gebhart/patrepeval huggingface dataset:
Field-Induced Layering of Colloidal Crystals (1996)

An electrohydrodynamic methodology has been developed that makes possible the precise assembly of two- and three-dimensional colloidal crystals on electrode surfaces. Electrophoretically deposited colloidal particles were observed to move toward one another over very large distances (greater than five particle diameters) to form two-dimensional colloidal crystals for both micrometer- and nanometer-size particles. This coalescence of particles with the same charge is opposite to what is expected from electrostatic considerations and appears to result from electrohydrodynamic fluid flow arising from an ionic current flowing through the solution. The ability to modulate this "lateral attraction" between particles, by adjusting field strength or frequency, facilitates the reversible formation of two-dimensional fluid and crystalline colloidal states on the electrode surface. Further manipulation allows controlled structures to be assembled.
Exploiting human-fish genome comparisons for deciphering gene regulation (2004)

Comparative genomics has served as an essential guide in the identification of functional coding and non-coding sequences in vertebrate genomes. Human-mouse pair-wise comparisons have limited utility for identifying functional conserved non-coding sequences, owing to the large number of sequences shared between these species. In searching for more stringent filters to uncover non-coding elements more likely to be of functional importance in the human genome, human-fish sequence comparisons have emerged as an important strategy, leading to the efficient identification of enhancer elements. These sequences are unevenly distributed in the genome, tending to cluster around genes involved in key developmental processes, with recent studies suggesting that they represent genomic segments in which sequence variation can result in morphological changes and innovation. These elements, conserved over long evolutionary time, emerge as primary candidates that are likely to harbor sequence variation contributing to susceptibility of human disease phenotypes.
Identification of a Novel Family of Oxidized Phospholipids That Serve as Ligands for the Macrophage Scavenger Receptor CD36 (2002)

The macrophage scavenger receptor CD36 plays an important role in the uptake of oxidized forms of low density lipoprotein (LDL) and contributes to lesion development in murine models of atherosclerosis. However, the structural basis of CD36 lipoprotein ligand recognition is unknown. We now identify a novel class of oxidized phospholipids that serve as high affinity ligands for CD36 and mediate recognition of oxidized forms of LDL by CD36 on macrophages. Small unilamellar vesicles of homogeneous phosphatidylcholine (PC) molecular species were oxidized by the myeloperoxidase (MPO)-H(2)O(2)-NO(2)(-) system, and products were separated by sequential LC/ESI/MS/MS. In parallel, fractions were tested for their ability to bind to CD36. Four major structurally related phospholipids with CD36 binding activity were identified from oxidized 1-palmitoyl-2-arachidonyl-PC, and four corresponding structural analogs with CD36 binding activity were identified from oxidized 1-palmitoyl-2-linoleoyl-PC. Each was then synthetically prepared, its structure confirmed by multinuclear NMR and high resolution mass spectrometry, and shown to possess identical CD36 binding activity and LC/ESI/MS/MS characteristics in both native and derivatized forms. Based upon the structures of the active compounds identified, and structure-function studies with a variety of synthetic analogs, we conclude that the structural characteristics required for high affinity binding of oxidized PC species to CD36 are a phospholipid with an sn-2 acyl group that incorporates a terminal gamma-hydroxy(or oxo)-alpha,beta-unsaturated carbonyl (oxPC(CD36)). LC/ESI/MS/MS studies demonstrate that oxPC(CD36) are formed during LDL oxidation by multiple distinct pathways. Formation of this novel class of oxidized PC species contributes to CD36-mediated recognition of LDL oxidized by MPO and other biologically relevant mechanisms. The present results offer structural insights into the molecular patterns recognized by the scavenger receptor CD36 and provide a platform for the development of potential therapeutic inhibitory agents.
N-demethylvancomycin, a novel antibiotic produced by a strain of Nocardia orientalis. Taxonomy and fermentation. (1984)

