gebhart/patrepeval huggingface dataset:
Structure-activity study of the actions of camptothecin derivatives on mammalian topoisomerase I: evidence for a specific receptor site and a relation to antitumor activity. (1989)

Twenty-two compounds related to camptothecin, a known inhibitor of eukaryotic topoisomerase I, were studied. The following effects on the actions of topoisomerase I were observed and were well correlated among most of the compounds studied: (a) inhibition of the first-order rate of relaxation of supercoiled DNA; (b) conversion of supercoiled DNA to nicked circles; and (c) single-strand cleavage of linear DNA at specific sites. The locations of the stimulated cleavage sites were the same for all of the active derivatives. Stereochemistry and the positions of substituents were found to be crucial for the presence or absence of effects on topoisomerase I, indicating that the compounds interact with an asymmetrical receptor site on the enzyme or enzyme-DNA complex. From the structure-activity relations, the regions of interaction between the camptothecin ring system and the receptor site were inferred. Striking correlations were observed between activity against topoisomerase I and reported activity against murine leukemias, indicating that an action on topoisomerase I is responsible for the antitumor activity of the camptothecins.
Time Course Profile of Serum Trypsinogen-2 and Trypsin-2-a1-Antitrypsin in Patients with Acute Pancreatitis (2000)

The time course profile of trypsinogen-2 and trypsin-2-alpha1-antitrypsin is favorable for diagnosing acute pancreatitis. The elevation starts within hours after the onset of the disease and it is very steep. Both markers remain elevated longer than amylase and the magnitude of the elevation correlates with the severity of the disease. This is further evidence to support the use of trypsinogen-2 and trypsin-2-alpha1-antitrypsin for the evaluation of patients suspected of having acute pancreatitis.
Series of Novel and Highly Potent Cyclic Peptide PCSK9 Inhibitors Derived from an mRNA Display Screen and Optimized via Structure-Based Design (2020)

Proprotein convertase subtilisin-like/kexin type 9 (PCSK9) is a key regulator of plasma LDL-cholesterol (LDL-C) and a clinically validated target for the treatment of hypercholesterolemia and coronary artery disease. In this paper, we describe a series of novel cyclic peptides derived from an mRNA display screen which inhibit the protein-protein interaction between PCSK9 and LDLR. Using a structure-based drug design approach, we were able to modify our original screening lead <b>2</b> to optimize the potency and metabolic stability and minimize the molecular weight to provide novel bicyclic next-generation PCSK9 inhibitor peptides such as <b>78</b>. These next-generation peptides serve as a critical foundation for continued exploration of potential oral, once-a-day PCSK9 therapeutics for the treatment of cardiovascular disease.
<title>Multilayer coated optics for an alpha-class extreme ultraviolet lithography system</title> (1999)

We present the results of coating the first set of optical elements for an alpha-class extreme-ultraviolet (EUV) lithography system, the Engineering Test Stand (ETS). The optics were coated with Mo/Si multilayer mirrors using an upgraded DC-magnetron sputtering system. Characterization of the near-normal incidence EUV reflectance was performed using synchrotron radiation from the Advanced Light Source at the Lawrence Berkeley National Laboratory. Stringent requirements were met for these multilayer coatings in terms of reflectance, wavelength matching among the different optics, and thickness control across the diameter of each individual optic. Reflectances above 65% were achieved at 13.35 nm at near-normal angles of incidence. The run-to-run reproducibility of the reflectance peak wavelength was maintained to within 0.4%, providing the required wavelength matching among the seven multilayer-coated optics. The thickness uniformity (or gradient) was controlled to within {+-}0.25% peak-to-valley (P-V) for the condenser optics and {+-}0.1% P-V for the four projection optics, exceeding the prescribed specification for the optics of the ETS.
Traffic Signal Phase and Timing Estimation From Low-Frequency Transit Bus Data (2014)

The objective of this paper is to demonstrate the feasibility of estimating traffic signal phase and timing from statistical patterns in low-frequency vehicular probe data. We use a public feed of bus location and velocity data in the city of San Francisco, CA, USA, as an example data source. We show that it is possible to estimate, fairly accurately, cycle times and the duration of reds for fixed-time traffic lights traversed by buses using a few days' worth of aggregated bus data. Furthermore, we also estimate the start of greens in real time by monitoring the movement of buses across intersections. The results are encouraging, given that each bus sends an update only sporadically ( $\approx$ every 200 m) and that bus passages are infrequent (every 5-10 min) . When made available on an open server, such information about the traffic signals' phase and timing can be valuable in enabling new fuel efficiency and safety functionalities in connected vehicles. Velocity advisory systems can use the estimated timing plan to calculate velocity trajectories that reduce idling time at red signals and therefore improve fuel efficiency and lower emissions. Advanced engine management strategies can shut down the engine in anticipation of a long idling interval at red. Intersection collision avoidance and active safety systems could also benefit from the prediction.
Servicing “mice”-streaming queries as a service (2013)

