gebhart/patrepeval huggingface dataset:
SU‐FF‐I‐59: A Machine Independent Threshold Method for PET Target Delineation (2007)

Purpose: We have developed a PET image segmentation method for accurate target delineation and volume estimation and compared the performance with other published methods without prior volume estimates from CT or MR. Method and Materials: Eight spheres containing a uniform concentration of FDG and ranging in size from 1 cc to 95 cc were imaged in a Jaszczak phantom. The spheres to background concentration ratio were variable from 3:1 to 12:1. Our hypothesis is that the optimal threshold depends on target volume and target/background concentration ratio and can be derived only from PET image. However, the target volume and concentration ratio both can not be obtained from image directly. For this work, a mean intensity segmentation method was used to obtain an initial target volume. Based on this initial volume estimate and source/background ratio, the concentration ratio was computed. This ratio combined with initial volume provided enough information to derive desired threshold to segment PET image and outline target volume. These volumes were compared with the actual measured sphere volumes. To determine the performance of this method, we also compared the segmentation results from adaptive thresholding, mean SUV and spatial derivative segmentation methods. Preliminary patient studies of lung lesion were also conducted. Results: The overall average error for sphere volume estimation was 8.7% . The performance was robust and uniform for all spheres in wide range of size and concentration ratio. Preliminary patient studies showed substantial clinic utility. Conclusions: This method results a high‐quality and uniform performance for PET image segmentation with acceptable clinic delineation. The method was shown to be superior compared to other methods in phantom studies overall, especially for small volumes.
Approximate Search in Very Large Files Using the Pigeonhole Principle (2013)

This paper presents a new technique for efficient searching with fuzzy criteria in very large information systems. The suggested technique uses the Pigeonhole Principle approach. This approach can be utilized with different embodiments, but the most effective realization would be to amplify some already given intrinsic approximate matching capabilities, like those in the FuzzyFind method [1][2]. Considering the following problem, a data to be searched is presented as a bit-attribute vector. The searching operation consists of finding a subset of this bit-attribute vector that is within particular Hamming distance. Normally, this search with approximate matching criteria requires sequential lookup for the whole collection of the attribute vector. This process can be easily parallelized, but in very large information systems this still would be slow and energy consuming. The suggested method, in this paper, of approximate search in very large files using the Pigeonhole Principle, circumvents the sequential search operations and reduces the calculations tremendously
Robust data transmission using the transmitter identification sequences in ATSC DVT signals (2005)

Transmitter identification (TxID, or transmitter fingerprinting) technique is used to detect, diagnose and classify the operating status of radio transmitters. Due to an ever-increasing number of transmitters, the need for transmitter identification is becoming an urgent issue, since it enables the broadcast authorities and operators to identify the source of interference. As a result, transmitter identification has been recognized as an important feature in the ATSC synchronization standard for distributed transmission. A new robust data transmission technique using the transmitter identification (TxID) sequences in the digital TV (DTV) signals is proposed in this paper. The major advantage of this low data transmission system is its robustness and extremely large coverage. The principle of the proposed data transmission system is presented. The modulation technique and throughput of the data transmission system is also evaluated.
A New Structural Optimization Method Based on the Level Set Method for Vibration Problems and Heat Conduction Problems (2008)

Various structural optimization methods have been proposed for design problems in many industries, such as mechanical, automotive, aerospace and civil industries. Recently, some structural optimization methods based on the level set method have been proposed. Although the previously proposed level set method&b ased structural optimization methods have some benefits, these methods have a difficulty with respect to updating the level set function. Therefore we proposed a new structural optimization method based on the level set method where the level set function is updated based on a simple scheme. In this paper, the newly proposed method is applied to vibration problems and heat conduction problems, and several numerical examples are provided to demonstrate that appropriate optimal structures can be obtained using the newly proposed method.
Automated registration and enhanced processing of clinical optical coherence tomography angiography (2016)

This automated registration method eliminates residual motion artifacts and enhances the visualization of vessels in OCTA.
Inhibition of pathogenic SHIV replication in macaques treated with antisense DNA of interleukin-4 (2004)

