gebhart/patrepeval huggingface dataset:
Alkylresorcinol Synthases Expressed in <i>Sorghum bicolor</i> Root Hairs Play an Essential Role in the Biosynthesis of the Allelopathic Benzoquinone Sorgoleone  (2010)

Sorghum bicolor is considered to be an allelopathic crop species, producing phytotoxins such as the lipid benzoquinone sorgoleone, which likely accounts for many of the allelopathic properties of Sorghum spp. Current evidence suggests that sorgoleone biosynthesis occurs exclusively in root hair cells and involves the production of an alkylresorcinolic intermediate (5-[(Z,Z)-8',11',14'-pentadecatrienyl]resorcinol) derived from an unusual 16:3Delta(9,12,15) fatty acyl-CoA starter unit. This led to the suggestion of the involvement of one or more alkylresorcinol synthases (ARSs), type III polyketide synthases (PKSs) that produce 5-alkylresorcinols using medium to long-chain fatty acyl-CoA starter units via iterative condensations with malonyl-CoA. In an effort to characterize the enzymes responsible for the biosynthesis of the pentadecyl resorcinol intermediate, a previously described expressed sequence tag database prepared from isolated S. bicolor (genotype BTx623) root hairs was first mined for all PKS-like sequences. Quantitative real-time RT-PCR analyses revealed that three of these sequences were preferentially expressed in root hairs, two of which (designated ARS1 and ARS2) were found to encode ARS enzymes capable of accepting a variety of fatty acyl-CoA starter units in recombinant enzyme studies. Furthermore, RNA interference experiments directed against ARS1 and ARS2 resulted in the generation of multiple independent transformant events exhibiting dramatically reduced sorgoleone levels. Thus, both ARS1 and ARS2 are likely to participate in the biosynthesis of sorgoleone in planta. The sequences of ARS1 and ARS2 were also used to identify several rice (Oryza sativa) genes encoding ARSs, which are likely involved in the production of defense-related alkylresorcinols.
Collaborative 3D DocuSpace: A platform for next-generation document services in 3D virtual worlds (2009)

In this paper, we propose a novel system, the collaborative 3D DocuSpace, that bridges a traditional document management system (such as Xerox DocuShare or Microsoft SharePoint) with a collaborative 3D virtual world (such as Second Life or Project Wonderland) to provide more immersive and engaging user experiences in document-centric collaborations. The collaborative 3D DocuSpace is a shared 3D virtual space that integrates document contents with collaborative interactions by a community of avatars (an avatar is the virtual representation of a user). It extends a document management system with an easy-to-use interface to a shared 3D virtual world so that a user not only can interact with document(s) alone, but also can collaborate with other avatars at the same time. It automatically brings in a collection of contents from a repository, and instantiates a shared 3D DocuSpace that can be customized based on contents' semantic contexts and user specified preferences. Therefore, this proposed system enhances the content-driven collaborations with much richer and more engaging user experiences that no existing document management systems or 3D virtual environments can provide alone.
Geometry-Based Circuit Modeling of Quasi-Static Cavity Resonators for Wireless Power Transfer (2022)

Wireless power transfer technology has seen steady advances in recent years, yet seamlessly charging devices within large volumes of space remains challenging. Although quasi-static cavity resonators have recently demonstrated safe wireless power transfer at room-scale sizes at significant power levels, previous work investigated this concept using coupled mode theory, lacking utility from the engineering perspective. This work presents a circuit model analysis of quasi-static cavity resonance-based wireless power transfer systems, which creates a critical conceptual bridge to the electrical engineering community and reveals factors that dominate the system performance and power transfer efficiency. A closed-form circuit model is derived from the geometrical properties of the system by analyzing the field distribution of a cylindrical cavity structure and is experimentally validated using a room-scale quasi-static cavity resonator. Finally, we demonstrate the utility of the derived circuit model through case studies for designing impedance matching circuits and optimization of the QSCR geometry.
An investigation of geographic mapping techniques for internet hosts (2001)

