gebhart/patrepeval huggingface dataset:
A Protein-Counting Mechanism for Telomere Length Regulation in Yeast (1997)

In the yeast Saccharomyces cerevisiae, telomere elongation is negatively regulated by the telomere repeat-binding protein Rap1p, such that a narrow length distribution of telomere repeat tracts is observed. This length regulation was shown to function independently of the orientation of the telomere repeats. The number of repeats at an individual telomere was reduced when hybrid proteins containing the Rap1p carboxyl terminus were targeted there by a heterologous DNA-binding domain. The extent of this telomere tract shortening was proportional to the number of targeted molecules, consistent with a feedback mechanism of telomere length regulation that can discriminate the precise number of Rap1p molecules bound to the chromosome end.
Polymer gel dosimetry utilizing a 2D (SE) and a 2D (HASTE) multiple echo sequences (2013)

Two pulse sequences were used for the estimation of dosimetric characteristics of VIPET polymer gels. The first one, multi- echo spin echo (MESE) is the well-established method for T2 measurements. The other method is a new multi-echo single shot turbo spin echo pulse sequence, MEHASTE that reduces the acquisition time significantly. Both techniques showed a linear R2-dose response. With MESE sequence, the dose sensitivity was slightly enhanced as compared to MEHASTE. The linear portion of the R2-dose curve was restricted using the MEHASTE sequence. For doses above 7 Gy both methods fulfill the 2% ICRU criterion limit for dose resolution estimations (95% confidence level). Finally, for a time period of one month the temporal stability of R2-dose response was maintained stable utilizing both MESE and MEHASTE pulse sequences. MEHASTE serves as an excellent means for fast 3D polymer gel dosimetry.
Nanocomposite Gold-Silk Nanofibers (2012)

Cell-biomaterial interactions can be controlled by modifying the surface chemistry or nanotopography of the material, to induce cell proliferation and differentiation if desired. Here we combine both approaches in forming silk nanofibers (SNFs) containing gold nanoparticles (AuNPs) and subsequently chemically modifying the fibers. Silk fibroin mixed with gold seed nanoparticles was electrospun to form SNFs doped with gold seed nanoparticles (SNF(seed)). Following gold reduction, there was a 2-fold increase in particle diameter confirmed by the appearance of a strong absorption peak at 525 nm. AuNPs were dispersed throughout the AuNP-doped silk nanofibers (SNFs(Au)). The Young's modulus of the SNFs(Au) was almost 70% higher than that of SNFs. SNFs(Au) were modified with the arginine-glycine-aspartic acid (RGD) peptide. Human mesenchymal stem cells that were cultured on RGD-modified SNF(Au) had a more than 2-fold larger cell area compared to the cells cultured on bare SNFs; SNF(Au) also increased cell size. This approach may be used to alter the cell-material interface in tissue engineering and other applications.
Domain-wall memory buffer for low-energy NoCs (2015)

Networks-on-chip (NoCs) have become a leading energy consumer in modern multi-core processors, with a considerable portion of this energy originating from the large number of virtual channel (FIFO) buffers. While emerging memories have been considered for many architectural components such as caches, the asymmetric access properties and relatively small size of network-FIFOs compared to the required peripheral circuitry has led to few such replacements proposed for NoCs. In this paper, we propose control schemes that leverage the\shift-register" nature of spintronic domain-wall memory (DWM) to replace conventional memory buffers for the NoC. Our results indicate that the best shift-based scheme utilizes a dual-nanowire approach to ensure that reads and writes can be more effectively aligned with access ports for simultaneous access in the same cycle. Our approach provides a 2.93X speedup over a DWM buffer using a traditional FIFO memory control scheme with a 1.16X savings in energy. Compared to a SRAM-FIFO it exhibits an 8% message latency degradation versus a 56% energy reduction. The resulting approach achieves a 53% reduction in energy delay product compared to SRAM and a 42% reduction in energy delay product versus STT-MRAM.
Enhanced Photoresponse in Metasurface-Integrated Organic Photodetectors (2018)

