gebhart/patrepeval huggingface dataset:
ApoE is necessary and sufficient for the binding of large triglyceride-rich lipoproteins to the LDL receptor; apoB is unnecessary. (1986)

Large triglyceride-rich very low density lipoproteins (VLDL) Sf 60-400 from hypertriglyceridemic (HTG) patients, but not VLDL from normal subjects, bind to the LDL receptor of human skin fibroblasts because they contain apolipoprotein E (apoE) of the correct conformation, accessible both to the LDL receptor and to specific proteolysis by alpha-thrombin. Trypsin treatment of HTG-VLDL Sf 60-400 causes extensive apoB hydrolysis (fragments less than 100,000 mol wt), total degradation of apoE, and thus complete loss of LDL receptor binding. The reincorporation of apoE (1 mol/mol VLDL) into trypsin-treated HTG-VLDL completely restored the ability of HTG-VLDL to interact with the LDL receptor, suggesting that apoE probably does not induce a conformational change in apoB which results in receptor recognition, nor is intact apoB necessary to maintain the appropriate conformation of apoE for LDL receptor binding. As a model of large triglyceride-rich VLDL Sf greater than 60, we fractionated Intralipid by the Lindgren method of cumulative flotation and prepared apoE-Intralipid complexes. Competitive binding studies demonstrated that apoE-Intralipid is at least as effective as LDL for uptake and degradation of 125I-labeled LDL. Control Intralipid complexes containing apoA-I instead of apoE do not compete with iodinated LDL. Since these TG-rich complexes contain no apoB, apoB is, therefore, not only not sufficient for receptor-mediated uptake of large particles, it is not necessary. ApoE of the correct conformation is not only necessary but is sufficient to mediate receptor binding of large triglyceride-rich particles to the LDL receptor.
A urokinase-activated recombinant diphtheria toxin targeting the granulocyte-macrophage colony-stimulating factor receptor is selectively cytotoxic to human acute myeloid leukemia blasts (2004)

Novel agents to treat acute myeloid leukemia (AML) are needed with increased efficacy and specificity. We have synthesized a dual-specificity fusion toxin DTU2GMCSF composed of the catalytic and translocation domains of diphtheria toxin (DT) fused to the granulocyte-macrophage colony-stimulating factor (GM-CSF) in which the DT furin cleavage site 163RVRRSV170 is modified to a urokinase plasminogen activator (uPA) cleavage site 163GSGRSA170, termed U2. DTU2GMCSF was highly toxic to the TF1-vRaf AML cell line (proliferation inhibition assay; IC50 = 3.14 pM), and this toxicity was greatly inhibited following pretreatment with anti-uPA and anti-GM-CSF antibodies. The activity of this toxin was then tested on a larger group of 13 human AML cell lines; 5 of the 13 cell lines were sensitive to DTU2GMCSF. An additional 5 of the 13 cell lines became sensitive when exogenous pro-uPA was added. Sensitivity to DTU2GMCSF strongly correlated with the expression levels of uPA receptors (uPARs) and GM-CSF receptors (GM-CSFRs) as well as with total uPA levels. DTU2GMCSF was less toxic to normal cells expressing uPAR or GMCSFR alone, that is, human umbilical vein endothelial cells and peripheral macrophages, respectively. These results indicate that DTU2GMCSF may be a selective and potent agent for the treatment of patients with AML.
Induction of Dendritic Cell Differentiation by IFN-α in Systemic Lupus Erythematosus (2001)

Dendritic cells (DCs) are important in regulating both immunity and tolerance. Hence, we hypothesized that systemic lupus erythematosus (SLE), an autoimmune disease characterized by autoreactive B and T cells, may be caused by alterations in the functions of DCs. Consistent with this, monocytes from SLE patients' blood were found to function as antigen-presenting cells, in vitro. Furthermore, serum from SLE patients induced normal monocytes to differentiate into DCs. These DCs could capture antigens from dying cells and present them to CD4-positive T cells. The capacity of SLE patients' serum to induce DC differentiation correlated with disease activity and depended on the actions of interferon-alpha (IFN-alpha). Thus, unabated induction of DCs by IFN-alpha may drive the autoimmune response in SLE.
The kinetics of assembly of normal and variant human oxyhemoglobins. (1987)

