gebhart/patrepeval huggingface dataset:
Efficient production of a human tumour necrosis factor in Escherichia coli. (1985)

To examine the effect of altering the nucleotide sequence of the Shine-Dalgarno (SD) region and the spacer sequence between the SD sequence and the AUG translation start signal, several plasmids were constructed which directed the synthesis of mature human tumour necrosis factor (TNF) under the control of the E. coli trp leader promoter. We found that the presence of the SD sequence, AAGGAGGT, which is complementary to the 3' end of 16S rRNA, gave the higher translational efficiency, and also, the presence of the spacer sequence which consists of only A and T residues raised the production of TNF 2-3 fold. The levels of expression of TNF were elevated over 20-fold by the alteration of the SD and spacer sequences and amounted to 20% of the total cellular proteins or approx. 5 X 10(6) molecules of TNF per cell.
Costimulatory protein B7-1 enhances the cytotoxic T cell response and antibody response to hepatitis B surface antigen. (1996)

There is a need for more effective therapy for chronic virus infections. A principle natural mechanism for elimination of virus-infected host cells is activation of viral antigen-specific cytotoxic T lymphocytes (CTL). In an effort to develop methods of inducing virus-specific CTL responses that might be utilized in therapy of virus infections, we have investigated the effect of B7, a costimulatory factor for T-cell activation. In this study we show that delivery of genes encoding human B7-1 and a viral antigen in the same recombinant viral vector to cells of mice induces a greater viral antigen-specific CTL response than does similar delivery of the viral antigen gene alone. Two recombinant adenovirus vectors were constructed with the foreign genes inserted in the early region 3. One of them (Ad1312) directed expression of the surface antigen gene of hepatitis B virus (HBS); the other (Ad1310) directed coexpression of HBS and human B7-1 (CD80) by means of an internal ribosomal entry site placed between the two coding sequences. When inoculated into BALB/c mice, both vectors induced a viral surface antigen-specific CTL response. The response induced by Ad1310 was stronger than that by Adl312 as measured by a chromium release assay for CTL activity and limiting dilution analysis for CTL precursor frequency, indicating that the B7-1 gene co-delivered with the HBS gene had an enhancing effect on the CTL response against surface antigen. Ad1310 also induced a higher titer of antibody against surface antigen than did Ad1312. This result suggests that expression of a costimulatory protein and a viral antigen in the same cells in vivo induces stronger immune responses than expression of the antigen alone. This could be a novel strategy for development of both preventive and therapeutic vaccines against infectious agents.
Strongly coupled inorganic–nano-carbon hybrid materials for energy storage (2013)

The global shift of energy production from fossil fuels to renewable energy sources requires more efficient and reliable electrochemical energy storage devices. In particular, the development of electric or hydrogen powered vehicles calls for much-higher-performance batteries, supercapacitors and fuel cells than are currently available. In this review, we present an approach to synthesize electrochemical energy storage materials to form strongly coupled hybrids (SC-hybrids) of inorganic nanomaterials and novel graphitic nano-carbon materials such as carbon nanotubes and graphene, through nucleation and growth of nanoparticles at the functional groups of oxidized graphitic nano-carbon. We show that the inorganic-nano-carbon hybrid materials represent a new approach to synthesize electrode materials with higher electrochemical performance than traditional counterparts made by simple physical mixtures of electrochemically active inorganic particles and conducting carbon materials. The inorganic-nano-carbon hybrid materials are novel due to possible chemical bonding between inorganic nanoparticles and oxidized carbon, affording enhanced charge transport and increased rate capability of electrochemical materials without sacrificing specific capacity. Nano-carbon with various degrees of oxidation provides a novel substrate for nanoparticle nucleation and growth. The interactions between inorganic precursors and oxidized-carbon substrates provide a degree of control over the morphology, size and structure of the resulting inorganic nanoparticles. This paper reviews the recent development of inorganic-nano-carbon hybrid materials for electrochemical energy storage and conversion, including the preparation and functionalization of graphene sheets and carbon nanotubes to impart oxygen containing groups and defects, and methods of synthesis of nanoparticles of various morphologies on oxidized graphene and carbon nanotubes. We then review the applications of the SC-hybrid materials for high performance lithium ion batteries, rechargeable Li-S and Li-O2 batteries, supercapacitors and ultrafast Ni-Fe batteries, and new electrocatalysts for oxygen reduction, oxygen evolution and hydrogen evolution reactions.
Structural and Functional Consequences of Altering a Peptide MHC Anchor Residue (2001)