In this work, we experimentally demonstrate metasurface-enhanced photoresponse in organic photodetectors. We have designed and integrated a metasurface with broadband functionality into an organic photodetector, with the goal of significantly increasing the absorption of light and generated photocurrent from 560 up to 690 nm. We discuss how the metasurface can be integrated with the fabrication of an organic photodiode. Our results show large gains in responsivity from 1.5× to 2× between 560 and 690 nm.
The 14-3-3 protein interacts directly with the C-terminal region of the plant plasma membrane H(+)-ATPase. (1997)

Accumulating evidence suggests that 14-3-3 proteins are involved in the regulation of plant plasma membrane H(+)-ATPase activity. However, it is not known whether the 14-3-3 protein interacts directly or indirectly with the H(+)-ATPase. In this study, detergent-solubilized plasma membrane H(+)-ATPase isolated from fusicoccin-treated maize shoots was copurified with the 14-3-3 protein (as determined by protein gel blotting), and the H(+)-ATPase was recovered in an activated state. In the absence of fusicoccin treatment, H(+)-ATPase and the 14-3-3 protein were well separated, and the H(+)-ATPase was recovered in a nonactivated form. Trypsin treatment removed the 10-kD C-terminal region from the H(+)-ATPase as well as the 14-3-3 protein. Using the yeast two-hybrid system, we could show a direct interaction between Arabidopsis 14-3-3 GF14-phi and the last 98 C-terminal amino acids of the Arabidopsis AHA2 plasma membrane H(+)-ATPase. We propose that the 14-3-3 protein is a natural ligand of the plasma membrane H(+)-ATPase, regulating proton pumping by displacing the C-terminal autoinhibitory domain of the H(+)-ATPase.
Comparison of the Rotating Cylinder and Pipe Flow Tests for Flow-Sensitive Carbon Dioxide Corrosion (1995)

The effects of various hydrodynamic parameters on the corrosion rate of low-carbon steel in carbon dioxide (CO2) environments were studied. Two different flow geometries, rotating cylinder (RC) and pipe flow, were studied simultaneously in the same electrolyte within a glass loop. Comparisons were made over a wide range of parameters: temperature (T) = 20°C to 80°C, pH = 4 to 6, CO2 partial pressure (PCO2)=0bar to 1 bar (0 kPa to 100 kPa), velocity (v) = 0 m/s to 13 m/s. The hydrodynamic conditions studied covered the range from static to highly turbulent flow. The corrosion process was monitored using polarization resistance, potentiodynamic sweep, and electrochemical impedance methods. The comparison of the two flow geometries was carried out in terms of hydrodynamics, mass transfer, and CO2 corrosion. The measured mass transfer rates agreed well with published correlations for the RC and straight pipe (SP) flow. In the case of CO2 corrosion, it was possible to achieve good agreement between corrosion rates in the two flow geometries at low temperatures by having the same water chemistry and mass-transfer conditions. This conclusion was valid for cases where no protective corrosion products, scale, or inhibitor films were present. However, at higher temperatures, films with a certain degree of protectiveness were observed. In those cases, lower corrosion rates were obtained on the SP specimen because of more dense and protective films.
Injecting light of high-power LEDs into thin light guides (2010)

A new method using a thin-film multilayer filter is described to couple light from high-power LEDs into a thin light guide such as an LCD backlight. Light emitted below the critical angle is reflected back to the LED and recycled. Largeangle emitted light passes the filter and is transported by total internal reflection in the light guide. The light guide can be as thin as 0.3mm for an LED of 1x1mm<sup>2</sup>, and the best coupling efficiency is estimated to be around 80%. With this approach, a backlight system can be greatly simplified but also compact collimators can be realized. In this paper the optical design and testing of the filter is described, and a 1mm thick, 6.5mm diameter collimator is presented that emits in a cone of 2×13°. Measurements on prototypes show good agreement with the designed characteristics.
Changes in Plasma ACTH Levels and Corticotroph Tumor Size in Patients With Cushing's Disease During Long-term Treatment With the Glucocorticoid Receptor Antagonist Mifepristone (2014)

