gebhart/patrepeval huggingface dataset:
Confocal theta microscope with three objective lenses (1994)

A microscope using three water immersion objective lenses which realizes confocal, 4Pi-confocal and various confocal theta microscopies in fluorescence, transmission, scattered, and reflection mode is described. An argon-ion laser is the primary light source. A pulsed titanium-sapphire laser allows two-photon absorption fluorescence microscopy. The instrument has a predicted resolution of 100 nm along the illumination axis and a three-dimensional resolution of 5×106 nm3 for lenses each with a numerical aperture of 0.75. This is an improvement of an order of magnitude over a confocal fluorescence microscope using the same lens. Applications of the microscope range from observation of a sample at three different angles, to confocal theta fluorescence microscopy with multiphoton absorption. Since mounting and immersion media are identical, aberrations become negligible. The large working distance of 2 mm makes the instrument ideal for the observation of biological samples of up to 1.5 mm in diameter such as drosophila embryos.
Synthesis of 4-alkyl-, 4-aryl- and 4-arylamino-5-aminoisoquinolin-1-ones and identification of a new PARP-2 selective inhibitor (2010)

The considerable interest in substituted isoquinolin-1-ones related to 5-aminoisoquinolin-1-one (5-AIQ) as drugs points to a need for an efficient and straightforward synthesis of the 4,5-disubstituted bicycles. Bromination of 5-nitroisoquinolin-1-one gave 4-bromo-5-nitroisoquinolin-1-one but neither this nor 5-amino-4-bromoisoquinolin-1-one would participate in Pd-catalysed couplings. Protection of the lactam as 1-methoxy- and 1-benzyloxy-4-bromo-5-nitroisoquinolines, however, permitted Stille, Suzuki and Buchwald-Hartwig couplings to take place in high yields, insensitive to electronic demands and severe steric bulk in the arylboronic acids. Lithiation of 4-bromo-1-methoxy-5-nitroisoquinoline and quench with iodomethane gave 1-methoxy-4-methyl-5-nitroisoquinoline in low yield. Demethylation of the 1-methoxy-4-substituted-5-nitroisoquinolines with hydrogen bromide gave 4-substituted-5-nitroisoquinolin-1-ones, whereas hydrogenolytic debenzylation was achieved with simultaneous reduction of the 5-nitro group. 5-Amino-4-(4-trifluoromethylphenyl)isoquinolin-1-one was identified as a new potent and selective inhibitor of poly(ADP-ribose)polymerase-2 (PARP-2).
A survey on motion prediction and risk assessment for intelligent vehicles (2014)

Abstract With the objective to improve road safety, the automotive industry is moving toward more “intelligent” vehicles. One of the major challenges is to detect dangerous situations and react accordingly in order to avoid or mitigate accidents. This requires predicting the likely evolution of the current traffic situation, and assessing how dangerous that future situation might be. This paper is a survey of existing methods for motion prediction and risk assessment for intelligent vehicles. The proposed classification is based on the semantics used to define motion and risk. We point out the tradeoff between model completeness and real-time constraints, and the fact that the choice of a risk assessment method is influenced by the selected motion model.
Uptake of Glycylglycine by the Scutellum of Germinating Barley Grain (1978)

The scutella separated from germinating barley grains (Hordeum vulgare L. cv. Himalaya) took up the dipeptide [(14)C]glycylglycine (Gly-Gly) rapidly from incubation media. The pH optimum of the process was about 4.5, and the rate of uptake conformed to Michaelis-Menten kinetics with an apparent K(m) of 2.3 mm and V(max) of 41 mumole gram(-1) hour(-1). The uptake was strongly inhibited by dinitrophenol and cyanide and by lack of O(2).After incubation of the scutella with Gly-Gly, no intact Gly-Gly was detectable in the scutella but the level of free glycine increased. The poorly hydrolyzed "model" dipeptide glycylsarcosine, which is actively taken up and accumulated by the scutella, was a competitive inhibitor of the uptake of Gly-Gly and completely inhibited the uptake at infinitely high inhibitor concentration. This suggests that Gly-Gly is taken up by the same mechanism as glycylsarcosine as an intact dipeptide (without hydrolysis in the membrane) and is hydrolyzed to free glycine by the abundant peptidases of the scutella.The uptake of Gly-Gly was not affected by glycine or leucine, but was strongly inhibited by all of the 10 dipeptides tested for inhibition. The three dipeptides tested for uptake, Ala-Gly, Pro-Gly, and Gly-Pro, were all taken up by the scutella. Thus, the uptake mechanism for the dipeptides seems to be rather nonspecific with respect to the side chains of the amino acids. The high rates of the uptake suggest that this process has an essential role in the mobilization of reserve proteins in the germinating grain.
Early post-treatment with 9-cis retinoic acid reduces neurodegeneration of dopaminergic neurons in a rat model of Parkinson’s disease (2012)

