gebhart/patrepeval huggingface dataset:
Neural Geometric Level of Detail: Real-time Rendering with Implicit 3D Shapes (2021)

Neural signed distance functions (SDFs) are emerging as an effective representation for 3D shapes. State-of-the-art methods typically encode the SDF with a large, fixed-size neural network to approximate complex shapes with implicit surfaces. Rendering with these large networks is, however, computationally expensive since it requires many forward passes through the network for every pixel, making these representations impractical for real-time graphics. We introduce an efficient neural representation that, for the first time, enables real-time rendering of high-fidelity neural SDFs, while achieving state-of-the-art geometry reconstruction quality. We represent implicit surfaces using an octree-based feature volume which adaptively fits shapes with multiple discrete levels of detail (LODs), and enables continuous LOD with SDF interpolation. We further develop an efficient algorithm to directly render our novel neural SDF representation in real-time by querying only the necessary LODs with sparse octree traversal. We show that our representation is 2-3 orders of magnitude more efficient in terms of rendering speed compared to previous works. Furthermore, it produces state-of-the-art reconstruction quality for complex shapes under both 3D geometric and 2D image-space metrics.
An inverse-scattering model for an all-optical logic gate (1991)

Electromagnetic inverse scattering theory is used to model the ON and OFF states of an all-optical logic gate. The scattering data are two phase-conjugate reflection coefficients that were obtained by pole reflection.
Novel Monitoring System for Detecting Malfunctioning In-Canopy Sprinklers on a Center Pivot Irrigation System (2021)

The preservation of limited aquifer resources in the US Great Plains has driven the innovation and deployment of more efficient sprinkler packages for center pivot irrigation systems. One of the more efficient sprinkler packages available are in-canopy sprinkler packages, which hang low in the canopy. Although effective, they have the potential to become entangled in crop biomass and detach from the center pivot. Such detachments impact the efficiency and uniformity of the system, resulting in disrupted flow and pressure conditions, ultimately decreasing crop yield. Therefore, it is crucial that producers detect and replace missing in-canopy sprinklers immediately. A novel prototype monitoring system was designed using low-cost, publicly available technologies to monitor in-canopy sprinklers on a center pivot irrigation system and alert the user when and where an in-canopy sprinkler has become detached from the center pivot span. Later design revisions of the monitoring system introduced the ability of the monitoring system to also detect when a sprinkler became clogged. Experimental trials verified that the monitoring system operates efficiently and accurately; however, minor changes need to be made before large-scale implementation is possible.
Partially occluded object detection by finding the visible features and parts (2015)

We address the problem of partially occluded object detection by implementing a model which includes latent visibility flags that are attached to cells and parts of a Deformable Part Model (DPM) [1]. A visibility flag indicates whether an image portion is part of a target object or part of an occluder. To compute the visibility flags and the score of the detector simultaneously, we maximize a concave objective function that is composed of the following four terms: (1) the detection scores of visible cells and parts, (2) a cell-to-cell consistency term which encourages neighboring cells to have the same visibility flags, (3) a cell-to-part consistency term which encourages compatible labeling among overlapping cells and parts, and (4) a penalty term for cells and parts that are labeled as occluded. The maximization of the concave objective function is done using the Alternating Direction Method of Multipliers (ADMM). By removing scores of occluded cells and parts from the final detection score we significantly improve detection performance on partially occluded pedestrians. In experiments we show that our system outperforms the standard DPM and other state-of-art methods on a benchmark database of partially occluded pedestrians.
Targeted 2′-O Methylation at a Nucleotide within the Pseudoknot of Telomerase RNA Reduces Telomerase Activity <i>In Vivo</i> (2010)

Telomerase RNA is an essential component of telomerase, a ribonucleoprotein enzyme that maintains chromosome ends in most eukaryotes. Here we employ a novel approach, namely, RNA-guided RNA modification, to assess whether introducing 2'-O methylation into telomerase RNA can influence telomerase activity in vivo. We generate specific 2'-O methylation sites in and adjacent to the triple helix (within the conserved pseudoknot structure) of Saccharomyces cerevisiae telomerase RNA (TLC1). We show that 2'-O methylation at U809 reduces telomerase activity, resulting in telomere shortening, whereas 2'-O methylation at A804 or A805 leads to moderate telomere lengthening. Importantly, we also show that targeted 2'-O methylation does not affect TLC1 levels and that 2'-O-methylated TLC1 appears to be efficiently assembled into telomerase ribonucleoprotein. Our results demonstrate that RNA-guided RNA modification is a highly useful approach for modulating telomerase activity.
Multiplexed Nucleic Acid Sensing with Single-Molecule FRET (2019)

