gebhart/patrepeval huggingface dataset:
Framework for Engineering Finite State Machines in Gene Regulatory Networks (2014)

Finite state machines are fundamental computing devices at the core of many models of computation. In biology, finite state machines are commonly used as models of development in multicellular organisms. However, it remains unclear to what extent cells can remember state, how they can transition from one state to another reliably, and whether the existing parts available to the synthetic biologist are sufficient to implement specified finite state machines in living cells. Furthermore, how complex multicellular behaviors can be realized by multiple cells coordinating their states with signaling, growth, and division is not well understood. Here, we describe a method by which any finite state machine can be built using nothing more than a suitably engineered network of readily available repressing transcription factors. In particular, we show the mathematical equivalence of finite state machines with a Boolean model of gene regulatory networks. We describe how such networks can be realized with a small class of promoters and transcription factors. To demonstrate the effectiveness of our approach, we show that the behavior of the coarse grained ideal Boolean network model approximates a fine grained delay differential equation model of gene expression. Finally, we explore a framework for the design of more complex systems via an example, synthetic bacterial microcolony edge detection, that illustrates how finite state machines could be used together with cell signaling to construct novel multicellular behaviors.
Decreased cytotoxicity of cis-diamminedichloroplatinum(II) by alpha-difluoromethylornithine depletion of polyamines in 9L rat brain tumor cells in vitro. (1982)

Before treatment with the cytotoxic drug cis-dichlorodiammineplatinum(II) (cis-platinum), 9L rat brain gliosarcoma cells grown in vitro were depleted of intracellular polyamines by alpha-difluoromethylornithine (DFMO; 10 mM, 48 hr), an enzyme-activated, irreversible inhibitor of the polyamine-synthetic enzyme ornithine decarboxylase. In contrast to studies that showed that the cytotoxicity of 1,3-bis (2-chloroethyl)-1-nitrosourea as measured by colony-forming efficiency is enhanced by DFMO depletion of intracellular polyamines, the cytotoxicity of cis-platinum was significantly decreased in polyamine-depleted 9L cells. At 10, 1, and 0.1% survival levels, the dose modification factors were 2.0 to 2.1. Addition of exogenous putrescine to polyamine-depleted 9L cells 24 hr before treatment with cis-platinum partially reversed this phenomenon. When 9L cells were treated either with DFMO and cis-platinum or with DFMO, putrescine, and cis-platinum for 1 hr, a time period that is too short for DFMO to affect intracellular polyamine levels, the cytotoxicity of cis-platinum was decreased, but to a significantly lesser extent than by the 48-hr DFMO pretreatment. Putrescine alone did not alter the cytotoxic effect of cis-platinum when administered either 24 or 1 hr before treatment. DFMO appears to affect cis-platinum cytotoxicity by two different mechanisms, the first mediated through polyamine depletion and the second through a direct interaction with cis-platinum.
An active headrest for personal audio (2006)

There is an increasing need for personal audio systems, which generate sounds that are clearly audible to one listener but are not audible to other listeners nearby. Of particular interest in this paper are listeners sitting in adjacent seats in aircraft or land vehicles. Although personal audio could then be achieved with headsets, it would be safer and more comfortable if loudspeakers in the seat headrests could be actively controlled to generate an acceptable level of acoustic isolation. In this paper a number of approaches to this problem are investigated, but the most successful involves a pair of loudspeakers on one side of the headrest, driven together to reproduce an audio signal for a listener in that seat and also to attenuate the pressures in the adjacent seat. The performance of this technique is investigated using simple analytic models and also with a practical implementation, tested in an anechoic chamber and a small room. It is found that significant attenuations, of between 5 and 25 dB, can be achieved in the crosstalk between the seats for frequencies up to about 2 kHz.
Peptides Derived from Fibronectin Type III Connecting Segments Promote Endothelial Cell Adhesion but Not Platelet Adhesion: Implications in Tissue-Engineered Vascular Grafts (2007)

The development of a completely tissue-engineered small-caliber prosthesis suitable for incorporation into an in vivo vascular network is fraught with many challenges, including overcoming resistance to endothelialization and susceptibility to thrombogenesis. In this work, recombinant human fibronectin-derived low-molecular-weight peptide fragments were studied for their ability to promote cell type-specific alpha(4) integrin-mediated adhesion. Two populations of primary human endothelial cells were examined and found to express alpha(4) integrin receptors on their surfaces; on the contrary, human platelets were not found to be expressers of alpha(4) integrins. A peptide fragment isolated from the variably spliced human fibronectin type III connecting segment-1 (CS-1) domain was determined to mediate statistically significant endothelial cell alpha(4) integrin-mediated adhesion. In contrast, the fibronectin type III CS-1 fragment did not support human platelet adhesion under physiological fluid shear conditions, although fully intact human fibronectin molecules supported shear-induced platelet adhesion. This suggests that platelets bind to fibronectin in regions not encompassing the CS-1 domain. In conclusion, this work has demonstrated that the low-molecular-weight peptide CS-1 could serve as a cell-selective adhesion mediator in the engineering of a more-compatible small-caliber vascular graft lumen interface.
Cytochrome P450 2E1 genotype and chlorzoxazone metabolism in healthy and alcoholic Caucasian subjects (1995)