Our data suggests that early post-treatment with 9cRA has a protective effect against neurodegeneration in nigrostriatal DA neurons in an animal model of PD.
Urinary Recovery of N -Formimidoyl Thienamycin (MK0787) as Affected by Coadministration of N -Formimidoyl Thienamycin Dehydropeptidase Inhibitors (1983)

N-Formimidoyl thienamycin (MK0787) undergoes renal metabolism by a dipeptidase, dehydropeptidase I, located on the brush border of the proximal tubular cells. The effects of two inhibitors (MK-789 and MK-791) of dehydropeptidase I on the pharmacokinetics of N-formimidoyl thienamycin were studied in 41 healthy subjects receiving various combinations of N-formimidoyl thienamycin and MK-789 or MK-791. Both inhibitors affected the plasma kinetics of N-formimidoyl thienamycin only to a small extent. Plasma concentrations and the area under the plasma concentration curve increased about 20% with a proportional decrease in plasma clearance. Plasma half-life was not altered significantly. Coadministration of MK-789 or MK-791 resulted in uniform and marked increases in urinary recovery and renal clearance of N-formimidoyl thienamycin. Thus, at an N-formimidoyl thienamycin/MK-791 ratio of 1:0.25 or higher, the urinary recovery was about 72% in all subjects, whereas it varied between 7.7 and 43% when N-formimidoyl thienamycin was given alone. The ratio of the N-formimidoyl thienamycin and MK-791 doses affected response. At relatively higher doses of MK-791, significant increases of N-formimidoyl thienamycin urinary recovery, renal clearance, and urine concentrations occurred during the later part of the 10-h observation period after each administration. At a 1:1 ratio of the two drugs, the inhibition of renal metabolism of N-formimidoyl thienamycin was maintained for at least 8 h, whereas renal clearance declined as soon as 4 h after the administration of a 1:0.25 ratio. The results indicated that MK-789 and MK-791 alter the renal excretion of N-formimidoyl thienamycin from glomerular filtration plus tubular secretion to glomerular filtration only, possibly by competitively inhibiting the penetration of N-formimidoyl thienamycin into the proximal tubular cells.
Structurally different bisphosphonates exert opposing effects on alkaline phosphatase and mineralization in marrow osteoprogenitors (1998)

Bisphosphonates (BPs) are inhibitors of bone resorption and soft tissue calcification. The biological effects of the BPs in calcium-related disorders are attributed mainly to their incorporation in bone, enabling direct interaction with osteoclasts and/or osteoblasts through a variety of biochemical pathways. Structural differences account for the considerable differences in the pharmacological activity of BPs. We compared the effects of two structurally different compounds, alendronate and 2-(3'-dimethylaminopyrazinio)ethylidene-1,1-bisphosphonic acid betaine (VS-6), in an osteoprogenitor differentiation system. The BPs were examined in a bone marrow stromal-cell culture system, which normally results in osteoprogenitor differentiation. The drugs were present in the cultures from days 2 to 11 of osteogenic stimulation, a period estimated as being comparable to the end of proliferation and the matrix-maturation stages. We found that the two different BPs have opposing effects on specific alkaline phosphatase (ALP) activity, on stromal-cell proliferation, and on cell-mediated mineralization. These BPs differentially interact with cell-associated phosphohydrolysis, particularly at a concentration of 10(-2) of ALP Km, in which alendronate inhibits whereas VS-6 did not inhibit phosphatase activity. VS-6 treatment resulted in similar and significantly increased mineralization at 10 and 1 microM drug concentrations, respectively. In contrast, mineralization was similar to control, and significantly decreased at 10 and 1 microM drug concentrations, respectively, under alendronate treatment.
A Monoclonal Antibody, GR7A4, Reacting with the T10 Antigen (1987)

