gebhart/patrepeval huggingface dataset:
Fast and Efficient Strategies for Cubic and Non-Cubic Allocation in Hypercube Multiprocessors (1993)

A new approach for dynamic processor allo cation in hypercube multiprocessors which sup ports a multi-user environment is proposed. A dynamic binary tree is used for processor allo cation along with an array of free lists. Two al gorithms are proposed based on this approach that are capable of handling cubic as well as non-cubic allocation efficiently. The time com plexities for both allocation and deallocation are shown to be polynomial; orders of mag nitude improvement over the existing expo nential and even super-exponential algorithms. Unlike the existing strategies, the proposed strategies are best-fit strategies and do not ex cessively fragment the hypercube. Simulation results indicate that the proposed strategies outperform the existing ones in terms of pa rameters such as average delay in honoring a request, average allocation time and average deallocation time.
Multiple-alphabet amino acid sequence comparisons of the immunoglobulin kappa-chain constant domain. (1985)

We compare the amino acid sequences of the constant domains of the immunoglobulin kappa chain of human, mouse, and rabbit by using four classification schemes ("alphabets") of the 20 amino acids based on their chemical, functional, charge, and structural properties. The comparison reveals three regions of pronounced similarity across the three species, independent of allotype. Two of these regions (residues 65-73 and 99-103) entail a high degree of identity at the DNA level and are distinguished from the rest of the constant domain in codon usage and in the dinucleotide sequence at abutting sites of adjacent codons. Residues 22-29 are highly conserved among the three species in the chemical and functional alphabets but do not show any three-sequence significant amino acid block identities. These results are discussed in terms of transcript processing, effector functions, and structural interactions within the constant domain and with the heavy chain.
A sound projector for acoustic tomography and global ocean monitoring (2003)

Long-range underwater acoustic systems, such as those used in ocean acoustic tomography, require low-frequency signals covering a broad frequency band. To meet this requirement, a novel design based on a tunable narrow-band high-efficiency sound projector has been used. The projector transmits a frequency sweep signal by mechanically tuning a resonator tube (or organ pipe) to match the frequency and phase of a reference signal. The resonator tube projector consists of a symmetrical pressure-balanced Tonpilz driver placed between two coaxially mounted tubes. The Tonpilz acoustic driver is composed of two pistons separated by preloaded ceramic stacks. The resonant tube is a simple, efficient, narrow-band, medium-output projector that operates at any ocean depth. Both projector tubes have slots (or vents) which are progressively covered or uncovered by sliding coaxial tubular sleeves. The frequency varies with the sleeve position. A computer-controlled electromechanical actuator moves the cylindrical sleeves along the tubes, keeping the projector in resonance at the instantaneous frequency of a swept frequency signal. The actuator smoothly tunes the resonator tube frequency in a bandwidth of 200 to 300 Hz during a 135-s transmission. A computer synthesizes the linear frequency-modulated signal; compares the phase between transmitted and reference signals; and, using a phase-lock loop (PLL) system, keeps the resonator tube frequency in resonance with the driver frequency. The estimated PLL precision is better than 3° phase error. The system was analyzed by means of finite element analysis and electrical equivalent circuit simulation. The projector prototype was first tested at the Woods Hole Oceanographic Institution (WHOI) dock in Woods Hole, MA and later in the Pacific Ocean during a voyage of the R/V "Point Sur" in November 2001.
Revealing the reversible rotation of magnetization in exchange-coupled composite media switching (2009)

We present a study of the magnetic reversal mechanism for exchange coupled composite perpendicular media, i.e., hard granular layer/exchange-coupling layer (ECL)/soft layer (SL) systems, without soft underlayer. Using a vibrating sample magnetometer, the out-of-plane and in-plane components of the magnetization are monitored simultaneously, while sweeping an external out-of-plane magnetic field. The in-plane signal reveals the reversible rotation of the magnetization during the switching process. The amplitude of this rotation is correlated with the variations in coercivity and angular dependence of the remanent coercivity for different ECL and SL thicknesses.
Spectral interference in multiplexed volume Bragg gratings: theoretical calculations and experimental verification (2014)

