gebhart/patrepeval huggingface dataset:
Compartmentation protects trypanosomes from the dangerous design of glycolysis (2000)

Unlike in other organisms, in trypanosomes and other Kinetoplastida the larger part of glycolysis takes place in a specialized organelle, called the glycosome. At present it is impossible to remove the glycosome without changing much of the rest of the cell. It would seem impossible, therefore, to assess the metabolic consequences of this compartmentation. Therefore, we here develop a computer experimentation approach, which we call computational cell biology. A validated molecular kinetic computer replica was built of glycolysis in the parasite Trypanosoma brucei. Removing the glycosome membrane in that replica had little effect on the steady-state flux, which argues against the prevalent speculation that glycosomes serve to increase flux by concentrating the enzymes. Removal of the membrane did cause (i) the sugar phosphates to rise to unphysiologically high levels, which must have pathological effects, and (ii) a failure to recover from glucose deprivation. We explain these effects on the basis of the biochemical organization of the glycosome. We conclude (i) that the glycosome protects trypanosomes from the negative side effects of the "turbo" structure of glycolysis and (ii) that computer experimentation based on solid molecular data is a powerful tool to address questions that are not, or not yet, accessible to experimentation.
Demonstration of a POMDP voice dialer (2008)

This is a demonstration of a voice dialer, implemented as a partially observable Markov decision process (POMDP). A real-time graphical display shows the POMDP's probability distribution over different possible dialog states, and shows how system output is generated and selected. The system demonstrated here includes several recent advances, including an action selection mechanism which unifies a hand-crafted controller and reinforcement learning. The voice dialer itself is in use today in AT&T Labs and receives daily calls.
Microstructure fiber optical parametric oscillator with femtosecond output in the 1200 to 1350 nm wavelength range (2010)

We describe an ultrafast fiber optical parametric oscillator operating in the 1210 nm to 1340 nm wavelength range. The system consists of a microstructure fiber placed in a Fabry-Perot cavity which is optically pumped with 1030-nm light from an Ytterbium mode-locked fiber laser. The output wavelength is tunable over a 130-nm span by adjusting the position of one cavity mirror. SHG FROG measurements reveal that the output pulse quality varies as a function of pump power and wavelength. Ultrafast sources operating in this range are particularly instrumental for deep-tissue nonlinear biophotonics applications.
Unsupervised Learning-Based Fast Beamforming Design for Downlink MIMO (2018)

In the downlink transmission scenario, power allocation and beamforming design at the transmitter are essential when using multiple antenna arrays. This paper considers a multiple input–multiple output broadcast channel to maximize the weighted sum-rate under the total power constraint. The classical weighted minimum mean-square error (WMMSE) algorithm can obtain suboptimal solutions but involves high computational complexity. To reduce this complexity, we propose a fast beamforming design method using unsupervised learning, which trains the deep neural network (DNN) offline and provides real-time service online only with simple neural network operations. The training process is based on an end-to-end method without labeled samples avoiding the complicated process of obtaining labels. Moreover, we use the “APoZ”-based pruning algorithm to compress the network volume, which further reduces the computational complexity and volume of the DNN, making it more suitable for low computation-capacity devices. Finally, the experimental results demonstrate that the proposed method improves computational speed significantly with performance close to the WMMSE algorithm.
Improved Placement of Multi-mapping Small RNAs (2016)

High-throughput sequencing of small RNAs (sRNA-seq) is a popular method used to discover and annotate microRNAs (miRNAs), endogenous short interfering RNAs (siRNAs), and Piwi-associated RNAs (piRNAs). One of the key steps in sRNA-seq data analysis is alignment to a reference genome. sRNA-seq libraries often have a high proportion of reads that align to multiple genomic locations, which makes determining their true origins difficult. Commonly used sRNA-seq alignment methods result in either very low precision (choosing an alignment at random), or sensitivity (ignoring multi-mapping reads). Here, we describe and test an sRNA-seq alignment strategy that uses local genomic context to guide decisions on proper placements of multi-mapped sRNA-seq reads. Tests using simulated sRNA-seq data demonstrated that this local-weighting method outperforms other alignment strategies using three different plant genomes. Experimental analyses with real sRNA-seq data also indicate superior performance of local-weighting methods for both plant miRNAs and heterochromatic siRNAs. The local-weighting methods we have developed are implemented as part of the sRNA-seq analysis program ShortStack, which is freely available under a general public license. Improved genome alignments of sRNA-seq data should increase the quality of downstream analyses and genome annotation efforts.
Detailed study of a high-finesse planar waveguide for evanescent wave atomic mirrors (1996)

International audience
Memory-efficient volume ray tracing on GPU for radiotherapy (2011)

