gebhart/patrepeval huggingface dataset:
Pleiotropic Effects of Ubp6 Loss on Drug Sensitivities and Yeast Prion Are Due to Depletion of the Free Ubiquitin Pool (2003)

Mutation of the mouse Usp14 gene, encoding the homolog of yeast deubiquitinating enzyme Ubp6, causes ataxia. Here we show that deletion of the UBP6 gene in Saccharomyces cerevisiae causes sensitivity to a broad range of toxic compounds and antagonizes phenotypic expression and de novo induction of the yeast prion [PSI+], a functionally defective self-perpetuating isoform of the translation termination factor Sup35. Conversely, overexpression of ubiquitin (Ub) increases phenotypic expression and induction of [PSI+] in the wild type cells and suppresses all tested ubp6Delta defects, indicating that they are primarily due to depletion of cellular Ub levels. Several lines of evidence suggest that Ubp6 functions on the proteasome. First, Ub levels in the ubp6Delta cells can be partly restored by proteasome inhibitors, suggesting that deletion of Ubp6 decreases Ub levels by increasing proteasome-dependent degradation of Ub. Second, fluorescence microscopy analysis shows that Ubp6-GFP fusion protein is localized to the nucleus of yeast cell, as are most proteasomes. Third, the N-terminal Ub-like domain, although it is not required for nuclear localization of Ubp6, targets Ubp6 to the proteasome and cannot be functionally replaced by Ub. The human ortholog of Ubp6, USP14, probably plays a similar role in higher eukaryotes, since it fully compensates for ubp6Delta defects and binds to the yeast proteasome. These data link the Ub system to prion expression and propagation and have broad implications for other neuronal inclusion body diseases.
Revised absolute configuration of mitomycin C. X-ray analysis of 1-N-(p-bromobenzoyl)mitomycin C (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRevised absolute configuration of mitomycin C. X-ray analysis of 1-N-(p-bromobenzoyl)mitomycin CKunikatsu Shirahata and Noriaki HirayamaCite this: J. Am. Chem. Soc. 1983, 105, 24, 7199–7200Publication Date (Print):November 1, 1983Publication History Published online1 May 2002Published inissue 1 November 1983https://pubs.acs.org/doi/10.1021/ja00362a046https://doi.org/10.1021/ja00362a046research-articleACS PublicationsRequest reuse permissionsArticle Views145Altmetric-Citations35LEARN 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 Get e-Alerts
Early Steps in Hematogenous Metastasis of B16F1 Melanoma Cells in Chick Embryos Studied by High-Resolution Intravital Videomicroscopy (1992)

Intravital videomicroscopy can provide new information about steps in metastasis. This procedure is applicable to other hosts and can be used in future studies to test hypotheses about molecular mechanisms of tumor spread.
Response to ‘‘Comment on ‘Visible photoluminescence in crystallized amorphous Si:H/SiN<i>x</i>:H multiquantum-well structures’ ’’ [Appl. Phys. Lett. <b>61</b>, 2069 (1992)] (1995)

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<title>In vivo and in vitro absorption spectrum of disulphonated aluminum phthalocyanine in tumor-bearing mice</title> (1994)

The absorption spectrum of disulphonated aluminum phthalocyanine (AlS<sub>2</sub>Pc) between 650 nm and 695 nm was measured in vivo by means of time-resolved reflectance. The experiments were performed on mice bearing the L1210 leukemia 1, 4, and 7 hr after the i.p. administration of 2.5 mg/kg body weight (b.w.) of AlS<sub>2</sub>Pc. The absorption peak is centered at 685 nm, red-shifted of 10 - 15 nm with respect to the spectra obtained in solution in various environments. Measurements performed in vitro confirm the results in vivo and seem to suggest that the extracellular environment can cause the shift in the absorption line shape.
Induction of target cell DNA release by the cytotoxic T lymphocyte granule protease granzyme A. (1989)

