gebhart/patrepeval huggingface dataset:
Extended Release Antibacterial Layer-by-Layer Films Incorporating Linear-Dendritic Block Copolymer Micelles (2007)

The electrostatic layer-by-layer (LbL) assembly approach offers large potential in the area of drug delivery from thin films; however, because the processing technique is aqueous-based, there have been few strategies proposed to incorporate hydrophobic molecules into these films. Here we create an LbL film that is capable of incorporating hydrophobic drug at high loadings via encapsulation with linear-dendritic block copolymer micelles and demonstrate for the first time release times of a hydrophobic antibacterial agent over a period of several weeksa significant improvement over reports of other micelle-encapsulated thin films with release times of several minutes. The amphiphilic linear-dendritic block copolymer is composed of poly(propylene oxide) (PPO), which forms the hydrophobic core creating the compartment for hydrophobic drug encapsulation, and poly(amidoamine) (PAMAM), which forms the outer corona of the micelle. The PAMAM is polycationic, enabling LbL deposition with negatively charged poly(acrylic acid) (PAA). The stable PPO−PAMAM micelles incorporated into the LbL films encapsulated a hydrophobic bactericide, triclosan, which have loading capacities as high as 80−90%. Film thickness and UV−vis measurements confirm the formation of the LbL film and incorporation of triclosan into the film. Fluorescence measurements of PPO−PAMAM/PAA films with pyrene indicated the presence of hydrophobic domains in the film. GISAXS revealed regular spacing of approximately 10.5 nm in the direction parallel to the film substrate, which is approximately the same size as the PPO−PAMAM micelles in aqueous solution. Volume fraction measurements based on elemental analysis and TGA confirm the GISAXS data. An in vitro release study revealed long release times of triclosan on the order of weeks, and a Kirby Bauer test was performed on Staphylococcus aureus, demonstrating that the drug released was still active to inhibit the growth of bacteria.
Increased frequency of NGF in sera of rheumatoid arthritis and systemic lupus erythematosus patients (1993)

Nerve growth factor (NGF) levels were measured by a two-site enzyme-linked immunosorbent assay (ELISA) in sera of patients with three autoimmune diseases, rheumatoid arthritis (RA), systemic lupus erythematosus (SLE) and thyroiditis. Serum NGF levels were variable (15 pg ml(-1)-1.6 ng ml-1) but not significantly different among these groups compared with control subjects. However the frequency of detectable circulating NGF was significantly higher in RA and SLE patients but not in thyroiditis patients compared with controls. The present data provides evidence for NGF involvement in two autoimmune rheumatic diseases and suggests a possible differential role of NGF as immunomodulatory agent in systemic versus certain organ-specific autoimmune diseases.
The coated pit and macropinocytic pathways serve distinct endosome populations (1994)

Clathrin-coated vesicle endocytosis and macropinocytosis are distinct endocytic pathways demonstrable in several cell types including human epidermoid A431 cells (West, M.A., M.S. Bretscher, and C. Watts. 1989. J. Cell Biol. 109:2731-2739). Here we analyze the extent of mixing of macropinocytic endosome (macropinosome) content with that of conventional endosomes served by coated vesicle endocytosis. Using laser scanning confocal fluorescence microscopy we detected very little delivery of macropinosome content to either early or late endosomes-lysosomes as defined by labeling with transferrin or with LDL. Mixing of the contents of the macropinosomes and conventional endosomes was not induced by the addition of brefeldin A. Moreover, the morphology of macropinosomes was not grossly altered in the presence of brefeldin A, whilst in the same cells there were dramatic tubulation effects on conventional endosomes as reported by others. Although refractory to fusion with conventional endosomes, macropinosomes were nonetheless dynamic structures which sometimes exhibited vesiculo-tubular morphology in living cells and were capable of fusing with each other. We suggest that different endocytic mechanisms can give rise to distinct endosome populations.
The Influence of Localized Chemical Modifications of the Basic Pancreatic Trypsin Inhibitor on Static and Dynamic Aspects of the Molecular Conformation in Solution (1979)

