gebhart/patrepeval huggingface dataset:
The C-terminal domain is essential for protective activity of the Bordetella pertussis adenylate cyclase-hemolysin (1995)

The adenylate cyclase-hemolysin of Bordetella pertussis consists of a cell-invasive N-terminal adenylate cyclase domain linked to a C-terminal RTX hemolysin containing extensive glycine-rich repeats. The toxin is an essential virulence factor required in the initial stages of infection. Adenylate cyclase-hemolysin was also shown to be a potent vaccinating antigen inducing protection against B. pertussis colonization of the mouse respiratory tract. This protective activity depends on a posttranslational fatty-acylation modification. We used a set of deletion derivatives of the recombinant adenylate cyclase-hemolysin to localize the protective epitopes on the 1,706-residue toxin. We show that specific anti-adenylate cyclase-hemolysin antibodies present in the sera of B. pertussis-infected mice and humans are directed predominantly against the modification-and-repeat portion of the toxin, contained in the last 800 residues of the adenylate cyclase-hemolysin. These antibodies appear to recognize conformational epitopes present only in a structure formed by the intact C-terminal half of the toxin. There was no correlation between the capacity of the truncated adenylate cyclase-hemolysin derivatives to induce both toxin-neutralizing antibodies upon immunization of mice and protective immunity. However, only the truncated proteins which were recognized by the sera of infected mice and humans and which had their last 800 residues intact had the capacity to induce protection of mice against colonization by B. pertussis. This indicates that the structure of the modification-and-repeat region of adenylate cyclase-hemolysin is critical for its protective activity.
Origin of High Li+ Conduction in Doped Li7La3Zr2O12 Garnets (2015)

Substitution of a native ion in the crystals with a foreign ion that differs in valence (<i>aliovalent doping</i>) has been widely attempted to upgrade solid-state ionic conductors for various charge carriers including O²⁻, H⁺, Li⁺, Na⁺, etc. The doping helps promote the high-conductive framework and dredge the tunnel for fast ion transport. The garnet-type Li₇La₃Zr₂O₁₂ (LLZO) is a fast Li⁺ solid conductor, which received much attention as an electrolyte candidate for all-solid-state lithium ion batteries, showing great potential to offer high energy density and minimize battery safety concerns to meet extensive applications in large energy storage systems such as those for electric vehicles and aerospace. In the Li-stuffed garnet framework of LLZO, the 3D pathway formed by the incompletely occupied tetrahedral sites bridged by a single octahedron enables the superior Li⁺ conductivity. For optimal performance, many aliovalent-doping efforts have been made throughout metal elements (Al³⁺, Ta⁵⁺) and metalloid elements (Ga³⁺, Te⁶⁺) in the periodic table with various valences to stabilize the high-conductive phase and increase the Li vacancy concentration.
MCPIP1 Down-Regulates IL-2 Expression through an ARE-Independent Pathway (2012)

IL-2 plays a key role in the survival and proliferation of immune cells, especially T lymphocytes. Its expression is precisely regulated at transcriptional and posttranscriptional level. IL-2 is known to be regulated by RNA binding proteins, such as tristetraprolin (TTP), via an AU-rich element (ARE) in the 3'-untranslated region (3'UTR) to influence the stability of mRNA. MCPIP1, identified as a novel RNase, can degrade IL-6, IL-12 and TNF-α mRNA by an ARE-independent pathway in the activation of macrophages. Here, we reported that MCPIP1 was induced in the activation of T lymphocytes and negatively regulated IL-2 gene expression in both mouse and human primary T lymphocytes through destabilizing its mRNA. A set of Luciferase reporter assay demonstrated that a non-ARE conserved element in IL-2 3'UTR, which formed a stem-loop structure, responded to MCPIP1 activity.RNA immunoprecipitation and Biotin pulldown experiments further suggested that MCPIP1 could modestly bind to IL-2 mRNA. Taken together, these data demonstrate that MCPIP1 down-regulates IL-2 via an ARE-independent pathway.
Four types of Ca2+ signals in naive CD8+ cytotoxic T cells after stimulation with T cell agonists, partial agonists and antagonists (1997)

