gebhart/patrepeval huggingface dataset:
Nuclear Oncoprotein Prothymosin α Is a Partner of Keap1: Implications for Expression of Oxidative Stress-Protecting Genes (2005)

Animal cells counteract oxidative stress and electrophilic attack through coordinated expression of a set of detoxifying and antioxidant enzyme genes mediated by transcription factor Nrf2. In unstressed cells, Nrf2 appears to be sequestered in the cytoplasm via association with an inhibitor protein, Keap1. Here, by using the yeast two-hybrid screen, human Keap1 has been identified as a partner of the nuclear protein prothymosin alpha. The in vivo and in vitro data indicated that the prothymosin alpha-Keap1 interaction is direct, highly specific, and functionally relevant. Furthermore, we showed that Keap1 is a nuclear-cytoplasmic shuttling protein equipped with a nuclear export signal that is important for its inhibitory action. Prothymosin alpha was able to liberate Nrf2 from the Nrf2-Keap1 inhibitory complex in vitro through competition with Nrf2 for binding to the same domain of Keap1. In vivo, the level of Nrf2-dependent transcription was correlated with the intracellular level of prothymosin alpha by using prothymosin alpha overproduction and mRNA interference approaches. Our data attribute to prothymosin alpha the role of intranuclear dissociator of the Nrf2-Keap1 complex, thus revealing a novel function for prothymosin alpha and adding a new dimension to the molecular mechanisms underlying expression of oxidative stress-protecting genes.
Annexin A2 Heterotetramer: Structure and Function (2013)

Annexin A2 is a pleiotropic calcium- and anionic phospholipid-binding protein that exists as a monomer and as a heterotetrameric complex with the plasminogen receptor protein, S100A10. Annexin A2 has been proposed to play a key role in many processes including exocytosis, endocytosis, membrane organization, ion channel conductance, and also to link F-actin cytoskeleton to the plasma membrane. Despite an impressive list of potential binding partners and regulatory activities, it was somewhat unexpected that the annexin A2-null mouse should show a relatively benign phenotype. Studies with the annexin A2-null mouse have suggested important functions for annexin A2 and the heterotetramer in fibrinolysis, in the regulation of the LDL receptor and in cellular redox regulation. However, the demonstration that depletion of annexin A2 causes the depletion of several other proteins including S100A10, fascin and affects the expression of at least sixty-one genes has confounded the reports of its function. In this review we will discuss the annexin A2 structure and function and its proposed physiological and pathological roles.
A reagent for peptide synthesis. Copoly(ethylene-N-hydroxymaleimide) (1968)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA reagent for peptide synthesis. Copoly(ethylene-N-hydroxymaleimide)Daniel A. Laufer, T. M. Chapman, D. I. Marlborough, V. M. Vaidya, and E. R. BloutCite this: J. Am. Chem. Soc. 1968, 90, 10, 2696–2698Publication Date (Print):May 1, 1968Publication History Published online1 May 2002Published inissue 1 May 1968https://doi.org/10.1021/ja01012a045RIGHTS & PERMISSIONSArticle Views186Altmetric-Citations45LEARN 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 InReddit PDF (357 KB) Get e-Alertsclose Get e-Alerts
Faulty Node Detection in Wireless Sensor Networks Using Cluster (2013)

Abstract- Since the accuracy of data is important to the whole system’s performance, detecting nodes with faulty readings is an essential issue in network management. Removing nodes with faulty readings from a system or replacing them with good ones improve the whole system’s performance and at the same time prolong the lifetime of the network. In general, wireless sensor nodes may experience two types of faults that would lead to the degradation of performance. One type is function fault, which typically results in the crash of individual nodes, packet loss, routing failure or network partition. The other type of error is data fault, in which a node behaves normally in all aspects except for its sensing results, leading to either significant biased or random errors.
Genomic Characterization of Methanomicrobiales Reveals Three Classes of Methanogens (2009)