In the largest prospective study to date, long-term mifepristone treatment increased ACTH in approximately two-thirds of patients with CD. ACTH elevations were observed within the first few weeks of treatment, were dose-dependent, and generally remained stable over time. Corticotroph tumor progression and regression may occur over time, but patients may have significant increases in ACTH levels without evidence of tumor growth.
Respiratory Effects of Amyotrophic Lateral Sclerosis: Problems and Solutions (2006)

Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease. Most patients die from respiratory complications. Fortunately, there are a growing number of treatment options that can improve both survival and quality of life for patients with ALS. This review discusses the respiratory evaluation and treatment of patients with ALS, about which a great deal is known. It also includes material on related problems, such as speech and swallowing difficulties and end-of-life care.
Gefitinib: current and future status in cancer therapy. (2003)

The epidermal growth factor receptor (EGFR) is recognized as a key modulator of tumor cell function and is considered to be a viable drug target in a range of solid malignancies. Current knowledge of its role in tumor growth and progression has led to a newly active area of anticancer research, investigating agents that target the activity of this receptor. Of these agents, gefitinib is furthest in clinical development, having received regulatory approval in Japan in 2002, and in the United States and Australia in 2003. Gefitinib is an orally active, EGFR-tyrosine kinase inhibitor that blocks signal transduction pathways implicated in the proliferation and survival of cancer cells and other host-dependent processes promoting cancer cell growth. A plethora of preclinical studies have suggested promising outcomes for this agent and have led to ongoing clinical trials in a wide range of tumors, including non-small-cell lung, head and neck, colorectal, prostate, and breast, either as monotherapy or in combination with standard chemotherapy, hormonal therapy, or radiotherapy. Furthermore, as biologic agents are specifically designed to attack different pathways of tumor growth and progression, the potential for the combination of gefitinib with other agents, given either concurrently or sequentially, to prevent or delay disease recurrence is also being investigated. This article provides a detailed overview of gefitinib, the rationale for its use in a wide range of tumor types, and the current clinical development status of this novel agent.
A visual data-mining methodology for seismic facies analysis: Part 2 — Application to 3D seismic data (2009)

Abstract A visual data-mining approach to unsupervised clustering analysis can be an effective tool for visualizing and understanding patterns inherent in seismic data (i.e., seismic facies). The unsupervised clustering analysis is completely data-driven, requiring no external information (e.g., well logs) to guide the seismic-trace classification. We demonstrate the application of the visual data-mining approach to seismic facies analysis on a real 3D seismic data volume. We select two stratigraphic intervals, the first including a Devonian pinnacle reef system and the second containing a Jurassic siliciclastic channel system. Both analyses show major stratigraphic features that can be defined in horizon slices or other types of visualization. However, the visual data-mining approach creates seismic facies maps with improved visual detail, distinguishing seismic trace-shape variability in the data. We also compare the facies maps with those obtained from a commercial package for seismic facies classification. Both approaches created similar facies maps, but the visual strategy better depicts subtle stratigraphic changes in the bodies being imaged, offering insight into the nature of these features.
Rhodium-Catalyzed Coupling Reaction of Salicyl Aldehydes with Alkynes via Cleavage of the Aldehyde C−H Bond (1997)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTRhodium-Catalyzed Coupling Reaction of Salicyl Aldehydes with Alkynes via Cleavage of the Aldehyde C−H BondKen Kokubo, Kenji Matsumasa, Masahiro Miura, and Masakatsu NomuraView Author Information Department of Applied Chemistry, Faculty of Engineering, Osaka University, Suita, Osaka 565, Japan Cite this: J. Org. Chem. 1997, 62, 14, 4564–4565Publication Date (Web):July 11, 1997Publication History Received29 May 1997Published online11 July 1997Published inissue 1 July 1997https://pubs.acs.org/doi/10.1021/jo9709458https://doi.org/10.1021/jo9709458rapid-communicationACS PublicationsCopyright © 1997 American Chemical SocietyRequest reuse permissionsArticle Views2086Altmetric-Citations129LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Addition reactions,Aldehydes,Aromatic compounds,Hydrocarbons,Ligands Get e-Alerts
IntelliGen: Automatic Driver Synthesis for Fuzz Testing (2021)

