gebhart/patrepeval huggingface dataset:
Overcoming performance collapse for 100Gbps cyber security (2013)

In this paper, we present a series of performance tests carried out on R-Scope Dominate-T (RDT), a 1U network security appliance configured with four Tilera Gx-36 processors and with an aggregated network IO capacity of 160Gbps. RDT is optimized with several high-performance computing techniques. On the software side, RDT runs Linux and a modified version of Bro--the open source network security monitor developed by the International Computer Science Institute--optimized with (1) intelligent IDS-aware packet queuing, (2) Bro-programmable packet shunting, (3) zero-locking IPC data structures, and (4) layer-4 packet prioritization. On the hardware side, the system leverages a many-core architecture with (1) 144 cores servicing 16 x 10Gbps network interfaces, (2) an on-chip ASIC-assisted engine delivering packets directly to Bro at wire rates, and (3) core-programmable zero-overhead/zero-interrupt Linux. The objective of this work is to make a contribution towards maximizing the amount of cyber security intelligence that a system can detect per unit of cost, where cost includes the processing time, space, energy, and capital equipment expenses incurred to perform such detection.
Neutrino event selection in the MicroBooNE liquid argon time projection chamber using Wire-Cell 3D imaging, clustering, and charge-light matching (2021)

Abstract An accurate and efficient event reconstruction is required to realize the full scientific capability of liquid argon time projection chambers (LArTPCs). The current and future neutrino experiments that rely on massive LArTPCs create a need for new ideas and reconstruction approaches. Wire-Cell, proposed in recent years, is a novel tomographic event reconstruction method for LArTPCs. The Wire-Cell 3D imaging approach capitalizes on charge, sparsity, time, and geometry information to reconstruct a topology-agnostic 3D image of the ionization electrons prior to pattern recognition. A second novel method, the many-to-many charge-light matching, then pairs the TPC charge activity to the detected scintillation light signal, thus enabling a powerful rejection of cosmic-ray muons in the MicroBooNE detector. A robust processing of the scintillation light signal and an appropriate clustering of the reconstructed 3D image are fundamental to this technique. In this paper, we describe the principles and algorithms of these techniques and their successful application in the MicroBooNE experiment. A quantitative evaluation of the performance of these techniques is presented. Using these techniques, a 95% efficient pre-selection of neutrino charged-current events is achieved with a 30-fold reduction of non-beam-coincident cosmic-ray muons, and about 80% of the selected neutrino charged-current events are reconstructed with at least 70% completeness and 80% purity.
Prevention of infection in a porous tracheal prosthesis by omental wrapping. (1991)

The ideal tracheal prosthesis has to permit complete incorporation by epithelialization of the luminal surface. This is not possible with the currently available impermeable solid silicone tube. The authors developed a reinforced, porous polyurethane tubular prosthesis which has the potential for complete incorporation. However, because these prostheses are implanted in a contamined area such as the airway, they all become infected. In order to prevent infection, the authors evaluated the effect of omental wrapping in guinea pigs. The authors' tubular prosthesis was implanted subcutaneously in the abdominal area with the ends open to the air. Ten prostheses were wrapped with omentum and 10 prostheses were not. In 4 weeks, all control prostheses were infected and marsupialized. All the wrapped prostheses remained in place and were macroscopically not infected. Microscopically, all wrapped prostheses were well vascularized and were incorporated by granulation tissue, which did not occur in the prostheses of the control group. From these results the authors conclude that omental wrapping would be an effective way to prevent infection of porous tracheal prostheses in an open-to-the-air situation, and allow rapid tissue ingrowth and incorporation in the host.
A competitive mechanism for self-organized learning of sensorimotor mappings (2011)

How can a robot learn sensorimotor knowledge in a developmental way based on its own experiences solely? An important step is the acquisition of a body-schema-learning about the physical behavior of its own body, and how incoming sensory stimuli can be put in relation to the own body. In this work, we study how a competitive learning mechanism, which is related to the EM algorithm, can help to simplify the learning problem. We demonstrate how a robot can learn the way visual stimuli move as a consequence of the robots own actions of moving its camera or moving its end-effector in front of its camera. We show how the robot can discriminate stimuli originating from these two kinds of actions and learn the position of the end-effector in its visual input. Previous approaches have relied on a preprocessing step to “self-detect”, which we find is not necessary. The robot acquires a set of sensorimotor estimates, which could later be used, e.g. in visually guided reaching.
50th Anniversary Perspective: Block Polymers—Pure Potential (2016)

