gebhart/patrepeval huggingface dataset:
Separation-Dependent Electronic Transparency of Monolayer Graphene Membranes on III−V Semiconductor Substrates (2010)

Ultrahigh vacuum scanning tunneling microscopy and first-principles calculations have been carried out to study monolayer graphene nanomembranes deposited in situ onto UHV-cleaved GaAs(110) and InAs(110) surfaces. A bias-dependent semitransparency effect is observed in which the substrate atomic structure is clearly visible through the graphene monolayer. Statistical data analysis and density functional theory calculations suggest that this semitransparency phenomenon is due to the scanning tunneling microscope tip pushing the graphene membrane away from its equilibrium location and closer to the substrate surface, causing their electronic states to intermix.
A vaccine carrier derived from Neisseria meningitidis with mitogenic activity for lymphocytes. (1992)

Protein carriers vary in their ability to increase the immunogenicity of poorly immunogenic or T-lymphocyte-independent antigens. We examined one such carrier, the outer membrane protein complex derived from Neisseria meningitidis serogroup B strain B11, in an attempt to determine why this outer membrane protein complex was more immunogenic in young infants and in relevant animal models than two other carriers used in conjugates made with Haemophilus influenzae type b polysaccharide, a T-cell-independent antigen. A single protein of the outer membrane protein complex, the class 2 porin protein, was purified and shown to function as a T-helper lymphocyte carrier protein. Unexpectedly, it was also found to have mitogenic activity for lymphocytes that was not due to lipopolysaccharide. This mitogenic activity appears to date to be unique to this carrier protein of the carrier proteins tested and may contribute to the ability of the H. influenzae type b conjugate vaccine made with the outer membrane protein complex to generate IgG anti-polysaccharide antibody responses in mice and infant monkeys and protective immune responses in infants less than 6 months of age.
Identification and the Information Matrix: How to Get Just Sufficiently Rich? (2009)

In prediction error identification, the information matrix plays a central role. Specifically, when the system is in the model set, the covariance matrix of the parameter estimates converges asymptotically, up to a scaling factor, to the inverse of the information matrix. The existence of a finite covariance matrix thus depends on the positive definiteness of the information matrix, and the rate of convergence of the parameter estimate depends on its ¿size¿. The information matrix is also the key tool in the solution of optimal experiment design procedures, which have become a focus of recent attention. Introducing a geometric framework, we provide a complete analysis, for arbitrary model structures, of the minimum degree of richness required to guarantee the nonsingularity of the information matrix. We then particularize these results to all commonly used model structures, both in open loop and in closed loop. In a closed-loop setup, our results provide an unexpected and precisely quantifiable trade-off between controller degree and required degree of external excitation.
.alpha.-Adrenergic agents. 1. Direct-acting .alpha.1 agonists related to methoxamine (1981)

A series of phenylethylamines related to methoxamine has been prepared and evaluated for direct alpha 1-receptor agonist activity. It has been observed that for open-chain compounds such as methoxamine, in which the amine-containing portion is free to adopt numerous conformations, an hydroxyl group is necessary for direct alpha 1-adrenergic activity. When the hydroxyl is removed, however, the direct component of activity is greatly reduced unless the amine is incorporated into a more sterically defined structure. From our studies we have concluded that in order for a phenylethylamine to be active as a direct alpha 1-receptor agonist it should have a beta nitrogen in a fully extended conformation relative to a substituted phenyl ring. For optimum potency, the nitrogen should be exocyclic to a saturated six-membered ring. It may be further incorporated exocyclic or endocyclic into an additional ring as long as the amine occupies a well-defined region of space relative to the aromatic portion of a molecule. The ED50 values of some of the more potent compounds as alpha 1-receptor agonists are on the order of 1 X 10(-7) M.
Fundamental aspects of regenerative cerium oxide nanoparticles and their applications in nanobiotechnology (2006)