In this paper, we ask whether it is possible to build an IP address to geographic location mapping service for Internet hosts. Such a service would enable a large and interesting class of location-aware applications. This is a challenging problem because an IP address does not inherently contain an indication of location.We present and evaluate three distinct techniques, collectively referred to as IP2Geo, for determining the geographic location of Internet hosts. The first technique, Geo Track, infers location based on the DNS names of the target host or other nearby network nodes. The second technique, GeoPing, uses network delay measurements from geographically distributed locations to deduce the coordinates of the target host. The third technique, GeoCluster, combines partial (and possibly inaccurate) host-to-location mapping information and BGP prefix information to infer the location of the target host. Using extensive and varied data sets, we evaluate the performance of these techniques and identify fundamental challenges in deducing geographic location from the IP address of an Internet host.
Design issues and physics for high-performance quantum-cascade lasers (2013)

The quantum-cascade lasers (QCL), first demonstrated in 1994, has since been developed into a mature laser emitting within nearly the entire spectrum from 2.6 to 250 <i>μ</i>m, particular within the mid-infrared part of the spectrum from 3 to 12 <i>μ</i>m for applications in gas sensing for security, environmental and medical uses, as well as for defense-related IR countermeasures. The QCL heterostructure is generally based on the InGaAs/InAlAs system lattice-matched to InP or on its strain-compensated extension to maximize the conduction band discontinuity between well and barrier material. A refinement is the use of mixed-height barriers to engineer the interface scattering of the different levels involved in the lasing process. This design strategy appears to be universally applicable, across the entire range of QCL emission wavelengths. By using low barriers where the upper laser state has its maximum probability and high barriers where the lower laser state has its maximal probability in strain-compensated designs for short wavelength emission, the lifetime of the upper laser state can be increased, while decreasing the lifetime of the lower laser state. First realizations of this design result in <i>J</i><sub>th</sub> = 1.7kA/cm<sup>2</sup> at 300 K, slope efficiency <i>η</i> = 1.4 W/A, <i>T</i><sub>0</sub> = 175 K, and <i>T</i><sub>1</sub> = 550 K. Further increases in efficiency can be achieved through designs in which parasitic states near the upper laser level are separated from it, either energetically or oscillator strength. These states may be associated with other k values, or with higher-lying subbands.
Reaction Coupling between Wild-Type and Disease-Associated Mutant EZH2 (2014)

EZH2 and EZH1 are protein methyltransferases (PMTs) responsible for histone H3, lysine 27 (H3K27) methylation. Trimethylation of H3K27 (H3K27me3) is a hallmark of many cancers, including non-Hodgkin lymphoma (NHL). Heterozygous EZH2 point mutations at Tyr641, Ala677, and Ala687 have been observed in NHL. The Tyr641 mutations enhance activity on H3K27me2 but have weak or no activity on unmethylated H3K27, whereas the Ala677 and Ala687 mutations use substrates of all methylation states effectively. It has been proposed that enzymatic coupling of the wild-type and mutant enzymes leads to the oncogenic H3K27me3 mark in mutant-bearing NHL. We show that coupling with the wild-type enzyme is needed to achieve H3K27me3 for several mutants, but that others are capable of achieving H3K27me3 on their own. All forms of PRC2 (wild-type and mutants) display kinetic signatures that are consistent with a distributive mechanism of catalysis.
Robust Multipose Face Detection in Images (2004)

Automatic human face detection from images in surveillance and biometric applications is a challenging task due to variations in image background, view, illumination, articulation, and facial expression. We propose a novel three-step face detection approach to addressing this problem. The approach adopts a simple-to-complex strategy. First, a linear-filtering algorithm is applied to enhance detection performance by removing most nonface-like candidates rapidly. Second, a boosting chain algorithm is adopted to combine the boosting classifiers into a hierarchical "chain" structure. By utilizing the inter-layer discriminative information, this algorithm reveals a higher efficiency than traditional approaches. Last, a postfiltering algorithm, consisting of image preprocessing; support vector machine-filter and color-filter, is applied to refine the final prediction. As only a few candidate windows remain in the final stage, this algorithm greatly improves detection accuracy with small computation cost. Compared with conventional approaches, this three-step approach is shown to be more effective and capable of handling more pose variations. Moreover, together with a two-level hierarchy in-plane pose estimator, a rapid multiview face detector is built. Experimental results demonstrate a significant performance improvement for the proposed approach over others.
WE‐C‐108‐01: JUNIOR INVESTIGATOR WINNER — Towards Radiation Therapy with Very High‐Energy Electron Beams (2013)

