gebhart/patrepeval huggingface dataset:
Mechanism of pH-dependentN-Acetylgalactosamine Binding by a Functional Mimic of the Hepatocyte Asialoglycoprotein Receptor (2000)

Efficient release of ligands from the Ca(2+)-dependent carbohydrate-recognition domain (CRD) of the hepatic asialoglycoprotein receptor at endosomal pH requires a small set of conserved amino acids that includes a critical histidine residue. When these residues are incorporated at corresponding positions in an homologous galactose-binding derivative of serum mannose-binding protein, the pH dependence of ligand binding becomes more like that of the receptor. The modified CRD displays 40-fold preferential binding to N-acetylgalactosamine compared with galactose, making it a good functional mimic of the asialoglycoprotein receptor. In the crystal structure of the modified CRD bound to N-acetylgalactosamine, the histidine (His(202)) contacts the 2-acetamido methyl group and also participates in a network of interactions involving Asp(212), Arg(216), and Tyr(218) that positions a water molecule in a hydrogen bond with the sugar amide group. These interactions appear to produce the preference for N-acetylgalactosamine over galactose and are also likely to influence the pK(a) of His(202). Protonation of His(202) would disrupt its interaction with an asparagine that serves as a ligand for Ca(2+) and sugar. The structure of the modified CRD without sugar displays several different conformations that may represent structures of intermediates in the release of Ca(2+) and sugar ligands caused by protonation of His(202).
One-shot vaccination with an insect cell-derived low-dose influenza A H7 virus-like particle preparation protects mice against H7N9 challenge (2013)

Human infections with a novel influenza A H7N9 subtype virus were reported in China recently. The virus caused severe disease with high mortality rates and it raised concerns over its pandemic potential. Here, we assessed in the mouse model protective efficacy of single immunisations with low vaccine doses of insect cell-derived H7 virus-like particles, consisting of hemagglutinin and matrix protein. Vaccinated mice were fully protected and survived a stringent lethal challenge (100 mLD50) with H7N9, even after a single, unadjuvanted, low vaccine dose (0.03 μg). Serum analysis revealed broad reactivity and hemagglutination inhibition activity across a panel of divergent H7 strains. Moreover, we detected significant levels of cross-reactivity to related group 2 hemagglutinins. These data demonstrate that virus-like particle vaccines have the potential to induce broadly protective immunity against the novel H7N9 virus and a variety of other H7 strains.
Cell cycle and cell size dependence of susceptibility to hydrodynamic forces (1995)

Exposure of animal cells to intense hydrodynamic forces exerted in turbulent capillary flow, and by controiled agitation and aeration, resulted in preferential destruction of S and G(2) cells and the extent of destruction of these cells was dependent upon the intensity of the action. The loss of these cells was possibly due to their larger size. However, the appearance of large numbers of membrane-bound vesicular structures similar to apoptotic bodies as well as cells with low DNA stainability (in a sub-G(1) peak) suggested that the action of adverse hydrodynamic forces on these large cells may at least in part be to induce an apoptotic response. (c) 1995 John Wiley & Sons, Inc.
Accumulation of 15-Kilodalton Zein in Novel Protein Bodies in Transgenic Tobacco (1995)

Zeins, the seed storage proteins of maize, are a group of alcohol-soluble polypeptides of different molecular masses that share a similar amino acid composition but vary in their sulfur amino acid composition. They are synthesized on the rough endoplasmic reticulum (ER) in the endosperm and are stored in ER-derived protein bodies. Our goal is to balance the amino acid composition of the methionine-deficient forage legumes by expressing the sulfur amino acid-rich 15-kD zeins in their leaves. However, it is crucial to know whether this protein would be stable in nonseed tissues of transgenic plants. The major focus of this paper is to compare the accumulation pattern of the 15-kD zein protein with a vacuolar targeted seed protein, [beta]-phaseolin, in nonseed tissues and to determine the basis for its stability/instability. We have introduced the 15-kD zein and bean [beta]-phaseolin-coding sequences behind the 35S cauliflower mosaic virus promoter into tobacco (Nicotiana tabacum) and analyzed the protein's accumulation pattern in different tissues. Our results demonstrate that the 15-kD seed protein is stable not only in seeds but in all nonseed tissues tested, whereas the [beta]-phaseolin protein accumulated only in mid- and postmaturation seeds. Interestingly, zein accumulates in novel protein bodies both in the seeds and in nonseed tissues. We attribute the instability of the [beta]-phaseolin protein in nonseed tissues to the fact that it is targeted to protease-rich vacuoles. The stability of the 15-kD zein could be attributed to its retention in the ER or to the protease-resistant nature of the protein.
Liver Transplantation in European Patients with the Hepatitis B Surface Antigen (1993)

