gebhart/patrepeval huggingface dataset:
Anti-pneumococcal antibody titre measurement: what useful information does it yield? (2006)

Measuring and interpretation of the immune response to pneumococcal polysaccharides is a complex field, owing to the diversity of the pneumococcal polysaccharide capsular types, different vaccine formulations including both polysaccharide and conjugate vaccines, diverse pneumococcal serological assays, lack of immunogenicity data for the conjugate in a number of at-risk groups and complex vaccine schedules. Even the reasons for performing pneumococcal serology can be complex, as assays may be performed for one of two reasons: either to assess an individual’s immune status to the pneumococcus or to discriminate between normal and abnormal humoral immunity. This review details a history of the pneumococcal serological assays and provides some insight into when serology can prove useful, including vaccination data for certain at-risk groups.
Integrin (alpha v beta 3)-ligand interaction. Identification of a heterodimeric RGD binding site on the vitronectin receptor. (1990)

The vitronectin receptor mediates cell adhesion to the extracellular matrix proteins vitronectin, fibrinogen, von Willebrand factor, and thrombospondin in an RGD-dependent manner. We previously demonstrated the direct interaction between the vitronectin receptor and an RGD-containing peptide by photoaffinity labeling the receptor with 125I-sulfosuccinimidyl-2-(p-azido-salicylamido)-1,3'-dithioprop ion ate (SASD)-GRGDSPK (Smith, J. W., and Cheresh, D. A. (1988) J. Biol. Chem. 263, 18726-18731). In that report, we identified amino acid residues 61-203 of the beta-subunit as proximal to the ligand binding site. Here we demonstrate that 125I-SASD-GRGDSPK affinity labels the alpha-subunit of the receptor at least two distinct sites within the region encompassing residues 139-349. Both of these regions are within the putative divalent cation binding region of the alpha-subunit. Collectively, our results suggest that discrete amino-terminal domains of both subunits of the receptor contribute to the structure of the ligand binding domain and furthermore that the ligand and divalent cation binding domains are spatially and functionally linked.
Blood vessel remodeling in pig ovarian follicles during the periovulatory period: an immunohistochemistry and SEM-corrosion casting study (2009)

These data allow us to hypothesize that EPerOFs are in a quiescent status. LPerOFs represent the "metamorphic" follicles that rapidly turn-on angiogenesis to sustain a successful corpus luteum formation. Particularly, it is interesting to underlie that the non-sprouting angiogenesis, typical of structures in rapid neovascularization, occurred only in the LPerOFs. Moreover, vascular geometric relations showed as blood vessel remodeling occurs with the "maximum output and the minimum energetic expense".This knowledge will allow to better understand the mechanisms regulating the reproductive success and to clarify the complex physiological angiogenic process in adult tissues.
Orally Administered DNA Vaccine Delivery by Attenuated Salmonella typhimurium Targeting Fetal Liver Kinase 1 Inhibits Murine Lewis Lung Carcinoma Growth and Metastasis (2010)

The vascular endothelial growth factor (VEGF) receptor 2 (VEGFR-2), also called fetal liver kinase 1 (FLK1) in mice and kinase insert domain receptor (KDR) in humans, is an endothelial cell specific receptor tyrosine kinase that mediates lung cancer angiogenesis. We hypothesized that an active immunotherapy approach targeting FLK1 may inhibit lung cancer growth and metastasis. To test this hypothesis, we evaluated whether immune responses to FLK1 could be elicited in mice by immunization with an orally administered DNA vaccine encoding the extracellular domain (ECD) of FLK1 (pcDNA3.1-FLK1(ECD)) carried by attenuated Salmonella typhimurium. We found that the vaccine was effective at protective antitumor immunity in Lewis lung carcinoma models in mice by breaking immune tolerance to FLK1 self-antigen. Both FLK1-specific humoral and cellular immune responses against endothelial cells can be induced in mice by immunization with pcDNA3.1-FLK1(ECD). Immunization with pcDNA3.1-FLK1(ECD) resulted in tumor suppression and prolonged survival in mice challenged with Lewis lung carcinomas cells. Experimental pulmonary metastases were strongly inhibited in pcDNA3.1-FLK1(ECD) immunized mice challenged with Lewis lung carcinoma cells. Thus, we conclude that the plasmid DNA vaccine encoding the extracellular domain of FLK1 could be an important component of FLK1 DNA vaccine to prevent lung carcinoma recurrence and metastasis after surgery.
Migration of dorsal aorta mesenchymal stem cells induced by mouse embryonic circulation (2010)

