gebhart/patrepeval huggingface dataset:
Measurements by filter elution of DNA single- and double-strand breaks in rat hepatocytes: effects of nitrosamines and gamma-irradiation. (1982)

This work presents a filter elution method for measuring DNA single- and double-strand breaks in primary rat hepatocytes without radioactive labeling of DNA. We have studied the effects of a series of nitrosamines and of gamma-irradiation on DNA single- and double-strand break induction. The repair of DNA single-strand breaks in the hepatocytes was measured after treatment with 60Co, 1-methyl-1-nitrosourea, and N-nitrosodimethylamine. The hepatocytes were isolated by ethylene glycol-bis(beta-aminoethyl ether)-N,N'-tetra acetic acid-collagenase perfusion and had a mean viability of 91 +/- 4% (S.D.). The isolated cells were treated for varying lengths of time with nitrosamines in suspension culture in L-15 medium containing 10% fetal bovine serum. After treatment, the cells were chilled, loaded onto 2 micrometers polycarbonate filters, and lysed in a 2% sodium dodecyl sulfate-proteinase K solution, pH 9.6. The DNA was eluted from the filter at either native or denaturing pH with fractions collected every 3 hr. The quantity of DNA in each fraction was determined by measuring the fluorescent product formed between it and diaminobenzoic acid after ethanol-sodium acetate precipitation and trapping of the DNA on 0.2-micrometer polycarbonate filters. The results show that the carcinogens, N-nitrosodimethylamine, N-nitrosodiethylamine, N-nitrosodipropylamine, N-nitrosodibutylamine, and 1-nitrosopiperidine all made dose- and time-related increases in the number of single-strand breaks in rat hepatocytes. N-Nitrosodiphenylamine produced small numbers of single-strand breaks. No double-strand breaks were formed by any of the nitrosamines. Single-strand breaks induced by N-nitrosodimethylamine were repaired very slowly relative to repair of either gamma-ray of 1-methyl-1-nitrosourea-induced single-strand breaks. This system has many advantages for studying carcinogen metabolism and DNA damage in hepatocytes, one of the major target cells for many carcinogens.-
Biosynthesis and glycosylation of the human complement regulatory protein decay-accelerating factor. (1986)

The biosynthesis and oligosaccharide structure of the human complement regulatory glycoprotein decay-accelerating factor (DAF) were studied in erythrocytes and cell lines. Initial information relative to carbohydrate moieties of DAF was obtained by enzymatic digestions. The 74,000 Mr erythrocyte DAF was lowered 3000 by endoglycosidase F, whereas endoglycosidase H had no effect, indicating one N-linked complex-type unit. Treatment with endo-alpha-N-acetylgalactosaminidase to remove O-linked oligosaccharides resulted in a 48,000 Mr molecule (67% of the Mr shift being due to sialic acid), which decreased to 45,000 Mr after sequential endoglycosidase F treatment. To additionally define the oligosaccharide structure and identify precursors in biosynthetic pathways, DAF was studied in the HL-60 cell line differentiated by vitamin D toward monocytes. Pulse-chase experiments with [35S]methionine revealed a precursor species of 43,000 Mr that underwent an early post-translational modification to a 46,000 Mr intermediate, and subsequently was chased into a mature species of 80,000 Mr that aligned with 125I surface-labeled DAF from these cells. All three forms of DAF were approximately 3000 lower in Mr in the presence of tunicamycin. The two lower Mr DAF species were sensitive to endoglycosidases F and H but not to neuraminidase or endo-alpha-N-acetylgalactosaminidase. In summary, DAF is synthesized as a 43,000 Mr precursor species containing one N-linked high-mannose unit. Before entering the central region of the Golgi, it is converted to a 46,000 Mr species by an as yet unknown post-translational modification. The 46,000 Mr form is converted to the 74,000 Mr (erythrocyte) or 80,000 Mr (leukocyte) membrane form of DAF by the addition of multiple, sialylated O-linked oligosaccharide chains (responsible for the large electrophoretic mobility shift) and conversion of the single N-linked high-mannose unit to a complex-type structure. The cell-specific Mr variation between red and white blood cells arises during this post-translational modification from the 46,000 Mr biosynthetic intermediate to the mature DAF species expressed on the cell surface.
Super‐resolution<i>T</i><sub>1</sub>estimation: Quantitative high resolution<i>T</i><sub>1</sub>mapping from a set of low resolution<i>T</i><sub>1</sub>‐weighted images with different slice orientations (2016)