The monoclonal antibody GR7A4 was produced against a human lymphoblastic leukemia (ALL-B). Biochemical characterization of GR7A4 was carried out with Raji cells in SDS-PAGE studies. GR7A4 precipitated a 43 kd molecule. The tissue distribution and molecular weight were similar to the T10 antigen. Modulation and capping of GR7A4 antigen reduced its binding ability to cells with either GR7A4 or OKT10. However, the cell surface distribution pattern observed was somewhat different from other similar monoclonal antibodies. Thus GR7A4 reacted greatly with pre-B-cell lines, Burkitt cell lines, EBV cell lines and activated PHA, ConA and PWM lymphocytes, however reactivity with leukemic cells was very limited. The kinetics of appearance of GR7A4 antigen on PWM blasts show that this molecule seems to represent an intermediate stage in lymphocytic activation. The differences in comparison with other similar MAbs are discussed and correlated with the peculiar discontinous pattern of appearance of this antigen.
The unusual properties of effective blood substitutes. (2002)

Blood substitutes or oxygen carrying plasma expanders were originally formulated to simulate the transport properties of blood, particularly oxygen carrying capacity, viscosity, p50, and colloid osmotic pressure, under the hypothesis that blood is the most desirable fluid in volume restitution. However, changes introduced into the organism during hemorrhage adversely affect microvascular function due to reflex vasoconstriction which causes the fall of functional capillary density, and lowers tissue oxygenation, conditions that are not universally reversed with retransfusion of blood. The restoration of microvascular function is seldom complete upon retransfusion of blood. New formulations of hemoglobin molecules in solutions whose oncotic pressure is in the range of 60-100 mmHg, p50 is about 5 mmHg, viscosity 3-4 cP, and oxygen carrying capacity in the range of 4-7 g/dl equivalent hemoglobin deliver better microvascular function after resuscitation when compared to whole blood and oxygen carrying plasma expanders with transport properties similar to those of blood. The improved performance is in part due to the increased plasma viscosity which increases capillary transmural pressure which reverses capillary collapse induced during low perfusion pressures. High oncotic pressure reinforces this effect, since it brings more fluid into the circulation. Microvascular transport studies of the effects of resuscitation in shock show that functional capillary density is the primary determinant of survival, thus maintenance of an open and fully perfused microcirculation is more critical than insuring oxygen supply, since closed capillaries lead to the accumulation of slowly diffusing byproducts of metabolism which ultimately become toxic. The required combination of properties can be achieved by conjugating hemoglobin and polyethylene glycol. Resuscitation fluids based on hemoglobin containing vesicles may provide the next level of functional improvement in the formulation of volume restitution fluids since their biophysical properties can be specifically controlled through the inclusion of specialized compounds into the vesicles, and the formulation of the suspending medium.
GIS based suitability evaluation of the Differential Radar Interferometry method (D-InSAR) for detection and deformation monitoring of landslides (2009)

In recent years differential radar interferometry (D- InSAR) has proven to be a powerful remote sensing technique to detect and measure deformation of the Earth’s crust, such as landslides, with an accuracy of a few millimeters. However, as a consequence of the inclined imaging geometry, areas with a topographic relief (where landslides usually occur) appear heavily distorted in the radar image. Thereby slopes inclined towards the radar appear shortened (foreshortening) and in extreme even can cause an overlapping of different radar signals (layover effect); slopes oriented away from the radar seem stretched (elongation) or even can be shadowed by a steep mountain (shadowing). These effects limit or even prohibit the use of a radar image for interferometric applications. Besides these geometric distortions, the land cover has great influence on the applicability of differential radar interferometry. For example vegetation-free areas such as buildings, roads and rocks show a high stability in their backscattering properties, whereas areas covered by vegetation, especially forests, have varying backscattering properties at different times (e.g. due to wind). Areas with a high constancy of their backscattering properties are better suited for the D-InSAR-technique. To date prior to an investigation using D-InSAR these limiting effects usually are only estimated, sometimes leading to disappointing results when the actual radar images are analyzed. Therefore in the present work a GIS routine was developed, which based on freely available DEM data (SRTM) not only accurately predicts the areas in which layover and shadowing will occur, but also determines the measurable percentage of the movement (portion oriented in radar line of sight) for a given radar acquisition geometry. Additionally land cover classification data (CORINE) is used to assess the influence of the land cover to D-InSAR deformation measurements. Thus by using this new GIS application, in future it is possible to evaluate the usability of D-InSAR landslide deformation measurements in a certain region quite accurately before the expensive actual radar records are ordered.
Levels of hypoxia‐inducible factor‐1α independently predict prognosis in patients with lymph node negative breast carcinoma (2003)