In this retrospective study of HBsAg-positive patients, liver transplantation had better results in those who had fulminant hepatitis or delta virus superinfection. An absence of viral replication at the time of transplantation and long-term immunoprophylaxis were associated with a reduced risk of recurrent HBV infection and reduced mortality.
EcoGene 3.0 (2012)

EcoGene (http://ecogene.org) is a database and website devoted to continuously improving the structural and functional annotation of Escherichia coli K-12, one of the most well understood model organisms, represented by the MG1655(Seq) genome sequence and annotations. Major improvements to EcoGene in the past decade include (i) graphic presentations of genome map features; (ii) ability to design Boolean queries and Venn diagrams from EcoArray, EcoTopics or user-provided GeneSets; (iii) the genome-wide clone and deletion primer design tool, PrimerPairs; (iv) sequence searches using a customized EcoBLAST; (v) a Cross Reference table of synonymous gene and protein identifiers; (vi) proteome-wide indexing with GO terms; (vii) EcoTools access to >2000 complete bacterial genomes in EcoGene-RefSeq; (viii) establishment of a MySql relational database; and (ix) use of web content management systems. The biomedical literature is surveyed daily to provide citation and gene function updates. As of September 2012, the review of 37 397 abstracts and articles led to creation of 98 425 PubMed-Gene links and 5415 PubMed-Topic links. Annotation updates to Genbank U00096 are transmitted from EcoGene to NCBI. Experimental verifications include confirmation of a CTG start codon, pseudogene restoration and quality assurance of the Keio strain collection.
Identification of a Nuclear Localization Signal in OCT4 and Generation of a Dominant Negative Mutant by Its Ablation (2004)

OCT4 plays a critical role in maintaining stem cell pluripotency in a dose-dependent manner by activating and repressing multiple downstream genes. The precise mechanism by which OCT4 achieves these diverse biological functions remains unknown. In this report, we identify and characterize (195)RKRKR as a nuclear localization signal responsible for its localization in the nuclei and required for the transactivation of its target genes. Point mutations within this motif yielded a mutant that localizes randomly throughout the cells and is defective in transactivating target genes. However, restoration of nuclear localization with a heterologous nuclear localization signal failed to rescue its transactivation function, suggesting that this (195)RKRKR motif has additional function in mediating transactivation function. We further demonstrate that this mutant is competent in dimerization with not only itself but also wild type OCT4 and can interfere with the activity of wild type OCT4, thus acting as a dominant negative mutant. Indeed, this mutant can induce the differentiation of P19 cells into trophoblast-like giant cells. These data suggest that this dominant negative form of OCT4 may be a useful tool for modulating the activity of OCT4 in pluripotent cells such as embryonic stem cells to achieve the desired cell types for therapeutic applications.
Star pinch scalable EUV source (2003)

