gebhart/patrepeval huggingface dataset:
Online Network Coding for Time-Division Duplexing (2010)

We study an online random linear network coding approach for time division duplexing (TDD) channels under Poisson arrivals. We model the system as a bulk-service queue with variable bulk size and with feedback, i.e., when a set of packets are serviced at a given time, they might be reintroduced to the queue to form part of the next service batch. We show that there is an optimal number of coded data packets that the sender should transmit back-to-back before stopping to wait for an acknowledgement from the receiver. This number depends on the latency, probability of packet erasure, degrees of freedom at the receiver, the size of the coding window, and the arrival rate of the Poisson process. Random network coding is performed across a moving window of packets that depends on the packets in the queue, design constraints on the window size, and the feedback sent from the receiver. We study the mean time between generating a packet at the source and it being "seen", but not necessarily decoded, at the receiver. We also analyze the mean time between a decoding event and the next, defined as the decoding of all the packets that have been previously "seen" and those packets involved in the current window of packets. Inherently, a decoding event implies an in-order decoding of a batch of data packets. We present numerical results illustrating the trade-off between mean delay and mean time between decoding events.
Studies on the Kinetics and Application of L-Carnitine Amidase for the Production of L-Carnitine (1995)

The kinetics of L-carnitine amidase from the newly isolated microorganism DSM 6320 is complex; the enzyme is competitively inhibited by the product L-carnitine as well as the unreactive enantiomer of the substrate, D-carnitine amide. The second reaction product, ammonia, does not affect the rate of hydrolysis. D-carnitine is an inhibitor, but should not be present normally. In batch hydrolysis experiments complete conversion of the L-enantiomer was achieved starting with DL-carnitine amide as substrate in concentrations up to 1000 mM. The L-carnitine obtained was of high optical purity (>99% enantiomeric excess) independent of the degree of conversion, of the specific activity of the enzyme employed, and of the method used to control the pH in the optimal range, around pH 8.5. A simple model was established describing the reaction kinetics of the enzyme. The model was used to simulate the time course of batch conversions. In continuous experiments the stability of the L-carnitine amidase was investigated under operating conditions. Enzyme deactivation of 1.2–1.7 U/h was observed. A space time yield of 460 g/(1.d) was reached.
A proposed nomenclature system for the cytosolic sulfotransferase (SULT) superfamily (2004)

A nomenclature system for the cytosolic sulfotransferase (SULT) superfamily has been developed. The nomenclature guidelines were applied to 65 SULT cDNAs and 18 SULT genes that were characterized from eukaryotic organisms. SULT cDNA and gene sequences were identified by querying the GenBank databases and from published reports of their identification and characterization. These sequences were evaluated and named on the basis of encoded amino acid sequence identity and, in a few cases, a necessity to maintain historical naming convention. Family members share at least 45% amino acid sequence identity whereas subfamily members are at least 60% identical. cDNAs which encode amino acid sequences of at least 97% identity to each other were assigned identical isoform names. We also attempted to categorize orthologous enzymes between various species, where these have been identified, and the nomenclature includes a species descriptor. We present recommendations for the naming of allelic variants of SULT genes and their derived allozymes arising from single nucleotide polymorphisms and other genetic variation. The superfamily currently comprises 47 mammalian SULT isoforms, one insect isoform and eight plant enzymes, and collectively these sequences represent nine separate SULT families and 14 subfamilies. It is hoped that this nomenclature system will be widely adopted and that, as novel SULTs are identified and characterized, investigators will name their discoveries according to these guidelines.
Improving the Oral Efficacy of CNS Drug Candidates:  Discovery of Highly Orally Efficacious Piperidinyl Piperidine M<sub>2</sub> Muscarinic Receptor Antagonists (2002)

In search of a backup M(2) muscarinic receptor antagonist to the previously reported compound 1, we discovered compound (+)-14, which showed superior oral efficacy in animal models. The improvement of oral efficacy was achieved by modulating both the molecular weight and lipophilicity of the lead compounds.
QoE Doctor (2014)

