gebhart/patrepeval huggingface dataset:
Contribution of Surface Salt Bridges to Protein Stability<sup>,</sup> (2000)

The role of surface salt bridges in protein stabilization has been a source of controversy. Here we present the NMR structure of a hyperthermophilic rubredoxin variant (PFRD-XC4) and the thermodynamic analysis of two surface salt bridges by double mutant cycles. This analysis shows that the surface side chain to side chain salt bridge between Lys 6 and Glu 49 does not stabilize PFRD-XC4. The main chain to side chain salt bridge between the N-terminus and Glu 14 was, however, found to stabilize PFRD-XC4 by 1. 5 kcal mol(-)(1). The entropic cost of making a surface salt bridge involving the protein's backbone is reduced, since the backbone has already been immobilized upon protein folding.
Bone Marrow Osteoblastic Niche: A New Model to Study Physiological Regulation of Megakaryopoiesis (2009)

The mechanism by which megakaryocytes (Mks) proliferate, differentiate, and release platelets into circulation are not well understood. Growing evidence indicates that a complex regulatory mechanism, involving cellular interactions, composition of the extracellular matrix and physical parameters such as oxygen tension, may contribute to the quiescent or permissive microenvironment related to Mk differentiation and maturation within the bone marrow.
Examples (2016)

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Isolation and functional characterization of cofactors of RNA polymerase II transcription (1996)

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 1996.
Light extraction efficiency enhancement of GaN-based light emitting diodes by a ZnO current spreading layer (2009)

Gallium nitride (GaN) based light emitting diodes (LEDs) with a thick and high quality ZnO film as a current spreading layer grown by metal-source vapor phase epitaxy (MVPE) are fabricated successfully. Compared with GaN-based LEDs employing a Ni/Au or an indium tin oxide transparent current spreading layer, these LEDs show an enhancement of the external quantum efficiency of 93% and 35% at a forward current of 20 mA, respectively. The full width at half maximum of the ZnO (002) ω-scan rocking curve is 93 arcsec, which corresponds to a high crystal quality of the ZnO film. Optical microscopy and atomic force microscopy are used to observe the surface morphology of the ZnO film, and many regular hexagonal features are found. A spectrophotometer is used to study the different absorption properties between the ZnO film and the indium tin oxide film of the GaN LED. The mechanisms of the extraction quantum efficiency increase and the series resistance change of the GaN-based LEDs with ZnO transparent current spreading layers are analyzed.
Analysis and design of integrated electronic circuits (1980)

Semiconductors and the p-n Junction Diode The Junction Transistor The Field Effect Transistor Integrated Circuit Fabrication Graphical Analysis Linear Models for Electronic Devices Pulse and Large-Signal Models for Electronic Devices Fundamental Elements of Digital Systems Logic Families Sequential Circuits and Their Design Memories Small-Signal Untuned Amplifiers - Broadband Amplifiers Operational Amplifier Applications Operational Amplifier Circuitry - The Practical Operational Amplifier Untuned Power Amplifiers Feedback Amplifiers Bandpass Amplifiers Oscillators Power Supplies.
Systematic investigations on the reduction of 4-aryl-4-oxoesters to 1-aryl-1,4-butanediols with methanolic sodium borohydride (2010)

4-Aryl-4-oxoesters undergo facile reduction of both the keto and the ester groups with methanolic NaBH₄ at room temperature to yield the corresponding 1-aryl-1,4-butanediols whereas 4-alkyl-4-oxoesters furnish the corresponding 1,4-butanolides via selective reduction of the keto moiety. Results of a detailed and systematic investigation of the reaction are described.
Sharing across Multiple MapReduce Jobs (2014)