Multiplex detection of biomolecules is important in bionanotechnology and clinical diagnostics. Multiplexing using engineered solutions such as microarrays, synthetic nanopores, and DNA barcodes is promising, but they require sophisticated design/engineering and typically yield semiquantitative information. Single-molecule fluorescence resonance energy transfer (smFRET) is an attractive tool in this regard as it enables both sensitive and quantitative detection. However, multiplexing with smFRET remains a great challenge as it requires either multiple excitation sources, an antenna system created by multiple FRET pairs, or multiple acceptors of the donor fluorophore, which complicates not only the labeling schemes but also data analysis, due to overlapping of FRET efficiencies ( E<sub>FRET</sub>). Here, we address these currently outstanding issues by designing interconvertible hairpin-based sensors (iHabSs) with nonoverlapping E<sub>FRET</sub> utilizing a single donor/acceptor pair and demonstrate a high-confidence multiplex detection of unlabeled nucleic acid sequences. We validated the reliability of our approach by systematically omitting one target at a time. Further, we demonstrate that these iHabSs are fully recyclable, sensitive with a limit of detection of ∼200 pM, and able to discriminate against single base mismatches. The multiplexed approach developed here has the potential to benefit the fields of biosensing and diagnostics by allowing simultaneous and quantitative detection of unlabeled nucleic acid biomarkers.
Specific enzyme-linked immunoassay for rotavirus serotypes 1 and 3 (1985)

We prepared monoclonal antibodies against two serotypically distinct rotavirus strains: Wa, a serotype 1 virus of human origin, and rhesus rotavirus, a simian serotype 3 virus. Monoclonal antibodies which react specifically with VP7 of each serotype were identified by hemagglutination inhibition tests, plaque reduction neutralization studies, and solid-phase immunoassays which used wild-type and reassortant strains of rotavirus. An enzyme-linked immunoassay was designed which utilizes two of these antibodies to correctly identify serotype 1 and serotype 3 viruses.
Curcumin‐induced antiproliferative and proapoptotic effects in melanoma cells are associated with suppression of IκB kinase and nuclear factor κB activity and are independent of the B‐Raf/mitogen‐activated/extracellular signal‐regulated protein kinase pathway and the Akt pathway (2005)

Curcumin has potent antiproliferative and proapoptotic effects in melanoma cells. These effects were associated with the suppression of NF-kappaB and IKK activities but were independent of the B-Raf/MEK/ERK and Akt pathways.
An Efficient and Scalable Method for the Isolation of Costatolide, A Naturally-Occurring Anti-HIV Agent, from the Latex of Calophyllum teysmannii var. inophylloide (1999)

AbstractAn efficient and scalable method is reported for the isolation of costatolide (2), a naturally-occurring and HIV-1-specific non-nucleoside reverse transcriptase inhibitor, from the latex of Calophyllum teysmannii Miq. var. inophylloide (King.) P. F. Stevens (Clusiaceae). An overall yield of 10.6% of costatolide (2), with a purity of 96%, was obtained by repetitive recrystallization of the latex from a single organic solvent, subsequent to the pre-treatment of latex with hexane and dichloromethane to remove undesirable oily material. A second major component of the latex, soulattrolide (3), another HIV-1 non-nucleoside reverse transcriptase inhibitor, was also isolated. Both compounds were characterized by spectroscopic and chromatographic analyses and their in vitro anti-HIV activities were also confirmed. The results suggest that sufficient quantities of costatolide for preclinical and clinical development can be obtained in a relatively low-cost manner from the natural source.
Multiscale superpixel-based fusion framework for hyperspectral image classification (2018)

Since it is usually difficult and time-consuming to obtain sufficient labeled samples in practice, the samll number of sample is one of the challenging issue for hyperspectral image classifiction. Fortunately, due to the spatial correlation of the surface of the materials, it is feasible to improve classification performance from the perspective of superpixel. In this paper, a multiscale superpixel-based fusion (MSSF) framework has been proposed for hyperspectral image classification. First, several superpixel maps of different scales are generated from the hyperspectral images. Then, calculate the spectral mean of superpixels and each class of training sample, the label of the superpixel is determined by the label of the training sample which distance is closest to the superpixel. Finally, we use majority voting strategy to determine the final label of each pixel. The experimental results on two real HSI data sets show that the performance of the proposed framework is better than support vector machine(SVM), K nearest neighbor(KNN), sparse representation-based classifier(SRC).
Environmental Factors That Control Microbial Perchlorate Reduction (2002)

