gebhart/patrepeval huggingface dataset:
Mucosal Immunity against Neuraminidase Prevents Influenza B Virus Transmission in Guinea Pigs (2019)

Despite efforts to control influenza virus infection and transmission, influenza viruses still cause significant morbidity and mortality in the global human population each year. Most of the current vaccines target the immunodominant hemagglutinin surface glycoprotein of the virus. However, reduced severity of disease and viral shedding have also been linked to antibodies targeting the second viral surface glycoprotein, the neuraminidase. Importantly, antineuraminidase immunity was shown to be relatively broad, in contrast to vaccine-induced antibodies to the hemagglutinin head domain. In this study, we assessed recombinant neuraminidase protein vaccination for its ability to prevent or limit virus transmission. We vaccinated guinea pigs either intramuscularly or intranasally with a recombinant influenza B virus neuraminidase to assess whether neuraminidase vaccination via these routes could prevent transmission of the homologous virus to a naive recipient. Guinea pigs vaccinated with neuraminidase showed reduced virus titers; however, only vaccination via the intranasal route fully prevented virus transmission to naive animals. We found high levels of antineuraminidase antibodies capable of inhibiting neuraminidase enzymatic activity in the nasal washes of intranasally vaccinated animals, which may explain the observed differences in transmission. We also determined that mucosal immunity to neuraminidase impaired the transmission efficiency of a heterologous influenza B virus, although to a lesser extent. Finally, we found that neuraminidase-vaccinated animals were still susceptible to infection via the airborne and contact transmission routes. However, significantly lower virus titers were detected in these vaccinated recipients. In summary, our data suggest that supplementing vaccine formulations with neuraminidase and vaccinating via the intranasal route may broadly prevent transmission of influenza B viruses.<b>IMPORTANCE</b> Recently, the protective effect of anti-neuraminidase immunity has been highlighted by several studies in humans and animal models. However, so far the role that anti-neuraminidase immunity plays in inhibition of virus transmission has not been explored. In addition, neuraminidase has been ignored as an antigen for influenza virus vaccines. We show here that neuraminidase-based vaccines can inhibit the transmission of influenza virus. Therefore, neuraminidase should be considered as an antigen for improved influenza virus vaccines that not only protect individuals from disease but also inhibit further spread of the virus in the population.
Revealing anelasticity and structural rearrangements in nanoscale metallic glass films using in situ TEM diffraction (2016)

We used a novel diffraction-based method to extract the local, atomic-level elastic strain in nanoscale amorphous TiAl films during <i>in situ</i> transmission electron microscopy deformation, while simultaneously measuring the macroscopic strain. The complementary strain measurements revealed significant anelastic deformation, which was independently confirmed by strain rate experiments. Furthermore, the distribution of first nearest-neighbor distances became narrower during loading and permanent changes were observed in the atomic structure upon unloading, even in the absence of macroscopic plasticity. The results demonstrate the capability of <i>in situ</i> electron diffraction to probe structural rearrangements and decouple elastic and anelastic deformation in metallic glasses.
Variable bit rate video traffic prediction based on kernel least mean square method (2015)

In this study, the problem of variable bit rate (VBR) video traffic prediction is addressed. VBR traffic prediction is necessary in dynamic bandwidth allocation for multimedia quality of service control strategies. Autoregressive (AR) models have been widely used in VBR traffic prediction where the least mean square (LMS)‐based methods were utilised for parameter estimation. However, they are ineffective when the traffic is dynamic in nature. In this study, using the Brock, Dechert, and Scheinkman (BDS) test, it is shown that the video traffic is non‐linear. Kernel is an efficient tool to convert non‐linear data into linear one in a higher‐dimensional space. The kernel LMS (KLMS) method is proposed to forecast the next frame sizes of I, B and P frames as well as the next group‐of‐pictures (GOP) size of video traffic. Extensive simulations were performed on different video traces where different performance metrics were considered. KLMS results were very close to those of the Wiener–Hopf optimum solution and better than the results of commonly used normalised LMS and other algorithms such as the least mean kurtosis (LMK), wavelet LMK, adaptive network fuzzy inference system (ANFIS) and neural networks.
IP Encapsulation within IP (1996)