Multiplexed volume Bragg gratings can be applied to many types of broad- and narrowband spectral systems. However, there are often deleterious side effects to combining several gratings into a single holographic optical element, including loss of efficiency in diffracted waves of interest and the introduction of spurious waves. Design of these spectral systems requires analysis methods that are flexible and efficient and that take these side effects into account. We present a matrix-based algorithm for determining diffraction efficiencies of significant coupled waves in these multiplexed grating Holographic optical elements (HOEs). Several carefully constructed experiments with spectrally multiplexed gratings in dichromated gelatin verify our conclusions.
Synthesis of α‐Substituted Fosmidomycin Analogues as Highly Potent Plasmodium falciparum Growth Inhibitors. (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Understanding the performance of streaming applications deployed on hybrid systems (2008)

Significant performance gains have been reported by exploiting the specialized characteristics of hybrid computing architectures for a number of streaming applications. While it is straightforward to physically construct these hybrid systems, application development is often quite difficult. We have built an application development environment, Auto-Pipe, that targets streaming applications deployed on hybrid architectures. Here, we describe some of the current and future characteristics of the Auto-Pipe environment that facilitate an understanding of the performance of an application that is deployed on a hybrid system.
High-level real-time programming in Java (2005)

Real-time systems have reached a level of complexity beyond the scaling capability of the low-level or restricted languages traditionally used for real-time programming.While Metronome garbage collection has made it practical to use Java to implement real-time systems, many challenges remain for the construction of complex real-time systems, some specific to the use of Java and others simply due to the change in scale of such systems.The goal of our current research is the creation of a comprehensive Java-based programming environment and methodology for the creation of complex real-time systems. Our goals include construction of a provably correct real-time garbage collector capable of providing worst case latencies of 100 μs, capable of scaling from sensor nodes up to large multiprocessors; specialized programming constructs that retain the safety and simplicity of Java, and yet provide sub-microsecond latencies; the extension of Java's "write once, run anywhere" principle from functional correctness to timing behavior; on-line analysis and visualization that aids in the understanding of complex behaviors; and a principled probabilistic analysis methodology for bounding the behavior of the resulting systems.While much remains to be done, this paper describes the progress we have made towards these goals.
Supplementary Tables 1-2, Figures 1-6 from HB-EGF and PDGF Mediate Reciprocal Interactions of Carcinoma Cells with Cancer-Associated Fibroblasts to Support Progression of Uterine Cervical Cancers (2023)

&lt;p&gt;PDF file - 428K&lt;/p&gt;
Two isoforms of Saccharomyces cerevisiae glutaredoxin 2 are expressed in vivo and localize to different subcellular compartments (2002)

Glutaredoxin (Grx)2 from Saccharomyces cerevisiae is a member of the two-cysteine (dithiol) subfamily of Grxs involved in the defence against oxidative stress in yeast. Recombinant yeast Grx2p, expressed in Escherichia coli, behaves as a ‘classical’ Grx that efficiently catalyses the reduction of hydroxyethyl disulphide by GSH. Grx2p also catalyses the reduction of GSSG by dihydrolipoamide with even higher efficiency. Western blot analysis of S. cerevisiae crude extracts identifies two isoforms of Grx2p of 15.9 and 11.9kDa respectively. The levels of these two isoforms reach a peak during the exponential phase of growth in normal yeast extract/peptone/dextrose ('YPD') medium, with the long form predominating over the short one. From immunochemical analysis of subcellular fractions, it is shown that both isoforms are present in mitochondria, but only the short one is detected in the cytosolic fraction. On the other hand, only the long form is prominent in microsomes. Mitochondrial isoforms should represent the processed and unprocessed products of an open reading frame (YDR513W), with a putative start codon 99bp upstream of the GRX2 start codon described thus far. These results indicate that GRX2 contains two in-frame start codons, and that translation from the first AUG results in a product that is targeted to mitochondria. The cytosolic form would result either by initiation from the second AUG, or by differential processing of one single translation product.
CRISPR/Cas9 for Human Genome Engineering and Disease Research (2016)