A new direct discharge source of 13.5nm radiation addresses the heat load problem by creating the plasma remote from all surfaces. The plasma is initially formed at the intersection of many pulsed xenon beamlets. Further heating is then applied via a high current pulse to induce efficient radiation from Xe<sup>10+</sup> ions. The plasma is compact, with a single pulse FWHM diameter of 0.7mm and length of 3mm. It is positionally stable, as illustrated by re-imaging onto a fluorescent screen sensitive to EUV and time-integrating over 250 pulses. In this mode the averaged FWHM is 0.9mm. The conversion efficiency from stored electrical energy to radiation within 2&pi; sterad and 2% bandwidth at 13.5nm is currently 0.55%, using xenon. Power is delivered to the plasma by a solid state-switched modulator operated at a stored energy of 25J of which 10J is dissipated in the plasma plus circuit, and 15J is recovered. The EUV output in 2% bandwidth at 13.5nm is 9mJ/sterad. Repetition rate scaling of the star pinch EUV source to 1kHz there is negligible electrode erosion at 10<sup>6</sup> pulses. This is possible because the cathode for the main heating discharge is distributed into 24-fold parallel hollow cathodes, with a combined operational surface aera of approximately 20cm<sup>2</sup>. The anode is similarly distributed. The walls facing the plasma are 22mm distant from it and when scaled to 6kHz will see a heat load of less than 1kWcm<sup>-2</sup>. The cathode electrode is then expected to receive a heat load of less than 500W cm<sup>-2</sup>. The plasma is expected to clear between pulses and be reproducible at frequencies up to at least 10kHz, at which rate the usable EUV power available at a second focus, assuming colleciton in 2sterad, is predicted to be more than 80W. The star pinch has properties that favor long life and appears to scale to the 50-100W powers needed for high throughput lithography.
Differences in the Crosslinking Activities of Native and Recombinant Erythrina corallodendron Lectin with Asialofetuin. Evidence for Carbohydrate-Carbohydrate Interactions in Lectin-Glycoprotein Complexes (1994)

A previous study showed that several multivalent galactose-specific lectins including the 14-kDa lectin from calf spleen and the lectins from Erythrina indica, Erythrina cristagalli, and soybean agglutinin formed specific cross-linked complexes with the glycoprotein asialofetuin (ASF) [Mandal, D. K., & Brewer, C. F. (1992) Biochemistry 31, 8465-8472]. In the present study, we have used quantitative precipitation analysis to compare the cross-linking activities of the Gal/GalNAc-specific lectin from Erythrina corallodendron (ECorL) and the recombinant protein (rECorL) which lacks the covalently linked heptasaccharide chains of the native lectin, with ASF. At low concentrations of ASF relative to the lectin, native dimeric ECorL binds to each of the three terminal Gal residues of the three N-linked triantennary chains of ASF and precipitates as a cross-linked complex at a ratio of 1:9 ASF/lectin (monomer). With increasing concentrations of ASF, the 1:9 complex changes to a 1:3 ASF/lectin complex, and at higher ASF concentrations, a 1:1 cross-linked complex forms. However, rECorL, which possesses the same specificity and binding affinity as the native lectin, forms only the 1:9 and 1:3 ASF/lectin complexes. Other Erythrina lectins examined, all of which have covalently attached carbohydrate and are structurally similar to ECorL, show the same cross-linking behavior as native ECorL. On the other hand, the dimeric 14-kDa calf spleen lectin which lacks covalently attached carbohydrate forms only 1:9 and 1:3 cross-linked complexes with ASF [Mandal, D. K., & Brewer, C. F. (1992) Biochemistry 31, 8465-8472].(ABSTRACT TRUNCATED AT 250 WORDS)
The Changing Face of Staphylococcus aureus: A Continuing Surgical Challenge (2011)

Staphylococcus aureus continues to be a major pathogen for surgical patients. The scope of infections has expanded recently to include toxic shock syndrome, severe community-acquired soft tissue infections with unique virulence characteristics, and highly resistant pathogens. The adaptability of the organism requires that new prevention and treatment strategies be developed continuously to meet the challenge of future infections.
Vitamin B12and folate in relation to the development of Alzheimer’s disease (2001)

