gebhart/patrepeval huggingface dataset:
Antigen‐Independent Selection of T15 Idiotype During B‐Cell Ontogeny In Mice (1990)

Precursors of B cells capable of responding to a T-independent form of phosphorylcholine (PC) in splenic focus assays were detected in the spleens of neonatal mice as early as 4 days after birth. The earliest anti-PC B cells were T15-. T15+ foci-forming B cells were first detected 6 days after birth and expanded rapidly to constitute greater than 80% of the total PC-specific foci by day 10. Injection of heat-killed S. pneumoniae (R36A) into neonatal mice resulted in priming of the antibody response to PC, with an idiotype profile reflecting that of precursors of foci-forming B cells at the time of antigen administration. Priming of 2-day-old mice with 2 x 10(6) and 2 x 10(7) R36A induced a five- and ten-fold increase in the antibody response to phosphorylcholine 6 to 8 weeks later. However, only 10 to 15% of the serum antibodies expressed the normally dominant T15 idiotype. Doses below 2 x 10(5) R36A showed no detectable priming activity. PC-specific hybridomas derived from mice injected with 2 x 10(7) R36A 2 days after birth lacked the idiotypic and molecular characteristics typical of T15+ antibodies. Antibodies to phosphorylcholine, raised by immunization of 6-week-old mice are normally protective against pneumococcal infection. However, serum antibodies from mice treated with R36A 2 days after birth and responding to phosphorylcholine following challenge with R36A at 6 weeks of age failed to protect against deliberate infection with virulent S. pneumoniae. These observations imply that the antigen phosphorylcholine does not play a role in the selective expansion and dominant expression of the T15 idiotype.
Multiresolution Tiling (1994)

Abstract This paper describes an efficient method for constructing a tiling between a pair of planar contours. The problem is of interest in a number of domains, including medical imaging, biological research and geological reconstructions. Our method, based on ideas from multiresolution analysis and wavelets, requires O(n) space and appears to require O(n log n) time for average inputs, compared to the O(n 2 ) space and O(n 2 log n) time required by the optimizing algorithm of Fuchs, Kedem and Uselton 1 . The results computed by our algorithm are in many cases nearly the same as those of the optimizing algorithm, but at a small fraction of the computational cost. The performance improvement makes the algorithm usable for large contours in an interactive system. The use of multiresolution analysis provides an efficient mechanism for data compression by discarding wavelet coefficients smaller than a threshold value during reconstruction. The amount of detail lost can be controlled by appropriate choice of the threshold value. The use of lower resolution approximations to the original contours yields significant savings in the time required to display a reconstructed object, and in the space required to store it.
The Structure of the Macrophage Signal Regulatory Protein α (SIRPα) Inhibitory Receptor Reveals a Binding Face Reminiscent of That Used by T Cell Receptors (2007)

Signal regulatory protein (SIRP) alpha is a membrane receptor that sends inhibitory signals to myeloid cells by engagement of CD47. The high resolution x-ray structure of the N-terminal ligand binding domain shows it to have a distinctive immunoglobulin superfamily V-like fold. Site-directed mutagenesis suggests that CD47 is bound at a surface involving the BC, FG, and DE loops, which distinguishes it from other immunoglobulin superfamily surface proteins that use the faces of the fold, but resembles antigen receptors. The SIRP interaction is confined to a single domain, and its use of an extended DE loop strengthens the similarity with T cell receptor binding and the suggestion that they are closely related in evolution. The employment of loops to form the CD47-binding surface provides a mechanism for small sequence changes to modulate binding specificity, explaining the different binding properties of SIRP family members.
Cytokines Regulate Proteolysis in Major Histocompatibility Complex Class II–Dependent Antigen Presentation by Dendritic Cells (2001)

