gebhart/patrepeval huggingface dataset:
Targeted Therapy with aSalmonella TyphimuriumLeucine-Arginine Auxotroph Cures Orthotopic Human Breast Tumors in Nude Mice (2006)

We report here a modified auxotrophic strain of Salmonella typhimurium that can target and cure breast tumors in orthotopic mouse models. We have previously reported development of a genetically modified strain of S. typhimurium, selected for prostate tumor targeting and therapy in vivo. The strain, termed S. typhimurium A1, selectively grew in prostate tumors in xenograft models causing tumor regression. In contrast, normal tissue was cleared of these bacteria even in immunodeficient athymic mice with no apparent side effects. A1 is auxotrophic (leucine-arginine dependent) but apparently receives sufficient nutritional support only from tumor tissue. The ability to grow in viable tumor tissue may account, in part, for the unique antitumor efficacy of the strain. In the present report, to increase tumor-targeting capability of A1, the strain was reisolated after infection of a human colon tumor growing in nude mice. The tumor-isolated strain, termed A1-R, had increased targeting for tumor cells in vivo as well as in vitro compared with A1. Treatment with A1-R resulted in highly effective tumor targeting, including viable tumor tissue and significant tumor shrinkage in mice with s.c. or orthotopic human breast cancer xerographs. Survival of the treated animals was significantly prolonged. Forty percent of treated mice were cured completely and survived as long as non-tumor-bearing mice. These results suggest that amino acid auxotrophic virulent bacteria, which selectively infect and attack viable tumor tissue, are a promising approach to cancer therapy.
Magnet field profiling: Analysis and correcting coil design (1984)

A full mathematical framework for the analysis and production of localized magnetic field profiles is presented. Of primary use in the production of highly homogeneous fields for nuclear magnetic resonance studies, the paper details the analysis of fields in terms of spherical harmonics, describes how field plotting in the appropriate manner may be used to obtain a direct measure of which harmonics are present, and shows how to combine basic "building blocks" to produce the various lower-order zonal and tesseral harmonics. "Building blocks" described include coils, arcs, and sinusoids of current as well as rings and arcs of steel. The use of shaped magnets is also briefly mentioned. Attention is drawn to the presence, in high-order designs, of possibly dominant lower orders of harmonics created by errors in fabrication. The goal of the paper is to present a design philosophy, backed by the appropriate mathematics, which is applicable to the variety of situations encountered in magnet design. Practical examples of correcting coils and "shims" are also given.
microRNA-guided posttranscriptional gene regulation (2005)

microRNAs (miRNAs) form an evolutionarily conserved and highly abundant class of non-coding RNAs that are 21-24 nucleotides (nt) in length. They are processed from double-stranded (ds) RNA precursors and sequence-specifically guide posttranscriptional gene silencing. The processing steps are facilitated by members of the RNAse III enzyme family, whereas gene silencing events are mediated by members of the highly conserved Argonaute (Ago) protein family. Initially discovered in Caenorhabditis elegans, in which they are essential for proper developmental timing, hundreds of miRNAs have been discovered to date in a variety of different organisms, including plants, flies and mammals. Expression profiling approaches demonstrated that miRNAs are specifically expressed not only during embryonic development, but also during cell differentiation and other cellular events such as hormonal signaling. Although miRNAs have been the object of extensive research in recent years, very little is known about their target mRNAs. Their identification along with a comprehensive description of the miRNA/target-mRNA interaction network will add a new level to our knowledge of gene regulation and will also provide new insights into the biology of so far poorly understood diseases, including various forms of cancer.
Infrared and Raman Spectroscopic Imaging (1994)

Introduction Microscopies based on the vibrational spectrum of a molecule provide perhaps the closest approach to universally applicable, chemically selective contrast generation techniques. Infrared and Raman microscopic imaging both use the technology of light microscopy, although in modified form. The mid-infrared and the near-infrared are both employed for microscopic observation. Raman imaging uses the visible region. Like the underlying spectroscopies, infrared microscopy is more widely practiced than Raman microscopy. And like the underlying spectroscopies, each has its characteristic advantages and drawbacks.
Effective migration of antigen-pulsed dendritic cells to lymph nodes in melanoma patients is determined by their maturation state. (2003)