Stimulation of T cells via the T cell receptor (TCR) leads to an increase intracellular in free Ca2+ levels ([Ca2+]i) and the activation of the MAP kinase signaling pathway. This study analyzes for the first time Ca2+ fluxes in naive cytotoxic T cells stimulated with full agonists, partial agonists, or antagonists. Four different types of Ca2+ responses could be observed. Full agonists triggered a strong and sustained increase in [Ca2+]i. In contrast, partial T cell agonists induced either a strong but transient Ca2+ flux or very low to no increases in [Ca2+]i, while T cell antagonists failed to induce any measurable Ca2+ flux. The ability of peptides to induce elevated [Ca2+]i perfectly paralleled their ability to trigger TCR internalization and T cell activation. Thus, stimulation of naive cytotoxic T cells with a panel of defined altered peptide ligands reveals a consistent picture, where Ca2+ fluxes predict agonist, partial agonist and antagonist properties of peptides.
Cloning and Characterization of a Dihydrolipoamide Acetyltransferase (E2) Subunit of the Pyruvate Dehydrogenase Complex from Arabidopsis thaliana (1995)

A cDNA encoding a dihydrolipoamide acetyltransferase (E2) subunit of the pyruvate dehydrogenase complex has been isolated from Arabidopsis thaliana. A cell culture cDNA expression library was screened with a monoclonal antibody (JIM 63) raised against nuclear matrix proteins, and four clones were isolated. One of these was 2175 base pairs in length, and it contained an open reading frame with an amino acid sequence and domain structure with strong similarity to the E2s of other eukaryotic and prokaryotic organisms. The organization and number of functional domains within the Arabidopsis protein are identical to those of the human E2, although the amino acid sequences within these domains are equally similar to those of the yeast and human proteins. The predicted amino acid sequence reveals the presence of a putative amino-terminal leader sequence with characteristics similar to those of other proteins, which are targeted to the plant mitochondrial matrix. The cross-reactivities of plant mitochondrial matrix proteins with JIM 63 and antibodies raised against the E2 and protein X components of eukaryotic pyruvate dehydrogenase complexes are consistent with the clone encoding a mitochondrial form of E2 and not the smaller protein X. The E2 mRNA of 2.2 kilobases was expressed in a range of Arabidopsis and Brassica napus tissues.
Polymer Composites of Carbon Nanotubes Aligned by a Magnetic Field (2002)

Anisotropic carbon nanotube–polyester composites have been realized by polymerization of the nanotube–monomer dispersion in a constant magnetic field (see Figure for method). Magnetic susceptibilities, electrical conductivities, and mechanical properties of the composite show clear anisotropy, indicating magnetic field-induced alignment of carbon nanotubes in the polymer matrix.
Mechanism of complement activation in the hyperacute rejection of porcine organs transplanted into primate recipients. (1992)

The authors investigated the importance of natural antibody and complement in the pathogenesis of hyperacute xenograft rejection using in vivo and in vitro pig to primate models. Studies were carried out in rhesus monkeys transplanted with a pig heart or kidney in which hyperacute rejection was observed within a few hours. The rejected organs showed deposits of IgM, C3, C4, C5, and C9 neoantigen along small blood vessels, but few deposits of factors B and P. Removal of anti-endothelial cell "natural" antibodies by plasmapheresis, immunoabsorption, and immunosuppression techniques resulted in marked prolongation of the survival of a subsequently transplanted heart, even when complement levels were within the normal range. Thus, complement, in the absence of natural antibodies, did not initiate hyperacute rejection in this species combination. The requirements for complement activation in human serum to cause cytotoxicity of porcine endothelial cells were then evaluated. Cytotoxicity was abrogated by depleting human serum of IgM, C2, or C5, but not of factor B. Restoration of the effect of serum on endothelial cells was achieved by reconstitution of the respective depleted sera with purified IgM or with the corresponding complement proteins, indicating that IgM and the classical, but not the alternative, pathway of complement, were involved. Identical conclusions were drawn from experiments to ascertain the requirements for complement activation in human serum to mediate binding of iC3b to porcine endothelial cells. The authors conclude that in a pig to primate xenograft complement does not directly initiate injury to the graft but rather requires activation by bound xenoreactive natural antibodies; IgM antibodies directed against endothelial cells activate the classical complement pathway, which then contributes to endothelial cell activation and subsequent events characteristic of hyperacute rejection.
CD20 Mimicry by a mAb Rituximab-Specific Linear Peptide: A Potential Tool for Active Immunotherapy of Autoimmune Diseases (2005)

