gebhart/patrepeval huggingface dataset:
Color Clusterization using Modified HSL Space (1996)

This paper describes a clusterization procedure based on a set of new transformations for HSL color space. The clusterization is applied for color layer extraction from the large blue print documents overdrawn with color pens and pencils. The process of color layer extraction requires a segmentation and a classification of segmented area to recompose each color layer. Overlapped colors are identified based on extraction of primary and secondary clusters. The new HSL transformations are based on the modification of lightness function in a standard HSL space. The modified HSL color space remains device dependent space, but the RGB regulate domain is not transformed into a HSL regulate domain. The clusterization procedure is based on the Mahalanobis distance in new HSL space. A 3D visualization procedure is used for illustration the efficiency of the clusterization process.
Expression of Fungal Cutinase and Swollenin in Tobacco Chloroplasts Reveals Novel Enzyme Functions and/or Substrates (2013)

In order to produce low-cost biomass hydrolyzing enzymes, transplastomic lines were generated that expressed cutinase or swollenin within chloroplasts. While swollenin expressing plants were homoplasmic, cutinase transplastomic lines remained heteroplasmic. Both transplastomic lines showed interesting modifications in their phenotype, chloroplast structure, and functions. Ultrastructural analysis of chloroplasts from cutinase- and swollenin-expressing plants did not show typical lens shape and granal stacks. But, their thylakoid membranes showed unique scroll like structures and chloroplast envelope displayed protrusions, stretching into the cytoplasm. Unusual honeycomb structures typically observed in etioplasts were observed in mature chloroplasts expressing swollenin. Treatment of cotton fiber with chloroplast-derived swollenin showed enlarged segments and the intertwined inner fibers were irreversibly unwound and fully opened up due to expansin activity of swollenin, causing disruption of hydrogen bonds in cellulose fibers. Cutinase transplastomic plants showed esterase and lipase activity, while swollenin transplastomic lines lacked such enzyme activities. Higher plants contain two major galactolipids, monogalactosyldiacylglycerol (MGDG) and digalactosyldiacylglycerol (DGDG), in their chloroplast thylakoid membranes that play distinct roles in their structural organization. Surprisingly, purified cutinase effectively hydrolyzed DGDG to MGDG, showing alpha galactosidase activity. Such hydrolysis resulted in unstacking of granal thylakoids in chloroplasts and other structural changes. These results demonstrate DGDG as novel substrate and function for cutinase. Both MGDG and DGDG were reduced up to 47.7% and 39.7% in cutinase and 68.5% and 67.5% in swollenin expressing plants. Novel properties and functions of both enzymes reported here for the first time should lead to better understanding and enhanced biomass hydrolysis.
Aluminum nitride for 6H-SiC power devices (1997)

Aluminum nitride (AlN) is a potential gate insulator material for 6H-SiC metal-insulator-semiconductor (MIS) devices for high temperature and high power applications. A critical requirement for a viable gate insulator material is that the insulator/semiconductor interface must have a very low interface state density, low insulator fixed charge density, as well as a low density of interfacial trapping centers. Our capacitance-voltage (CV) measurements have shown that it is possible to obtain an AlN/6H-SiC interface with such characteristics. Although CV measurements done at 573 K have shown evidence of the activation of deeper interfacial charged centers, they still reveal the presence of a low number of interface states and low insulator charge density. The disadvantage of this material system is the high leakage current density. However, by using a stacked AlN structure, we have found that it is possible to obtain MIS structures that are able to sustain breakdown fields close to the theoretical values. The possible use of a very thin AlN layer to enhance the characteristics of a Au-6H-SiC Schottky diode will also be discussed.
Re: Marked Protection against Acute Renal and Hepatic Injury after Nitrited Myoglobin + Tin Protoporphyrin Administration (2016)

No AccessJournal of UrologyInvestigative Urology1 Jun 2016Re: Marked Protection against Acute Renal and Hepatic Injury after Nitrited Myoglobin + Tin Protoporphyrin Administration Anthony AtalaMD Anthony AtalaAnthony Atala More articles by this author View All Author Informationhttps://doi.org/10.1016/j.juro.2016.03.017AboutFull TextPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail "Re: Marked Protection against Acute Renal and Hepatic Injury after Nitrited Myoglobin + Tin Protoporphyrin Administration." The Journal of Urology, 195(6), pp. 1947–1948 © 2016 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 195Issue 6June 2016Page: 1947-1948 Advertisement Copyright & Permissions© 2016 by American Urological Association Education and Research, Inc.MetricsAuthor Information Anthony Atala More articles by this author Expand All Advertisement PDF downloadLoading ...
Structure, dynamics, and regulation of TRF1-TIN2-mediated trans- and cis-interactions on telomeric DNA (2021)