Interleukin-4 is implicated in the pathogenesis of HIV-induced AIDS and causes enhancement of replication of virus strains that use the CXCR4 (X4) coreceptor. In this study, we explored the effects of interleukin-4 (IL-4) antisense (AS) DNA on replication of X4, simian human immunodeficiency viruses, SHIV(KU-2) and SHIV89.6P. AS IL-4 oligomer caused inhibition of virus replication in cultures of CD4+ T cells and macrophages derived from macaques. Plasmid expressing AS IL-4 DNA was also effective in abrogating virus replication in macrophage cultures. Relevance of these cell culture studies was confirmed in vivo by treating SHIV89.6P-infected macaques with AS IL-4 DNA. Six macaques were inoculated with the virus, and 4 were treated with AS IL-4 DNA. This resulted in a significant decrease in viral RNA concentrations in the liver, lungs, and spleen tissues that are all sites of virus replication in macrophages. This is the first demonstration of effective inhibition of an HIV-like virus in tissues by AS DNA of a cytokine. In the present era of increasing resistance of HIV to antiviral compounds, exploration of adjunct therapies directed at host responses in combination with antiretroviral drugs may be of value for the treatment of AIDS.
Personalizing web search results by reading level (2011)

Traditionally, search engines have ignored the reading difficulty of documents and the reading proficiency of users in computing a document ranking. This is one reason why Web search engines do a poor job of serving an important segment of the population: children. While there are many important problems in interface design, content filtering, and results presentation related to addressing children's search needs, perhaps the most fundamental challenge is simply that of providing relevant results at the right level of reading difficulty. At the opposite end of the proficiency spectrum, it may also be valuable for technical users to find more advanced material or to filter out material at lower levels of difficulty, such as tutorials and introductory texts. We show how reading level can provide a valuable new relevance signal for both general and personalized Web search. We describe models and algorithms to address the three key problems in improving relevance for search using reading difficulty: estimating user proficiency, estimating result difficulty, and re-ranking based on the difference between user and result reading level profiles. We evaluate our methods on a large volume of Web query traffic and provide a large-scale log analysis that highlights the importance of finding results at an appropriate reading level for the user.
Threshold Logical Clocks for Asynchronous Distributed Coordination and\n Consensus (2019)

Consensus protocols for asynchronous networks are usually complex and\ninefficient, leading practical systems to rely on synchronous protocols. This\npaper attempts to simplify asynchronous consensus by building atop a novel\nthreshold logical clock abstraction, which enables upper layers to operate as\nif on a synchronous network. This approach yields an asynchronous consensus\nprotocol for fail-stop nodes that may be simpler and more robust than Paxos and\nits leader-based variants, requiring no common coins and achieving consensus in\na constant expected number of rounds. The same approach can be strengthened\nagainst Byzantine failures by building on well-established techniques such as\ntamper-evident logging and gossip, accountable state machines, threshold\nsignatures and witness cosigning, and verifiable secret sharing. This\ncombination of existing abstractions and threshold logical clocks yields a\nmodular, cleanly-layered approach to building practical and efficient Byzantine\nconsensus, distributed key generation, time, timestamping, and randomness\nbeacons, and other critical services.\n
<i>X</i>-pinch soft x-ray source for microlithography (1990)

A novel soft x-ray source for submicron resolution lithography is described. Exploratory experiments with the x-pinch dense plasma radiation source have been performed using a 500 kA, 40 ns pulsed power generator. About 33 J of magnesium K-shell radiation (1.3–1.5 keV) and 10 J of aluminum K-shell radiation (1.6–1.7 keV) have been produced in a source approximately 0.5 mm or less in diameter during a single pulse. The yield increased rapidly with current, implying the possibility of exposing a resist at a distance of 40 cm using a&lt;750 kA pulser in as few as ten pulses.
Preparation and Characterization of Newly Discovered Fibrous Aggregates of Single‐Walled Carbon Nanohorns (2016)