This document specifies a method by which an IP datagram may be encapsulated (carried as payload) within an IP datagram. Encapsulation is suggested as a means to alter the normal IP routing for datagrams, by delivering them to an intermediate destination that would otherwise not be selected by the (network part of the) IP Destination Address field in the original IP header. Encapsulation may serve a variety of purposes, such as delivery of a datagram to a mobile node using Mobile IP.
Biomimetic magnetic nanoparticles (2005)

Magnetic nanoparticles are of considerable interest because of their potential use in high-density memory devices, spintronics, and applications in diagnostic medicine. The conditions for synthesis of these materials are often complicated by their high reaction temperatures, costly reagents, and post-processing requirements. Practical applications of magnetic nanoparticles will require the development of alternate synthetic strategies that can overcome these impediments. Biomimetic approaches to materials chemistry have provided a new avenue for the synthesis and assembly of magnetic nanomaterials that has great potential for overcoming these obstacles.
Synthesis of Amphiphilic Amino Alcohols (2008)

Abstract An efficient and general approach for the synthesis of amphiphilic 1,2-amino alcohols is reported. The use of N-benzyl protecting groups is essential for obtaining good yields when opening a long-chain terminal epoxide with an amine. Keywords: Amino alcoholsamphiphilesepoxide opening N-benzyl protecting group Notes a Isolated yield. b Ncd—no conversion detected.
Fabrication and Characterization of Paper-Based Microfluidics Prepared in Nitrocellulose Membrane By Wax Printing (2009)

Paper-based microfluidics is a promising technology to develop a simple, low-cost, portable, and disposable diagnostic platform for resource-limited settings. Here we report the fabrication of paper-based microfluidic devices in nitrocellulose membrane by wax printing for protein immobilization related applications. The fabrication process, which can be finished within 10 min, includes mainly printing and baking steps. Wax patterning will form hydrophobic regions in the membrane, which can be used to direct the flow path or separate reaction zones. The fabrication parameters like printing mode and baking time were optimized, and performances of the wax-patterned nitrocellulose membrane such as printing resolution, protein immobilization, and sample purification capabilities were also characterized in this report. We believe the wax-patterned nitrocellulose membrane will enhance the capabilities of paper microfluidic devices and bring new applications in this field.
Characterization of CamH from Methanosarcina thermophila , Founding Member of a Subclass of the γ Class of Carbonic Anhydrases (2009)

The homotrimeric enzyme Mt-Cam from Methanosarcina thermophila is the archetype of the gamma class of carbonic anhydrases. A search of databases queried with Mt-Cam revealed that a majority of the homologs comprise a putative subclass (CamH) in which there is major conservation of all of the residues essential for the archetype Mt-Cam except Glu62 and an acidic loop containing the essential proton shuttle residue Glu84. The CamH homolog from M. thermophila (Mt-CamH) was overproduced in Escherichia coli and characterized to validate its activity and initiate an investigation of the CamH subclass. The Mt-CamH homotrimer purified from E. coli cultured with supplemental zinc (Zn-Mt-CamH) contained 0.71 zinc and 0.15 iron per monomer and had k(cat) and k(cat)/K(m) values that were substantially lower than those for the zinc form of Mt-Cam (Zn-Mt-Cam). Mt-CamH purified from E. coli cultured with supplemental iron (Fe-Mt-CamH) was also a trimer containing 0.15 iron per monomer and only a trace amount of zinc and had an effective k(cat) (k(cat)(eff)) value normalized for iron that was 6-fold less than that for the iron form of Mt-Cam, whereas the k(cat)/K(m)(eff) was similar to that for Fe-Mt-Cam. Addition of 50 mM imidazole to the assay buffer increased the k(cat)(eff) of Fe-Mt-CamH more than 4-fold. Fe-Mt-CamH lost activity when it was exposed to air or 3% H(2)O(2), which supports the hypothesis that Fe(2+) has a role in the active site. The k(cat) for Fe-Mt-CamH was dependent on the concentration of buffer in a way that indicates that it acts as a second substrate in a "ping-pong" mechanism accepting a proton. The k(cat)/K(m) was not dependent on the buffer, consistent with the mechanism for all carbonic anhydrases in which the interconversion of CO(2) and HCO(3)(-) is separate from intermolecular proton transfer.
Theory of the damping of excited molecules located above a metal surface (1978)

