gebhart/patrepeval huggingface dataset:
Model System for Growing and Quantifying <i>Streptococcus pneumoniae</i> Biofilms In Situ and in Real Time (2004)

Streptococcus pneumoniae forms biofilms, but little is known about its extracellular polymeric substances (EPS) or the kinetics of biofilm formation. A system was developed to enable the simultaneous measurement of cells and the EPS of biofilm-associated S. pneumoniae in situ over time. A biofilm reactor containing germanium coupons was interfaced to an attenuated total reflectance (ATR) germanium cell of a Fourier transform infrared (FTIR) laser spectrometer. Biofilm-associated cells were recovered from the coupons and quantified by total and viable cell count methods. ATR-FTIR spectroscopy of biofilms formed on the germanium internal reflection element (IRE) of the ATR cell provided a continuous spectrum of biofilm protein and polysaccharide (a measure of the EPS). Staining of the biofilms on the IRE surface with specific fluorescent probes provided confirmatory evidence for the biofilm structure and the presence of biofilm polysaccharides. Biofilm protein and polysaccharides were detected within hours after inoculation and continued to increase for the next 141 h. The polysaccharide band increased at a substantially higher rate than did the protein band, demonstrating increasing coverage of the IRE surface with biofilm polysaccharides. The biofilm total cell counts on germanium coupons stabilized after 21 h, at approximately 10(5) cells per cm(2), while viable counts decreased as the biofilm aged. This system is unique in its ability to detect and quantify biofilm-associated cells and EPS of S. pneumoniae over time by using multiple, corroborative techniques. This approach could prove useful for the study of biofilm processes of this or other microorganisms of clinical or industrial relevance.
Functionalization of Graphene <i>via</i> 1,3-Dipolar Cycloaddition (2010)

Few-layer graphenes (FLG) produced by dispersion and exfoliation of graphite in N-methylpyrrolidone were successfully functionalized using the 1,3-dipolar cycloaddition of azomethine ylides. The amino functional groups attached to graphene sheets were quantified by the Kaiser test. These amino groups selectively bind to gold nanorods, which were introduced as contrast markers for the identification of the graphene reactive sites. The interaction between gold nanorods and functionalized graphene was followed by UV-vis spectroscopy. The presence of the organic groups was confirmed by X-ray photoelectron spectroscopy and thermogravimetric analysis. The sheets were characterized by transmission electron microscopy, demonstrating the presence of gold nanorods distributed uniformly all over the graphene surface. This observation indicates that reaction has taken place not just at the edges but also at the internal C horizontal lineC bonds of graphene. Our results identify exfoliated graphene as a considerably more reactive structure than graphite and hence open the possibility to control the functionalization for use as a scaffold in the construction of organized composite nanomaterials.
Performance Analysis of Large Receive Offload in a Xen Virtualized System (2009)

System-level virtualization provides us various advantages including independent and isolated computing environments on which multiple operating systems can be executed, and improved resource utilization. These benefits come with performance overheads and network operation is one of most typical cases. In this paper, we first present the experimental results of network performance with LRO under varying message sizes and maximum transmission unit (MTU). We analyze the effectiveness of large receive offload (LRO) in a consolidated execution environment based on Xen. When SPECjbb, a CPU-intensive workload, and network receiver are executed on separated domains, LRO in physical and virtual NICs improve the throughput up to 8 and 14%, respectively.
Electromagnetic fields and waves (2013)

The latest edition of Electromagnetic Fields and Waves retains an authoritative, balanced approach, in-depth coverage, extensive analysis, and use of computational techniques to provide a complete understanding of electromagnetic—important to all electrical engineering students. An essential feature of this innovative text is the early introduction of Maxwell's equations, together with the quantifying experimental observations made by the pioneers who discovered electromagnetics. This approach directly links the mathematical relations in Maxwell's equations to real experiments and facilitates a fundamental understanding of wave propagation and use in modern practical applications, especially in today's wireless world. New and expanded topics include the conceptual relationship between Coulomb's law and Gauss's law for calculating electric fields, the relationship between Biot-Savart's and Ampere's laws and their use in calculating magnetic fields from current sources, the development of Faraday's law from experimental observations, and a comprehensive discussion and analysis of the displacement current term that unified the laws of electromagnetism. The text also includes sections on computational techniques in electromagnetics and applications in electrostatics, in transmission lines, and in wire antenna designs. The antennas chapter has been substantially broadened in scope; it now can be used as a stand-alone text in an introductory antennas course. Advantageous pedagogical features appear in every chapter: examples that illustrate key topics and ask the reader to render a solution to a question or problem posed; an abundant number of detailed figures and diagrams, enabling a visual interpretation of the developed mathematical equations; and multiple review questions and problems designed to strengthen and accelerate the learning process. Helpful material is included in six appendices, including answers to selected problems. Unlike other introductory texts, Electromagnetic Fields and Waves does not bog readers down with equations and mathematical relations. Instead, it focuses on the fundamental understanding and exciting applications of electromagnetics. Not-for-sale instructor resource material available to college and university faculty only; contact publisher directly.
Interaction in Semi-Immersive Large Display Environments (1998)