Dendritic cells are the professional antigen-presenting cells of the immune system. To induce an effective immune response, these cells should not only express high levels of MHC and costimulatory molecules but also migrate into the lymph nodes to interact with naïve T cells. Here, we demonstrate that in vitro-generated mature, but not immature dendritic cells, efficiently migrate into the T-cell areas of lymph nodes of melanoma patients. This difference is confirmed by in vitro studies, in which immature dendritic cells are strongly adherent, whereas mature dendritic cells remain highly motile. Our present findings demonstrate that the ability of dendritic cells to mount a proper immune response correlates with their ability to migrate both in vitro and in vivo.
Adam-Gibbs formulation of enthalpy relaxation near the glass transition (1997)

The entropically based nonlinear Adam-Gibbs equation is discussed in the context of phenomenologies for nonlinear enthalpy relaxation within the glass transition temperature range. In many materials for which adequate data are available, the nonlinear Adam-Gibbs parameters are physically reasonable and agree with those obtained from linear relaxation data and thermodynamic extrapolations. Observed correlations between the traditional Tool-Narayanaswamy-Moynihan parameters are rationalized in terms of the Adam-Gibbs primary activation energy (Δ<i>μ</i>) determining how close the kinetic glass transition temperature can get to the thermodynamic Kauzmann temperature. It is shown that increased nonlinearity in the glass transition temperature range is associated with greater fragility in the liquid/rubber state above <i>T</i><sub>g</sub>.
Passively Driven Integrated Microfluidic System for Separation of Motile Sperm (2003)

This paper describes a self-contained integrated microfluidic system that can separate motile sperm from small samples that are difficult to handle using conventional sperm-sorting techniques. The device isolates motile sperm from nonmotile sperm and other cellular debris, based on the ability of motile sperm to cross streamlines in a laminar fluid stream. The device is small, simple, and disposable yet is an integrated system complete with sample inlets, outlets, sorting channel, and a novel passively driven pumping system that provides a steady flow of liquid; it requires no external power source or controls. The device fulfills a need in clinical settings where small amounts of sperm need to be sorted. It also opens the way for convenient bioassays based on sperm motility including at-home motile sperm tests.
A comprehensive machine-readable view of the mammalian cholesterol biosynthesis pathway (2013)

Cholesterol biosynthesis serves as a central metabolic hub for numerous biological processes in health and disease. A detailed, integrative single-view description of how the cholesterol pathway is structured and how it interacts with other pathway systems is lacking in the existing literature. Here we provide a systematic review of the existing literature and present a detailed pathway diagram that describes the cholesterol biosynthesis pathway (the mevalonate, the Kandutch-Russell and the Bloch pathway) and shunt pathway that leads to 24(S),25-epoxycholesterol synthesis. The diagram has been produced using the Systems Biology Graphical Notation (SBGN) and is available in the SBGN-ML format, a human readable and machine semantically parsable open community file format.
A New Site Selective Synthesis of Benzoin Esters. Synthesis of Symmetrically and Unsymmetrically Substituted Benzils (1988)

A series of novel benzoin esters has been obtained in high yield, in a site selective synthesis, by the acid hydrolysis of a series of 4-benzoyloxy-2-azabuta-1, 3-dienes. The oxidation of the benzoin esters allows the preparation of symmetrically and unsymmetrically substituted benzils by a route that is superior, in some cases, to those previously reported.
Fungal Metabolites. XVIII. New Membrane-Modifying Peptides, Trichorozins I-IV, from the Fungus Trichoderma harzianum. (1995)

New membrane-modifying peptides, trichorozins I-IV, have been isolated from conidia of the fungus Trichoderma harzianum. Their amino acid sequences were clearly determined by spectrometric methods and, furthermore, they were synthesized by the solution-phase method. Trichorozins are a family of the class of peptaibols and are composed of 11 residues including an amino alcohol. Trichorozins exhibited voltage-dependent ion channel-like activity in lipid bilayers.
60.2: Intermediate Connector with Suppressed Voltage Loss for White Tandem OLEDs (2009)

Abstract In order to attain low drive voltage and high power conversion efficiency in tandem OLEDs, the mechanism for carrier generation/separation at the intermediate connecting parts, which are interposed between emission units, has been examined, and a new intermediate connector has been proposed. Voltage increase due to the provision of the new intermediate connector is minimized, and marked decrease in drive voltage of the tandem OLEDs has been attained.
Genetic analysis of CYP2C9 polymorphism in a Japanese population (1997)