To better understand TCR discrimination of multiple ligands, we have analyzed the crystal structures of two Hb peptide/I-E(k) complexes that differ by only a single amino acid substitution at the P6 anchor position within the peptide (E73D). Detailed comparison of multiple independently determined structures at 1.9 A resolution reveals that removal of a single buried methylene group can alter a critical portion of the TCR recognition surface. Significant variance was observed in the peptide P5-P8 main chain as well as a rotamer difference at LeuP8, approximately 10 A distal from the substitution. No significant variations were observed in the conformation of the two MHC class II molecules. The ligand alteration results in two peptide/MHC complexes that generate bulk T cell responses that are distinct and essentially nonoverlapping. For the Hb-specific T cell 3.L2, substitution reduces the potency of the ligand 1000-fold. Soluble 3.L2 TCR binds the two peptide/MHC complexes with similar affinity, although with faster kinetics. These results highlight the role of subtle variations in MHC Ag presentation on T cell activation and signaling.
Various ways to improve whole cancer cell vaccines (2014)

Immunotherapy based on whole cancer cell vaccines is regarded as a promising avenue for cancer treatment. However, limited efficacy in the first human clinical trials calls for more optimized whole cancer cell vaccines and better patient selection. It is suggested that whole cancer cell vaccines consist preferably of immunogenically killed autologous cancer stem cells associated with dendritic cells. Adjuvants should stimulate both immune effector cells and memory cells, which could be achieved through their correct dosage and timing of administration. There are indications that whole cancer cell vaccination is less effective in patients who are immunocompromised, who have specific genetic defects in their immune or cancer cells, as well as in patients in an advanced cancer stage. However, such patients form the bulk of enrolled patients in clinical trials, prohibiting an objective evaluation of the true potential of whole cancer cell immunotherapy. Each key point will be discussed.
A metabolic pathway leading to mannosylfructose biosynthesis in Agrobacterium tumefaciens uncovers a family of mannosyltransferases (2007)

A metabolic pathway for biosynthesis of the nonreducing disaccharide mannosylfructose (beta-fructofuranosyl-alpha-mannopyranoside), an important osmolyte in Agrobacterium tumefaciens, was discovered. We have identified and functionally characterized two ORFs that correspond to genes (named mfpsA and mfppA) encoding the rare enzymes mannosylfructose-phosphate synthase and mannosylfructose-phosphate phosphatase, an associated phosphohydrolase. The mfpsA and mfppA genes are arranged in an operon structure, whose transcription is up-regulated by NaCl, resulting in the accumulation of mannosylfructose in the cells. Not only is the biosynthesis of mannosylfructose mechanistically similar to that of sucrose, but the corresponding genes for the biosynthesis of both disaccharides are also phylogenetic close relatives. Importantly, a protein phylogeny analysis indicated that mannosylfructose-phosphate synthase defines a unique group of mannosyltransferases.
Chemical definition of an epitope/adhesin molecule on Candida albicans. (1993)

An antigen (Ag), as defined by reactivity with a monoclonal antibody (mAb 10G), was found on the cell wall surface and on the plasma membrane of Candida albicans yeast cells (Li, R. K., and Cutler, J. E. (1991) J. Gen. Microbiol. 137, 455-464). The 10G Ag from the cell surface location was solubilized by treatment with beta-mercaptoethanol and Zymolyase. Antigenic activity of the extract was lost following periodate oxidation, but was stable to proteolytic enzyme and heat treatments. Mannoproteins in the extract were fractionated by hexadecyltrimethylammonium bromide. A fraction containing the 10G Ag was degraded by mild acid hydrolysis and a tetrahexose eluted from a P-2 size exclusion column was found to be the epitope (10G epitope) part of the 10G Ag. By use of gas-liquid chromatography, mass spectroscopy, and H-1 proton NMR analysis, the 10G epitope was determined to be a linear beta-1,2-linked tetramannose. The 10G Ag, which was immunopurified from the Zymolyase extract, and the 10G epitope were involved in the attachment of C. albicans to mouse spleen marginal zone macrophages. Both the 10G Ag and the purified 10G epitope specifically inhibited C. albicans adherence in an ex vivo binding assay. Latex beads adsorbed with the 10G Ag or the 10G epitope adhered specifically to the splenic marginal zone macrophages. These data show that a beta-1,2-linked mannotetraose part of a C. albicans cell wall mannoprotein is an adhesin site that may play a role in pathogenesis of disseminated candidiasis.
New Robot for Power Line Inspection (2008)