Fibrous aggregates composed of radially assembled graphene-based single-walled nanotubules are prepared, named here as fibrous aggregates of single-walled carbon nanohorns (fib-CNHs), whose structure resembles that of chenille stems. The newly discovered fib-CNHs are 30-100 nm in diameter and 1-10 μm in length. The fib-CNHs show high dispersibility and conductivity. The fib-CNHs increase the advantages of nanocarbons in various fields.
Upscaling of elastic properties for large scale geomechanical simulations (2004)

Abstract Large scale geomechanical simulations are being increasingly used to model the compaction of stress dependent reservoirs, predict the long term integrity of under‐ground radioactive waste disposals, and analyse the viability of hot‐dry rock geothermal sites. These large scale simulations require the definition of homogenous mechanical properties for each geomechanical cell whereas the rock properties are expected to vary at a smaller scale. Therefore, this paper proposes a new methodology that makes possible to define the equivalent mechanical properties of the geomechanical cells using the fine scale information given in the geological model. This methodology is implemented on a synthetic reservoir case and two upscaling procedures providing the effective elastic properties of the Hooke's law are tested. The first upscaling procedure is an analytical method for perfectly stratified rock mass, whereas the second procedure computes lower and upper bounds of the equivalent properties with no assumption on the small scale heterogeneity distribution. Both procedures are applied to one geomechanical cell extracted from the reservoir structure. The results show that the analytical and numerical upscaling procedures provide accurate estimations of the effective parameters. Furthermore, a large scale simulation using the homogenized properties of each geomechanical cell calculated with the analytical method demonstrates that the overall behaviour of the reservoir structure is well reproduced for two different loading cases. Copyright © 2004 John Wiley & Sons, Ltd.
Salicylic Acid Signaling Pathway in Rice and the Potential Applications of Its Regulators (2010)

The salicylic acid (SA) signaling pathway plays a crucial role in systemic acquired resistance in dicots. Several chemical inducers, which are also called “plant activators,” such as benzothiadiazole (BTH), protect plants from diseases by acting on the SA signaling pathway. Several studies by us and other groups have revealed that rice also has the SA signaling pathway that shares signaling components with the SA signaling pathway in dicots. OsNPR1 is a rice counterpart of NPR1, a transcriptional coactivator that plays a central role in the SA pathway in Arabidopsis. OsWRKY45 is a BTH-inducible rice-specific transcription factor. Knockdown experiments have demonstrated that both these transcriptional regulators are essential for BTH-induced blast resistance in rice. Unlike the SA pathway in Arabidopsis, wherein most of the SA/BTH-regulated genes are controlled by NPR1, the pathway in rice branches into OsNPR1-and OsWRKY45dependent pathways. OsWRKY45 overexpression confers very high resistance to blast and leaf blight diseases in rice, and it causes only minor growth retardation through the “priming effect”an action mechanism characteristic of plant activators. OsWRKY45 is a potential target for genetic manipulation of rice in order to confer broad-spectrum disease resistance; however, it is necessary to improve the construct to drive OsWRKY45 expression in rice in order to optimize the growth and disease resistance of the plants. Here, we have reviewed recent advances in the studies on the SA pathway in rice, with particular focus on the potential practical applications of the signaling components.
Closed-Loop Vagus Nerve Stimulation Based on State Transition Models (2017)

Closed-loop multiparametric stimulation may improve response and minimize side effects on current pathologies treated by VNS.
Utility of Polymerase Chain Reaction for Analysis of Antigen Receptor Rearrangement in Staging and Predicting Prognosis in Dogs with Lymphoma (2006)

