gebhart/patrepeval huggingface dataset:
Microplasma generation in artificial media and its potential applications (2010)

Unlike the generation of uniform plasmas in a large volume, structured plasma comprising microplasmas has attracted increasing scientific and technological interest in recent years. Similarly, the concept of plasma generation in artificial media with gas–gas, gas–liquid, and gas–solid interfaces under intentionally organized and controlled conditions has the potential to open a new field in plasma science and technology. Amongst the subtopics of plasma generation in artificial media, we discuss here those dealing with micro-plasma jets in flowing gas channels, microdischarges within microbubbles generated in aqueous electrolyte solutions, and discharges in bubbled water and misted air. Our discussion is supported by preliminary results and aims to stimulate future systematic and quantitative investigations.
Lack of interference of DNA single-strand breaks with the measurement of double-strand breaks in mammalian cells using the neutral filter elution assay (1991)

In this study, the effect of DNA single strand breaks (ssb) on the neutral (pH 9.6) filter elution of DNA from Chinese hamster ovary (CHO K1) cells containing DNA double strand breaks (dsb) was investigated. Protein associated ssb were induced by the inhibition of DNA topoisomerase I with camptothecin (cpt). Protein associated dsb were introduced by treating cells with the DNA topoisomerase II poison; etoposide (VP-16). Protein associated ssb and dsb were converted to ssb and dsb by proteinase K present in the lysis solution. In some experiments dsb were generated by the restriction endonuclease Pvu II. It was found that elution of DNA in the presence and absence of ssb was similar under neutral conditions. This finding is consistent with the view that the fast component of the bi-phasic repair kinetics observed in irradiated mammalian cells with the neutral filter elution technique is not attributable to the interference of ssb with the measurement of dsb, and thus suggests that the two components of repair observed with the neutral filter elution elution technique may represent two different types of dsb or modes of repair of dsb.
Recent progress in microfluidic devices for nucleic acid and antibody assays (2003)

Microfluidic devices are increasingly important in biomedical assays. In this paper, we review recent progress on these devices for chemical amplification, hybridization, separation, and detection of nucleic acids. Recent developments in microfluidic technologies for detection of protein binding events in immunoassay applications are also reviewed.
Building near-surface models with velocity inversions and evaluating their impact on depth imaging (2014)

Summary Complex near-surface geology in arid environments poses many challenges for building near-surface velocity models. High-impedance contrasts, velocity inversions and screening of reflected energy are among the most significant challenges for velocity estimation and imaging in these areas. Here we demonstrate that the recovery of detailed velocity variations in the near surface is essential for depth imaging of deep targets. Specifically, we focus on a case from an arid environment where low-velocity zones and layers are present in the near surface and shingling of first arrivals is observed. We confirm that traveltime tomography is unable to recover them properly and as a consequence leads to poor depth images. In contrast, full-waveform inversion can reconstruct a better velocity model with inversion resulting in more accurate depth images.
Polymeric Dibromomaleimides As Extremely Efficient Disulfide Bridging Bioconjugation and Pegylation Agents (2011)

A series of dibromomaleimides have been shown to be very efficacious at insertion into peptidic disulfide bonds. This conjugation proceeds with a stoichiometric balance of reagents in buffered solutions in less than 15 min to give discrete products while maintaining the disulfide bridge and thus peptide conformation. The insertion is initiated by disulfide reduction using a water-soluble phosphine, tris(2-carboxyethyl)phosphine (TCEP) which allows for subsequent substitution of the two maleimide bromides by the generated thiols. Reaction of salmon calcitonin (sCT) with 2,3-dibromomaleimide (1.1 excess) in the presence of TCEP (1.1 equiv) in aqueous solution at pH 6.2 gives complete production of a single conjugate which requires no workup. A linear methoxy poly(ethylene glycol) (PEG) was functionalized via a Mitsunobu reaction and used for the successful site-specific and rapid pegylation of sCT. This reaction occurs in 15 min with a small stoichiometry excess of the pegylating agent to give insertion at the disulfide with HPLC showing a single product and MALDI-ToF confirming conjugation. Attempts to use the group in a functional ATRP polymerization initiator led to polymerization inhibition. Thus, in order to prepare a range of functional polymers an indirect route was chosen via both azide and aniline functional initiators which were converted to 2,3-dibromomaleimides via appropriate reactions. For example, the azide functional polymer was reacted via a Huisgen CuAAC click reaction to an alkyne functional 2,3-dibromomaleimide. This new reagent allowed for the synthesis of conjugates of sCT with comb polymers derived from PEG methacrylic monomers which in addition gave appropriate cloud points. This reaction represents a highly efficient polymer conjugation method which circumvents problems of purification which normally arise from having to use large excesses of the conjugate. In addition, the tertiary structure of the peptide is efficiently maintained.
Plant polyphenols : synthesis, properties, significance (1992)