Endo/lysosomal proteases control two key events in antigen (Ag) presentation: the degradation of protein Ag and the generation of peptide-receptive major histocompatibility complex (MHC) class II molecules. Here we show that the proinflammatory cytokines tumor necrosis factor alpha and interleukin (IL)-1beta rapidly increase the activity of cathepsin (cat) S and catB in human dendritic cells (DCs). As a consequence, a wave of MHC class II sodium dodecyl sulfate stable dimer formation ensues in a catS-dependent fashion. In contrast, the antiinflammatory cytokine IL-10 renders DCs incapable of upregulating catS and catB activity and in fact, attenuates the level of both enzymes. Suppressed catS and catB activity delays MHC class II sodium dodecyl sulfate stable dimer formation and impairs Ag degradation. In DCs exposed to tetanus toxoid, IL-10 accordingly reduces the number of MHC class II-peptide complexes accessible to tetanus toxoid-specific T cell receptors, as analyzed by measuring T cell receptor downregulation in Ag-specific T cell clones. Thus, the control of protease activity by pro- and antiinflammatory cytokines is an essential feature of the Ag presentation properties of DCs.
Influence of Chemical Composition of CoFeB on Tunneling Magnetoresistance and Microstructure in Polycrystalline CoFeB/MgO/CoFeB Magnetic Tunnel Junctions (2006)

We report, for the first time, the correlation between tunneling magnetoresistance (TMR) and the microstructure of polycrystalline CoFeB/MgO/CoFeB magnetic tunnel junctions with various Co/Fe ratios in the (CoFe)81B19 reference and free layers. It is found that the Co/Fe ratio in the (CoFe)81B19 reference layer strongly affects the (001) out-of-plane texture of the MgO tunnel barrier, resulting in the variation in TMR ratio. Further microstructure characterization of the magnetic tunnel junction with a higher TMR ratio and a stronger (001) out-of-plane texture in the MgO tunnel barrier reveals a grain-to-grain lattice match between the crystallized bcc CoFeB reference layer and MgO with a 45° rotational epitaxial relationship, that is, CoFeB(001)[110]∥MgO(001)[100].
Regulation of G1progression by thePTENtumor suppressor protein is linked to inhibition of the phosphatidylinositol 3-kinase/Akt pathway (1999)

PTEN/MMAC1 is a tumor suppressor gene located on chromosome 10q23. Inherited PTEN/MMAC1 mutations are associated with a cancer predisposition syndrome known as Cowden's disease. Somatic mutation of PTEN has been found in a number of malignancies, including glioblastoma, melanoma, and carcinoma of the prostate and endometrium. The protein product (PTEN) encodes a dual-specificity protein phosphatase and in addition can dephosphorylate certain lipid substrates. Herein, we show that PTEN protein induces a G1 block when reconstituted in PTEN-null cells. A PTEN mutant associated with Cowden's disease (PTEN;G129E) has protein phosphatase activity yet is defective in dephosphorylating inositol 1,3,4,5-tetrakisphosphate in vitro and fails to arrest cells in G1. These data suggest a link between induction of a cell-cycle block by PTEN and its ability to dephosphorylate, in vivo, phosphatidylinositol 3,4,5-trisphosphate. In keeping with this notion, PTEN can inhibit the phosphatidylinositol 3,4, 5-trisphosphate-dependent Akt kinase, a downstream target of phosphatidylinositol 3-kinase, and constitutively active, but not wild-type, Akt overrides a PTEN G1 arrest. Finally, tumor cells lacking PTEN contain high levels of activated Akt, suggesting that PTEN is necessary for the appropriate regulation of the phosphatidylinositol 3-kinase/Akt pathway.
Structure of a New Type of Transient Network:  Entangled Wormlike Micelles Bridged by Telechelic Polymers (2007)

The thermodynamics and structural behavior of a new type of transient network are reported. The network is obtained by adding in a solution of entangled surfactant wormlike micelles a telechelic triblock copolymer whose hydrophobic ends anchor into the micelles and whose hydrophilic tails are swollen in the aqueous solvent and reversibly link the entangled cylindrical micelles. For comparison, we have also studied the same surfactant system decorated with an amphiphilic diblock copolymer which corresponds exactly to a triblock telechelic copolymer cut into two identical diblock copolymers. We find that the addition of telechelic polymers induces an effective attraction of entropic origin between the surfactant that may result, in equilibrium, in the coexistence of a dilute phase and a connected network, as predicted by theory. Small-angle neutron scattering experiments show first that the locally cylindrical structure of the micelles is maintained upon copolymer addition over a wide range of copolymer-to-surfactant molar ratio. On the other hand, the addition of telechelic polymer correlates with (i) the emergence of a broad peak in the structure factor at a finite scattering vector, q, due to the short-range steric repulsion induced by the polymer between the cylinders, and (ii) the large rise of the scattered intensity at low q's (for small enough surfactant concentration), which indicates an increase of the osmotic compressibility of the solution due to the effective attractive interaction between cylinders provoked by the telechelic polymers linking them.
A hundred years of public education: A personal comment (1980)

