gebhart/patrepeval huggingface dataset:
Complete genome sequence and comparative analysis of the metabolically versatile <i>Pseudomonas putida</i> KT2440 (2002)

Pseudomonas putida is a metabolically versatile saprophytic soil bacterium that has been certified as a biosafety host for the cloning of foreign genes. The bacterium also has considerable potential for biotechnological applications. Sequence analysis of the 6.18 Mb genome of strain KT2440 reveals diverse transport and metabolic systems. Although there is a high level of genome conservation with the pathogenic Pseudomonad Pseudomonas aeruginosa (85% of the predicted coding regions are shared), key virulence factors including exotoxin A and type III secretion systems are absent. Analysis of the genome gives insight into the non-pathogenic nature of P. putida and points to potential new applications in agriculture, biocatalysis, bioremediation and bioplastic production.
Methanol Production By Reduction Of Formic Acid Over Cu Catalyst Under Hydrothermal Conditions (2010)

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation Min Cheng, Bing Wu, Fangming Jin, Xiaokun Duan, Yuanqing Wang; Methanol Production By Reduction Of Formic Acid Over Cu Catalyst Under Hydrothermal Conditions. AIP Conf. Proc. 24 November 2010; 1251 (1): 234–237. https://doi.org/10.1063/1.3529286 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAIP Publishing PortfolioAIP Conference Proceedings Search Advanced Search |Citation Search
Development and Use of an Attenuated Total Reflectance/Fourier Transform Infrared (ATR/FT-IR) Spectral Database To Identify Foreign Matter in Cotton (2006)

The presence of foreign matter in cotton seriously affects the cotton grade and thus the price per bale paid by the spinner to the grower, the efficiency of the spinning and ginning operations, and the quality of the final woven product. Rapid identification of the nature of the extraneous matter in cotton at each stage of cleaning and processing is necessary to permit actions to eliminate or reduce its presence and improve efficiency and quality. Although several instruments are being successfully employed for the measurement of contamination in cotton fibers based on particle size/weight, no commercial instrument is capable of accurate qualitative identification of contaminants. To this end, ATR/FT-IR spectra of retrieved foreign matter were collected and subsequently rapidly matched to an authentic spectrum in a spectral database. The database includes contaminants typically classified as "trash", cotton plant parts (hull, shale, seed-coat fragments, bract, cacyx, leaf, bark, sticks, and stems) and grass plant parts (leaf and stem); "foreign objects and materials", synthetic materials (plastic bags, film, rubber, bale wrapping and strapping); organic materials (other fibers, yarns, paper, feathers, and leather); plus entomological and physiological sugars and inorganic materials (sand and rust). The spectral matching resulted in consistently high-score identification of the foreign matter based on chemical composition, irrespective of its particle size. The method is envisioned to be employed with stand-alone rugged infrared instrumentation to provide specific identification of extraneous materials in cotton as opposed to only general classification of the type by particle size or shape.
Adding <scp>l</scp>-3-(2-Naphthyl)alanine to the Genetic Code of <i>E. coli</i> (2002)

An unnatural amino acid, L-3-(2-naphthyl)alanine, has been site-specifically incorporated into proteins in Escherichia coli. An orthogonal aminoacyl-tRNA synthetase was evolved that uniquely aminoacylates the unnatural amino acid onto an orthogonal amber suppressor tRNA, which delivers the acylated amino acid in response to an amber nonsense codon with translational fidelity greater than 99%. This result, together with the in vivo site-specific incorporation of O-methyl-L-tyrosine reported previously, demonstrate that this methodology may be applicable to a host of amino acids. The expansion of the genetic code to include amino acids beyond the common 20 would provide an opportunity to better understand and possibly enhance protein (and perhaps organismal) function.
How much can an electric dipole stabilize a nematic phase? Polar and non-polar isosteric derivatives of [closo-1-CB9H10]− and [closo-1,10-C2B8H10] (2010)

Replacement of a C–C fragment with an N+–B− fragment leads to pairs of isosteric non-polar/polar nematics with a difference in the calculated molecular dipole moment of about 12 D. Contrary to the expectations, the uniform increase of the dipole moment does not affect phase stability equally, and a strong dependence on the substituent structure is observed. For one of the polar derivatives (5b, µ = 20 D) a record high dielectric anisotropy (Δε = 113) was measured in dilute nematic solutions.
The ultimate invasion of privacy: Identity theft (2011)