Susceptibility to cancer or ethanol-related liver diseases may be associated with a large variability in cytochrome P450 2E1 activity. This variability may be of genetic origin or reflect environmental factors. To test the role of genetics, the phenotype and genotype of this enzyme were determined in 42 non-alcoholic and 74 alcoholic patients hospitalized for detoxification treatment. Chlorzoxazone metabolism was used to assess CYP2E1 phenotype. Restriction length fragment polymorphisms with Rsa I or Pst I, and Dra I endonucleases were used to determine the two mutant alleles, Pst I/Rsa I-c2 and Dra I-C. A significant gender difference in basal CYP2E1 activity was observed in non-smoking controls (p < 0.05) but not in alcoholics or smokers. Subjects heterozygous for the C or c2 mutated allele did not show any difference in CYP2E1 activity at the basal level, compared with the wild type homozygotes. Conversely, patients with the mutated genotype appeared less inducible than the others after ethanol induction (p < 0.01).
Dynamic economic dispatch: feasible and optimal solutions (2001)

Dynamic economic dispatch is an extension of the conventional economic dispatch problem that takes into consideration the limits on the ramp rate of the generating units. This paper examines the factors that affect the feasibility and optimality of solutions to this problem. It proposes two new solution methods. The first is guaranteed to find a feasible solution even when the load profile is nonmonotonic. The second is an efficient technique for funding the optimal solution. The results obtained with these methods are compared with those obtained using previously published methods.
Clinical and microbiological characteristics of communityacquired methicillin-resistant Staphylococcus aureus pneumonia (2012)

Methicillin-resistant <em>Staphylococcus aureus</em> (MRSA) infections now occur in healthy adults in community settings. We searched the PubMed database to identify relevant articles on the clinical presentation, epidemiology, virulence, and treatment of community-acquired MRSA (CA-MRSA) infections, including pneumonia. This information was summarized in a narrative review.MRSA infections cause approximately 30 infections per 100,000 people per year in the USA, and twenty percent of these infections are secondary to CA-MRSA. These community-acquired infections often involve the skin and subcutaneous tissue but can also involve visceral tissues such as the lung and bone. The overall mortality in patients with invasive disease is approximately 10%; it approaches 50% in patients with pneumonia. The bacterial isolates from these infections have the staphylococcal chromosome cassette <em>mec</em> types 4 and 5. This genetic characteristic produces beta-lactam resistance and helps distinguish these isolates from hospital- acquired MRSA, which usually have <em>mec</em> types 1-3. Some CA-MRSA isolates release the Panton-Valentine leukocidin (PVL), which causes neutropenia and tissue necrosis; other toxins also contribute to the virulence of these infections. Empiric therapy should include vancomycin or linezolid. CA-MRSA infections can have fulminant courses and high mortality rates. Physicians should consider these infections as possible emergencies with a high risk for organ system failure and shock.
Far-infrared reflectance spectra of some hexachlorotellurates and other hexachlorometallates (1971)

Far-i.r. reflectance spectra of M2IMCl6 complexes where M = Sn, Pt, or Te, have been used to estimate the half-bandwidths of the v3 vibration of the [MCl6]2– ions. The values are substantially lower than those found from absorption spectra of powdered samples but those for the tellurates are greater than those for the platinates and stannates. An earlier interpretation of the mull i.r. spectra is supported by these results.
Characterization of a Novel Negative Regulator (DOC-2/DAB2) of c-Src in Normal Prostatic Epithelium and Cancer (2003)

DOC-2/DAB2 is a potent tumor suppressor in many cancer types including prostate cancer. In prostate cancer, expression of DOC-2/DAB2 can inhibit its growth. Our recent studies demonstrate that DOC-2/DAB2 can suppress both protein kinase C and peptide growth factor-elicited signal pathways via the Ras-mitogen-activated protein kinase pathway. In this study, we further showed that the proline-rich domain of DOC-2/DAB2 could also interact with proteins containing the Src homology 3 domain, such as Src and Fgr. The binding of c-Src to DOC-2/DAB2 was enhanced in cells treated with growth factor, and this interaction resulted in c-Src inactivation. The c-Src inactivation was evidenced by the decreased tyrosine 416 phosphorylation of c-Src and reduced downstream effector activation. It appears that DOC-2/DAB2 can bind to Src homology 3 domain of c-Src and maintain it in an inactive conformation. Thus, this study provides a new mechanism for modulating c-Src in prostatic epithelium and cancer.
Electrochemical performance of Li(NMC)O2 cathode materials for Li-ion batteries (2010)