TIN2 is a core component of the shelterin complex linking double-stranded telomeric DNA-binding proteins (TRF1 and TRF2) and single-strand overhang-binding proteins (TPP1-POT1). In vivo, the large majority of TRF1 and TRF2 exist in complexes containing TIN2 but lacking TPP1/POT1; however, the role of TRF1-TIN2 interactions in mediating interactions with telomeric DNA is unclear. Here, we investigated DNA molecular structures promoted by TRF1-TIN2 interaction using atomic force microscopy (AFM), total internal reflection fluorescence microscopy (TIRFM), and the DNA tightrope assay. We demonstrate that the short (TIN2S) and long (TIN2L) isoforms of TIN2 facilitate TRF1-mediated DNA compaction (cis-interactions) and DNA-DNA bridging (trans-interactions) in a telomeric sequence- and length-dependent manner. On the short telomeric DNA substrate (six TTAGGG repeats), the majority of TRF1-mediated telomeric DNA-DNA bridging events are transient with a lifetime of ~1.95 s. On longer DNA substrates (270 TTAGGG repeats), TIN2 forms multiprotein complexes with TRF1 and stabilizes TRF1-mediated DNA-DNA bridging events that last on the order of minutes. Preincubation of TRF1 with its regulator protein Tankyrase 1 and the cofactor NAD<sup>+</sup> significantly reduced TRF1-TIN2 mediated DNA-DNA bridging, whereas TIN2 protected the disassembly of TRF1-TIN2 mediated DNA-DNA bridging upon Tankyrase 1 addition. Furthermore, we showed that TPP1 inhibits TRF1-TIN2L-mediated DNA-DNA bridging. Our study, together with previous findings, supports a molecular model in which protein assemblies at telomeres are heterogeneous with distinct subcomplexes and full shelterin complexes playing distinct roles in telomere protection and elongation.
Cytoplasmic Delivery and Selective, Multicomponent Labeling with Oligoarginine-Linked Protein Tags (2015)

Strategies that leverage bio-orthogonal interactions between small molecule ligands and genetically encoded amino acid sequences can be used to attach high-performance fluorophores to proteins in living cells. However, a major limitation of chemical protein labeling is that cells' plasma membranes are impermeable to many useful probes and biolabels. Here, we show that conjugation to nonaarginine, a cell penetrating peptide (CPP), enables passive cytoplasmic delivery of otherwise membrane-impermeant, small molecule protein labels. Heterodimers consisting of a luminescent Tb(3+) complex, Lumi4, linked to benzyl guanine, benzyl cytosine, and trimethoprim were conjugated to the peptide CysArg9 with a reducible disulfide linker. When added to culture medium, the peptide conjugates rapidly (<30 min) enter the cytoplasm and diffuse freely throughout cells. The benzyl guanine, benzyl cytosine, and trimethoprim derivatives bind selectively to fusion proteins tagged with SNAP-Tag, CLIP-Tag, and Escherichia coli dihydrofolate reductase (eDHFR), respectively. Furthermore, eDHFR and SNAP-Tag fusions can be labeled with Lumi4 analogues in the same cell, and this labeling can be detected using two-color, time-gated Förster resonance energy transfer (FRET) microscopy. Finally, we present quantitative data showing that cytoplasmic uptake of nonaarginine-conjugated probes occurs in multiple cell types (MDCK, HeLa, NIH 3T3), most cells in a culture (>75%) are loaded with probe, and the cellular probe concentration can be controlled by varying incubation conditions. CPP-mediated delivery of Lumi4-linked protein labels will greatly increase the utility of lanthanide-based FRET microscopy. Moreover, our results strongly suggest that this approach can be adapted to deliver a wide variety of protein-targeted fluorophores or other functional probes that were previously unavailable for intracellular imaging studies.
Corrigendum to “Some aspects of the venom proteome of the Colubridae snake Philodryas olfersii revealed from a Duvernoy's (venom) gland transcriptome” [FEBS Lett. 580 (2006) 4417–4422] (2006)

