p-hydroxyphenyl-lignin model) with ∼20% yield (mol/mol) without supplement of glucose. The dissolved oxygen concentration of 5–10% was effective to produce ccMA with a higher yield. The Sphingobium sp. SYK-6-based strain produced ccMA from vanillic acid with ∼45% yield (mol/mol) while growing on syringic acid (a syringyl-lignin model). These ccMA-producing strains can synthesize ccMA from lignin extracts of Japanese cedar and birch without using glucose.
Specific roles of 5' RNA secondary structures in stabilizing transcripts in chloroplasts (2005)

RNA secondary structures, e.g. stem-loops that are often found at the 5' and 3' ends of mRNAs, are in many cases known to be crucial for transcript stability but their role in prolonging the lifetime of transcripts remains elusive. In this study we show for an essential RNA-stabilizing stem-loop at the 5' end of rbcL gene transcripts in Chlamydomonas that it neither prevents ribonucleases from binding to the RNA nor impedes their movement along the RNA strand. The stem-loop has a formative function in that it mediates folding of a short sequence around its base into a specific RNA conformation, consisting of a helical and single-stranded region, i.e. the real structure required for longevity of rbcL transcripts in chloroplasts. Disturbing this structure renders transcripts completely unstable, even if the sequence of this element is not altered. The requirement of a specific 5' sequence and structure for RNA longevity suggests an interaction of this element with a trans-acting factor that protects transcripts from rapid degradation in chloroplasts.
Functional Proteomics Mapping of a Human Signaling Pathway (2004)

Access to the human genome facilitates extensive functional proteomics studies. Here, we present an integrated approach combining large-scale protein interaction mapping, exploration of the interaction network, and cellular functional assays performed on newly identified proteins involved in a human signaling pathway. As a proof of principle, we studied the Smad signaling system, which is regulated by members of the transforming growth factor beta (TGFbeta) superfamily. We used two-hybrid screening to map Smad signaling protein-protein interactions and to establish a network of 755 interactions, involving 591 proteins, 179 of which were poorly or not annotated. The exploration of such complex interaction databases is improved by the use of PIMRider, a dedicated navigation tool accessible through the Web. The biological meaning of this network is illustrated by the presence of 18 known Smad-associated proteins. Functional assays performed in mammalian cells including siRNA knock-down experiments identified eight novel proteins involved in Smad signaling, thus validating this integrated functional proteomics approach.
Signalling with official interest rates: the case of the German discount and lombard rate (2005)

A major characteristic of the operating procedure of the European Central Bank (ECB) is its reliance on standing facilities. It is intended that the official rates on those facilities also serve the function of signalling. The case of Germany, where the Bundesbank followed a similar signalling strategy, is analysed. In particular the paper investigates whether announcements of official interest rates provide information not already contained in other policy measures and whether the resulting revisions of expectations are efficient. Significant differences are found between signalling in the case of increasing and decreasing interest rates.
A Position Fixing Algorithm for the Low-Cost GPS Receiver (1976)

The global positioning system (GPS) is a satellite navigation system currently under development by the Department of Defense. This correspondence describes a new position fix algorithm for a low-cost GPS receiver. The algorithm uses Hotelling's method to iteratively update the inverse of the measurement matrix for correction of the
Poor Survival Associated with the <i>BRAF</i> V600E Mutation in Microsatellite-Stable Colon Cancers (2005)