A novel vancomycin analog, N-demethylvancomycin, is produced by a soil isolate collected in Yucatan, Mexico. Taxonomic studies indicated this microorganism, designated NRRL 15232, is a strain of Nocardia orientalis. Unlike some glycopeptide antibiotics, virtually none of the N-demethylvancomycin synthesized remained bound to the cells of the producing culture. Antibiotic production was markedly depressed by the addition of orthophosphate to the fermentation medium. Enrichment of the medium with tyrosine, p-hydroxyphenylglycine, p-hydroxyphenylglyoxylic acid, or leucine, all putative precursors of the aglycone, stimulated the biosynthesis of N-demethylvancomycin.
Locating objects in mobile computing (2001)

In current distributed systems, the notion of mobility is emerging in many forms and applications. Mobility arises naturally in wireless computing since the location of users changes as they move. Besides mobility in wireless computing, software mobile agents are another popular form of moving objects. Locating objects, i.e., identifying their current location, is central to mobile computing. We present a comprehensive survey of the various approaches to the problem of storing, querying, and updating the location of objects in mobile computing. The fundamental techniques underlying the proposed approaches are identified, analyzed, and classified along various dimensions.
Hemozoin (Malarial Pigment) Directly Promotes Apoptosis of Erythroid Precursors (2009)

Severe malarial anemia is the most common syndrome of severe malaria in endemic areas. The pathophysiology of chronic malaria is characterised by a striking degree of abnormal development of erythroid precursors (dyserythropoiesis) and an inadequate erythropoietic response in spite of elevated levels of erythropoietin. The cause of dyserythropoiesis is unclear although it has been suggested that bone-marrow macrophages release cytokines, chemokines or lipo-peroxides after exposure to hemozoin, a crystalloid form of undigested heme moieties from malarial infected erythrocytes, and so inhibit erythropoiesis. However, we have previously shown that hemozoin may directly inhibit erythroid development in vitro and the levels of hemozoin in plasma from patients with malarial anemia and hemozoin within the bone marrow was associated with reduced reticulocyte response. We hypothesized that macrophages may reduce, not enhance, the inhibitory effect of hemozoin on erythropoiesis. In an in vitro model of erythropoiesis, we now show that inhibition of erythroid cell development by hemozoin isolated from P. falciparum is characterised by delayed expression of the erythroid markers and increased apoptosis of progenitor cells. Crucially, macrophages appear to protect erythroid cells from hemozoin, consistent with a direct contribution of hemozoin to the depression of reticulocyte output from the bone marrow in children with malarial anemia. Moreover, hemozoin isolated from P. falciparum in vitro inhibits erythroid development independently of inflammatory mediators by inducing apoptotic pathways that not only involve activation of caspase 8 and cleavage of caspase 3 but also loss of mitochondrial potential. Taken together these data are consistent with a direct effect of hemozoin in inducing apoptosis in developing erythroid cells in malarial anemia. Accumulation of hemozoin in the bone marrow could therefore result in inadequate reticulocytosis in children that have adequate levels of circulating erythropoietin.
Multilinear Independent Components Analysis (2005)

Independent components analysis (ICA) maximizes the statistical independence of the representational components of a training image ensemble, but it cannot distinguish between the different factors, or modes, inherent to image formation, including scene structure, illumination, and imaging. We introduce a nonlinear, multifactor model that generalizes ICA. Our multilinear ICA (MICA) model of image ensembles learns the statistically independent components of multiple factors. Whereas ICA employs linear (matrix) algebra, MICA exploits multilinear (tensor) algebra. We furthermore introduce a multilinear projection algorithm which projects an unlabeled test image into the N constituent mode spaces to simultaneously infer its mode labels. In the context of facial image ensembles, where the mode labels are person, viewpoint, illumination, expression, etc., we demonstrate that the statistical regularities learned by MICA capture information that, in conjunction with our multilinear projection algorithm, improves automatic face recognition.
Transposons for Gene Therapy! (2006)