Power line inspection is of the utmost importance for the reliability and stability of electric power distribution. However, manual inspection is a hazardous, slow, expensive and unreliable task. Therefore, new highly specialized robots are required to improve the overall quality and safety of the power line inspection. The research conducted so far has been mainly focused on the development of climbing and flying robots. This paper first addresses the main achievements in the field of robotic power line inspection. The proposed solutions are critically assessed and the associated problems are outlined. Based on these findings, a new concept for robot-assisted power line inspection, combining both climbing and flying principles, is proposed in the second part of the paper. The proposed concept is critically assessed and related to the other established concepts so as to demonstrate its advantages and feasibility for a routine power line inspection.
Antibody response that protects against disseminated candidiasis (1995)

We previously showed that surface mannans of Candida albicans function as adhesins during yeast cell attachment to mouse splenic marginal zone macrophages. The mannan adhesin fraction was encapsulated into liposomes and used to vaccinate mice over a 5- to 6-week period. Circulating agglutinins specific for the fraction correlated with increased resistance to disseminated candidiasis. Antiserum from vaccinated animals protected naive BALB/cByJ mice against C. albicans serotype A and B strains and Candida tropicalis. Antiserum also protected SCID mice against disseminated disease. The serum protective ability was stable at 56 degrees C, but this ability was adsorbed by C. albicans cells. The antiserum was divided into three fractions after separation by high-performance liquid chromatography. One fraction contained all of the agglutinin activity and transferred resistance to naive mice. A second fraction also transferred resistance. Two monoclonal antibodies (MAbs) specific for candidal surface determinants were obtained. MAb B6.1 is specific for a mannan epitope in the adhesin fraction, and MAb B6 is specific for a different epitope in the fraction. Both MAbs are immunoglobulin M, and both strongly agglutinate candidal cells, but only MAb B6.1 protected both normal and SCID mice against disseminated candidiasis. In one experiment, 10 normal mice were given MAb B6.1 and challenged with yeast cells. Six mice survived the 67-day observation period; 4 of the survivors were cured as evidenced by the lack of CFU in the kidney and spleen. Our studies show that antibodies against certain cell surface antigens of C. albicans help the host resist disseminated candidiasis.
Modeling the Repertoire of True Tumor-Specific MHC I Epitopes in a Human Tumor (2009)

DNA replication has a finite measurable error rate, net of repair, in all cells. Clonal proliferation of cancer cells leads therefore to accumulation of random mutations. A proportion of these mutational events can create new immunogenic epitopes that, if processed and presented by an MHC allele, may be recognized by the adaptive immune system. Here, we use probability theory to analyze the mutational and epitope composition of a tumor mass in successive division cycles and create a double Pölya model for calculating the number of truly tumor-specific MHC I epitopes in a human tumor. We deduce that depending upon tumor size, the degree of genomic instability and the degree of death within a tumor, human tumors have several tens to low hundreds of new, truly tumor-specific epitopes. Parenthetically, cancer stem cells, due to the asymmetry in their proliferative properties, shall harbor significantly fewer mutations, and therefore significantly fewer immunogenic epitopes. As the overwhelming majority of the mutations in cancer cells are unrelated to malignancy, the mutation-generated epitopes shall be specific for each individual tumor, and constitute the antigenic fingerprint of each tumor. These calculations highlight the benefits for personalization of immunotherapy of human cancer, and in view of the substantial pre-existing antigenic repertoire of tumors, emphasize the enormous potential of therapies that modulate the anti-cancer immune response by liberating it from inhibitory influences.
Range–azimuth-coupling aberrations in pulse-scanned imaging systems (1973)

An aberration peculiar to imaging systems that employ pulse-ranging techniques in one dimension and are conventional in the other is described. The aberration imposes limitations on the resolution achievable. Means for correcting this aberration are given.
The macular pigment. I. Absorbance spectra, localization, and discrimination from other yellow pigments in primate retinas. (1984)