Large-scale data analysis lies in the core of modern enterprises and scientific research. With the emergence of cloud computing, the use of an analytical query processing infrastructure can be directly associated with monetary cost. MapReduce has been a popular framework in the context of cloud computing, designed to serve long-running queries (jobs) which can be processed in batch mode. Taking into account that different jobs often perform similar work, there are many opportunities for sharing. In principle, sharing similar work reduces the overall amount of work, which can lead to reducing monetary charges for utilizing the processing infrastructure. In this article we present a sharing framework tailored to MapReduce, namely, <tt>MRShare</tt>. Our framework, <tt>MRShare</tt>, transforms a batch of queries into a new batch that will be executed more efficiently, by merging jobs into groups and evaluating each group as a single query. Based on our cost model for MapReduce, we define an optimization problem and we provide a solution that derives the optimal grouping of queries. Given the query grouping, we merge jobs appropriately and submit them to MapReduce for processing. A key property of <tt>MRShare</tt> is that it is independent of the MapReduce implementation. Experiments with our prototype, built on top of Hadoop, demonstrate the overall effectiveness of our approach. <tt>MRShare</tt> is primarily designed for handling I/O-intensive queries. However, with the development of high-level languages operating on top of MapReduce, user queries executed in this model become more complex and CPU intensive. Commonly, executed queries can be modeled as evaluating pipelines of CPU-expensive filters over the input stream. Examples of such filters include, but are not limited to, index probes, or certain types of joins. In this article we adapt some of the standard techniques for filter ordering used in relational and stream databases, propose their extensions, and implement them through <tt>MRAdaptiveFilter</tt>, an extension of <tt>MRShare</tt> for expensive filter ordering tailored to MapReduce, which allows one to handle both single- and batch-query execution modes. We present an experimental evaluation that demonstrates additional benefits of <tt>MRAdaptiveFilter</tt>, when executing CPU-intensive queries in <tt>MRShare</tt>.
Make an impression by showing off your classroom… (2004)

A good display is not just down to aesthetics; it should showcase the real learning that takes place in a setting, says Ailsa Chapman.
Effects of sulfonylureas on the synthesis and secretion of plasminogen activator from bovine aortic endothelial cells. (1988)

The effects of sulfonylureas on the production of plasminogen activator (PA) and antiactivator (PAI) were investigated using bovine aortic endothelial cells. All compounds studied stimulated PA release (1.3- to 5.2-fold), with glipizide being the most potent, followed by tolazamide, chlorpropamide, and tolbutamide, in that order, while glyburide was the least effective. Both tissue-type and urokinase-type PA production was enhanced. Studies using metabolic inhibitors indicated that both RNA and protein syntheses are required for the sulfonylurea-mediated stimulation of PA release. In addition to continuous release of the two PAs, there was also a continuous release of a single PAI, which did not show an increase after the sulfonylureas. These results suggest that, in addition to their beneficial effects in the treatment of diabetes mellitus, some sulfonylurea compounds may also have significant thrombolytic effects. These results also suggest that pharmacological enhancement of PA production by vascular endothelial cells may be a promising antithrombotic mechanism.
A Delphic consensus assessment: imaging and biomarkers in gastroenteropancreatic neuroendocrine tumor disease management (2016)