Gene therapy is a promising strategy for the treatment of several inherited and acquired human diseases. Several vector platforms exist for the delivery of therapeutic nucleic acids into cells. Vectors based on viruses are very efficient at introducing gene constructs into cells, but their use has been associated with genotoxic effects of vector integration or immunological complications due to repeated administration in vivo. Non-viral vectors are easier to engineer and manufacture, but their efficient delivery into cells is a major challenge, and the lack of their chromosomal integration precludes long-term therapeutic effects. Transposable elements are non-viral gene delivery vehicles found ubiquitously in nature. Transposon-based vectors have the capacity of stable genomic integration and long-lasting expression of transgene constructs in cells. Molecular reconstruction of Sleeping Beauty, an ancient transposon in fish, represents a cornerstone in applying transposition-mediated gene delivery in vertebrate species, including humans. This review summarizes the state-of-the-art in the application of transposable elements for therapeutic gene transfer, and identifies key targets for the development of transposon-based gene vectors with enhanced efficacy and safety for human applications.
Absorption Coefficients for the Bound-to-continuum Transitions in a Biased Quantum-well Infrared Photodetector (2005)

We have proposed a method to calculate the absorption coefficients for the bound-to-continuum transitions in a strong biased quantum-well infrared photodetector. We have applied this method to a manufactured sample of typical device parameters, and obtained good agreements with experiments. The absorption coefficients evaluated are up to 5,700/cm at some particular operating conditions. We have also been able to make a qualitative explanation for the bias dependence of response.
Analytical capabilities of coherent anti-Stokes Raman scattering microspectroscopy (2008)

Nonlinear Raman scattering is an emerging spectroscopy technique for non-invasive microscopic imaging. It can produce a fluorescence background free vibrational spectrum from a microscopic volume of a sample providing chemically specific information about its molecular composition. We analyze the ability of nonlinear Raman microspectroscopy to detect low concentrated molecular species and evaluate its applicability to study complex solutions.
Mechanical Properties of Stapedial Tendon in Human Middle Ear (2007)

Measurement on mechanical properties of the stapedial tendon in human middle ear has not been reported in the literature. In this paper, we used the material testing system to conduct uniaxial tensile, stress relaxation, and failure tests on stapedial tendon specimens harvested from human temporal bones. The digital image correlation method was employed to assess the boundary effect on experimental data. The stress-strain relationship of the tendon obtained from experiments was analyzed using the hyperelastic Ogden model. The results presented include (1) the constitutive equation of the tendon for stretch ratio of 1-1.4 or stress range of 0-1.45 MPa, (2) the mean ultimate stress and stretch ratio of the tendon at 4.04 MPa and 1.65, respectively, and (3) the hysteresis and normalized stress relaxation function of the tendon. The data reported in this paper contribute to ear mechanics, especially for theoretical analysis of human ear function.
GATES: a grid-based middleware for processing distributed data streams (2004)

Increasingly, a number of applications rely on, or can potentially benefit from, analysis and monitoring of data streams. Moreover, many of these applications involve high volume data streams and require distributed processing of data arising from a distributed set of sources. Thus, we believe that a grid environment is well suited for flexible and adaptive analysis of these streams. This paper reports the design and initial evaluation of a middleware for processing distributed data streams. Our system is referred to as GATES (grid-based adaptive execution on streams). This system is designed to use the existing grid standards and tools to the extent possible. It flexibly achieves the best accuracy that is possible while maintaining the real-time constraint on the analysis. We have developed a self-adaptation algorithm for this purpose. Results from a detailed evaluation of this system demonstrate the benefits of distributed processing, and the effectiveness of our self-adaptation algorithm.
Tacrolimus (FK 506)—A New Therapeutic Agent for Severe Recalcitrant Psoriasis (1992)

Tacrolimus, a new immunosuppressive agent, is effective in treating patients with severe recalcitrant psoriasis. The mechanism of its action in psoriasis is unknown, but it may be related to its ability to modulate immune function. Further studies will establish criteria for patient selection and drug dosage, to maximize efficacy of this agent in psoriasis, while minimizing its toxicity.
Characterization of cis‐elements required for vascular expression of the Cinnamoyl CoA Reductase gene and for protein–DNA complex formation (2000)