Presents a theory for how excited molecules, located above a metal surface, are damped due to excitation of electron-hole pairs and bulk plasmons in the metal. A detailed study of how the excitation energy will be spread into the metal is also given. The theory is compared with experiments for the special case of vibrationally excited molecules adsorbed directly on the metal surface. The author shows the usefulness of a particular vector field decomposition in treating surface problems.
Expression in Escherichia coli of a high-molecular-weight protective surface antigen found in nontypeable and type b Haemophilus influenzae (1990)

An Escherichia coli clone producing a high-molecular-weight surface antigen of Haemophilus influenzae type b (Hib) was isolated from a library of Hib DNA fragments cloned as lysogens in a lambda replacement vector. The antigen is found in sarcosyl-insoluble outer membrane protein preparations and was produced by all 36 H. influenzae isolates tested. Absorption studies indicated that the antigen is a surface determinant on all isolates tested. Antibodies to the antigen (D15) were found in eight of nine convalescent-phase sera from children with invasive Hib infection. Affinity-purified antibodies prepared against the cloned antigen gave protection against the development of bacteremia in a rat pup model.
Pseudotypes of vesicular stomatitis virus with the envelope properties of mammalian and primate retroviruses (1977)

By employing improved techniques it has been possible to produce and characterize a representative spectrum of mammalian and primate retrovirus pseudotypes of vesicular stomatitis virus (VSV). Selection of appropriate cell lines for both the production and subsequent detection of the VSV pseudotypes has been the most important factor in permitting their demonstration. The host range for penetration of these retrovirus pseudotypes of VSV has been defined and found to differ from that reported for the replication of the corresponding retroviruses. Additionally, retroviruses having an identical host range for replication were distinguishable by differences in their host range for penetration, implying that restriction of replication may be occurring by different mechanisms. Studies of the plaque-forming efficiency of retrovirus pseudotypes of VSV in cell lines nonpermissive for replication of the corresponding retroviruses permitted a distinction to be made between the restriction of replication occurring as a consequence of postpenetration events and that occurring as a consequence of a block of penetration itself. The demonstration of primate retrovirus pseudotypes of VSV permits the use of VSV as a probe for the detection of this group of viruses.
Multidimensional profiling of plasma lipoproteins by size exclusion chromatography followed by reverse-phase protein arrays (2011)

The composition of lipoproteins and the association of proteins with various particles are of much interest in the context of cardiovascular disease. Here, we describe a technique for the multidimensional analysis of lipoproteins and their associated apolipoproteins. Plasma is separated by size exclusion chromatography (SEC), and fractions are analyzed by reverse-phase arrays. SEC fractions are spotted on nitrocellulose slides and incubated with different antibodies against individual apolipoproteins or antibodies against various apolipoproteins. In this way, tens of analytes can be measured simultaneously in 100 μl of plasma from a single SEC separation. This methodology is particularly suited to simultaneous analysis of multiple proteins that may change their distribution to lipoproteins or alter their conformation, depending on factors that influence circulating lipoprotein size or composition. We observed changes in the distribution of exchangeable apolipoproteins following addition of recombinant apolipoproteins or interaction with exogenous compounds. While the cholesteryl ester transfer protein (CETP)-dependent formation of pre-β-HDL was inhibited by the CETP inhibitors torcetrapib and anacetrapib, it was not reduced by the CETP modulator dalcetrapib. This finding was elucidated using this technique.
Observation of phonon-assisted laser operation of AlxGa1−xAs-GaAs quantum well heterostructures (1989)

