gebhart/patrepeval huggingface dataset:
Detection of Carbon Nanotubes in Environmental Matrices Using Programmed Thermal Analysis (2012)

Carbon nanotube (CNT) production is rapidly growing, and there is a need for robust analytical methods to quantify CNTs at environmentally relevant concentrations in complex organic matrices. Because physical and thermal properties vary among different types of CNTs, we studied 14 single-walled (SWCNTs) and multiwalled CNTs (MWCNTs). Our aim was to apply a classic analytical air pollution method for separating organic (OC) and elemental carbon (EC) (thermal optical transmittance/reflectance, TOT/R) to environmental and biological matrices and CNTs. The TOT/R method required significant modification for this analysis, which required a better understanding of the thermal properties of CNTs. An evaluation of the thermal properties of CNTs revealed two classes that could be differentiated using Raman spectroscopy: thermally "weak" and "strong." Using the programmed thermal analysis (PTA) method, we optimized temperature programs and instituted a set of rules for defining the separation of OC and EC to quantify a broad range of CNTs. The combined Raman/PTA method was demonstrated using two environmentally relevant matrices (cyanobacteria (CB) and urban air). Thermal evaluation of CB revealed it to be a complex matrix with interference occurring for both weak and strong CNTs, and thus a pretreatment method was necessary. Strong CNT masses of 0.51, 2.7, and 11 μg, corresponding to concentrations of 10, 54, and 220 μg CNT/g CB, yielded recoveries of 160 ± 29%, 99 ± 1.9%, and 96 ± 3.0%, respectively. Urban air was also a complex matrix and contained a significant amount (12%) of background EC that interfered greatly with weak CNTs and minimally with strong CNTs. The current detection limit at 99% confidence for urban air samples and strong CNTs is 55 ng/m(3) (0.33 μg). Overall, the PTA method presented here provides an initial approach for quantifying a wide range of CNTs, and we identify specific future research needs to eliminate potential interferences and lower detection limits.
Expression of interleukin 1β and interleukin 1β converting enzyme by intestinal macrophages in health and inflammatory bowel disease (1998)

Exposure of normal colonic macrophages to LPS only induces the production of the precursor form of IL-1 beta, because the cells fail to activate ICE. In contrast, IBD colonic macrophages are able to activate ICE and hence release mature IL-1 beta in a manner similar to circulating monocytes. This is consistent with IBD macrophages being recently recruited from the circulating monocyte population. Targeted inhibition of ICE may represent a novel form of therapy in IBD.
Catalytic Asymmetric [3+2] Cycloaddition of Azomethine Ylides. Development of a Versatile Stepwise, Three-Component Reaction for Diversity-Oriented Synthesis (2003)

We report a new catalyst system that should enhance the use of enantioselective 1,3-dipolar cycloadditions of azomethine ylides with electronic-deficient olefins in the divergent pathways of diversity-oriented synthesis (DOS). The underlying reaction is of considerable interest in DOS because its stereospecificity enables stereochemical diversification of up to four tetrahedral centers on pyrrolidine rings. This new catalyst system extends the scope and selectivity of the azomethine ylide cycloaddition and is compatible with reagents used in a one-bead/one-stock solution technology platform for DOS.
Sinusitis in children (1988)

Upper respiratory tract infection and allergic inflammation are recognized as the important risk factors for acute sinusitis, with upper respiratory tract infection being most common. In children with acute or chronic sinusitis, the respiratory symptoms of nasal discharge, nasal congestion and cough are usually prominent. Radiography has traditionally been used to determine the presence or absence of sinus disease. The radiographic findings most diagnostic of bacterial sinusitis are diffuse opacification, mucous membrane thickening or an air-fluid level. The predominant organisms include Streptococcus pneumoniae, Branhamella catarrhalis and nontypable Haemophilus influenzae. Several viruses including adenovirus and parainfluenzae have also been recovered. Clinical improvement is prompt in nearly all children treated with an appropriate antimicrobial agent.
Bioconversion of waste cellulose by using an attrition bioreactor (1983)