Mesenchymal stem cells (MSCs) represent powerful tools for regenerative medicine for their differentiation and migration capacity. However, ontogeny and migration of MSCs in mammalian mid-gestation conceptus is poorly understood. We identified canonical MSCs in the mouse embryonic day (E) 11.5 dorsal aorta (DA). They possessed homogenous immunophenotype (CD45(-)CD31(-)Flk-1(-)CD44(+)CD29(+)), expressed perivascular markers (α-SMA(+)NG2(+)PDGFRβ(+)PDGFRα(+)), and had tri-lineage differentiation potential (osteoblasts, adipocytes, and chondrocytes). Of interest, MSCs were also detected in E12.5-E13.5 embryonic circulation, 24 hr later than in DA, suggesting migration like hematopoietic stem cells. Functionally, E12.5 embryonic blood could trigger efficient migration of DA-MSCs through platelet-derived growth factor (PDGF) receptor-, transforming growth factor-beta receptor-, but not basic fibroblast growth factor receptor-mediated signaling. Moreover, downstream JNK and AKT signaling pathway played important roles in embryonic blood- or PDGF-mediated migration of DA-derived MSCs. Taken together, these results revealed that clonal MSCs developed in the mouse DA. More importantly, the embryonic circulation, in addition to its conventional transporting roles, could modulate migration of MSC during early embryogenesis.
HUNGARIAN PHYTOSOCIOLOGICAL DATABASE (COENODATRE F): SAMPLING METHODOLOGY, NOMENCLATURE AND ITS ACTUAL STAGE (2007)

The article contains the methodological guide of the national phytocoenological database, called CoenoDat Reference Database, which was prepared to build up the first Hungarian reference databank of the natural and semi-natural vegetation types in 2003. Nomenclature of plants follows Dobolyi (2002). Syntaxonomical nomenclature follows Borhidi &amp;amp;amp; S&amp;amp;aacute;nta (1999) and Borhidi (2003). For databasing the authors used TurboVeg for Windows. Up to now, CoenoDatRef contains some 9,000 relev&amp;amp;eacute;s of app. 400 natural and/or semi-natural associations. The number of entered relev&amp;amp;eacute;s of different vegetation classes is included.
S-layer proteins as basic building blocks in a biomolecular construction kit (2000)

Crystalline bacterial cell surface layer (S-layer) proteins have been optimized during billions of years of biological evolution as constituent elements of one of the simplest self-assembly systems. Isolated S-layer proteins possess the intrinsic property of being able to recrystallize into two-dimensional arrays at a broad spectrum of surfaces (e.g. silicon) and interfaces (e.g. air-water interface or planar lipid films). The well-defined arrangement of functional groups on S-layer lattices allows the binding of molecules and particles in defined regular arrays. S-layers recrystallized on solid supports can be patterned in the submicrometre range using standard optical lithography. S-layers also represent templates for the formation of inorganic nanocrystal superlattices (e.g. CdS, Au, Ni, Pt, or Pd) as required for molecular electronics and nonlinear optics.
Smart Protocol for Communication in Mobile Ad Hoc Network of Vehicles (2007)

In this paper we present a smart protocol for intervehicle communication based on mobile ad hoc networks. The protocol is capable of handling both broadcast as well as unicast messages for a particular node. The protocol implements controlled flooding in an efficient manner to reduce unnecessary communication overheads. The protocol avoids forming clusters and clusterheads by using the concept of selective forwarding. Thus it gets the advantages related to clusters without actually forming one itself. It effectively deals with blind flooding by introducing a comprehensive retransmission time delay in the nodes. This retransmission delay favors the nodes in the direction of the destination and restricts other nodes from transmitting the same message again. The proposed protocol avoids the use of routing tables which have a short life in mobile networks needing frequent updates. Instead the protocol relies on directing the messages to geographic locations which are forwarded by any available intermediary nodes. The protocol also provides techniques for handling network fragmentation which is a frequent problem for the vehicular networks. The protocol is implemented using NS2 and simulation results are compared with AODV.
Leakage-resilient approach to fault-tolerant quantum computing with superconducting elements (2015)

