gebhart/patrepeval huggingface dataset:
Microtubule Disruption in Keratinocytes Induces Cell-Cell Adhesion through Activation of Endogenous E-Cadherin (2001)

The association of the cytoskeleton with the cadherin--catenin complex is essential for strong cell-cell adhesion in epithelial cells. In this study, we have investigated the effect of microtubule organization on cell-cell adhesion in differentiating keratinocytes. When microtubules of normal human epidermal keratinocytes (NHEKs) grown in low calcium media (0.05 mM) were disrupted with nocodazole or colcemid, cell-cell adhesion was induced through relocalization of the E-cadherin-catenin-actin complex to the cell periphery. This was accompanied by actin polymerization. Also, it was found that microtubule disruption-induced cell-cell adhesion was significantly reduced in more advanced differentiated keratinocytes. For example, when NHEK cells cultured under high calcium (1.2 mM) for 8 d and then in low calcium for 1 d were treated with nocodazole, there was no induction of cell-cell adhesion. Also long-term treatment of a phorbol ester for 48 h inhibited nocodazole-induced cell-cell adhesion of NHEK. Furthermore, this nocodazole-induced cell-cell adhesion could be observed in squamous cancer cell lines (A431 and SCC-5, -9, and -25) under low calcium condition, but not in the keratinocyte cell lines derived from normal epidermis (HaCaT, RHEK). On the other hand, HaCaT cells continuously cultivated in low calcium media regained a less differentiated phenotype such as decreased expression of cytokeratin 10, and increased K5; these changes were accompanied with inducibility of cell-cell adhesion by nocodazole. Together, our results suggest that microtubule disruption can induce the cell-cell adhesion via activation of endogenous E-cadherin in non- or early differentiating keratinocytes. However, this is no longer possible in advanced terminally differentiating keratinocytes, possibly due to irreversible changes effected by cell envelope barrier formation.
Kinetic properties and stability of glucose dehydrogenase from Bacillus amyloliquefaciens SB5 and its potential for cofactor regeneration (2015)

Glucose dehydrogenases (GluDH) from Bacillus species offer several advantages over other NAD(P)H regeneration systems including high stability, inexpensive substrate, thermodynamically favorable reaction and flexibility to regenerate both NADH and NADPH. In this research, characteristics of GluDH from Bacillus amyloliquefaciens SB5 (GluDH-BA) was reported for the first time. Despite a highly similar amino acid sequence when comparing with GluDH from Bacillus subtilis (GluDH-BS), GluDH-BA exhibited significantly higher specific activity (4.7-fold) and stability when pH was higher than 6. While an optimum activity of GluDH-BA was observed at a temperature of 50 °C, the enzyme was stable only up to 42 °C. GluDH-BA exhibited an extreme tolerance towards n-hexane and its respective alcohols. The productivity of GluDH obtained in this study (8.42 mg-GluDH/g-wet cells; 1035 U/g-wet cells) was among the highest productivity reported for recombinant E. coli. With its low K M-value towards glucose (5.5 mM) and NADP(+) (0.05 mM), GluDH-BA was highly suitable for in vivo applications. In this work, a recombinant solvent-tolerant B. subtilis BA overexpressing GluDH-BA was developed and evaluated by coupling with B. subtilis overexpressing an enzyme P450 BM3 F87V for a whole-cell hydroxylation of n-hexane. Significantly higher products obtained clearly proved that B. subtilis BA was an effective cofactor regenerator, a valuable asset for bioproduction of value-added chemicals.
Plasma-Fluorination Synthesis of High Surface Area Aluminum Trifluoride from a Zeolite Precursor (2001)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTPlasma-Fluorination Synthesis of High Surface Area Aluminum Trifluoride from a Zeolite PrecursorJames L. Delattre, Peter J. Chupas, Clare P. Grey, and Angelica M. StacyView Author Information Department of Chemistry, University of California at Berkeley, Berkeley, California 94720 Department of Chemistry, State University of New York at Stony Brook, Stony Brook, New York 11794 Cite this: J. Am. Chem. Soc. 2001, 123, 22, 5364–5365Publication Date (Web):May 10, 2001Publication History Received7 February 2001Revised13 April 2001Published online10 May 2001Published inissue 1 June 2001https://pubs.acs.org/doi/10.1021/ja015645thttps://doi.org/10.1021/ja015645trapid-communicationACS PublicationsCopyright © 2001 American Chemical SocietyRequest reuse permissionsArticle Views720Altmetric-Citations38LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Aluminum,Halogenation,Materials,Plasma,Precursors Get e-Alerts
Replication-timing-correlated spatial chromatin arrangements in cancer and in primate interphase nuclei (2008)