Fuzzing is a technique widely used in vulnerability detection. The process usually involves writing effective fuzz driver programs, which, when done manually, can be extremely labor intensive. Previous attempts at automation leave much to be desired, in either degree of automation or quality of output. In this paper, we propose IntelliGen, a framework that constructs valid fuzz drivers automatically. First, IntelliGen determines a set of entry functions and evaluates their respective chance of exhibiting a vulnerability. Then, IntelliGen generates fuzz drivers for the entry functions through hierarchical parameter replacement and type inference. We implemented IntelliGen and evaluated its effectiveness on real-world programs selected from the Android Open-Source Project, Google's fuzzer-testsuite and industrial collaborators. IntelliGen covered on average 1.08X-2.03X more basic blocks and 1.36X-2.06X more paths over state-of-the-art fuzz driver synthesizers FUDGE and FuzzGen. IntelliGen performed on par with manually written drivers and found 10 more bugs.
Framework for a Cloud-Based Multimedia Surveillance System (2014)

The new generation of multimedia surveillance systems integrates a large number of heterogeneous sensors to collect, process, and analyze multimedia data for identifying events of potential security threats. Some of the major concerns facing these systems are scalability, ubiquitous access to sensory data, event processing overhead, and massive storage requirements—all of which demand novel scalable approach. Cloud computing can provide a powerful and scalable infrastructure for large-scale storage, processing, and dissemination of sensor data. Furthermore, the integration of sensor technology and cloud computing offers new possibilities for efficient development and deployment of sensor-based systems. This paper proposes a framework for a cloud-based multimedia surveillance system and highlights several research and technical issues. A prototype surveillance system is also designed and analyzed in the context of the proposed surveillance framework. The paper finally reports that cloud-based multimedia surveillance system can effectively support the processing overload, storage requirements, ubiquitous access, security, and privacy in large-scale surveillance settings.
Evolution of vertebrate steroid receptors from an ancestral estrogen receptor by ligand exploitation and serial genome expansions (2001)

The evolution of novelty in tightly integrated biological systems, such as hormones and their receptors, seems to challenge the theory of natural selection: it has not been clear how a new function for any one part (such as a ligand) can be selected for unless the other members of the system (e.g., a receptor) are already present. Here I show-based on identification and phylogenetic analysis of steroid receptors in basal vertebrates and reconstruction of the sequences and functional attributes of ancestral proteins-that the first steroid receptor was an estrogen receptor, followed by a progesterone receptor. Genome mapping and phylogenetic analyses indicate that the full complement of mammalian steroid receptors evolved from these ancient receptors by two large-scale genome expansions, one before the advent of jawed vertebrates and one after. Specific regulation of physiological processes by androgens and corticoids are relatively recent innovations that emerged after these duplications. These findings support a model of ligand exploitation in which the terminal ligand in a biosynthetic pathway is the first for which a receptor evolves; selection for this hormone also selects for the synthesis of intermediates despite the absence of receptors, and duplicated receptors then evolve affinity for these substances. In this way, novel hormone-receptor pairs are created, and an integrated system of increasing complexity elaborated. This model suggests that ligands for some "orphan" receptors may be found among intermediates in the synthesis of ligands for phylogenetically related receptors.
An Ink Spreading Model for Dot-On-Dot Spectral Prediction (2006)