Cinnamoyl-CoA reductase (CCR) catalyses the first specific step in the biosynthesis of monolignols, the monomeric units of lignins. We examined the developmental regulation of the Eucalyptus gunnii EgCCR promoter by analysing the expression of EgCCR-GUS fusions in tobacco. EgCCR promoter activity was strongest in lignified organs (stems and roots) consistent with the EgCCR mRNA level in these organs. Histochemical analysis showed expression in vascular tissues (cambium, young differentiating xylem, ray cells, internal and external phloem) of stems and roots in agreement with in situ hybridization data. Promoter deletion analysis and gain-of-function experiments identified the sequences between positions -119 and -77 as necessary and sufficient for expression in vascular tissues of stems. Electrophoretic mobility-shift assays showed that this region is specifically recognized by nuclear proteins present in tobacco stems, giving rise to two retarded complexes, LMC1 and LMC2. Using overlapping EgCCR fragments and mutated oligonucleotides as competitors in gel-shift assays, two DNA-protein interaction sites were mapped. Finally, the role of protein-protein interactions in the formation of the LMC1 and LMC2 complexes was investigated using the detergent sodium deoxycholate, and protein fractionation onto a heparin Sepharose column.
Levamisole causes differential cytokine expression by elicited mouse peritoneal macrophages (1992)

Thioglycolate-elicited peritoneal macrophages from normal C57B1/6J mice were examined in vitro for bacterial lipopolysaccharide (LPS)-stimulated interleukin-1 (IL-1), IL-6, and tumor necrosis factor (TNF) production. Macrophages from mice administered a single oral dose of levamisole (3 mg/kg) 1 to 4 days prior to macrophage harvest demonstrated a twofold enhancement of IL-1 production compared to vehicle-treated mice. In contrast, IL-6 production and TNF production by the same macrophages were inhibited up to 36 and 62%, respectively, compared to production by macrophages harvested from vehicle-treated mice. Similar results were observed when IL-1 production and TNF production were followed in peritoneal exidate cells directly stimulated with levamisole in vitro. The ex vivo LPS-stimulated IL-1 production was enhanced 4 days after macrophage elicitation, whereas TNF and IL-6 production returned to baseline by 72 h after macrophage recruitment and augmentation. No evidence could be found for the presence of inhibitors of TNF or IL-6. The specificity of the IL-1, IL-6, and TNF bioactivities was demonstrated by neutralization with specific antisera. Immunoprecipitation studies of supernatants from biosynthetically labeled macrophages also revealed augmented IL-1 production and decreased IL-6 and TNF, indicating that levamisole may have affected cytokine production at the translational level. Kinetics studies revealed that ex vivo release of IL-6 and TNF by macrophages from levamisole-dosed mice was delayed compared to production of these cytokines by macrophages harvested from mice given vehicle only. The results may explain, in part, the reported ability of levamisole to ameliorate cases of rheumatoid arthritis or other autoimmune and inflammatory diseases by affecting the relative levels of cytokines produced by macrophages recruited to sites of injury, which are associated with inflammation and acute-phase protein synthesis.
A review of block polymer surfactants (1977)

Abstract and Summary A brief historical review of four series of commercially available block polymer surface‐active agents—the PLURONIC R , TETRONIC R , PLURADOT R , and PLURONIC R R polyols—is presented. A comparison is made of the physical properties within each series, in the form of trend lines. These parameters encompass solubility, rate of solubility, wetting, foaming, defoaming, emulsification, thickening, cleansing, and toxicity. The physical property relationships which depend upon variation in the hydrophobe molecular weight and variation in the hydrophile hydrophobe balance are shown to be similar in each series of surfactants. Differences among the four series of polymers, where they exist, are seen to vary from little to significant. The many controversial articles on the micellar nature of the block polymers and their critical micelle concentrations are examined. Considerations of the important physical properties which lead to practical applications are discussed. Some of the more important newly developed potential uses of these polymeric surfactants are then described in various application areas, including the cosmetic, medical, paper, pharmaceutical, and textile industries.
Embryological changes induced by weak, extremely low frequency electromagnetic fields. (1982)