Data are presented showing that the key to observing the phonon-assisted photopumped laser operation of narrow rectangular samples of AlxGa1−xAs-GaAs quantum well heterostructures (QWHs) is the control of the edge-to-edge resonator Q across the sample. If the sample is heat sunk in metal, with metal reflectors folded upward along the edges, the resonator Q across the sample is high, and laser operation across the sample on confined-particle states (a reference) and along the sample a phonon lower in energy (ΔE≊ℏωLO) is observed. If the sample edges across the sample are left uncoated (weakly reflecting, low Q), laser operation is observed only along the sample (longitudinal modes) but shifted (ΔE≊ℏωLO) below the confined-particle states and absorption. A QWH rectangle, with proper heat sinking and control of its edge-to-edge resonator Q, can act as a hot-phonon ‘‘spectrometer’’ if it is fully photopumped across its width and is only partially pumped along its length.
Pathogen- and NaCl-Induced Expression of the SCaM-4 Promoter Is Mediated in Part by a GT-1 Box That Interacts with a GT-1-Like Transcription Factor (2004)

The Ca(2+)-binding protein calmodulin mediates cellular Ca(2+) signals in response to a wide array of stimuli in higher eukaryotes. Plants express numerous CaM isoforms. Transcription of one soybean (Glycine max) CaM isoform, SCaM-4, is dramatically induced within 30 min of pathogen or NaCl stresses. To characterize the cis-acting element(s) of this gene, we isolated an approximately 2-kb promoter sequence of the gene. Deletion analysis of the promoter revealed that a 130-bp region located between nucleotide positions -858 and -728 is required for the stressors to induce expression of SCaM-4. A hexameric DNA sequence within this region, GAAAAA (GT-1 cis-element), was identified as a core cis-acting element for the induction of the SCaM-4 gene. The GT-1 cis-element interacts with an Arabidopsis GT-1-like transcription factor, AtGT-3b, in vitro and in a yeast selection system. Transcription of AtGT-3b is also rapidly induced within 30 min after pathogen and NaCl treatment. These results suggest that an interaction between a GT-1 cis-element and a GT-1-like transcription factor plays a role in pathogen- and salt-induced SCaM-4 gene expression in both soybean and Arabidopsis.
Mutation and expression of PDGFRA and KIT in malignant peripheral nerve sheath tumors, and its implications for imatinib sensitivity (2005)

Platelet-derived growth factor receptor alpha (PDGFRalpha) and c-Kit are receptor tyrosine kinases. Both are targets of the tyrosine kinase inhibitor imatinib mesylate which is approved for treatment of some cancers. In order to assess the role of PDGFRalpha and c-Kit in malignant peripheral nerve sheath tumours (MPNST) we examined human tumours for structural alterations, protein and ligand expression. We investigated 34 MPNST, 6 corresponding plexiform neurofibromas (pNF) and 1 MPNST cell culture from 31 patients for mutations and polymorphisms in PDGFRA (exon 2-21) and KIT (exon 9, 11, 13, 17). PDGFRA was amplified in seven tumours from six patients and MPNST cell culture S462. KIT was amplified in five tumours from four patients and in the cell culture. Two MPNST carried somatic PDGFRA mutations in exons coding for the extracellular domain. In addition we detected several polymorphisms in PDGFRA. No point mutations or polymorphisms were detected in the four KIT exons analysed. PDGFRalpha expression was present in 21 of 28 MPNST patients (75%) and the MPNST cell culture. Expression analysis of PDGFRalpha ligands in MPNST and neurofibromas revealed that PDGF-A was more widely expressed than PDGF-B. Focal c-Kit expression was detected in 2 of 29 (7%) MPNST patients. Imatinib treatment of MPNST cell culture S462 exerted a growth inhibitory effect and prevented PDGF-AA induced PDGFRalpha phosphorylation. In summary, PDGFRA, PDGF and KIT dysregulation as well as growth inhibition of cell culture S462 by imatinib may suggest that MPNST patients benefit from treatment with imatinib.
Direct analysis of the binding of the abl Src homology 2 domain to the activated epidermal growth factor receptor. (1993)