Processing streaming queries at scale has received a lot of attention recently. Systems, such as S4, Storm, Photon, MillWheel, and Kinesis, can efficiently execute (“elephant”) queries that process streams with high rates, and typically scale-out the execution of each query. We envision a platform in the opposite side of the spectrum. Our queries process relatively slower streams, but the challenge is to handle very high density of queries per server. Such a system democratizes the access to a streaming platform, and enable “mice” queries, on behalf of users, to consume stream data, e.g. news, weather, travel related information, and so on. A challenging problem for the design of such a system is how to place queries among available servers. On one hand, we expect balanced workload among servers. On the other hand, we expect queries are packed into servers such that the network traffic is minimized by reducing the chance of sending identical data streams to multiple servers. This trade-off makes it hard to effectively place queries into servers. When we consider queries subscribing to more than one sources and query/server dynamics, this problem becomes even harder. In this paper, we formalize the problem of placing “mice” queries into the servers of a streaming platform. We propose approximation algorithms and derive approximation bounds for the cases, including (1) the offline case where queries are stable and known ahead of time, akin to an “oracle”, and (2) the online case without departures and known query popularities.For the general online problem, we propose effective heuristic algorithms. An extensive set of experiments demonstrate that the proposed algorithms provide good performance in a wide-range of scenarios.
The separate contribution of head-shadow and binaural interactions to directional hearing in noise (1993)

A replication of Bronkhorst and Plomp [J. Acoust. Soc. Am. 83, 1508–1516 (1988)] was undertaken to study the separate contributions of interaural level differences (ITDs); produced by head shadow, and interaural time differences (ITDs), which produce binaural interactions, to directional hearing in noise. Digital filtering of speech and noise signals was performed using head-related transfer functions (HRTFs) measured on a KEMAR mannequin to simulate sound field conditions under headphones. Speech materials from the hearing in noise test (HINT) were presented at a simulated 0-deg azimuth, while a noise signal matched to the spectral shape of the speech was filtered to include the ILDs and ITDs from either a 0-, 90-, or 270-deg presentation, including mixed combinations, e.g., 0-deg ILDs with 90-deg ITDs. Results from 19 normal hearing subjects showed the ILDs alone benefited the listener slightly more [3.97-dB improvement in sentence speech reception threshold (sSRT) versus a 0-deg condition] than ITDs alone (3.22-dB improvement in sSRT), as compared to 6.21-dB improvement in sSRT when both ILDs and ITDs are present. If the sSRT is calculated relative to the noise level in the shadowed ear, the ITDs alone produced the same sSRT as ITDs and ILDs together. Data from hearing impaired listeners will also be presented.
ChemInform Abstract: Targeted Polymeric Therapeutic Nanoparticles: Design, Development and Clinical Translation (2012)

Abstract Review: 444 refs.
SERS nano-imaging probes for characterizing extracellular surfaces (2007)

Across extracellular surfaces, lipid rafts are believed to be an important organizing membrane microdomain component, facilitating specific protein-protein interactions by selectively excluding or including proteins into them. The lipid-based sorting mechanism of these microdomains has been implicated in many cellular processes including; membrane trafficking, signal transduction and cell growth regulation. However, since individual rafts are estimated to range in size from the nanoscale to the microscale, in many cases, they cannot be easily monitored by conventional imaging techniques. We have developed surface enhanced Raman scattering (SERS)-based nanoimaging probes for nanoscale imaging of biochemical species on and within extracellular environments. These probes synergistically combine the qualitative and quantitative information of SERS with the nanoscale imaging capabilities of tapered fiber optic bundles, potentially allowing for chemical imaging of extracellular components and chemical exchange events across cellular surfaces. These probes are fabricated from coherent fiber optic bundles containing 30,000 individual fiber elements that have been tapered to have diameters as small as 140 nm, thus allowing for image magnification and submicron spatial resolution. Due to the uniformly roughened surface features across the probe's imaging surface onto which silver island arrays are fabricated, these probes exhibit less than 3% RSD in SERS signal across the imaging area. In this work, tunability, multiplex detection capabilities and an application of these SERS nanoimaging probes to biological systems are demonstrated.
A High-Dimensional Set Top Box Ad Targeting Algorithm Including Experimental Comparisons to Traditional TV Algorithms (2013)