The complexity of the clinical management of neuroendocrine neoplasia (NEN) is exacerbated by limitations in imaging modalities and a paucity of clinically useful biomarkers. Limitations in currently available imaging modalities reflect difficulties in measuring an intrinsically indolent disease, resolution inadequacies and inter-/intra-facility device variability and that RECIST (Response Evaluation Criteria in Solid Tumors) criteria are not optimal for NEN. Limitations of currently used biomarkers are that they are secretory biomarkers (chromogranin A, serotonin, neuron-specific enolase and pancreastatin); monoanalyte measurements; and lack sensitivity, specificity and predictive capacity. None of them meet the NIH metrics for clinical usage. A multinational, multidisciplinary Delphi consensus meeting of NEN experts (n = 33) assessed current imaging strategies and biomarkers in NEN management. Consensus (>75%) was achieved for 78% of the 142 questions. The panel concluded that morphological imaging has a diagnostic value. However, both imaging and current single-analyte biomarkers exhibit substantial limitations in measuring the disease status and predicting the therapeutic efficacy. RECIST remains suboptimal as a metric. A critical unmet need is the development of a clinico-biological tool to provide enhanced information regarding precise disease status and treatment response. The group considered that circulating RNA was better than current general NEN biomarkers and preliminary clinical data were considered promising. It was resolved that circulating multianalyte mRNA (NETest) had clinical utility in both diagnosis and monitoring disease status and therapeutic efficacy. Overall, it was concluded that a combination of tumor spatial and functional imaging with circulating transcripts (mRNA) would represent the future strategy for real-time monitoring of disease progress and therapeutic efficacy.
THE THERMAL DECOMPOSITION OF α-TOCOPHEROL (1937)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTTHE THERMAL DECOMPOSITION OF α-TOCOPHEROLE. FernholzCite this: J. Am. Chem. Soc. 1937, 59, 6, 1154–1155Publication Date (Print):June 1, 1937Publication History Published online1 May 2002Published inissue 1 June 1937https://pubs.acs.org/doi/10.1021/ja01285a508https://doi.org/10.1021/ja01285a508research-articleACS PublicationsRequest reuse permissionsArticle Views210Altmetric-Citations40LEARN 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 Get e-Alerts
RESEARCH ON THE AMENITY CHARACTERISTICS OF PORTSCAPE IN THE WHARF With the Yokohama Port Used as Example case (1993)

The purposes of this research are to examine the characteristics of portscape perceived as amenable to general citizens and to determine the distance suitable for viewing them. Thus, it is intended to identify the areas appropriate to be opened to residents.As a result of an on-the-spot investigation at the Port of Yokohama, it was clear that such amenity characteristics of ports are activity, safety, and unobstructed views. In this regard, specific factors responsible for these characteristics and the distance ensuring a clear recognition of these were successfully identified.
Skeletal Characterization of Smurf2-Deficient Mice and In Vitro Analysis of Smurf2-Deficient Chondrocytes (2016)

Overexpression of Smad ubiquitin regulatory factor 2 (Smurf2) in chondrocytes was reported to cause spontaneous osteoarthritis (OA) in mice. However, it is unclear whether Smurf2 is involved in bone and cartilage homeostasis and if it is required for OA pathogenesis. Here we characterized age-related changes in the bone and articular cartilage of Smurf2-deficient (MT) mice by microCT and histology, and examined whether reduced Smurf2 expression affected the severity of OA upon surgical destabilization of the medial meniscus (DMM). Using immature articular chondrocytes (iMAC) from MT and wild-type (WT) mice, we also examined how Smurf2 deficiency affects chondrogenic and catabolic gene expressions and Smurf2 and Smurf1 proteins upon TGF-β3 or IL-1β treatment in culture. We found no differences in cortical, subchondral and trabecular bone between WT and MT in young (4 months) and old mice (16-24 months). The articular cartilage and age-related alterations between WT and MT were also similar. However, 2 months following DMM, young MT showed milder OA compared to WT (~70% vs ~30% normal or exhibiting only mild OA cartilage phenotype). The majority of the older WT and MT mice developed moderate/severe OA 2 months after DMM, but a higher subset of aged MT cartilage (27% vs. 9% WT) remained largely normal. Chondrogenic gene expression (Sox9, Col2, Acan) trended higher in MT iMACs than WT with/without TGF-β3 treatment. IL-1β treatment suppressed chondrgenic gene expression, but Sox9 expression in MT remained significantly higher than WT. Smurf2 protein in WT iMACs increased upon TGF-β3 treatment and decreased upon IL-1β treatment in a dose-dependent manner. Smurf1 protein elevated more in MT than WT upon TGF-β3 treatment, suggesting a potential, but very mild compensatory effect. Overall, our data support a role of Smurf2 in regulating OA development but suggest that inhibiting Smurf2 alone may not be sufficient to prevent or consistently mitigate post-traumatic OA across a broad age range.
NAD‐malic enzyme from plants (1985)