An attractive, whether alternative or complementary, approach to passive immunotherapy (IT) with the anti-CD20 mAb rituximab for the treatment of autoimmune diseases is to stimulate the host to produce an anti-CD20 immune response by using peptides that mimic CD20 (mimotopes). The only mimotope reported to target CD20 antigen is a 43-mer polypeptide corresponding to the exposed domain of the molecule (from amino acid 142 to 184). Owing to its length, however, it failed to efficiently induce a CD20-specific response. A search has now been made for a smaller mimotope by biopanning a phage-display peptide library with rituximab. A total of 10 positive phage clones expressing six distinct sequences were isolated. Their alignment produced a motif that did not match any portion of the CD20 extracellular loop, whereas the motif bearing the 12-mer linear peptide Rp10-L specifically reacted with rituximab and inhibited its binding to CD20. Furthermore, in BALB/c mice Rp10-L-induced antibodies that reacted with the CD20(+) B lymphoid cell line Raji but not with the C20(-) T lymphoid cell line CEM. This peptide is currently being investigated to determine the effectiveness of CD20-based active IT for the treatment of autoimmune diseases.
Structural Organization and Chromosomal Assignment of the Gene Encoding Endothelin (1989)

Endothelin is a 21-amino acid vasoconstrictor synthesized and secreted by vascular endothelial cells. The human peptide is derived from a 212-amino acid precursor, preproendothelin. A nearly full length clone containing DNA complementary to human preproendothelin mRNA was isolated, and its nucleotide sequence was determined. Using this cDNA as a probe, the genomic organization of the human endothelin gene was determined and the promoter region delineated. The gene contains five exons and four intervening sequences. Nucleotide sequences encoding endothelin are contained within the second exon, and the third exon specifies a portion of preproendothelin that is homologous to endothelin. The second and third exons may represent descendants of a common progenitor exon. The 3'-untranslated portion of the gene contains a 250-base pair region that is highly conserved between human and porcine genomes and may have an important role in endothelin mRNA stability. On the basis of DNA isolated from human-mouse somatic hybrid cell lines, the endothelin gene was assigned to human chromosome 6.
Effect of spin-valve sensor magnetostatic fields on nanobead detection for biochip applications (2005)

Spin valves are being used in biochip applications via the detection of biomolecular recognition using magnetic nanoparticles as labels. The magnetic moment of the labels and the sensor response depend on the magnetic fields involved. A calculation based on an external magnetizing field, incorporating the contribution from the magnetostatic fields created by the free and pinned layers of the sensor and the field due to the sensing current, showed that these fields are important. Experimental detection signals of high particle numbers agree with the model, showing that reasonable detection signals are possible even in the absence of an external field.
The Use Of Variable Celestial X-ray Sources For Spacecraft Navigation (2005)

Accurate control and guidance of spacecraft require continuous high performance three-dimensional navigation solutions. Celestial sources that produce fixed radiation have demonstrated benefits for determining location near Earth and vehicle attitude. Many interplanetary navigation solutions have also relied on Earth-based radio telescope observations and substantial ground processing. This dissertation investigates the use of variable celestial sources to compute an accurate navigation solution for autonomous spacecraft operation and presents new methodologies for determining time, attitude, position, and velocity. A catalogue of X-ray emitting variable sources has been compiled to identify those that exhibit characteristics conducive to navigation. Many of these sources emit periodic signals that are stable and predictable, and all are located at vast distances such that the signal visibility is available throughout the solar system and beyond. An important subset of these sources is pulsar stars. Pulsars are rapidly rotating neutron stars, which generate pulsed radiation throughout the electromagnetic spectrum with periods ranging from milliseconds to thousands of seconds. A detailed analysis of several X-ray pulsars is presented to quantify expected spacecraft range accuracy based upon the source properties, observation times, and X-ray photon detector parameters. High accuracy time transformation equations are developed, which include important general relativistic corrections. Using methods that compare measured and predicted pulse time of arrival within an inertial frame, approaches are presented to determine absolute and relative position, as well as corrections to estimated solutions. A recursive extended Kalman filter design is developed to incorporate the spacecraft dynamics and pulsar-based range measurements. Simulation results demonstrate that absolute position determination depends on the accuracy of the pulse phase measurements and initial solutions within several tens of kilometers are achievable. The delta-correction method can improve this position solution to within 100 m MRSE and velocity to within 10 mm/s RMS using observations of 500 s and a 1-m2 detector. Comparisons to recorded flight data obtained from Earth-orbiting X-ray astrophysics missions are also presented. Results indicate that the pulsed radiation from variable celestial X-ray sources presents a significant opportunity for developing a new class of navigation system for autonomous spacecraft operation.
Structural Analysis of Arabidopsis thaliana Chromosome 3. I. Sequence Features of the Regions of 4,504,864 bp Covered by Sixty P1 and TAC Clones (2000)