Increased levels of HIF-1alpha were associated independently with shortened survival in patients with lymph node negative breast carcinoma. Therefore, the use of immunohistochemical assessment of HIF-1alpha as a new predictor of poor outcome may improve clinical decision-making regarding adjuvant treatment of patients with lymph node negative breast carcinoma.
High-Activity, Single-Site Catalysts for the Alternating Copolymerization of CO2 and Propylene Oxide (2002)

Despite recent advances regarding catalysts for CO2/epoxide copolymerization, the development of high-activity catalysts for alternating polymerization of CO2 and commodity epoxides, such as propylene oxide, remains a challenge. A new class of unsymmetrically substituted beta-diiminate zinc complexes is reported that exhibits unprecedented activity for CO2/propylene oxide copolymerization. The polymers formed are of high molecular weight (Mn approximately 35 kg/mol) and have narrow polydispersities (PDI approximately 1.1), consistent with a living polymerization.
Senescent Human Fibroblasts Show Increased Glycolysis and Redox Homeostasis with Extracellular Metabolomes That Overlap with Those of Irreparable DNA Damage, Aging, and Disease (2015)

Cellular senescence can modulate various pathologies and is associated with irreparable DNA double-strand breaks (IrrDSBs). Extracellular senescence metabolomes (ESMs) were generated from fibroblasts rendered senescent by proliferative exhaustion (PEsen) or 20 Gy of γ rays (IrrDSBsen) and compared with those of young proliferating cells, confluent cells, quiescent cells, and cells exposed to repairable levels of DNA damage to identify novel noninvasive markers of senescent cells. ESMs of PEsen and IrrDSBsen overlapped and showed increased levels of citrate, molecules involved in oxidative stress, a sterol, monohydroxylipids, tryptophan metabolism, phospholipid, and nucleotide catabolism, as well as reduced levels of dipeptides containing branched chain amino acids. The ESM overlaps with the aging and disease body fluid metabolomes, supporting their utility in the noninvasive detection of human senescent cells in vivo and by implication the detection of a variety of human pathologies. Intracellular metabolites of senescent cells showed a relative increase in glycolysis, gluconeogenesis, the pentose-phosphate pathway, and, consistent with this, pyruvate dehydrogenase kinase transcripts. In contrast, tricarboxylic acid cycle enzyme transcript levels were unchanged and their metabolites were depleted. These results are surprising because glycolysis antagonizes senescence entry but are consistent with established senescent cells entering a state of low oxidative stress.
Weathering the unexpected (2012)

Failures happen, and resilience drills help organizations prepare for them.
Normal pressure hydrocephalus in a patient with systemic lupus erythematosus. (1990)

We describe a patient who had concomitant systemic lupus erythematosus (SLE) and a normal pressure hydrocephalus. She improved only after appropriate therapy for each. Although 6 patients with arthritis and normal pressure hydrocephalus have been described, this is the first report of it occurring in a patient with SLE. It has been emphasized that normal pressure hydrocephalus can easily be overlooked in elderly patients with arthritic conditions. Since neuropsychiatric symptoms are likelier to occur in patients with SLE than in other rheumatologic conditions, the diagnosis of normal pressure hydrocephalus may be delayed or overlooked. Because normal pressure hydrocephalus is a potentially reversible cause of neurologic dysfunction, it should be considered in appropriate populations.
Calculation of the total electrostatic energy of a macromolecular system: Solvation energies, binding energies, and conformational analysis (1988)