This year we are celebrating the Centenary of Public Education in the State of New South Wales. The inaugural date was the First of May, 1880. May Day was traditionally, from Roman times, associated with social and sporting activities. In Merrie England people went a-maying, enjoyed maypole and morris dancing, held archery contests, lit bonfires, and chose the Queen of the May. In modern times the day has become associated with trade union processions; and by a rare coincidence, it was on May Day, 1976, that our present State Government came to power; since when, one of its major problems has been the public education system!
Oxidative Effects during Irreversible Electroporation of Melanoma Cells—In Vitro Study (2020)

Irreversible electroporation (IRE) is today used as an alternative to surgery for the excision of cancer lesions. This study aimed to investigate the oxidative and cytotoxic effects the cells undergo during irreversible electroporation using IRE protocols. To do so, we used IRE-inducing pulsed electric fields (PEFs) (eight pulses of 0.1 ms duration and 2-4 kV/cm intensity) and compared their effects to those of PEFs of intensities below the electroporation threshold (eight pulses, 0.1 ms, 0.2-0.4 kV/cm) and the PEFs involving elongated pulses (eight pulses, 10 ms, 0.2-0.4 kV/cm). Next, to follow the morphology of the melanoma cell membranes after treatment with the PEFs, we analyzed the permeability and integrity of their membranes and analyzed the radical oxygen species (ROS) bursts and the membrane lipids' oxidation. Our data showed that IRE-induced high cytotoxic effect is associated both with irreversible cell membrane disruption and ROS-associated oxidation, which is occurrent also in the low electric field range. It was shown that the viability of melanoma cells characterized by similar ROS content and lipid membrane oxidation after PEF treatment depends on the integrity of the membrane system. Namely, when the effects of the PEF on the membrane are reversible, aside from the high level of ROS and membrane oxidation, the cell does not undergo cell death.
Generation of Breast Cancer Stem Cells through Epithelial-Mesenchymal Transition (2008)

Recently, two novel concepts have emerged in cancer biology: the role of so-called "cancer stem cells" in tumor initiation, and the involvement of an epithelial-mesenchymal transition (EMT) in the metastatic dissemination of epithelial cancer cells. Using a mammary tumor progression model, we show that cells possessing both stem and tumorigenic characteristics of "cancer stem cells" can be derived from human mammary epithelial cells following the activation of the Ras-MAPK pathway. The acquisition of these stem and tumorigenic characters is driven by EMT induction.
Characteristics of hepatic fatty acid compositions in patients with nonalcoholic steatohepatitis (2014)

The fatty acid composition in liver tissue and expression of genes related to fatty acid metabolism were different between the SS and NASH groups, suggesting that the acceleration of fatty acid metabolism is deeply involved in pathogenesis of NASH.
An update on Cryptococcus among HIV-infected patients (2010)

Cryptococcus remains an important opportunistic infection in HIV patients despite considerable declines in prevalence during the highly active antiretroviral therapy era. This is particularly apparent in sub-Saharan Africa, where Cryptococcus continues to cause significant mortality and morbidity. This review discusses the microbiology, epidemiology, pathogenesis and clinical presentation of cryptococcal infections in HIV patients. Additionally, a detailed approach to the management of cryptococcosis is provided.
Detection of Antibodies to Mycoplasma gallisepticum Vaccine ts-11 by an Autologous pMGA Enzyme-Linked Immunosorbent Assay (2002)

Mycoplasma gallisepticum is a poultry pathogen that causes respiratory disease and loss of egg production worldwide. A live attenuated vaccine, ts-11, has been used for control of M. gallisepticum in several countries. The rapid serum agglutination test is usually used as an indicator of flock response to vaccination; however, in some flocks, the detected response may be weak or absent. With the use of specific monoclonal antibodies against M. gallisepticum strain S6 pMGA in immunoaffinity purification, the major membrane antigen of ts-11 was purified. An indirect enzyme-linked immunosorbent assay (ELISA) was developed with the purified antigen, and its potential for detection of antibodies induced after ts-11 vaccination was compared with an indirect ELISA with M. gallisepticum strain S6 pMGA. In the presence of high levels of ts-11-induced antibodies, both antigens detected similar numbers of positive sera. However, when lower levels of antibodies were present, ts-11 pMGA showed a higher sensitivity than S6 pMGA. Further examination of ts-11 pMGA with Mycoplasma synoviae-infected chicken sera revealed that ts-11 pMGA is specific for M. gallisepticum antibodies. With a panel of sera from ts-11-vaccinated or non-ts-11-vaccinated field chickens, the ts-11 pMGA ELISA was found to be more sensitive than the commercial rapid serum agglutination test in detecting antibodies to ts-11 vaccine. The results from this study suggest that the major membrane antigen of M. gallisepticum may have slightly different antigenic profiles in different strains, thereby necessitating the use of autologous antigens in serodiagnostic assays to increase sensitivity of the tests for mycoplasma antibodies. Thus, the low level of antibody response after ts-11 vaccination is, at least partially, due to the low ability of the current diagnostic antigens to bind ts-11 antibodies.
Truncation of the carboxy-terminal 28 amino acids of glycoprotein B specified by herpes simplex virus type 1 mutant amb1511-7 causes extensive cell fusion (1993)