Won the first prize of Best Paper on Materials 2010 organized by Materials Division of Hong Kong Institution of Engineers (HKIE).
Piezotronic and Piezophototronic Effects (2010)

Owing to the polarization of ions in a crystal that has noncentral symmetry, a piezoelectric potential (piezopotential) is created in the material by applying a stress. The creation of piezopotential together with the presence of Schottky contacts are the fundamental physics responsible for a few important nanotechnologies. The nanogenerator is based on the piezopotential-driven transient flow of electrons in the external load. On the basis of nanomaterials in the wurtzite semiconductors, such as ZnO and GaN, electronics fabricated by using a piezopotential as a gate voltage are called piezotronics, with applications in strain/force/pressure-triggered/controlled electronic devices, sensors, and logic gates. The piezophototronic effect is a result of three-way coupling among piezoelectricity, photonic excitation, and semiconductor transport, which allows tuning and controlling of electro-optical processes by a strain-induced piezopotential.
Chemical sources of current. [Review of Russian book] (1981)

This book thoroughly illuminates general problems associated with the layout and operation of primary cells, storage batteries and electrochemical generators, and it describes various concrete types of chemical sources of current. The book is intended for engineers, technicians and scientists involved in the development, production and use of chemical current sources, college students, graduate students and instructors, and the numerous users of current sources in radiotechnical, instrument making, motor vehicle, aviation and ship building industry, power engineering and so on.
Redeposition—A serious problem in rf sputter etching of structures with micronmeter dimensions (1977)

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation H. W. Lehmann, L. Krausbauer, R. Widmer; Redeposition—A serious problem in rf sputter etching of structures with micronmeter dimensions. J. Vac. Sci. Technol. 1 January 1977; 14 (1): 281–284. https://doi.org/10.1116/1.569140 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAVS: Science & Technology of Materials Interfaces and ProcessingJournal of Vacuum Science and Technology Search Advanced Search |Citation Search
Alkylation of Amines by Esters and Lithium Aluminum Hydride. II (1962)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAlkylation of Amines by Esters and Lithium Aluminum Hydride. IIWilliam B. Wright Jr.Cite this: J. Org. Chem. 1962, 27, 3, 1042–1045Publication Date (Print):March 1, 1962Publication History Published online1 May 2002Published inissue 1 March 1962https://pubs.acs.org/doi/10.1021/jo01050a511https://doi.org/10.1021/jo01050a511research-articleACS PublicationsRequest reuse permissionsArticle Views424Altmetric-Citations28LEARN 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
Green's function for migration: Continuous recording geometry (2000)

Abstract Analytical formulas are derived to give the point scatterer responses for the zero-offset and nonzero-offset migration operators. These formulas are derived under the far-field approximation for a continuous distribution of sources and receivers, and are denoted as migration Green's functions. By specifying a homogeneous velocity model with irregular layers, these Green's functions can be used to quickly compute the synthetic migrated sections without having to compute the modeled data. Thus, these formulas provide a fundamental understanding of migration artifacts and their relationship to the image point location and source-receiver configuration. This understanding lays the foundation for the next step, elimination of these artifacts by migration deconvolution.
Precise deterministic change detection for smooth surfaces (2016)

We introduce a precise deterministic approach for pixel-wise change detection in images taken of a scene of interest over time. Our motivation is for applications such as artefact condition monitoring and structural inspection, where a common problem is the need to efficiently and accurately identify subtle signs of damage and deterioration. The approach we describe is designed to compensate for the three most common sources of nuisance variation encountered when tackling the problem of change detection, namely: viewpoint variation due to camera motion between images, photometric variation due to lighting differences, and changes in image resolution/focal settings. To tackle viewpoint variation, particularly in areas of low texture, we propose the use of the generalised PatchMatch (PM) correspondence algorithm to compute a dense flow field. The flow field is regularized using a Thin Plate Spline (TPS) model which assumes a smooth underlying geometry and allows registration to be interpolated precisely through areas of low texture or uncertain flow. To compensate for low-frequency lighting variation, we fit a second TPS model to the photometric differences between registered images. Finally, to account for changes in focal settings, we estimate and apply a blurring kernel via optimisation over image differences. We provide a thorough evaluation of the performance of our method on an illustrative toy dataset and on two recent, real-world inspection datasets. Our approach performs favourably versus state-of-the-art baselines in both cases, while remaining relatively transparent to understand and simple to compute.
Computational Delay and Free Mode Environment Design for Haptic Display (1999)