Introduction: Reflections on the Chemistry and Affinities of the Major Commercial Tannins in the Context of their Industrial Use D.G. Roux. Biogenesis and Synthesis: Enzymes in the Biosynthesis of Hydrolyzable Tannins G.G. Gross. Biosynthesis of Flavenoids G. Hrazdina. Chemical Properties: Gallic Acid at its Metabolites E. Haslam. Chinquapinic Acid M. Adamczeski, et al. Biological Significance: Plant Phenolics as Expressions of Biological Diversity O.R. Gottlieb. Pharmacologically Active Tannins Isolated from Medicinal Plants T. Okuda, et al. Commercial Significance: Flavor, Color, and Stability in Fruit Products A.G.H. Lea. Tannins and the Qualities of Wines V.L. Singleton. Conclusions: Concluding Remarks P.E. Laks, R.W. Hemmingway. 54 additional articles. Index.
Eminent role of ICOS costimulation for T cells interacting with plasmacytoid dendritic cells (2006)

CD4+ CD45RO+ T cells could mature freshly isolated human plasmacytoid dendritic cells (PDC) in a superantigen-driven culture in a similar way to recombinant interleukin-3 (IL-3). Mature PDC expressed significantly higher levels of inducible costimulator ligand (ICOS-L), but similar levels of CD80 and CD86, when compared to mature monocyte-derived DC (moDC). We therefore directly compared the capacities of mature PDC and moDC to activate T cells. A similar T helper type 1 (Th1)/Th2 pattern of cytokines was generated in both systems, but significantly higher levels of IL-3, IL-4 and IL-10 were induced by PDC. In T cells interacting with PDC, the ICOS/ICOS-L costimulatory pathway played a pre-eminent role in the generation of IL-3 and IL-10, CD28 was central to the induction of IL-2, and both pathways were equally important for the generation of other cytokines. In cocultures with moDC, the CD28 pathway was dominant over ICOS under all circumstances, except for the ICOS-mediated release of IL-10. In general, our data demonstrate an eminent role of ICOS in the interaction of T cells with PDC, and thus modify the current paradigm of CD28 dominance for the costimulation of T cells interacting with professional antigen-presenting cells. In particular, our data highlight the role of ICOS in the generation of IL-3, a factor central to the biology of human PDC.
Synthesis of Biocompatible Dextran‐Coated Nanoceria with pH‐Dependent Antioxidant Properties (2008)

Biocompatible dextran-coated nanoceria (cerium oxide nanoparticles) are found to exhibit excellent, pH-dependent antioxidant properties (see image). They provide cytoprotection from free radicals to normal cells but not to cancer cells, and thus have potential applications in antioxidant and anti-inflammatory coatings for prosthetic devices and tissue engineering and in improved cancer therapeutics. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2296/2008/smll200700824_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
A comparative study of immunosuppressive acidic protein (IAP), CA 125 and acute-phase proteins as parameters for ovarian cancer monitoring. (1988)