The kinetics of assembly have been monitored spectrophotometrically for normal and variant human oxyhemoglobins in 0.1 M Tris, 0.1 M NaCl, 1 mM Na2EDTA, pH 7.4, at 21.5 degrees C. Oxyhemoglobin versus oxy chain static difference spectra were performed and revealed subtle but significant absorption changes in both the visible and Soret regions. Kinetic experiments were performed by rapidly mixing equivalent (in heme) concentrations of alpha and beta A chains and following the change in absorbance at 583 nm with time. Over a protein concentration range of 10-100 microM in heme prior to mixing, these time courses were homogeneous and followed first-order kinetics, yielding a value of 0.069 s-1 for the apparent rate constant of dissociation of oxygenated beta A chain tetramers. Under these conditions, the overall assembly of oxyhemoglobins S (beta 6Glu----Val) and N-Baltimore (beta 95Lys----Glu) were also governed by the rates of dissociation of their respective oxygenated beta S and beta N-Baltimore chain tetramers with the apparent first-order rate constants of 0.044 and 0.15 s-1, respectively. In the Soret region, the alpha, beta monomer combination reaction could be observed if the protein concentration (heme basis) was lowered and if protein nonequivalency (beta chain exceeded alpha chain concentration) mixing experiments were performed. A kinetic oxyhemoglobin A, oxy-alpha, oxy-beta A monomer difference spectrum could be generated, and simple second-order kinetics were observed (415 nm) yielding rate constants of 2.3, 3.3, and 4.8 X 10(5) M-1 s-1 for the assembly of oxyhemoglobins S, A, and N-Baltimore, respectively. To our knowledge, this is the first kinetic study to reveal significant differences between the rate of association of alpha and beta monomers of hemoglobin A and those of two distinctly charged hemoglobin variants.
Cell Type Specific Upregulation of Vascular Endothelial Growth Factor in an MCA-occlusion Model of Cerebral Infarct (1999)

Vascular endothelial growth factor (VEGF) is an endothelial cell specific mitogen that has been implicated in hypoxia-mediated angiogenesis under physiological and pathological conditions. We used the middle cerebral artery occlusion model (MCAO) in the rat to investigate VEGF mRNA and protein localization, and VEGFR-1 mRNA and VEGFR-2 mRNA expression in cerebral ischemia. By nonradioactive in situ hybridization we observed upregulation of VEGF mRNA and VEGFR-1 mRNA, but not of VEGFR-2 mRNA in the hemisphere ipsilateral to MCA occlusion. VEGF mRNA was upregulated in the periphery of the ischemic area commencing 3 hours (h) after onset of MCAO, reached a peak after 24 h, and remained expressed at lower levels until 7 days (d) after MCAO. Double labelling experiments revealed that the majority of VEGF expressing cells in the penumbra and within the infarct were immunoreactive for Ox-42, Iba-1, and Ed1, but not for GFAP and neurofilament proteins, suggesting that microglial cells/macrophages are the major cell type expressing VEGE Since VEGF was also expressed in Ox-42 immunoreactive cells distant from the infarct (e.g. in the corpus callosum and hippocampus), activated microglial cells expressing VEGF may migrate towards the ischemic stimulus. VEGF protein was also detected on capillaries within the peri-ischemic area, suggesting that VEGF produced and secreted by microglial cells/macrophages binds to its receptors on nearby vascular endothelial cells and initiates an angiogenic response which counterbalances tissue hypoxia. Accordingly, apoptosis of neuroectodermal cells in the penumbra was highly depressed after the onset of angiogenesis. The spatial and temporal correlation between the induction of angiogenesis with VEGF and VEGFR-1 expression suggests that the ischemic upregulation of VEGF represents a physiological response of the brain to counterbalance hypoxia/ischemia in order to protect neuroectodermal tissue.
The Genome Sequence of the SARS-Associated Coronavirus (2003)

We sequenced the 29,751-base genome of the severe acute respiratory syndrome (SARS)-associated coronavirus known as the Tor2 isolate. The genome sequence reveals that this coronavirus is only moderately related to other known coronaviruses, including two human coronaviruses, HCoV-OC43 and HCoV-229E. Phylogenetic analysis of the predicted viral proteins indicates that the virus does not closely resemble any of the three previously known groups of coronaviruses. The genome sequence will aid in the diagnosis of SARS virus infection in humans and potential animal hosts (using polymerase chain reaction and immunological tests), in the development of antivirals (including neutralizing antibodies), and in the identification of putative epitopes for vaccine development.
Pharmacological and immunocytochemical characterization of metabotropic glutamate receptors in cultured Purkinje cells (1992)