Using published high-resolution data on S-phase replication timing, we determined the three-dimensional (3D) nuclear arrangement of 33 very-early-replicating and 31 very-late-replicating loci. We analyzed diploid human, non-human primate and rearranged tumor cells by 3D fluorescence in situ hybridization with the aim of investigating the impact of chromosomal structural changes on the nuclear organization of these loci. Overall, their topology was found to be largely conserved between cell types, species and in tumor cells. Early-replicating loci were localized in the nuclear interior, whereas late-replicating loci showed a broader distribution with a higher preference for the periphery than for late-BrdU-incorporation foci. However, differences in the spatial arrangement of early and late loci of chromosome 2, as compared with those from chromosome 5, 7 and 17, argue against replication timing as a major driving force for the 3D radial genome organization in human lymphoblastoid cell nuclei. Instead, genomic properties, and local gene density in particular, were identified as the decisive parameters. Further detailed comparisons of chromosome 7 loci in primate and tumor cells suggest that the inversions analyzed influence nuclear topology to a greater extent than the translocations, thus pointing to geometrical constraints in the 3D conformation of a chromosome territory.
Photoconductive power switches (1985)

This paper outlines the advantages and the potential of photoconductive switches applied to high-power systems. The photoconductive effect can be used to switch large amounts of energy by changing the conductivity of a solid-state circuit element many orders of magnitude with a high-power laser. The simplicity of these devices offers many advantages in high-power applications when combined with high-power pulsed lasers. The surge capability, the switched energy gain, and the maximum average power for photoconductive power switches are discussed. In addition, the results of a 100-kV, 100-MW photoconductive switch experiment transferring 20 J in 200 ns are presented.
Super-resolution reconstruction of MR image sequences with contrast modeling (2009)

Quantitative MR imaging experiments (e.g., to measure relaxation and diffusion properties of tissues) often require image sequences with different contrast in each frame. However, high-resolution acquisition of each frame can lead to prohibitively long experiments. In this work, we investigate the possibility of utilizing a parametric contrast model to synthesize high-resolution information. Theoretical analysis and empirical evidence indicates that this kind of super-resolution can be possible, though robustness is dependent on a number of factors (e.g., the contrast model and the experiment design). In particular, it is found that conventional low-frequency sampling leads to significant information loss, but that alternative experiments can overcome this limitation. Experimental results are shown in the context of T <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">*</sup> relaxation mapping.
Venous Insufficiency Of The Lower Limb And Stasis Ulceration (1983)

In a group of patients studied for venous insufficiency, the incidence of deep venous insufficiency was much higher than previously suspected. Insufficiency of the superficial system, when present, was associated invariably with deep venous insufficiency, suggesting a leading role for the latter condition. Evidence is presented to show that in many instances, such reflux is probably non-thrombotic. The results of various types of direct venous valve surgery in a group of patients are presented.
Analyzing a Multi-Lateral Well Failure in the East Wilmington Field of California (1997)