Purpose: To experimentally validate Monte Carlo (MC) simulations for dose calculations with very high‐energy electron (VHEE) beams in the presence of heterogeneities and to use MC simulations for treatment planning optimization of ultra‐fast radiation therapy with VHEE beams. Methods: Polystyrene phantom with heterogeneities made of nine materials of various thicknesses was irradiated at a VHEE beam line at SLAC National Accelerator Laboratory. Films were used to measure the dose delivered to the phantom by 60–110MeV VHEE beams of 0.6–2.2mm in size. A MC model of the beam line was built and validated against the experimental data based on percentage depth‐dose (PDD) curves. The MC validated code was used for VHEE radiotherapy planning of three patients. More specifically, MC beamlets were exported into a modified version of RayStation for spot‐scanning optimization. The quality of VHEE dose distributions as a function of electron beam energy, beamlet size and spacing, source‐to‐isocenter distance, and number of beams was studied. Results: MC calculated PDD curves for heterogeneous phantoms were in agreement with the experimental PDD curves obtained at the VHEE beam line for all beam energies and beam sizes. VHEE treatment planning optimization study for a pediatric patient brain tumor revealed that significant normal tissue sparing was achieved in 60–100MeV VHEE plans compared to the state‐of‐the‐art 6MV VMAT plan. The mean dose to the cochleae was by 56–72% lower in the VHEE plans. Out of the studied parameters, electron beam energy had the largest effect on the quality of VHEE treatment plans. In order to generate a VHEE plan matching a VMAT plan for a large patient, VHEE beams of 100–150MeV are needed. Conclusion: We have validated VHEE beam MC dose calculations and we have developed a MC/RayStation treatment planning optimization tool for evaluation of the potential to rapidly treat cancer with VHEE beams. This work has been supported by the 2012 AAPM Research Seed Grant.
Photoinduced nucleation: A novel tool for detecting molecules in air at ultra-low concentrations (2000)

This paper describes the development of a novel detection method and the demonstration of its capability to detect substances at concentrations as small as a few parts per trillion. It is shown that photoinduced nucleation is not in itself a nucleation process; rather, supersaturated vapor condenses onto long-lasting clusters formed by chemical reaction of photo-excited molecules. The role of the supersaturated vapor is to increase the size of these photoproducts by condensation to a size readily detectable by light scattering. Furthermore, the measured nucleation rate variation with illumination wavelength exactly matches the substance’s vapor-phase UV light absorption wavelength dependence, thus providing species identification. The ability to detect and identify molecules of substances at extremely low concentrations from ambient air is useful for detecting and monitoring pollutants, and for detecting explosives such as TNT.
Reprofiled anthelmintics abate hypervirulent stationary-phase Clostridium difficile (2016)

Prolonged use of broad-spectrum antibiotics disrupts the indigenous gut microbiota, which consequently enables toxigenic Clostridium difficile species to proliferate and cause infection. The burden of C. difficile infections was exacerbated with the outbreak of hypervirulent strains that produce copious amounts of enterotoxins and spores. In recent past, membrane-active agents have generated a surge of interest due to their bactericidal property with a low propensity for resistance. In this study, we capitalized on the antimicrobial property and low oral bioavailability of salicylanilide anthelmintics (closantel, rafoxanide, niclosamide, oxyclozanide) to target the gut pathogen. By broth microdilution techniques, we determined the MIC values of the anthelmintics against 16 C. difficile isolates of defined PCR-ribotype. The anthelmintics broadly inhibited C. difficile growth in vitro via a membrane depolarization mechanism. Interestingly, the salicylanilides were bactericidal against logarithmic- and stationary-phase cultures of the BI/NAP1/027 strain 4118. The salicylanilides were poorly active against select gut commensals (Bacteroides, Bifidobacterium and Lactobacillus species), and were non-hemolytic and non-toxic to mammalian cell lines HepG2 and HEK 293T/17 within the range of their in vitro MICs and MBCs. The salicylanilide anthelmintics exhibit desirable properties for repositioning as anti-C. difficile agents.
Generation of Recombinant Skin <i>in Vitro</i> by Adeno-Associated Virus Type 2 Vector Transduction (2004)