Metabotropic glutamate receptor (mGluR) is highly expressed in cerebellar Purkinje cells. The purpose of this study was pharmacological and immunocytochemical characterization of the mGluR in single cerebellar neurons, especially Purkinje cells. Ca2+ imaging with fura-2 in cultured cerebellar neurons, identified immunocytochemically, was used to record the direct effects of drugs in stable conditions. In addition, the expression of mGluR was examined, and expression of the intracellular receptor for inositol trisphosphate (IP3) produced by mGluR activation was studied immunocytochemically with specific antibodies. Purkinje neurons and some other neurons showed Ca(2+)-mobilizing responses to mGluR agonists. These responses were mediated by mGluR because they were not blocked by ionotropic GluR antagonists, were independent of the caffeine-sensitive Ca2+ pool, and were blocked by inhibitors of IP3-induced Ca2+ release. This is the first pharmacological characterization of mGluR at single Purkinje cells. The results differed as follows from those in earlier studies in which phosphoinositide turnover of the entire population of cerebellar cells was monitored: (1) the mGluR responses were not blocked by pertussis toxin or D,L-2-amino-3-phosphonopropionic acid; (2) glutamate was a potent agonist, whereas L-aspartate was ineffective; and (3) the dose-response relationship showed an all-or-none tendency. The metaboltropic response of Purkinje cells changed markedly during development, with a sharp peak after day 4 of culture, whereas mGluR and IP3 receptor proteins increased steadily during maturation. This apparent desensitization of mGluR was not blocked by inhibitors of protein kinase C (PKC) or ADP-ribosyltransferase. The metabotropic responses were mainly localized to the center of the somata of Purkinje cells even on day 4, whereas both receptor proteins were expressed throughout the cell. These results suggest that the function of mGluR is spatially and developmentally controlled by a posttranslational mechanism involving a mechanism other than phosphorylation by PKC or ADP-ribosylation.
Characterization of SP1, a Stress-Responsive, Boiling-Soluble, Homo-Oligomeric Protein from Aspen (2002)

sp1 cDNA was isolated from aspen (Populus tremula) plants by immunoscreening an expression library using polyclonal antibodies against BspA protein. BspA, which is a boiling-stable protein, accumulates in aspen plants in response to water stress and abscisic acid application (Pelah et al., 1995). The sp1 cDNA was found to encode a 12.4-kD generally hydrophilic protein with a hydrophobic C terminus, which is different from the BspA protein and was termed SP1 (stable protein 1). Northern-blot analysis revealed that sp1 encodes a small mRNA (about 0.6 kb) that is expressed in aspen plants under non-stress conditions and is accumulated after salt, cold, heat, and desiccation stress, and during the recovery from stress. The SP1 detected in plants remained soluble upon boiling, migrated both as a 12.4-kD band and a much higher mass of 116 kD on a 17% (w/v) Tricine-sodium dodecyl sulfate-polyacrylamide gel. Comparative protease digestion patterns, amino acid analyses, and the N-terminal sequences of the 12.4- and 116-kD proteins revealed that SP1 is homo-oligomeric. Furthermore, gel filtration chromatography analysis indicated that SP1 exists in aspen plants as a complex, composed of 12 subunits of 12.4 kD. A large number of sequences deduced from expressed sequence tags and genomic sequences of other organisms with unknown function show high homology to SP1. Thus, SP1 may represent a new protein family. Here, we present the first report on this putative protein family: the cloning, isolation, and characterization of SP1, a stress-responsive, boiling-soluble, oligomeric protein.
Functionalities for automatic metadata generation applications: a survey of metadata experts' opinions (2006)

This paper reports on the automatic metadata generation applications (AMeGA) project's metadata expert survey. Automatic metadata generation research is reviewed and the study's methods, key findings and conclusions are presented. Participants anticipate greater accuracy with automatic techniques for technical metadata (e.g., ID, language, and format metadata) compared to metadata requiring intellectual discretion (e.g., subject and description metadata). Support for implementing automatic techniques paralleled anticipated accuracy results. Metadata experts are in favour of using automatic techniques, although they are generally not in favour of eliminating human evaluation or production for the more intellectually demanding metadata. Results are incorporated into Version 1.0 of the Recommended Functionalities for automatic metadata generation applications (Appendix A).
Complete Enantiomeric Separation of Phenylthiocarbamoylated Amino Acids on a Tandem Column of Reversed and Chiral Stationary Phases (1997)