A new type of reactor, an attrition bioreactor, was tested to achieve a higher rate and extent of enzymatic saccharification of cellulose than is possible with conventional methods. The reactor consisted of a jacketted stainless-steel vessel with shaft, stirrer, and milling media, which combined the effect of the mechanical action of wet milling with cellulose hydrolysis. The substrates tested were newsprint and white-pine heartwood. The performance of the reactor was excellent. The extent and rate of enzymatic hydrolysis could be markedly improved over other methods. The power consumption of the attrition bioreactor was also measured. The cellulase enzyme deactivation during attrition milling was not significant.
Isolation and Structure Elucidation of Five New Asterriquinones from Aspergillus, Humicola and Botryotrichum Species. (1996)

Five new quinone pigments have been discovered from the fermentation broth of Aspergillus, Humicola and Botryotrichum species isolated from different soil samples. These compounds inhibit serine proteases of the coagulation pathway. Their structures which differ in the identity and position of a 5-carbon side chain on the indole moiety have been elucidated based on NMR and FAB-MS experiments.
<title>Three-dimensional imaging of nucleolin trafficking in normal cells, transfectants, and heterokaryons</title> (1996)

The study of intracellular trafficking using labeled molecules has been aided by the development of the cyanine fluorochromes, which are easily coupled, very soluble, resist photobleaching, and fluoresce at far-red wavelengths where background fluorescence is minimal. We have used Cy3-, Cy5-, and Cy5.5-labeled antibodies, antigen-binding fragments, and specifically binding single-stranded oligonucleotides to follow expression and trafficking of nucleolin, the most abundant protein of the nucleolus. Nucleolin shuttles between the nucleolus and the cytoplasm, and is also expressed on the cell surface, allowing us to test our techniques at all three cellular sites. Differentially cyanine-labeled non-specific antibodies were used to control for non-specific binding. Similarly, the differentially labeled non-binding strand of the cloned oligonucleotide served as a control. The multimode microscope allowed us to follow both rapid and slow redistributions of labeled ligands in the same study. We also performed 3-D reconstructions of nucleolin distribution in cells using rapid acquisition and deconvolution. Microinjection of labeled ligands was used to follow intracellular distribution, while incubation of whole cells with antibody and antigen-binding fragments was used to study uptake. To unambiguously define trafficking, and eliminate the possibility of interference by cross-reactive proteins, we transfected mouse renal cell carcinoma cells that express cell surface nucleolin with human nucleolin. We used microinjection and cell surface staining with Cy3- or Cy5- labeled monoclonal antibody D3 (specific for human nucleolin) to assess the cellular distribution of the human protein. Several clones expressed human nucleolin on their surfaces and showed high levels of transport of the human protein into the mouse nucleus and nucleolus. This distribution roughly parallels that of mouse nucleolin as determined by labeled polyclonal antibody. We have used these engineered transfectants to determine whether the cell surface-expressed xenogeneic nucleolin can serve as a target for antibodies in vivo.
Revalidation of description of constipation in terms of recall bias and visual scale analog questionnaire (2003)

The prevalence of constipation in the questionnaire form based on self-reported, symptom-based and diary-based criteria were highly compatible with the result obtained on readministration. Recall bias was negligibly low. Also, the present results suggest that the diagnosis of constipation is more accurate when >2 criteria are present. In addition, the VSAQ seems to be sensitive enough to differentiate subjects with constipation from those without, when a score of 3 has been chosen as the cut-off value for discrimination. However, this sensitivity was less in the group who stated they were constipated.
4-1BB Engagement Costimulates NKT Cell Activation and Exacerbates NKT Cell Ligand-Induced Airway Hyperresponsiveness and Inflammation (2008)