An unfortunate error occurred during the preparation of Fig. 4B. In the second block of the alignment, the amino acid sequence segment “EALAGGTTALRRDVTEEQQQQLVAEESSG” should not be part of the AAC60341 protein, but part of the protein AAY47072 in the line below in the alignment. Note that the phylogenetic tree on Fig. 4 C was constructed from the correct sequences.
Triangulating polygons without large angles (1992)

We show how to triangulate an n-vertex polygonal region—adding extra vertices as necessary—with triangles of guaranteed quality. Using only O(n) triangles, we can guarantee that the smallest height (shortest dimension) of a triangle is approximately as large as possible. Using O(n log n) triangles, we can also guarantee that the largest angle is no greater than 150°. Finally we give a nonobtuse triangulation algorithm for convex polygons that uses O(n1.85) triangles.
Staphylococcus aureus infection of human endothelial cells potentiates Fc receptor expression. (1990)

Vasculitis, a recognized complication of staphylococcal-endovascular infections, may result in part, from the expression of FcR by Staphylococcus aureus-infected endothelial cells. FcR were measured using [51]Cr labeled SRBC preincubated with rabbit anti-SRBC IgG. FcR were not detected on uninfected endothelial cells, but were demonstrated on S. aureus infected cells using IgG, but not IgM labeled SRBC. FcR expression was dependent on the initial bacterial density (greater than or equal to 8 x 10(7) cfu/ml) and on phagocytosis of the staphylococci, but not on new protein synthesis. IgG labeled SRBC binding was blocked by aggregated IgG but not IgM. SRBC coated with the F(ab')2 portion of IgG did not bind, thus confirming that FcR were specifically involved in this interaction. FcR are expressed after S. aureus invasion of human endothelial cells and may contribute to the vasculitis which often accompanies S. aureus-endovascular infections.
Multilocus Binding Increases the Relaxivity of Protein‐Bound MRI Contrast Agents (2005)

Spinning around: The sensitivity of MRI contrast agents can be increased through multilocus binding. This restricts the internal motion and therefore increases the relaxivity of a bound protein multimer (see picture; A) relative to a single binding group (B), whose flexibility and internal motion limits the relaxivity gain. Protein-targeting groups (TG) can be used to anchor the multimer. Supporting information (synthesis of 1, 2, and 3) for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2005/z502245_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.
Effects of polymeric substrate roughness on head-medium spacing and recording properties of sputtered magnetic tape (2005)

We investigated the spacing dependence of recording characteristics on head-medium spacing due to the surface roughness of substrates. CoCrPt-sputtered tape media with a magnetic thickness of 25 nm were deposited onto polymeric substrates possessing very different roughnesses for this investigation. The degradation in the write and read processes due to spacing was a significant limiting factor at high densities. By utilizing smooth polymeric substrates, a substantial improvement in system bandwidth as well as effective write field gradient can be achieved. As a result, overwrite performance was also considerably improved over the frequency range of interest.
Spectroscopic characterization of dissolved organic matter from sludge solubilization treatment by micro-bubble technology (2017)

In this study, the micro-bubble were used for the sludge solubilization process. In order to investigate the enhancement of sludge solubilization by micro-bubbles, the performance of the micro-bubble system and a conventional bubble system (the control one) was compared in terms of sludge solubilization. The performance in the micro-bubble reactor was much better than the control one, as a result total suspended solid (TSS) was rapidly decreased to 2325.19 TSS L−1. To investigate the mechanism of the sludge solubilization, the constituents of dissolved organic matter (DOM) from the sludge solubilization was investigated using fluorescence spectroscopy. Compared to the DOM from the reactor using conventional bubbles, the DOM from the micro-bubbles reactor contained higher protein- and humic-like substances. Moreover, the total integrated fluorescence intensity (TOT) were constantly decreased by 18.37% in the control one and increased by 34.39% in the micro-bubble reactor. The results mean that the sludge were effectively solubilized, and organic molecules were released. Polymerase chain reactions-denaturing gradient gel electrophoresis (PCR-DGGE) was used to analyse the microbial communities after a micro-bubble process. The dominant bacteria in the micro-bubble reactor were identified as Delftia sp., Sphenophorus levis and Stenotrophomonas sp., which were benefit to the cleavage of refractory organics. Scanning Electron Microscopy (SEM) inspection showed that the sludge after the micro-bubble process presented more pores and channels on the sludge surface; the micro-bubbles was good at forming zoogloea, which was helpful for oxygen and mass transfer. Overall, the results indicate that the micro-bubbles aeration could improve the solubilization of sludge.
Extracellular superoxide dismutase is a thyroid differentiation marker down-regulated in cancer (2010)