We present a method for targeting ads on television that works on today's TV systems. The method works by mining vast amounts of Set Top Box data, as well as advertiser customer data. From both sources the system builds demographic profiles, and then looks for media that have the highest match per dollar to the customer profile. The method was tested in four live television campaigns, comprising over 22,000 airings, and we present experimental results.
High-Performance Recommender System Training Using Co-Clustering on CPU/GPU Clusters (2017)

Recommender systems are becoming the crystal ball of the Internet because they can anticipate what the users may want, even before the users know they want it. However, the machine-learning algorithms typically involved in the training of such systems can be computationally expensive, and often may require several days for retraining. Here, we present a distributed approach for load-balancing the training of a recommender system based on state-of-art non-negative matrix factorization principles. The approach can exploit the presence of a cluster of mixed CPUs and GPUs, and results in a 466-fold performance improvement compared with the serial CPU implementation, and a 15-fold performance improvement compared with the best previously reported results for the popular Netflix data set.
Towards a next generation open-source video codec (2013)

Google has recently been developing a next generation opensource video codec called VP9, as part of the experimental branch of the libvpx repository included in the WebM project (http://www.webmproject.org/). Starting from the VP8 video codec released by Google in 2010 as the baseline, a number of enhancements and new tools have been added to improve the coding efficiency. This paper provides a technical overview of the current status of this project along with comparisons and other stateoftheart video codecs H. 264/AVC and HEVC. The new tools that have been added so far include: larger prediction block sizes up to 64x64, various forms of compound INTER prediction, more modes for INTRA prediction, ⅛pel motion vectors and 8tap switchable subpel interpolation filters, improved motion reference generation and motion vector coding, improved entropy coding and framelevel entropy adaptation for various symbols, improved loop filtering, incorporation of Asymmetric Discrete Sine Transforms and larger 16x16 and 32x32 DCTs, frame level segmentation to group similar areas together, etc. Other tools and various bitstream features are being actively worked on as well. The VP9 bitstream is expected to be finalized by earlyto mid2013. Results show VP9 to be quite competitive in performance with mainstream stateoftheart codecs.
Simple dense-pattern optical multipass cells (2005)

Multiple-pass optical cells with dense spot patterns are useful for many applications, especially when the cell volume must be minimized relative to the optical path length. Present methods to achieve these dense patterns require expensive, highly precise astigmatic mirrors and complex alignment procedures. This work describes a new, simpler, and less demanding mirror system, comprising either a pair of cylindrical mirrors or one cylindrical and one spherical mirror.
Three-Dimensional Sheaf of Ultrasound Planes Reconstruction (SOUPR) of Ablated Volumes (2014)

This paper presents an algorithm for 3-D reconstruction of tumor ablations using ultrasound shear wave imaging with electrode vibration elastography. Radio-frequency ultrasound data frames are acquired over imaging planes that form a subset of a sheaf of planes sharing a common axis of intersection. Shear wave velocity is estimated separately on each imaging plane using a piecewise linear function fitting technique with a fast optimization routine. An interpolation algorithm then computes velocity maps on a fine grid over a set of C-planes that are perpendicular to the axis of the sheaf. A full 3-D rendering of the ablation can then be created from this stack of C-planes; hence the name "Sheaf Of Ultrasound Planes Reconstruction" or SOUPR. The algorithm is evaluated through numerical simulations and also using data acquired from a tissue mimicking phantom. Reconstruction quality is gauged using contrast and contrast-to-noise ratio measurements and changes in quality from using increasing number of planes in the sheaf are quantified. The highest contrast of 5 dB is seen between the stiffest and softest regions of the phantom. Under certain idealizing assumptions on the true shape of the ablation, good reconstruction quality while maintaining fast processing rate can be obtained with as few as six imaging planes suggesting that the method is suited for parsimonious data acquisitions with very few sparsely chosen imaging planes.
Frontiers in Tissue Engineering (1999)

Cartilage tissue engineering can provide functional cartilaginous constructs that can be used for controlled in vitro studies of chondrogenesis and potentially for in vivo articular cartilage repair. Ideally, engineered cartilage should be indistinguishable from native articular cartilage with respect to zonal organization, biochemical composition, and mechanical properties. In the model system presented here, chondrogenic cells are expanded in vitro as required, seeded onto three-dimensional polymeric scaffolds, and cultured in bioreactor vessels. During the course of in vitro cultivation, construct cellularity plateaus at a physiologic level, fractions of glycosaminoglycan and Type II collagen increase progressively, and the scaffold biodegrades. Construct structure (composition, morphology) and function (biosynthetic activity, mechanical properties) depend on cultivation conditions. This paper reviews recent studies of in vitro modulation of chondrogenesis by: (1) cell seeding density and source; (2) the tissue regeneration template; (3) biochemical regulatory signals; (4) mixing, mass transport and hydrodynamic forces; and (5) cultivation time. Key requirements and some of the critical research needs for successful cartilage tissue engineering are discussed.
Offshore Field Test of a New System for Model Integrated Closed-Loop Drilling Control (2009)