The BRAF V600E mutation has been associated with microsatellite instability and the CpG island methylator phenotype (CIMP) in colon cancer. We evaluated a large population-based sample of individuals with colon cancer to determine its relationship to survival and other clinicopathologic variables. The V600E BRAF mutation was seen in 5% (40 of 803) of microsatellite-stable tumors and 51.8% (43 of 83) of microsatellite-unstable tumors. In microsatellite-stable tumors, this mutation was related to poor survival, CIMP high, advanced American Joint Committee on Cancer (AJCC) stage, and family history of colorectal cancer [odds ratio, 4.23; 95% confidence interval (95% CI), 1.65-10.84]. The poor survival was observed in a univariate analysis of 5-year survival (16.7% versus 60.0%; P < 0.01); in an analysis adjusted for age, stage, and tumor site [hazard rate ratio (HRR), 2.97; 95% CI, 2.05-4.32]; in stage-specific, age-adjusted analyses for AJCC stages 2 to 4 (HRR, 4.88, 3.60, and 2.04, respectively); and in Kaplan-Meier survival estimates for AJCC stages 2 to 4 (P < 0.01 for all three stages). Microsatellite-unstable tumors were associated with an excellent 5-year survival whether the V600E mutation was present or absent (76.2% and 75.0%, respectively). We conclude that the BRAF V600E mutation in microsatellite-stable colon cancer is associated with a significantly poorer survival in stages 2 to 4 colon cancer but has no effect on the excellent prognosis of microsatellite-unstable tumors.
Tau Positron Emission Tomography (PET) Imaging: Past, Present, and Future (2015)

Alzheimer's disease (AD) is a chronic neurodegenerative disorder and the most common cause of dementia among the elderly population. The good correlation of the density and neocortical spread of neurofibrillary tangles (NFTs) with clinical AD disease progression offers an opportunity for the early diagnosis and staging using a noninvasive imaging technique such as positron emission tomography (PET). Thus, PET imaging of NFTs not only holds promise as a diagnostic tool but also may enable the development of disease modifying therapeutics for AD. In this review, we focus on the structural diversity of tau PET tracers, the challenges related to the identification of high affinity and highly selective NFT ligands, and recent progress in the clinical development of tau PET radioligands.
Latent infection of KB cells with adeno-associated virus type 2 (1986)

Adeno-associated virus (AAV) is a prevalent human virus whose replication requires factors provided by a coinfecting helper virus. AAV can establish latent infections in vitro by integration of the AAV genome into cellular DNA. To study the process of integration as well as the rescue of AAV replication in latently infected cells after superinfection with a helper virus, we established a panel of independently derived latently infected cell clones. KB cells were infected with a high multiplicity of AAV in the absence of helper virus, cloned, and passaged to dilute out input AAV genomes. AAV DNA replication and protein synthesis were rescued from more than 10% of the KB cell clones after superinfection with adenovirus type 5 (Ad5) or herpes simplex virus types 1 or 2. In the absence of helper virus, there was no detectable expression of AAV-specific RNA or proteins in the latently infected cell clones. Ad5 superinfection also resulted in the production of infectious AAV in most cases. All mutant adenoviruses tested that were able to help AAV DNA replication in a coinfection were also able to rescue AAV from the latently infected cells, although one mutant, Ad5hr6, was less efficient at AAV rescue. Analysis of high-molecular-weight cellular DNA indicated that AAV sequences were integrated into the cell genome. The restriction enzyme digestion patterns of the cellular DNA were consistent with colinear integration of the AAV genome, with the viral termini present at the cell-virus junction. In addition, many of the cell lines appeared to contain head-to-tail concatemers of the AAV genome. The understanding of the integration of AAV DNA is increasingly important since AAV-based vectors have many advantages for gene transduction in vitro and in vivo.
Disaggregated memory for expansion and sharing in blade servers (2009)