Introduction As the industry pursues optimum cost drilling techniques, more focus is being applied to multi-lateral technology. The presently available literature invariably focuses on the cost and efficiency benefits of drilling multi-lateral wells. What is missing in the media, however, are the benefits associated with publication of the negative aspects or costly failures of higher-technology multiple-lateral projects that require a mechanical tie-back or pressure seal at the junction of the laterals (i.e. Class 3 or 4 type multi-lateral wells, respectively). This paper is a case study of a Class 4 multilateral well attempted by Thums Long Beach Company in the East Wilmington Field of California. To date, this case study represents the only detailed analysis of an unsuccessful attempt to drill a Class 4 multi-lateral well. Starting with a field and well profile, this case study explores Well B743A in the Long Beach Unit of the East Wilmington Field of California. The discussion progresses from the original proposal through the drilling and completion of the lower lateral to the drilling of the upper lateral, and then to the plugging and abandonment both laterals. Finally, the analysis provides an examination of six critical problem areas encountered during the drilling of Well B743A: hole cleaning, cementing and junction stability, whipstock orientation, tubular size, re-entry, and risk management. These are areas that are problematic for most operators and contractors struggling with multi-lateral technology, especially the drilling of Class 3 or Class 4 multi-lateral wells. Field and Well Profile The Long Beach Unit of the East Wilmington Oil Field is located just offshore at the southwestern extension of the Los Angeles Basin of California (Fig. 1). The field produces from three major zones, the Ranger, Terminal, and Union Pacific-Ford zones (Fig. 2). Individual sand units are continuous and can be correlated over the Long Beach Unit and beyond. The structural setting is an asymmetrical northwest to southeasterly trending, faulted anticline. P. 169^
Efficient pagerank approximation via graph aggregation (2004)

We present a framework for approximating random-walk based probability distributions over Web pages using graph aggregation. We (1) partition the Web's graph into classes of quasi-equivalent vertices, (2) project the page-based random walk to be approximated onto those classes, and (3) compute the stationary probability distribution of the resulting class-based random walk. From this distribution we can quickly reconstruct a distribution on pages. Inparticular, our framework can approximate the well-known PageRank distribution by setting the classes according to the set of pages on each Web host. We experimented on a Web-graph containing over 1.4 billion pages, and were able to produce a ranking that has Spearman rank-order correlation of 0.95 with respect to PageRank. A simplistic implementation of our method required less than half the running time of a highly optimized implementation of PageRank, implying that larger speedup factors are probably possible.
Memory Effects Of Aronia Melanocarpa Fruit Juice In A Passive Avoidance Test In Rats (2014)

These findings suggest that Aronia melanocarpa fruit juice could improve memory in rats. The effect is probably due to the polyphenolic ingredients of the juice which have been shown to be involved in learning and memory processes.
Expression of non-signaling membrane-anchored death receptors protects murine livers in different models of hepatitis (2006)

Fas and tumor necrosis factor receptor 1 (TNFR1) are death receptors involved in various diseases such as hepatitis, sepsis, or graft rejection. Neutralizing antibodies to death ligands or soluble death receptors can inhibit cell death; however, they induce side effects because of their systemic actions. To specifically block death signaling to target cells, we created death domain-deficient (DeltaDD) membrane-anchored receptors, delivered to the liver by either recombinant adenovirus or hydrodynamic pressure of nonviral recombinant plasmids. In anti-Fas antibody-induced fulminant hepatitis, mice expressing recombinant Fas-decoy receptors (FasDeltaDD) in their livers were completely protected against apoptosis and survived fulminant hepatitis. In T-cell-dependent concanavalin A-induced autoimmune hepatitis, FasDeltaDD antagonist expression prevented hepatocyte damage and mouse death. Finally, TNFR1DeltaDD effectively protected mice against LPS-induced septic shock. In conclusion, such DeltaDD-decoy receptors act as dominant-negative receptors exerting local inhibition, while avoiding systemic neutralization of apoptosis ligands, and might have therapeutic potential in hepatitis.
Fast parallel cosine K-nearest neighbor graph construction (2016)