Summary A new system for real-time optimization and automated control of the drilling process has been tested successfully on the Statfjord C platform in the Norwegian sector of the North Sea. The demonstrated system uses continuously calibrated dynamic process models combined with real-time drilling-data input to calculate available parameter windows, and forward-model simulations are applied to provide optimized operational parameter sequences. The calculation results are applied directly in machine control. The system further applies automated testing combined with continuous diagnostics to provide process advisory. In the field test, pipe-movement control automation, pump-rate control automation, and automated wellbore-condition diagnostics were demonstrated, proving fail-safe application of process safeguard enforcement and optimization of operational procedures. Results from active and passive testing indicated that the new methodology has the ability to improve drilling-process reliability, safely increase drilling efficiency, and reduce the risk of human error. The authors provide a thorough description of the preparations and testing and present an evaluation of the test results, with reference to success criteria that were developed in cooperation with the field operator and drilling contractors involved in the test. Implications for the work organization are also discussed, particularly in relation to control of data input, decision making, and responsibility. The demonstrated technology applies direct integration of current know-how and best practices into the drilling-control system, and available real-time information is applied directly in controlling the drilling process.
LayerP2P: Using Layered Video Chunks in P2P Live Streaming (2009)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> Although there are several successful commercial deployments of live P2P streaming systems, the current designs 1) lack incentives for users to contribute bandwidth resources, 2) lack adaptation to aggregate bandwidth availability, and 3) exhibit poor video quality when bandwidth availability falls below bandwidth supply. In this paper, we propose, prototype, deploy, and validate <emphasis emphasistype="italic">LayerP2P</emphasis>, a P2P live streaming system that addresses all three of these problems. LayerP2P combines layered video, mesh P2P distribution, and a tit-for-tat-like algorithm, in a manner such that a peer contributing more upload bandwidth receives more layers and consequently better video quality. We implement LayerP2P (including seeds, clients, trackers, and layered codecs), deploy the prototype in PlanetLab, and perform extensive experiments. We also examine a wide range of scenarios using trace-driven simulations. The results show that LayerP2P has high efficiency, provides differentiated service, adapts to bandwidth deficient scenarios, and provides protection against free-riders. </para>
Sysplex time synchronization using IEEE 1588 Precision Time Protocol (PTP) (2020)

Timekeeping and highly accurate, precise time synchronization are key requirements for modern information technology systems. While true for several industries, this is especially true for industries involved in transaction processing such as the financial industry. As such, the IBM Z Sysplex needs highly accurate timing/timekeeping and synchronization technology to ensure data integrity, and to also provide the ability to reconstruct a database based upon logs. Recently enacted changes and new regulatory requirements, both in Europe and the United States, have brought increasing attention to time synchronization accuracy. These regulations spurred an interest, both from IBM Z and from our IBM Z clients, in the IEEE 1588 Precision Time Protocol (PTP) being implemented in IBM Z. This article explains the history of PTP, PTP technology, the regulations that led IBM to introduce PTP to IBM Z, PTP's implementation on IBM Z, and IBM's involvement and leadership in the development of the PTP technology and standards going forward.
A New Approach for Fluorescence Subtraction in Raman Spectroscopy (2011)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text Q. Li, K. R. Wang, and S. X. Wang, "A New Approach for Fluorescence Subtraction in Raman Spectroscopy," in CLEO:2011 - Laser Applications to Photonic Applications, OSA Technical Digest (CD) (Optica Publishing Group, 2011), paper CFN7. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Modeling customer demand in print service environments using bootstrapping (2015)

For simulation modeling, what-if analysis and optimization studies of many service and production operations, demand models that are reliable statistical representations of current and future operating conditions are required. Current simulation tools allow demand modeling using known closed-form statistical distributions or raw demand data collected from operations. In many instances, demand data cannot be described by known closed-form statistical distributions and the raw data collected from operations is not representative of future demand. This paper describes an approach to demand modeling where historical demand data collected over a finite time period is combined with user-input using two-tier bootstrapping to produce synthetic demand data that preserves the statistical distribution of the original data but has overall metrics such as volume, workflow mix and individual task and job sizes that represent projected future state scenarios. When the customer demand data follows highly non-normal distributions, a modified procedure is presented.
Estimation of Phase Shifts in Structured Illumination for Optically Sectioned Imaging of Moving Objects (2008)

Structured illumination has been used to obtain optically sectioned images. We estimate unknown, random phase shifts in the multiple sinusoidally patterned images in post-processing, permitting the application of this technique to translating objects.