Ray tracing within a uniform grid volume is a fundamental process invoked frequently by many radiation dose calculation methods in radiotherapy. Recent advances of the graphics processing units (GPU) help real-time dose calculation become a reachable goal. However, the performance of the known GPU methods for volume ray tracing is all bounded by the memory-throughput, which leads to inefficient usage of the GPU computational capacity. This paper introduces a simple yet effective ray tracing technique aiming to improve the memory bandwidth utilization of GPU for processing a massive number of rays. The idea is to exploit the coherent relationship between the rays and match the ray tracing behavior with the underlying characteristics of the GPU memory system. The proposed method has been evaluated on 4 phantom setups using randomly generated rays. The collapsed-cone convolution/superposition (CCCS) dose calculation method is also implemented with/without the proposed approach to verify the feasibility of our method. Compared with the direct GPU implementation of the popular 3DDDA algorithm, the new method provides a speedup in the range of 1.8-2.7X for the given phantom settings. Major performance factors such as ray origins, phantom sizes, and pyramid sizes are also analyzed. The proposed technique was also shown to lead to a speedup of 1.3-1.6X over the original GPU implementation of the CCCS algorithm.
The Asn505 mutation of the c-MPL gene, which causes familial essential thrombocythemia, induces autonomous homodimerization of the c-Mpl protein due to strong amino acid polarity (2009)

We previously reported that a dominant-positive activating mutation (Asn505) in the transmembrane domain (TMD) of c-MPL, which encodes the thrombopoietin receptor, caused familial essential thrombocythemia. Here, we show that the Asn505 mutation induces both autonomous dimerization of c-Mpl and signal activation in the absence of its ligand. Signal activation was preserved in a truncated mutant of Asn505 that lacked the extracellular domain of c-MPL. We also found that the substitution of the amino acid (AA) residue at position 505 with others of strong polarity (Glu, Asp, or Gln) also resulted in activated dimerization without ligand stimulation. Overall, these data show that the Asn505 mutation transduced the signal through the autonomous dimerization of the c-MPL protein due to strong AA polarity. This finding provides a new insight into the mechanism of disease causation by mutations in the TMD of cytokine/hematopoietic receptors.
P-Systems: A Structural Model for Kinship Studies (2001)

We dedicate this paper to the memory of Oystein Ore Several mathematical models have been proposed for kinship studies.We propose an alternate structural model designed to be so simple logically and intuitively that it can be understood and used by anyone, with a minimum of complication.It is called a P-system, which is short for parental system.The P-system incorporates the best features of each of the previous models of kinship: a single relation of parentage, graphs embedded within the nodes of other graphs, and segregation of higher level descent and marriage structure from nuclear family structure.The latter is also the key conceptual distinction used by Lvi-Strauss (1969) in the theory of marriage alliance.While a P-system is used to represent a concrete network of kinship and marriage relationships, this network also constitutes a system in the sense that it contains multiple levels where each level is a graph in which each node contains another graph structure.In sum, the connections between the nodes at the outer level in a P-system are especially useful in the analysis of marriage and descent, while at inner level we can describe how individuals are embedded in the kinship structure.
ANTS: a toolkit for building and dynamically deploying network protocols (2002)

The authors present a novel approach to building and deploying network protocols. The approach is based on mobile code, demand loading, and caching techniques. The architecture of the system allows new protocols to be dynamically deployed at both routers and end systems, without the need for coordination and without unwanted interaction between co-existing protocols. They describe the architecture and its realization in a prototype implementation. To demonstrate how to exploit the architecture, they present two simple protocols that operate within the prototype to introduce multicast and mobility services into a network that initially lacks them.
Do You Have Suggestions To Help Me Find Quality Childcare (2001)

Do You Have Suggestions To Help MeFind
The design and implementation of active power filters based on variable structure system concepts (2003)

The authors consider the design and implementation of active power filter systems based on concepts from variable structure systems (VSSs) and sliding mode control. The equivalent control concept from VSSs proves to be a very useful tool in the design of the filter. It is shown how the power circuit parameters are integrally tied to the equivalent control, and how circuit performance can be likewise judged. A design procedure is outlined using this approach. In addition, the authors discuss a closed-loop control for an active power filter based on a three-phase switchmode voltage-source inverter. The controller is composed of an inner current control loop which utilizes a sliding-mode control law, and an outer linear control loop which regulates the average voltage across the DC bus of the inverter. Simulations are presented to document converter performance.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
The Impact of Highly Active Antiretroviral Therapy and Immunodeficiency on Human Papillomavirus Infection of the Oral Cavity of Human Immunodeficiency Virus–Seropositive Adults (2005)

Treatment of HIV, rather than HIV immunosuppression, appears to play a role in oral HPV infections in HIV+ individuals.
Absorption and Fluorescence Spectra of Polydiacetylenes (4BCMU and 3BCMU) in Solution (1985)