Abstract In lymphoid neoplasia, molecular assays to confirm clonality rely on the fact that lymphoid cells normally contain DNA regions with unique sequences, resulting from recombination of the V, D, and J genes. The purpose of this study was to determine the utility of polymerase chain reaction (PCR) for antigen receptor rearrangements (PARR) for molecular staging and predicting prognosis in canine lymphoma. We hypothesized that the PARR assay would offer a sensitive method for detecting neoplastic cells in blood, and that the presence of such cells would be a negative prognostic finding compared with dogs with no detectable circulating tumor cells. Eighty-six patients with histologically or cytologically confirmed lymphoma were studied from initial diagnosis until death or euthanasia. All patients had PARR assays of a representative tumor-infiltrated lymph node and peripheral whole blood. Sixty-two patients had clonal rearrangements detected in the lymph node and were able to be staged by PARR. Seventeen patients (27%) had no detectable tumor in their blood and 45 (73%) were blood positive. Our findings showed that (1) PARR correlated with clinical stage in that the PARR assay was more likely to detect tumor cells in blood in stage 5 lymphomas, (2) PARR was more sensitive for detecting circulating tumor cells than visual assessment of blood or bone marrow because 80% of stage 3 lymphomas were blood-PARR-positive, and (3) PCR stage was not prognostic for disease-free interval (DFI) or survival.
Modelling the colonisation of maize by toxigenic and non-toxigenic Aspergillus flavus strains: implications for biological control (2008)

To successfully exploit biological control it is desirable to understand how the introduced agent colonises the host and interferes with establishment of the pest. This study assessed field colonisation of maize by Aspergillus flavus strains as biological control agents to reduce aflatoxin contamination. Maize (corn, Zea mays L.) ears were inoculated with A. flavus using a pin-bar technique in 2004 and 2005. Non-aflatoxigenic strains K49 (NRRL 30797) & CT3 (NRRL 30798) and toxigenic F3W4 (NRRL 30798) were compared against a carrier control (0.2% aqueous Tween 20). Ten ears were sampled over 12 to 20 days, visually assessed, and curves fit to a three compartment Gompertz equation or other best appropriate regressions. Aflatoxin was determined by HPLC and cyclopiazonic acid (CPA) by LC/MS. The Gompertz model describes growth parameters, e.g. growth constant, lag phase and maximum colonisation characterised patterns of maize colonisation for most inoculated treatments. Aflatoxin accumulation in maize inoculated with F3W4 was about 35,000 ng/g in 2004 and 2005, with kinetics of aflatoxin accumulation in 2005 well described by the Gompertz equation. Less than 200 ng/g was observed in maize inoculated with strains CT3 & K49 and accumulation was described by a linear or logistic model. Maize inoculated with strains CT3 and F3W4 accumulated a maximum of 220 and 169 µg/kg CPA, respectively, compared to 22 and 0.2 µg/kg in the control and K49 inoculated, respectively. This technique can be used to elucidate colonisation potential of non-toxigenic A. flavus in maize in relation to biological control of aflatoxin. The greatest reduction of aflatoxin and CPA in maize inoculated with strain K49 and Gompertz parameters on colonisation indicates its superiority to CT3 as a biological control agent. The dynamics of maize colonisation by A. flavus strains and subsequent mycotoxin accumulation generated by using the pin-bar technique has implications for characterising the competence of biocontrol strains for reducing aflatoxin contamination.
Mode multiplexing and holographic demultiplexing communication channels on a multimode fiber (1991)

Spatial mode multiplexing is used to transmit several communication channels on a single multimode optical fiber. Each channel is encoded by an orthogonal pattern produced by a spatial light modulator. A photorefractive medium holographically decodes the output speckle pattern at a receiver station. We demonstrate ring and star architectures for interconnection networks. Typical cross-talk-to-signal ratios, for fully interconnected three-processor networks, are -24 and -26 dB for the ring and star, respectively.
P3‐051: UPTAKE OF TAU ANTIBODIES INTO PHF PRETREATED TRANSFECTED HUMAN NEUROBLASTOMA CELLS LEADS TO A DECREASE IN TAU PROTEIN LEVELS (2014)