High‐resolution 1 H nuclear magnetic resonance was used to characterize the molecular conformations in solution of the basic pancreatic trypsin inhibitor and three chemical modifications of this protein. It was found that, except for local variations near the modification site, the average spatial structure was preserved after reduction of the disulfide bond 14–38, after cleavage of the reactive peptide bond Lys‐15–Ala‐16, and after removal of the residues Ala‐16 and Arg‐17 from the reactive‐site‐cleaved inhibitor. In all four species the average solution conformation corresponds closely to the crystal structure of the native inhibitor. The stability of the globular conformation in the modified proteins is, however, markedly reduced, i.e. the denaturation temperature is lowered and the interior amide protons exchange more rapidly with the solvent. In contrast, the internal mobility of the aromatic rings is essentially unaffected by these modifications of the covalent structure. These observations and inspection of the molecular structure of the native inhibitor provide direct evidence for the occurrence of hydrophobic stability domains within these relatively small proteins. Functional roles of hydrophobic clusters in the architecture of globular proteins are discussed.
Combination of Photoinduced Alignment and Self-Assembly to Realize Polarized Emission from Ordered Semiconductor Nanorods (2015)

One-dimensional semiconductor nanorods are a very promising class of materials for applications in modern optoelectronic devices, such as light-emitting diodes, solar cells, displays, and lasers. Their ability to emit linearly polarized light is considered to simplify device structures and improve the overall efficiencies. To ensure macroscopic polarization in such devices, the biggest challenge is the long-range alignment of nanorods by controllable means. We propose a technique that combines photoinduced alignment with nanorod's self-assembly. With this approach, we are able to actively control the alignment directions of highly emissive semiconductor nanorods in both microscopic and macroscopic scale with the order parameter as high as 0.87. As a result, polarized emission has been achieved with the degree of polarization of 0.62. Furthermore, patterned alignment of nanorods with spatially varying local orientations has been realized to demonstrate the great flexibility of this approach. Besides opportunities for applications, our method of alignment offers insights into host-guest interactions governing self-assembly of colloidal nanocrystals within the host molecular matrix.
RelEx—Relation extraction using dependency parse trees (2006)

The used natural language preprocessing tools are free for use for academic research. Test sets and relation term lists are available from our website (http://www.bio.ifi.lmu.de/publications/RelEx/).
Ligation of Cell Surface CD38 Protein with Agonistic Monoclonal Antibody Induces a Cell Growth Signal in Myeloid Leukemia Cells (1998)

CD38 is expressed during early stages of differentiation in normal and leukemic myeloid cells. Recently, CD38 has been shown to participate in intracellular signal transduction pathways following its ligation with CD38-specific mAbs. In this study we report that ligation of CD38 by one such agonistic mAb (IB4) induced proliferation of cultured leukemic cells in vitro. In HL-60, KG-1A, NB4, and OCI-AML-3 myeloid leukemia cell lines, IB4 mAb induced an increase in the proliferating cell fraction as determined by cell number, clonogenic assay, and flow cytometric analysis. The presence of Ab caused a dose-dependent increase in the number of CFU and an increase in cell divisions. HL-60-Dox cells (a HL-60-doxorubicin-resistant cell line), which have no detectable CD38 expression, failed to respond to IB4 mAb. The effect of CD38 ligation on cell growth was also evaluated in freshly isolated leukemic cells from patients with acute myelogenous leukemia (AML). A significant increase in the proliferating cell fraction (S+G2M) was observed in 50% of the patients incubated with IB4 mAb. In five of the six AML patients, anti-CD38 mAb stimulated the proliferation of AML colony-forming cells. These results suggest that ligation of CD38 can induce the proliferation of leukemic cells and may play a role in the propagation of leukemic cell clones in certain cohorts of AML patients.
Modeling the Fluid Dynamics in a Human Stomach to Gain Insight of Food Digestion (2010)

This study illustrates the capability of computational fluid dynamic techniques to provide a unique insight into the dynamics of the gastric contents, pointing out its potential to develop a fundamental understanding and modeling of the human digestion process.
Modest Gaze-Related Discharge Modulation in Monkey Dorsal Premotor Cortex During a Reaching Task Performed With Free Fixation (2002)