The rapid breakdown of target cell DNA during CTL-mediated lysis has been difficult to explain by the granule exocytosis model of cytotoxicity. The involvement of CTL granule proteases in this process was strongly suggested by experiments in which CTL were pretreated with the serine protease inhibitor PMSF, in combination with agents that raise the pH of acidic intracellular compartments. While PMSF pretreatment alone had little effect on target lysis or DNA breakdown, the combination of PMSF and NH4Cl or monensin profoundly reduced target cell DNA release, while little effect was observed on target lysis, as measured by 51Cr release. CTL granule extracts cause release of 125I-DNA from detergent-permeabilized cells. This nuclear DNA-releasing (NDR) activity is inhibited by serine esterase inhibitors that also inhibit the granule BLT-esterase activity, and is specifically immunoabsorbed by antibodies to the CTL granule protease granzyme A. The NDR activity comigrates with BLT-esterase activity during subcellular fractionation, solubilization, gel filtration, and aprotinin-Sepharose affinity chromatography. SDS-PAGE analysis of the affinity-purified product indicates a molecular mass of 60,000 daltons under non-reducing conditions, which moves to 30,000 daltons upon reduction, consistent with previously reported behavior of granzyme A. When the purified material was reduced and alkylated, both esterase and NDR activities comigrated at 30,000 daltons upon gel filtration. Although fully lytic concentrations of purified LGL granule cytolysin alone failed to induce target cell DNA release, a combination of purified granzyme A and the cytolysin induces substantial DNA release.
Tutorial: Computer architecture (1986)

This book presents the state-of-the-art in advanced computer architecture. It deals with the concepts underlying current architectures and covers approaches and techniques being used in the design of advanced computer systems.
Esterification and transesterification of 9(10)‐carboxystearic acid and its methyl esters. Kinetic studies (1972)

Abstract 9(10)‐Carboxystearic acid and its mono‐ and dimethyl esters were esterified and transesterified with 1‐butanol, 2‐methoxyethanol, 2‐chloroethanol, 2,2‐dimethylpentanol, 2‐ethylhexanol and 1‐octanol. Rate studies for the sulfuric acid‐catalyzed esterification of 9(10)‐carboxystearic acid to alkyl 9(10)‐carboxystearate and alkyl 9(10)‐carboalkoxystearate indicate than on an average the terminal carboxyl is approximately 26–27 times more reactive than the branched carboxyl group. Esterification is highly dependent on catalyst concentration. Steric hindrance in 2,2‐dimethylpentanol and the electrophilic character of 2‐methoxyethanol and 2‐chloroethanol markedly retard the rate. In addition to the expected diesters, 2‐chloroethanol yields esters containing extra‐O‐CH 2 CH 2 ‐ groups. The rate of transesterification of the terminal ester group of mono‐ and dimethyl esters of 9(10)‐carboxystearic acid is about two times faster than the rate of esterification of the branched carboxyl group. Transesterification of the branched 9(10)‐ester group is extremely slow.
Transformation of VHDL descriptions into DEVS models for fault modeling (2004)

We propose in this article an approach for the transformation of VHDL descriptions into DEVS models for an easy and fast fault simulation. VHDL allows description of the structure of a design, that is how it is decomposed into sub-designs, and how those designs are interconnected. The specification of the function of designs are performed using familiar programming language forms. One of the main problems is that today tools are unable to quickly and easily create and simulate fault models directly from the VHDL descriptions. A way to solve this problem is to encapsulate these descriptions in easily simulating and evolutive models. We propose to use the DEVS formalism to achieve this encapsulation.
Quantum Language Processing (2019)