Smartphones have become increasingly prevalent and important in our daily lives. To meet users' expectations about the Quality of Experience (QoE) of mobile applications (apps), it is essential to obtain a comprehensive understanding of app QoE and identify the critical factors that affect it. However, effectively and systematically studying the QoE of popular mobile apps such as Facebook and YouTube still remains a challenging task, largely due to a lack of a controlled and reproducible measurement methodology, and limited insight into the complex multi-layer dynamics of the system and network stacks.
Genomic Deletions Suggest a Phylogeny for the<i>Mycobacterium tuberculosis</i>Complex (2002)

To better understand the evolution of the Mycobacterium tuberculosis complex, subspecies were tested for large sequence polymorphisms. Samples with greater numbers of deletions, without exception, were missing all the same regions that were deleted from samples with lesser numbers of deletions. Principal genetic groups based on single-nucleotide polymorphisms were restricted to one of the deletion-based groups, and isolates that shared genotypes based on molecular epidemiological markers were assigned almost exclusively to the same deletion type. The data provide compelling evidence that human tuberculosis did not originate from the present-day bovine form. Genomic deletions present themselves as an attractive modality to study the evolution of the M. tuberculosis complex.
Effective Infiltration of Gel Polymer Electrolyte into Silicon-Coated Vertically Aligned Carbon Nanofibers as Anodes for Solid-State Lithium-Ion Batteries (2015)

This study demonstrates the full infiltration of gel polymer electrolyte into silicon-coated vertically aligned carbon nanofibers (Si-VACNFs), a high-capacity 3D nanostructured anode, and the electrochemical characterization of its properties as an effective electrolyte/separator for future all-solid-state lithium-ion batteries. Two fabrication methods have been employed to form a stable interface between the gel polymer electrolyte and the Si-VACNF anode. In the first method, the drop-casted gel polymer electrolyte is able to fully infiltrate into the open space between the vertically aligned core-shell nanofibers and encapsulate/stabilize each individual nanofiber in the polymer matrix. The 3D nanostructured Si-VACNF anode shows a very high capacity of 3450 mAh g(-1) at C/10.5 (or 0.36 A g(-1)) rate and 1732 mAh g(-1) at 1C (or 3.8 A g(-1)) rate. In the second method, a preformed gel electrolyte film is sandwiched between an Si-VACNF electrode and a Li foil to form a half-cell. Most of the vertical core-shell nanofibers of the Si-VACNF anode are able to penetrate into the gel polymer film while retaining their structural integrity. The slightly lower capacity of 2800 mAh g(-1) at C/11 rate and ∼1070 mAh g(-1) at C/1.5 (or 2.6 A g(-1)) rate have been obtained, with almost no capacity fade for up to 100 cycles. Electrochemical impedance spectroscopy does not show noticeable changes after 110 cycles, further revealing the stable interface between the gel polymer electrolyte and the Si-VACNFs anode. These results show that the infiltrated flexible gel polymer electrolyte can effectively accommodate the stress/strain of the Si shell due to the large volume expansion/contraction during the charge-discharge processes, which is particularly useful for developing future flexible solid-state lithium-ion batteries incorporating Si-anodes.
Coumamidines, new broad spectrum antibiotics of the cinodine type. I. Discovery, taxonomy of the producing organism and fermentation. (1989)

Coumamidines are water-soluble basic antibiotics related to the glycocinnamoylspermidines. They are produced by a soil isolate designated Saccharopolyspora sp. AB 1167L-65. The coumamidines have broad spectrum activity and were selected in a screen for substances which inhibit Pseudomonas aeruginosa.
SU‐FF‐J‐46: A Probabilistic Method for Online Treatment Plan Modification (2005)