As part of a study to elucidate the environmental parameters that control microbial perchlorate respiration, we investigated the reduction of perchlorate by the dissimilatory perchlorate reducer Dechlorosoma suillum under a diverse set of environmental conditions. Our results demonstrated that perchlorate reduction by D. suillum only occurred under anaerobic conditions in the presence of perchlorate and was dependent on the presence of molybdenum. Perchlorate reduction was dependent on the presence of the enzyme chlorite dismutase, which was induced during metabolism of perchlorate. Anaerobic conditions alone were not enough to induce expression of this enzyme. Dissolved oxygen concentrations less than 2 mg liter(-1) were enough to inhibit perchlorate reduction by D. suillum. Similarly to oxygen, nitrate also regulated chlorite dismutase expression and repressed perchlorate reduction by D. suillum. Perchlorate-grown cultures of D. suillum preferentially reduced nitrate in media with equimolar amounts of perchlorate and nitrate. In contrast, an extended (40 h) lag phase was observed if a similar nitrate-perchlorate medium was inoculated with a nitrate-grown culture. Perchlorate reduction commenced only when nitrate was completely removed in either of these experiments. In contrast to D. suillum, nitrate had no inhibitory effects on perchlorate reduction by the perchlorate reducer Dechloromonas agitata strain CKB. Nitrate was reduced to nitrite concomitant with perchlorate reduction to chloride. These studies demonstrate that microbial respiration of perchlorate is significantly affected by environmental conditions and perchlorate reduction is directly dependent on bioavailable molybdenum and the presence or absence of competing electron acceptors. A microbial treatment strategy can achieve and maintain perchlorate concentrations below the recommended regulatory level, but only in environments in which the variables described above can be controlled.
Specificity and heregulin regulation of Ebp1 (ErbB3 binding protein 1) mediated repression of androgen receptor signalling (2004)

Although ErbB receptors have been implicated in the progression of prostate cancer, little is known about proteins that may mediate their interactions with the androgen receptor (AR). Ebp1, a protein cloned via its association with the ErbB3 receptor, binds the AR and inhibits androgen-regulated transactivation of wild-type AR in COS cells. As the complement of coregulators in different cells are important for AR activity, we determined the effect of Ebp1 on AR function in prostate cancer cell lines. In addition, we examined the regulation of Ebp1 function by the ErbB3/4 ligand heregulin (HRG). In this study, we demonstrate, using several natural AR-regulated promoters, that Ebp1 repressed transcriptional activation of wild-type AR in prostate cancer cell lines. Downregulation of Ebp1 expression in LNCaP cells using siRNA resulted in activation of AR in the absence of androgen. Ebp1 associated with ErbB3 in LNCaP cells in the absence of HRG, but HRG induced the dissociation of Ebp1 from ErbB3. In contrast, HRG treatment enhanced both the association of Ebp1 with AR and also the ability of Ebp1 to repress AR transactivation. These studies suggest that Ebp1 is an AR corepressor whose biological activity can be regulated by the ErbB3 ligand, HRG.
Cytomegalovirus Vectors Violate CD8 <sup>+</sup> T Cell Epitope Recognition Paradigms (2013)

CD8(+) T cell responses focus on a small fraction of pathogen- or vaccine-encoded peptides, and for some pathogens, these restricted recognition hierarchies limit the effectiveness of antipathogen immunity. We found that simian immunodeficiency virus (SIV) protein-expressing rhesus cytomegalovirus (RhCMV) vectors elicit SIV-specific CD8(+) T cells that recognize unusual, diverse, and highly promiscuous epitopes, including dominant responses to epitopes restricted by class II major histocompatibility complex (MHC) molecules. Induction of canonical SIV epitope-specific CD8(+) T cell responses is suppressed by the RhCMV-encoded Rh189 gene (corresponding to human CMV US11), and the promiscuous MHC class I- and class II-restricted CD8(+) T cell responses occur only in the absence of the Rh157.5, Rh157.4, and Rh157.6 (human CMV UL128, UL130, and UL131) genes. Thus, CMV vectors can be genetically programmed to achieve distinct patterns of CD8(+) T cell epitope recognition.
Microreactors for efficient on-chip fuel processing and hydrogen generation (2005)

This paper provides an overview of several on-going research projects on microreactors and microchemical systems in our group. Microchemical systems are a new generation of miniature chemical systems that carry out chemical reactions and separations in precisely fabricated three dimensional microreactor configurations in the size range of a few microns to a few hundred microns. Typical microchemical systems combine fluid handling and reaction capabilities with electronic sensing and actuation, are fabricated using integrated circuit (IC) manufacturing techniques and use silicon and related IC industry materials, polymers, ceramics, glass or quartz as their material of construction. The use of such systems for in-situ and on-demand chemical production is gaining increasing importance as the field of microreaction engineering transitions from a theoretical concept to a technology with significant industrial applications. The paper presents a review of our work on MEMS-based microfabrication, modeling and control of microreformers for hydrogen delivery systems in micro-fuel cells and suggests possible areas of future research.
Hot‐Gas‐Jet Method and Apparatus for Thermal‐Shock Testing (1989)