Analysis of technology and application trends reveals a growing imbalance in the peak compute-to-memory-capacity ratio for future servers. At the same time, the fraction contributed by memory systems to total datacenter costs and power consumption during typical usage is increasing. In response to these trends, this paper re-examines traditional compute-memory co-location on a single system and details the design of a new general-purpose architectural building block-a memory blade-that allows memory to be "disaggregated" across a system ensemble. This remote memory blade can be used for memory capacity expansion to improve performance and for sharing memory across servers to reduce provisioning and power costs. We use this memory blade building block to propose two new system architecture solutions-(1) page-swapped remote memory at the virtualization layer, and (2) block-access remote memory with support in the coherence hardware-that enable transparent memory expansion and sharing on commodity-based systems. Using simulations of a mix of enterprise benchmarks supplemented with traces from live datacenters, we demonstrate that memory disaggregation can provide substantial performance benefits (on average 10X) in memory constrained environments, while the sharing enabled by our solutions can improve performance-per-dollar by up to 57% when optimizing memory provisioning across multiple servers.
Plasmid gene organization: naphthalene/salicylate oxidation. (1982)

Genes for naphthalene metabolism are localized on nah7, an 83-kilobase (kb) plasmid, in two gene clusters under salicylate control. Polar mutations formed by insertion of the transposon Tn5 permit detection of the transcription direction and the gene organization within two approximately 10-kb DNA segments separated by a approximately 7-kb regulatory gene region. The gene cluster specifying conversion of naphthalene to salicylate lies near the left initiation of a 25-kb DNA fragment A released by EcoRI; that for the salicylate pathway via catechol meta-fission lies near the right terminus with extension into the adjoining 5.9-kb fragment C. The genetic organization and regulation resemble the tol plasmid-encoded "upper" and "lower" pathways of toluene/xylene oxidation in Pseudomonas putida mt2.
Energy transfer and device performance in phosphorescent dye doped polymer light emitting diodes (2003)

Singlet and triplet–triplet energy transfer in phosphorescent dye doped polymer light emitting devices were investigated. Poly(N-vinylcarbazol) and poly[9,9′-di-n-hexyl-2,7-fluorene-alt- 1,4-(2,5-di-n-hexyloxy)phenylene] (PFHP) were selected as the host polymer for the phosphorescent dopants fac-tris(2-phenylpyridine) iridium(III) [Ir(ppy)3] and 2,3,7,8,12,13, 17,18-octaethyl-21H,23H-porphyrin platinum(II) (PtOEP) because of their high triplet energy levels and long phosphorescence lifetimes. In case of PVK film, efficient triplet energy transfers to both PtOEP and Ir(ppy)3 were observed. In contrast, the triplet energy transfer did not occur or was very weak from PFHP to both PtOEP and Ir(ppy)3 although usual requirements for triplet energy transfer were satisfied. Furthermore, the singlet–singlet energy transfer did not take place from PFHP to Ir(ppy)3 in doped films even though the Förster radius is more than 30 Å. However, the blended film of Ir(ppy)3 with PFHP and PMMA showed the green emission from Ir(ppy)3 via singlet energy transfer. In addition, the solution of PFHP and Ir(ppy)3 (8 wt. %) in p-xylene also showed green emission. The blocking of the energy transfers in the phosphorescent dye doped PFHP films is found to be originated from the formation of aggregates which is evident from the microscopic images taken by transmission electron microscope, atomic force microscope, and fluorescence microscope. The formation of aggregates prevents dopant molecules from being in close proximity with host molecules thereby inhibiting energy transfer processes. The phase separation deteriorates the device performance also. Therefore, the chemical compatibility of a dopant with a host polymer as well as conventional requirements for energy transfers must be significantly considered to fabricate efficient phosphorescent dye doped polymer light emitting devices.
Polar codes: Primary concepts and practical decoding algorithms (2014)

Polar codes represent an emerging class of error-correcting codes with power to approach the capacity of a discrete memoryless channel. This overview article aims to illustrate its principle, generation and decoding techniques. Unlike the traditional capacity-approaching coding strategy that tries to make codes as random as possible, the polar codes follow a different philosophy, also originated by Shannon, by creating a jointly typical set. Channel polarization, a concept central to polar codes, is intuitively elaborated by a Matthew effect in the digital world, followed by a detailed overview of construction methods for polar encoding. The butterfly structure of polar codes introduces correlation among source bits, justifying the use of the SC algorithm for efficient decoding. The SC decoding technique is investigated from the conceptual and practical viewpoints. State-of-the-art decoding algorithms, such as the BP and some generalized SC decoding, are also explained in a broad framework. Simulation results show that the performance of polar codes concatenated with CRC codes can outperform that of turbo or LDPC codes. Some promising research directions in practical scenarios are also discussed in the end.
Influence of bore and rail geometry on an electromagnetic naval railgun system (2005)