<b><i>Objective: </i></b> To explore the associations of low serum levels of vitamin B<sub>12</sub> and folate with AD occurrence. <b><i>Methods:</i></b> A population-based longitudinal study in Sweden, the Kungsholmen Project. A random sample of 370 nondemented persons, aged 75 years and older and not treated with B<sub>12</sub> and folate, was followed for 3 years to detect incident AD cases. Two cut-off points were used to define low levels of vitamin B<sub>12</sub> (≤150 and ≤250 pmol/L) and folate (≤10 and ≤12 nmol/L), and all analyses were performed using both definitions. AD and other types of dementia were diagnosed by specialists according to DSM-III-R criteria. <b><i>Results:</i></b> When using B<sub>12</sub> ≤150pmol/L and folate ≤10 nmol/L to define low levels, compared with people with normal levels of both vitamins, subjects with low levels of B<sub>12</sub><i>or</i> folate had twice higher risks of developing AD (relative risk [RR] = 2.1, 95% CI = 1.2 to 3.5). These associations were even stronger in subjects with good baseline cognition (RR = 3.1, 95% CI = 1.1 to 8.4). Similar relative risks of AD were found in subjects with low levels of B<sub>12</sub><i>or</i> folate and among those with both vitamins at low levels. A comparable pattern was detected when low vitamin levels were defined as B<sub>12</sub> ≤250 pmol/L and folate ≤12 nmol/L. <b><i>Conclusions:</i></b> This study suggests that vitamin B<sub>12</sub> and folate may be involved in the development of AD. A clear association was detected only when both vitamins were taken into account, especially among the cognitively intact subjects. No interaction was found between the two vitamins. Monitoring serum B<sub>12</sub> and folate concentration in the elderly may be relevant for prevention of AD.
Multiple discrete encephalitogenic epitopes of the autoantigen myelin basic protein include a determinant for I-E class II-restricted T cells. (1988)

Immunization with the autoantigen myelin basic protein (MBP) causes experimental allergic encephalomyelitis (EAE). Initial investigations indicated that encephalitogenic murine determinants of MBP were located only within MBP 1-37 and MBP 89-169. Encephalitogenic T cell epitopes within these fragments have been identified. Each epitope is recognized by T cells in association with separate allelic I-A molecules. A hybrid I-E-restricted T cell clone that recognizes intact mouse (self) MBP has been examined. The epitope recognized by this clone includes MBP residues 35-47. When tested in vivo, p35-47 causes EAE. T cell recognition of p35-47 occurs only in association with I-E molecules. These results provide the first clear example that antigen-specific T cells restricted by I-E class II molecules participate in murine autoimmune disease. Furthermore, it is clear that there are multiple (at least three) discrete encephalitogenic T cell epitopes of this autoantigen, each recognized in association with separate allelic class II molecules. These results may be relevant to human autoimmune diseases whose susceptibility is associated with more than one HLA-D molecule.
Molecular Modeling on the PC (1997)

Introduction to Molecular Modeling PC Molecular Modeling Hardware and Software Input and Output Input File Formats The Molecular Mechanics Force Field Applications Appendices References Index.
4-[(3-Bromo-4-hydroxyphenyl)amino]-6,7-dimethoxyquinazolin-1-ium chloride methanol solvate and 4-[(3-hydroxyphenyl)amino]-6,7-dimethoxy-1-quinazolinium chloride (2001)

The title compounds, C16H15BrN3(O3)(+).Cl(-).CH4O (WHI-P154) and C16H16N3(O3)(+).Cl(-) (WHI-P180), are potent inhibitors [WHI-P154 with IC50 = 5.6 microM and WHI-P180 with IC50 = 4.0 microM for epidermal growth factor receptor (EGFR) kinase inhibition] of the EGFR tyrosine kinase as well as Janus Kinase 3. The molecular structures of these compounds are very similar except for the dihedral angle between the anilino and quinazoline moieties which is 1.10 (5) degrees for WHI-P154, and 45.66 (6) and 25.29 (7) degrees for the two molecules of WHI-P180 in the asymmetric unit. The nitrogen at the N3 position is protonated in both structures and participates in hydrogen bonding with the chlorine anions.
The anti-CD30 monoclonal antibody SGN-30 promotes growth arrest and DNA fragmentation in vitro and affects antitumor activity in models of Hodgkin's disease. (2002)