Absorption and fluorescence spectra have been measured on soluble poly-diacetylenes (4BCMU, 3BCMU), having the side group R=n-BCMU (n-butoxy carbonyl methyl urethane, n=4, 3), in chloroform/n-hexane mixture solvents for various solvent compositions and temperatures. The observed features of the absorption spectra are interpreted by assuming that two types of the coil-to-rod conformational transition take place in the two distinct isomeric bond-structures, which presumably correspond to the acetylenic and butatrienic types, respectively. Experimental phase-diagrams are presented as functions of solvent composition and temperature. Fluorescence bands were observed in rod-like polymer solutions at low temperatures. It is suggested that these largely Stokes-shifted emission bands are due to the self-trapped π-π * excitons on the one-dimensional polymer chains.
The use of multi-pulse nuclear quadrupole resonance techniques for the detection of explosives containing RDX (1997)

The multi-pulse method of detecting nuclear quadrupole resonance (NQR) in explosives containing polycrystalline RDX has been investigated. The following sequences were used: a spin-locking type sequence (SLS), a phase-alternated pulse sequence (PAPS) and a sequence without a preparatory pulse. The SLS, PAPS and strong off-resonance comb methods with the same parameters are of great interest for practical applications. The influence of the frequency offset on NQR signals in multi-pulse experiments was studied.
Depressed Cd4+ T Lymphocyte Proliferative Response and Enhanced Antibody Response to Viral Antigen in Chronic Lentivirus-Induced Arthritis (1995)

The proliferative response of peripheral blood mononuclear cells (PBMC) stimulated with caprine arthritis-encephalitis virus (CAEV) surface glycoprotein (SU) was depressed 4- to 20-fold in Saanen goats with chronic CAEV-induced arthritis compared with asymptomatic goats. Phytohemagglutinin-stimulated responses were not depressed. Complement depletion of PBMC with anti-CD4 or anti-CD8 monoclonal antibodies identified CD4+ T lymphocytes as the antigen-responsive cells in both high-responder asymptomatic goats and low-responder arthritic goats. Serum antibody titers to CAEV SU were 8- to 32-fold higher in goats with chronic arthritis. Increased anti-CAEV SU titers as early as 3 months after infection predicted the eventual development of clinical arthritis. Thus, CAEV-induced arthritis is associated with chronic B cell activation resulting from dominant type 2 immune responses to viral antigen. The clinical outcome of CAEV infection may be determined by differential activation of type 1 or 2 T lymphocyte phenotypes at or near the time of initial exposure to CAEV.
Second-harmonic tomography of tissues (1997)

A novel noninvasive second-harmonic-generation tomographic method of mapping the structure of animal tissues by use of 100-fs laser pulses at 625nm is described. Subsurface structures were measured with this approach, which is potentially a symmetry-sensitive tool for optical histological reconstruction.
A Facile Synthesis of Two Isomeric Components of San Jose Scale Pheromone (1985)

Two components, 1 and 2, of the San Jose scale pheromone were synthesized from nerol and geraniol via regioselective allylic chloride formation and subsequent reduction.
A simulation study of fair queueing and policy enforcement (1990)

article Free Access Share on A simulation study of fair queueing and policy enforcement Authors: James R. Davin View Profile , Andrew T. Heybey View Profile Authors Info & Claims ACM SIGCOMM Computer Communication ReviewVolume 20Issue 5Oct 1 1990 pp 23–29https://doi.org/10.1145/381906.381926Online:01 October 1990Publication History 40citation250DownloadsMetricsTotal Citations40Total Downloads250Last 12 Months8Last 6 weeks3 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my AlertsNew Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Automatic generation of large scale 3D cloud based on weather forecast data (2012)

3D cloud scenes generation is widely used in computer graphics and virtual reality. Most of the existing methods for 3D cloud visualization first model the cloud based on the physical mechanism of cloud, and then solve the illumination model of the cloud to generate 3D scenes. However, this kind of methods cannot show the real weather condition. Moreover, the existing cloud visualization methods based on the weather forecast data cannot be applied to the large scale 3D cloud scenes due to the complicated solution of the illumination model. Borrowing the idea of particle system, this paper proposes an algorithm for automatic generation of large scale 3D cloud based on weather forecast data. The algorithm considers each grid point in the data as a particle, whose optical parameters can be determined by the input data. Multiple forward scattering is used to calculate the incident color of each particle, and the first order scattering is utilized to determine the incident color to the observer. Experimental results demonstrate that our algorithm could not only generate realistic 3D cloud scenes from the weather forecast data, but also obtain an interactive frame rates for the data that contains millions of grids.
Virtual networking (2010)