Cerium oxide has been used extensively for various applications over the past two decades. The use of cerium oxide nanoparticles is beneficial in present applications and can open avenues for future applications. The present study utilizes the microemulsion technique to synthesize uniformly distributed cerium oxide nanoparticles. The same technique was also used to synthesize cerium oxide nanoparticles doped with trivalent elements (La and Nd). The fundamental study of cerium oxide nanoparticles identified variations in properties as a function of particle size and also due to doping with trivalent elements (La and Nd). It was found that the lattice parameter of cerium oxide nanoparticles increases with decrease in particle size. Also Raman allowed mode shift to lower energies and the peak at 464 cm-1 becomes broader and asymmetric. The size dependent changes in cerium oxide were correlated to increase in oxygen vacancy concentration in the cerium oxide lattice. The doping of cerium oxide nanoparticles with trivalent elements introduces more oxygen vacancies and expands the cerium oxide lattice further (in addition to the lattice expansion due to the size effect). The lattice expansion is greater for La-doped cerium oxide nanoparticles compared to Nd-doping due to the larger ionic radius of La compared to Nd, the lattice expansion is directly proportional to the dopant concentration. The synthesized cerium oxide nanoparticles were used to develop an electrochemical biosensor of hydrogen peroxide (H2O2). The sensor was useful to detect H2O2 concentrations as low as 1µM in water. Also the preliminary testing of the sensor on tomato stem and leaf extracts indicated that the sensor can be used in practical applications such as plant physiological studies etc. The nanomolar concentrations of cerium oxide nanoparticles were also found to be useful in decreasing ROS (reactive oxygen species) mediated cellular damages in various in vitro cell cultures. Cerium oxide nanoparticles reduced the cellular damages to the normal breast epithelial cell line (CRL 8798) induced by X-rays and to the Keratinocyte cell line induced by UV irradiation. Cerium oxide nanoparticles were also found to be neuroprotective to adult rat spinal cord and retinal neurons. We propose that cerium oxide nanoparticles act as free radical scavenger (via redox reactions on its surface) to decrease the ROS induced cellular damages. Additionally, UV-visible spectroscopic studies indicated that cerium oxide nanoparticles possess auto-regenerative property by switching its oxidation state between Ce3+ and Ce4+. The auto-regenerative antioxidant property of these nanoparticles appears to be a key component in all the biological applications discussed in the present study.
Behavior of DNA fibers stretched by precise meniscus motion control (2001)

A modified DNA combing method, which can precisely locate straightened DNA fibers on a substrate, has been developed. Precise motion control of a DNA solution droplet on hydrophobic surfaces has allowed detailed analyses of DNA straightening behavior. Our method provides a technique for consistently straightening lambda phage DNA on a trace of droplet motion, though the straightened DNAs had several variations in their alignments. The dependence of the straightened DNA frequency upon motion rate, fluidity in the droplet and environmental humidity was investigated. Visualization of the solution flow in the moving droplet indicated that flows circulating parallel to the contour of the droplet markedly bias the direction of straightening in relation to the site in the droplet. As a result, the alignment variations caused by the site specificity of the bias direction revealed that environmental humidity significantly alters the straightening behavior.
Host Range, Host–Virus Interactions, and Virus Transmission (2018)

Three intricate and intertwined biological features in the replication cycle of viruses are covered in this chapter: The range of cellular entities that support virus replication and/or virus transmission, and the various relationships viruses establish with their hosts and biological vectors. Although in its infancy, an explosion of research on virus–host interactions has already revealed surprising relationships ranging from strictly parasitic to mutualistic, and some others in between. A clearer picture is emerging as regards to our understanding of the full spectrum of these interactions, even with varying experimental approaches and differing opinions on terminology and data interpretation.
Dystrophins carrying spectrin-like repeats 16 and 17 anchor nNOS to the sarcolemma and enhance exercise performance in a mouse model of muscular dystrophy (2009)