1Center for Molecular Biology and Cytotjenetics. SRL. Inc.. Hachioji. Tokyo. Japan 2Department of Clinical Pharmacology, Research Institute. International Medical Center of Japan. Tokyo. Japan
Cryptosporidium parvum metalloaminopeptidase inhibitors prevent in vitro excystation (1996)

Cryptosporidium parvum arginine aminopeptidase (RAP) was studied during in vitro excystation. Specific RAP inhibitors were identified by using C. parvum extracts. Amastatin, a series of alpha-aminoboronic acids, and the chelating agents EDTA and 1,10-phenanthrolene, but not endoproteinase inhibitors, blocked enzymatic activity. RAP inhibitors found to be effective in soluble enzymatic assays were then studied for their effect on in vitro excystation. 1,10-Phenanthrolene, amastatin, and H-boronorleucine (pinacol) inhibited excystation by 84, 57, and 61%, respectively, compared with solvent-treated control oocysts. Sporozoites remained viable within the oocyst as determined by propidium iodide and fluorescein diacetate dye uptake, suggesting that alpha-aminoboronic acids were not directly lethal to the parasite.
Angiogenin is a cytotoxic, tRNA-specific ribonuclease in the RNase A superfamily. (1992)

Angiogenin is a 14.4-kDa human plasma protein with 65% homology to RNase A that retains the key active site residues and three of the four RNase A disulfide bonds. We demonstrate that recombinant angiogenin functions as a cytotoxic tRNA-specific RNase in cell-free lysates and when injected into Xenopus oocytes. Inhibition of protein synthesis by angiogenin correlates with degradation of endogenous oocyte tRNA. Exogenous, radiolabeled tRNA is also hydrolyzed by angiogenin, whereas oocyte rRNA and mRNA are not detectably degraded by angiogenin. Protein synthesis was restored to angiogenin-injected oocytes by injecting the RNase inhibitor RNasin plus total Xenopus or calf liver tRNAs, thereby demonstrating that the tRNA degradation induced by angiogenin was the sole cause of cytotoxicity. A similar tRNA-reversible inhibition of protein synthesis was seen in rabbit reticulocyte lysates. Angiogenin therefore appears to be a specific cellular tRNase, whereas five homologues in the RNase A superfamily lack angiogenin's specificity for tRNA. One of these homologues purified from human eosinophils, eosinophil-derived neurotoxin, nonspecifically degrades oocyte RNA similar to RNase A and is also cytotoxic at very low concentrations.
PP.13.15 (2015)

Objective: Hypercholesterolemia can cause damage to the artery before the atherosclerotic lesion has formed. Intermedin (IMD) is a novel member of the calcitonin gene-related peptide family. Endogenous IMD is reported to participate in several cardiovascular pathological states. Using the rats fed with high-cholesterol diet, this study aims to investigate the aortic expression of IMD and its receptors in hypercholesterolemia without atherosclerosis. Furthermore, by the antioxidant intervention, we also explore the influence of oxidative stress. Design and method: Male Wistar rats were fed with high cholesterol diet, with or without concurrent administration of simvastatin and vitamin C. The serum lipid levels were measured, and the aortic histopathology features were examined. Both the malondialdehyde (MDA) and superoxide dismutase (SOD) in plasma and aorta were determined as the oxidative stress biomarkers. The plasma IMD was assessed by radioimmunoassay. Within the aorta, the mRNA expression of IMD along with its receptor components were determined by quantitative Real-Time Polymerase Chain Reaction (qRT-PCR), and the corresponding protein level of the CRLR/RAMPs were assessed by Western blot analysis. Results: The hypercholesterolemia rats without atherosclerotic lesion manifested higher level of MDA and SOD. The IMD in plasma was elevated. Within the aorta, increased expression of IMD and all its receptor components (CRLR, RAMP1, RAMP2, and RAMP3) were displayed. The simvastatin indirectly attenuated oxidative stress by improving lipid profiles, while the vitamin C directly reduced oxidative stress without interfering with the serum lipids. Both simvastatin and vitamin C ameliorated the aortic injury, decreased the plasma IMD level, and recovered the expression of IMD and its receptors within the aorta. Conclusions: For the first time, the up-regulated expression of IMD is observed within the aorta of the hypercholesterolemia rats, demonstrating the pathophysiological role which IMD has performed in hypercholesterolemia absent of atherosclerosis lesion. In addition, the oxidative stress is evidenced to participate in the up-regulation.
Serologic aspects of IgG4 antibodies. I. Prolonged immunization results in an IgG4-restricted response. (1983)