This paper evaluates interaction methods within the general framework of navigation, selection, and manipulation. It considers large display environments and, in particular, the virtual workbench, comparing this system with HMD and CAVE systems. The paper addresses three issues: (a) identifying the characteristics that set the workbench apart from other virtual environments; (b) determining types, organization, and examples of interaction techniques: (c) evaluating how these techniques perform on the workbench to determine which perform best. The evaluations are based on an extensive set of user observations. Also discussed are some problems that stereoscopic display coupled with interaction bring out.
Relapsed Multiple Myeloma (2010)

Advances in treatment options for patients with multiple myeloma have made a significant impact on the overall survival of patients and have helped achieve levels of response and duration of remission previously not achievable with standard chemotherapy-based approaches. These improvements are due, in large part, to the development of the novel agents thalidomide, bortezomib, and lenalidomide, each of which has substantial single-agent activity. In addition, a large number of second-generation agents are also in clinical development, such that the repertoire of available treatment options continues to expand. To better interpret clinical trials performed in the relapsed setting, it is important that definitions of relapse categories are used to help better pinpoint the specific benefit for a given therapy, especially in the combination therapy setting as it aids in determining if ongoing work should be continued or abandoned for a given new agent. Insights from preclinical modeling and in vitro work have identified several new combinations, new targets and second- or third-generation versions of existing targets that hold great promise in the setting of relapsed myeloma. Combinations of thalidomide, bortezomib, and lenalidomide with conventional agents or among each other have resulted in enhanced response rates and efficacy. Clinical trials of agents such as carfilzomib, pomalidomide, vorinostat, panobinostat, and elotuzomab are just a few of the many exciting new compounds that are being tested in phase 1 and phase 2 clinical trials for relapsed patients. Further clinical and translational testing are critical to better understanding how best to combine these new agents, as well as identifying patient populations that may best benefit from treatment with these developing new agents.
PRED-TMBB: a web server for predicting the topology of  -barrel outer membrane proteins (2004)

The beta-barrel outer membrane proteins constitute one of the two known structural classes of membrane proteins. Whereas there are several different web-based predictors for alpha-helical membrane proteins, currently there is no freely available prediction method for beta-barrel membrane proteins, at least with an acceptable level of accuracy. We present here a web server (PRED-TMBB, http://bioinformatics.biol.uoa.gr/PRED-TMBB) which is capable of predicting the transmembrane strands and the topology of beta-barrel outer membrane proteins of Gram-negative bacteria. The method is based on a Hidden Markov Model, trained according to the Conditional Maximum Likelihood criterion. The model was retrained and the training set now includes 16 non-homologous outer membrane proteins with structures known at atomic resolution. The user may submit one sequence at a time and has the option of choosing between three different decoding methods. The server reports the predicted topology of a given protein, a score indicating the probability of the protein being an outer membrane beta-barrel protein, posterior probabilities for the transmembrane strand prediction and a graphical representation of the assumed position of the transmembrane strands with respect to the lipid bilayer.
Avian sarcoma virus gag precursor polypeptide is not processed in mammalian cells (1982)

We studied intracellular avian gag proteins (internal structural proteins of virions) in several mammalian cell lines transformed by Rous sarcoma virus. All lines examined contain gag antigens as determined by radioimmune assay. We used the techniques of protein blotting from polyacrylamide gels, which detects nanogram quantities of viral protein, to investigate the size of intracellular viral polypeptides. All of the lines that contained enough viral protein to be amenable to this type of analysis synthesized Pr76, the avian sarcoma virus gag precursor polypeptide, but failed to process it into mature virion proteins. In some cell lines, the recovery of Pr76 was greatly enhanced by the addition of a mixture of protease inhibitors, including the sulfhydryl-blocking reagent N-ethylmaleimide, to the lysis buffer. At least several of the mammalian cells also synthesized a viral polypeptide the size of Pr180, the precursor to reverse transcriptase. Since Rous sarcoma virus does not replicate or replicates extremely poorly in mammalian cells, the lack of processing suggests that cleavage and virion assembly are invariably associated.
A Monopole Antenna Made of a Transparent Conductive Film (2007)