A large-scale railgun is being considered by the U.S. navy as a future long range (>200 nm) naval weapon system. The notional concept includes a 15 kg projectile with a 2.5 km/sec muzzle velocity. The choice of bore and rail geometry for such a weapon can influence key aspects of the total system design. This study explored a range of bore and rail geometries and looked at their effects on key railgun system parameters such as parasitic mass, inductance gradient, linear current density, required pulse forming network (PFN) size, and barrel mass. Preliminary solid modeling and structural analysis of the integrated launch package was performed in order to quantify parasitic mass. Inductance gradient calculations were based on a current density distribution analysis. A PFN/Launcher numerical simulation model was then used to determine linear current density and PFN size. Finally, barrel mass was estimated by structural analysis based on calculated rail repulsive forces. Trends and sensitivities of the different parameters to changes in the bore and rail geometries are presented and conclusions are given.
Ontologies as background knowledge to explore document collections (2004)

This paper introduces a new approach to provide users with solutions to explore a domain via an information space. A key point in our approach is that information searching and exploring takes place in a domaindependent semantic context. A given context is described through its vocabulary organised along hierarchies that structure the information space. These hierarchies are simplified views on a more complex domain specific ontology, that form a shared and coherent background knowledge representation. So the system benefits from the combination of two innovations that make the exploration of the document space more effective. First, hierarchies (extracted from the ontology) provide with a language and synthetic representation to be explored by the users to express their information need. Additionally, a visual interface presents answers to their queries using multi-dimensional analysis and a global visualisation of document collections. At both stages, ontology is the key structure that guides a meaningful browsing for query formulation and for the document set exploration.
Adiponectin Specifically Increased Tissue Inhibitor of Metalloproteinase-1 Through Interleukin-10 Expression in Human Macrophages (2004)

Adiponectin selectively increased TIMP-1 expression in human monocyte-derived macrophages through IL-10 induction. This study identified, for the first time, the adiponectin/IL-10 interaction against vascular inflammation.
Electron dynamics in gold and gold–silver alloy nanoparticles: The influence of a nonequilibrium electron distribution and the size dependence of the electron–phonon relaxation (1999)

Electron dynamics in gold nanoparticles with an average diameter between 9 and 48 nm have been studied by femtosecond transient absorption spectroscopy. Following the plasmon bleach recovery after low power excitation indicates that a non-Fermi electron distribution thermalizes by electron–electron relaxation on a time scale of 500 fs to a Fermi distribution. This effect is only observed at low excitation power and when the electron distribution is perturbed by mixing with the intraband transitions within the conduction band (i.e., when the excitation wavelength is 630 or 800 nm). However, exciting the interband transitions at 400 nm does not allow following the early electron thermalization process. Electron thermalization with the lattice of the nanoparticle by electron–phonon interactions occurs within 1.7 ps under these conditions, independent of the excitation wavelength. In agreement with the experiments, simulations of the optical response arising from thermalized and nonthermalized electron distributions show that a non-Fermi electron distribution leads to a less intense bleach of the plasmon absorption. Furthermore, the difference between the response from the two electron distributions is greater for small temperature changes of the electron gas (low excitation powers). No size dependence of the electron thermalization dynamics is observed for gold nanoparticles with diameters between 9 and 48 nm. High-resolution transmission electron microscopy (HRTEM) reveals that these gold nanoparticles possess defect structures. The effect of this on the electron–phonon relaxation processes is discussed. 18 nm gold–silver alloy nanoparticles with a gold mole fraction of 0.8 are compared to 15 nm gold nanoparticles. While mixing silver leads to a blue-shift of the plasmon absorption in the ground-state absorption spectrum, no difference is observed in the femtosecond dynamics of the system.
Differences in CT Perfusion Maps Generated by Different Commercial Software: Quantitative Analysis by Using Identical Source Data of Acute Stroke Patients (2009)