Due to increasing printing accuracies and the possibility of printing several droplets at the same pixel location, there is a renewed interest in dot-on-dot printing models. In the present contribution, we improve a dot-on-dot spectral prediction model relying on the Yule-Nielsen modified Spectral Neugebauer model by taking into account ink spreading in all ink superposition conditions. Since ink spreading is different when ink dots are printed alone, printed in superposition with one ink or printed in superposition with two inks, we create for each superposition condition an ink spreading function mapping nominal to effective dot surface coverages. When predicting the reflection spectrum of a dot-on-dot halftone patch, its known nominal surface coverage values are converted into effective coverage values by weighting the contributions from different ink spreading functions according to the corresponding ratio of colorant surface coverages. We analyze the colorimetric prediction improvement brought by our ink spreading model for dot-on-dot thermal transfer prints and for ink-jet prints. Accounting for ink spreading according to different ink superposition conditions considerably improves the prediction accuracy. In the case of ink jet prints at 120 lpi, the mean ΔE94 difference between predictions and measurements is reduced from 4.54 to 1.55 (accuracy improvement factor: 3). Due to the slight misregistration between the ink layers, spectral predictions accounting for ink spreading in the case of dot-on-dot screens are less accurate than corresponding predictions for classical mutually rotated screens.
Calibration of a Shack–Hartmann sensor for absolute measurements of wavefronts (2005)

We demonstrate a method with which to calibrate a Shack-Hartmann sensor for absolute wavefront measurement of collimated laser beams. Nearly perfect spherical wavefronts originating from a single-mode fiber were used as references. After the calibration, the uncertainty of the wavefront was less than lambda/100 peak to valley across a diameter of 6 mm. For example, this method allowed us to balance aberrations and prepare collimated beams with wavefronts that are plane to lambda/500 across 1 mm.
Inhibition of a Gi-activated Potassium Channel (GIRK1/4) by the Gq-coupled m1 Muscarinic Acetylcholine Receptor (2001)

The G protein-coupled inwardly rectifying K+ channel, GIRK1/GIRK4, can be activated by receptors coupled to the Galpha(i) subunit. An opposing role for Galpha(q) receptor signaling in GIRK regulation has only recently begun to be established. We have studied the effects of m1 muscarinic acetylcholine receptor (mAChR) stimulation, which is known to mobilize calcium and activate protein kinase C (PKC) by a Galpha(q)-dependent mechanism, on whole cell GIRK1/4 currents in Xenopus oocytes. We found that stimulation of the m1 mAChR suppresses both basal and dopamine 2 receptor-activated GIRK 1/4 currents. Overexpression of Gbetagamma subunits attenuates this effect, suggesting that increased binding of Gbetagamma to the GIRK channel can effectively compete with the G(q)-mediated inhibitory signal. This G(q) signal requires the use of second messenger molecules; pharmacology implicates a role for PKC and Ca2+ responses as m1 mAChR-mediated inhibition of GIRK channels is mimicked by PMA and Ca2+ ionophore. We have analyzed a series of mutant and chimeric channels suggesting that the GIRK4 subunit is capable of responding to G(q) signals and that the resulting current inhibition does not occur via phosphorylation of a canonical PKC site on the channel itself.
Statistical analysis of real-time PCR data (2006)

Practical statistical solutions with SAS programs were developed for real-time PCR data and a sample dataset was analyzed with the SAS programs. The analysis using the various models and programs yielded similar results. Data quality control and analysis procedures presented here provide statistical elements for the estimation of the relative expression of genes using real-time PCR.
Modeling of multi-resolution active network measurement time-series (2008)

Active measurements on network paths provide end-to-end network health status in terms of metrics such as bandwidth, delay, jitter and loss. Hence, they are increasingly being used for various network control and management functions on the Internet. For purposes of network health anomaly detection and forecasting involved in these functions, it is important to accurately model the time-series process of active measurements. In this paper, we describe our time-series analysis of two typical active measurement data sets collected over several months: (i) routine, and (ii) event-laden. Our analysis suggests that active network measurements follow the moving average process. Specifically, they possess ARIMA(0,1,q) model characteristics with low q values, across multi-resolution timescales. We validate our model selection accuracy by comparing how well our predicted values using our model match the actual measurements.