The k-nearest neighbor graph is an important structure in many data mining methods for clustering, advertising, recommender systems, and outlier detection. Constructing the graph requires computing up to n2 similarities for a set of n objects. This has led researchers to seek approximate methods, which find many but not all of the nearest neighbors. In contrast, we leverage shared memory parallelism and recent advances in similarity joins to solve the problem exactly, via a filtering based approach. Our method considers all pairs of potential neighbors but quickly filters those that could not be a part of the k-nearest neighbor graph, based on similarity upper bound estimates. We evaluated our solution on several real-world datasets and found that, using 16 threads, our method achieves up to 12.9x speedup over our exact baseline and is sometimes faster even than approximate methods. Moreover, an approximate version of our method is up to 21.7× more efficient than the best approximate state-of-the-art baseline at similar high recall.
On-Line Expectation–Maximization Algorithm for latent Data Models (2009)

Summary We propose a generic on-line (also sometimes called adaptive or recursive) version of the expectation–maximization (EM) algorithm applicable to latent variable models of independent observations. Compared with the algorithm of Titterington, this approach is more directly connected to the usual EM algorithm and does not rely on integration with respect to the complete-data distribution. The resulting algorithm is usually simpler and is shown to achieve convergence to the stationary points of the Kullback–Leibler divergence between the marginal distribution of the observation and the model distribution at the optimal rate, i.e. that of the maximum likelihood estimator. In addition, the approach proposed is also suitable for conditional (or regression) models, as illustrated in the case of the mixture of linear regressions model.
Biodistribution and clearance of quantum dots in small animals (2010)

CdSe-core, ZnS-capped semiconductor nanoparticles - quantum dots (QDs) - have been at the forefront of biomedical nanotechnology research thanks to their unique optical Η photophysical properties. In the present study the impact of the particle coating and size on their in vivo fate after intravenous (IV) injection into mice was studied by fluorescence methods. For this study, we compared organ-selective biodistribution and elimination routes of synthesized QDs coated with 3-mercaptopropionic acid (QD MPA) and commercially available Qtracker 705 nontargeted quantum dots with poly(ethylene glycol) coating (QD PEG). We observed primary accumulation of these QDs in lung. Experiments demonstrated that QD MPA and QD PEG have both remained fluorescent in lung after at least 24 hours postinjection. Moreover, QDs was seen to deposit mainly in liver, spleen, kidney and lymph nodes. We also concluded that QDs MPA and QDs 705 are both sequestered and not excreted with feces or urine.
ZCURVE: a new system for recognizing protein-coding genes in bacterial and archaeal genomes (2003)

A new system, ZCURVE 1.0, for finding protein- coding genes in bacterial and archaeal genomes has been proposed. The current algorithm, which is based on the Z curve representation of the DNA sequences, lays stress on the global statistical features of protein-coding genes by taking the frequencies of bases at three codon positions into account. In ZCURVE 1.0, since only 33 parameters are used to characterize the coding sequences, it gives better consideration to both typical and atypical cases, whereas in Markov-model-based methods, e.g. Glimmer 2.02, thousands of parameters are trained, which may result in less adaptability. To compare the performance of the new system with that of Glimmer 2.02, both systems were run, respectively, for 18 genomes not annotated by the Glimmer system. Comparisons were also performed for predicting some function-known genes by both systems. Consequently, the average accuracy of both systems is well matched; however, ZCURVE 1.0 has more accurate gene start prediction, lower additional prediction rate and higher accuracy for the prediction of horizontally transferred genes. It is shown that the joint applications of both systems greatly improve gene-finding results. For a typical genome, e.g. Escherichia coli, the system ZCURVE 1.0 takes approximately 2 min on a Pentium III 866 PC without any human intervention. The system ZCURVE 1.0 is freely available at: http://tubic. tju.edu.cn/Zcurve_B/.
Signal processing requirements in pan-European digital mobile communications (2003)

The authors give an overview of the basic functions and techniques of the user equipment of the proposed pan-European digital communications system. The multipath equalizer and channel decoder of the receiver together with the speech codec are identified to be the most complicated devices from the viewpoint of signal processing and integration. Three different approaches for implementation, using general-purpose digital signal processing (DSPs), application-oriented DSPs, and dedicated full custom VLSI, are discussed. With particular reference to the speech codec, a detailed analysis of the full-custom VLSI implementation is made and the results are compared with the other approaches. It is concluded that even though the full-custom approach offers considerable benefits in terms of power consumption and use of silicon area, other matters such as flexibility in operation and further development also have to be taken into account.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Oral treatment of ichthyosis by the cytochrome P-450 inhibitor liarozole (1997)