The serum concentrations of immunosuppressive acidic protein (IAP), CA 125, alpha-1-antitrypsin (AL-1-AT), C-reactive protein (CRP) and ceruloplasmin (COP) were determined in 63 patients with ovarian carcinoma (mean age 56.9 +/- 11.1 years). The threshold value of IAP was 640 micrograms/ml (means + 2SD), of CA 125 35 U/ml, of AL-1-AT 4 mg/ml, of CRP 12 micrograms/ml, and of COP 600 ng/ml. Eighty-three analyses of the patients with ovarian cancer coincided with tumor progression and 124 samples with remission. In women with progressive ovarian carcinoma the median IAP serum concentrations (799.3 +/- 292 micrograms/ml) were significantly increased as compared to the values of the healthy control group (48 volunteers, mean age 37.8 +/- 13.8 years; IAP 452.0 +/- 146.0 micrograms/ml). The median serum concentrations of IAP (799.3 +/- 292.2 micrograms/ml), CA 125 (933.8 +/- 1442.1 U/ml). AL-1-AT (3.8 +/- 8.7 mg/ml), CRP (31 +/- 39 micrograms/ml) were significantly elevated with progression as compared to remission (IAP 511.8 +/- 111.9 micrograms/ml, CA 125 18.4 +/- 14.4 U/ml, AL-1-AT 2.8 +/- 4.1 mg/ml, CRP 13 +/- 11 micrograms/ml). This was not the case with COP (509 +/- 761 vs. 466 +/- 106 ng/ml). A correlation between increased serum values and confirmed tumor progression was encountered in 65.1% of the patients for IAP, in 80.7% for CA 125 and in 34.9% for CRP and AL-1-AT. 98.8% false negative serum values were found for COP. Seven out of 16 and 4 out of 16 CA 125 negative samples showed right positive IAP and right positive CRP and AL-1-AT values, respectively. 88.7% of the IAP values, 92.7% of the CA 125 values, 71% of the AL-1-AT values, 93.5% of the CRP and 100% of the COP values were right negative. Our results indicate that the simultaneous determination of CA 125 and IAP enhance the efficiency of tumor monitoring in patients with ovarian cancer.
Degradation of Opioids and Opiates During Acid Hydrolysis Leads to Reduced Recovery Compared to Enzymatic Hydrolysis (2016)

Drug monitoring laboratories utilize a hydrolysis process to liberate the opiates from their glucuronide conjugates to facilitate their detection by tandem mass spectrometry (MS). Both acid and enzyme hydrolysis have been reported as viable methods, with the former as a more effective process for recovering codeine-6-glucuronide and morphine-6-glucuronide. Here, we report concerns with acid-catalyzed hydrolysis of opioids, including a significant loss of analytes and conversions of oxycodone to oxymorphone, hydrocodone to hydromorphone and codeine to morphine. The acid-catalyzed reaction was monitored in neat water and patient urine samples by liquid chromatography-time-of-flight and tandem MS. These side reactions with acid hydrolysis may limit accurate quantitation due to loss of analytes, possibly lead to false positives, and poorly correlate with pharmacogenetic profiles, as cytochrome P450 enzyme (CYP2D6) is often involved with oxycodone to oxymorphone, hydrocodone to hydromorphone and codeine to morphine conversions. Enzymatic hydrolysis process using the purified, genetically engineered β-glucuronidase (IMCSzyme<sup>®</sup>) addresses many of these concerns and demonstrates accurate quantitation and high recoveries for oxycodone, hydrocodone, oxymorphone and hydromorphone.
Pattern of Plasma Dehydroepiandrosterone Sulfate Levels in Humans from Birth to Adulthood: Evidence for Testicular Production* (1978)

Plasma levels of dehydroepiandrosterone sulfate (DHAS) were measured in 513 normal full term newborns, infants, children, adolescents, and adults and the results were expressed in micrograms per dl. In infancy and childhood, DHAS levels were similar in both sexes. In 74 neonates, mixed cord blood mean values ± SD were 134.6 ± 64. During the first day of life, plasma DHAS levels were 140 ± 125 in 33 neonates. During the first month of life, DHAS decreased drastically, then more progressively until the 6th month of life. Between 1-6 months of age, mean levels were 5.9 ± 4.7 in 40 children. DHAS was very low between 1-6 yr of life (2.3 ± 1.6) and rose abruptly at the 7th year of life. Thereafter, DHAS continued to increase correlatively with age and pubertal stages in both sexes; a further increase after age 16 or pubertal stage P5 was noted only in male subjects. In adults, DHAS was significantly higher in male (224 ± 93) than in female (138.3 ± 51) subjects. DHAS levels were compared to those of dehydroepiandrosterone; at two periods of life, early infancy and adulthood, their patterns differed. After long term hCG stimulation, DHAS increased significantly in 45 normal prepubertal boys and in 2 boys with adrenal insufficiency. These data would suggest a direct testicular production of DHAS.
A cobalt complex that selectively disrupts the structure and function of zinc fingers (1998)