Three amber mutations were introduced proximal to the syn3 locus of the herpes simplex virus type 1 glycoprotein B (gB) gene specifying gB derivatives lacking the carboxy-terminal 28, 49, or 64 amino acids. A complementation system that utilized gBs expressed in COS cells to complement gB-null virus K delta T was established. The 49- or 64-amino-acid-truncated gBs failed to complement gB-null virus K delta T, while the 28-amino-acid-truncated gB complemented K delta T efficiently. Mutant herpes simplex virus type 1 KOS (amb1511-7) specifying the 28-amino-acid-truncated gB fused Vero cells extensively.
The N-terminal part of theE.ColiDNA binding protein FIS is essential for stimulating site-specific DNA inversion but is not required for specific DNA binding (1991)

FIS protein is involved in several different cellular processes stimulating site-specific recombination in phages Mu and lambda as well as transcription of stable RNA operons in E.coli. We have performed a mutational analysis of fis and provide genetic and biochemical evidence that a truncated version of FIS lacking the N-terminal region is sufficient for specific DNA binding and for stimulating lambda excision. These mutants also retain their ability to autoregulate fis gene expression. Such mutant proteins, however, cannot stimulate the enhancer dependent DNA inversion reaction.
Cloning, Expression, and Characterization of Bacterial l-Arabinose 1-Dehydrogenase Involved in an Alternative Pathway of l-Arabinose Metabolism (2005)

Azospirillum brasiliense converts L-arabinose to alpha-ketoglutarate via five hypothetical enzymatic steps. We purified and characterized L-arabinose 1-dehydrogenase (EC 1.1.1.46), catalyzing the conversion of L-arabinose to L-arabino-gamma-lactone as an enzyme responsible for the first step of this alternative pathway of L-arabinose metabolism. The purified enzyme preferred NADP+ to NAD+ as a coenzyme. Kinetic analysis revealed that the enzyme had high catalytic efficiency for both L-arabinose and D-galactose. The gene encoding L-arabinose 1-dehydrogenase was cloned using a partial peptide sequence of the purified enzyme and was overexpressed in Escherichia coli as a fully active enzyme. The enzyme consists of 308 amino acids and has a calculated molecular mass of 33,663.92 Da. The deduced amino acid sequence had some similarity to glucose-fructose oxidoreductase, D-xylose 1-dehydrogenase, and D-galactose 1-dehydrogenase. Site-directed mutagenesis revealed that the enzyme possesses unique catalytic amino acid residues. Northern blot analysis showed that this gene was induced by L-arabinose but not by D-galactose. Furthermore, a disruptant of the L-arabinose 1-dehydrogenase gene did not grow on L-arabinose but grew on D-galactose at the same growth rate as the wild-type strain. There was a partial gene for L-arabinose transport in the flanking region of the L-arabinose 1-dehydrogenase gene. These results indicated that the enzyme is involved in the metabolism of L-arabinose but not D-galactose. This is the first identification of a gene involved in an alternative pathway of L-arabinose metabolism in bacterium.
Photonic band gap formation in certain self-organizing systems (1998)