Our laboratory has pioneered targeting pathological tau proteins for clearance with immunotherapies. We have shown that this approach leads to antibody uptake into neurons, clears tau aggregates from the brain and prevents functional impairments, such as cognitive decline, in mouse tauopathy models. To clarify the mechanism of action of tau antibodies, we are using naïve and transfected (0N4R P301L tau) SHSY5Y human neuroblastoma cells. To mimic a pathological state, we have incubated these cells with paired helical filaments (PHF) enriched from Alzheimer's disease (AD) brain for 3 days, and subsequently incubated with tau antibody (Ser396/404 epitope) for 1, 4, or 6 days. Incubation was performed at 10% (normal) and 1% (compromising) FBS media conditions. In parallel, these cells were analyzed using our flow cytometry protocol and western blot analysis for antibody and PHF uptake as well as tau protein profile, respectively. Transfected cells with 1% FBS had more PHF uptake than all other groups at 1, 4, and 6 days (p<0.0001, p=0.0005, and p=0.0003, respectively, n=3). In both controls and sequentially (PHF and tau antibody) treated samples we observed a gradual increase in tau antibody uptake from 1 to 4 days in both cell lines and additional increase from 4 to 6 days in our transfected line. Only at 6 days of tau antibody incubation and in 1% FBS the transfected cells had significantly greater uptake of tau antibody compared to all other groups (26-39%, p= 0.0002, n=3) and a decrease in total tau and phospho Ser199 tau (64%, p=0.0013 and 49%, p=0.0925, respectively, n=3) levels compared to its PHF incubated control. The compromised transfected cells at 1% FBS and 6 days of antibody incubation show the most promising results as antibody uptake increases and tau levels decrease. Also, PHF seems to have limited effect on antibody uptake, but provides a condition for tau degradation. This neuroblastoma flow cytometry protocol may give us a new high throughput method to better understand the underlying cellular mechanisms and further development of this immunotherapy approach to treat AD and related tauopathies.
Segmentation-free statistical image reconstruction for polyenergetic x-ray computed tomography with experimental validation (2003)

This paper describes a statistical image reconstruction method for x-ray CT that is based on a physical model that accounts for the polyenergetic x-ray source spectrum and the measurement nonlinearities caused by energy-dependent attenuation. Unlike our earlier work, the proposed algorithm does not require pre-segmentation of the object into the various tissue classes (e.g., bone and soft tissue) and allows mixed pixels. The attenuation coefficient of each voxel is modelled as the product of its unknown density and a weighted sum of energy-dependent mass attenuation coefficients. We formulate a penalized-likelihood function for this polyenergetic model and develop an iterative algorithm for estimating the unknown density of each voxel. Applying this method to simulated x-ray CT measurements of objects containing both bone and soft tissue yields images with significantly reduced beam hardening artefacts relative to conventional beam hardening correction methods. We also apply the method to real data acquired from a phantom containing various concentrations of potassium phosphate solution. The algorithm reconstructs an image with accurate density values for the different concentrations, demonstrating its potential for quantitative CT applications.
Colony immunoblot assay of botulinal toxin (1993)

Botulinal neurotoxin in and around colonies of Clostridium botulinum types A, B, and E and of toxigenic Clostridium butyricum was detected by an enzyme-linked immunoassay procedure whereby the toxin was transferred from the agar medium to a nitrocellulose support and the immobilized toxin was probed with type-specific antibodies. The method identified the toxin types of the colonies grown from a mixed inoculum of C. botulinum serotypes. The specificity of the antitoxins for type A and B toxins was improved by adsorption of the antitoxins with the antigens of heterologous type cultures.
Dynamic measurement of the corneal tear film with a Twyman-Green interferometer (2014)

An interferometer for measuring dynamic properties of the in vivo tear film on the human cornea has been developed. The system is a near-infrared instantaneous phase-shifting Twyman-Green interferometer. The laser source is a 785 nm solidstate laser; the system has been carefully designed and calibrated to ensure that the system operates at eye safe levels. Measurements are made over a 6 mm diameter on the cornea. Successive frames of interferometric height measurements are combined to produce movies showing both the quantitative and qualitative changes in the topography of the tear film surface and structure. To date, measurement periods of up to 120 seconds at 28.6 frames per second have been obtained. Several human subjects have been examined using this system, demonstrating a surface height resolution of 25 nm and spatial resolution of 6 μm. Examples of features that have been observed in these in preliminary studies of the tear film include: post-blink disruption, evolution, and stabilization of the tear film; tear film artifacts generated by blinking; tear film evaporation and break-up; and the propagation of foreign objects in the tear film. This paper discusses the interferometer design and presents results from in vivo measurements.