The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) system, a versatile RNA-guided DNA targeting platform, has been revolutionizing our ability to modify, manipulate, and visualize the human genome, which greatly advances both biological research and therapeutics development. Here, we review the current development of CRISPR/Cas9 technologies for gene editing, transcription regulation, genome imaging, and epigenetic modification. We discuss the broad application of this system to the study of functional genomics, especially genome-wide genetic screening, and to therapeutics development, including establishing disease models, correcting defective genetic mutations, and treating diseases.
The Development of a Postmodern Self: A Computer-Assisted Comparative Analysis of Personal Documents. (1990)

Illustrations Introduction The Background of the Postmodern Self: Industrial and Postindustrial Society Speculations on a New Culture and Overdeveloped Modernism The Challenge of Studying Self and Social Change The Use of Personal Documents in Social Science Research Qualitative Analysis of Personal Documents: From Resolution to Realization The Computer-Assisted Analysis of Diaries: Self and Social Change Quantitive Analysis of Personal Documents: Institution vs. Impulse/Product vs. Process The Postmodern Self: Summary and Discussion Recasting the Theory: From Modern to Postmodern Self, Therapeutic Ethic, and Organizational Process Appendices: A: Content Analysis Dictionary B: Diary Bibliographic Sources Not Cited in Text Bibliography Index
Preparation of optically active 6′-fluorocarbocyclic nucleosides utilising an enantiospecific enzyme-catalysed Baeyer–Villiger type oxidation (1990)

M. S. Levitt, R. F. Newton, S. M. Roberts and A. J. Willetts, J. Chem. Soc., Chem. Commun., 1990, 619 DOI: 10.1039/C39900000619
Exploration of Structure-Function Relationships in Human Factor VIII by Site-directed Mutagenesis (1986)

Hemophilia A is an X-linked bleeding disorder (which occurs in ∼ 10-20 males in every 100,000) caused by deficiency or abnormality of a particular clotting protein, factor VIII. Afflicted individuals suffer episodes of uncontrolled bleeding and are currently treated with concentrates rich in factor VIII derived from human plasma. The available therapy, although reasonably effective, is very costly and is associated with a finite risk of infection.
Fabrication of a tungsten master stamp using self-ordered porous alumina (2005)

We describe the preparation of a tungsten pillar nanoimprint stamp without the use of lithography and etching techniques. Structures with heights of 15 nm were prepared on the basis of self-ordered porous alumina templates and this was followed by DC sputtering of tungsten. The stamp was successfully used to prepare an aluminium surface to obtain highly ordered porous anodic alumina films after a single anodization step. The preparation efficiency for highly ordered porous alumina was dramatically improved as compared to the more conventional two-step anodization-strip-anodization method, as a sacrificial layer with a thickness of a few hundred micrometres was not required. In addition, by fractal calculations, we have evaluated the degree of ordering of the asperities on the nanoimprint master stamp.
Gold Electrodes Wired for Coupling with the Deeply Buried Active Site of Arthrobacter globiformis Amine Oxidase (2003)

Diethylaniline-terminated oligo(phenyl-ethynyl)-thiol (DEA-OPE-SH) wires on Au-bead electrodes facilitate electron tunneling to and from the deeply buried topaquinone (TPQ) cofactor in Arthrobacter globiformis amine oxidase (AGAO). Reversible cyclic voltammograms were observed when AGAO was adsorbed onto this DEA-OPE-SAu surface: the 2e-/2H+ reduction potential is -140 mV versus SCE.
M1 muscarinic receptor is a key target of neuroprotection, neuroregeneration and memory recovery by i-Extract from Withania somnifera (2019)

