gebhart/patrepeval huggingface dataset:
Characterization of biofilm-like structures formed by Pseudomonas aeruginosa in a synthetic mucus medium (2012)

The thick, viscous ASM+, which contains mucin and extracellular DNA levels similar to those found in the CF lung, supports the formation of biofilm-like structures similar to the aggregates described within CF airways. Alterations in environmental conditions or in the QS genes of P. aeruginosa, as occurs naturally during the progression of CF lung infection, affect the architecture and quantitative structural features of these BLS. Thus, ASM+ provides an in vitro medium in which the effect of changing levels of substances produced by the host and the bacteria can be analyzed to determine the effect on such structures and on the susceptibility of the bacteria within the BLS to various treatments.
Second solid cancers after radiotherapy for breast cancer in SEER cancer registries (2009)

Most second solid cancers in breast cancer survivors are not related to radiotherapy.
A Regulatory Role for CD37 in T Cell Proliferation (2004)

CD37 is a leukocyte-specific protein belonging to the tetraspanin superfamily. Previously thought to be predominantly a B cell molecule, CD37 is shown in this study to regulate T cell proliferation. CD37-deficient (CD37(-/-)) T cells were notably hyperproliferative in MLR, in response to Con A, or CD3-TCR engagement particularly in the absence of CD28 costimulation. Hyperproliferation was not due to differences in memory to naive T cell ratios in CD37(-/-) mice, apoptosis, or TCR down-modulation. Division cycle analyses revealed CD37(-/-) T cells to enter first division earlier than wild-type T cells. Importantly, proliferation of CD37(-/-) T cells was preceded by enhanced early IL-2 production. We hypothesized CD37 to be involved in TCR signaling and this was supported by the observation that CD4/CD8-associated p56(Lck) kinase activity was increased in CD37(-/-) T cells. Remarkably, CD37 cross-linking on human T cells transduced signals that led to complete inhibition of CD3-induced proliferation. In the presence of CD28 costimulation, CD37 engagement still significantly reduced proliferation. Taken together, these results demonstrate a regulatory role for CD37 in T cell proliferation by influencing early events of TCR signaling.
Monoclonal antibodies to the leukocyte common antigen (CD45) inhibit IgE-mediated histamine release from human basophils (1991)

mAb were selected that inhibited IgE-mediated histamine release from human basophils. The two mAb, HB 9AB6 and HB 10AB2, are of the IgG1 subclass and have a 50% inhibitory concentration of 0.16 to 1.1 micrograms/ml. The mAb required several hours of incubation with the basophils at 37 degrees C to induce maximum inhibition. Neither mAb directly released histamine from human basophils nor did they inhibit release induced by formylmethionine tripeptide, calcium ionophore A23187, or PMA. There was little inhibition of IgE-mediated release when the cells were preincubated with the mAb at 4 degrees C. By FACS analysis the 2 mAb bound to all peripheral blood leukocytes and immunoprecipitated a approximately 200-kDa protein from peripheral blood leukocytes and several cell lines of human origin. In binding studies and by sequential immunoprecipitation the 2 mAb and a known anti-CD45 mAb bound to the same protein. However, the mAb recognized different epitopes. Therefore, mAb to the CD45 surface Ag, a membrane protein tyrosine phosphatase, inhibits IgE-receptor mediated histamine release from human basophils. The data suggest a link between protein tyrosine phosphorylation and high affinity IgE receptor-mediated signal transduction in human basophils.
A novel monoclonal antibody DC63 reveals that inhibitor 1 of protein phosphatase 2A is preferentially nuclearly localised in human brain (2007)