Sarcolemma-associated neuronal NOS (nNOS) plays a critical role in normal muscle physiology. In Duchenne muscular dystrophy (DMD), the loss of sarcolemmal nNOS leads to functional ischemia and muscle damage; however, the mechanism of nNOS subcellular localization remains incompletely understood. According to the prevailing model, nNOS is recruited to the sarcolemma by syntrophin, and in DMD this localization is altered. Intriguingly, the presence of syntrophin on the membrane does not always restore sarcolemmal nNOS. Thus, we wished to determine whether dystrophin functions in subcellular localization of nNOS and which regions may be necessary. Using in vivo transfection of dystrophin deletion constructs, we show that sarcolemmal targeting of nNOS was dependent on the spectrin-like repeats 16 and 17 (R16/17) within the rod domain. Treatment of mdx mice (a DMD model) with R16/17-containing synthetic dystrophin genes effectively ameliorated histological muscle pathology and improved muscle strength as well as exercise performance. Furthermore, sarcolemma-targeted nNOS attenuated alpha-adrenergic vasoconstriction in contracting muscle and improved muscle perfusion during exercise as measured by Doppler and microsphere circulation. In summary, we have identified the dystrophin spectrin-like repeats 16 and 17 as a novel scaffold for nNOS sarcolemmal targeting. These data suggest that muscular dystrophy gene therapies based on R16/17-containing dystrophins may yield better clinical outcomes than the current therapies.
Polymerase Chain Reaction Amplification of DNA from Aged Blood Stains:  Quantitative Evaluation of the “Suitability for Purpose” of Four Filter Papers as Archival Media (2002)

In collaboration with the Armed Forces Institute of Pathology's Department of Defense DNA Registry, the National Institute of Standards and Technology recently evaluated the performance of a short tandem repeat multiplex with dried whole blood stains on four different commercially available identification card matrixes. DNA from 70 stains that had been stored for 19 months at ambient temperature was extracted or directly amplified and then processed using routine methods. All four storage media provided fully typeable (qualitatively identical) samples. After standardization, the average among-locus fluorescence intensity (electropherographic peak height or area) provided a suitable metric for quantitative analysis of the relative amounts of amplifiable DNA in an archived sample. The amounts of DNA in Chelex extracts from stains on two untreated high-purity cotton linter pulp papers and a paper treated with a DNA-binding coating were essentially identical. Average intensities for the aqueous extracts from a paper treated with a DNA-releasing coating were somewhat lower but also somewhat less variable than for the Chelex extracts. Average intensities of directly amplified punches of the DNA-binding paper were much larger but somewhat more variable than the Chelex extracts. Approximately 25% of the observed variation among the intensity measurements is shared among the four media and thus can be attributed to intrinsic variation in white blood count among the donors. All of the evaluated media adequately "bank" forensically useful DNA in well-dried whole blood stains for at least 19 months at ambient temperature.
Infrared Depletion Spectroscopy and Structure of the 2-Aminopyridine Dimer (2004)

The electronic and vibrational spectra of the 2-aminopyridine (2AP) dimer have been measured using resonant two-photon ionization (R2PI) and IR ion depletion (IR/R2PI) spectroscopy. Only two vibrational bands in the N−H stretch region have been observed at 3319 and 3529 cm-1, which are red-shifted by 120 and 17 cm-1, respectively, relative to the symmetric and antisymmetric N−H vibrations of the monomer. This provides evidence of the cyclic structure of this dimer with two antiparallel N−H· · ·N hydrogen bonds. In addition, ab initio calculations at the B3LYP/6-311++G(d,p) level have been carried out. The cyclic structure is also the calculated minimum energy conformation. Each NH2 group forms a σ-hydrogen bond with the ring nitrogen of the partner. Compared to the dimers of 2-pyridone ((2PY)2) and 2-hydroxypyridine ((2HP)2) and to the mixed dimer ((2PY)·(2HP)), the hydrogen bonds in (2AP)2 are weaker. This is confirmed by the differences in the vibrational spectra and by the computational results. The binding energy of the 2AP dimer is the lowest among these dimers, and its hydrogen bonds are the longest. The weaker hydrogen bonds in 2AP may be rationalized by the nonplanar structure of the molecule in the ground state. The theoretical results are in good agreement with the experimental data.
Kinetics and dynamics of the dissociative chemisorption of oxygen on Ir(111) (1997)