Memory loss is one of the most tragic symptoms of Alzheimer's disease. Our laboratory has recently demonstrated that 'i-Extract' of Ashwagandha (Withania somnifera) restores memory loss in scopolamine (SC)-induced mice. The prime target of i-Extract is obscure. We hypothesize that i-Extract may primarily target muscarinic subtype acetylcholine receptors that regulate memory processes. The present study elucidates key target(s) of i-Extract via cellular, biochemical, and molecular techniques in a relevant amnesia mouse model and primary hippocampal neuronal cultures. Wild type Swiss albino mice were fed i-Extract, and hippocampal cells from naïve mice were treated with i-Extract, followed by muscarinic antagonist (dicyclomine) and agonist (pilocarpine) treatments. We measured dendritic formation and growth by immunocytochemistry, kallikrein 8 (KLK8) mRNA by reverse transcription polymerase chain reaction (RT-PCR), and levels of KLK8 and microtubule-associated protein 2, c isoform (MAP2c) proteins by western blotting. We performed muscarinic receptor radioligand binding. i-Extract stimulated an increase in dendrite growth markers, KLK8 and MAP2. Scopolamine-mediated reduction was significantly reversed by i-Extract in mouse cerebral cortex and hippocampus. Our study identified muscarinic receptor as a key target of i-Extract, providing mechanistic evidence for its clinical application in neurodegenerative cognitive disorders.
Surface-Coil Magnetic Resonance Imaging of the Internal Auditory Canal (1985)

Computed tomography is effective for detecting acoustic neuromas, but not for resolving individual nerves in the internal auditory canal. Surface-coil magnetic resonance (MR) images of the internal auditory canal were obtained using a 1.5 T superconducting magnet, a 13.5-cm-diameter surface coil, 3- and 5-mm-thick slices, and partial-saturation pulse sequences. Cranial nerves VII and VIII (three branches) were identified on MR images in volunteers and on corresponding cryomicrotomic sections. The nerves were obscured in one patient with an acoustic neuroma. Because high-resolution surface-coil images can demonstrate specific nerves in the internal auditory canal, MR should be a sensitive study to evaluate cranial nerves VII and VIII in patients with facial paralysis and neurosensory hearing loss that is congenital or caused by small acoustic neuromas.
Search for weakly decaying Λn‾ and ΛΛ exotic bound states in central Pb–Pb collisions at sNN=2.76 TeV (2015)

We present results of a search for two hypothetical strange dibaryon states, i.e. the H-dibaryon and the possible n bound state. The search is performed with the ALICE detector in central (0-10%) Pb-Pb collisions at s NN = 2.76 TeV, by invariant mass analysis in the decay modes n d + and Hdibaryon p -. No evidence for these bound states is observed. Upper limits are determined at 99% confidence level for a wide range of lifetimes and for the full range of branching ratios. The results are compared to thermal, coalescence and hybrid UrQMD model expectations, which describe correctly the production of other loosely bound states, like the deuteron and the hypertriton.
Characterization of DNA-binding proteins that recognize the replication origin of the rRNA genes of Tetrahymena thermophila (1993)

Proteins that bind to specific sequences in replication origins have been shown to be important components of both prokaryotic and eukaryotic DNA replication systems. An origin of DNA replication is located within the 5' non-transcribed spacer region of the rRNA genes (rDNA) of Tetrahymena thermophila. Previous work has shown that several cis-acting mutations responsible for rDNA replication defects lie in upstream repeats of a transcriptional promoter element, the Type I repeat. Using FE(II)EDTA cleavage footprinting and gel-mobility shift assays, I identified and characterized two distinct DNA-binding activities that interact with the Type I repeat. One of these activities, designated ds-TIBF, binds preferentially to duplex DNA whereas the other, ssA-TIBF, binds preferentially to single-stranded DNA. Competition studies revealed that although ds-TIBF binds with high affinity to Type I sequences, it has only moderate sequence specificity and binds with high affinity to other duplex oligonucleotides containing dA/T stretches of greater than 6 nucleotides. In contrast, ssA-TlBF does not bind to generally A-rich oligonucleotides, but specifically interacts with single-stranded oligonucleotides corresponding to the Type I repeat. UV crosslinking of the partially purified protein to A-rich strand oligonucleotides followed by SDS gel electrophoresis demonstrated the binding activity of ssA-TIBF is associated with a polypeptide of
Total acknowledgements (extended abstract) (1998)