Recent studies have shown that gaze angle modulates reach-related neural activity in many cortical areas, including the dorsal premotor cortex (PMd), when gaze direction is experimentally controlled by lengthy periods of imposed fixation. We looked for gaze-related modulation in PMd during the brief fixations that occur when a monkey is allowed to look around freely without experimentally imposed gaze control while performing a center-out delayed arm-reaching task. During the course of the instructed-delay period, we found significant effects of gaze angle in 27-51% of PMd cells. However, for 90-95% of cells, these effects accounted for <20% of the observed discharge variance. The effect of gaze was significantly weaker than the effect of reach-related variables. In particular, cell activity during the delay period was more strongly related to the intended movement expressed in arm-related coordinates than in gaze-related coordinates. Under the same experimental conditions, many cells in medial parietal cortex exhibited much stronger gaze-related modulation and expressed intended movement in gaze-related coordinates. In summary, gaze direction-related modulation of cell activity is indeed expressed in PMd during the brief fixations that occur in natural oculomotor behavior, but its overall effect on cell activity is modest.
Longitudinal changes in cognition and behavior in asymptomatic carriers of the APOE e4 allele (2004)

Memory declined in APOE e4 carriers before the symptomatic presentation of MCI in a cohort whose mean age was 60 years over a median period of 33 months. The decline began prior to age 60.
Faecalibacterium prausnitzii A2-165 has a high capacity to induce IL-10 in human and murine dendritic cells and modulates T cell responses (2016)

Faecalibacterium prausnitzii strain A2-165 was previously reported to have anti-inflammatory properties and prevent colitis in a TNBS model. We compared the immunomodulatory properties of strain A2-165 to four different F. prausnitzii isolates and eight abundant intestinal commensals using human dendritic cells (DCs) and mouse BMDCs in vitro. Principal component analysis revealed that the cytokine response to F. prausnitzii A2-165 is distinct from the other strains in eliciting high amounts of IL-10 secretion. The mouse DNBS model of relapsing IBD was used to compare the protective effects of F. prausnitzii A2-165 and Clostridium hathewayi, a low secretor of IL-10, on the Th1-driven inflammatory response to DNBS; attenuation of disease parameters was only observed with F. prausnitzii. In an in vivo mouse model of nasal tolerance to ovalbumin, F. prausnitzii A2-165 enhanced ovalbumin-specific T cell proliferation and reduced the proportion of IFN-γ(+) T cells in CLNs. Similarly, in vitro F. prausnitzii A2-165 stimulated BMDCs increased ovalbumin-specific T cell proliferation and reduced the number of IFN-γ(+) T cells. These mechanisms may contribute to the anti-inflammatory effects of F. prausnitzii in colitis and support the notion that this abundant bacterium might contribute to immune homeostasis in the intestine via its anti-inflammatory properties.
Relationship between promoter structure and template specificities exhibited by the bacteriophage T3 and T7 RNA polymerases. (1983)

To explore the basis for the template specificities of the bacteriophage T3 and T7 RNA polymerases (EC 2.7.7.6), we determined the nucleotide sequences of six promoters recognized by the T3 RNA polymerase and compared them with the previously determined promoter sequences recognized by the bacteriophage T7 RNA polymerase. Recombinant plasmids containing random Hpa II and Taq I fragments of T3 DNA were screened for T3 promoter activity in vitro in a transcription assay using purified T3 RNA polymerase. Five promoters for the T3 RNA polymerase were identified in this manner and their sequences were determined; the sequence of an additional promoter was determined directly from a genomic DNA fragment. In five of the T3 promoters an identical 16-base-pair sequence (A-C-C-C-T-C-A-C-T-A-A-A-G-G-G-A) extends from -12 to +4 (initiation occurring with GTP at +1); this sequence is preceded by a 6-base-pair A + T region. The remaining promoter contains an inserted C at position -1 and an A at the +1 position. The sequence of the 5' end of the RNA transcript from the latter promoter confirms that transcription is initiated with ATP at the +1 position. Previously, late T3 or T7 transcripts had not been found to initiate with ATP. The highly conserved T3 promoter sequence was compared to the T7 promoter consensus sequence. The fundamental difference between the two kinds of phage promoters is the occurrence of G-A at positions -11 and -10 in the T7 promoter, whereas there is a single C at position -10 in the T3 promoter.
Widespread gene transfer in the central nervous system of cynomolgus macaques following delivery of AAV9 into the cisterna magna (2014)