Identity theft has become one of the fastest growing crimes. Most people are unaware of the amount of data they disclose over all the Internet services proposed by search engines, social networking sites, e-commerce web sites, free online tools, etc. They are also unaware that this data can be easily aggregated, data-mined and linked together, which may lead to a potential identity theft should it fall into the wrong hands. If one adds up all of his online searching, communicating, shopping, browsing, blogging, chatting, reading and news sharing, one would realize that one revealed a complete picture of oneself and perhaps some information about his relatives, friends, colleagues, employer, etc. The potential value of this data is considerable for criminals. This paper deals with identity theft and all the issues raised by this type of computer crime. More precisely, it illustrates the variety of information that hackers may want to sift through, the attacks that they may perform and the locations where they can find the information.
Laparoscopic video analysis for training and image-guided surgery (2011)

Automatic analysis of Minimally Invasive Surgical video has the potential to drive new solutions for alleviating needs of safe and reproducible training programs, objective and transparent evaluation systems and navigation tools to assist surgeons and improve patient safety. Surgical video is an always available source of information, which can be used without any additional intrusive hardware in the operating room. This paper is focused on surgical video analysis methods and techniques. It describes authors' contributions in two key aspects, the 3D reconstruction of the surgical field and the segmentation and tracking of tools and organs based on laparoscopic video images. Results are given to illustrate the potential of this field of research, like the calculi of the 3D position and orientation of a tool from its 2D image, or the translation of a preoperative resection plan into a hepatectomy surgical procedure using the shading information of the image. Research efforts are required to further develop these technologies in order to harness all the valuable information available in any video-based surgery.
Automatic Clock Abstraction from Sequential Circuits (1995)

Our goal is to transform a low-level circuit design into a more abstract representation. A pre-existing tool, Tranalyze [4], takes a switch-level circuit and generates a functionally equivalent gatelevel representation. This work focuses on taking that gate-level sequential circuit and performing a temporal analysis which abstracts the clocks from the circuit. The analysis generates a cycle-level gate model with the detailed timing abstracted from the original circuit. Unlike other possible approaches, our analysis does not require the user to identify state elements or give the timings of internal state signals. The temporal analysis process has applications in simulation, formal verification, and reverse engineering of existing circuits. Experimental results show a 40%-70% reduction in the size of the circuit and a 3X-150X speedup in simulation time.
A Novel Machine Learning Data Preprocessing Method for Enhancing Classification Algorithms Performance (2015)

Data preprocessing describes any type of processing methods performed on raw data to prepare it for another processing procedure. Commonly used as a preliminary data mining practice, data preprocessing methods transforms the data into a format that will be more easily and effectively processed for the classification algorithms. In this paper, a novel data preprocessing method is proposed and evaluated in three difficult classification data sets of the well known UCI Repository, in which various classifiers have average performance lower than 75%. The three UCI repository datasets that have been used are the Mammographic masses, Indian Liver and Contraceptive Method. The performance of our proposed data preprocessing method and Principal Component Analysis preprocessing method was evaluated using the 10-fold cross validation method assessing five classification algorithms, Nearest-neighbour classifier (IB1), C4.5 algorithm implementation (J48), Random Forest, Multilayer Perceptron and Rotation Forest, respectively. The classification results are presented and compared analytically. The results indicate that the generated features after our proposed preprocessing method implementation to the original dataset markedly improve the performance of the classification algorithms.
Performance evaluation of novel distributed coverage techniques for swarms of flying robots (2014)

This paper focuses on the coverage of specific Zones of Interest that can change dynamically over time by using a swarm of flying robots. The mobility of the flying devices is achieved by the design of two distributed and local algorithms. The first algorithm is based on Particle Swarm Optimization (PSO) and Virtual Forces Algorithm (VFA). We modify the classical PSO approach to propose a totally distributed algorithm, which only requires the flying robots to receive local information from the neighbors to update their velocity and trajectory (PSO-S). This new distributed version of the PSO is combined with a distributed version of the Virtual Forces Algorithm. The second algorithm is a distributed implementation of the VFA (VFA-D). To the best of our knowledge, these two approaches are novel in their distributed character, scalability and implementability on resource-constrained devices. We show that the proposed algorithms are reactive, i.e. able to capture in an effective fashion the events happening within the field even if the position of the events changes over time. To show the effectiveness of the proposed techniques, we perform extensive simulations to compare both the PSO-S and the VFA-D schemes with a centralized version of the VFA. Simulations show the good performance in terms of coverage and traveled distance as well as the high reactivity of both PSO-S and VFA-D when the ZoI changes.
Ultrahigh-Speed Low-Power DACs Using InP HBTs for Beyond-100-Gb/s/ch Optical Transmission Systems (2011)

This paper presents the circuit designs and measured performance of two ultrahigh-speed low-power 6-b digital-to-analog converters (DACs) using InP-based heterojunction bipolar transistors (HBTs) for beyond-100-Gb/s/ch optical transmission systems. The first design is based on an R-2R ladder-based current-steering architecture with a novel double-sampling technique that relaxes the speed restraints for the DAC and helps achieve ultrahigh-speed operation. The DAC with the double-sampling technique achieves an excellent sampling speed of up to 32 GS/s with low power consumption of 1.4 W. The second design is based on a new timing alignment technique. The DAC with the timing alignment technique operates at a sampling rate of 28 GS/s with very low power consumption of 0.95 W and achieves an excellent figure of merit (0.53 pJ per conversion step). It provides a clear multilevel modulated signal for QAM transmission and can be applied to beyond-100-Gb/s/ch optical transmission systems.
Estimating Gait Phase using Low-Level Motion (2008)