Labeled antigen-binding tests were used to determine quantitatively the contribution of IgG4 antibodies to the total IgG antibody response in humans. In agreement with literature, we found no IgG4-restricted antibody responses with tetanus toxoid or streptococcal carbohydrate. In the serum of individuals immunized for several years with phospholipase (PLA) from honey bee venom, grass pollen allergen, or house dust mite allergen, we often found that more than 50% of the total antigen-binding capacity was due to IgG4 antibodies. In the case of beekeepers, it could clearly be shown that during prolonged immunization a shift in the IgG4:IgG1 antibody ratio occurs that finally results in an IgG4-dominated antibody response. Evidence is provided that antigen-binding assays may even underestimate the contribution of IgG4 antibodies, because in contrast to IgG1 antibodies, IgG4 antibodies act as monovalent antibodies in being unable to cross-link immunosorbent-bound antigen and radiolabeled antigen.
Studies of inactivation mechanism of non-enveloped icosahedral virus by a visible ultrashort pulsed laser (2014)

We conclude that our model non-enveloped virus, MNV-1, is inactivated by the ISRS process. These studies provide fundamental knowledge on photon-virus interactions on femtosecond time scales. From the analysis of the transmission electron microscope (TEM) images of viral particles before and after USP laser irradiation, the locations of weak structural links on the capsid of MNV-1 were revealed. This important information will greatly aid our understanding of the structure of non-enveloped, icosahedral viruses. We envision that this non-invasive, efficient viral eradication method will find applications in the disinfection of pharmaceuticals, biologicals and blood products in the near future.
Focusing light with a single subwavelength aperture flanked by surface corrugations (2003)

In this letter, we show theoretically how a single subwavelength aperture surrounded by a finite array of grooves made on a metallic film can act as a “lens” for electromagnetic radiation within a certain frequency range. The dependence of this resonant focusing ability with the geometrical parameters defining the structure is extensively analyzed. Universal curves for the depth, length and width of the focus as a function of the number of grooves are also given.
A novel immunoradiometric assay for human liver ferritin. (1983)

Rivanol, the cationic salt of an acridine base, has been used as a novel separation procedure in an immunoradiometric assay for human liver ferritin. The separation step is based on the differences in charge and molecular weight between the labelled antibody-ferritin complex and free labelled immunoglobulins. The resultant assay is simple, reproducible and sufficiently sensitive to determine serum concentrations of ferritin.
β-Catenin stabilization dysregulates mesenchymal cell proliferation, motility, and invasiveness and causes aggressive fibromatosis and hyperplastic cutaneous wounds (2002)

Fibroproliferative processes are a group of disorders in which there is excessive proliferation of spindle (mesenchymal fibroblast-like) cells. They range from hypertrophic scars to neoplasms such as aggressive fibromatosis. Cells from these disorders share cytologic similarity with fibroblasts present during the proliferative phase of wound healing, suggesting that they represent a prolonged wounding response. A critical role for beta-catenin in mesenchymal cells in fibroproliferative processes is suggested by its high rate of somatic mutation in aggressive fibromatosis. Using a Tcf-reporter mouse we found that beta-catenin protein level and Tcf-transcriptional activity are elevated in fibroblasts during the proliferative phase of healing. We generated a transgenic mouse in which stabilized beta-catenin is expressed in mesenchymal cells under control of a tetracycline-regulated promoter. Fibroblasts from the transgenic mice exhibited increased proliferation, motility, and invasiveness when expressing stabilized beta-catenin and induced tumors after induction of the transgene when grafted into nude mice. Mice developed aggressive fibromatoses and hyperplastic gastrointestinal polyps after 3 months of transgene induction and healed with hyperplastic cutaneous wounds compared with control mice, which demonstrates an important function for beta-catenin in mesenchymal cells and shows a central role for beta-catenin in wound healing and fibroproliferative disorders.
Recombinant Vaccinia Virus Coexpressing the F Protein of Respiratory Syncytial Virus (RSV) and Interleukin-4 (IL-4) Does Not Inhibit the Development of RSV-Specific Memory Cytotoxic T Lymphocytes, whereas Priming Is Diminished in the Presence of High Levels of IL-2 or Gamma Interferon (1998)