The enantiomeric separation of phenylthiocarbamoyl derivatives of amino acids (PTC-AAs) was studied on a series of reversed phase HPLC columns coupled to the chiral phase HPLC columns. First, the five chiral phases (native, 0.2, 3.3, 7.5 and 16.9 phenylcarbamoylated/β-cyclodextrins, Ph/CD) were newly prepared by modification of β-cyclodextrin with phenyl isocyanate and were examined for the enantiomeric separation of PTC-AAs. Among them, the 3.3Ph/CD phase gave the best enantiomeric separation (α ≥ 1.04). However, the separation of the individual PTC-AAs was not sufficient. Next, these separations were investigated on various reversed phase HPLC columns, and octyl silica was selected in terms of the suitability of the mobile phase adopted for the enantiomeric separation mentioned above. The effects of the column temperature, the ion-pairing reagent, and the final content of methanol were also studied on the tandem column of octyl silica and the 3.3Ph/CD phase. Under the best conditions (100 mM ammonium acetate (pH 6.5) containing 1 mM butanesulfonate with 0-40% methanol as the mobile phase), all the individual PTC-AAs were well separated within 150 min. The applicability of the method was demonstrated by the sequence/configuration analysis of a peptide containing a d-amino acid ([d-Thr(2)]leucine enkephalin-Thr).
Application containers without virtual machines (2009)

This position paper introduces lightweight cryptographic jails (CryptoJails) that protect the privacy of application data by intercepting write accesses and redirecting them to encrypted application containers. CryptoJails ensure that application data (for example, cached emails or web pages) cannot be read or undetectably altered by other applications. Unlike existing approaches, CryptoJails do not require kernel modifications or even superuser (i.e., root) privileges, do not impose significant performance overhead, and may even be used with already installed applications.
Pharmacological activity and toxicity of apyramide: comparison with non-steroidal anti-inflammatory agents. (1987)

An experimental and comparative study was conducted on 1-(p-chlorobenzoyl)-2-methyl-5-methoxyindole-3-p-acetamidophenol acetate (Apyramide) and known anti-inflammatory agents. Apyramide was far less toxic than indomethacin in rats and mice by the oral or the i.p. route. It exhibited anti-inflammatory activity on carrageenin-induced paw oedema, cotton pellet granuloma and adjuvant arthritis, as well as analgesic and antipyretic activities. The acute ulcerogenic effect of Apyramide was lower than that of indomethacin.
Failure of aminoglycoside antibiotics to kill anaerobic, low-pH, and resistant cultures (1988)

The critical inhibition of ribosome function by aminoglycosides has long been established. But the binding of drug to ribosomes is reversible: why then are aminoglycosides bactericidal? Several groups have shown that irreversible action (lethality) results from irreversible uptake into susceptible cells; conversely, resistance in cases such as anaerobiosis is associated with the failure of uptake. Oddly, the pattern of results excludes all traditional transport mechanisms; most unusual is the apparent dependence of uptake on the interaction of drug with ribosomes. A traditional view that ribosomes may function during uptake as a "sink" for aminoglycosides cannot explain all the data. Instead, the alternative is considered that cycling ribosomes at the cell membrane help to induce "one-way endocytic pores." Although no detailed mechanism is formulated, the results do suggest a way that the permeation of antibiotics might be systematically controllable to render them more cidal.
Self-Assembled Monolayer Growth of Octadecylphosphonic Acid on Mica (1996)

Self-assembled monolayers are formed by exposing freshly cleaved mica to a solution of octadecylphosphonic acid in tetrahydrofuran. Atomic force microscope images of samples immersed in solution for varying exposure times show that prior to forming a complete monolayer the molecules aggregate into dense islands (1.8 ± 0.2 nm high) on the surface. The islands have a compact, rounded morphology. The cosine of the contact angle between hexadecane and the partial monolayers has an approximately linear dependence on coverage. However, the cosine of the contact angle of water decreases linearly to about 50% coverage (the percolation threshold of the phosphonate islands) and then appears to saturate.
Respiratory quinone profile as a tool for refractory chemical biodegradation study (1997)