Adeno-associated virus serotype 9 (AAV9) vectors have recently been shown to transduce cells throughout the central nervous system of nonhuman primates when injected into the cerebrospinal fluid (CSF), a finding which could lead to a minimally invasive approach to treat genetic and acquired diseases affecting the entire CNS. We characterized the transduction efficiency of two routes of vector administration into the CSF of cynomolgus macaques-lumbar puncture, which is typically used in clinical practice, and suboccipital puncture, which is more commonly used in veterinary medicine. We found that delivery of vector into the cisterna magna via suboccipital puncture is up to 100-fold more efficient for achieving gene transfer to the brain. In addition, we evaluated the inflammatory response to AAV9-mediated GFP expression in the nonhuman primate CNS. We found that while CSF lymphocyte counts increased following gene transfer, there were no clinical or histological signs of immune toxicity. Together these data indicate that delivery of AAV9 into the cisterna magna is an effective method for achieving gene transfer in the CNS, and suggest that adapting this uncommon injection method for human trials could vastly increase the efficiency of gene delivery.
An immunodominant SSX-2–derived epitope recognized by CD4+ T cells in association with HLA-DR (2004)

Ectopic gene expression in tumors versus normal somatic tissues provides opportunities for the specific immunotargeting of cancer cells. SSX gene products are expressed in tumors of different histological types and can be recognized by tumor-reactive CTLs from cancer patients. Here, we report the identification of an SSX-2derived immunodominant T cell epitope recognized by CD4 + T cells from melanoma patients in association with HLA-DR. The epitope maps to the 37-58 region of the protein, encompassing the sequence of the previously defined HLA-A2-restricted immunodominant epitope SSX-2 41-49 . SSX-2 37-58 -specific CD4 + T cells were detected among circulating lymphocytes from the majority of melanoma patients analyzed and among tumorinfiltrating lymphocytes, but not in healthy donors. Together, our data suggest a dominant role of the 37-58 sequence in the induction of cellular CD4 + T cell responses against SSX antigens and will be instrumental for both the onset and the monitoring of upcoming cancer-vaccine trials using SSX-derived immunogens.
Copolymerization of Vinyl Acetate with Ethylene by Palladium/Alkylphosphine−Sulfonate Catalysts (2009)

Coordination copolymerization of vinyl acetate (VAc) with ethylene, leading to linear copolymers that possess in-chain -CH(2)CH(OAc)- units, has been accomplished using novel palladium complexes bearing alkylphosphine-sulfonate ligands.
Spontaneous deletions in lg heavy chain genes: flanking sequences influence splice site selection (1991)

The cell line G403.4.7, isolated as a spontaneous variant of the MPC-11 derived myeloma G403.4, produces a truncated gamma 2b HC protein, but no light chain (LC), and a single gamma 2b specific transcript of 2.4kb. This gamma 2b transcript consists of the VDJ and CH1 exons, the CH1 to Hinge (Hi) intervening sequence (IVS) and HI exon, part of the IVS between the two membrane exons M1 and M2, and most of the membrane 3' untranslated (UT) region. Even though the mature mRNA contains intronic sequences, it is abundant in the cytoplasm. Analysis of the gamma 2b genomic organization reveals that this unusual transcript results in part from two genomic deletions of 2.5kb and 588bp and in part from an altered splicing pattern. This altered splicing pattern is probably a consequence of the sequence alterations resulting from the genomic deletions. Analysis of these events provides some interesting insights into the mechanism of splice site selection and the evolution of introns and exons.
Redox status of cells influences constitutive or induced NF-kappa B translocation and HIV long terminal repeat activity in human T and monocytic cell lines (1992)