CT perfusion imaging maps were significantly different among commercial software even when using identical source data, presumably because of differences in tracer-delay sensitivity.
High-Performance Liquid Chromatographic/Mass Spectrometric Studies on the Susceptibility of Heparin Species to Cleavage by Heparanase (2007)

Heparanase is an endo-beta-D-glucuronidase that cleaves the heparan sulfate chains of heparan sulfate proteoglycans and is implicated in angiogenesis and metastasis. With the aim of establishing a simple and reliable method for studying the susceptibility of heparin/heparan sulfate oligosaccharides to be cleaved by heparanase, an on-line ion pair reversed-phase high-performance liquid chromatographic/electrospray ionization mass spectrometric method was set up. The method works in the micromolar range of concentration and does not require derivatization of the substrate or of the products. It is based on mass identification of oligosaccharide fragments generated by heparanase and their quantification with reference to an internal heparin disaccharide standard. Substrates were (1) the synthetic pentasaccharides GlcN (NS,6S) - GlcA - GlcN (NS,3S,6S) - IdoA (2S) - GlcN (NS,6S) - OMe (AGA*IA (M)) and GlcN (NS,6S) - GlcA - GlcN (NS,6S) - IdoA (2S) - GlcN (NS,6S) - OMe (AGAIA (M)), corresponding to the heparin/heparan sulfate active site for antithrombin, and to the same sequence devoid of the 3- O-sulfate group in the central glucosamine, respectively; and (2) two natural heparin octasaccharides containing the AGA*IA sequence in different locations along the chain. The two pentasaccharides exhibited a higher susceptibility to heparanase cleavage with respect to the octasaccharides. The commercial availability of AGA*IA (M) makes it an ideal substrate to determine the specific activity of heparanase preparations. The present method could also be used for rapid screening of potential heparanase inhibitors.
An Attenuated Strain of Enterovirus 71 Belonging to Genotype A Showed a Broad Spectrum of Antigenicity with Attenuated Neurovirulence in Cynomolgus Monkeys (2007)

Enterovirus 71 (EV71) is a causative agent of hand, foot, and mouth disease and is also sometimes associated with serious neurological disorders. In this study, we characterized the antigenicity and tissue specificity of an attenuated strain of EV71 [EV71(S1-3')], which belongs to genotype A, in a monkey infection model. Three cynomolgus monkeys were inoculated with EV71(S1-3'), followed by lethal challenge with the parental virulent strain EV71(BrCr-TR) via an intravenous route on day 45 postinoculation of EV71(S1-3'). Monkeys inoculated with EV71(S1-3') showed a mild neurological symptom (tremor) but survived lethal challenge by virulent EV71(BrCr-TR) without exacerbation of the symptom. The immunized monkey sera showed a broad spectrum of neutralizing activity against different genotypes of EV71, including genotypes A, B1, B4, C2, and C4. For the strains examined, the sera showed the highest neutralization activity against the homotype (genotype A) and the lowest neutralization activity against genotype C2. The order of decreasing neutralization activity of sera was as follows: A > B1 > C4 > B4 > C2. To examine the tissue specificity of EV71(S1-3'), two monkeys were intravenously inoculated with EV71(S1-3'), followed by examination of virus distribution in the central nervous system (CNS) and extraneural tissues. In the CNS, EV71(S1-3') was isolated only from the spinal cord. These results indicate that EV71(S1-3') acts as an effective antigen, although this attenuated strain was still neurotropic when inoculated via the intravenous route.