Abnormal phosphorylation of tau protein represents one of the major candidate pathological mechanisms leading to Alzheimer's disease (AD) and related tauopathies. Altered phosphorylation status of neuronal tau protein may result from upregulation of tau-specific kinases or from inhibition of tau-specific phosphatases. Increased expression of the protein inhibitor 1 of protein phosphatase 2A (I1PP2A) could therefore indirectly regulate the phosphorylation status of tau. As an important step towards elucidation of the role of I1PP2A in the physiology and pathology of tau phosphorylation, we developed a novel monoclonal antibody, DC63, which recognizes I1PP2A. Specificity of the antibody was examined by mass spectrometry and Western blot. This analysis supports the conclusion that the antibody does not recognize any of the other proteins of the 9-member leucine-rich acidic nuclear phosphoprotein family to which I1PP2A belongs. Immunoblot detection revealed that the inhibitor I1PP2A is expressed throughout the brain, including the hippocampus, temporal cortex, parietal cortex, subcortical nuclei and brain stem. The cerebellum displayed significantly higher levels of expression of I1PP2A than was seen elsewhere in the brain. Imunohistochemical analysis of normal human brain showed that I1PP2A is expressed in both neurons and glial cells and that the protein is preferentially localized to the nucleus. We conclude that the novel monoclonal antibody DC63 could be successfully employed as a mass spectrometry-validated molecular probe that may be used for in vitro and in vivo qualitative and quantitative studies of physiological and pathological pathways involving I1PP2A.
MDS array codes with independent parity symbols (1996)

A new family of maximum distance separable (MDS) array codes is presented. The code arrays contain p information columns and r independent parity columns, each column consisting of p-1 bits, where p is a prime. We extend a previously known construction for the case r=2 to three and more parity columns. It is shown that when r=3 such extension is possible for any prime p. For larger values of r, we give necessary and sufficient conditions for our codes to be MDS, and then prove that if p belongs to a certain class of primes these conditions are satisfied up to r/spl les/8. One of the advantages of the new codes is that encoding and decoding may be accomplished using simple cyclic shifts and XOR operations on the columns of the code array. We develop efficient decoding procedures for the case of two- and three-column errors. This again extends the previously known results for the case of a single-column error. Another primary advantage of our codes is related to the problem of efficient information updates. We present upper and lower bounds on the average number of parity bits which have to be updated in an MDS code over GF (2/sup m/), following an update in a single information bit. This average number is of importance in many storage applications which require frequent updates of information. We show that the upper bound obtained from our codes is close to the lower bound and, most importantly, does not depend on the size of the code symbols.
Mechanical and rheological properties of HDPE/graphite composite with enhanced thermal conductivity (2001)

Abstract Having been treated with coupling agent and pan‐milling, graphite is incorporated into HDPE to make a HDPE/graphite composite with enhanced thermal conductivity as well as good mechanical properties and processibility. This paper focuses on the study of mechanical properties, thermal stability and rheological behavior of HDPE/graphite composite. The experimental results show that with increase of the graphite content, Young's modulus of HDPE/graphite increases and the elongation at break and impact strength decrease. However, when the graphite content is 35% in HDPE/graphite, the elongation at break and impact strength still remain 22.4% and 85.8J/m. respectively. Also, the yield strength increases with the increase of the graphite content, and reaches the maximum at 55% graphite content, and reduces afterwards. The crystallization temperature and thermal stability of HDPE/graphite increase with the increase of the graphite content. The melt viscosity of the filled HDPE remains almost unchanged, but the shear sensitivity increases, and the temperature sensitivity decreases with the increase of the graphite content. By optimizing the experimental conditions, a HDPE/graphite composite with fairly good comprehensive properties such as enhanced thermal conductivity and stability, good mechanical properties, and processability could be prepared, which has potential application in the field of heat transfer.
A sequence motif involved in the donor substrate binding by 1,6-fucosyltransferase: the role of the conserved arginine residues (2000)