The nonbleaching yellow pigments of the primate fovea were studied by microspectrophotometry (MSP). Retinas fixed with glutaraldehyde/paraformaldehyde mixtures retained yellow pigments with absorbance spectra very similar to those recorded by MSP in fresh retinas. This allowed the authors to prepare retinal sections for localization of the pigments. The spectrum of the macular pigment in fixed tissue is shifted slightly (about 6 nm) toward longer wavelengths, with maximum absorbance at 460 nm. Two short-wavelength yellow pigments also have been identified, with absorbance maxima at 410 nm ( P410 ) and 435 nm ( P435 ), respectively. All three yellow pigments are present in the fovea. The short-wavelength pigments are detected more easily outside the central foveal region because the macular pigment does not obscure them there. They are especially apparent when the MSP beam is confined to the outer nuclear layer or the inner segment layer of retinal sections. The macular pigment is most dense in the fiber layers (receptor axon layer and inner plexiform layer); its density declines markedly with retinal eccentricity. The maximal absorbance of P410 and P435 is usually lower than that of the macular pigment in the central fovea, but their densities and relative proportions change more gradually with eccentricity. Consequently, their maximal absorbance is higher than that of the macular pigment outside the foveal center. The P410 and P435 pigments may be two different oxidation states of one or more respiratory hemoproteins. Commonly used procedures for estimating the absorbance spectrum of the macular pigment by comparing the foveal center with a parafoveal region may be influenced by the amounts and the oxidation states of the short-wavelength pigments in the living eye.
Identification of Proteins Associating with Glycosylphosphatidylinositol- Anchored T-Cadherin on the Surface of Vascular Endothelial Cells: Role for Grp78/BiP in T-Cadherin-Dependent Cell Survival (2008)

There is scant knowledge regarding how cell surface lipid-anchored T-cadherin (T-cad) transmits signals through the plasma membrane to its intracellular targets. This study aimed to identify membrane proteins colocalizing with atypical glycosylphosphatidylinositol (GPI)-anchored T-cad on the surface of endothelial cells and to evaluate their role as signaling adaptors for T-cad. Application of coimmunoprecipitation from endothelial cells expressing c-myc-tagged T-cad and high-performance liquid chromatography revealed putative association of T-cad with the following proteins: glucose-related protein GRP78, GABA-A receptor alpha1 subunit, integrin beta3, and two hypothetical proteins, LOC124245 and FLJ32070. Association of Grp78 and integrin beta3 with T-cad on the cell surface was confirmed by surface biotinylation and reciprocal immunoprecipitation and by confocal microscopy. Use of anti-Grp78 blocking antibodies, Grp78 small interfering RNA, and coexpression of constitutively active Akt demonstrated an essential role for surface Grp78 in T-cad-dependent survival signal transduction via Akt in endothelial cells. The findings herein are relevant in the context of both the identification of transmembrane signaling partners for GPI-anchored T-cad as well as the demonstration of a novel mechanism whereby Grp78 can influence endothelial cell survival as a cell surface signaling receptor rather than an intracellular chaperone.
Human Clara cell 10-kDa protein is the counterpart of rabbit uteroglobin. (1993)

Human Clara cell 10-kDa protein has been suggested to be a counterpart of rabbit uteroglobin, an immunomodulatory and antiinflammatory secretory protein. Since this human protein is not readily available in substantial quantity for detailed characterization of its biochemical, biological, and pharmacological properties, we sought to express it in Escherichia coli in order to study its structure-function relationship. However, bacterial overproduction of homodimeric proteins with interchain disulfide bonds, such as Clara cell 10-kDa protein, was thought to be impossible until we achieved expression of native uteroglobin (Miele, L., Cordella-Miele, E., and Mukherjee, A.B. (1990) J. Biol. Chem. 265, 6427-6435). Here, we report high level production of recombinant native dimeric human Clara cell 10-kDa protein in E. coli and its characterization. Recombinant human Clara cell 10-kDa protein forms its disulfide bonds within the bacterial cytoplasm. The purified protein possesses two of the most important activities characteristic of uteroglobin: (i) it is an excellent substrate of transglutaminase, and (ii) it is a potent inhibitor of porcine pancreatic and, more importantly, human synovial phospholipase A2. These results demonstrate that human Clara cell 10-kDa protein and rabbit uteroglobin have very similar biochemical properties. Our data suggest that this protein may possess immunomodulatory and antiinflammatory activities of potential physiological and pharmacological importance.
CXCR3 Expression and Activation of Eosinophils: Role of IFN-γ-Inducible Protein-10 and Monokine Induced by IFN-γ (2000)