Super resolution T<sub>1</sub> estimation enables resolution enhancement in T<sub>1</sub> mapping with the use of standard (inversion recovery) T<sub>1</sub> acquisition sequences. Magn Reson Med 77:1818-1830, 2017. © 2016 International Society for Magnetic Resonance in Medicine.
Three-Dimensional Nonlinear Image Reconstruction for Microwave Biomedical Imaging (2004)

Active microwave imaging has attracted significant interests in biomedical applications, in particular for breast imaging. However, the high electrical contrasts in breast tissue also increases the difficulty of forming an accurate image because of the increased multiple scattering. To model such strong three-dimensional (3-D) multiple scattering effects in biomedical imaging applications, we develop a full 3-D inverse scattering algorithm based on the combination of the contrast source inversion and the fast Fourier transform algorithm. Numerical results show that our algorithm can accurately invert for the high-contrast media in breast tissue.
Transliteration as Alignment vs. Transliteration as Generation for Crosslingual Information Retrieval (2010)

Crosslingual Information Retrieval (CLIR) usually requires query tran slation and, due to named entities in the case of IR, query translation requires a good tra nsliteration system when writing systems differ. Transliteration can be seen as a problem of ge neration or align- ment. For IR, since we can extract a word list from the corpus being sear ched, it should be seen as an alignment problem. The shift from generation to alignment can lead to h igher translit- eration accuracies and significant improvements in the CLIR results. We w ere able to achieve an increase (over generation) in the CLIR Mean Average Precision by 2 2.66% and 29.08% for
A Deep Learning Based Printing Defect Classification Method with Imbalanced Samples (2019)

Deep learning has been successfully applied to classification tasks in many fields due to its good performance in learning discriminative features. However, the application of deep learning to printing defect classification is very rare, and there is almost no research on the classification method for printing defects with imbalanced samples. In this paper, we present a deep convolutional neural network model to extract deep features directly from printed image defects. Furthermore, considering the asymmetry in the number of different types of defect samples—that is, the number of different kinds of defect samples is unbalanced—seven types of over-sampling methods were investigated to determine the best method. To verify the practical applications of the proposed deep model and the effectiveness of the extracted features, a large dataset of printing detect samples was built. All samples were collected from practical printing products in the factory. The dataset includes a coarse-grained dataset with four types of printing samples and a fine-grained dataset with eleven types of printing samples. The experimental results show that the proposed deep model achieves a 96.86% classification accuracy rate on the coarse-grained dataset without adopting over-sampling, which is the highest accuracy compared to the well-known deep models based on transfer learning. Moreover, by adopting the proposed deep model combined with the SVM-SMOTE over-sampling method, the accuracy rate is improved by more than 20% in the fine-grained dataset compared to the method without over-sampling.
TSLP regulates intestinal immunity and inflammation (2009)

This thesis characterizes and explores the role of thymic stromal lymphopoietin (TSLP) – TSLP receptor (TSLPR) interactions in the regulation of intestinal immunity and inflammation. TSLP is known to promote TH2 cytokine-mediated inflammation in the skin and the lung. Firstly, this thesis focuses on the characterization of TSLP and TSLPR expression within the gastrointestinal (GI) tract and in the immune cells of the associated lymphoid tissues. Our findings suggest that TSLP is primarily produced by intestinal epithelial cells (IECs) under homeostatic conditions. Expression of the heterodimeric TSLPR complex was exhibited on gut-associated lymphoid tissue (GALT) CD4+ T cells and CD11c+ dendritic cells (DCs) as well as on splenic mast cells and basophils in naïve mice. Second, this thesis explores the role of TSLP in the generation of a TH2 cytokine-mediated host-protective immune response to the gastrointestinal helminth pathogen Trichuris muris. We demonstrate that in an intact animal TSLP-TSLPR interactions are critical for resistance to Trichuris as disruption of the TSLP-TSLPR pathway either through genetic deletion of the TSLPR, or antibody-mediated depletion of TSLP, resulted in susceptibility to infection. Further, these mice exhibited increased infection-induced proinflammatory cytokine production and inflammation. However, TSLP-TSLPR interactions were not required for the generation of a host-protective TH2 cytokine-mediated immune response to Trichuris in the absence of IFN-γ, indicating TSLP-independent intestinal TH2 immune responses. Third, we examine the potential for TSLP-TSLPR interactions to regulate intestinal proinflammatory cytokine production. Examination of naïve TSLPR-/- mice revealed a trend towards increased CD4+ T cell production of IFN-γ in the GALT compared to TSLPR+/+ mice. Further, TSLPR-/- mice were more susceptible to DSS-induced colitis, exhibiting increased proinflammatory cytokine production and more severe intestinal inflammation compared to control mice. We demonstrate that TSLP can regulate DC-derived IL-12/23p40 production both in vitro and in vivo and that rTSLP is able to inhibit CD4+ T cell production of IFN-γ in splenocyte cultures in the absence of IL-4. Taken as a whole, this thesis identifies an important role for TSLP-TSLPR interactions in regulating intestinal immunity and inflammation and in the maintenance of intestinal immune homeostasis.
Electromagnetic fields act <i>via</i> activation of voltage‐gated calcium channels to produce beneficial or adverse effects (2013)