The leukocyte activation marker CD30 is highly expressed on the Reed Sternberg cells of Hodgkin's disease (HD). On normal tissues, CD30 has a restricted expression profile limited to activated T cells, activated B cells, and activated natural killer cells. This expression profile makes CD30 an ideal target for monoclonal antibody (mAb)-based therapies of Hodgkin's disease. CD30 mAbs have been shown to be effective in in vitro and in vivo models of hematologic malignancies such as anaplastic large cell lymphoma, yet these mAb have not been efficacious in HD models. We have found that a mAb against CD30, AC10, was able to inhibit the growth of HD cell lines in vitro. To generate a more clinically relevant molecule, the variable regions from AC10 were cloned into an expression construct containing the human gamma1 heavy chain and kappa light chain constant regions. The resulting chimeric antibody, designated SGN-30, retained the binding and in vitro growth-inhibitory activities of the parental antibody. Treatment of HD cell lines with SGN-30 in vitro resulted in growth arrest in the G(1) phase of the cell cycle and DNA fragmentation consistent with apoptosis in the HD line L540cy. Severe combined immunodeficient mouse xenograft models of disseminated HD treated with SGN-30 produced significant increases in survival. Similarly, xenograft models of localized HD demonstrated dose-dependent reduction in tumor mass in response to SGN-30 therapy. SGN-30 is being developed for the treatment of patients who have HD that is refractory to initial treatment or who have relapsed and have limited therapeutic options.
Preparation and purification of Flavobacterium heparinum chondroitinases AC and B by hydrophobic interaction chromatography (1999)

Flavobacterium heparinum is a soil bacterium that produces several mucopolysaccharidases such as heparinase, heparitinases I and II, and chondroitinases AC, B, C and ABC. The purpose of the present study was to optimize the preparation of F. heparinum chondroitinases, which are very useful tools for the identification and structural characterization of chondroitin and dermatan sulfates. We observed that during the routine procedure for cell disruption (ultrasound, 100 kHz, 5 min) some of the chondroitinase B activity was lost. Using milder conditions (2 min), most of the chondroitinase B and AC protein was solubilized and the enzyme activities were preserved. Tryptic soy broth without glucose was the best culture medium both for bacterial growth and enzyme induction. Chondroitinases AC and B were separated from each other and also from glucuronidases and sulfatases by hydrophobic interaction chromatography on HP Phenyl-Sepharose. A rapid method for screening of the column fractions was also developed based on the metachromatic shift of the color of dimethylmethylene blue.
3D printing and international security: risks and challenges of an emerging technology (2017)

"3D printing - or additive manufacturing - is a challenging dual-use technology: One and the same device can print toys or guns. The author explains the basics of the technology, describes its current applications, and provides an overview of its global diffusion. He shows the potential of this emerging technology and analyzes its possible risks with respect to the pro­lif­eration of small arms, major weapon systems, and even weapons of mass destruction. He investigates how 3D printing might pose serious challenges to national and international security. The author discusses first proposals of risk mitigation through safeguards, export controls, cyber security, awareness raising, and industry self-regulation." (author's abstract)
Mannose-binding lectin enhances phagocytosis and killing ofNeisseria meningitidisby human macrophages (2004)

Deficiency of mannose-binding lectin (MBL) is probably the most common human immunodeficiency and is associated with an increased risk of mucosally acquired infections including meningococcal disease. Tissue macrophages are an important component of mucosal defense, and so we determined the effect of MBL on uptake of meningococci by human monocyte-derived macrophages. Opsonization with MBL significantly increased the capture and doubled the amount of internalization of Neisseria meningitidis. Inhibition of f-actin polymerization indicated that MBL exerted this effect by a dose-dependent acceleration of uptake into phagosomes, which was maximal within the normal physiological concentration of MBL (1.5 microg/ml) and was independent of scavenger receptors. MBL accelerated the acquisition and subsequent loss of the early endosome marker, early endosomal antigen-1, and enhanced the acquisition of the late endosomal marker, lysosome-associated membrane protein-1. MBL reduced the survival of meningococci within macrophages by more than half, despite the increased uptake of organisms, and significantly reduced the number of viable extracellular bacteria by 80%. We conclude that MBL is a dependent opsonin able to accelerate microbial uptake and killing. These results suggest that MBL could modify disease susceptibility by modulating macrophage interactions with mucosal organisms at the site of initial acquisition.