gebhart/patrepeval huggingface dataset:
Oxygen-Sensing Reporter Strain of <i>Pseudomonas fluorescens</i> for Monitoring the Distribution of Low-Oxygen Habitats in Soil (1999)

ABSTRACT The root-colonizing bacterium Pseudomonas fluorescens CHA0 was used to construct an oxygen-responsive biosensor. An anaerobically inducible promoter of Pseudomonas aeruginosa , which depends on the FNR (fumarate and nitrate reductase regulation)-like transcriptional regulator ANR (anaerobic regulation of arginine deiminase and nitrate reductase pathways), was fused to the structural lacZ gene of Escherichia coli . By inserting the reporter fusion into the chromosomal att Tn 7 site of P. fluorescens CHA0 by using a mini-Tn 7 transposon, the reporter strain, CHA900, was obtained. Grown in glutamate-yeast extract medium in an oxystat at defined oxygen levels, the biosensor CHA900 responded to a decrease in oxygen concentration from 210 × 10 2 Pa to 2 × 10 2 Pa of O 2 by a nearly 100-fold increase in β-galactosidase activity. Half-maximal induction of the reporter occurred at about 5 × 10 2 Pa. This dose response closely resembles that found for E. coli promoters which are activated by the FNR protein. In a carbon-free buffer or in bulk soil, the biosensor CHA900 still responded to a decrease in oxygen concentration, although here induction was about 10 times lower and the low oxygen response was gradually lost within 3 days. Introduced into a barley-soil microcosm, the biosensor could report decreasing oxygen concentrations in the rhizosphere for a 6-day period. When the water content in the microcosm was raised from 60% to 85% of field capacity, expression of the reporter gene was elevated about twofold above a basal level after 2 days of incubation, suggesting that a water content of 85% caused mild anoxia. Increased compaction of the soil was shown to have a faster and more dramatic effect on the expression of the oxygen reporter than soil water content alone, indicating that factors other than the water-filled pore space influenced the oxygen status of the soil. These experiments illustrate the utility of the biosensor for detecting low oxygen concentrations in the rhizosphere and other soil habitats.
Genetic interactions among Chlamydomonas reinhardtii mutations that confer resistance to anti-microtubule herbicides. (1992)

We previously described two types of genetic interactions among recessive mutations in the APM1 and APM2 loci of Chlamydomonas reinhardtii that may reflect a physical association of the gene products or their involvement in a common structure/process: (1) allele-specific synthetic lethality, and (2) unlinked noncomplementation, or dominant enhancement. To further investigate these interactions, we isolated revertants in which the heat sensitivity caused by the apm2-1 mutation is lost. The heat-insensitive revertants were either fully or partially suppressed for the drug-resistance caused by the apm2-1 allele. In recombination tests the revertants behaved as if the suppressing mutation mapped within the APM2 locus; the partial suppressors of apm2-1 herbicide resistance failed to complement apm2-1, leading to the conclusion that they were likely to be intragenic pseudorevertants. The apm2-1 partial suppressor mutations reversed apm1-apm2-1 synthetic lethality in an allele-specific manner with respect both to apm1- alleles and apm2-1 suppressor mutations. Those apm1- apm2-1rev strains that regained viability also regained heat sensitivity characteristic of the original apm2-1 mutation, even though the apm2-1 suppressor strains were fully heat-insensitive. The Hs+ phenotypes of apm2-1 partial suppressors were also reversed by treatment with the microtubule-stabilizing agent deuterium oxide (D2O). In addition to the above interactions, we observed interallelic complementation and phenotypic enhancement of temperature conditionality among apm1- alleles. Evidence of a role for the products of the two genes in microtubule-based processes was obtained from studying flagellar assembly in apm1- and apm2- mutants.
DX-8951F, a water-soluble camptothecin analog, exhibits potent antitumor activity against a human lung cancer cell line and its SN-38-resistant variant (1997)

We previously reported that DX-8951f, a novel water-soluble camptothecin analog, significantly inhibits the growth of various human and murine tumors in vitro and in vivo. The antitumor effects and topoisomerase I inhibitory activity of DX-8951f are stronger than those of other current camptothecin analogs. In this study, we established an SN-38-resistant cell line, PC-6/SN2-5, from the human oat cell carcinoma PC-6 cell line by a stepwise selection system, investigated the mechanism of resistance of this cell line and then compared the antitumor activity of camptothecin analogs against the cell line. PC-6/SN2-5 cells were resistant to SN-38 (32-fold) and SK&F 104864 (topotecan; 14-fold), but barely resistant to CPT-11 (3-fold) and DX-8951f (2-fold). Topoisomerase I protein levels and topoisomerase I activities of parental cells were similar to those of resistant cells. Determination of the cellular drug concentration by either flow cytometric analysis or the high-performance liquid chromatography method confirmed that the cellular accumulation of SN-38 and topotecan was significantly reduced in PC-6/SN2-5 cells, whereas that of DX-8951f was only slightly reduced. Furthermore, DX-8951f stabilized the cleavable complex formations in intact PC-6/SN2-5 cells as well as in parental cells, but SN-38 and topotecan did not in the resistant cells. Our data suggest that PC-6/SN2-5 cells may have acquired resistance to camptothecin analogs by a decrease in intracellular drug accumulation and that DX-8951f may have the potency to overcome such a type of resistance mechanism induced by camptothecin compounds.
Hereditary Juvenile Haemochromatosis and Idiopathic Dilated Cardiomyopathy (2015)

Hereditary hemochromatosis (HH), a common autosomal recessive disease, is characterized by excessive iron overload/toxicity in multiple organs (joints, liver, heart, pancreas, pituitary, adrenals and skin). Symptoms and signs depend upon the location of the excess iron deposition. Dilated cardiomyopathy is a typical complication of HH. Juvenile haemochromatosis is a rare disorder of iron metabolism with clinical manifestations before 30 years of age. Two common mutations of the haemochromatosis associated gene (HFE), cys282tyr (C282Y) and his63asp (H63D), have been implicated in the HH. These genes also appear to be modulators in cardiovascular disease. In fact the HFE gene defects are related to idiopathic dilated cardiomyopathy (IDCM) in some patients, even though the results of genotype analyses were conflicting. In this case report we investigate a 21 year-old male patient affected by juvenile haemochromatosis associated with heterozygosity for the H63D mutation with an idiopathic dilated cardiomyopathy.
Phenotypic characterization of metaplastic intestinal glands and ductular hepatocytes in cholangiofibrotic lesions rapidly induced in the caudate liver lobe of rats treated with furan. (1991)

In order to investigate the early cellular changes in liver associated with furan cholangiocarcinogenesis, young adult male Fischer 344 rats were administered furan by gavage once a day, 5 days a wk for 2 to 3 wk at doses ranging from 15 to 60 mg/kg of body weight per day. The most conspicuous feature observed in the liver of animals receiving the higher doses of furan was a rapidly developed cholangiofibrosis characterized by the presence of bile ductular hyperplasia, intestinal metaplasia, and fibrosis. Moreover, this lesion was found to be almost exclusively localized to the caudate liver lobe, which by morphometric analysis was further determined to be largely replaced by cholangiofibrotic tissue. Both the hyperplastic bile ductular epithelial cells and the intestinal-like epithelial cells in these areas selectively exhibited a strongly positive immunohistochemical staining for cytokeratin 19 and were supported by well-developed basement membranes enriched in both laminin and type IV collagen. However, in contrast to the hyperplastic bile ductules, electron microscopy of the metaplastic intestinal glands revealed them to be composed mostly of columnar epithelial cells with well-developed striated borders, less numerous mucin-secreting goblet cells, and occasional neuroendocrine-like cells, thus closely resembling in their cellular composition that of intestinal mucosa. These metaplastic glands also showed a more heterogeneous pattern of staining for both gamma-glutamyl transpeptidase and the placental form of glutathione S-transferase than did the hyperplastic bile ductules. At the 60-mg/kg/day furan dose, cholangiolar-like structures composed of biliary epithelial cells and ductular hepatocytic cells at different stages of morphological differentiation were also observed. Phenotypically, the biliary epithelial and "ductular hepatocytes" of these cholangioles shared a common basement membrane containing laminin and type IV collagen, as well as a luminal plasma membrane gamma-glutamyl transpeptidase. On the other hand, only the biliary epithelial cells of the newly appearing mixed cell cholangioles stained positive for cytokeratin 19. Interestingly, unlike hepatocarcinogen-induced oval cells, alpha-fetoprotein expression was not detected in any of the cell types comprising the furan-induced cholangiofibrotic tissue. These results support a novel in vivo model for investigating cell lineages in the development in liver of intestinal metaplasia, "ductular hepatocytes," and cholangiofibrosis in relation to intrahepatic cholangiocarcinogenesis.
Optofluidic Waveguides in Teflon AF-Coated PDMS Microfluidic Channels (2009)

We report a new method for fabricating an optofluidic waveguide that is compatible with polydimethylsiloxane (PDMS). The light path follows the microfluidic channels, an architecture that can maximize detection efficiency and make the most economic use of chip area in many lab-on-chip applications. The PDMS-based microfluidic channels are coated with Teflon amorphous fluoropolymers (Teflon AF) which has a lower refractive index (n = 1.31) than water (n = 1.33) to form a water/Teflon AF optical waveguide. Driven by a vacuum pump, the Teflon AF solution was flowed through the channels, leaving a thin (5-15 µm) layer of coating on the channel wall as the cladding layer of optical waveguides. This coating process resolves the limitations of spin-coating processes by reducing the elasticity mismatch between the Teflon AF cladding layer and the PDMS device body. We demonstrate that the resulting optofluidic waveguide confines and guides the laser light through the liquid core channel. Furthermore, the light in such a waveguide can be split when the fluid flow is split. This new method enables highly integrated biosensors such as lab-on-chip flow cytometers and micro-fabricated fluorescence-activated cell sorter with on-chip excitation.
Improved hollow-core photonic crystal fiber design for delivery of nanosecond pulses in laser micromachining applications (2005)

We report the delivery of high-energy nanosecond pulses (~65 ns pulse width) from a high-repetition-rate (up to 100 kHz) Q-switched Nd:YAG laser through the fundamental mode of a hollow-core photonic crystal fiber (HC-PCF) at 1064 nm. The guided mode in the HC-PCF has a low overlap with the glass, allowing delivery of pulses with energies above those attainable with other fibers. Energies greater than 0.5 mJ were delivered in a single spatial mode through the hollow-core fiber, providing the pulse energy and high beam quality required for micromachining of metals. Practical micromachining of a metal sheet by fiber delivery has been demonstrated.
PATTERN MATCHING WITH DIFFERENTIAL VOTING AND MEDIAN TRANSFORMATION DERIVATION Improved Point-Pattern Matching Algorithm for Two-Dimensional Coordinate Lists (2006)

We describe an algorithm for matching two-dimensional coordinate lists. Such matching should be immune to translation, rotation, scaling and flipping. We assume that coordinate lists may be only partially overlapping and we allow some random perturbations in the lists. Our goal is to match enough points to be able to derive a coordinates transformation with high confidence. The implementation described here is a part of SkySpy automated sky survey system. The presented algorithm is used to perform matching of stars detected during observations with star catalogues.
Autoimmune Oophoritis: A Clinicopathologic Assessment of 12 Cases (1990)

Summary: Twelve cases of histologically confirmed autoimmune oophoritis are described. Eight presented with symptoms and laboratory evidence of premature ovarian failure (POF). Four were diagnosed unexpectedly after hysterectomy for endometrial pathology or for sequelae of cystic enlargement of the ovaries. Two of eight patients tested had serum anti-ovarian autoantibodies (Aab), while five of seven had anti-adrenal Aab. Two women had, or subsequently developed, Addison's disease, and two patients had Hashimoto's disease at presentation. All women with this disease risk the development of adrenal failure and hypothyroidism. Microscopically, 11 cases showed a lymphoplasmacytic infiltrate that spared primordial follicles but involved, with progressive intensity, early and late preovulatory follicles and corpora lutea. Sparse perivascular and perineural inflammatory infiltrates were also present. The twelfth case appeared to be a unique case of granulomatous oophoritis, considered autoimmune because of the folliculotropic nature of the inflammatory process. Three cases showed evidence of follicular dysplasia.
Review Article: Shakespeare and Cognitive Literary and Performance Studies (2013)

Questions are, and need to be, raised when scientific terms and ideas are reapplied in apparently non-scientific disciplines.The modern English restriction of the term 'science', a Latin derived term for knowledge, to those branches of study that deal with the natural and physical sciences, in itself suggests what can be an increasingly skewed modern perception of what are significant forms of human understanding (OED 5b).The concern then when the humanities adopt and apply such forms of scientific knowledge is that it entails an overbearing constraint on, and a further reduction of the value of, their own complex matter and methodologies.This has led to sceptical responses, such as Raymond Tallis's dismissal of what he terms the current 'neuromania' or 'Darwinitis'.Tallis's book Aping Mankind warns that the reach of neuroscience and evolutionary psychology are being overestimated, with too much of a focus on the physical rather than the cultural contributions that make us human.This is potentially a valuable counterpoint.Yet such critiques of scientific disciplines often themselves err by focusing on only overly simplified versions of scientific data and claims.Besides, in the humanities it is the reach of the cultural rather than of the physical that has tended to be overestimated, with postmodernist notions of humans as sociocultural constructs overly dominating discourses (notably in new historicism, cultural materialism, and feminist, queer and globalisation studies).
Adaptations of alpha2- and beta-cells of rat and mouse pancreatic islets to starvation, to refeeding after starvation, and to obesity. (1980)

The effects of starvation and refeeding and of obesity on pancreatic alpha2- and beta-cell responses to glucose or tolbutamide were studied with the isolated rat or mouse pancreas perfused with an amino acid mixture in the presence and absence of glucose. It was observed that the physiological adaptation to a regimen of fasting and realimentation and to obesity differed greatly in the two types of endocrine cells. Whereas beta-cells of rats showed a dramatic reduction of glucose- and tolbutamide-stimulated insulin release during starvation that was reversed by refeeding, alpha2-cells preserved their response to stimulators and inhibitors during this experimental manipulation. Amino acid stimulation of glucagon release occurred equally well with the pancreas from fed and starved rats and was suppressed efficiently by glucose and tolbutamide in both nutritional states. Surprisingly, the rate of onset of glucose suppression of alpha2-cells was significantly higher in the fasted than in the fed state. This glucose hypersensitivity was apparent 2 d after after food deprivation and had disappeared again on the 2nd d of refeeding. In the pancreas from animals starved for 3 d, glucose and tolbutamide suppression of alpha2-cells took place in the absence of demonstrable changes of insulin release. In the isolated perfused pancreas taken from the hyperphagic obese hyperglycemic mouse (C57 Black/6J; ob/ob), the observed rate of insulin secretion as a result of a combined stimulus of amino acids and glucose and of glucagon release stimulated by amino acids was about four times higher than achieved by the pancreas of lean controls. However, glucose was unable to suppress the alpha2-cells in the pancreas of obese animals, in spite of the hypersection of the beta-cells, again in contrast to the alpha2-cells of controls that were readily inhibited by glucose. These data imply that the acute suppression of alpha2-cells by glucose is largely independent of a concomitant surge of extracellular insulin levels and that the adaptation of the islet organ to starvation leads to decreased glucose sensitivity of beta-cells, which contrasts with an improved glucose responsiveness of alpha2-cells. However, hyperphagia, which is assumed to be the primary abnormality in the ob/ob mouse, leads to overproduction of insulin and glucagon by the pancreas while greatly reducing the alpha2-cell sensitivity to glucose. An attempt is made to incorporate these data on starvation, refeeding, and obesity, as well as previous results with experimental diabetes, in a comprehensive picture describing a regulative principle underlying the glucose responsivness of alpha2-cells.
Anode substrate with continuous porosity gradient for tubular solid oxide fuel cells (2013)

Tubular solid oxide fuel cells (SOFCs) are fabricated using a modified phase inversion process to obtain anode structure with graded pore distribution. The novel structure is achieved using an additional graphite layer to control the phase separation reaction in the ceramic layer and to remove the skin layer, which always presents in phase inversion process. The graded anode can effectively eliminate the concentration polarization loss at high current density as observed for the anode with the skin layer. In addition, improved peak power density is obtained with the graded-anode based cell, demonstrating that the modified process is promise in fabricating tubular SOFCs.
Design optimization of main, gradient and RF field coils for MR imaging (1990)

Image quality in magnetic resonance imaging (MRI) is closely connected to the quality of three types of magnetic fields. The geometry design of their generating coils is based on algorithmic optimization codes. The author discusses the strategies used and shows examples of solutions related to coil design optimization.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Building Upon Patterned Organic Monolayers Produced via Catalytic Stamp Lithography (2010)

Soft lithographic sub-100 nm chemical patterning was demonstrated on organic monolayer surfaces using poly(dimethylsiloxane)-based stamps decorated with Pd nanostructures, structures termed "catalytic stamps". Chemically reactive azide or alkene functionalities were incorporated on oxide-capped silicon surfaces and utilized for patterning via Pd-catalyzed hydrogenation or Heck reactions. The catalytic stamps were soft lithographic stamps based on PDMS with embedded nanoscale palladium catalysts, prepared via block copolymer-based templating. Nanoscale chemical patterns were readily generated on the azide or alkene precursor surfaces simply by applying the Pd catalytic stamps and the reactive molecule, the molecular ink, to the surface, thanks to the highly localized catalytic transformations induced by the patterned, immobilized solid Pd catalysts. A series of successful postfunctionalization reactions on the resulting patterned surfaces further demonstrated the utility of this approach to construct novel designs of nanoarchitectures, with potentially unique and innovative properties.
Endogenous hepcidin and its agonist mediate resistance to selected infections by clearing non–transferrin-bound iron (2017)

The iron-regulatory hormone hepcidin is induced early in infection, causing iron sequestration in macrophages and decreased plasma iron; this is proposed to limit the replication of extracellular microbes, but could also promote infection with macrophage-tropic pathogens. The mechanisms by which hepcidin and hypoferremia modulate host defense, and the spectrum of microbes affected, are poorly understood. Using mouse models, we show that hepcidin was selectively protective against siderophilic extracellular pathogens (<i>Yersinia enterocolitica</i> O9) by controlling non-transferrin-bound iron (NTBI) rather than iron-transferrin concentration. NTBI promoted the rapid growth of siderophilic but not nonsiderophilic bacteria in mice with either genetic or iatrogenic iron overload and in human plasma. Hepcidin or iron loading did not affect other key components of innate immunity, did not indiscriminately promote intracellular infections (<i>Mycobacterium tuberculosis</i>), and had no effect on extracellular nonsiderophilic <i>Y enterocolitica</i> O8 or <i>Staphylococcus aureus</i> Hepcidin analogs may be useful for treatment of siderophilic infections.
Self‐Assembly of Folic Acid Derivatives: Induction of Supramolecular Chirality by Hierarchical Chiral Structures (2004)

Hierarchical chiral structures made up of dendritic oligo(L- or D-glutamic acid) moieties of folic acid derivatives induce supramolecular chirality in the self-assembled columnar structures of the folic acids. These folic acids self-assemble through the intermolecular hydrogen bonds of the pterin rings to form disklike tetramers. In the neat states, the stacked tetramers form thermotropic hexagonal columnar phases over wide temperature ranges, including room temperature. Addition of alkali metal salts induces chirality in the columnar phases. In dilute solution states in a relatively polar solvent (chloroform), the folic acid derivatives form non-chiral, self-assembled structures. In the presence of sodium triflate, the folic acid forms chiral columnar assemblies through the oligo(L-glutamic acid) moiety, similar to those formed in the liquid-crystalline (LC) states. The enantiomer of the folic acid induces columnar assemblies with reversed helicity. In the case of the diastereomer, no induced helicity is observed. Application of an apolar solvent (dodecane) drives the folic acid derivatives to form chiral assemblies in the absence of ions. In this case, lipophilic interactions promote nanophase segregation, which enhances the formation of chiral columns. Interestingly, the chiral supramolecular structure of the diastereomer induces the most intense circular dichroism. In both cases, the molecular chirality in the oligo(glutamate) moieties yields supramolecular chirality of the folic acids that self-assemble through cooperative molecular interactions.
Trans-septal catheterization for radiofrequency catheter ablation of cardiac arrhythmias. Results and safety of a simplified method (1998)

In experienced hands and according to the method described in this paper, the elective use of transseptal catheterization for radiofrequency catheter ablation in a large cohort of patients with cardiac arrhythmias is feasible, safe and allows successful ablation in the vast majority of the patients.