The direct targets of extremely low and microwave frequency range electromagnetic fields (EMFs) in producing non-thermal effects have not been clearly established. However, studies in the literature, reviewed here, provide substantial support for such direct targets. Twenty-three studies have shown that voltage-gated calcium channels (VGCCs) produce these and other EMF effects, such that the L-type or other VGCC blockers block or greatly lower diverse EMF effects. Furthermore, the voltage-gated properties of these channels may provide biophysically plausible mechanisms for EMF biological effects. Downstream responses of such EMF exposures may be mediated through Ca(2+) /calmodulin stimulation of nitric oxide synthesis. Potentially, physiological/therapeutic responses may be largely as a result of nitric oxide-cGMP-protein kinase G pathway stimulation. A well-studied example of such an apparent therapeutic response, EMF stimulation of bone growth, appears to work along this pathway. However, pathophysiological responses to EMFs may be as a result of nitric oxide-peroxynitrite-oxidative stress pathway of action. A single such well-documented example, EMF induction of DNA single-strand breaks in cells, as measured by alkaline comet assays, is reviewed here. Such single-strand breaks are known to be produced through the action of this pathway. Data on the mechanism of EMF induction of such breaks are limited; what data are available support this proposed mechanism. Other Ca(2+) -mediated regulatory changes, independent of nitric oxide, may also have roles. This article reviews, then, a substantially supported set of targets, VGCCs, whose stimulation produces non-thermal EMF responses by humans/higher animals with downstream effects involving Ca(2+) /calmodulin-dependent nitric oxide increases, which may explain therapeutic and pathophysiological effects.
Using interleaved execution to resolve cyclic dependencies in time-based block diagrams (2004)

Time-based block diagrams are a convenient formalism for describing dynamic systems such as those found in control system design. The block-diagram model of the control system is used to capture implementation effects such as sample rates and fixed-point data types. One implementation decision concerns the desired software partitioning used in performing simulation and program synthesis. This paper shows how software partitioning may yield undesirable side-effects involving 'false' algebraic loops, which affects model execution and program synthesis. It presents an approach to resolve these pathological cases for a class of block diagram models.
Genome Sequence of the Chemolithoautotrophic Nitrite-Oxidizing Bacterium <i>Nitrobacter winogradskyi</i> Nb-255 (2006)

The alphaproteobacterium Nitrobacter winogradskyi (ATCC 25391) is a gram-negative facultative chemolithoautotroph capable of extracting energy from the oxidation of nitrite to nitrate. Sequencing and analysis of its genome revealed a single circular chromosome of 3,402,093 bp encoding 3,143 predicted proteins. There were extensive similarities to genes in two alphaproteobacteria, Bradyrhizobium japonicum USDA110 (1,300 genes) and Rhodopseudomonas palustris CGA009 CG (815 genes). Genes encoding pathways for known modes of chemolithotrophic and chemoorganotrophic growth were identified. Genes encoding multiple enzymes involved in anapleurotic reactions centered on C2 to C4 metabolism, including a glyoxylate bypass, were annotated. The inability of N. winogradskyi to grow on C6 molecules is consistent with the genome sequence, which lacks genes for complete Embden-Meyerhof and Entner-Doudoroff pathways, and active uptake of sugars. Two gene copies of the nitrite oxidoreductase, type I ribulose-1,5-bisphosphate carboxylase/oxygenase, cytochrome c oxidase, and gene homologs encoding an aerobic-type carbon monoxide dehydrogenase were present. Similarity of nitrite oxidoreductases to respiratory nitrate reductases was confirmed. Approximately 10% of the N. winogradskyi genome codes for genes involved in transport and secretion, including the presence of transporters for various organic-nitrogen molecules. The N. winogradskyi genome provides new insight into the phylogenetic identity and physiological capabilities of nitrite-oxidizing bacteria. The genome will serve as a model to study the cellular and molecular processes that control nitrite oxidation and its interaction with other nitrogen-cycling processes.
Designing multi-core architecture using folded torus concept to minimize the number of switches (2011)