NAD‐malic enzyme (NAD‐ME) is a primary regulatory enzyme for the metabolism of malate in plant mitochondria. NAD‐ME serves an anaplerotic function for the production of pyruvate, and provides CO 2 for refixation in the Calvin cycle in certain C 4 and Crassulacean acid metabolism plants. Clues regarding the mechanism of control of NAD‐ME in vivo come from numerous studies on the physical and kinetic properties of the enzyme. The kinetics are complex and are altered by the pH of the assay medium as well as by serveral effectors, including divalent cations. CoA, sulfate, acetyl CoA, and fructose 1,6‐bisphosphate (activators) and chloride, citrate, and bicarbonate (inhibitors). The enzyme is functional as a dimer, tetramer and octamer and the variation in kinetics is at least in part due to its association/dissociation.
Expression and signaling of the tyrosine kinase FGFR2b/KGFR regulates phagocytosis and melanosome uptake in human keratinocytes (2010)

Membrane and actin cytoskeleton dynamics during phagocytosis can be triggered and amplified by the signal transduction of receptor tyrosine kinases. The epidermal keratinocytes appear to use the phagocytic mechanism of uptake to ingest melanosomes released by the melanocytes and play a pivotal role in the transfer process. We have previously demonstrated that the keratinocyte growth factor KGF/FGF7 promotes the melanosome uptake through activation of its receptor tyrosine kinase FGFR2b/KGFR. The aim of the present study was to investigate the contribution of KGFR expression, activation, and signaling in regulating the phagocytic process and the melanosome transfer. Phagocytosis was analyzed in vitro using fluorescent latex beads on human keratinocytes induced to differentiate. Melanosome transfer was investigated in keratinocyte-melanocyte cocultures. KGFR depletion by small interfering RNA microinjection and overexpression by transfection of wild type or defective mutant KGFR were performed to demonstrate the direct effect of the receptor on phagocytosis and melanosome transfer. Colocalization of the phagocytosed beads with the internalized receptors in phagolysosomes was analyzed by optical sectioning and 3-dimensional reconstruction. KGFR ligands triggered phagocytosis and melanosome transfer in differentiated keratinocytes, and receptor kinase activity and signaling were required for these effects, suggesting that FGFR2b/KGFR expression/activity and PLCγ signaling pathway play crucial roles in phagocytosis.
A toolbox for power system dynamics and control engineering education and research (1992)

The design concept and use of the power system toolbox (PST), a Matlab-based power system dynamics simulation and control design package, are discussed. The motivation for developing the package was to provide a flexible environment for teaching power system simulation techniques and control design concepts to advanced undergraduate and graduate students, and for graduate students to perform research and development on power systems. The authors discuss the capabilities of PST and the software development philosophy. Sample applications are given. Some potential educational usage is suggested. The future enhancement to the package is outlined.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Radio proximity fuze design (1946)

The general principles governing the design of radio proximity fuzes are presented.
Run-time compilation of bytecode in wireless sensor networks (2010)

Recent work on virtual machines for wireless sensor networks has demonstrated the benefits of using a Java programming paradigm for resource constrained sensor networks. Results have shown that a virtual machine approach greatly suffers from interpretation overheads. We present run-time compilation of bytecode which leverages from a compact platform independent bytecode application encoding as well as an efficient program execution platform by converting bytecode to native code in situ.
A Bandit Approach to Price-Aware Energy Management in Cellular Networks (2017)

We introduce a reinforcement learning algorithm inspired by the combinatorial multi-armed bandit problem to minimize the time-averaged energy cost at individual base stations (BSs), powered by various energy markets and local renewable energy sources, over a finite-time horizon. The algorithm sustains traffic demands by enabling sparse beamforming to schedule dynamic user-to-BS allocation and proactive energy provisioning at BSs to make ahead-of-time price-aware energy management decisions. Simulation results indicate a superior performance of the proposed algorithm in reducing the overall energy cost, as compared with recently proposed cooperative energy management designs.
Effects of low concentrations of bisulfite-sulfite and nitrite on microorganisms (1978)