Our results indicate that Methanomicrobiales, rather than being similar to Class I methanogens or Methanomicrobiales, share some features of both and have some unique properties. We find that there are three distinct classes of methanogens: the Class I methanogens, the Methanomicrobiales (Class II), and the Methanosarcinales (Class III).
Transplant-lite: induction of graft-versus-malignancy using fludarabine-based nonablative chemotherapy and allogeneic blood progenitor-cell transplantation as treatment for lymphoid malignancies. (1998)

These findings indicate the feasibility of allogeneic hematopoietic transplantation with a nonablative preparative regimen to produce engraftment and GVL against lymphoid malignancies. The ability to induce remissions with donor lymphocyte infusion in patients with CLL, Richter's, and low-grade and intermediate-grade lymphoma is direct evidence of GVL activity against these diseases. This approach appears to be most promising in patients with chemotherapy-responsive disease and low tumor burden.
Novel rat Alzheimer's disease models based on AAV-mediated gene transfer to selectively increase hippocampal Aβ levels (2007)

The results show that AAV-mediated gene transfer is a valuable tool to model aspects of AD pathology in vivo, and demonstrate that whilst expression of Abeta42 alone is sufficient to initiate Abeta deposition, both Abeta40 and Abeta42 may contribute to cognitive deficits.
Surface-plasmon-assisted nanoscale photolithography by polarized light (2005)

We demonstrate that photolithography can be extended to a subwavelength resolution for patterning of virtually any substrate by exciting surface plasmons on both a metallic mask and a substrate. Without any additional equipment or added complexity to mask design, one-to-one pattern transfer has been achieved. In this letter, a polarized laser beam of 355 nm wavelength was used as light source to photoinitiate an 80 nm thick photoresist on a silicon substrate coated with titanium of 80 nm thick. Array of line apertures of 100 nm in width were made on gold film or titanium film deposited on a quartz substrate, serving as the mask. Simulation results by finite-difference time-domain method have shown that surface plasmons excited on both the metallic mask and the Ti shield help to spatially confine the light behind the apertures. Experimental results show a strong dependence of pattern transfer on the polarization of light as well as the energy dosage of the light. The feature size using such method could be further scaled down, limited theoretically by the validity of the dielectric function of the material, and practically by the fabrication of the mask.
Characterization of a Very High Density Lipoprotein Allergen, Dpt 4, from the House Dust Mite <i>Dermatophagoides pteronyssinus</i> (1983)

The allergen Dpt 4 from the house dust mite Dermatophagoides pteronyssinus was shown to be a lipoprotein as judged by its Sudan black B staining properties. Ultracentrifugal studies confirmed this finding and showed that Dpt 4 was polydisperse, although the majority of the allergen belonged to a very high density lipoprotein class. Physicochemical studies using gradient polyacrylamide gel electrophoresis showed that Dpt 4 had an apparent molecular weight of 244,000 daltons and a particle diameter of 10.73 nm. Agarose gel electrophoresis showed that the allergen had an electrophoretic mobility 0.86 times that of human alpha-lipoprotein. The observation that Dpt 4 is a lipoprotein is consistent with earlier studies which showed that the allergen was heterogeneous with regard to its molecular weight and that it contained the hapten phosphorylcholine.
Dendritic Molecules: Concepts, Syntheses, Perspectives (1996)

Masses, Sizes, and Shapes of Macromolecules from Multifunctional Monomers From Theory to Practice: Historical Perspectives Nomenclature Synthetic Methodologies: Divergent Procedures Synthetic Methodologies: Convergent Procedures Synthetic Methodologies: One-step (Hyperbranched) Procedures Chiral Dendritic Macromolecules Dendrimers Containing Metal Sites Dendritic Networks Utilitarian Aspects Appendices Index.
Flow-Through Microvial Facilitating Interface of Capillary Isoelectric Focusing and Electrospray Ionization Mass Spectrometry (2011)