Purpose: To develop an IMRT treatment planning method that accounts for increased knowledge of tumor and normal tissue location gained from inter‐ or intra‐fractional imaging. Method and Materials: Knowledge of tumor location in each fraction or sub‐fraction is represented by a probability density function (pdf), p(n,n′,t) , that describes the probability that a voxel at index n in the planning image will be located at voxel n ′ at a later time t . The pdf is changing as the new information becomes available. A set of beam profiles for each fraction or sub‐fraction is then obtained by minimizing the quadratic objective function by accounting for probabilistic nature of the beamlet dose distribution: in each fraction. This optimization problem is set with the intention that the beamlets that have the highest risk of missing the tumor will not be delivered until adequate knowledge of tumor location becomes available. We apply this method to a case of a disk‐shaped tumor inside a disk‐shaped phantom with a tomotherapy beam geometry. Results: The method proved to deliver more conservative dose distributions at the beginning of treatment than at the end for both inter‐ and intra‐fractional cases. For early fractions and sub‐fractions, low‐risk doses were delivered to regions where the probability was high that the tumor would be present during the treatment. As knowledge of tumor location improved, the remaining dose at the periphery of the tumor was filled‐in. Conclusion: We showed that incorporating increased knowledge about tumor and normal tissue location, obtained by repeatitive on‐line imaging leads to superior treatment plans.
Communication: Partial polarization transfer for single-scan spectroscopy and imaging (2011)

A method is presented to partially transfer nuclear spin polarization from one isotope S to another isotope I by the way of heteronuclear spin couplings, while minimizing the loss of spin order to other degrees of freedom. The desired I spin polarization to be detected is a design parameter, while the sequence of pulses at the two Larmor frequencies is optimized to store the greatest unused S spin longitudinal polarization for subsequent use. The unitary evolution for the case of I(N)S spin systems illustrates the potentially ideal efficiency of this strategy, which is of particular interest when the spin-lattice relaxation time of S greatly exceeds that of I. Explicit timing and pulses are tabulated for the cases for which M ≤ 10 partial transfers each result in equal final polarization of 1/M or more compared to the final I polarization expected in a single transfer for N = 1, 2, or 3 I spins. Advantages for the ratiometric study of reacting molecules and hyperpolarized initial conditions are outlined.
Weighted iterative reconstruction for magnetic particle imaging (2010)

Magnetic particle imaging (MPI) is a new imaging technique capable of imaging the distribution of superparamagnetic particles at high spatial and temporal resolution. For the reconstruction of the particle distribution, a system of linear equations has to be solved. The mathematical solution to this linear system can be obtained using a least-squares approach. In this paper, it is shown that the quality of the least-squares solution can be improved by incorporating a weighting matrix using the reciprocal of the matrix-row energy as weights. A further benefit of this weighting is that iterative algorithms, such as the conjugate gradient method, converge rapidly yielding the same image quality as obtained by singular value decomposition in only a few iterations. Thus, the weighting strategy in combination with the conjugate gradient method improves the image quality and substantially shortens the reconstruction time. The performance of weighting strategy and reconstruction algorithms is assessed with experimental data of a 2D MPI scanner.
Carboxyterminal Region of Hybrid Leukocyte Interferons Affects Antiviral Specificity (1982)

Four hybrid human leukocyte interferon (IFN-alpha) genes have been constructed and expressed in Escherichia coli using molecular cloning methods. Plasmids containing genes encoding human interferons, IFN-alpha A, IFN-alpha D, IFN-alpha I and several hybrids of the different IFN-alpha genes (formed by in vitro recombination at common restriction endonuclease sites located within the DNA sequence encoding mature polypeptides) joined identically to an E. coli trp promoter gave rise to bacterial-produced interferons with distinctly different antiviral activities. The expression plasmid which directs the synthesis of IFN-alpha I was constructed using a gene isolated from a human genomic library in a manner similar to the previous expression of IFN-alpha A and IFN-alpha D cDNA clones. The use of a cell-free transcription-translation system has allowed the calculation of the specific activities of IFN-alpha made from isolated DNA fragments containing these hybrid IFN-alpha genes. These bacterially-derived interferons vary considerably in their ability to inhibit vesicular stomatitis virus (VSV) in different mammalian cells. The results show that the cloned hybrid interferons have unique antiviral activities when compared with the parent interferons, and they demonstrate that more active IFN-alpha s can be made using recombinant DNA techniques.
Mass-Conserving Eulerian Liquid Simulation (2013)