Block polymers have undergone extraordinary evolution since their inception more than 60 years ago, maturing from simple surfactants to an expansive class of macromolecules encoded with exquisite attributes. Contemporary synthetic accessibility coupled with facile characterization and rigorous theoretical advances have conspired to continuously generate fundamental insights and enabling concepts that target applications spanning chemistry, biology, physics, and engineering. Here, we parse the vast literature to examine the forefront of the field and identify exciting themes and challenging opportunities that portend a bracing future trajectory. This Perspective celebrates the visionary role played by Macromolecules in advancing our understanding of this remarkable class of materials.
Deterministic approximation algorithms for the nearest codeword problem (2010)

The Nearest Codeword Problem (NCP) is a basic algorithmic question in the theory of error-correcting codes. Given a point v in F_2^n and a linear space L in F_2^n of dimension k NCP asks to find a point l in L that minimizes the (Hamming) distance from v. It is well-known that the nearest codeword problem is NP-hard. Therefore approximation algorithms are of interest. The best effcient approximation algorithms for the NCP to date are due to Berman and Karpinski. They are a deterministic algorithm that achieves an approximation ratio of O(k/c) for an arbitrary constant c; and a randomized algorithm that achieves an approximation ratio of O(k/ log n). In this paper we present new deterministic algorithms for approximating the NCP that improve substantially upon the earlier work, (almost) de-randomizing the randomized algorithm of Berman and Karpinski. We also initiate a study of the following Remote Point Problem (RPP). Given a linear space L in F_2^n of dimension k RPP asks to find a point v in F_2^n that is far from L. We say that an algorithm achieves a remoteness of r for the RPP if it always outputs a point v that is at least r-far from L. In this paper we present a deterministic polynomial time algorithm that achieves a remoteness of Omega(n log k / k) for all k < n/2. We motivate the remote point problem by relating it to both the nearest codeword problem and the matrix rigidity approach to circuit lower bounds in computational complexity theory.
Conformational dynamics of bacteriophage T7 DNA polymerase and its processivity factor, Escherichia coli thioredoxin (2010)

Gene 5 of bacteriophage T7 encodes a DNA polymerase (gp5) responsible for the replication of the phage DNA. Gp5 polymerizes nucleotides with low processivity, dissociating after the incorporation of 1 to 50 nucleotides. Thioredoxin (trx) of Escherichia coli binds tightly (Kd = 5 nM) to a unique segment in the thumb subdomain of gp5 and increases processivity. We have probed the molecular basis for the increase in processivity. A single-molecule experiment reveals differences in rates of enzymatic activity and processivity between gp5 and gp5/trx. Small angle X-ray scattering studies combined with nuclease footprinting reveal two conformations of gp5, one in the free state and one upon binding to trx. Comparative analysis of the DNA binding clefts of DNA polymerases and DNA binding proteins show that the binding surface contains more hydrophobic residues than other DNA binding proteins. The balanced composition between hydrophobic and charged residues of the binding site allows for efficient sliding of gp5/trx on the DNA. We propose a model for trx-induced conformational changes in gp5 that enhance the processivity by increasing the interaction of gp5 with DNA.
Quantification of EBV DNA In Whole Blood In Newly Diagnosed Patients with Diffuse Large B-Cell Lymphoma (2010)