A capillary electrophoresis mass spectrometry (CE-MS) interface utilizing a flow-through microvial is used to ensure the electric continuity and supply the catholyte and mobilizer solutions during the capillary isoelectric focusing (cIEF) and mobilization process. The flow-through microvial provides a stable chemical environment and helps to improve the ionization efficiency without significantly diluting the analyte. The CE-MS interface facilitates the transfer of the mobilized cIEF effluent to the site of electrospray ionization, and the gaseous ions can be detected directly by a mass spectrometer. It also allows for complete focusing and mobilization processes to be performed automatically in programmed sequences with commercial CE systems. Two different strategies, using either a part of the capillary or the flow-through microvial of the CE-MS interface as the catholyte reservoir for bare fused silica capillaries or neutral coated capillaries, respectively, were developed for automated cIEF-electrospray ionization (ESI)-MS. Reasonable separation efficiency was achieved using proper concentration of carrier ampholytes and suitable strategies of electroosmotic/electrophoretic mobilization.
A cooperative model for receptor recognition and cell adhesion: evidence from the molecular packing in the 1.6-A crystal structure of the pheromone Er-1 from the ciliated protozoan Euplotes raikovi. (1995)

The crystal structure of the pheromone Er-1 from the unicellular eukaryotic organism Euplotes raikovi was determined at 1.6 A resolution and refined to a crystallographic R factor of 19.9%. In the tightly packed crystal, two extensive intermolecular helix-helix interactions arrange the Er-1 molecules into layers. Since the putative receptor of the pheromone is a membrane-bound protein, whose extracellular C-terminal domain is identical in amino acid sequence to the soluble pheromone, the interactions found in the crystal may mimic the pheromone-receptor interactions as they occur on a cell surface. Based on this, we propose a model for the interaction between soluble pheromone molecules and their receptors. In this model, strong pheromone-receptor binding emerges as a consequence of the cooperative utilization of several weak interactions. The model offers an explanation for the results of binding studies and may also explain the adhesion between cells that occurs during mating.
Tissue-specific transformation by epidermal growth factor receptor: a single point mutation within the ATP-binding pocket of the erbB product increases its intrinsic kinase activity and activates its sarcomagenic potential. (1990)

Avian c-erbB is activated to a leukemia oncogene following truncation of its amino-terminal, ligand-binding domain by retroviral insertion. The insertionally activated transcripts encode protein products that have constitutive tyrosine kinase activity and that can induce erythro-leukemia but not sarcomas. We have found that a single point mutation within the ATP-binding pocket of the tyrosine kinase domain in this truncated molecule can increase the ability of this oncogene to induce anchorage-independent growth of fibroblasts in vitro and fibrosarcoma formation in vivo. Associated with this increased transforming potential is a corresponding increase in the kinase activity of the mutant erbB protein product. The mutation, which converts a valine to isoleucine at position 157 of the insertionally activated c-erbB product, is at a residue that is highly conserved within the protein kinase family. To our knowledge, this is the first demonstration of a point mutation in the ATP-binding pocket that activates a tyrosine kinase.
Microstrip fractal patch antenna for multi-bandcommunication (2000)

A novel square microstrip fractal patch antenna in a Sierpinski carpet is proposed for three-band operation. Measured results indicate that the return loss is better than 10 dB and that the gain is greater than 7 dB in each band. This antenna is an attractive candidate for wireless, satellite and mobile communication applications.
Targeting Melanoma Cells with Human High Molecular Weight-Melanoma Associated Antigen-Specific Antibodies Elicited by a Peptide Mimotope: Functional Effects (2006)