Reactive oxygen species, specifically hydrogen peroxide (H(2)O(2)), have a significant role in hormone production in thyroid tissue. Although recent studies have demonstrated that dual oxidases are responsible for the H(2)O(2) synthesis needed in thyroid hormone production, our data suggest a pivotal role for superoxide dismutase 3 (SOD3) as a major H(2)O(2)-producing enzyme. According to our results, Sod3 is highly expressed in normal thyroid, and becomes even more abundant in rat goiter models. We showed TSH-stimulated expression of Sod3 via phospholipase C-Ca(2+) and cAMP-protein kinase A, a pathway that might be disrupted in thyroid cancer. In line with this finding, we demonstrated an oncogene-dependent decrease in Sod3 mRNA expression synthesis in thyroid cancer cell models that corresponded to a similar decrease in clinical patient samples, suggesting that SOD3 could be used as a differentiation marker in thyroid cancer. Finally, the functional analysis in thyroid models indicated a moderate role for SOD3 in regulating normal thyroid cell proliferation being in line with our previous observations.
Spin Transition in a Manganese(III) Porphyrin Cation Radical, Its Transformation to a Dichloromanganese(IV) Porphyrin, and Chlorination of Hydrocarbons by the Latter (1997)

Chemical oxidation of (TMP)Mn(III)(Cl) (TMP = the tetramesitylporphyrinato dianion) by Fe(ClO(4))(3) leads to the porphyrin-oxidized product (TMP(*)(+))Mn(III)(ClO(4))(2). Magnetic measurements and EPR spectroscopy show that the total spin of the complex changes from S = (5)/(2) at high temperature to S = (3)/(2) at low temperature. Ligand exchange of the perchlorato ligands in (TMP(*)(+))Mn(III)(ClO(4))(2) by chloride anions is accompanied by a change of the oxidation site from porphyrin to metal, resulting in (TMP)Mn(IV)(Cl)(2). This high-valent-metal complex can effect chlorine atom transfer to olefins, as well as to dimedone and chlorodimedone, natural substrates of chloroperoxidases.
Remote C−H Olefination of Heterocyclic Biaryls Enabled by Reversibly Bound Templates (2023)

Remote C-H functionalization of heterocyclic biaryls will be of great importance in synthesis and medicinal chemistry. Through adjusting the geometric relationship of the directing atom and target C-H bonds, two new catalytic templates have been developed to enable the functionalization of the more hindered ortho-C-H bonds of heterobiaryls bearing directing heteroatom at the meta- or para-positions, affording unprecedented site-selectivity. The use of template chaperone also overcomes product inhibition and renders the directing templates catalytic. The utility of this protocol was demonstrated by olefination of heterocyclic biaryls with various substituents, overriding conventional steric and electronic effects. These ortho-C-H olefinated heterobiaryls are sterically hindered and can often be challenging to prepare through aryl-aryl coupling reactions.
Chemical and immunological analysis of the complex structure of Escherichia coli alpha-hemolysin (1985)

Escherichia coli alpha-hemolysin (AH) purified from culture supernatants by gel filtration and ion-exchange chromatography was heterogeneous in charge and size. A 107,000-dalton protein was identified as the product of the hlyA gene by its reactivity with anti-AH monoclonal antibodies. Proteolysis of the product of the hlyA gene occurred but was not required for transport of the protein through the cell wall. Active AH had a larger size and lower pI than analysis of the hlyA gene sequence would predict, thus suggesting that the hlyA protein is complexed with other bacterial products. Lipopolysaccharide was detected in purified hemolysin complex preparations and may be a major component of the complexes. These findings suggest several possible mechanisms for release of AH from the bacterial cell including release by outer membrane fragmentation. The existence of AH complexed with lipopolysaccharide may have important implications in understanding its toxicity.
Bit-stream extraction to maximize perceptual quality using quality information table in SVC (2006)