This paper presents a method that is capable of robustly estimating gait phase of a human walking from a sequence of images using only low-level motion. The approach we adopt is first to learn statistical motion models of the trajectories we would expect to observe for each of the main limbs. We then extract a sparse cloud of motion features from an image sequence using a standard feature tracker. By comparing the motion of the tracked features to our models and integrating over all feature points, a HMM can be used to estimate the most likely sequence of phases. This method is then extended to be invariant to translation by using a particle filter to track the dominant foreground object. Experimental results show that the presented system is capable of extracting gait phase to a high level of accuracy, demonstrating robustness to changes in height of the walker, gait frequency and individual gait characteristics. The purpose of this work is to ask the question "how much information can we extract if we choose to throw away all appearance cues and rely only on motion? ".
Cytotoxic effects of Mn(III)<i>N</i>-alkylpyridylporphyrins in the presence of cellular reductant, ascorbate (2011)

Due to the ability to easily accept and donate electrons Mn(III)N-alkylpyridylporphyrins (MnPs) can dismute O(2)(·-), reduce peroxynitrite, but also generate reactive species and behave as pro-oxidants if conditions favour such action. Herein two ortho isomers, MnTE-2-PyP(5+), MnTnHex-2-PyP(5+), and a meta isomer MnTnHex-3-PyP(5+), which differ greatly with regard to their metal-centered reduction potential, E(1/2) (Mn(III)P/Mn(II)P) and lipophilicity, were explored. Employing Mn(III)P/Mn(II)P redox system for coupling with ascorbate, these MnPs catalyze ascorbate oxidation and thus peroxide production. Consequently, cancer oxidative burden may be enhanced, which in turn would suppress its growth. Cytotoxic effects on Caco-2, Hela, 4T1, HCT116 and SUM149 were studied. When combined with ascorbate, MnPs killed cancer cells via peroxide produced outside of the cell. MnTE-2-PyP(5+) was the most efficacious catalyst for peroxide production, while MnTnHex-3-PyP(5+) is most prone to oxidative degradation with H(2) , and thus the least efficacious. A 4T1 breast cancer mouse study of limited scope and success was conducted. The tumour oxidative stress was enhanced and its microvessel density reduced when mice were treated either with ascorbate or MnP/ascorbate; the trend towards tumour growth suppression was detected.
Optimization models and algorithms: an emerging technology for the motor carrier industry (1991)

Optimization models and algorithms for transportation are reviewed with the intent the providing lay management with at least a feeling of the range of technologies that are available and a sense of the strengths and weaknesses of each. The different types of applications of optimization to transportation that have evolved are described, and it is indicated how different methods are suited to different types of problems. Special attention is given to real-time optimization for truckload motor carriers. An interactive graphic simulation system, called MIDAS (micro dispatch and simulation), that was developed for demonstrating optimization methods is reported. It allows the user to compete against the optimization model in a real-time framework.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Design, Synthesis, and Cytoprotective Effect of 2-Aminothiazole Analogues as Potent Poly(ADP-Ribose) Polymerase-1 Inhibitors (2009)

A series of novel poly(ADP-ribose) polymerase-1 (PARP-1) inhibitors were designed within 2-aminothiazole analogues (4-10) based on a constructed three-dimensional pharmacophore model. After synthesis, the inhibitory effect on PARP-1 activity and the cytoprotective action of these compounds were tested and evaluated. Among them, compounds 4-6 and 10 appeared to be potent PARP-1 inhibitors with IC(50) values less than 1 microM, which had been perfectly predicted by pharmacophore model. These compounds proved to be highly potent against cell injury induced by H(2)O(2) and oxygen-glucose deprivation (OGD) in PC12 cells. These novel 2-aminothiazole analogues are potentially applicable as neuroprotective agents for the treatment of neurological diseases.
Cooperative Communications (2007)

This article reviews progress in cooperative communication networks. Our survey is by no means exhaustive. Instead, we assemble a representative sample of recent results to serve as a roadmap for the area. Our emphasis is on wireless networks, but many of the results apply to cooperation in wireline networks and mixed wireless/wireline networks. We intend our presentation to be a tutorial for the reader who is familiar with information theory concepts but has not actively followed the field. For the active researcher, this contribution should serve as a useful digest of significant results. This article is meant to encourage readers to find new ways to apply the ideas of network cooperation and should make the area sufficiently accessible to network designers to contribute to the advancement of networking practice.
3D prestack depth migration by hybrid method (2006)