Thesis (M.S.)--Wichita State University, College of Engineering, Dept. of Electrical Engineering and Computer Science.
Titanium-doped indium oxide: A high-mobility transparent conductor (2005)

We report on the effects of titanium doping (0–7at.%) on the optical and electrical properties of In2O3 using combinatorial deposition and analysis techniques. Maximum mobilities are observed at Ti concentrations of 1.5–2.5at.% and are &gt;80cm2∕Vs in sputtered films. The carrier concentration increased with titanium content to a high of 8.0×1020cm−3. Data show that one carrier is generated per added Ti between 1 and 3at.%. Conductivities up to 6260Ω−1cm−1 were observed. These remained very high &gt;5000Ω−1cm−1 across a wide compositional range. The optical transparency is high (&gt;85%) in a wide spectral range from 400nm to at least 1750nm. The work function of titanium-doped indium oxide varies substantially over the studied compositional range.
Effect of red pepper and black pepper on the stomach. (1987)

Spices have long been implicated as a cause of gastric mucosal injury. We assessed the effects of red and black pepper on the gastric mucosa using double-blind intragastric administration of test meals containing red pepper (0.1-1.5 g) or black pepper (1.5 g) to healthy human volunteers; aspirin (655 mg) and distilled water were used as positive and negative controls, respectively. Serial gastric washes were performed after test meal administration and gastric contents were analyzed for DNA, pepsin, blood, sodium, potassium, parietal cell secretion, and nonparietal cell secretion. Both red pepper and black pepper caused significant increases in parietal secretion, pepsin secretion, and potassium loss. Gastric cell exfoliation (as reflected in DNA loss into gastric contents) was increased after red or black pepper administration; the increase after red pepper administration was dose dependent. Mucosal microbleeding was seen after spice administration and one subject had grossly visible gastric bleeding after both red pepper and black pepper administration. There were no significant differences from control between the test meals, in nonparietal volume, fractional recovery of the gastric secretions, or sodium secretion. Finally, no spice was significantly different from aspirin in any parameter studied; indeed, aspirin was comparable to the higher doses of pepper. The long-term result of daily pepper ingestion is unknown. Whether spices are detrimental, beneficial (e.g., inducing an adaptive cytoprotective response), or have no significant long-term effect on the gastric mucosa is unknown and deserves further study.
Effect of Silver Nitrate, Aminoethoxyvinylglycine, and Gibberellins A4+7 plus 6-Benzylamino purine on Fruit Set and Development of ‘Delicious’ Apples1 (1980)

Abstract Sprays of silver nitrate (AgNO 3 ), aminoethoxyvinylglycine (AVG) and gibberellins A 4+7 (GA 4+7 ) plus 6-benzylamino purine (BA) were applied with 0.1% Triton B-1956 at bloom to ‘Richared Delicious’ apple trees ( Malus domestica Borkh.). AVG at 200 ppm alone or when applied with 50 ppm each of GA 4+7 and BA increased fruit set whereas GA 4+7 plus BA applied alone at 50 ppm caused fruit thinning. AVG reduced endogenous ethylene production and overcame the increased ethylene production brought about by GA 4+7 plus BA application. AVG applied alone at 200 ppm or when combined with GA 4+7 plus BA reduced fruit size and increased the L/D ratio at harvest.
Device for intracellular increase of oxygen free radicals and inhibition of MethA tumour cell proliferation: in vitro and in vivo studies. (1988)