In order to investigate if immune responses to the fusion (F) protein of respiratory syncytial virus (RSV) could be influenced by cytokines, recombinant vaccinia viruses (rVV) carrying both the F gene of RSV and the gene for murine interleukin-2 (IL-2), IL-4, or gamma interferon (IFN-gamma) were constructed. In vitro characterization of rVV revealed that insertion of the cytokine gene into the VP37 locus of the vaccinia virus genome resulted in 100- to 1,000-fold higher expression than insertion of the same gene into the thymidine kinase (TK) locus. In comparison, only a two- to fivefold difference in the level of expression of the F protein was observed when the gene was inserted into either of these two loci. Mice vaccinated with rVV expressing the F protein and high levels of IL-2 or IFN-gamma cleared rVV more rapidly than mice inoculated with a control rVV and developed only low levels of RSV-specific serum antibody. In addition, these recombinants were much less effective at priming RSV-specific memory cytotoxic T lymphocytes (CTL) and IFN-gamma production by spleen cells than rVV expressing the F protein alone. In contrast, mice vaccinated with rVV expressing high levels of IL-4 showed signs of delayed rVV clearance. RSV-specific serum antibody responses were biased in favor of immunoglobulin G1 (IgG1) in these mice, as there was a significant reduction in IgG2a antibody responses compared with serum antibody responses in mice vaccinated with rVV expressing the F protein alone. However, vaccination with rVV expressing the F protein together with high levels of IL-4 did not alter the development of RSV-specific memory CTL or IFN-gamma production by RSV-restimulated splenocytes.
Enhanced Specificity and Efficiency of the CRISPR/Cas9 System with Optimized sgRNA Parameters in Drosophila (2014)

The CRISPR/Cas9 system has recently emerged as a powerful tool for functional genomic studies in Drosophila melanogaster. However, single-guide RNA (sgRNA) parameters affecting the specificity and efficiency of the system in flies are still not clear. Here, we found that off-target effects did not occur in regions of genomic DNA with three or more nucleotide mismatches to sgRNAs. Importantly, we document for a strong positive correlation between mutagenesis efficiency and sgRNA GC content of the six protospacer-adjacent motif-proximal nucleotides (PAMPNs). Furthermore, by injecting well-designed sgRNA plasmids at the optimal concentration we determined, we could efficiently generate mutations in four genes in one step. Finally, we generated null alleles of HP1a using optimized parameters through homology-directed repair and achieved an overall mutagenesis rate significantly higher than previously reported. Our work demonstrates a comprehensive optimization of sgRNA and promises to vastly simplify CRISPR/Cas9 experiments in Drosophila.
Correlation of Expression of H/LeY/LeBAntigens with Survival in Patients with Carcinoma of the Lung (1992)

Positivity for MIA (i.e., immunohistologic staining by MIA-15-5, which defines H/Le(y)/Le(b) antigens) is inversely correlated with survival among patients with primary lung cancer and may be of prognostic value.
Adaptive image retrieval using the fuzzy integral (2003)

The paper proposes an alternative and iterative image retrieval system which takes into account the subjectivity of human perception of visual content. The proposed system uses a dynamic similarity measure based on the Choquet integral. Both positive and negative user's feedback are modeled by fuzzy sets, and are used to refine the feature relevance weights. The experimental results on more than 3000 texture images illustrate the learning behaviour of the retrieval system.
Imaging of ferroelectric domain walls by force microscopy (1990)

We have imaged ferroelectric domain walls in the ferroelectric-ferroelastic material Gd2(Mo)3 using force microscopy. By using a mode of imaging developed for the detection of static surface charge, the force gradient due to the polarization charge at the sample surface was imaged. The signal was seen to change sign at the domain wall, consistent with the reversal in sign of the polarization across a wall. By modeling the wall as a step function in the electric potential, the general features of the force microscope domain wall image could be explained.