We present a representation for linguistic structure that we call a Fock-space representation, which allows us to embed problems in language processing into small quantum devices. We further develop a formalism for understanding both classical as well as quantum linguistic problems and phrase them both as a Harmony optimization problem that can be solved on a quantum computer which we show is related to classifying vectors using quantum Boltzmann machines. We further provide a new training method for learning quantum Harmony operators that describe a language. This also provides a new algorithm for training quantum Boltzmann machines that requires no approximations and works in the presence of hidden units. We additionally show that quantum language processing is BQP-complete, meaning that it is polynomially equivalent to the circuit model of quantum computing which implies that quantum language models are richer than classical models unless BPP=BQP. It also implies that, under certain circumstances, quantum Boltzmann machines are more expressive than classical Boltzmann machines. Finally, we examine the performance of our approach numerically for the case of classical harmonic grammars and find that the method is capable of rapidly parsing even non-trivial grammars. This suggests that the work may have value as a quantum inspired algorithm beyond its initial motivation as a new quantum algorithm.
Improved performance of multi-bit delta-sigma analog to digital converters via requantization (1991)

System performance of an oversampled analog to digital converter (ADC) with feedback noise shaping is limited by the precision of the digital to analog converter (DAC) in the feedback path as well as by the number of integrators in the loop(s). Standard designs avoid the DAC precision problem by restricting the ADC and DAC to a single bit, while stability and matching considerations limit systems to three loops. This limit in turn defines the oversample ratio for a given effective bandwidth and noise performance. A simple modification to the oversampled ADC which avoids these limitations via requantization in the feedback path of the original delta-sigma loop structure is presented.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Microarray Analysis of Retinal Gene Expression in the DBA/2J Model of Glaucoma (2006)

DBA/2J retina shows evidence of glial activation and an immune-related response after IOP elevation, similar to what has been reported after acute elevation of IOP in other models.
Low-complexity integer transform and high-definition coding (2004)

In H.264/AVC, an integer 4×4 transform is used instead of traditional float DCT transform due to its low complexity and exact reversibility. Combined with the normalization for the integer transform together, a division-free quantization scheme is used in H.264/AVC. H.264/AVC is the most outstanding video coding standard at far. But at first H.264/AVC targets to low bit-rate coding, and almost all experimental results of the proposals for H.264/AVC are tested at low bit-rate. In the near, experimental results show that 8×8 transform can further improve the coding efficiency on high definition (HD) coding. In this paper a kind of 8×8 low complexity integer transforms are studied and corresponding quantization schemes are developed for HD coding. Compared with 4×4 transform/prediction based coder, the proposed 8×8 based coder can achieve better performance on HD coding while with much lower encoder/decoder complexity.
Retrieving interesting images using fuzzy image segmentation and fuzzy data mining model (2004)

We propose a novel image mining model to address three issues. First, we utilize a scalable region-based representation for an image. Users can retrieve desired images according to their visual interesting. Second, we take users' intuition into consideration. We design a such that users can select some important portions from an image and directly search the database. Also the relevance feedback can achieve a higher performance. Third, the processes to search for interesting images can be treated as transaction records and be transformed into useful information. Through the data mining analysis, the system can discover the users' intentions in retrieving images. The discovered rules may in turn be used to improve the retrieval efficiency. We exploit fuzzy clustering method and data mining model to design an image retrieval model. The designing methodology is illustrated and the system performance is evaluated in the paper.
From the Bottom-Up: Toward Area-Selective Atomic Layer Deposition with High Selectivity (2018)

Bottom-up nanofabrication by area-selective atomic layer deposition (ALD) is currently gaining momentum in semiconductor processing, because of the increasing need for eliminating the edge placement errors of top-down processing. Moreover, area-selective ALD offers new opportunities in many other areas such as the synthesis of catalysts with atomic-level control. This Perspective provides an overview of the current developments in the field of area-selective ALD, discusses the challenge of achieving a high selectivity, and provides a vision for how area-selective ALD processes can be improved. A general cause for the loss of selectivity during deposition is that the character of surfaces on which no deposition should take place changes when it is exposed to the ALD chemistry. A solution is to implement correction steps during ALD involving for example surface functionalization or selective etching. This leads to the development of advanced ALD cycles by combining conventional two-step ALD cycles with correction steps in multistep cycle and/or supercycle recipes.
Visual learning by integrating descriptive and generative methods (2002)