CXC chemokine receptor 3 (CXCR3), predominately expressed on memory/activated T lymphocytes, is a receptor for both IFN-gamma-inducible protein-10 (gamma IP-10) and monokine induced by IFN-gamma (Mig). We report a novel finding that CXCR3 is also expressed on eosinophils. gamma IP-10 and Mig induce eosinophil chemotaxis via CXCR3, as documented by the fact that anti-CXCR3 mAb blocks gamma IP-10- and Mig-induced eosinophil chemotaxis. gamma IP-10- and Mig-induced eosinophil chemotaxis are up- and down-regulated by IL-2 and IL-10, respectively. Correspondingly, CXCR3 protein and mRNA expressions in eosinophils are up- and down-regulated by IL-2 and IL-10, respectively, as detected using flow cytometry, immunocytochemical assay, and a real-time quantitative RT-PCR technique. gamma IP-10 and Mig act eosinophils to induce chemotaxis via the cAMP-dependent protein kinase A signaling pathways. The fact that gamma IP-10 and Mig induce an increase in intracellular calcium in eosinophils confirms that CXCR3 exists on eosinophils. Besides induction to chemotaxis, gamma IP-10 and Mig also activate eosinophils to eosinophil cationic protein release. These results indicate that CXCR3-gamma IP-10 and -Mig receptor-ligand pairs as well as the effects of IL-2 and IL-10 on them may be especially important in the cytokine/chemokine environment for the pathophysiologic events of allergic inflammation, including initiation, progression, and termination in the processes.
Local passive immunization by monoclonal antibodies against streptococcal antigen I/II in the prevention of dental caries (1985)

Local passive immunization with monoclonal antibodies (Mc Ab) to Streptococcus mutans was attempted as an alternative approach to active systemic immunization. We prepared an immunoglobulin G class Mc Ab to the cell surface protein determinant of streptococcal antigen I/II and applied it repeatedly to the teeth of rhesus monkeys. This resulted in decreased colonization by S. mutans in fissures and smooth surfaces of teeth and no dental caries, unlike the results in control animals, which developed caries and showed a high proportion of S. mutans on their teeth. There was no significant difference in serum, salivary, or gingival fluid antibodies to S. mutans between the two groups of animals. Any objections raised over systemic immunization inducing cross-reactive antibodies are therefore overcome by local passive immunization. The mechanism of prevention of colonization has not been established, but we postulate that the Mc Ab which is directed against an important cell surface antigenic determinant of S. mutans (streptococcal antigen I/II) prevents adherence of S. mutans to the acquired pellicle on the tooth surface. S. mutans reacts with the Mc Ab and becomes opsonized, phagocytosed, and killed by the local gingival traffic of neutrophils.
High‐performance functional ecopolymers based on flora and fauna (2007)

Liquid crystalline (LC) polymers of rigid monomers based on flora and fauna were prepared by in-bulk polymerization. Para-coumaric (p-coumaric) acid [4-hydroxycinnamic acid (4HCA)] and its derivatives were selected as phytomonomers and bile acids were selected as biomonomers. The 4HCA homopolymer showed a thermotropic LC phase only in a state of low molecular weight. The copolymers of 4HCA with bile acids such as lithocholic acid (LCA) and cholic acid (CA) showed excellent cell compatibilities but low molecular weights. However, P(4HCA-co-CA)s allowed LC spinning to create molecularly oriented biofibers, presumably due to the chain entanglement that occurs during in-bulk chain propagation into hyperbranching architecture. P[4HCA-co-3,4-dihydroxycinnamic acid (DHCA)]s showed high molecular weight, high mechanical strength, high Young's modulus, and high softening temperature, which may be achieved through the entanglement by in-bulk formation of hyperbranching, rigid structures. P(4HCA-co-DHCA)s showed a smooth hydrolysis, in-soil degradation, and photo-tunable hydrolysis. Thus, P(4HCA-co-DHCA)s might be applied as an environmentally degradable plastic with extremely high performance.