In this report we describe an accurate numerical method for calculating the total electrostatic energy of molecules of arbitrary shape and charge distribution, accounting for both Coulombic and solvent polarization terms. In addition to the solvation energies of individual molecules, the method can be used to calculate the electrostatic energy associated with conformational changes in proteins as well as changes in solvation energy that accompany the binding of charged substrates. The validity of the method is examined by calculating the hydration energies of acetate, methyl ammonium, ammonium, and methanol. The method is then used to study the relationship between the depth of a charge within a protein and its interaction with the solvent. Calculations of the relative electrostatic energies of crystal and misfolded conformations of Themiste dyscritum hemerythrin and the VL domain of an antibody are also presented. The results indicate that electrostatic charge-solvent interactions strongly favor the crystal structures. More generally, it is found that charge-solvent interactions, which are frequently neglected in protein structure analysis, can make large contributions to the total energy of a macromolecular system.
Predictors of bronchial hyperresponsiveness in chronic rhinosinusitis with nasal polyp (2008)

Taken together, these results indicate that moderate to severe sneezing and a serum eosinophil count > or = 300 cells/microl may be predictive factors for BHR in patients with CRSNP.
Fibronectin promotes epithelial migration of cultured rabbit cornea in situ. (1983)

We investigated the effect of fibronectin on epithelial migration onto the stroma in cultured rabbit cornea. Rabbit plasma fibronectin was purified by affinity chromatography using gelatin-Sepharose 4B, and its purity was confirmed by SDS polyacrylamide slab gel electrophoresis. Antibody against rabbit plasma fibronectin raised in guinea pigs formed a single precipitin line against rabbit plasma and purified rabbit plasma fibronectin by Ouchterlony double diffusion test. When rabbit cornea was cut into small blocks and cultured in TCM-199 medium alone, corneal epithelial cells began to migrate on the cut edge of the corneal stroma. The addition of purified rabbit plasma fibronectin to the culture medium significantly enhanced epithelial migration. The degree of enhancement depended on the amount of fibronectin added. When guinea pig IgG anti-rabbit plasma fibronectin was added, epithelial migration was significantly inhibited when compared with that in control cultured corneal blocks. The results demonstrate that fibronectin promotes epithelial migration in the cornea and thus plays an important role in corneal wound healing.
Genetic and morphological characterization of an Escherichia coli chromosome segregation mutant (1992)

The temperature-sensitive nucleoid segregation mutant of Escherichia coli, PAT32, formerly described as a parA mutant, has been shown to carry a mutation near 66 min on the genetic map. Fine mapping with phages from the collection of Kohara et al. is consistent with its being a parC allele. Observation by fluorescence microscopy revealed the formation, at a nonpermissive temperature, of filaments containing one or two large nucleoids and of normal-size anucleate cells. There was also a significant loss of viability.
The opsX locus of Xanthomonas campestris affects host range and biosynthesis of lipopolysaccharide and extracellular polysaccharide (1993)

Xanthomonas campestris pv. citrumelo strain 3048 is the causal agent of citrus bacterial leaf spot disease and has a wide host range that includes rutaceous and leguminous plants. A spontaneous prototrophic mutant of strain 3048 (strain M28) that had lost virulence on citrus but retained virulence on bean plants was recovered. Growth studies in planta showed that M28 cells died rapidly in citrus leaves but grew normally in bean leaves. In addition to the loss of citrus-specific virulence, M28 displayed the following mutant phenotypes in culture: decreased growth rate, reduction of the amount of exopolysaccharide (to ca. 25% of the amount in 3048), loss of capsules, and significant alterations of the two 3048 lipopolysaccharide (LPS) bands visualized by silver stain on polyacrylamide gels, consistent with a defect(s) in LPS assembly. A 38-kb DNA fragment from a 3048 total DNA library that complemented the mutant phenotypes of M28 was identified. The 38-kb fragment did not hybridize to two similarly sized fragments carrying different hrp (hypersensitive response and pathogenicity) genes cloned from 3048. Subcloning, DNA sequence analyses, and gene disruption experiments were used to identify a single gene, opsX (for outer-membrane polysaccharide), responsible for the mutant phenotypes of M28. At least one other gene downstream from opsX also affected the same phenotypes and may be part of a gene cluster. We report here the DNA sequence and transcriptional start site of opsX. A search of protein sequence data bases with the predicted 31.3-kDa OpsX sequence found strong similarity to Lsi-1 of Neisseria gonorrhoeae and RfaQ of Escherichia coli (both are involved in LPS core assembly). The host-specific virulence function of opsX appears to involve biosynthesis of the extracellular polysaccharide and a complete LPS. Both may be needed in normal amounts for protection from citrus, but not bean, defense compounds.