Based on the physical map of Arabidopsis thaliana chromosome 3 previously constructed with CIC YAC, TAC, P1 and BAC clones (Sato, S. et al., DNA Res., 5, 163-168, 1998), a total of 60 P1 and TAC clones were sequenced, and the sequence features of the resulting 4,504,864 bp regions were analyzed by applying various computer programs for similarity search and gene modeling. As a result, a total of 1054 potential protein-coding genes were identified. The average density of the genes identified was 1 gene per 4066 bp. Introns were observed in 77% of the genes, and the average number per gene and the average length of the introns were 3.9 and 156 bp, respectively. These sequence features are essentially identical to those of chromosome 5 in our previous reports, but the gene density was slightly higher than that observed for chromosomes 2 and 4. The regions also contained 10 tRNA genes when searched by similarity to reported tRNA genes and the tRNA scan-SE program. The sequence data and information on the potential genes are available through the World Wide Web database KAOS (Kazusa Arabidopsis data Opening Site) at http://www.kazusa.or.jp/kaos/.
Incidence and Predictors of Pulmonary Vein Stenosis Following Catheter Ablation of Atrial Fibrillation Using the Anatomic Pulmonary Vein Ablation Approach: Results from Paired Magnetic Resonance Imaging (2005)

The results of this study demonstrate that detectable PV narrowing occurs in 38% of PVs following anatomic PV ablation. Moderate or severe PV stenosis occurs in 3.8% of PVs. The high incidence of mild stenosis likely reflects reverse remodeling rather than pathological PV stenosis. The probability of moderate or severe PV stenosis appears to be related to creation of individual encircling rather than encircling in pairs lesion.
The Nuclear Factor κ-B Signaling Pathway Participates in Dysregulation of Vascular Smooth Muscle Cells in Vitroand in Human Atherosclerosis (1997)

In the lesions of atherosclerosis, vascular smooth muscle cells (SMC) display many functions characteristic of cytokine activation that likely contribute importantly to ongoing inflammation during human atherogenesis. The transcription factor nuclear factor kappa-B (NFkappaB) often mediates the effects of cytokines on target cells, but the identity of Rel family members important in human SMC activation remains uncertain. In vitro, human SMC express multiple Rel family members. Of these, dimers of p65 and p50, but not a putative SMC-Rel, comprise basal and inducible NFkappaB binding activities. SMC express two inhibitor proteins IkappaBbeta and IkappaBalpha. Interleukin-1beta stimulation caused transient loss of IkappaBalpha and a sustained decrease of IkappaBbeta that correlated with increased and persistent levels of p65/p50 protein and binding activity in the nucleus. SMC cultured under serum-free conditions displayed little NFkappaB activity, but addition of serum or platelet-derived growth factor did activate NFkappaB. In situ analyses showed no evidence for basal NFkappaB activity in SMC in vivo as nonatherosclerotic arteries did not contain nuclear p65 or p50 protein. However, the nuclei of intimal SMC within human atheroma did contain both Rel proteins. We conclude that (i) dimers of p65 and p50, but not SMC-Rel, comprise NFkappaB complexes in human SMC; (ii) stimulatory components in serum activate NFkappaB and likely account for previously reported "constitutive" NFkappaB activity in cultured SMC; and (iii) exposure to inflammatory cytokines may produce prolonged NFkappaB activation in SMC because of sustained decreases in the inhibitory subunit IkappaB-beta.
Programmable high speed (~1MHz) Vernier-mode-locked frequency-swept laser for OCT imaging (2008)