Over a decade ago, virtual networking started with a simple bridging of VM's virtual network adapter to host's physical network adapter in VMware's Workstation product. With VMware's vSphere 4 product, virtual networking has evolved to a distributed virtual networking infrastructure with pluggable packet switching and filtering modules, under the umbrella marketing name of vNetwork. It is clear that in a virtualized environment, traditional network access layer has migrated from physical switches to virtual switches in the hypervisor. We are beginning to see virtualized solutions in layer 3 to 7 network services and we expect this trend of service migration from physical to virtual to continue in the coming years
Finteraction : Finger Interaction with Mobile Phone (2008)

Touch interaction with mobile phones enable users to have a more natural interaction with the device, since touch is a natural way of direct accessing an object of interest. But one disadvantage is occlusion; i.e., the user loses a high percentage of information presented on the small screen of the mobile phone during the interaction using his ”big finger”. On the other hand, interaction enhanced with accelerometers can react according to the device movements, e.g., while the user is tilting the mobile phone, the UI will be rotated. A drawback is that the user needs to move the whole device while interacting and consequently loses his eye contact on the phone’s screen (screen-absence problem). Finteraction (Finger Interaction) is a new interaction concept that solves the occlusion and screen-absence problems. User interact with a large public display using his mobile phone. Moving the index finger in front of the camera at the backside of the mobile phone, the user can interact with the large public display even on the move.
Talking Yourself Out of Exhaustion (2013)

This study is the first to demonstrate that ST significantly reduces RPE and enhances endurance performance. The findings support the psychobiological model of endurance performance and illustrate that psychobiological interventions designed to specifically target favorable changes in the perception of effort are beneficial to endurance performance. Consequently, this psychobiological model offers an important and novel perspective for future research investigations.
54.5L: <i>Late‐News Paper:</i> A 24‐inch AM‐OLED Display with XGA Resolution by Novel Seamless Tiling Technology (2003)

Abstract We developed a novel seamless tiling technology for full color AM‐OLED display. This technology is based on three items: 1) TAC‐based tiling structure, 2) High precision tiling process, 3) Brightness and color matching system. As a result, a 24‐inch panel, the largest OLED display ever reported, has been fabricated using 2×2 tiles with no apparent seams.
Effects of Arginine-Based Supplements on the Physical Working Capacity at the Fatigue Threshold (2010)

The purpose of the present study was to examine the effects of daily oral administration of arginine-based supplements for 4 weeks on the physical working capacity at the fatigue threshold (PWCFT). The PWCFT test is an electromyographic (EMG) procedure for estimating the highest power output that can be maintained without neuromuscular evidence of fatigue. The study used a double-blind, placebo-controlled design. Fifty college-aged men (mean age +/- SD = 23.9 +/- 3.0) were randomized into 1 of 3 groups: (a) placebo (n = 19); (b) 1.5 g arginine (n = 14); or (c) 3.0 g arginine (n = 17). The placebo was microcrystalline cellulose. The 1.5-g arginine group ingested 1.5 g of arginine and 300 mg of grape seed extract, whereas the 3.0 g arginine group ingested 3.0 g of arginine and 300 mg of grape seed extract. All subjects performed an incremental test to exhaustion on a cycle ergometer to determine their PWCFT before supplementation (PRE) and after 4 weeks of supplementation (POST). Surface EMG signals were recorded from the vastus lateralis using a bipolar electrode arrangement during the incremental tests for the determination of the PRE and POST supplementation PWCFT values. There were significant mean increases (PRE to POST) in PWCFT for the 1.5 g (22.4%) and 3.0 g (18.8%) supplement groups, but no change for the placebo group (-1.6%). These findings supported the use of arginine-based supplements, at the dosages examined in the present investigation, as an ergogenic aid for untrained individuals.
Choline Ion Interactions with DNA Atoms Explain Unique Stabilization of A–T Base Pairs in DNA Duplexes: A Microscopic View (2013)

Under physiological conditions, G-C base pairs are more stable than A-T base pairs. In a previous study, we showed that in the hydrated ionic liquid of choline dihydrogen phosphate, the stabilities of these base pairs are reversed. In the present study, we elucidated the unique binding interactions of choline ions with DNA atoms from a microscopic viewpoint using molecular dynamics simulations. Three times more choline ions bind to the DNA duplex than sodium ions. Sodium ions bind closely but not stably; in contrast, the choline ions bind through multiple hydrogen bonding networks with DNA atoms stably. The affinity of choline ion for the minor groove of A-T base pairs is more than 2 times that for other groove areas. In the narrow A-T minor groove, choline ion has high affinity for the ribose atoms of thymine. Choline ions also destabilize the formation of hydrogen bonds between G-C base pairs by binding to base atoms preferentially for both of duplex and single-strand DNA, which are associated with the bonds between G-C base pairs. Our new finding will not only lead to better control of DNA stability for use in DNA nanodevices, but also provide new insight into the stability of DNA duplexes under crowding conditions found in living cells.