End-to-end data transport protocols have two main functions: error recovery and congestion control. The information required by the sender to perform these functions is provided by acknowledgements (ACKs) from the receiver. The Internet transport protocol, TCP/IP, uses cumulative acknowledgements (CACKs), which provide a robust but minimal mechanism for error recovery which is inadequate for heterogeneous networks with random loss. Furthermore, TCP's congestion control mechanism is based on counting ACKs, and is therefore vulnerable to loss of ACKs on the reverse path, particularly when the latter may be slower than the forward path, as in asymmetric networks. The contributions of this paper are as follows:(a) We show that a simple enhancement of CACK provides sufficient information for end-to-end congestion control. We term this ACK format total ACKs (TACKs).(b) We devise a novel ACK format that uses TACKs for congestion control, and negative ACKs (NACKs) for efficient error recovery. Typically, the main concern with NACKs is that of robustness to ACK loss, and we address this using an implementation that provides enough redundancy to provide such robustness.(c) We use the TACK+NACK acknowledgement format as the basis for a new transport protocol that provides efficient error recovery and dynamic congestion control. The protocol provides large performance gains over TCP in an environment with random loss, and is robust against loss of ACKs in the reverse path. In particular, the protocol gives high throughput upto a designed level of random loss, independent of the bandwidth-delay product. This is in contrast to TCP, whose throughput deteriorates drastically if the random loss probability is higher than the inverse square of the bandwidth-delay product.
Demand-Aware Onboard Payload Processor Management for High Throughput NGSO Satellite Systems (2023)

High-Throughput Satellite (HTS) systems with digital payload technology have been identified as a key enabler to support 5G/6G high-data connectivity with wider coverage area. The satellite community has extensively explored resource allocation methods to achieve this target. Typically, these methods do not consider the intrinsic architecture of the flexible satellite digital payload, which consists of multiple processors responsible for receiving, processing, and transmitting the signals. This paper presents a demand-aware onboard processor management scheme for broadband Non-Geostationary (NGSO) satellites. In this context, we formulate an optimization problem to minimize the number of active on-board processors while meeting the system constraints and user requirements. As the problem is non-convex, we solve it in two steps. First, we transform the problem into demand-driven bandwidth allocation while fixing the number of processors. Second, using the bandwidth allocation solution, we determine the required number of processors with two methods: 1) sequential optimization with the Branch & Bound method and 2) Bin Packing with Next Fit, First Fit, and Best Fit methods. Finally, we demonstrate the proposed methods with extensive numerical results. It is shown that the Branch & Bound, Best Fit, and First Fit methods manage the processors better than the Next Fit method. Furthermore, Branch & Bound requires fewer processors than the above methods.
NEMS (Nanoelectromechanicsl Systems) Networks: A Novel Validation Platform for Controlling Interconnected Dynamical Networks (2015)

Abstract : We review the experimental role NanoElectroMechanical System (NEMS) networks play vis a vis the MURIs scientific and validation goals which target new theoretical understanding of the dynamics of large-scale interconnected networks and their control. Our plans for NEMS networks are substantially updated based on our theoretical and experimental results during the MURIs first two years, providing a clear roadmap for the coming years that discusses relative benefits and costs. For example, we briefly compare how NEMS networks compare to alternative, potential validation platforms, including one based on Field-Programmable Gate Arrays (FPGAs). We also provide a relatively detailed outline of system-on-chip implementation of large-scale NEMS networks that will allow us to explore the nonlinear dynamics, statistical mechanics, and control of very large oscillator networks.