This paper presents a mathematical framework for visual learning that integrates two popular statistical learning paradigms in the literature: (I). Descriptive learning, such as Markov random fields and minimax entropy learning, and (II). Generative learning, such as PCA, ICA, TCA, image coding and HMM. We apply this integrated learning framework to texton modeling, and we assume that an observed texture image is generated by multiple layers of hidden stochastic "texton processes" with each texton being a window function, like a mini-template or a wavelet, under affine transformations. The spatial arrangements of the textons are characterized by minimax entropy models. The texton processes generate images by occlusion or linear addition. Thus given a raw input image, the learning framework achieves four goals: (i). Computing the appearance of the textons. (ii) Inferring the hidden stochastic texton processes. (iii). Learning Gibbs models for each texton process and (iv). Verifying the learnt textons and Gibbs models through random sampling and texture synthesis. The integrated framework subsumes the minimax entropy learning paradigm and creates a richer class of probability models for visual patterns, which are suited for middle level vision representations. Furthermore we show that the integration of description and generative methods yields a natural and general framework of visual learning. We demonstrate the proposed framework and algorithms on many real images.
Enhancing the immunogenicity of a permissive binding T cell epitope derived from the simian immunodeficiency virus-encoded negative regulatory factor (1992)

Using the murine system we have analyzed an immunogenic T cell peptide epitope corresponding to amino acids 96-112 of the simian immunodeficiency virus-negative regulatory protein sequence. This epitope was unusual in that it was strongly immunogenic in mice of five of the six H-2 haplotypes tested. We generated a T cell hybridoma (SVNF) specific for this peptide in order to determine how manipulating the peptide might alter its immunogenicity. Substitution analysis showed that His 103, Pro 104, Val 106, and Pro 107 were important amino acids for stimulating SVNF because substitutions at these positions diminished the reactivity of SVNF. However, we also found that substituting an Ala for a Val at position 100 or a Val for an Ala at position 110 enhanced reactivity of SVNF. We were able to further enhance the immunogenicity of this epitope by extending the carboxyl terminus two amino acids and making the resulting carboxyl-terminal Lys an amide and by adding a Glu to the amino terminus. These modifications shifted the in vitro activity of SVNF at least two orders of magnitude. We also compared the ability of this modified peptide and the wild-type SIV nef 96-112 to prime a T cell response in vivo. We primed mice with various doses of either the wild-type or the modified peptide and looked at the ability of the draining lymph node cells to proliferate to wild-type peptide. We found that the modified peptide was 10- to 100-fold better at priming a T cell response than the wild-type peptide. Therefore, we were able to create a peptide that was more immunogenic than the wild-type peptide in vivo as well as in vitro. Manipulations such as these that enhance the immunogenicity of T cell epitopes must be considered in developing peptide vaccines against HIV or other infectious agents.
ChemInform Abstract: REACTION OF EPOXIDES WITH PHOSPHONIC ACID MONOESTERS AND PHOSPHONIC ACIDS (1976)

Abstract Die Phosphonsäureester (Ia) setzen sich mit Epoxiden, wie (II), zu Phosphonsäurealkyl‐ β‐hydroxyalkylestern, wie z.B. (IIIa) (die als Stellungsisomere in bezug auf die Positionen von R3 und R4 anfallen) um.
Study on the Propagation of Love Waves across Irregular Structures of the Moho Discontinuity (1997)

An ICP sets out best practice guidance. One health-care team applied ICPs to stroke care, which can be unpredictable. Stroke care was arranged in 'bite-sized chunks' with ICPs for each separate aspect.
Effective improved artificial potential field-based regression search method for autonomous mobile robot path planning (2013)

This paper presents an effective improved artificial potential field-based regression search (improved APF-based RS) method that can obtain a better and shorter path efficiently without local minima and oscillations in an environment including known, partially known or unknown, static, and dynamic environments. We redefine potential functions to eliminate oscillations and local minima problems, and use improved wall-following methods for the robots to escape non-reachable target problems. Meanwhile, we develop a regression search method to optimise the planned path. The optimisation path is calculated by connecting the sequential points produced by improved APF. The simulations demonstrate that the improved APF method easily escapes from local minima, oscillations, and non-reachable target problems. Moreover, the simulation results confirm that our proposed path planning approach can calculate a shorter or more nearly optimal than the general APF can. Results prove our improved APF-based RS method’s feasibility and efficiency for solving path planning.
Laboratory-Scale Studies on Chemical Reactions Between Fracturing Fluid and Shale Core From the Marcellus Shale Energy and Environmental Laboratory (MSEEL) Site (2017)