Multiple studies have demonstrated that 4-1BB (CD137), a member of the TNF receptor superfamily, is expressed on several immune cells including activated T cells. However, the expression and the role of 4-1BB on natural killer T (NKT) cells have not been fully characterized. In this study, it was shown that 4-1BB was not expressed on naive NKT cells but was rapidly induced on activated NKT cells by TCR engagement with alpha-galactosylceramide (alpha-GalCer). Also, 4-1BB signaling provided by 3H3, an agonistic anti-4-1BB mAb, promoted NKT cell activation resulting in enhanced cytokine production of NKT cells driven by alpha-GalCer. When NKT cell-driven airway immune responses were evaluated by intranasal administration of alpha-GalCer, airway hyperresponsiveness (AHR) and lung inflammation were significantly more aggravated in mice treated with 3H3 and alpha-GalCer than in mice treated with alpha-GalCer alone. These aggravations were accompanied by up-regulation of IL-4, IL-13, and IFN-gamma production. Interestingly, AHR was not developed in IL-4Ralpha-deficient mice treated with alpha-GalCer with or without 3H3 but was exacerbated in IFN-gamma-deficient mice. Our study suggests that 4-1BB on NKT cells functions as a costimulatory molecule and exacerbates the induction of NKT cell-mediated AHR, which is dependent on the IL-4Ralpha-mediated pathway.
Identification of an Enhancer Element for the Endosperm-Specific Expression of High Molecular Weight Glutenin (1990)

Mark S. Thomas, Richard B. Flavell, Identification of an Enhancer Element for the Endosperm-Specific Expression of High Molecular Weight Glutenin, The Plant Cell, Vol. 2, No. 12 (Dec., 1990), pp. 1171-1180
Nonmetric calibration of camera lens distortion: differential methods and robust estimation (2005)

This paper addresses the problem of calibrating camera lens distortion, which can be significant in medium to wide angle lenses. Our approach is based on the analysis of distorted images of straight lines. We derive new distortion measures that can be optimized using nonlinear search techniques to find the best distortion parameters that straighten these lines. Unlike the other existing approaches, we also provide fast, closed-form solutions to the distortion coefficients. We prove that including both the distortion center and the decentering coefficients in the nonlinear optimization step may lead to instability of the estimation algorithm. Our approach provides a way to get around this, and, at the same time, it reduces the search space of the calibration problem without sacrificing the accuracy and produces more stable and noise-robust results. In addition, while almost all existing nonmetric distortion calibration methods needs user involvement in one form or another, we present a robust approach to distortion calibration based on the least-median-of-squares estimator. Our approach is, thus, able to proceed in a fully automatic manner while being less sensitive to erroneous input data such as image curves that are mistakenly considered projections of three-dimensional linear segments. Experiments to evaluate the performance of this approach on synthetic and real data are reported.
Pulsed-field gel electrophoresis analysis of retinoic acid receptor-alpha and promyelocytic leukemia rearrangements. Detection of the t(15;17) translocation in the diagnosis of acute promyelocytic leukemia. (1993)

Acute promyelocytic leukemia (APL) is characterized cytogenetically by a balanced reciprocal chromosomal translocation t(15;17) (q22;q21). This translocation involves the retinoic acid receptor-alpha (RAR-alpha) on chromosome 17 and the promyelocytic leukemia locus (PML) on chromosome 15 and results in the transcription of novel fusion messenger RNAs. In this study, pulsed-field gel electrophoresis (PFGE) was applied to the detection of the t(15;17) translocation in twenty-six clinical specimens cytologically diagnosed by French-American-British criteria as APL. This technique could readily be applied to both fresh and nonviably frozen tumor samples. In 24 of 26 samples, rearrangements of the PML and RAR-alpha, loci could be detected by Southern blotting after digestion with MluI and BssHII. Furthermore, co-migration of the rearranged fragments, detected by hybridization to probes for the PML and RAR-alpha genes, demonstrated that these loci were juxtaposed. The translocation was detected in specimens at the time of initial diagnosis, on differentiation therapy with retinoic acid and at the time of relapse. The diagnostic accuracy was compared to cytogenetics and the reverse transcriptase-polymerase chain reaction for the novel PML-RAR-alpha fusion transcript. The samples from two patients were negative by all three diagnostic methods, and both of these patients failed to respond to all-trans retinoic acid. In the other 24 APL samples, cytogenetics was positive in only 76.9% of the cases, whereas both reverse transcriptase-polymerase chain reaction and PFGE methods detected the translocation in 100% of the cases. Thus, PFGE can readily detect the t(15;17) translocation in both viable and nonviable clinical specimens and can improve the diagnostic accuracy of morphology and cytogenetics in APL. In contrast to conventional electrophoresis based on rearrangement of RAR-alpha, the ability to demonstrate directly co-migration of the PML and RAR-alpha loci enables this method to distinguish the t(15;17) translocation from variant translocations such as the t(11;15). Because PFGE can be performed on nonviable, frozen tumor samples, it could be diagnostically useful in APL when the RNA-based reverse transcriptase-polymerase chain reaction cannot be performed.
Bacteriophage T4 multiplication in a glucose-limited Escherichia coli biofilm (2001)