Abstract This paper develops a technique for the design of haptic systems that guarantees the absence of oscillations. Valid components of the haptic system are general devices, virtual couplings and virtual environments, linear or nonlinear, however the current work focuses on linear components. Once developed, the method will be applied to a haptic system to investigate stability conditions for passive environments versus those for non-passive environments. Examples of computational delay and free mode environment design will be developed as meaningful design problems that fall into the category of non-passive environments.
Gates, beads and Danubians. The defences and garrison of the auxiliary fort at Castell Collen: a speculative relationship (2006)

Davies, Jeffrey, 'Gates, beads and Danubians. The defences and garrison of the auxiliary fort at Castell Collen: a speculative relationship', Bayerische Vorgeschichtsblatter (2006) 71 pp.3-13 RAE2008
Modeling of transient modal instability in fiber amplifiers (2013)

A model of transient modal instability in fiber amplifiers is presented. This model combines an optical beam propagation method that incorporates laser gain through local solution of the rate equations and refractive index perturbations caused by the thermo-optic effect with a time-dependent thermal solver with a quantum defect heating source term. This model predicts modal instability a fiber amplifier operating at 241, 270, and 287 Watts of output power characterized by power coupling to un-seeded modes, the presence of stable and unstable regions within the fiber, and rapid intensity variations along the fiber. The instability becomes more severe as the power is increased.
Deterministic Memory Abstraction and Supporting Multicore System Architecture (2017)

Poor time predictability of multicore processors has been a long-standing challenge in the real-time systems community. In this paper, we make a case that a fundamental problem that prevents efficient and predictable real-time computing on multicore is the lack of a proper memory abstraction to express memory criticality, which cuts across various layers of the system: the application, OS, and hardware. We, therefore, propose a new holistic resource management approach driven by a new memory abstraction, which we call Deterministic Memory. The key characteristic of deterministic memory is that the platform - the OS and hardware - guarantees small and tightly bounded worst-case memory access timing. In contrast, we call the conventional memory abstraction as best-effort memory in which only highly pessimistic worst-case bounds can be achieved. We propose to utilize both abstractions to achieve high time predictability but without significantly sacrificing performance. We present deterministic memory-aware OS and architecture designs, including OS-level page allocator, hardware-level cache, and DRAM controller designs. We implement the proposed OS and architecture extensions on Linux and gem5 simulator. Our evaluation results, using a set of synthetic and real-world benchmarks, demonstrate the feasibility and effectiveness of our approach.
Domains, Motifs, and Scaffolds: The Role of Modular Interactions in the Evolution and Wiring of Cell Signaling Circuits (2006)

Living cells display complex signal processing behaviors, many of which are mediated by networks of proteins specialized for signal transduction. Here we focus on the question of how the remarkably diverse array of eukaryotic signaling circuits may have evolved. Many of the mechanisms that connect signaling proteins into networks are highly modular: The core catalytic activity of a signaling protein is physically and functionally separable from molecular domains or motifs that determine its linkage to both inputs and outputs. This high degree of modularity may make these systems more evolvable-in principle, novel circuits, and therefore highly innovative regulatory behaviors, can arise from relatively simple genetic events such as recombination, deletion, or insertion. In support of this hypothesis, recent studies show that such modular systems can be exploited to engineer nonnatural signaling proteins and pathways with novel behavior.
Kerr Enhancement by Layer Modulation in Co/Pt Multilayers (1992)

Thus far, a good Kerr hysteresis loop has been obtained only for thickness ratios of Co to Pt lower than 0.6 in Co/Pt multilayers. It has been found in this study that perfect squareness can be obtained for ultrathin films even with a high thickness ratio of t Co / t Pt =1. This is caused by diminished magnetostatic energy. Furthermore, layer-modulated structures were investigated in order to increase the Kerr rotation angle. The Co/Pt multilayers were prepared by two-source rf-magnetron sputtering. Co/Pt multilayers with perfect squareness were deposited with a Pt interlayer, which resulted in excellent magneto-optical properties. In particular, the Kerr rotation angle measured from the glass-substrate side showed a very large value, 0.73 degrees. This Kerr enhancement is due to optical interference and multiple reflection. On the other hand, another interesting phenomenon was also obtained. Kerr hysteresis showed characteristic stepwise hysteresis loops when the interlayer Pt thickness was increased. Such layer-modulated multilayers have potentiality for high-density magneto-optical recording.