The initial dissociative chemisorption probability, S0, of O2 on Ir(111) has been investigated with molecular beam techniques and electron energy loss spectroscopy (EELS). The adsorption process on the clean surface occurs by distinct dynamical mechanisms. At incident kinetic energies, Ei, of 0.1 eV and below, the dissociative chemisorption probability decreases with increasing kinetic energy, indicating the dominance of a trapping-mediated mechanism. A decrease in the value of S0 with increasing surface temperature, Ts, is also characteristic of this regime. This temperature dependence reflects the participation of a physically adsorbed state and molecularly chemisorbed state in the dissociation scheme. Additionally, the dependence of S0 on incident angle, θi, in the low kinetic energy regime exhibits near normal energy scaling. At high kinetic energy (Ei&amp;gt;0.1 eV), the initial dissociative chemisorption probability rises with increasing Ei indicating that translational energy is effective in surmounting a potential barrier to adsorption. Direct access of a molecularly chemisorbed state followed by dissociation, rather than direct access of the dissociated state, is hypothesized to be the primary initial adsorption step. Several observations support this mechanism, including a temperature dependence in the high kinetic energy regime and no observed increase in oxygen saturation coverage with increasing kinetic energy. In addition, EEL spectra show that molecularly chemisorbed states of oxygen are formed on the Ir(111) surface at Ts&amp;lt;70 K after exposure to a 1.36 eV beam and partial saturation of the atomic overlayer. Attempts to identify molecularly chemisorbed oxygen at low coverages were unsuccessful and limited by the experimental setup which provides cooling of the iridium crystal to only ∼68 K.
Directed Antigen Presentation Using Polymeric Microparticulate Carriers Degradable at Lysosomal pH for Controlled Immune Responses (2005)

The types of the immune responses generated against an antigen are determined by the intracellular fate of the antigen. Endogenous antigens are processed in the cytoplasm and initiate cytotoxic T lymphocyte (CTL) activation. In contrast, exogenous antigens are degraded in the lysosome (or phagolysosome) of antigen presenting cells (APCs), and induce antibody-mediated immune responses and assist CTL activation. Therefore, maximizing a desired response by controlling delivery pathways is indispensable in vaccine development and immunotherapy. New cleavable microparticles have been prepared for use as protein-based vaccine carriers by polymerizing water soluble monomers including a newly developed aliphatic monomer with a pendant primary amine group and a cleavable acetal linkage with a wholly aliphatic cleavable acetal cross-linker. Incorporation of the cleavable amine monomer in the polymerization mixture increased the encapsulation efficiency of a model antigen, ovalbumin. Ex vivo assays showed that the composition of the particles greatly affected the magnitude and the pathway of antigen presentations, which determine the type of immune responses. The degradable particles synthesized with the new cross-linker enhanced MHC I antigen presentation 2-3-fold over nondegradable particles. It was also found that, by adding 10% cationic cleavable monomers to the microparticles, MHC I restricted antigen presentation was enhanced ca. 75 times over that achieved with nondegradable particles. The microparticles introduced in this study can be further used for targeting and gene delivery due to functionalizable and cleavable cationic monomers in addition to degradability.
High-performance, graded-base AlGaAs/InGaAs collector-up heterojunction bipolar transistors using a novel selective area regrowth process (1999)

Graded-base AlGaAs/InGaAs collector-up heterojunction bipolar transistors (C-up HBTs) were successfully fabricated using a novel selective area regrowth process to reduce the base resistance and their dc and microwave performances were evaluated. The base is compositionally graded to provide a quasi-built-in field which decreases the base transit time for high-frequency response and increases the base transport factor at low-temperature operation. A unity-gain cutoff frequency f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</sub> =55 GHz and a maximum frequency of oscillation f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">max</sub> =74 GHz for the C-up n-p-n HBT, and an f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</sub> =48 GHz and an f <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">max</sub> = 39 GHz for the C-up p-n-p HBT were obtained for devices with a 5-μm×10-μm collector area. The nonself-aligned C-up HBT's reported here show great promise for future high-speed C-up complementary bipolar IC's.
The Relationship of Blood Lymphocytes to the Recirculating Lymphocyte Pool (1998)