The respiratory quinone profile was successfully used as a tool for identifying the change of bacterial phase in the microbial film of aerobic submerged biofilter treating refractory chemicals such as dimethylformamide (DMF). It was ascertained that the coexistence of easily biodegradable substances such as glucose and peptone hindered the acclimation of bacteria inhabiting the microbial film in biofilter to DMF. The higher initial microbial concentration and the feeding of DMF as a sole organic substance accelerated the acclimation of microbial film to DMF. Appreciable changes in quinone profile were detected through the acclimation to DMF, and the results showed that DMF degrading bacteria such as Methylobacterium and Mycobacterium had grown in the biofilter.
Nanoscale Energy Deposition by X-ray Absorbing Nanostructures (2007)

Here we wish to demonstrate a unique property of nanomaterials: energy deposition with nanometer precision from low-energy electrons released from these nanostructures interacting with hard X-ray radiation in aqueous solution. Three effects combine to cause this phenomenon: (1) localized absorption of X-rays by nanostructures, (2) effective release of low-energy electrons from small nanostructures, and (3) efficient deposition of energy in water in the form of radicals and electrons. This combination creates localized X-ray absorption and localized energy deposition of nanometer precision. We confirmed the theoretically predicted nanoscale energy deposition distribution by measuring hydroxyl radical-induced DNA strand breaks, and observed enhanced damage to a 5600-bp DNA molecule from approximately 10 chemically conjugated small gold nanoparticles under X-ray radiation. These results provide a general guidance to applications of this new concept in many fields including radiation chemistry, radiology, radiation oncology, biochemistry, biology, and nanotechnology.
Optimization of All-to-All Communication on the Blue Gene/L Supercomputer (2008)

All-to-all communication is a well known performance bottleneck for many applications, such as the ones that use the Fast-Fourier-transform (FFT) algorithm. We analyze the performance of all-to-all communication on the BlueGene/L torus interconnect that has link contention even for all-to-all operations with short messages. We observed that the performance of all-to-all depends on the shape of the processor partition. We present a performance analysis of all-to-all on partitions of various shapes. We then present optimization schemes that substantially improve the performance of all-to-all with short and large messages.In particular, throughput improved from 64% to over 99% of peak on the 65,536 (64 times 32 times 32) node Blue Gene/L machine at the Lawrence Livermore National Lab. We show the impact of the all-to-all performance optimizations in 1-D and 3-D FFT benchmarks. We achieved a performance of over 2.8 TF for the HPC Challenge 1D FFT benchmark with our optimized all-to-all.
Estrogen Receptor-Associated Proteins: Possible Mediators of Hormone-Induced Transcription (1994)

The estrogen receptor is a transcription factor which, when bound to estradiol, binds DNA and regulates expression of estrogen-responsive genes. A 160-kilodalton estrogen receptor-associated protein, ERAP160, was identified that exhibits estradiol-dependent binding to the receptor. Mutational analysis of the receptor shows that its ability to activate transcription parallels its ability to bind ERAP160. Antiestrogens are unable to promote ERAP160 binding and can block the estrogen-dependent interaction of the receptor and ERAP160 in a dose-dependent manner. This evidence suggests that ERAP160 may mediate estradiol-dependent transcriptional activation by the estrogen receptor. Furthermore, the ability of antiestrogens to block estrogen receptor-ERAP160 complex formation could account for their therapeutic effects in breast cancer.
The role of manganese superoxide dismutase in health and disease (1998)

Manganese superoxide dismutase (MnSOD) is the mitochondrial enzyme that disposes of superoxide generated by respiratory chain activity. Of all electrons passing down the mitochondrial respiratory chain, 1-2% are diverted to form superoxide; thus production of hydrogen peroxide occurs at a constant rate due to MnSOD activity. Mice lacking MnSOD develop cardiomyopathy and basal ganglia lesions, have no lipid peroxidation products, but show destruction of enzymes with 4Fe-4S centres. Patients with complex I (NADH-CoQ oxidoreductase) deficiency show variable hyperinduction of MnSOD that is at least partially dependent on the extent of disturbance of redox state. This in turn appears to result in production of excess hydroxyl radicals, which are damaging to proteins, lipids and DNA. An alternative method of protection from oxygen radicals is employed by complex I-deficient cell types that do not induce MnSOD in that they show induction of the bcl-2 protein.