Alpha1,6-fucosyltransferase catalyzes the transfer of fucose to the innermost GlcNAc residue of an N-linked oligosaccharide. In order to identify the amino acid residue(s) which are associated with the enzyme activity and to investigate their function, we prepared a series of mutant human alpha1,6-fucosyltransferases in which the conserved residues in the region homologous to alpha1,2-fucosyltransferase had been replaced. These proteins were then characterized by kinetic analyses. The wild-type and mutant alpha1,6-fucosyltransferases were expressed using a baculovirus-insect cell system. The activity assay showed that replacement of Arg-365 by Ala or Lys led to a complete loss of activity while substitution of Ala or Lys for the neighboring Arg-366 decreased the activity to about 3% that of the wild type. Kinetic analyses revealed that the replacements of Arg-366 lead to an increase in the apparent K (m) value for both GDP-fucose and the acceptor oligosaccharide but did not markedly affect the apparent V (max). When these mutants were inhibited by GDP in a competitive manner with respect to the donor substrate, the K (i) values were found to be 50-100 times higher than the value in the wild type. On the other hand, in the inhibition by GMP, the K (i) values for the mutants were very similar to that of the wild type. These findings suggest that Arg-366 contributes to the binding of GDP-fucose via an interaction with the beta-phosphoryl group of the GDP moiety of the donor, and that Arg-365 may also play an essential role in substrate binding. The results suggest that the motif common to alpha1,2- and alpha1,6-fucosyltransferases is critical for binding of the donor substrate, GDP-fucose.
ES cells derived from cloned and fertilized blastocysts are transcriptionally and functionally indistinguishable (2006)

Reproductive cloning is uniformly rejected as a valid technology in humans because of the severely abnormal phenotypes seen in cloned animals. Gene expression aberrations observed in tissues of cloned animals have also raised concerns regarding the therapeutic application of "customized" embryonic stem (ES) cells derived by nuclear transplantation (NT) from a patient's somatic cells. Although previous experiments in mice have demonstrated that the developmental potential of ES cells derived from cloned blastocysts (NT-ES cells) is identical to that of ES cells derived from fertilized blastocysts, a systematic molecular characterization of NT-ES cell lines is lacking. To investigate whether transcriptional aberrations, similar to those observed in tissues of cloned mice, also occur in NT-ES cells, we have compared transcriptional profiles of 10 mouse NT- and fertilization-derived-ES cell lines. We report here that the ES cell lines derived from cloned and fertilized mouse blastocysts are indistinguishable based on their transcriptional profiles, consistent with their normal developmental potential. Our results indicate that, in contrast to embryonic and fetal development of clones, the process of NT-ES cell derivation rigorously selects for those immortal cells that have erased the "epigenetic memory" of the donor nucleus and, thus, become functionally equivalent. Our findings support the notion that ES cell lines derived from cloned or fertilized blastocysts have an identical therapeutic potential.
Reduction of amyloid load and cerebral damage in transgenic mouse model of Alzheimer's disease by treatment with a β‐sheet breaker peptide (2002)

Genetic, neuropathological, and biochemical studies have provided strong evidence for a central role of amyloid in the pathogenesis of Alzheimer's disease (AD). We have proposed previously that peptides designed as beta-sheet breakers may be useful in preventing the formation of amyloid plaques. In this study, we describe a modified beta-sheet breaker peptide with improved pharmacological properties, a high rate of penetration across the blood-brain barrier, and the ability to induce a dramatic reduction in amyloid deposition in two different transgenic AD models. In addition, we report for the first time a significant increase in neuronal survival and a decrease in brain inflammation associated with the reduction of amyloid plaques. These results demonstrate that the process of amyloid deposition is one of the causes of neurodegeneration in AD. Moreover, our findings indicate that beta-sheet breaker peptides provide a valuable tool for evaluating further the importance of amyloid in the etiology of AD and suggest that these peptides or some of their derivatives might be good candidates for AD treatment.
Simple extension to the Fabry–Perot technique for accurate measurement of losses in semiconductor waveguides (1990)

A simple modification to the Fabry-Perot technique for the measurement of semiconductor waveguide losses is described. The modification dispenses with the need for knowing implicitly the reflectivities of end faces of the waveguide, which are usually difficult to ascertain experimentally.
Artificial skin I. Preparation and properties of pluronic F‐127 gels for treatment of burns (1972)