In scalable video coding (SVC), video quality can be controlled by bit-stream extraction. The bit-stream extraction is to extract network abstraction layer (NAL) units for the required quality. Since scalable bit-stream is packed in NAL units, quality control of SVC video is highly related to NAL unit extraction policy at a given bit-rate. Therefore, effective extraction policy is required to provide SVC video with optimal quality. In this paper, a SVC bit-stream extraction method based on perceptual quality is proposed. The main goal of this work is to find the optimal extraction policy for SVC bit-stream that contain the spatial, temporal, and SNR scalability at a given bit-rate. Also, to consider perceptual quality relied on video characteristics, the video segments are classified into different classes, namely action, crowd, dialog, scenery, and text&graphic. As a result of a subjective test on the classified video scenes, consistent characteristic of perceptual quality preference is achieved. Based on this, quality information table (QIT) has been determined for each class which guides the bit-stream extraction process. The determined QIT is applied to SVC bit-stream extraction depending on to which class a video segment belongs. In the experiment, the proposed extraction scheme is applied for SVC bit-stream extraction belongs to action class. Extraction policy to maximize perceptual quality of action class is applied based on QIT for action class. The extracted video and multi-dimensional scalability resulted from the proposed scheme are also described.
A novel tunable matching network for dynamic load modulation of high power amplifiers (2012)

Dynamic load modulation (DLM) has been proposed as a promising technique to improve the backoff efficiency of power amplifier (PA) for wireless communication systems with high peak-to-average power ratio (PAPR), where the design of a tunable matching network (TMN) with wide impedance tuning range and low loss is essential. This work proposes a novel TMN circuit topology that has three main features satisfying closely to the requirements of DLM: able to generate impedance trajectory close to the pure resistance, easy to produce impedance trajectory of a wide tuning range, e.g., with reflection coefficient Gcoverage up to 0.9, and possessing high potential to generate a TMN having low loss especially at high G. A TMN circuit for load modulation of 2.14GHz Class-B GaN HEMT PAs based on the proposed topology is built and measured. Static measurements show that, given a properly selected PA, the drain efficiency is improved by 30% at 7.5dB backoff by the load modulation.
MicroRNA-181a* targets nanog in a subpopulation of CD34+ cells isolated from peripheral blood (2012)

Background and Objectives: Hematopoietic stem cells (HSC) are the most widely studied and characterized adult stem cells, which play an essential role in sustaining the formation of blood and immune system. The ease of their manipulation, the lack of serious ethical issues, and, in the autologous setting, the absence of their immunogenicity, have made them an attractive tool for developing stem cell-based therapies. Exploiting the properties of HSC by microRNA (miRNA) profiling offers an attractive approach to identify new regulators of stem cell fate. Although numerous miRNA have been screened from hematopoietic stem cells (HSC), the targets corresponding to many of these miRNA have not yet been fully elucidated. Therefore the objective of this study is to generate a miRNA profile from a subpopulation of adherent CD34+ HSC isolated from G- colony-stimulating factor mobilized peripheral blood aiming to understand the role of selected miRNA in regulating HSC stemness. Methods: CD34+ cells from patients' blood were isolated using a CD34+ isolation kit (Miltenyi Biotec) according to the manufacturer's protocol. miRNA profiling of adherent and nonadherent CD34+ cells was done using TaqMan Array MicroRNA Cards. Nanog expression levels was tested using a dual-luciferase reporter construct for miR-181a* or its mutant variant and Nanog 3′ UTR mRNA. Results: In this study, we have identified eight clusters of miRNA that were differentially expressed in an adherent subpopulation of CD34+ stem cells. Further analysis of one of the clusters by bioinformatics revealed that a miRNA, miR-181a*, which is highly expressed in the adherent CD34+ cells, affects the expression levels of Nanog, a stem cell surrogate marker. We show specifically by reporter assay and mutational analysis that miR-181a* targets a seedless 3′ compensatory site in the 3′UTR of Nanog and affects gene expression. We demonstrate that inhibiting miR-181a* upregulates the Nanog expression level, in addition to an increase in alkaline phosphatase activity. Conclusions: In conclusion, our results highlight a new stem cell-related target for the miR-181 family and show that miR-181a* directly targets Nanog in a subpopulation of CD34+ stem cells suggesting a possible role of miR-181a* in regulation of adherent CD34+ HSC cells stemness.