We have tested the hypothesis that cellular activation events occurring in T lymphocytes and monocytes and mediated through translocation of the transcription factor NF-kappa B are dependent upon the constitutive redox status of these cells. We used phenolic, lipid-soluble, chain-breaking antioxidants (butylated hydroxyanisole (BHA), nordihydroquairetic acid, or alpha-tocopherol (vitamin E) to show that peroxyl radical scavenging in unstimulated and PMA- or TNF-stimulated cells blocks the functions depending on NF-kappa B activation. BHA was found to suppress not only PMA- or TNF-induced, but also constitutive, HIV-enhancer activity concomitant to an inhibition of NF-kappa B binding activity in both lymphoblastoid T (J.Jhan) and monocytic (U937) cell lines. This was also true for KBF (p50 homodimer) binding activity in U937 cells. Secretion of TNF, the product of another NF-kappa B-dependent gene, was abolished by BHA in PMA-stimulated U937 cells. The anti-oxidative effect of BHA was accompanied by an increase in thiol, but not glutathione, content in stimulated and unstimulated T cell, whereas TNF stimulation itself barely modified the cellular thiol level. Oxidative stress obtained by the addition of H2O2 to the culture medium of J.Jhan or U937 cells could not by itself induce NF-kappa B activation. These observations suggest that TNF and PMA do not lead to NF-kappa B activation through induction of changes in the cell redox status. Rather, TNF and PMA can exert their effect only if cells are in an appropriate redox status, because prior modification toward reduction with BHA treatment prevents this activation. It appears that a basal redox equilibrium tending toward oxidation is a prerequisite for full activation of transduction pathways regulating the activity of NF-kappa B-dependent genes.
NF-kappaB and its regulation on the immune system. (2004)

NF-kappaB is a transcription factor of eukaryote, whose family comprises five members in mammals and three in drosophila. Transcription factors of the NF-kappaB family are activated in response to signals that lead to cell growth, differentiation, apoptosis and other events. NF-kappaB takes part in expression of numerous cytokines and adhesion molecules which are critical elements involved in the regulation of immune responses. In this review, we focus on our current understanding of NF-kappaB signal pathway and its role in the innate and adaptive immune responses in which these transcription factors have a key regulatory function. Furthermore we review what is currently known about their effects associated with apoptosis.
Progressive multifocal leukoencephalopathy (1975)

Progressive multifocal leukoencephalopathy developed in a patient with rheumatoid arthritis after treatment with an immunosuppressive agent (chlorambucil). We fell that this case lends further support to the concept that an altered immunologic state is important in the appearance of this infection, which is probably viral in origin.
Aquaporin-1–Independent Microvessel Proliferation in a Neonatal Mouse Model of Oxygen-Induced Retinopathy (2007)

Microvessel proliferation in oxygen-induced retinopathy is AQP1-independent. Retinal endothelia have the capacity to express AQP1, though intact retinal vessels chronically suppress AQP1 expression.
Ultrafast spectroscopy of wavelength-dependent coherent photoionization cross sections of Li2 wave packets in the E1Σg+ state: The role of Rydberg states (2001)

The significance of Rydberg states in the probing (via ionization) of Li2 wave packets has been studied through quantitative measurements of the relative coherent ionization cross sections in a two-color pump–probe femtosecond experiment. Following the preparation of a single intermediate rovibronic state with a cw laser, a femtosecond pump pulse (around 800 nm) creates a single two-state rotational wave packet by coherent excitation of the E1Σg+ (ν=9; J=27 and 29) states. The wave packet is then probed through ionization using time-delayed, wavelength tunable pulses (in the region 508–690 nm) while the total energy of the system is kept below the dissociation limit of Li2+. The background-free coherent ionization yield (for each probe wavelength) is measured as the relative oscillation amplitude of the single quantum beat time-dependent signal. The experimental results closely follow a relatively simple theoretical model, which is based on the assumption that the coherent ionization predominantly takes place via the excitation of high-n bound singly excited Rydberg states in the ionization continuum converging to the X 2Σg+ ground electronic state of Li2+. The best interpretation is that the high-n Rydberg states (above n∼25) undergo collisional ionization or autoionization and contribute to the measured coherent ionization signal, while the low-n Rydberg states undergo predissociation and do not contribute to the measured signal. An implication of the results is that the final states of the Li2 system, accessed by the above probe pulses, can be better approximated by a corresponding set of isolated discrete levels rather than by a continuum. This conclusion is important to experimental, as well as theoretical, coherent control and wave packet dynamics studies, in particular, when phase- and amplitude-shaped pump and probe pulses are employed. This study is also the first to investigate ionization of lithium dimer slightly below the E 1Σg+ shelf region with visible light.