It has long been recognized that skin may be a particularly good target for pharmacologic gene therapy and as a platform for the secretion of systemically distributed molecules. Adeno-associated virus type 2 (AAV) is a useful vector for skin gene therapy because skin is the natural host tissue for AAV, in which it functions as an autonomous parvovirus. We demonstrate here that recombinant (r) AAV vectors carrying the granulocyte-macrophage colony-stimulating factor (GM-CSF), human papillomavirus E6, or green fluorescent protein (GFP) transgene could transduce primary human keratinocytes in ex vivo culture. We further demonstrate that these transduced cells could be used to form a transgene-positive recombinant skin (r-skin), using the organotypic epithelial raft culture system. Transduction of keratinocytes was demonstrated by reverse transcriptase-polymerase chain reaction (RT-PCR) for RNA expression, enzyme-linked immunosorbent assay (ELISA) for product secretion, intracellular staining for protein expression, vector-chromosomal junction PCR and Southern blot analysis of proviral sequences, in situ immunohistochemistry analysis of protein expression, and ultraviolet light fluorescence for GFP expression. AAV/GM-CSF/Neo-infected keratinocyte/raft skins secreted GM-CSF at levels as high as 25 ng/cm(2) of skin and maintained expression to 60 days postinfection. These data support the utility and efficiency of AAV-based gene delivery to produce genetically altered keratinocytes and r-skin.
P1‐253: Research and development of anti‐Aß oligomers antibodies for the treatment of Alzheimer's disease (2012)

Amyloid beta oligomers (AbOs) are promising target for the treatment of Alzheimer's disease (AD) because they are believed as major pathogenic factor of AD. One of the hopeful therapeutic approaches is passive immunotherapy using anti- AbOs specific antibody. This approach has two merits, which are efficient therapeutic effect and decrease of side effects, because the antibody does not bind to amyloid precursor protein (APP) nor naturally existed Abeta. At AAIC2011 last year, we reported the screening results of the best anti-AbOs antibody by in vitro tests and in vivo test using AD model mouse. Here, the progress will be presented. Anti-AbOs antibodies were generated by immunization of antigens prepared by our original method to mouse. The initial screening was performed by ELISA and dotblot assay. The amino acid sequences of all positive clones were analyzed and sequence-redundant clones were eliminated. Then, antibodies that have higher selectivity to AbOs were selected by competitive ELISA. Next, antibodies that displayed non-binding property to normal human tissue array were chosen. Then, their affinities to AbOs were measured by SPR (Surface Plasmon Resonance) analysis, following that the antibodies were divided into high or low affinity groups. Next, passive immunization test using Tg2576 mouse was performed in several antibodies from each group. 184 antibodies were obtained in the results of first screening and subsequent determination of amino acid sequence. Then, 49 antibodies which have higher selectivity to AbOs were selected by the competitive ELISA. Moreover, dozens of antibodies were chosen from 49 antibodies by their non-binding feature to normal human tissue array. Next, these antibodies were divided into high and low affinity groups by SPR analysis. Then in vivo efficacy in several antibodies in each groups were examined by passive immunization test by using Tg2576 mouse. The results showed that high affinity antibodies have better efficacy of improvement of learning memory than low affinity ones, and also there were difference in clearance of Abeta in the brains among the high affinity antibodies. We have obtained the best antibody which has high specificity and affinity to AbOs and also has high efficacy in in vivo experiments.
SU-8 microfluidic device for scintillating particle detection (2009)