We propose and demonstrate a programmable high-speed, frequency-swept laser for swept-source optical coherence tomography (SS-OCT). This new technique is based on Vernier effect of two pieces of Fabry-Perot electro-optic modulators. This technique offers a non-mechanical optical filter with high resolution and wide tuning range. By applying it to a Fourier domain mode-locked laser, such sweeps are generated. The Vernier effect filter can be modulated by arbitrary wave forms, thus this laser source can eliminate the rescaling process which is the main bottle-neck of the operation time in SS-OCT by applying frequency sweep to equidistant spacing in frequency. Effective repetition frequencies of 100kHz~1MHz are demonstrated with a tuning range of 17THz (140nm) at 1550nm center wavelength. OCT imaging of <i>in vivo </i>human sweat duct with A-line rate of 100kHz and 300kHz are also demonstrated. The resolution of 12&mu;m~ is realized without rescaling process. We present an analysis which suggests design approaches for optimization performance.
Molecular characterization of the 128-kDa immunodominant antigen of Helicobacter pylori associated with cytotoxicity and duodenal ulcer. (1993)

Helicobacter pylori has been associated with gastritis, peptic ulcer, and gastric adenocarcinoma. We report the nucleotide sequence and expression of an immunodominant antigen of H. pylori and the immune response to the antigen during disease. The antigen, named CagA (cytotoxin-associated gene A), is a hydrophilic, surface-exposed protein of 128 kDa produced by most clinical isolates. The size of the cagA gene and its protein varies in different strains by a mechanism that involves duplication of regions within the gene. Clinical isolates that do not produce the antigen do not have the gene and are unable to produce an active vacuolating cytotoxin. An ELISA to detect the immune response against a recombinant fragment of this protein detects 75.3% of patients with gastroduodenal diseases and 100% of patients with duodenal ulcer (P < 0.0005), suggesting that only bacteria harboring this protein are associated with disease.
Synthesis of Marine Sponge Alkaloids Oroidin, Clathrodin, and Dispacamides. Preparation and Transformation of 2-Amino-4,5-dialkoxy-4,5-dihydroimidazolines from 2-Aminoimidazoles (1998)

The preparation and transformation of 2-amino-4,5-dialkoxy-4,5-dihydroimidazolines A from 2-aminoimidazoles (AIs) is described. The oxidation of 2-aminoimidazole 8 with NCS in methanol affords cyclic guanidine adduct 9 which, upon heating, affords vinylogous AI derivative 3 and 2-aminoimidazolinone (glycocyamidine) 13. Olefin 3 comprises the core structure found in the oroidin alkaloids. Furthermore, oxidation of 8 with Br2 and DMSO affords directly α,β-unsaturated imidazolinone 14 which is the key structural unit comprising the dispacamides (2). A highly facile and practical synthesis of the C11N5 marine sponge alkaloids oroidin (1a), clathrodin (1c), and dispacamides (2) is outlined.
Multifunctional platinum porphyrin dendrimers as emitters in undoped phosphorescent based light emitting devices (2006)

The authors report on a class of platinum porphyrin based phosphorescent multifunctional first generation dendrimers (Pt-8Cn-TPP) incorporating a platinum porphyrin core as the emissive center and carbazole side groups as the hole, as well as energy transport fragments. Furthermore, the alkyl groups prevent aggregation and allow for the formation of transparent homogeneous films directly from solution. The intra- and intermolecular energy transfers by Förster and Dexter mechanisms from the carbazole side groups to the platinum porphyrin core have been investigated. Light emitting devices were fabricated and bright red electrophosphorescence was achieved from a single undoped emitting layer of Pt-8C4-TPP. The results indicate that platinum porphyrin dendrimers are very promising to make bright, red saturated and spin-coated phosphorescent devices with a simplified undoped emissive layer.