As mobile wireless communications have progressed dramatically in recent years, many mobile terminals are becoming smaller and smaller and miniaturization of the antennas employed in mobile devices is required accordingly. In this paper, a monopole antenna that consists of one-half of a bow-tie dipole antenna, made of optically transparent conductive thin film and mounted above a ground plane, is investigated. The antenna is designed to work at 2.4 GHz and the radiation element of the antenna is made of several transparent conductive films with different sheet resistivities. It is found that the gain lowering of the antenna varies from 4.4 dB to 0.2 dB at 2.4 GHz, and the efficiency of the antenna increases from 46% to 93% at the same frequency, as the sheet resistivity of the film decreases from 19.8 Omega/sq to 1.3 Omega/sq, respectively. The antenna is analyzed by a wire-grid model based on the moment method. The resistance of the film is taken into account by parallelly loading a resistance on every discretized element. It is demonstrated after that the analyzed results are in good agreement with the experimental ones
Chloroquine causes lysosomal dysfunction in neural retina and RPE: Implications for retinopathy (2004)

Chronic use of chloroquine has been shown to induce numerous pathophysiological defects in the retina. This drug has the ability to alter pH of intracellular compartments and lysosomal function of the retinal pigment epithelium (RPE) and retinal neurons may constitute the basis of chloroquine retinopathy. The aim of the current study was to investigate pathogenic alterations in retinal cells continuously exposed to chloroquine using appropriate in vivo and in vitro models. Male hooded Lister rats were implanted with osmotic mini pumps which released chloroquine continuously over a period of seven days. The eyes were processed for electron microscopy and ultrastructural abnormalities determined in the neural retina and quantified using stereology in the retinal pigment epithelium (RPE). RPE were also exposed to chloroquine in vitro and lysosomal pH changes were investigated using a pH sensitive probe. Degradative capacity was also analysed using FITC labeled rod outer segments (ROS). Chloroquine-treated animals displayed several ultrastructural abnormalities including numerous membranous cytoplasmic bodies (MCBs) in retinal neurons. Cone photoreceptors displayed numerous MCBs although rods did not. The RPE of the treated groups all showed significantly higher numbers of lysosomal associated organelles (LAO) than the control group (p < 0.001). The in vitro experiments demonstrated chloroquine-mediated rises in lysosomal pH and an increase in lysosome/phagosome accumulation of ROS in the chloroquine treated group (p < 0.01). The current study demonstrates that chloroquine disrupts lysosomal function in retinal neurons and RPE. The evidence presented provides a clear pathogenic basis for the functional defects experienced by patients with chloroquine retinopathy.
Adaptive predictive control using recurrent neural network identification (2009)

This paper presents a new adaptive predictive control algorithm which consists of an on-line process identification part and a predictive control strategy which is updated every time a process model change is identified. The identification method is based on recurrent neural network (RNN) nonlinear AutoRegressive with eXternal input (NARX) model derived from dynamic feedforward neural network by adding feedback connection between output and input layers. Two model-based predictive control strategies have been studied: the generalized predictive controller (GPC) and nonlinear adaptive model predictive controller (NAMPC). The neural network training and validation data are obtained from the open-loop simulation of a validated first principles plant model. The identified neural network (NN) model is validated using the following three different validation algorithms: (1) one-step ahead cross-correlation; (2) Akaike's final prediction error (AFPE) estimate; and (3) 5-step ahead prediction simulations. The algorithm has been applied to the temperature control of a fluidized bed furnace reactor of the steam deactivation unit of a fluid catalytic cracking (FCC) pilot plant used to evaluate catalyst performance. The validation results show that the RNN models the reactor to a high degree of accuracy. Simulation results show that the proposed NAMPC control strategy outperforms the GPC at the expense of extra computation time.
An accelerated separable median filter with sorting networks (2015)

Since the computer vision technologies are used to extract features from the edges of images, the median filter is frequently used as a pre-processing operation to improve the quality of feature objects. However, the median filter algorithms still have the limitation on integrating with the mobile systems due to the large computation overhead. Since the median filter accounts for a large proportion of total computation, this paper proposes a separable median filter to resolve the limitation. The proposed separable median filter is implemented with the sorting network, and reuses the data sorted at neighbor pixels, reducing duplicated comparisons.
Experiment on Solitons in the Dissipative Toda Lattice Using Nonlinear Transmission Line (1979)