This paper presents the study of a novel scintillation detector based on standard microfabrication techniques. It consists of a fine pitch array of hollow waveguides filled with a liquid scintillator and optically coupled to photodetectors. The detector has been fabricated by patterning the SU-8 photoresist on silicon wafers. Experimental studies have been performed by exciting the liquid scintillator contained in the SU-8 waveguides with electrons. The scintillation light produced was read out by an external photodetector. The results obtained with this set-up demonstrate the concept of microfluidic scintillation detection and are very encouraging for future developments.
A Microsystem with Varying-Length Electrode Arrays for Auditory Nerve Prostheses (2006)

This paper reports the design, fabrication and simulation of a novel array of micromachined electrodes with different lengths for use in auditory nerve prostheses. A 10 x 10 array is created in a 1 mm2 on silicon with bulk micromachining technology. The electrode lengths vary from 200 microm to 400 microm. This design could provide access to most fascicles within the auditory nerve and thus allow stimulation of a broad tonotopic range within the nerve fiber. A multichannel ultra-low power circuit is also designed, fabricated, and tested for neural signal recording. The chip is fabricated in 0.5 microm AMI CMOS technology with a die size of 1.5 mm x 1.5 mm. The total power consumption is less than 100 microW.
Validation of an Immunohistochemistry Assay for Detection of CD155, the Poliovirus Receptor, in Malignant Gliomas (2017)

- Anti-CD155 antibody D3G7H achieves monospecific detection of CD155 in immunoblots of tumor homogenates and immunohistochemistry of tumor FFPE sections. Our assay has utility in defining appropriate use of PVSRIPO in oncolytic immunotherapy against malignant glioma and other cancer histotypes.
Distribution-Aware Weight Compression for Federated Averaging Learning Over Wireless Edge Networks (2021)

Recently, federated learning (FL) over wireless edge networks has aroused much research interest due to its merits in mitigating the privacy risks. On the basis of the standard FL, a federated averaging (FedAvg) learning algorithm emerges to reduce the communication rounds between the edge nodes and the central server. Even though the number of communication rounds of FedAvg learning is significantly reduced, exchanging all model parameters is still of heavy communication cost. To reduce the communication cost, this paper proposes a model compression method for FedAvg learning that adapts to the model weights distribution, namely distribution-aware weight compression (DAWC). In the proposed DAWC, we propose a parameter-oriented quantization algorithm (POQA) according to the distribution properties of different parameters of the model weights to iterate out the optimal quantization intervals, with the target of minimizing the mean square quantization errors. When the quantization is finished, Huffman coding is used to minimize the average code length. It is analyzed that FedAvg using the proposed DAWC converges at a fast speed. Experiment results show that DAWC exhibits the optimal performance in comparison with existing benchmarks.
Optimal illumination pattern for transport-of-intensity quantitative phase microscopy (2018)

The transport-of-intensity equation (TIE) is a well-established non-interferometric phase retrieval approach, which enables quantitative phase imaging (QPI) of transparent sample simply by measuring the intensities at multiple axially displaced planes. Nevertheless, it still suffers from two fundamentally limitations. First, it is quite susceptible to low-frequency errors (such as \cloudy" artifacts), which results from the poor contrast of the phase transfer function (PTF) near the zero frequency. Second, the reconstructed phase tends to blur under spatially low-coherent illumination, especially when the defocus distance is beyond the near Fresnel region. Recent studies have shown that the shape of the illumination aperture has a significant impact on the resolution and phase reconstruction quality, and by simply replacing the conventional circular illumination aperture with an annular one, these two limitations can be addressed, or at least significantly alleviated. However, the annular aperture was previously empirically designed based on intuitive criteria related to the shape of PTF, which does not guarantee optimality. In this work, we optimize the illumination pattern to maximize TIE's performance based on a combined quantitative criterion for evaluating the \goodness" of an aperture. In order to make the size of the solution search space tractable, we restrict our attention to binary coded axis-symmetric illumination patterns only, which are easier to implement and can generate isotropic TIE PTFs. We test the obtained optimal illumination by imaging both a phase resolution target and HeLa cells based on a small-pitch LED array, suggesting superior performance over other suboptimal patterns in terms of both signal-to-noise ratio (SNR) and spatial resolution.