Superconducting qubits, while promising for scalability and long coherence times, contain more than two energy levels, and therefore are susceptible to errors generated by the leakage of population outside of the computational subspace. Such leakage errors constitute a prominent roadblock towards fault-tolerant quantum computing (FTQC) with superconducting qubits. FTQC using topological codes is based on sequential measurements of multiqubit stabilizer operators. Here, we first propose a leakage-resilient procedure to perform repetitive measurements of multiqubit stabilizer operators, and then use this scheme as an ingredient to develop a leakage-resilient approach for surface code quantum error correction with superconducting circuits. Our protocol is based on swap operations between data and ancilla qubits at the end of every cycle, requiring read-out and reset operations on every physical qubit in the system, and thereby preventing persistent leakage errors from occurring.
Thermoregulated expression of virulence genes in enteropathogenic Escherichia coli (2002)

Enteropathogenic Escherichia coli (EPEC) causes severe diarrhoea in young children. The locus of enterocyte effacement (LEE) pathogenicity island comprises a cluster of operons encoding a type III secretion system and related proteins that are associated with EPEC virulence. The LEE1 operon encodes Ler that positively regulates the LEE2, LEE3, LEE4, LEE5 and espG transcriptional units. The LEE operons are repressed at 27 degrees C and expressed at 37 degrees C. This paper describes a regulatory cascade of the thermoregulation of LEE operons. LEE1 including ler is repressed by H-NS at 27 degrees C but not at 37 degrees C. In contrast, the expression of the LEE2, LEE3, LEE4, LEE5 and espG transcriptional units is repressed by H-NS at both 27 degrees C and 37 degrees C. Upon shifting the culture temperature from 27 degrees C to 37 degrees C, Ler is synthesized and in turn activates the expression of LEE2, LEE3, LEE4 and espG by releasing the H-NS mediated repression. In the case of LEE5, Ler acts both by alleviating the H-NS mediated repression and by an additional mechanism, as yet to be defined.
Cross-reacting antigens between Neorickettsia helminthoeca and Ehrlichia species, shown by immunofluorescence and Western immunoblotting (1991)

Dogs orally infected with Neorickettsia helminthoeca developed immunoglobulin G titers against Erlichia risticii, Erlichia sennetsu, and Erlichia canis similar to those against N. helminthoeca antigen, as determined by immunofluorescence. Western immunoblotting showed that the major common antigens shared among the microorganisms were 80- or 78-kDa and 64-kDa polypeptides. In contrast, horse anti-E. risticii and anti-E. sennetsu and dog anti-E. canis sera reacted more weakly to N. helminthoeca antigen than to homologous antigens in both immunofluorescence and Western immunoblotting. Antisera raised in other species of animals, i.e., mouse anti-E. canis and rabbit anti-E. risticii and anti-E. sennetsu sera, however, all reacted with the 64-kDa antigen of N. helminthoeca. This strong antigenic cross-reactivity and similarity in Western immunoblotting reaction profiles indicate that N. helminthoeca is antigenically closely related to E. risticii and E. sennetsu and less so to E. canis. In both immunofluorescence and Western immunoblotting, E. canis shared fewer common antigens with E. risticii and E. sennetsu than N. helminthoeca did. It is reasonable to conclude that these results may have both diagnostic and taxonomic significance.
Direct measurement of gap-state absorption in hydrogenated amorphous silicon by photothermal deflection spectroscopy (1982)

We have measured the subgap optical absorption of undoped, singly doped, and compensated hydrogenated amorphous silicon down to 0.6 eV using the sensitive technique of photothermal deflection spectroscopy. We show that this absorption is due to silicon dangling-bond defects located \ensuremath{\sim}1.3 eV below the conduction band. While doping also creates defects \ensuremath{\sim}1.3 eV below the conduction band, compensation removes them. The results suggest that for the undoped material the density-of-states maximum found in field-effect measurements is due to silicon dangling bonds.
Differentiation and Proliferation of Mast Cells in Nasal Mucosa (2001)