Human high molecular weight-melanoma associated Ag (HMW-MAA) mimics have been shown to elicit HMW-MAA-specific humoral immune responses that appear to be clinically beneficial. This finding has stimulated interest in characterizing the mechanism(s) underlying the ability of the elicited Abs to exert an anti-tumor effect. To address this question, in the present study, we have generated HMW-MAA-specific Abs by sequentially immunizing rabbits with the peptide P763.74, which mimics the HMW-MAA determinant recognized by mAb 763.74, and with HMW-MAA(+) melanoma cells. HMW-MAA-specific Abs isolated from immunized rabbits mediated cell-dependent cytotoxicity but did not mediate complement-dependent cytotoxicity of HMW-MAA(+) melanoma cells. These Abs also effectively inhibited spreading, migration and Matrigel invasion of HMW-MAA(+) melanoma cells. Besides contributing to our understanding of the role of HMW-MAA in the biology of melanoma cells, these results suggest that both immunological and nonimmunological mechanisms underlie the beneficial clinical effects associated with the induction of HMW-MAA-specific Abs in melanoma patients immunized with a HMW-MAA mimic.
The major outer membrane protein nucleotide sequence ofChlamydia trachomatis, serovar E (1990)

Journal Article The major outer membrane protein nucleotide sequence of Chlamydia trachomatis, serovar E Get access Ellena M. Peterson, Ellena M. Peterson * Pathology Department, University of California IrvineIrvine, CA 92717, USA *To whom correspondence should be addressed Search for other works by this author on: Oxford Academic PubMed Google Scholar Brian A. Markoff, Brian A. Markoff Pathology Department, University of California IrvineIrvine, CA 92717, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Luis M. de la Maza Luis M. de la Maza Pathology Department, University of California IrvineIrvine, CA 92717, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 18, Issue 11, 11 June 1990, Page 3414, https://doi.org/10.1093/nar/18.11.3414 Published: 11 June 1990 Article history Received: 03 April 1990 Published: 11 June 1990
Analysis Issues for Gene Expression Array Data (2001)

Gene expression array technologies are rapidly emerging for use in various genome-wide studies in biology and medicine (1)(2)(3). Results from the recently completed sequencing of the human genome predict that the number of genes in the human genome is much smaller (∼33 000 genes) than anticipated (4). This implies that the major complexity in biological mechanisms in humans lies in the synergistic effects among various genes. Therefore, to decipher the secrets of our life and, ultimately, to find the cures for many human diseases, biologists must deal with multiple genes and their interactive transcripts simultaneously. High-throughput biotechnologies, including gene chip approaches, will play an important role in these studies (5).

However, quality control over thousands of gene expression values and full utilization of the information from these high-throughput data are extremely difficult, and important issues in quality control and bioinformatic approaches have not been resolved (6)(7). A series of careful analyses on the variability of array instrumentation and on the statistical evaluation of gene expression intensities are required for reliable and consistent inference on gene chip data. Specifically, sources of error and their confidence levels on these high-throughput measurements need to be better understood because some can significantly alter our inferences and conclusions (8). The purpose of this report is to dispel three common misconceptions about array experiments.

It often is believed that reproducibility of gene expression data is high enough to perform bioinformatic discovery without a replicated chip experiment and that duplicated array data are necessary only for confirmation of such a discovery, which may help publication in high-standard journals. Investigators who have successfully obtained resources for high-cost gene chip experiments must optimize their experimental strategy for their study goals within limited resources. Therefore, for an initial study, single-chip experiments for each …
A Method of Measuring Escherichia Coli O157:H7 at 1 Cell/mL in 1 Liter Sample Using Antibody Functionalized Piezoelectric-Excited Millimeter-Sized Cantilever Sensor (2007)