Abstract The preparation of block polymer surface‐active agents derived solely from propylene oxide and ethylene oxide is described. The physical properties of a nonionic surfactant of 12,500 molecular weight, Pluronic F‐127, are presented. The toxicity data of the polymeric series is reviewed. The preparation of cold aqueous solutions of the F‐127 solution, to which silver salts and other medicaments are then added, is described. By raising the temperature, these fluid liquids are then converted to strong “ringing” gels or viscous ointments which are suitable for application to a burn wound or abraded skin area. The factors involved in altering the yield strength of the gel are presented.
A peptidomimetic antagonist of TNF-alpha-mediated cytotoxicity identified from a phage-displayed random peptide library. (1998)

Phage-displayed peptide libraries represent a vast collection of peptide sequences that can be used to identify novel therapeutic molecules. In this report, a 15-mer phage-displayed peptide library was used to identify potential TNF-alpha antagonists. After direct interaction of recombinant human TNF-alpha with the library, four randomly selected phage clones were shown to inhibit in a dose-dependent fashion both mouse and human TNF-alpha-induced cytotoxicity in vitro. DNA sequencing of the positive clones revealed a common amino acid sequence that does not bear any structural similarity to the known primary structures of the extracellular domains of either 55-kDa or 75-kDa TNF receptors. This sequence was synthesized, and the peptidomimotope was shown i) to bind to the recombinant human TNF-alpha using surface plasmon resonance (biosensor) technology and ii) to inhibit both recombinant mouse and human TNF-alpha-induced cytotoxicity in vitro in a dose-dependent fashion. These findings highlight the potential of phage-displayed random peptide libraries for the identification of novel low molecular antagonistic molecules that can block the biologic activities of TNF-alpha.
Towards the Chemical Synthesis of Proteins (1991)

Abstract The chemical total synthesis of proteins using solid supports has made great progress. It is therefore becoming a reality what E. Fischer already predicted in 1902 : “I foresee the time when physiological chemistry… is able to prepare synthetic enzymes.” The synthesis of peptides of up to 20 amino acids by the well‐established solid‐phase procedure on polymeric supports (SPPS) has made great progress through the development of newer supports. At the same time, methods have emerged which facilitate the separation and characterization of peptides, thus allowing optimization of the synthesis of pure materials. The new supports which enable one to synthesize peptides by a rapid continuous flow procedure are characterized by hydrophilicity, beads of approximately equal size, similar swelling properties in the solvents used for peptide synthesis, and stability at high pressure. With graft copolymers of weakly cross‐linked polystyrene and linear polyethylene glycol (PEG), the synthetic cycle for coupling of one amino acid can routinely be reduced to 10–20 min with a concomitant higher yield. With beads of monodispersed graft copolymer of 10 μm diameter, a synthetic cycle can, in principle, be shortened to 1–5 min. By utilizing this high‐speed solid‐phase procedure, larger peptides up to the size of proteins could also be prepared in a few hours. With newer mass spectroscopic methods such as ion‐spray mass spectrometry, peptides of up to a molecular mass of 100 kDa can be characterized, and with the advent of capillary electrophoresis, another very efficient separation tool, besides HPLC, is at our disposal.
Apoptosis Factor EI24/PIG8 Is a Novel Endoplasmic Reticulum–Localized Bcl-2–Binding Protein which Is Associated with Suppression of Breast Cancer Invasiveness (2005)