In the hot‐gas‐jet thermal‐shock‐testing method, a stream of high‐temperature air is impinged on the center of a ceramic disk. This test is suitable for determining the relative resistance of ceramics to thermal shock that involves fast heating from ambient, with convection as the principal heat‐transfer mode. The feasibility of this testing method was established using transparent polycrystalline La 2 O 3 ‐doped Y 2 O 3 . Thermal‐shock fracture initiates from the cold face of the disk. A smaller grain size in transparent Y 2 O 3 results in a higher probability of survival for a given critical temperature difference in the test. Toughened Y 2 O 3 shows more resistance to thermal‐shock fracture than the standard material.
Inside Cover: A New Class of Amphiphiles Bearing Rigid Hydrophobic Groups for Solubilization and Stabilization of Membrane Proteins (Chem. Eur. J. 31/2012) (2012)

A class of structurally new amphiphile based on steroidal lipophilic groups have been prepared by P. S. Chae et al. on page 9485 ff. The results show that the new amphiphiles confer enhanced stability to a variety of membrane proteins in solution relative to popular conventional detergent dodecylmaltoside (DDM). The potential of the new amphiphiles as tools for solubilization, isolation, and stabilization is evident from their success with a variety of membrane proteins.
Decrease in Formalin-Inactivated Respiratory Syncytial Virus (FI-RSV) Enhanced Disease with RSV G Glycoprotein Peptide Immunization in BALB/c Mice (2013)

Respiratory syncytial virus (RSV) is a high priority target for vaccine development. One concern in RSV vaccine development is that a non-live virus vaccine would predispose for enhanced disease similar to that seen with the formalin inactivated RSV (FI-RSV) vaccine. Since a mAb specific to RSV G protein can reduce pulmonary inflammation and eosinophilia seen after RSV infection of FI-RSV vaccinated mice, we hypothesized that RSV G peptides that induce antibodies with similar reactivity may limit enhanced disease after subunit or other non-live RSV vaccines. In support of this hypothesis, we show that FI-RSV vaccinated mice administered RSV G peptide vaccines had a significant reduction in enhanced disease after RSV challenge. These data support the importance of RSV G during infection to RSV disease pathogenesis and suggest that use of appropriately designed G peptide vaccines to reduce the risk of enhanced disease with non-live RSV vaccines merits further study.
Demonstration of a high-temperature fiber-optic gas sensor made with a sol-gel process to incorporate a fluorescent indicator (1999)

To make a gas sensor suitable for use at high temperatures, we have used a sol-gel-processing technique to bond a copper-exchanged zeolite fluorescence indicator onto the end of an all-silica optical fiber. Experimental results from single-fiber prototype sensors show they can be used to measure either the oxygen concentration or the equivalence ratio for gas mixtures containing weak or strong reductants, respectively.
The Histone Methyltransferase Inhibitor A-366 Uncovers a Role for G9a/GLP in the Epigenetics of Leukemia (2015)

Histone methyltransferases are epigenetic regulators that modify key lysine and arginine residues on histones and are believed to play an important role in cancer development and maintenance. These epigenetic modifications are potentially reversible and as a result this class of enzymes has drawn great interest as potential therapeutic targets of small molecule inhibitors. Previous studies have suggested that the histone lysine methyltransferase G9a (EHMT2) is required to perpetuate malignant phenotypes through multiple mechanisms in a variety of cancer types. To further elucidate the enzymatic role of G9a in cancer, we describe herein the biological activities of a novel peptide-competitive histone methyltransferase inhibitor, A-366, that selectively inhibits G9a and the closely related GLP (EHMT1), but not other histone methyltransferases. A-366 has significantly less cytotoxic effects on the growth of tumor cell lines compared to other known G9a/GLP small molecule inhibitors despite equivalent cellular activity on methylation of H3K9me2. Additionally, the selectivity profile of A-366 has aided in the discovery of a potentially important role for G9a/GLP in maintenance of leukemia. Treatment of various leukemia cell lines in vitro resulted in marked differentiation and morphological changes of these tumor cell lines. Furthermore, treatment of a flank xenograft leukemia model with A-366 resulted in growth inhibition in vivo consistent with the profile of H3K9me2 reduction observed. In summary, A-366 is a novel and highly selective inhibitor of G9a/GLP that has enabled the discovery of a role for G9a/GLP enzymatic activity in the growth and differentiation status of leukemia cells.
Human oocyte cryopreservation: new perspectives regarding oocyte survival (2001)

The success of human oocyte cryopreservation depends on morphological and biophysical factors that could influence oocyte survival after thawing. