gebhart/patrepeval huggingface dataset:
Pyogenic liver abscess: contrast-enhanced MR imaging in rats (1988)

MR imaging was used to evaluate experimentally induced pyogenic liver abscesses in an animal model. Rats were examined before and after IV administration of either gadolinium-diethylenetriaminepentaacetic acid (Gd-DTPA), ferrite particles, or both contrast agents together. Pyogenic liver abscesses appeared hypointense on T1-weighted images and hyperintense on T2-weighted images. Bolus administration of Gd-DTPA using a fast spin-echo sequence with repetition time of 250 msec and echo time of 20 msec (SE 250/20) showed transient selective enhancement of normal hepatic tissue and increased lesion conspicuity, quantitatively assessed by the contrast-to-noise ratio, which increased from -35.7 to -59.0. Delayed leakage of Gd-DTPA into the abscess center partially obscured small lesions at 30-60 min. Ferrite particles reduced the signal intensity of normal liver, and the abscess then appeared homogenously hyperintense. Applying the SE 500/32 sequence, the contrast-to-noise ratio increased from -1.2 to +74.0. Coordinated administration of both contrast agents showed a further increase in contrast to +94.0, with a hyperintense abscess rim surrounded by hypointense liver. Gd-DTPA increases abscess-liver contrast by rim enhancement of the abscess wall, and ferrite increases the abscess-liver contrast by selectively decreasing the signal intensity of surrounding normal liver. As a result of increased contrast-to-noise ratio, both contrast agents, alone or in combination, increase the conspicuity of hepatic abscesses.
Antitumor effect of taxol-containing liposomes in a taxol-resistant murine tumor model. (1993)

Taxol is a promising agent for use in ovarian cancer and other malignancies. One problem associated with taxol is its low aqueous solubility, requiring Cremophor EL (polyethoxylated castor oil) and ethanol as excipients (Diluent 12); these agents cause serious adverse effects. Liposomes containing taxol and phospholipid (in a 1:33 mole ratio, respectively) were prepared from phosphatidylglycerol and phosphatidylcholine in a 1:9 mole ratio. Antitumor effect was evaluated against Colon-26, a taxol-resistant murine tumor. Given as 1, 4, or 9 injections, free taxol given i.v. in Diluent 12 was ineffective at delaying tumor growth at doses < or = 30 mg/kg per injection (the maximum tolerated dose). In contrast, taxol-liposomes were well tolerated at doses greater than or equal to the maximum tolerated dose of free taxol and showed significant tumor growth inhibition at 10-45 mg/kg per injection.
Engineering of a glycosidase Family 7 cellobiohydrolase to more alkaline pH optimum: the pH behaviour of Trichoderma reesei Cel7A and its E223S/ A224H/L225V/T226A/D262G mutant (2001)

The crystal structures of Family 7 glycohydrolases suggest that a histidine residue near the acid/base catalyst could account for the higher pH optimum of the Humicola insolens endoglucanase Cel7B, than the corresponding Trichoderma reesei enzymes. Modelling studies indicated that introduction of histidine at the homologous position in T. reesei Cel7A (Ala224) required additional changes to accommodate the bulkier histidine side chain. X-ray crystallography of the catalytic domain of the E223S/A224H/L225V/T226A/D262G mutant reveals that major differences from the wild-type are confined to the mutations themselves. The introduced histidine residue is in plane with its counterpart in H. insolens Cel7B, but is 1.0 Å (= 0.1nm) closer to the acid/base Glu217 residue, with a 3.1 Å contact between N∊2 and O∊1. The pH variation of kcat/Km for 3,4-dinitrophenyl lactoside hydrolysis was accurately bell-shaped for both wild-type and mutant, with pK1 shifting from 2.22±0.03 in the wild-type to 3.19±0.03 in the mutant, and pK2 shifting from 5.99±0.02 to 6.78±0.02. With this poor substrate, the ionizations probably represent those of the free enzyme. The relative kcat for 2-chloro-4-nitrophenyl lactoside showed similar behaviour. The shift in the mutant pH optimum was associated with lower kcat/Km values for both lactosides and cellobiosides, and a marginally lower stability. However, kcat values for cellobiosides are higher for the mutant. This we attribute to reduced non-productive binding in the +1 and +2 subsites; inhibition by cellobiose is certainly relieved in the mutant. The weaker binding of cellobiose is due to the loss of two water-mediated hydrogen bonds.
Circos: An information aesthetic for comparative genomics (2009)

We created a visualization tool called Circos to facilitate the identification and analysis of similarities and differences arising from comparisons of genomes. Our tool is effective in displaying variation in genome structure and, generally, any other kind of positional relationships between genomic intervals. Such data are routinely produced by sequence alignments, hybridization arrays, genome mapping, and genotyping studies. Circos uses a circular ideogram layout to facilitate the display of relationships between pairs of positions by the use of ribbons, which encode the position, size, and orientation of related genomic elements. Circos is capable of displaying data as scatter, line, and histogram plots, heat maps, tiles, connectors, and text. Bitmap or vector images can be created from GFF-style data inputs and hierarchical configuration files, which can be easily generated by automated tools, making Circos suitable for rapid deployment in data analysis and reporting pipelines.
Characterization of Recombinant Mannan-Binding Lectin-Associated Serine Protease (MASP)-3 Suggests an Activation Mechanism Different from That of MASP-1 and MASP-2 (2004)

Mannan-binding lectin (MBL)-associated serine proteases (MASP-1, -2, and -3) are homologous modular proteases that each associate with MBL and L- and H-ficolins, which are oligomeric serum lectins involved in innate immunity. To investigate its physicochemical, interaction, and enzymatic properties, human MASP-3 was expressed in insect cells. Ultracentrifugation analysis indicated that rMASP-3 sedimented as a homodimer (s(20,w) = 6.2 +/- 0.1 S) in the presence of Ca(2+), and as a monomer (s(20,w) = 4.6 +/- 0.1 S) in EDTA. As shown by surface plasmon resonance spectroscopy, it associated with both MBL (K(D) = 2.6 nM) and L-ficolin (K(D) = 7.2 nM). The protease was produced in a single-chain, proenzyme form, but underwent slow activation upon prolonged storage at 4 degrees C, resulting from cleavage at the Arg(430)-Ile(431) activation site. Activation was prevented in the presence of protease inhibitors iodoacetamide and 1,10-phenanthroline but was not abolished upon substitution of Ala for the active site Ser(645) of MASP-3, indicating extrinsic proteolysis. In contrast, the corresponding mutations Ser(627)-->Ala in MASP-1 and Ser(618)-->Ala in MASP-2 stabilized the latter in their proenzyme form. Likewise, the MASP-1 and MASP-2 mutants were each activated by their active counterparts, but MASP-3 S645A was not. Activated MASP-3 did not react with C1 inhibitor; had no activity on complement proteins C2, C4, and C3; and only cleaved the N-carboxybenzyloxyglycine-L-arginine thiobenzyl ester substrate to a significant extent. Based on these observations, it is postulated that MASP-3 activation and control involve mechanisms that are different from those of MASP-1 and -2.
Augmentation for intratumoral accumulation and anti‐tumor activity of liposome‐encapsulated adriamycin by tumor necrosis factor‐α in mice (1990)

The effect of recombinant human tumor necrosis factor-alpha (rhTNF-alpha) on anti-tumor activity of adriamycin entrapped in small unilamellar liposomes (ADM-Lip) has been studied using BALB/c mice bearing subdermal Meth-A fibrosarcoma. Accumulation of i.v. injected ADM-Lip, but not of free ADM, into tumor tissue was augmented by a single i.v. injection of rhTNF-alpha. The maximum effect of rhTNF-alpha was expressed when it was injected 1 hr before ADM-Lip. This rhTNF-alpha treatment did not result in increased accumulation of ADM-Lip in normal organs. Based on these results, we treated mice bearing Meth-A tumor with rhTNF-alpha and then with ADM-Lip 1 hr later. By 2-cycle treatments using this regimen, tumor growth was markedly inhibited, and 5 out of 13 mice tested were cured of tumor, while treatment with rhTNF-alpha alone, ADM alone, ADM-Lip alone or rhTNF-alpha plus ADM resulted neither in prolongation of survival time nor in cure of mice. Our results indicate that ADM-Lip can express a potent and systemic anti-tumor activity after pretreatment of animals with TNF, but only when administration of these drugs is appropriately timed.
Fighting fit (1998)

Pat White discusses how conflict can be harnessed as a positive force for change when managed effectively
OsCSLD1, a Cellulose Synthase-Like D1 Gene, Is Required for Root Hair Morphogenesis in Rice (2007)

Root hairs are long tubular outgrowths that form on the surface of specialized epidermal cells. They are required for nutrient and water uptake and interact with the soil microflora. Here we show that the Oryza sativa cellulose synthase-like D1 (OsCSLD1) gene is required for root hair development, as rice (Oryza sativa) mutants that lack OsCSLD1 function develop abnormal root hairs. In these mutants, while hair development is initiated normally, the hairs elongate less than the wild-type hairs and they have kinks and swellings along their length. Because the csld1 mutants develop the same density and number of root hairs along their seminal root as the wild-type plants, we propose that OsCSLD1 function is required for hair elongation but not initiation. Both gene trap expression pattern and in situ hybridization analyses indicate that OsCSLD1 is expressed in only root hair cells. Furthermore, OsCSLD1 is the only member of the four rice CSLD genes that shows root-specific expression. Given that the Arabidopsis (Arabidopsis thaliana) gene KOJAK/AtCSLD3 is required for root hair elongation and is expressed in the root hair, it appears that OsCSLD1 may be the functional ortholog of KOJAK/AtCSLD3 and that these two genes represent the root hair-specific members of this family of proteins. Thus, at least part of the mechanism of root hair morphogenesis in Arabidopsis is conserved in rice.
Hydrothermal Synthesis of Ferroelectric PbHPO4 Nanowires from a Single-Source Precursor (2008)

Ferroelectric PbHPO4 nanowires have been successfully prepared from a Pb(II)−IP6 (IP6, inositol hexakisphosphate acid) complex, a novel single-source precursor, by a hydrothermal method at 180 °C for 24 h. The structure and morphology of the as-prepared PbHPO4 nanowires and the Pb(II)−IP6 complex were systematically studied by means of X-ray diffraction, scanning electron microscopy, transmission electron microscopy, and Fourier transform infrared spectroscopy. The possible formation mechanism for PbHPO4 nanowires is also proposed. The photoluminescence (PL) and ferroelectric properties of the obtained products were investigated in detail. PL measurements indicate that under the excitation of 375 nm the products have a broad emission peak at 460 nm. The ferroelectric hysteresis loop shows that the remnant polarization (PR) is equal to its maximum polarization (PS). The one-dimensional conducting protons chains in the PbHPO4 crystal structure may be responsible for this unique ferroelectric hysteresis loop.
Metabotropic Glutamate Receptors Are Involved in Long-Term Potentiation in Isolated Slices of Rat Medial Frontal Cortex (1997)

The prelimbic region of medial frontal cortex in the rat receives a direct input from the hippocampus and this functional connection is essential for aspects of spatial memory. Activity-dependent changes in the effectiveness of synaptic transmission in the medial frontal cortex, namely long-term potentiation (LTP) and long-term depression (LTD) can persist for tens of minutes or hours and may be the basis of learning and memory storage. Glutamatergic activation of ionotropic receptors is required to induce both LTP and LTD. We now present evidence of the involvement of metabotropic glutamate receptors in LTP in isolated slices of frontal cortex. Repetitive bursts of stimulation at theta frequencies (TBS) were applied to layer II, and monosynaptic EPSPs were monitored in layer V neurons of the prelimbic area. TBS was found to be more effective at inducing LTP than tetanic stimulation at 100 Hz and produced LTP that lasted >30 min in 8 out of 14 neurons. Tetanic stimulation at 100 Hz in the presence of the N-methyl--aspartate (NMDA)-antagonist 2-amino-5-phosphonopentanoate (AP5) was reported to be a reliable method of inducing LTD in prelimbic cortex (). However we found that this protocol did not facilitate the induction of LTD. The role of metabotropic glutamate receptors (mGluR) in LTP was assessed by using the selective, broad-spectrum antagonist (R, S)-alpha-methyl-4- carboxyphenylglycine (MCPG). This drug significantly reduced the incidence of LTP after TBS to only 1 of 14 neurons (P < 0.02, chi2 test). The pooled responses to TBS in MCPG showed significantly reduced potentiation [(P < 0.02, analysis of variance (ANOVA)]. The broad-spectrum mGluR agonist (1S, 3R)-1-aminocyclopentane-1,3-dicarboxylic acid (ACPD) and the selective group I agonist S-3 hydroxyphenylglycine(S-3HPG) both produced membrane depolarization, an increase in number of spikes evoked by depolarizing current pulses, and a reduction in the afterhyperpolarization. Similar effects were produced by these agonists even when synaptic transmission was blocked by use of the gamma-aminobutyric acid-B (GABAB) receptor agonist, 200 microM baclofen, which suggests that group I mGluRs are present on layer V neurons. We conclude that mGluRs participate in the production of LTP in prelimbic cortex, and that this excitatory effect could be mediated by the postsynaptic group I mGluRs.
Kinetics of nitroxide radical trapping. 2. Structural effects (1992)

Laser flash photolysis and kinetic competition product demonstrated that in isooctane at ambient temperature the rate constant for coupling of carbon-centered with presistent nitroxides, kT, upon the of steric hindrance to coupling and upon the extent of resonance stabilization of the carbon radical. Sterically induced reductions in the magnitude of kT are observed for changes in both the structure of the nitroxide the structure of the carbon radical. Thus, for any particular carbon kT is largest for the Bredt's rule protected nitroxides, 9-azabicyclo[3.3.1]nonane-N-oxyl (ABNO) and nortropane-N-oxyl, while for the "usual" di-tert-alkyl nitroxides kT decreases along the series, 1,1,3,3-tetra-methylisoindoline-2-oxyl ≥ 2,2,5,5-tetramethylpiperidin-1-oxyl (Tempo) > di-tert-butyl nitroxide, i.e., kT decreased on going from a five-membered ring to a six-membered ring to a noncyclic structure. Cyclopropyl triphenylmethyl are trapped at the fastest and slowest rates, respectively, the corresponding kT value 3.0 × 109 and 1.2 × 108 M-1 s-1 for ABNO and 2.1 × 109 <1 × 106 M-1 s-1 for Tempo. Steric effects in the carbon radicals are for Tempo than for ABNO. For example, the ratio of kT's for the trapping of nonyl tert-butyl is 1.7 for Tempo but 1.3 for ABNO, while for the trapping of benzyl cumyl the ratio of kT's is 4.1 for Tempo 0.9 for ABNO. The effect of resonance stabilization can be illustrated by the kT values for three sterically unhindered primary radicals, n-nonyl, benzyl, 2-naphthyhmethyl, viz., 1.2 × 109, 4.8 × 108, and 5.7 × 107 M-1 s-1, respectively, for Tempo and 2.2 × 109, 1.2 × 109, and 8.1 × 108 M-1 s-1, respectively, for ABNO.
An atomic-resolution atomic-force microscope implemented using an optical lever (1989)

We present the first atomic-resolution image of a surface obtained with an optical implementation of the atomic-force microscope (AFM). The native oxide on silicon was imaged with atomic resolution, and ≊5-nm resolution images of aluminum, mechanically ground iron, and corroded stainless steel were obtained. The relative merits of an optical implementation of the AFM as opposed to a tunneling implementation are discussed.
KVLQT1 C-Terminal Missense Mutation Causes a Forme Fruste Long-QT Syndrome (1997)

Our data show a wide KVLQT1 allelic heterogeneity among 20 families in which KVLQT1 causes RWS. We describe the first missense mutation in the C-terminal domain of KVLQT1, which is clearly associated with a fruste phenotype, which could be a favoring factor of acquired LQT syndrome.
Assembly, spatial distribution, and secretion activity of the curlin secretion lipoprotein, CsgG (2008)

Escherichia coli assembles functional amyloid fibers called curli. Produced by many Enterobacteriaceae spp., curli fibers are associated with biofilm formation, host cell adhesion and invasion, and immune system activation. CsgB nucleates the major curli subunit protein, CsgA, into a self-propagating amyloid fiber on the cell surface. CsgA and CsgB cell surface association and subsequent fiber polymerization are efficient processes, yet little is known about how the subunits reach and become positioned on the surface. I have characterized the role of CsgG in curli subunit secretion across the outer membrane, and found that CsgG is the central molecule of the curli secretion and assembly complex. CsgG formed an oligomeric complex in the outer membrane that interacted with at least three other csg encoded proteins. I found that the CsgG lipoprotein spanned the outer membrane, was sufficient for curlin transport across the outer membrane, and that a specific signal peptide on the N-terminus of the major fiber subunit directed protein secretion via the CsgG secretion apparatus. I also discovered that CsgG was non-uniformly distributed on the surface of curli-producing cells, and that the assembly, spatial organization, and secretion activity of CsgG was modified by other components of the curli assembly machine. One of the other curli assembly proteins, CsgE, was found to specifically function in the secretion pathway and to modulate both the secretion activity of CsgG and to act directly on CsgA to prevent self-polymerization. These results suggest a model where secretion and fiber assembly are tightly coupled and highly ordered processes.
Production Improvement of Heavy-Oil Recovery by Using Electromagnetic Heating (2008)

Abstract Heavy oil is produced primarily by reducing its viscosity using well-known processes such as steam injection, steamsoak, and in situ combustion. A recent technique for recovery consists of resistively heating the reservoir using electrical energy. Resistive heating can be particularly beneficial for reservoirs in which conventional steam operations are uneconomic. Resistive heating is a special case of a more general form of heating based on electromagnetic energy (EM). EM has the following advantages over steam injection: it can be used to recover extremely heavy hydrocarbon, is not susceptible to heat losses through a wellbore, and its water requirements are far less than for steam. Compared to resistive heating, EM heats within the formation. Thus (for downhole generation) larger well spacing may be possible. Although its potential was recognized in the late 70's, there are relatively few field applications of EM heating and even fewer engineering studies. The purpose of this paper is to examine how the performance response of EM compares to resistive heating. This paper presents a model for single-phase flow to calculate the temperature distribution, and the productivity improvement obtained when an EM heating source (an antenna) is placed in a well. We consider both counter-current flow, in which the well with the antenna is also a producer, and co-current flow where the flow is opposite to EM energy flow. Flow is taking place concurrently with the addition of EM energy. Steady-state solutions for counter-current flow showed a relative productivity index (PI) increase of 2.5 - 12.0 times cold oil production when the input power was varied from 20 to 150kw. A peak improvement occurred when the adsorption coefficient was between 1e−3 and le−1 m−1, which indicates that there is an optimum adsorption coefficient. Resistive heating is the special case of an infinite adsorption coefficient and the existence of an optimum suggests that EM heating can be more effective than resistive heating. For co-current flow, the improvement was even greater for the same input power. Calculated energy gains (the ratio of produced to injected energy) were in the 8 to 163 range; successful steam injection processes have gains of around 10.
T-cell adoptive immunotherapy for acute lymphoblastic leukemia (2013)

Substantial progress has been made in the treatment of precursor B-cell acute lymphoblastic leukemia (B-ALL), but recurrent disease remains a leading cause of death in children due to cancer and outcomes for adults with B-ALL remain poor. Recently, complete clinical responses have been observed in small numbers of patients with B-ALL treated with adoptive immunotherapy using T cells genetically engineered to express chimeric antigen receptors (CARs) targeting CD19, a cell surface molecule present in essentially all cases of B-ALL. Preclinical data suggest that CARs targeting CD22, another antigen present in the majority of B-ALL cases, are similarly potent. Several clinical studies already under way will soon more clearly define the rate of response to this novel therapy in B-ALL. Further work is needed to identify optimal platforms for CAR-based adoptive immunotherapy for leukemia, to establish guidelines for managing toxicity, and to determine whether the remissions induced by this approach can be rendered durable.
Penetration of mitomycin C in human bladder. (1993)

The penetration of mitomycin C (MMC) in bladder tissue was studied in patients who received intravesical chemotherapy at the time of radical cystectomy. An intravesical dose of MMC (20 mg/40 ml) was instilled and maintained in the bladder for 60 to 120 min at which time the solution was drained. Within 10 to 60 min after draining the drug solution, the bladder vasculature was ligated, and the bladder was removed. Tissues were sectioned serially in layers parallel to the urothelium and analyzed for MMC concentration. Of the 24 patients evaluated, 17 patients had a low final MMC concentration in urine (< 66 micrograms/ml) or had the MMC solution drained more than 30 min before ligation of the blood vessels. Among these 17 patients, the concentration in the urothelium was measurable in only 4 patients, while the concentrations in deeper tissues were not measurable. In the remaining 7 patients where the urine concentration was > 120 micrograms/ml and where the vasculature was ligated within 30 min after the MMC solution was drained, the bladder wall contained significant MMC concentrations. The drug penetration was studied in the latter 7 patients, using sections of bladder wall that were grossly normal and non-tumor bearing. Concentrations in the bladder wall declined semilogarithmically with tissue depth from the urothelium to the deep muscle and reached a plateau at about 2000 microns depth. The median MMC concentrations were 5.6 micrograms/g in the urothelium and lamina propria interface, 2.7 micrograms/g in the lamina propria, and 0.9 microgram/g in the muscularis. The distance over which the MMC concentration decreased by one-half was about 500 microns. The concentration ratio between the urine and urothelium/lamina propria interface was about 35-fold. The mean plasma concentrations were 0.003, 0.1, and 0.4% of the mean concentration in urine, urothelium, and the averaged bladder tissue concentrations, respectively. Paired superficial tumor and normal tissues were obtained from 5 bladders. In 4 of 5 cases, the concentration in tumors was higher than in normal tissues, while the reverse was seen in the remaining tumor. In one sessile bladder tumor a complete concentration-depth profile could be obtained. While the concentrations in the tumor tissue were 2-3-fold higher than that in the adjacent normal tissue, the rate of concentration declined with respect to tissue depth and hence the distance over which the MMC concentration decreased by one-half was similar in both tumors.(ABSTRACT TRUNCATED AT 400 WORDS)