Zinc finger domains are structures that mediate sequence recognition for a large number of DNA-binding proteins. These domains consist of sequences of amino acids containing cysteine and histidine residues tetrahedrally coordinated to a zinc ion. In this report, we present a means to selectively inhibit a zinc finger transcription factor with cobalt(III) Schiff-base complexes. 1H NMR spectroscopy confirmed that the structure of a zinc finger peptide is disrupted by axial ligation of the cobalt(III) complex to the nitrogen of the imidazole ring of a histidine residue. Fluorescence studies reveal that the zinc ion is displaced from the model zinc finger peptide in the presence of the cobalt complex. In addition, gel-shift and filter-binding assays reveal that cobalt complexes inhibit binding of a complete zinc finger protein, human transcription factor Sp1, to its consensus sequence. Finally, a DNA-coupled conjugate of the cobalt complexes selectively inhibited Sp1 in the presence of several other transcription factors.
Bandwidth Enhancement by Master Modulation of Optical Injection-Locked Lasers (2008)

In normal injection-locked semiconductor lasers, the modulation signals are applied to the slave laser. In this paper, we show that modulating the master light before injection exhibits distinctive modulation dynamics and frequency response. We first present a detailed theoretical model and simulation results. Experimentally, we have successfully demonstrated both master amplitude and master phase modulation. The resulting 3-dB bandwidths have been enhanced by up to three times, exceeding 50 GHz. The resonance frequency of the combined lasers is greater than 100 GHz.
Histidine 21 does not play a major role in diphtheria toxin catalysis. (1994)

It has been proposed that the histidine at position 21 (H21) of the diphtheria toxin A subunit (DTA) plays an important role in the ADP-ribosyltransferase (ADPRT) activity of the toxin. The region of DT encompassing H21 demonstrates sequence similarity with other toxins exhibiting ADPRT activity, is located along the catalytic cleft of DTA, and when H21 is chemically modified, ADPRT activity is abolished. H21 was mutagenized by a polymerase chain reaction-based system whereby all alternative amino acids were substituted in place of the histidine. The majority of the substitutions virtually abolished enzymatic activity, the exception being a mutant in which H21 was replaced with asparagine (DTA-H21N). This mutant demonstrated only a slight increase in Km and relatively small decreases in both reaction rate (kcat) and catalytic efficiency (kcat/Km). Asparagine is a sterically conserved substitution, but its side-chain is unable to replace the imidazole group of histidine in general acid-base mechanisms or to participate in electrostatic interactions. This suggests that H21 is important in maintaining a steric conformation required for catalysis rather than in participating in an electrostatic or acid-base type of exchange.
Distinct Domain Utilization by Smad3 and Smad4 for Nucleoporin Interaction and Nuclear Import (2003)

Smad proteins undergo rapid nuclear translocation upon stimulation by transforming growth factor-beta (TGFbeta) and in so doing transduce the signal into the nucleus. In this report we unraveled nuclear import mechanisms of Smad3 and Smad4 that are dependent on their interaction with FG-repeat-containing nucleoporins such as CAN/Nup214, without the involvement of importin molecules that are responsible for most of the known nuclear import events. A surface hydrophobic corridor within the MH2 domain of Smad3 is critical for association with CAN/Nup214 and nuclear import, whereas Smad4 interaction with CAN/Nup214, and nuclear import requires structural elements present only in the full-length Smad4. As exemplified by the different susceptibility to inhibition of import by cytoplasmic retention factor SARA (Smad anchor for receptor activation), such utilization of distinct domains for nuclear import of Smad3 and Smad4 suggests that nuclear transport of Smad3 and Smad4 is subject to control by different retention factors.
Optical and electrical properties of amorphous zinc tin oxide thin films examined for thin film transistor application (2008)

Structural, electronic, and optical properties of amorphous and transparent zinc tin oxide films deposited on glass substrates by pulsed laser deposition (PLD) were examined for two chemical compositions of Zn:Sn=1:1 and 2:1 as a function of oxygen partial pressure (PO2) used for the film deposition and annealing temperature. Different from a previous report on sputter-deposited films [Chiang et al., Appl. Phys. Lett. 86, 013503 (2005)], the PLD-deposited films crystallized at a lower temperature &amp;lt;450 °C to give crystalline ZnO and SnO2 phases. The optical band gaps (Tauc gaps) were 2.80−2.85 eV and almost independent of oxygen PO2, which are smaller than those of the corresponding crystals (3.35−3.89 eV). Films deposited at low PO2 showed significant subgap absorptions, which were reduced by postthermal annealing. Hall mobility showed steep increases when carrier concentration exceeded threshold values and the threshold value depended on the film chemical composition. The films deposited at low PO2&amp;lt;2 Pa had low carrier concentrations. It is thought that the low PO2 produced high-density oxygen deficiencies and generated electrons, but these electrons were trapped in localized states, which would be observed as the subgap absorptions. Similar effects were observed for 600 °C crystallized films and their resistivities were increased by formation of subgap states due to the reducing high-temperature condition. High carrier concentrations and large mobilities were obtained in an intermediate PO2 region for the as-deposited films.
Posttranslational modification and microtubule stability. (1987)