A wide range of microorganisms was tested to determine their sensitivity to low concentrations of bisulfite-sulfite and nitrite, solubility products of SO2 and NO2, respectively. Photosynthesis by blue-green algae (cyanobacteria) was more strongly inhibited by 0.1 mM bisulfite-sulfite and 1 mM nitrite at pH 6.0 than photosynthesis by eucaryotic algae and respiration of bacteria, fungi, and protozoa. At pH 7.7, blue-green algae were still more sensitive to bisulfite-sulfite and nitrite than eucaryotic algae, but the toxicity of bisulfite-sulfite and nitrite decreased as the pH increased. Photosynthesis by Anabaena flos-aquae at pH 6.0 was inhibited 25% by a bisulfite-sulfite concentration of 10 micrometer and 15% by a nitrite concentration of 50 micrometer. Photosynthesis by the blue-green alga, Lyngbya sp., was not exceptionally sensitive to chlorate and thiosulfate. Acetylene-reducing activity of Beijerinckia indica was completely inhibited by 0.1 mM bisulfite-sulfite at pH 4.0, the suppression being decreased with increasing pH.
Retrieval of volatile database output through hypermedia applications (2003)

This paper reports on research on the generation of hypermedia (Web) applications for querying multimedia databases. We have proposed a heuristic algorithm for generating navigational structures for multimedia database output, based on ideas from RMM. Here we discuss two extensions to our approach. The first extension concerns in more depth the generation of navigation for volatile database output. The semantics of the data are used to produce a navigational structure for the hypermedia presentation, while by adding elements to the query syntax we allow the user to influence this. The second extension deals with the automatic generation of a presentation for the multimedia database output. While many of the presentation issues can be settled at design time by the designer of the application, a number of issues should be tackled at query time. These issues concern the presentation of records and their relationships with other records.
The malonyl-CoA–long-chain acyl-CoA axis in the maintenance of mammalian cell function (1999)

Long-chain acyl-CoA esters have potent specific actions (e.g. on gene transcription, membrane trafficking) as well as non-specific ones (e.g. on phospholipid bilayers). They are synthesized on the cytosolic aspects of several intracellular membranes, to give rise to (a) cytosolic pool(s) to which a variety of enzymes and processes have access, including some localized in the nucleus. Their concentration in cells is highly regulated, interconversion with corresponding acylcarnitines being the most important mechanism involved. This reaction is catalysed by cytosol-accessible carnitine long-chain acyl (palmitoyl) transferase activities that are themselves located on multiple membrane systems. Regulation of these activities is through the inhibitory action of malonyl-CoA. Hence the existence of a potent malonyl-CoA-acyl-CoA axis through which many processes involved in the maintenance of mammalian cell function are regulated. The molecular, topographical and physiological interactions that make this possible are described and discussed.
Diminished responsibility: is it ‘substantial’? (1992)

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Opportunities and Challenges in Multi-Times-Programmable Floating-Gate Logic Non-Volatile Memories (2008)

Low bit count floating gate (FG) logic NVM (LNVM) developed in baseline logic process is finding increasing use in system-on-chip (SOC) ICs due to its low cost and absence of extra process integration needs. This paper reviews the opportunities this technology brings to the eNVM fields and the technical challenges it faces. It also demonstrates that FG logic NVM is scalable to have 50A tunneling oxide to store the charge at 65 nm CMOS technology node and beyond.
Architectures and technologies for enterprise application integration (2004)

Architects are faced with the problem of building enterprise scale information systems, with streamlined, automated internal business processes and Web-enabled business functions, all across multiple legacy applications. The underlying architectures for such systems are embodied in a range of diverse products known as enterprise application integration (EAI) technologies. In this paper, we highlight some of the major problems, approaches and issues in designing EAI architectures and selecting appropriate supporting technology. The tutorial presents a range of the common architectural patterns frequently used for EAI applications. It also explains service-oriented architectures as the current best practice architectural framework for EAI. It then describes the state-or-the-art in EAI technologies that support these architectural styles, and discusses some of the key design trade-offs involved when selecting an appropriate integration technology (including buy versus build decisions).