Adding dissipative elements to a nonlinear transmission line equivalent to the Toda lattice, we have studied the behavior of a soliton propagating in the dissipative system. The damping rate is found to be explained to large extent by the theory derived from the K-dV equation with a loss term, while its slight dependence on the initial amplitude of the soliton is explained by the theory of the dissipative Toda lattice given by Kako. For a relatively small conductance parallel to the nonlinear capacitor, a somewhat distorted shape of the soliton followed by the long `dip on tail' was observed, which is compared with the theory given by Karpman and Maslov. The `bump on tail' behind the soliton, which is considered as one of the features of the dissipative Toda lattice, was also observed only for the case of connecting a relatively large resistance in series to each inductance.
FS-FBMC: A flexible robust scheme for efficient multicarrier broadband wireless access (2012)

An alternative implementation of the filter bank multicarrier (FBMC) concept is introduced. It is based on an FFT whose size is the length of the prototype filter. The approach clarifies the connection with OFDM and its main benefit is in the receiver, where high performance sub-channel equalization and timing offset compensation are achieved in a straightforward manner without additional delay. The scheme is particularly appropriate for broadband wireless access, to cope with fragmented frequency bands and to optimize the utilization of the spectrum, for example with the help of water-filling based sub-channel loading algorithms. The context of TV white spaces is taken for illustration. An issue with the proposed scheme is the computational complexity in the receiver and an approach having the potential for substantial savings is mentioned.
[Studies on recombinant chitinase and SXP-1 antigens as antimicrofilarial vaccines]. (1999)

The recombinant chitinase, fragments F7R2 and F8R2 and SXP-1 could provide partial protection against microfilaremia in jirds.
Dimension Increase in Metal-Oxide-Semiconductor Memories and Transistors (2010)

In response to the ceaseless requirement for extended performance of transistor in LSI, continual scaling has been achieved since early 1970's. Sizes of transistors in products measured 12 m in 1970 and around 45 nm in 2009. The scaling of device size has been brought about 4-fold increase in memory's volume and processor's performance every three years. Since there existed a limitation of amount of signal charges in DRAM against the cell size scaling, DRAM had first encountered the imitation of the volume size at 1 megabit in mid 1980's. To overcome the limitation, it began to employ a 3-D capacitor structure such as trench capacitor or stack capacitor. Even with the 3-D structures, its maximum volume of DRAM in a chip is estimated to be 64 gigabit provided that the amount of signal charges stored in a cell must be kept constant against the cell scaling. To solve the deadlock, the employment of an extra high-k dielectrics, and a vertical stack of a cell transistor with a capacitor will be inevitable in near future. Regarding NAND flash memory, multi-stacks of flash transistors have already been proposed. Since flash memory cell consists of one cell transistor in a memory cell and no contact is needed to source and drain in a string of cell transistors, the multi-stack is relatively easier than that of DRAM. On the other hand, field-effect transistor itself will encounter the ultimate size limit of 5-10 nm. Only about several tens of silicon atoms exist in the channel region of 10-nm transistor. Normal filed-effect operation will be impossible due to fatal short-channel effects in that dimension range. Particularly a ratio of off current to on current becomes worse causing unacceptably large stand-by power consumption. If the scaling pace is still kept constant, the ultimate limit will be encountered within 15 years. Forecasting the limitation, various kinds of 3-D transistors have been proposed, however, they will still suffer from the short-channel effects same as 2-D transistors. Due to a limitation of invariable channel length of vertical transistor, it will be practical in products that the vertical transistor is employed together with 2-D one in an LSI chip. To cope with these fundamental limits in miniaturization of devices, various kinds of chip stack will be dominant in LSI products in response to the requirement for smaller package used in personal-use, hand-held products.
Christian name Rosee (1940)

Journal Article Christian name Rosee Get access S. E. Y. S. E. Y. Search for other works by this author on: Oxford Academic Google Scholar Notes and Queries, Volume 179, Issue 9, 31 August 1940, Page 154, https://doi.org/10.1093/nq/179.9.154c Published: 31 August 1940
Interface synthesis for heterogeneous multi-core systems from transaction level models (2007)

This paper presents a tool for automatic synthesis of RTL interfaces for heterogeneous MPSoC from transaction level models (TLMs). The tool captures the communication parameters in the platform and generates interface modules called universal bridges between buses in the design. The design and configuration of the bridges depend on several platform components including heterogeneity of the components, traffic on the bus, size of messages and so on. We define these parameters and show how the synthesizable RTL code for the bridge can be automatically derived based on these parameters. We use industrial strength design drivers such as an MP3 decoder to test our automatically generated bridges for a variety of platforms and compare them to manually designed bridges on different quality metrics. Our experimental results show that performance of automatically generated bridges are within 5% of manual design for simple platforms but surpasses them for more complex platforms. The area and RTL code size is consistently better than manual design while giving 5 orders of improvement in development time.