We determined the distribution of mast cells in nasal mucosa and studied their proliferation. Inferior turbinate mucosa was sampled in 13 patients with allergic rhinitis (allergic group) and 5 without (non allergic group) and stained immunohistochemically using anti mast cell tryptase antibody, anti-c-kit antibody, anti-PCNA antibody, and anti mast cell chymase antibody. Tissue sections stained with anti tryptase antibody revealed a higher degree of infiltration of tryptase-positive cells, i.e., mast cells, in the allergic group than in non allergic group. In the allergic group, the number of tryptase-positive cells, c-kit-positive cells, and PCNA-positive cells was significantly greater in the epithelium and shallow lamina propria than that in the deep lamina propria. Tryptase-positive, c-kit-positive cells, i.e., c-kit-positive mast cells, and tryptase-positive, PCNA-positive cells, i.e., PCNA-positive mast cells, were also abundunt in the epithelium and shallow lamina propria. The stem cell factor and c-kit receptor are reported to play a primary role in mast cell differentiation and proliferation. PCNA-positive cells represent actively proliferating cells. Based on the above, we concluded that mast cells in the epithelium and shallow lamina propria in the allergic group differentiated and proliferated more actively than those in the deep lamina propria.
Engineering subtilisin and its substrates for efficient ligation of peptide bonds in aqueous solution (1991)

Protein engineering techniques were used to construct a derivative of the serine protease subtilisin that ligates peptides efficiently in water. The subtilisin double mutant in which the catalytic Ser221 was converted to Cys (S221C) and Pro225 converted to Ala (P225A) has 10-fold higher peptide ligase activity and at least 100-fold lower amidase activity than the singly mutated thiolsubtilisin (S221C) that was previously shown to have some peptide ligase activity [Nakatsuka, T., Sasaki, T., & Kaiser, E.T. (1987) J. Am. Chem. Soc. 109, 3808-3810]. A 1.5-A X-ray crystal structure of an oxidized derivative of the double mutant (S221C/P225A) supports the protein design strategy in showing that the P225A mutation partly relieves the steric crowding expected from the S221C substitution, thus accounting for its improved catalytic efficiency. Stable and synthetically reasonable alkyl ester peptide substrates were prepared that rapidly acylate the S221C/P225A enzyme, and aminolysis of the resulting thioacyl-enzyme intermediate by various peptides is strongly preferred over hydrolysis. The efficiency of aminolysis is relatively insensitive to the sequence of the first two residues in the acyl acceptor peptide whose alpha-amino group attacks the thioacyl-enzyme. To obtain greater flexibility in the choice of coupling sites, a set of three additional peptide ligases were engineered by introducing mutations into the parent ligase (S221C/P225A) that were previously shown to change the specificity of subtilisin for the residue nearest the acyl bond (the P1 residue). The specificity properties of the parent ligase and derivatives of it paralleled those of wild type and corresponding specificity variants.(ABSTRACT TRUNCATED AT 250 WORDS)
Faster Isosurface Ray Tracing Using Implicit KD-Trees (2005)

The visualization of high-quality isosurfaces at interactive rates is an important tool in many simulation and visualization applications. Today, isosurfaces are most often visualized by extracting a polygonal approximation that is then rendered via graphics hardware or by using a special variant of preintegrated volume rendering. However, these approaches have a number of limitations in terms of the quality of the isosurface, lack of performance for complex data sets, or supported shading models. An alternative isosurface rendering method that does not suffer from these limitations is to directly ray trace the isosurface. However, this approach has been much too slow for interactive applications unless massively parallel shared-memory supercomputers have been used. In this paper, we implement interactive isosurface ray tracing on commodity desktop PCs by building on recent advances in real-time ray tracing of polygonal scenes and using those to improve isosurface ray tracing performance as well. The high performance and scalability of our approach will be demonstrated with several practical examples, including the visualization of highly complex isosurface data sets, the interactive rendering of hybrid polygonal/isosurface scenes, including high-quality ray traced shading effects, and even interactive global illumination on isosurfaces.
Biomechanical Effects of Microbubbles: From Radiosensitization to Cell Death (2015)