p53 is a critical tumor suppressor which removes cells with DNA damage by regulating expression and activity of a select group of p53-induced genes (PIG) that subsequently induce apoptosis. PIG8 was also identified as a gene induced by etoposide and named etoposide-induced gene 24 (EI24). Later experiments established EI24/PIG8 as a proapoptotic factor and suggested that it may function as a tumor suppressor. Indeed, EI24/PIG8 is relatively highly mutated in aggressive breast cancers and is located in a region which expresses frequent loss of heterozygosity. However, despite these important observations, the activity and role of EI24/PIG8 remain largely unknown. We used (immmuno)fluorescence microscopy and subcellular fractionation techniques to show that EI24/PIG8 is localized in the endoplasmic reticulum (ER). Pull-down experiments showed that it specifically binds with Bcl-2, a death regulator known to reside in mitochondria, ER, and the nuclear envelope. EI24/PIG8-Bcl-2 binding was corroborated by coimmunoprecipitation and other in vitro and in vivo protein-protein binding assays. Further analysis showed that EI24/PIG8 uses its N-terminal region to bind the BH3 domain in Bcl-2. Finally, we used immunohistochemical techniques to analyze expression of EI24/PIG8 in breast cancer tissue progression arrays and showed that loss of EI24/PIG8 is associated with tumor invasiveness but not with the development of the primary tumor. These results suggest that EI24/PIG8 is a novel, ER-localized Bcl-2-binding protein which may contribute to apoptosis by modulating the activity and/or function of Bcl-2 in this organelle. EI24/PIG8 may serve to prevent tumor spreading, consistent with its suspected role as a tumor suppressor.
Effects of fosthiazate and aldicarb on populations of plant‐growth‐promoting bacteria, root‐lesion nematodes and bacteria‐feeding nematodes in the root zone of potatoes (1999)

A 2‐year study investigated the relationship between the nematicides aldicarb and fosthiazate and populations of plant growth‐promoting (PGP) and plant‐growth‐inhibiting (PGI) bacteria, and root‐lesion nematodes and bacteria‐feeding nematodes in the root‐zone soils of potatoes. Fewer ( P &lt; 0.05) bacterial genera and species were recovered from aldicarb‐treated soils than from the fosthiazate and untreated soils but bacterial population densities were greatest in the aldicarb‐treated soils. In potato plantlet bioassays using root‐zone bacteria from the three soil sources, bacteria from the aldicarb‐treated soils reduced ( P &lt; 0.01) the mean wet and dry weight of shoots and roots compared with those from the fosthiazate and untreated soils. In the field, fosthiazate (but not aldicarb) significantly increased tuber yields and reduced nematode population densities of Pratylenchus penetrans in roots and soil. Population densities of bacteria‐feeding nematodes (primarily Diplogaster lheritieri ) were not affected by either nematicide. Aldicarb appeared to suppress the populations of plant‐growth‐promoting bacteria that contribute to enhanced growth in potatoes. This is attributed to the long‐term use of aldicarb at the trial site, which may have encouraged the selection, or adaptation, of soil microorganisms that degrade carbamate pesticides but do not enhance potato growth.
Inactivation of Viruses on Surfaces by Ultraviolet Germicidal Irradiation (2007)

In many outbreaks caused by viruses, the transmission of the agents can occur through contaminated environmental surfaces. Because of the increasing incidence of viral infections, there is a need to evaluate novel engineering control methods for inactivation of viruses on surfaces. Ultraviolet germicidal irradiation (UVGI) is considered a promising method to inactivate viruses. This study evaluated UVGI effectiveness for viruses on the surface of gelatin-based medium in a UV exposure chamber. The effects of UV dose, viral nucleic acid type (single-stranded RNA, ssRNA; single-stranded DNA, ssDNA; double-stranded RNA, dsRNA; and double-stranded DNA, dsDNA), and relative humidity on the virus survival fraction were investigated. For 90% viral reduction, the UV dose was 1.32 to 3.20 mJ/cm2 for ssRNA, 2.50 to to 4.47 mJ/cm2 for ssDNA, 3.80 to 5.36 mJ/cm2 for dsRNA, and 7.70 to 8.13 mJ/cm2 for dsDNA. For all four tested viruses, the UV dose for 99% viral reduction was 2 times higher than those for 90% viral reduction. Viruses on a surface with single-stranded nucleic acid (ssRNA and ssDNA) were more susceptible to UV inactivation than viruses with double-stranded nucleic acid (dsRNA and dsDNA). For the same viral reduction, the UV dose at 85% relative humidity (RH) was higher than that at 55% RH. In summary, results showed that UVGI was an effective method for inactivation of viruses on surfaces.