The hybrid migration approach does wavefield extrapolation using finite‐difference and phase‐shift operators. It has the advantages of adapting lateral velocity variations and high migration dips. In this paper, the hybrid method based on the approximation of the square root is presented. The error analysis and the comparisons with some typical methods are also given. The migration test for a 3D field data show that it has good imaging ability.
Urinary bladder temperature monitoring (1980)

A new method of core body temperature monitoring is introduced and compared to currently used methods. A close correlation exists between urinary bladder temperatures and each of the techniques studied. The correlation is good when compared to esophageal and rectal temperature and best when compared to pulmonary arterial blood temperature. During rapid rewarming after extracorporeal circulation, the urine temperature consistently increases faster than rectal or esophageal and seemingly is a better measure of blood temperature rather than muscle mass temperature. Urine temperature monitoring is reliable, safe, convenient, and accurate for routine intraoperative and postoperative continuous use in adult patients with urethral catheterization.
Cytokine-induced, nitric oxide-dependent, intracellular antirickettsial activity of mouse endothelial cells. (1997)

In a murine model of rickettsial disease in which, as in human rickettsioses, endothelial cells are the major target of infection, depletion of IFN-gamma or TNF-alpha converts a sublethal infection into a uniformly fatal disease with overwhelming rickettsial growth and decreased nitric oxide (NO) synthesis. The kinetics of NO production and rickettsial survival and growth were examined on Days 1, 2, and 3 after inoculation of endothelial cells with Rickettsia conorii under four different experimental conditions: (a) no cytokine treatment, (b) treatment with IFN-gamma and TNF-alpha, (c) treatment with cytokines and NG monomethyl-L-arginine, a competitive inhibitor of NO synthesis, and (d) treatment with sodium nitroprusside, a source of NO. Endothelial cells were examined for the presence of inducible nitric oxide synthase mRNA by specific reverse transcriptase-PCR after stimulation with IFN-gamma and TNF-alpha. Cytokine-stimulated and unstimulated rickettsiae-infected endothelial cells were examined by electron microscopy to observe the cellular and rickettsial events. Transformed and diploid mouse endothelial cells stimulated by the combination of recombinant murine IFN-gamma and TNF-alpha killed intracellular Rickettsia conorii by a mechanism that required the synthesis of NO. The antirickettsial effect and NO synthesis were inhibited by treatment of endothelial cells with NG monomethyl-L-arginine. Addition of nitroprusside, which released NO, also exerted a strong antirickettsial effect in the absence of IFN-gamma and TNF-alpha. Endothelial inducible nitric oxide synthase mRNA was detected 4 hours after cytokine stimulation, increased substantially at 8 hours, and decreased to low levels by 72 hours. Ultrastructural evaluation revealed that endothelial cells effected rickettsial killing in association with autophagy. Double membranes of endothelial cell granular endoplasmic reticulum surrounded rickettsiae, which were also observed being destroyed within phagolysosomes. This study demonstrated for the first time that endothelial cells are capable of killing rickettsiae. When stimulated by the combination of IFN-gamma and TNF-alpha, mouse endothelial cells kill Rickettsia conorii by an NO-dependent mechanism. Within the endothelium, NO exerts a rickettsicidal effect.
Entry of Influenza A Virus with a α2,6-Linked Sialic Acid Binding Preference Requires Host Fibronectin (2012)

The receptor binding specificity of influenza A virus is one of the major determinants of viral tropism and host specificity. In general, avian viral hemagglutinin prefers to bind to α2,3-linked sialic acid, whereas the human viral hemagglutinin prefers to bind to α2,6-linked sialic acid. Here, we demonstrate that host fibronectin protein plays an important role in the life cycle of some influenza A viruses. Treating cells with anti-fibronectin antibodies or fibronectin-specific small interfering RNA can inhibit the virus replication of human H1N1 influenza A viruses. Strikingly, these inhibitory effects cannot be observed in cells infected with H5N1 viruses. By using reverse genetics techniques, we observed that the receptor binding specificity, but not the origin of the hemagglutinin subtype, is responsible for this differential inhibitory effect. Changing the binding preference of hemagglutinin from α2,6-linked sialic acid to α2,3-linked sialic acid can make the virus resistant to the anti-fibronectin antibody treatment and vice versa. Our further characterizations indicate that anti-fibronectin antibody acts on the early phase of viral replication cycle, but it has no effect on the initial binding of influenza A virus to cell surface. Our subsequent investigations further show that anti-fibronectin antibody can block the postattachment entry of influenza virus. Overall, these results indicate that the sialic acid binding preference of influenza viral hemagglutinin can modulate the preferences of viral entry pathways, suggesting that there are subtle differences between the virus entries of human and avian influenza viruses.