Ultrasound-stimulated microbubbles have been demonstrated to mechanically perturb cell membranes, resulting in the activation of biological signaling pathways that significantly enhance the effects of radiation. The underlying mechanism involves augmented ceramide production following both microbubble stimulation and irradiation, leading to rapid and extensive endothelial apoptosis and tumor cell death as a result of vascular collapse. Endothelial cells are particularly sensitive to ceramide-induced cell death due to an enriched presence of sphingomyelinase in their membranes. In tumors, this consequent rapid vascular shutdown translates to an overall increase in tumor responses to radiation treatments. This review summarizes the groundwork behind endothelial-based radiation enhancement with ultrasound-stimulated microbubbles, and presents ongoing research on the use of microbubbles as therapeutic agents in cancer therapy.
Childhood ataxia with diffuse central nervous system hypomyelination (1994)

A significant number of patients with progressive leukodystrophy do not have a definitive diagnosis. This report describes the clinical, morphological, and biochemical characteristics of 4 unrelated girls with progressive ataxic diplegia of unknown etiology. These patients had normal development until the ages of 1.5 to 5 years. A diffuse confluent abnormality of the white matter of the central nervous system was present on computed tomography and magnetic resonance scans obtained early in the course of the illness. Dementia was not present and peripheral nerves were normal. All patients were evaluated for known metabolic and degenerative diseases and no abnormalities were observed. Light and electron microscopy of open-brain biopsy specimens from 2 girls showed selective white matter abnormalities including hypomyelination, demyelination, and gliosis. Myelin-specific proteins in the subcortical white matter were examined immunocytochemically and by Western blot analysis. They were of normal molecular size but were markedly reduced in quantity in both patients compared to control subjects. Lipid analysis revealed decreased levels of characteristic myelin lipids. When examined by magnetic resonance spectroscopic imaging, all patients showed a marked decrease of N-acetylaspartic acid, choline, and creatine in white matter only. The magnetic resonance spectroscopic imaging profile is a unique diagnostic feature of this clinicopathological syndrome.
A review of the ophidiid fish genus Sirembo with a new species from Australia (1986)

(Uploaded by Plazi from the Biodiversity Heritage Library) No abstract provided.
Release of heat shock proteins (Hsps) and the effects of extracellular Hsps on neural cells and tissues (2005)

Hsps were long thought to be cytoplasmic proteins with functions restricted to the intra-cellular compartment. However, an increasing number of observations show that they can be released into the extra-cellular space and can then have a wide variety of affects on other cells. The mechanism of release remains unknown, but may involve the shedding of exosomes, which are vesicles containing cytoplasmic constituents. In the nervous system, it appears that glial cells can release the 70 kD Hsps and that neurons exposed to extra-cellular Hsps are more likely to survive injury than their naïve counterparts. These phenomena have great potential significance in the development of neuroprotective therapeutic strategies utilizing the heat shock protein response.
Optimizing path tracing using noise reduction filters (1995)

The problem of global illumination can be solved using path tracing. Unfortunately path tracing gives very noisy images. This noise is mostly caused by the indirect illumination reflected diffusely. The common way to reduce the noise is to use more samples/rays pr. pixel. However, the convergence speed in path tracing makes this strategy very costly. In this paper we propose a technique in which light reflected diffusely two times is separated from the final solution. This light is filtered by different noise reduction filtres and then added to the remaining solution. In this way we avoid blurring the image and the the same time we are able to reduce the noise level significantly.
Pathogenesis of Borna Disease in Rats: Immune-Mediated Viral Ophthalmoencephalopathy Causing Blindness and Behavioral Abnormalities (1983)

Borna disease virus is an unclassified agent that causes a rare but fatal encephalitis in horses in Germany. In experimental animals the virus causes acute fatal encephalitis in some instances and chronic encephalitis with abnormal behavior in others. In initial studies of the pathogenesis of the latter disease in rats, the virus was shown to replicate only in the nervous system, with the greatest concentration of infectivity in the cerebrum and eyes. Viral replication continued indefinitely in both newborn and adult rats. The adult animals developed self-limiting, necrotizing encephalitis in the cerebrum, with inflammation spreading to the retina. Inflammation receded after two months, however, with concomitant cessation of necrosis; static hydrocephalus was observed at this point. Levels of viral replication were unaffected by these changes. Rats became frenzied and aggressive during the encephalitic period but became permanently passive and inactive after inflammation receded. Infected neonates and immunosuppressed adults did not become ill. The frenzied behavior and subsequent blindness in immunocompetent adults were therefore attributed to a uniquely transient immunopathologic reaction targeted to centers in the limbic system and retinal neurons.