Fertilized chicken eggs were incubated for 48 hours while exposed to extremely low frequency magnetic fields (ELMF) of 10 Hz, 100 Hz and 1000 Hz with intensities of 0.12, 1.2 and 12 micro T. Gross morphological and histological analysis of the exposed embryos revealed the following effects: (1) ELMF of 100 Hz/1.2 micro T had the most consistent and powerful inhibitory effect on embryogenesis. Development of embryos was reduced to the formation of the three primitive layers. Brain vesicles, auditory pit, neural tube, foregut, heart, vessels, and somites were not developed. Glycosaminoglycans were almost absent. (2) The above results demonstrate a window effect because embryos exposed to 100 Hz/1.2 micro T were less developed than embryos exposed at lower and higher intensities and frequencies. (3) Developing organs reacted with different sensitivity to ELMF of specific frequencies and intensities. Somites were not disturbed by exposure to 10 Hz with any of the intensities used. Formation of blood vessels was completely blocked by ELMF of 1000 Hz/12 micro T while traces of other organs were present. (4) The drastic embryological disturbances described were obtained with much lower intensities (1 micro T = 0.01 Gauss) than those used in studies by other investigators. (5) Embryological alterations induced by ELMF may depend on disturbances in the presence and structure of glycosaminoglycans which are essential elements in cellular activities, including cell migration. (6) The use of ELMF of low intensity may be a powerful method to investigate embryogenetic mechanisms and may also be a useful technique for investigation of other biological systems.
Interleukin-6 and new strategies for the treatment of cancer, hyperproliferative diseases and paraneoplastic syndromes (2005)

Interleukin-6 (IL-6) is a pleiomorphic cytokine whose growth factor properties play an important role in the development and progression of many types of cancer. IL-6 is produced in response to a variety of stimuli, and is required for the development of T and B lymphocytes to effector cells. In certain neoplasias, such as multiple myeloma, IL-6 is both produced and required for survival by the cancer cell itself. In other neoplasias, IL-6 may come from tissue surrounding the tumour. Thus, therapeutic strategies aimed at inhibiting the production, expression or action of IL-6 would be quite beneficial in the treatment of cancer. Moreover, IL-6 is a pathophysiological factor in several hyperproliferative diseases and the paraneoplastic syndromes that often accompany cancer, such as cachexia and osteoporosis; thus, anti-IL-6 therapy would be useful in treating these entities as well. This expert opinion acquaints the reader with IL-6, its physiological responses, the cancer types with which it is associated, and discusses the current state of therapy aimed at inhibiting it.
Interaction of the low-molecular weight salts with cationic polyelectrolytes (1997)

The interaction of several mono-, di-, and trivalent anions with cationic polyelectrolytes having different contents in N,N-dimethyl-2-hydroxypropylen ammonium chloride units (polymer A) or tertiary amine N-atoms and PEG (polymer PEGA) in the main chain was studied by viscosimetric and conductometric measurements. Both methods have shown a stronger interaction for tri- and bi- than for univalent counterions. © 1997 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 35: 2571–2581, 1997
Light scattering from cells: the contribution of the nucleus and the effects of proliferative status (2000)

As part of our ongoing efforts to understand the fundamental nature of light scattering from cells and tissues, we present data on elastic light scattering from isolated mammalian tumor cells and nuclei. The contribution of scattering from internal structures and in particular from the nuclei was compared to scattering from whole cells. Roughly 55% of the elastic light scattering at high-angles (> 40 degrees) comes from intracellular structures. An upper limit of 40% on the fractional contribution of nuclei to scattering from cells in tissue was determined. Using cell suspensions isolated from monolayer cultures at different stages of growth, we have also found that scattering at angles greater than about 110 degrees was correlated with the DNA content of the cells. Based on model calculations and the relative size difference of nuclei from cells in different stages of growth, we argue that this difference in scattering results from changes in the internal structures of the nucleus. This interpretation is consistent with our estimate of 0.2 micron as the mean size of the scattering centers in cells. Additionally, we find that while scattering from the nucleus accounts for a majority of internal scattering, a significant portion must result from scattering off of cytoplasmic structures such as mitochondria.