Presented by NETL at Unconventional Resources Technology Conference, 07/17
Activation of Wnt5A signaling is required for CXC chemokine ligand 12–mediated T-cell migration (2009)

Chemokines mediate the signaling and migration of T cells, but little is known about the transcriptional events involved therein. Microarray analysis of CXC chemokine ligand (CXCL) 12-treated T cells revealed that Wnt ligands are significantly up-regulated during CXCL12 treatment. Real-time polymerase chain reaction and Western blot analysis confirmed that the expression of noncanonical Wnt pathway members (eg, Wnt5A) was specifically up-regulated during CXCL12 stimulation, whereas beta-catenin and canonical Wnt family members were selectively down-regulated. Wnt5A augmented signaling through the CXCL12-CXCR4 axis via the activation of protein kinase C. Moreover, Wnt5A expression was required for CXCL12-mediated T-cell migration, and rWnt5A sensitized human T cells to CXCL12-induced migration. Furthermore, Wnt5A expression was also required for the sustained expression of CXCR4. These results were further supported in vivo using EL4 thymoma metastasis as a model of T-cell migration. Together, these data demonstrate that Wnt5A is a critical mediator of CXCL12-CXCR4 signaling and migration in human and murine T cells.
[Induced differentiation of mouse embryonic stem cell into endothelial cell in vitro]. (2007)

ESC can differentiate into endothelial cells under some conditions, and form vessel-like structure under condition culture, which can provide sources of seed cells for tissue engineered vessel.
Motor Nerve Root Monitoring During Percutaneous Transforaminal Endoscopic Sequestrectomy Under General Anesthesia for Intra- and Extraforaminal Lumbar Disc Herniation (2005)

PTFES under general anesthesia is a safe and easy-to-perform technique for surgical management of intra- and/or extraforaminal lumbar disc herniation if combined with intraoperative neurophysiological monitoring. General anesthesia reduces intraoperative stress to a minimum, so that a larger number of patients may benefit from this minimally invasive procedure in future.
Modeling, evaluation, and testing of paradyn instrumentation system (1996)

This paper presents a case study of modeling, evaluating, and testing the data collection services (called an instrumentation system) of the Paradyn parallel performance measurement tool using well-known performance evaluation and experiment design techniques. The overall objective of the study is to use modeling- and simulation-based evaluation to provide feedback to the tool developers to help them choose system configurations and task scheduling policies that can significantly reduce the data collection overheads. We develop and parameterize a resource occupancy (ROCC) model for Paradyn instrumentation system (IS) for an IBM SP-2 platform. This model is parameterized with a measurement-based workload characterization and subsequently used to answer several "what if" questions regarding configuration options and two policies to schedule instrumentation system tasks: collect-and-forward (CF) and batch-and-forward (BF) policies. Simulation results indicate that the BF policy can significantly reduce the overheads. Based on this feedback, the BF policy was implemented in Paradyn IS as an option to manage the data collection. Measurement-based testing results obtained from this enhanced version of Paradyn IS are reported in this paper and indicate more than 60% reduction in the direct IS overheads when the BF policy is used.
Modeling and comparing CMOS implementations of the C-element (1998)

Various applications have demonstrated that asynchronous circuits have great potential for energy-efficient and high-performance design. One of the primitives used in asynchronous control circuits is the C-element. Analytical delay and energy models are presented and applied to the most popular complementary metal-oxide-semiconductor (CMOS) implementations of the C-element. Optimization of these implementations are discussed. The implementations are also compared using simulations. The simulation results are in good agreement with the analytical predictions.