We present a detailed study of photonic band structure in certain self-organizing systems that self-assemble into large-scale photonic crystals with photonic band gaps (PBGs) or pseudogaps in the near-visible frequency regime. These include colloidal suspensions, inverted opals, and macroporous silicon. We show that complete three-dimensional PBGs spanning roughly 10% and 15% of the gap center frequency are attainable by incomplete infiltration of an opal with silicon and germanium, respectively. The photonic band structure of both face center cubic and hexagonal close packed photonic crystals are evaluated. We delineate how the PBG is modified by sintering the opal prior to infiltration and by applying strain along various crystallographic directions. We evaluate the total photon density of states as well as the local density of states (LDOS) projected onto various points within the photonic crystal. It is shown that the LDOS may exhibit considerable pseudogap structure even for systems that do not exhibit a complete PBG. These results are directly relevant to quantum optical experiments in which atoms, dye molecules, or other active materials are inserted into specific locations within the photonic crystal. When the resonant optical transition of these dopants is tuned close to a pseudogap or other abrupt structure in the LDOS, novel effects in radiative dynamics associated with a ``colored vacuum'' may be realized.
Tibiofemoral movement 1: the shapes and relative movements of the femur and tibia in the unloaded cadaver knee (2000)

In six unloaded cadaver knees we used MRI to determine the shapes of the articular surfaces and their relative movements. These were confirmed by dissection. Medially, the femoral condyle in sagittal section is composed of the arcs of two circles and that of the tibia of two angled flats. The anterior facets articulate in extension. At about 20° the femur ‘rocks’ to articulate through the posterior facets. The medial femoral condyle does not move anteroposteriorly with flexion to 110°. Laterally, the femoral condyle is composed entirely, or almost entirely, of a single circular facet similar in radius and arc to the posterior medial facet. The tibia is roughly flat. The femur tends to roll backwards with flexion. The combination during flexion of no antero-posterior movement medially (i.e., sliding) and backward rolling (combined with sliding) laterally equates to internal rotation of the tibia around a medial axis with flexion. About 5° of this rotation may be obligatory from 0° to 10° flexion; thereafter little rotation occurs to at least 45°. Total rotation at 110° is about 20°, most if not all of which can be suppressed by applying external rotation to the tibia at 90°.
Aerothionin and homoaerothionin: two tetrabromo spirocyclohexadienylisoxazoles from Verongia sponges (1972)

K. Moody, R. H. Thomson, E. Fattorusso, L. Minale and G. Sodano, J. Chem. Soc., Perkin Trans. 1, 1972, 18 DOI: 10.1039/P19720000018
Transcriptional activation of human mu‐opioid receptor gene by insulin‐like growth factor‐I in neuronal cells is modulated by the transcription factor REST (2008)

The human mu-opioid receptor gene (OPRM1) promoter contains a DNA sequence binding the repressor element 1 silencing transcription factor (REST) that is implicated in transcriptional repression. We investigated whether insulin-like growth factor I (IGF-I), which affects various aspects of neuronal induction and maturation, regulates OPRM1 transcription in neuronal cells in the context of the potential influence of REST. A series of OPRM1-luciferase promoter/reporter constructs were transfected into two neuronal cell models, neuroblastoma-derived SH-SY5Y cells and PC12 cells. In the former, endogenous levels of human mu-opioid receptor (hMOPr) mRNA were evaluated by real-time PCR. IGF-I up-regulated OPRM1 transcription in: PC12 cells lacking REST, in SH-SY5Y cells transfected with constructs deficient in the REST DNA binding element, or when REST was down-regulated in retinoic acid-differentiated cells. IGF-I activates the signal transducer and activator of transcription-3 signaling pathway and this transcription factor, binding to the signal transducer and activator of transcription-1/3 DNA element located in the promoter, increases OPRM1 transcription. We propose that a reduction in REST is a critical switch enabling IGF-I to up-regulate hMOPr. These findings help clarify how hMOPr expression is regulated in neuronal cells.
Toll-Like Receptor Agonists (2010)

Therapeutic immunization leading to cancer regression remains a significant challenge. Successful immunization requires activation of adaptive immunity, including tumor specific CD4 T cells and CD8 T cells. Generally, the activation of T cells is compromised in patients with cancer because of immune suppression, loss of tumor antigen expression, and dysfunction of antigen-presenting cells. Antigen-presenting cells such as dendritic cells (DCs) are key for the induction of adaptive antitumor immune responses. Recently, attention has focused on novel adjuvants that enhance dendritic cell function and their ability to prime T cells. Agonists that target toll-like receptors are being used clinically either alone or in combination with tumor antigens and showing initial success both in terms of enhancing immune responses and eliciting antitumor activity. This review summarizes the application of these adjuvants to treat cancer and the potential for boosting responses in vivo.