Piezoelectric-excited millimeter-sized cantilever (PEMC) sensors immobilized with antibody specific to Escherichia coli (EC) 0157:H7 is used to detect EC at 1 cell/mL in 1 mL and 1 L samples in a batch and flow mode, respectively. Two sensor designs were used. The first design (PEMC-a) has both the piezoelectric and non-piezoelectric layer anchored, while in the second design (PEMC-b) had only the piezoelectric layer anchored. PEMC-a, used in batch mode with 1 mL sample, showed limit of detection at 10 cells/ mL using the second bending mode at 85.5 kHz in air. PEMC-b exhibited resonant frequencies at 186.5, 883.5, and 1778.5 kHz in air and 162.5, 800.0, and 1725.5 kHz in sample flow conditions. A one-liter sample containing 1000 EC cells was introduced at 1.5, 2.5, 3, and 17 ml/min, and the change in resonant frequency was monitored. The total frequency change observed for the mode at 800 kHz and sample flow rates of 1.5, 2.5, 3, and 17 mL/min were 2230+/-11, 3069 +/-47, 4686+/-97, and 7188+/-52 Hz, respectively. Each detection experiment was confirmed by exposing the sensor to a low pH solution followed by a phosphate buffered saline (PBS) rinse, which caused the release of the attached EC. The final frequency change observed was nearly identical to the value prior to EC attachment. Kinetic analysis showed that the observed binding rate constant at 1.5, 2.5, 3 mL/min were 0.009, 0.015, and 0.021 min(-1), respectively. The significance of these results is that very low concentration of pathogens in large sample volumes can be measured in a short time period without the need for filtration or enrichment.
Double Carbon Coating of LiFePO4 as High Rate Electrode for Rechargeable Lithium Batteries (2010)

Micrometer-size LiFePO4 spheres with homogeneous double carbon coating layers have been prepared as potential electrode materials for battery applications. The double carbon-coated LiFePO4 electrodes in a lithium-ion cell exhibited discharge capacities of the order of 160 mAh g−1 and 115 mAh g−1 at 25 °C under 0.1 C-rate and 10 C-rate, respectively. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. 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.
Simplified PCR-based detection and typing strategy for human papillomaviruses utilizing a single oligonucleotide primer set. (1991)

Utilizing the PCR, we have devised a detection and typing system for the human papillomaviruses (HPVs) that are commonly associated with preneoplastic and cancerous lesions of the genital and aero-digestive tracts: HPV 6, 11, 16 and 18. Utilizing computer sequence analysis, we designed a single, "consensus" set of oligomeric nucleotide primers capable of amplifying a 571-594-bp region of the E1 open reading frame of all of these HPVs. Detection via PCR amplification is followed by restriction endonuclease digestion of the resultant products that yield distinctive and reproducible banding patterns by polyacrylamide gel electrophoresis because of their internal sequence diversity. The system is sensitive, does not require sophisticated molecular biology expertise or radioisotopes and can be modified as new information on HPV types and their relationship to diseases becomes available.
PDCI damping control analysis for the western North American power system (2013)

Transmission capacity in the western North American power system (termed the wNAPS) is often limited by poorly-damped electromechanical oscillations. To date, the primary damping controllers applied in the wNAPS are via generator controls using localized feedback signals. Such controls have limited effectiveness for inter-area modes. Recent development of reliable real-time wide-area measurement systems (WAMS) has enabled the potential for large-scale damping control approaches. One such approach is feedback modulation of the Pacific DC Intertie (PDCI). This paper summarizes simulation results from a study to evaluate PDCI damping control in the wNAPS. This includes developing a safe and effective control strategy, quantifying potential improved damping, and conducting open-loop actual-system probing tests.
Molecular Links between Endocytosis and the Actin Cytoskeleton (2000)

The endocytosis process is of critical importance for a variety of cellular life functions. Vesicle formation during receptor-mediated endocytosis involves a complex protein machinery and additional proteins to control it. Although our understanding of this endocytic machinery has grown rapidly
TGF-β-stimulated cooperation of Smad proteins with the coactivators CBP/p300 (1998)

TGF-beta and activin induce the phosphorylation and activation of Smad2 and Smad3, but how these proteins stimulate gene transcription is poorly understood. We report that TGF-beta receptor phosphorylation of Smad3 promotes its interaction with the paralogous coactivators CBP and p300, whereas CBP/p300 binding to nonphosphorylated Smad3 or its oligomerization partner Smad4 is negatively regulated by Smad-intramolecular interactions. Furthermore, p300 and TGF-beta receptor-phosphorylated Smad3 synergistically augment transcriptional activation. Thus, CBP/p300 are important components of activin/TGF-beta signaling and may mediate the antioncogenic functions of Smad2 and Smad4.