We present a GPU friendly, Eulerian, free surface fluid simulation method that conserves mass locally and globally without the use of Lagrangian components. Local mass conservation prevents small-scale details of the free surface from disappearing, a problem that plagues many previous approaches, while global mass conservation ensures that the total volume of the liquid does not decrease over time. Our method handles moving solid boundaries as well as cells that are partially filled with solids. Due to its stability, it allows the use of large time steps that makes it suitable for both offline and real-time applications. We achieve this by using density-based surface tracking with a novel, unconditionally stable, conservative advection scheme. We also propose mass conserving methods to sharpen the interface and to reveal subgrid features of the liquid. While our approach conserves mass, volume loss is still possible but only temporarily. With constant mass, local volume loss causes a local increase of the density used for surface tracking which we detect and correct over time. We show the effectiveness of the proposed methods in several practical examples all running either at interactive rates or in real time.
Species‐specific action of (Pro3)GIP – a full agonist at human GIP receptors, but a partial agonist and competitive antagonist at rat and mouse GIP receptors (2015)

When evaluating new compounds, it is important to consider interspecies differences both at the receptor and ligand level. Thus, in rodent models, human GIP is a comparatively weak partial agonist. Human (Pro3)GIP was not an antagonist at human GIP receptors, so there is still a need for a potent antagonist in order to elucidate the physiology of human GIP.
Terahertz pulse generation beyond excitation pulse limitation by &#x03C7;(2) cascaded processes (2009)

We propose a novel technique for the generation of high power monocycle terahertz (THz) pulse beyond excitation pulse width limitation. When intense THz electric field generated by optical rectification lies in EO crystal, optical pulse itself gets modulated by emitted THz electric field. It causes excitation pulse compression and consequently gives rise to the enhancement of generation efficiency and its bandwidth. We experimentally demonstrate it using tilted wavefront excitation beam by LiNbO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> from Yb doped fiber laser.
A Euthymic Hairless Mouse Model of <i>Helicobacter pylori</i> Colonization and Adherence to Gastric Epithelial Cells In Vivo (1998)

The hairless mouse strain NS:Hr/ICR was examined as a potential small animal model of Helicobacter pylori colonization, adherence to gastric epithelial cells in vivo, and gastritis. Among several small animals tested, NS:Hr/ICR mice proved to be the most highly susceptible to H. pylori infection. Challenge with clinical isolates of H. pylori consisting of either phenotype I or II (VacA and CagA positive and negative, respectively) resulted in colonization by mucus-resident and epithelial cell-adherent bacterial populations. Cell-adherent bacteria resisted 80 cycles of top-speed Vortex washing and were recovered only by homogenization of serially washed glandular stomach tissue, indicating intimate association with the mucosal surface. Immunoperoxidase staining of paraffin sections of gastric tissue from infected mice revealed H. pylori antigens localized in the glandular region of the mucosa, with some colonized areas seen in the vicinity of submucosal mononuclear cell infiltration. The latter inflammatory reaction was observed as a function of the H. pylori phenotype (only type I induced inflammation) and the challenge dose (only those mice challenged with 10(8) CFU or higher showed the reaction). The NS:Hr/ICR strain of mice is a suitable miniature model of H. pylori infection and may prove useful in the quest for an efficacious mode of treatment for this common infection in humans.
Effects of a constricted nozzle on the arc phenomena in TIG welding process (2014)

Effects of a constricted nozzle on the arc phenomena in Tungsten Inert Gas (TIG) welding process are investigated by numerical simulation. The obtained results show that the temperature and velocity of the arc plasma are increased by attaching an additional gas nozzle which is called "constricted nozzle". As a result, the iron vapor does not diffused upward but transported outward. In addition, the heat transfer to the base metal surface is enhanced.
<title>Empirical analysis of new methods for computing minimum cost paths with turn constraints</title> (1998)