An Escherichia coli K-12 biofilm was grown at a dilution rate of 0.028 h -1 for 48 h in a glucose-limited chemostat coupled to a modified Robbins' device to determine its susceptibility to infection by bacteriophage T4. Bacteriophage T4 at a multiplicity of infection (MOI) of 10 caused a log reduction in biofilm density (expressed as colony forming units (CFU) per cm 2 ) at 90 min postinfection. After 6 h, a net decrease and equilibrium in viral titer was seen. When biofilms were exposed to T4 phage at a MOI of 100, viral titer doubled after 90 min. After 6 h, viral titers (expressed as plaque forming units (PFU) per cm 2 ) stabilized at levels approximately one order of magnitude higher than seen at a MOI of 10. Scanning confocal laser microscopy images also indicated disruption of biofilm morphology following T4 infection with the effects being more pronounced at a MOI of 100 than at a MOI of 10. These results imply that biofilms under carbon limitation can act as natural reservoirs for bacteriophage and that bacteriophage can have some influence on biofilm morphology.Key words: bacteriophage T4, biofilm, biofilm morphology, bacteriophage ecology, carbon limitation.
A latency and fault-tolerance optimizer for online parallel query plans (2011)

We address the problem of making online, parallel query plans fault-tolerant: i.e., provide intra-query fault-tolerance without blocking. We develop an approach that not only achieves this goal but does so through the use of different fault-tolerance techniques at different operators within a query plan. Enabling each operator to use a different fault-tolerance strategy leads to a space of fault-tolerance plans amenable to cost-based optimization. We develop FTOpt, a cost-based fault-tolerance optimizer that automatically selects the best strategy for each operator in a query plan in a manner that minimizes the expected processing time with failures for the entire query. We implement our approach in a prototype parallel query-processing engine. Our experiments demonstrate that (1) there is no single best fault-tolerance strategy for all query plans, (2) often hybrid strategies that mix-and-match recovery techniques outperform any uniform strategy, and (3) our optimizer correctly identifies winning fault-tolerance configurations.
Development of murine ischemic cardiomyopathy is associated with a transient inflammatory reaction and depends on reactive oxygen species (2003)

We examined the effects of daily repetitive brief (15 min) myocardial ischemia and reperfusion (I/R) in WT C57BL6 and extracellular superoxide dismutase (EC-SOD)-overexpressing mice. In the absence of myocardial necrosis, I/R resulted in persistent fibrosis in ischemic areas of C57/BL6 mice associated with persistent global and segmental anterior wall dysfunction. The I/R protocol induced chemokines (peak 3 days) followed sequentially by infiltration of macrophages and myofibroblasts (5 days). Fibrosis peaked at 7 days and was stable at 28 days despite regression of the chemokine and cellular response. Discontinuation of I/R at 7 or 28 days led to regression of fibrosis and ventricular dysfunction. In contrast, the EC-SOD mice developed markedly less chemokine induction, cell response, and fibrosis, with no ventricular dysfunction. Reversible fibrosis and ventricular dysfunction are features of human hibernating myocardium. The reduction of the cellular and functional response in EC-SOD mice suggests a role for reactive O(2) in the pathogenesis of ischemic cardiomyopathy.
Rapid Evaporative Ionization Mass Spectrometry Imaging Platform for Direct Mapping from Bulk Tissue and Bacterial Growth Media (2015)