Abstract Abstract 3102 Introduction: Epstein-Barr virus (EBV) is a well-known oncogenic virus associated with the development of several lymphoproliferative disorders. The quantification of EBV viral load in plasma and peripheral blood mononuclear cells has been reported as a useful biomarker for EBV-associated non-Hodgkin lymphoma (NHL). The role of EBV in diffuse large B-cell lymphoma (DLBCL) is unclear at this time. METHODS: In the present prospective study, using real-time quantitative polymerase chain reaction (RQ-PCR), whole blood specimens from patients with a new diagnosis of DLBCL were used to quantitatively determine EBV viral load. Consecutive patients who presented from January 1, 2009 to December 30, 2009 were selected for this study. The pathological samples from the patients showing elevated EBV DNA levels were then investigated for the presence of EBV-encoded RNA (EBER) using a chromogenic in situ hybridization (CISH) technique. Clinical data from these patients was collected and analyzed, and will be presented using descriptive statistics. Overall survival estimates were obtained using the Kaplan-Meier method. Results: Forty six patients with a new diagnosis of DLBCL were included in our study; from which five cases showed elevated levels of EBV DNA by RQ-PCR (10.8%). These five patients (100%) were positive for EBER expression within the tumoral cells by EBER CISH. One patient was evaluated at the end of treatment and blood EBV DNA level was undetectable. All EBV DNA-positive cases were male with a median age of 69 years (range 25–73 years); only one case was younger than 50 years. The median EBV DNA viral load was 59 copies/uL (range 0.225–43200 copies/uL). Three patients (60%) presented with advanced clinical stage (III or IV) and three patients (60%) had a primary extranodal site of involvement. Four patients (80%) received CHOP-based chemotherapy regimens. The three patients with advanced stage have deceased with a survival of &lt;3 months. The two patients with early stage experienced a complete response with immunochemotherapy and are alive 6 and 9 months after diagnosis, respectively. The median overall survival is 4 months. Conclusions: These results, although preliminary, suggest that whole blood EBV DNA quantification might be useful at detecting patients with EBV-positive DLBCL. Further studies are needed to investigate the potential diagnostic and/or prognostic value of EBV DNA in DLBCL. Disclosures: No relevant conflicts of interest to declare.
Solid State Imaging Techniques. New Design and Implementation of On-sensor-compression circuit Based on Column Parallel Architecture. (1999)

新たに試作した128×128画素からなる動画像圧縮センサについて報告する.本プロトタイプでは列並列処理構成を採用し, 多画素化と共に処理回路の見直しによる大幅な高速化, 低消費電力化を実現する.試作したチップの動作検証を行い, 毎秒5000フレームの高速撮像下における処理回路の動作を確認する.
Hierarchical Modeling, Optimization, and Synthesis for System-Level Analog and RF Designs (2007)

The paper describes the recent state of the art in hierarchical analog synthesis, with a strong emphasis on associated techniques for computer-aided model generation and optimization. Over the past decade, analog design automation has progressed to the point where there are industrially useful and commercially available tools at the cell level-tools for analog components with 10-100 devices. Automated techniques for device sizing, for layout, and for basic statistical centering have been successfully deployed. However, successful component-level tools do not scale trivially to system-level applications. While a typical analog circuit may require only 100 devices, a typical system such as a phase-locked loop, data converter, or RF front-end might assemble a few hundred such circuits, and comprise 10 000 devices or more. And unlike purely digital systems, mixed-signal designs typically need to optimize dozens of competing continuous-valued performance specifications, which depend on the circuit designer's abilities to successfully exploit a range of nonlinear behaviors across levels of abstraction from devices to circuits to systems. For purposes of synthesis or verification, these designs are not tractable when considered "flat." These designs must be approached with hierarchical tools that deal with the system's intrinsic design hierarchy. This paper surveys recent advances in analog design tools that specifically deal with the hierarchical nature of practical analog and RF systems. We begin with a detailed survey of algorithmic techniques for automatically extracting a suitable nonlinear macromodel from a device-level circuit. Such techniques are critical to both verification and synthesis activities for complex systems. We then survey recent ideas in hierarchical synthesis for analog systems and focus in particular on numerical techniques for handling the large number of degrees of freedom in these designs and for exploring the space of performance tradeoffs early in the design process. Finally, we briefly touch on recent ideas for accommodating models of statistical manufacturing variations in these tools and flows
A functional test identifies dopamine agonists selective for D3 versus D2 receptors (1995)