In this paper we describe a recently developed algorithm for computing least cost paths under turn angle constraints. If a graph representation of a two or three dimensional routing problem contains V vertices and El edges, then the new algorithm scales as O(IEI log V). This result is substantially better than O((EIIVI) algorithms for the more general problem of routing with turn penalties, which cannot be applied to large scale graphs. We also describe an enhancement to the new algorithm that dramatically improves the performance in practice. We provide empirical results showing that the new algorithm can substantially reduce the computation time required for constrained vehicle routing. This performance is sufficient to allow for the dynamic re-routing of vehicles in uncertain or changing environments. Keywords: Dijkstra's algorithm, least cost paths, range searching, routing, turn constraints.
System development and performance of the Deep-ocean Assessment and Reporting of Tsunamis (DART) system from 1997-2001 (2001)

As part of the U.S. National Tsunami Hazard Mitigation Program, the Deep Ocean As- sessment and Reporting of Tsunamis (DART) Project is an ongoing effort by the Pacific Marine En- vironmental Laboratory (PMEL) to develop and implement a capability for the early detection and near real-time reporting of tsunamis in the open ocean. A DART system consists of a seafloor system, capable of detecting tsunamis as small as 1 cm, and a surface buoy for near real-time communica- tions. An acoustic link is used to transmit the data from the seafloor system to the surface buoy. The data are then relayed via a NOAA Geostationary Operational Environmental Satellite (GOES) satel- lite link to ground stations, which demodulate the signals for immediate dissemination to Tsunami Warning Centers and PMEL. A DART quality control page is made available to the public in near real time via the World Wide Web (http://tsunami.pmel.noaa.gov/dartqc/WaveWatcher). The general system design is fundamentally as envisioned in 1996, but many technical challenges had to be overcome during the development process. The surface buoys now incorporate redundant electronic packages to improve reliability and data return, and the seafloor system design now al- lows for 2-year deployments, to reduce the cost and effort of maintaining the oceanic network. The end-to-end DART system concept has been proven through numerous deployments, starting in July 1997 and continuing up to the present configuration of five operating DART stations. Performance measures such as cumulative data return, scheduled test transmissions, triggered transmissions, data dropouts, and system failures will be discussed. The results will show that during the past 5 years, the DART Project has successfully developed and tested a prototype system, which will lead directly to an operational Pacific DART Network.
Hard problems in elliptic curve scalar multiplication (2010)

Abstract Number Theory and Cryptography are based on mathematical problems that are considered difficult to solve. “Difficult” in this case refers more to the computational requirements in finding a solution than to the conception of the problem. These problems are formally called “hard” problems. Some of the most well known examples are factoring large numbers, finding the discrete logarithms, theorem-proving, and the Traveling Salesman Problem. In the theory of Double Base Number System (DBNS)/Multiple Base Number System (MBNS), finding the best approximation for a given integer is a hard problem. This approximation can be used to compute Elliptic curve scalar multiplication in an efficient way. In this paper, we have come up with an algorithm for DBNS, which expresses any integer n in the form of DBNS with decreasing order of exponents.
Method for the production of {sup 99m}Tc compositions from {sup 99}Mo-containing materials (1998)

An improved method for producing .sup.99m Tc compositions from .sup.99 Mo compounds. .sup.100 Mo metal or .sup.100 MoO.sub.3 is irradiated with photons in a particle (electron) accelerator to ultimately produce .sup.99 MoO.sub.3. This composition is then heated in a reaction chamber to form a pool of molten .sup.99 MoO.sub.3 with an optimum depth of 0.5-5 mm. A gaseous mixture thereafter evolves from the molten .sup.99 MoO.sub.3 which contains vaporized .sup.99 MoO.sub.3, vaporized .sup.99m TcO.sub.3, and vaporized .sup.99m TcO.sub.2. This mixture is then combined with an oxidizing gas (O.sub.2(g)) to generate a gaseous stream containing vaporized .sup.99m Tc.sub.2 O.sub.7 and vaporized .sup.99 MoO.sub.3. Next, the gaseous stream is cooled in a primary condensation stage in the reaction chamber to remove vaporized .sup.99 MoO.sub.3. Cooling is undertaken at a specially-controlled rate to achieve maximum separation efficiency. The gaseous stream is then cooled in a sequential secondary condensation stage to convert vaporized .sup.99m Tc.sub.2 O.sub.7 into a condensed .sup.99m Tc-containing reaction product which is collected.