We investigated the efficacy of chemical agents aimed at increasing and accumulating oxygen free radicals inside tumour cells to act as inhibitors of the proliferation of these cells. Using MethA tumour cells derived from Balb/c mice, diethyldithiocarbamate (DDC), a copper chelator which is known to inactivate superoxide dismutase, and ascorbic acid (AsA) which mediates catalase inhibition, were employed to accumulate oxygen free radicals inside the tumour cells. It was found that inhibition of the tumour-cell proliferation in vitro, along with greater than 95% reduction of tritiated thymidine uptake by these cells, was attained only when both DDC (5 x 10(-7) M) and AsA (2 x 10(-5) M approximately 2 x 10(-4) M) were added simultaneously and cultured for 48 h. A similar inhibitory effect was observed when the MethA tumour cells were pretreated simultaneously or separately with both DDC and AsA at 37 degrees C for 1 h and cultured for 48 h. The augmented inhibitory effect was completely inhibited by the addition of catalase (2000 U/ml). In vivo, two million MethA tumour cells were inoculated s.c. into the mice, and DDC and/or AsA were injected i.v. or i.t. 7 days later when the diameter of each tumour had reached about 8 mm. An early development of tumour necrosis, and a significant inhibition of the tumour growth, occurred when both agents were used together. Thus a marked augmentation of the inhibitory effect was observed when DDC and AsA were used in combination.(ABSTRACT TRUNCATED AT 250 WORDS)
Combining data compression and encryption (2002)

As data communication becomes more pervasive and complex and the use of digital data evermore wide spread, data security becomes a wider, more complex and more important problem. Encryption can be an important tool to help improve data security. At first thought, data compression and data encryption are incompatible because encrypted data cannot be compressed by any known compression algorithms. Encryption can be applied after compression, but this requires additional processing or hardware. However, fixed library autosophy tree network data compression can combine encryption by using the library as the code key. Under appropriate conditions the compression ratio can be high, the encryption strong, and no additional processing is required for encryption.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Congestion-free routing reconfiguration: Formulation and examples (2014)

We consider the network-layer problem of avoiding congestion while reconfiguring the routing paths. We formulate a flow-based and a switch-based model. For the flow-based model, we demonstrate that an optimal sequence of minimum update steps could always be found when the dependency graph is acyclic. For the switch-based model, we find a way to translate a feasible flow-based sequence to a feasible switch-based sequence subject to a tree topology constraint on the routing paths.
Development of wide-band gap InGaN solar cells for high-efficiency photovoltaics (2008)

Main objective of the present work is to develop wide-band gap InGaN solar cells in the 2.4 - 2.9 eV range that can be an integral component of photovoltaic devices to achieve efficiencies greater than 50%. In the present work, various challenges in the novel III-nitride technology are identified and overcome individually to build basic design blocks, and later, optimized comprehensively to develop high-performance InGaN solar cells. Due to the unavailability of a suitable modeling program for InGaN solar cells, PC1D is modified up to a source-code level to incorporate spontaneous and piezoelectric polarization in order to accurately model III-nitride solar cells. On the technological front, InGaN with indium compositions up to 30% (2.5 eV band gap) are developed for photovoltaic applications by controlling defects and phase separation using metal-organic chemical vapor deposition. InGaN with band gap of 2.5 eV is also successfully doped to achieve acceptor carrier concentration of 1e18 cm-3. A robust fabrication scheme for III-nitride solar cells is established to increase reliability and yield; various schemes including interdigitated grid contact and current spreading contacts are developed to yield low-resistance Ohmic contacts for InGaN solar cells. Preliminary solar cells are developed using a standard design to optimize the InGaN material, where the band gap of InGaN is progressively lowered. Subsequent generations of solar cell designs involve an evolutionary approach to enhance the open-circuit voltage and internal quantum efficiency of the solar cell. The suitability of p-type InGaN with band gaps as low as 2.5 eV is established by incorporating in a solar cell and measuring an open-circuit voltage of 2.1 V. Second generation InGaN solar cell design involving a 2.9 eV InGaN p-n junction sandwiched between p- and n-GaN layers yields internal quantum efficiencies as high as 50%; while sixth generation devices utilizing the novel n-GaN strained window-layer enhance the open circuit voltage of a 2.9 eV InGaN solar cell to 2 V. Finally, key aspects to further InGaN solar cell research, including integration of various designs, are recommended to improve the efficiency of InGaN solar cells. These results establish the potential of III-nitrides in ultra-high efficiency photovoltaics.