Lymphocyte recirculation facilitates the detection and elimination of pathogens and the dissemination of immunologic memory. It is generally assumed that all small lymphocytes in the blood are actively recirculating, yet there is little quantitative data directly comparing the migration of this population with actively recirculating, lymph-derived lymphocytes. In this study blood lymphocytes were labeled with fluorescein isothiocyanate (FITC), and lymph lymphocytes were labeled with CM-DiI, reinfused intravenously, and monitored in blood and lymph. After equilibration the concentration of blood lymphocytes was several times higher in blood than in lymph, whereas lymph lymphocytes displayed the opposite behavior. This suggested that blood lymphocytes did not recirculate as efficiently as lymph lymphocytes, so we examined the following blood lymphocyte subsets in greater detail: B cells, CD4+, CD8+, and γδ T cells. Within 4 hours postinjection the percentage of FITC+CD8+ and CD4+ lymphocytes fell in the blood and remained significantly lower than the injected sample. In contrast, the concentration of FITC+ γδ T cells did not change, and the percentage of FITC+ B cells increased. These data suggest that subpopulations of B and perhaps γδ T lymphocytes in the blood do not recirculate efficiently through lymph nodes.
Enhancement of Hepatitis C Virus RNA Replication by Cell Culture-Adaptive Mutations (2001)

Studies of the Hepatitis C virus (HCV) replication cycle have been made possible with the development of subgenomic selectable RNAs that replicate autonomously in cultured cells. In these replicons the region encoding the HCV structural proteins was replaced by the neomycin phosphotransferase gene, allowing the selection of transfected cells that support high-level replication of these RNAs. Subsequent analyses revealed that, within selected cells, HCV RNAs had acquired adaptive mutations that increased the efficiency of colony formation by an unknown mechanism. Using a panel of replicons that differed in their degrees of cell culture adaptation, in this study we show that adaptive mutations enhance RNA replication. Transient-transfection assays that did not require selection of transfected cells demonstrated a clear correlation between the level of adaptation and RNA replication. The highest replication level was found with an adapted replicon carrying two amino acid substitutions located in NS3 and one in NS5A that acted synergistically. In contrast, the nonadapted RNA replicated only transiently and at a low level. The correlation between the efficiency of colony formation and RNA replication was corroborated with replicons in which the selectable marker gene was replaced by the gene encoding firefly luciferase. Upon transfection of naive Huh-7 cells, the levels of luciferase activity directly reflected the replication efficiencies of the various replicon RNAs. These results show that cell culture-adaptive mutations enhance HCV RNA replication.
5-Azacytidine and RNA secondary structure increase the retrovirus mutation rate (1992)

A broad spectrum of mutations occurs at a high rate during a single round of retrovirus replication (V.K. Pathak and H. M. Temin, Proc. Natl. Acad. Sci. USA 87:6019-6023, 1990). We have now determined that this high rate of spontaneous mutation can be further increased by 5-azacytidine (AZC) treatment or by regions of potential RNA secondary structure. We found a 13-fold increase in the mutation rate after AZC treatment of retrovirus-producing cells and target cells. The AZC-induced substitutions were located at the same target sites as previously identified spontaneous substitutions. The concordance of the AZC-induced and spontaneous substitutions indicates the presence of reverse transcription "pause sites," where the growing point is error prone. An analysis of nucleotides that neighbored substitutions revealed that transversions occur primarily by transient template misalignment, whereas transitions occur primarily by misincorporation. We also introduced a 34-bp potential stem-loop structure as an in-frame insertion within a lacZ alpha gene that was inserted in the long terminal repeat (LTR) U3 region and determined whether this potential secondary structure increased the rate of retrovirus mutations. We found a threefold increase in the retrovirus mutation rate. Fifty-seven of 96 mutations were deletions associated with the potential stem-loop. We also determined that these deletion mutations occurred primarily during minus-strand DNA synthesis by comparing the frequencies of mutations in recovered provirus plasmids containing both LTRs and in provirus plasmids containing only one LTR.
Linux Means Business (1998)

Wireless Networking in Africa: The experiences of the members of an Italian project in establishing wireless networking with Linux in Africa