Src homology regions 2 (SH2) and 3 (SH3) are noncatalytic domains that are conserved among several proteins implicated in the regulation of cell proliferation. Using bacterially expressed fusion proteins containing the SH2 domain of the abl tyrosine kinase, we have quantitated the binding of these domains to the activated epidermal growth factor (EGF) receptor (EGFR). A 35S-labeled abl SH2 fusion protein binds to the human EGFR immunoprecipitated from EGF-treated NIH3T3 cells that overexpress the receptor. This binding is totally dependent on the pretreatment of cells with EGF. The interaction is rapid, reaching 50% of maximum within 1 min, and attaining apparent equilibrium by 10 min. Dissociation of the complex is biphasic with a rapidly dissociating component (t1/2 of less than 1 min), as well as a slowly dissociable component. The 35S-labeled abl SH2 fusion protein specifically binds to the EGFR in a saturable manner and is differentially inhibited by unlabeled fusion proteins containing SH2 domains from phospholipase C, the p85 subunit of phosphatidylinositol-3 kinase, and the GTPase activation protein of ras. To identify residues critical for abl SH2-EGFR binding, six point mutants were constructed in the highly conserved FLVRES motif. Three mutants (V170L, E172Q, and E174Q) display binding affinities similar to that of wild type. However, three other mutants (R171K, S173C, and S175C) have greatly reduced affinity. Interestingly, the binding affinity to the EGFR determined by the in vitro assay directly correlates with the transforming ability of the corresponding v-abl constructs in vivo (Mayer, B. J., Jackson, P. K., Etten, R. A. V., and Baltimore, D. (1992) Mol. Cell. Biol. 12, 609-618). These data indicate that the Arg-171, Ser-173, and Ser-175 are critical for both transformation and abl SH2 domain binding to phosphotyrosine-containing proteins.
RAxML and FastTree: Comparing Two Methods for Large-Scale Maximum Likelihood Phylogeny Estimation (2011)

Statistical methods for phylogeny estimation, especially maximum likelihood (ML), offer high accuracy with excellent theoretical properties. However, RAxML, the current leading method for large-scale ML estimation, can require weeks or longer when used on datasets with thousands of molecular sequences. Faster methods for ML estimation, among them FastTree, have also been developed, but their relative performance to RAxML is not yet fully understood. In this study, we explore the performance with respect to ML score, running time, and topological accuracy, of FastTree and RAxML on thousands of alignments (based on both simulated and biological nucleotide datasets) with up to 27,634 sequences. We find that when RAxML and FastTree are constrained to the same running time, FastTree produces topologically much more accurate trees in almost all cases. We also find that when RAxML is allowed to run to completion, it provides an advantage over FastTree in terms of the ML score, but does not produce substantially more accurate tree topologies. Interestingly, the relative accuracy of trees computed using FastTree and RAxML depends in part on the accuracy of the sequence alignment and dataset size, so that FastTree can be more accurate than RAxML on large datasets with relatively inaccurate alignments. Finally, the running times of RAxML and FastTree are dramatically different, so that when run to completion, RAxML can take several orders of magnitude longer than FastTree to complete. Thus, our study shows that very large phylogenies can be estimated very quickly using FastTree, with little (and in some cases no) degradation in tree accuracy, as compared to RAxML.
Thoracic Human Vertebrae Quantitative Three-Dimensional Anatomy (1991)

This study details the quantitative three-dimensional surface anatomy of thoracic vertebrae based on a study of 144 vertebrae. The thoracic spine was found to have three distinct regions: upper, middle, and lower segments. The two end segments appear to be transitional zones toward cervical and lumbar regions. The middle zone (T3 to T9) is of utmost importance due to the presence of the combination of narrow spinal canal and critical vascular supply. Means and standard errors of the means for linear, angular, and area dimensions of vertebral bodies, spinal canal, pedicle, pars articularis, spinous and transverse processes, and rib articulations are provided for all thoracic vertebrae. This information is necessary for constructing accurate mathematical models of the human spine. It will also provide a better understanding of the spine, and allow for a more precise clinical and surgical management of spinal problems.
Serial analysis of gene expression of lobular carcinoma in situ identifies down regulation of claudin 4 and overexpression of matrix metalloproteinase 9 (2008)

We have created the first global gene expression profile of LCIS, and demonstrated down regulation of cell junction proteins (an expected result) and overexpression of matrix metalloproteinase 9 (an unexpected result). Additional analysis of this data made available as an online resource should facilitate further molecular characterisation of LCIS.