The functional potency of a series of dopamine agonists for increasing mitogenesis, measured by incorporation of [3H]thymidine, was established in transfected cell lines expressing human D2 or D3 receptors. The functional selectivity of agonists markedly differs from their binding selectivity. (+)7-OH-DPAT, pramipexole, quinerolane and PD 128,907, the most D3 receptor-selective compounds in binding studies, were 7, 15, 21 and 54 times more potent, respectively, at the D3 than at the D2 receptor in the functional test. Bromocriptine displayed a 10-fold functional selectivity toward the D2 receptor. The known behavioural actions of D3 selective agonists support a role for the D3 receptor in motor inhibitions, which should be taken into account for the treatment of motor dysfunctions by dopamine agonists.
A Permanent Common Carotid Filter for Stroke Prevention in Atrial Fibrillation: Ex Vivo and In Vivo Pre-Clinical Testing (2020)

These favorable pre-clinical results prompt clinical testing of the CCA filter in stroke prevention clinical trials.
New Findings in Estimating Flow Rates Through Overflowing Manhole Covers (2008)

New Findings in Estimating Flow Rates Through Overflowing Manhole CoversWhen sewers overflow through manhole covers, the flow rate of the overflow is expected to depend, to some extent, on the head loss through the partly open manhole cover. In this study, the flow rate and head loss was measured through several manhole covers with different weights and number of holes to determine that relationship between head loss and flow. While it is common to model an...Author(s)Thomas WalskiBrian WhitmanBrandon KellyMike LeamanDanny LoughranSourceProceedings of the Water Environment FederationSubjectSession 12: Flow Monitoring that Pays Real DividendsDocument typeConference PaperPublisherWater Environment FederationPrint publication date Jan, 2008ISSN1938-6478SICI1938-6478(20080101)2008:5L.851;1-DOI10.2175/193864708788812839Volume / Issue2008 / 5Content sourceCollection Systems ConferenceFirst / last page(s)851 - 874Copyright2008Word count143
An integrated aluminum/CVD-W metallization process for sub-micron contact filling (2002)

The development of a contact metallization scheme which allows the planarized deposition of aluminum by sputtering methods is reported. Deposition of a thin (<or=0.2 mu m) CVD-W film onto a TiN adhesion layer provides good contact and junction properties, barrier integrity, and avoids a re-entrant profile for hot Al filling. The CVD-W/Al layerings withstood not only the temperature of hot (450 degrees C) Al deposition, but additional anneal periods at 500 degrees C without significant junction deterioration. In contrast, conventional PVD barriers alone (TiW, TiW-N, TiN) failed prematurely as a result of the high temperature Al deposition.<<ETX>>
Flow Field Features of the BEVERLI Hill Model (2021)

View Video Presentation: https://doi.org/10.2514/6.2021-1741.vid Wind tunnel tests and corresponding computational fluid dynamics simulations were performed to characterize surface and off-surface turbulent mean flow features of a novel superelliptic-shaped, wall-mounted, three-dimensional hill named BeVERLI (Benchmark Val- idation Experiment for RANS and LES Investigations). The wind tunnel tests were conducted at a hill-height-based Reynolds number of 650,000 and 0◦ model orientation with respect to the incoming flow. Detailed measurements needed for the highest level of uncertainty quantifica- tion, study of flow sensitivites, and extensive documentation of the flow boundary conditions as per Oberkampf and Smith [1] were additionally carried out. Deviations in the as-manufactured hill model as compared to the as-designed geometry and inflow non-uniformities at the inlet of the experimental facility were identified, quantified, and used to provide additional context to the analysis of the mean flow features. Measurements on the hill identified a large leeward flow separation region and the possibility of a small laminar windward separation region. Sim- ulations predicted flow reattachment to occur at the downstream foot of the hill. Despite the symmetric nature of the BeVERLI Hill, the measurements showed asymmetric flow. Quantified asymmetries in the as-manufactured model geometry were deemed a potential cause. Simu- lations predicted the same flow asymmetry using symmetric grids and boundary conditions, suggesting the possibility of a true asymmetric bi-modal flow behavior of the BeVERLI Hill. However, simulation parameters, such as the choice of turbulence model, were seen to affect the prediction of flow asymmetry, leaving the answer to the true nature of these asymmetries a subject of future work. The onset of deviations of the simulations from the measurements was observed at the windward transition to the hill top, where the flow experiences a strong favor- able pressure gradient, suggesting the occurrence of important flow dynamics in this region. Indeed, the measurements revealed the formation of a complex shear layer on the hill top and the potential for relaminarization upstream of this region.
Dynamic micromagnetic field measurement by stroboscopic electron beam tomography (1992)