Rapid evaporative ionization mass spectrometry (REIMS) technology allows real time intraoperative tissue classification and the characterization and identification of microorganisms. In order to create spectral libraries for training the classification models, reference data need to be acquired in large quantities as classification accuracy generally improves as a function of number of training samples. In this study, we present an automated high-throughput method for collecting REIMS data from heterogeneous organic tissue. The underlying instrumentation consists of a 2D stage with an additional high-precision z-axis actuator that is equipped with an electrosurgical diathermy-based sampling probe. The approach was validated using samples of human liver with metastases and bacterial strains, cultured on solid medium, belonging to the species P. aeruginosa, B. subtilis, and S. aureus. For both sample types, spatially resolved spectral information was obtained that resulted in clearly distinguishable multivariate clustering between the healthy/cancerous liver tissues and between the bacterial species.
TM7XN1, a novel human EGF‐TM7‐like cDNA, detected with mRNA differential display using human melanoma cell lines with different metastatic potential1 (1999)

We have identified a novel 3845 bp cDNA differentially expressed in a human melanoma metastasis model. Northern blot analysis showed expression in the poorly and intermediately metastasizing cell lines and a marked downregulation in the highly metastatic cell lines. Using RT-PCR expression was also seen in several other tumor cell lines and normal cell types of human origin. cDNA sequence analysis revealed an ORF of 687 amino acids containing seven putative transmembrane domains C-terminally and a long N-terminus. The gene was mapped to 16q13. Highest homology was observed with members of the EGF-TM7 subfamily of the secretin/calcitonin receptor family. We propose the delineation of a subfamily of TM7 proteins, LN-TM7, containing seven transmembrane proteins with a long N-terminal extracellular part.
Catalytic Activity of a Series of Zn(II) Phenoxides for the Copolymerization of Epoxides and Carbon Dioxide (1998)

A series of zinc phenoxides of the general formula (2,6-R2C6H3O)2Zn(base)2 [R = Ph, tBu, iPr, base = Et2O, THF, or propylene carbonate] and (2,4,6-Me3C6H2O)2Zn(pyridine)2 have been synthesized and characterized in the solid state by X-ray crystallography. All complexes crystallized as four-coordinate monomers with highly distorted tetrahedral geometry about the zinc center. The angles between the two sterically encumbering phenoxide ligands were found to be significantly more obtuse than the corresponding angles between the two smaller neutral base ligands, having average values of 140° and 95°, respectively. In a noninteracting solvent such as benzene or methylene chloride at ambient temperature, the ancillary base ligands are extensively dissociated from the zinc center, with the degree of dissociation being dependent on the base as well as the substituents on the phenolate ligands. That is, stronger ligand binding was found in zinc centers containing electron-donating tert-butyl substituents as opposed to electron-withdrawing phenyl substituents. In all instances, the order of ligand binding was pyridine > THF > epoxides. These bis(phenoxide) derivatives of zinc were shown to be very effective catalysts for the copolymerization of cyclohexene oxide and CO2 in the absence of strongly coordinating solvents, to afford high-molecular-weight polycarbonate (Mw ranging from 45 × 103 to 173 × 103 Da) with low levels of polyether linkages. However, under similar conditions, these zinc complexes only coupled propylene oxide and CO2 to produce cyclic propylene carbonate. Nevertheless, these bis (phenoxide) derivatives of zinc were competent at terpolymerization of cyclohexene oxide/propylene oxide/CO2 with little cyclic propylene carbonate formation at low propylene oxide loadings. While CO2 showed no reactivity with the sterically encumbered zinc bis(phenoxides), e.g., (2,6-di-tert-butylphenoxide)2Zn(pyridine)2, it rapidly inserted into one of the Zn−O bonds of the less crowded (2,4,6-trimethylphenoxide)2Zn(pyridine)2 to provide the corresponding aryl carbonate zinc derivative. At the same time, both sterically hindered and sterically nonhindered phenoxide derivatives of zinc served to ring-open epoxide, i.e., were effective catalysts for the homopolymerization of epoxide to polyethers. The relevance of these reactivity patterns to the initiation step of the copolymerization process involving these monomeric zinc complexes is discussed.