Liarozole, a novel imidazole derivative, inhibits the cytochrome P450‐dependent 4‐hydroxylation of retinoic acid. resulting in increased tissue levels of retinoic acid. Twelsve male patients with ichthyosis were given oral liarozole. 150mg twice daily. in an open study for 12 weeks. Immunohistochemical parameters of inflammation, epidermal proliferation and differentiation were assessed before and after treatment. Extent and severity of the skin lesions was markedly reduced in all prtients. Clinical side‐effects were reminiscent of those with synthetic retinoids. No relevant changes were found in the haematological. urinary and biochemical parameters. Immunohistochemical assessment showed a statistically significant induction of keratin 4 after liarozole treatment in 10 of 12 patients. In two of these patients keratin 13 was induced. This open study showed that oral liarozole treatment was efficacious and well tolerated in the treatment of different types of ichthyosis. The immunohisotchemical results suggest a retinoid mechanism as the mode of action.
Insights into the function of the WhiB‐like protein of mycobacteriophage TM4 – a transcriptional inhibitor of WhiB2 (2010)

WhiB-like proteins of actinomycetes are known to co-ordinate iron-sulfur (Fe-S) clusters and are believed to have regulatory functions in many essential bacterial processes. The systematic determination of the genome sequences of mycobacteriophages has revealed the presence of several whiB-like genes in these viruses. Here we focussed on the WhiB-like protein of mycobacteriophage TM4, WhiBTM4. We provide evidence that this viral protein is capable of co-ordinating a Fe-S cluster. The UV-visible absorption spectra obtained from freshly purified and reconstituted WhiBTM4 were consistent with the presence of an oxygen sensitive [2Fe-2S] cluster. Expression of WhiBTM4 in the mycobacterial host led to hindered septation resembling a WhiB2 knockout phenotype whereas basal expression of WhiBTM4 led to superinfection exclusion. The quantification of mRNA-levels during phage infection showed that whiBTM4 is a highly transcribed early phage gene and a dominant negative regulator of WhiB2. Strikingly, both apo-WhiB2 of Mycobacterium tuberculosis and apo-WhiBTM4 were capable of binding to the conserved promoter region upstream of the whiB2 gene indicating that WhiB2 regulates its own synthesis which is inhibited in the presence of WhiBTM4. Thus, we provide substantial evidence supporting the hypothesis of viral and bacterial WhiB proteins being important Fe-S containing transcriptional regulators with DNA-binding capability.
Effect of ozone on ruthenium species in alkaline medium – Part I: Oxidative dissolution of ruthenium dioxide hydrate (2006)

Summary Several ruthenium species compounds are typically encountered in waste management from nuclear fuel reprocessing operations. Ozone acting as a strong oxidizing agent in aqueous alkaline medium presents some advantages to dissolve rapidly solid deposits of RuO 2 , x H 2 O formed into process devices, without generating troublesome byproducts or secondary wastes. In this study, a three-phase solid-gas-liquid column was used for dissolution experiments where the ozone gas flow was contacted with RuO 2 , x H 2 O solid particles suspended in sodium hydroxide solution. The analysis of reaction by-products, ruthenate and perruthenate ions, leads us to propose a reaction mechanism. It points out the autocatalytic effect of ruthenate RuO 4 2- in the dissolution reaction mechanism. Parametric experimental study has been performed. It shows that increase of oxidative dissolution kinetics is obtained: (i) with a particular RuO 2 , x H 2 O solid morphology, (ii) for an optimum sodium hydroxide concentration near 0.5 M, (iii) by increasing gas-liquid exchange surface area, (iv) by increasing ozone concentration in the gas and (v) by increasing ruthenium initial concentration.