A stroboscopic electron beam tomography system for measuring the dynamic micromagnetic field of recording heads is presented. A pulsed electron beam, which is synchronized with the recording head driver, is scanned along the recording head surface from all directions. Integration of the magnetic field intensity along the beam path is calculated from the electron beam deflection angle. Intensity distributions of the dynamic magnetic field are calculated using a tomographic reconstruction algorithm. To obtain enough current even in pulsed electron beam operation, a high-brightness Ti/W thermal field emitter is used. This system was successfully applied in measuring the field distributions of a thin-film recording head, with 0.1 mu m spatial resolution and 1 ns time resolution at an operation frequency of 30 MHz.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Iron uptake from ferrichrome A and iron citrate in Ustilago sphaerogena (1983)

Double radioactive label transport assays with iron, chromium, and gallium chelates were used to investigate the mechanism of iron uptake by Ustilago sphaerogena. In iron-deficient cells, ferrichrome A iron was taken up without appreciable uptake of the ligand. Iron-sufficient cells partially accumulated the ligand with the metal. The chromium- and gallium-containing analogs of ferrichrome A were transported as intact chelates. Ferrichrome A iron uptake was inhibited by dipyridyl. The data suggest that the intact ferrichrome A chelate binds to a specific receptor, the iron is then separated from the ligand at the membrane by reduction, and the metal is released to the inside of the cell while the ligand is released to the exterior. The reduction step is not transport rate limiting. Iron chelated to citrate was taken up by an energy-dependent process. The citrate ligand was not taken up with the metal. Uptake was sensitive to dipyridyl and ferrozine. Chromic ion chelated to citrate was not transported, suggesting that the iron, rather than the chelate, is recognized by the receptor or that reduction of the metal is required for transport.
Effects of Chilling Treatment on Baicalin, Baicalein, and Wogonin Biosynthesis in Scutellaria baicalensis Plantlets (2022)

When plants are exposed to stressful conditions, they modulate their nutrient balance by regulating their primary and secondary metabolisms to adapt. In this study, changes in primary and secondary metabolites elicited by chilling stress treatment and the effects of treatment duration were examined in roots of <i>Scutellaria baicalensis</i> (<i>S. baicalensis</i>) plantlets. The concentrations of most sugars (maltose, glucose, sucrose, and fructose) and of several amino acids (proline and GABA), which are crucial regarding plant defense mechanisms, increased with increasing duration of chilling stress. Furthermore, salicylic acid levels increased after two-day chilling treatments, which may enhance plant tolerance to cold temperatures. The concentrations of flavones (baicalin, baicalein, and wogonin) increased during chilling stress, and those of phenolic acids (ferulic acid and sinapic acid) increased after two-day chilling treatments. The concentrations of these flavones were positively correlated with sucrose levels which acted as energy sources.
Immunoglobulin V/J recombination is accompanied by deletion of joining site and variable region segments. (1980)

A site-specific recombination event is responsible for the somatic activation of immunoglobulin genes and for generating a major share of immunoglobulin gene diversity. Although several possible mechanisms can be proposed to account for this process, recombinatio accompanied by deletion is a particularly attractive mechanism because it might utilize inverted repeat sequences noted on the 3' side of all variable regions and on the 5' side of all joining site segments thus far studied. Testing this model is complicated by the fact that antibody cells are at least diploid and gene segments on the inactive chromosome can obscure deletions occurring within the active gene. Accordingly, we have screened several immunoglobulin-producing plasmacytoma lines to select those in which both chromosomes are rearranged. By using appropriate cell lines and variable and joining region probes in in situ hybridization experiments, we show that recombination is accompanied by the deletion of both variable and joining region genes. These experiments also allow us to map the site of V/J recombination of several active immunoglobulin genes and suggest an order and orientation for variable, joining, and constant region sequences.