We have probed the relationship between tubulin posttranslational modification and microtubule stability, using a variation of the antibody-blocking technique. In human retinoblastoma cells we find that acetylated and detyrosinated microtubules represent congruent subsets of the cells' total microtubules. We also find that stable microtubules defined as those that had not undergone polymerization within 1 h after injection of biotin-tubulin were all posttranslationally modified; furthermore dynamic microtubules were all unmodified. We therefore conclude that in these cells the stable, acetylated, and detyrosinated microtubules represent the same subset of the cells' total network. Posttranslational modification, however, is not a prerequisite for microtubule stability and vice versa. Potorous tridactylis kidney cells have no detectable acetylated microtubules but do have a sizable subset of stable ones, and chick embryo fibroblast cells are extensively modified but have few stable microtubules. We conclude that different cell types can create specific microtubule subsets by modulating the relative rates of posttranslational modification and microtubule turnover.
In vitro organogenesis from pluripotent stem cells (2014)

Pluripotent stem cells (PSCs) have the ability to spontaneously generate structured tissues in vitro reminiscent of embryonic tissue development. Recently, complex organoids such as cortical tissues, cerebral brain organoids, optical cups, intestinal tissues, and liver buds have been generated from PSCs derived from healthy individuals and patients with genetic diseases, providing powerful tools to understand morphogenesis and disease pathology. This article highlights recent advances in the state-of-art generation of organoids from PSCs, possible signaling pathways and mechanisms involved in organogenesis, and the understanding of extracellular microenvironment. Challenges involved in the organoid generation such as increasing organoid size, enhancing the tissue complexity, and improving functional maturation are also discussed.
Cationic oligopeptide‐mediated delivery of dsRNA for post‐transcriptional gene silencing in plant cells (2004)

We have used cationic oligopeptide polyarginine-12mer (POA) to deliver double-stranded RNA (dsRNA), prepared in vitro, to tobacco (Nicotiana tabacum) suspension cells. POA interacts electrostatically with dsRNA to form a complex. When dsRNA for the GUS or NPTII gene was delivered into cells carrying the same genes, the corresponding mRNA was degraded. Using RNase protection assay we were able to detect 21-bp small interfering RNA in dsRNA/POA-treated cells. These results demonstrate that POA can be used to deliver dsRNA to induce post-transcriptional gene silencing in plant cells.
Induction of Defense Responses in Cucumber Plants ( Cucumis sativus L.) by the Biocontrol Agent Trichoderma harzianum (1999)

ABSTRACT The potential of the biocontrol agent Trichoderma harzianum T-203 to trigger plant defense responses was investigated by inoculating roots of cucumber seedlings with Trichoderma in an aseptic, hydroponic system. Trichoderma -treated plants were more developed than nontreated plants throughout the experiment. Electron microscopy of ultrathin sections from Trichoderma -treated roots revealed penetration of Trichoderma into the roots, restricted mainly to the epidermis and outer cortex. Strengthening of the epidermal and cortical cell walls was observed, as was the deposition of newly formed barriers. These typical host reactions were found beyond the sites of potential fungal penetration. Wall appositions contained large amounts of callose and infiltrations of cellulose. The wall-bound chitin in Trichoderma hyphae was preserved, even when the hyphae had undergone substantial disorganization. Biochemical analyses revealed that inoculation with Trichoderma initiated increased peroxidase and chitinase activities within 48 and 72 h, respectively. These results were observed for both the roots and the leaves of treated seedlings, providing evidence that T. harzianum may induce systemic resistance mechanisms in cucumber plants.
Platinum coil-mediated implantation of growth factor-secreting endovascular tissue grafts: an in vivo study. (1998)

Platinum coils can be used as a cell delivery device. Direct intravascular implantation of growth factor-secreting fibroblast grafts leads to improved intravascular scar formation, therefore theoretically reducing the potential for aneurysm regrowth or coil compaction.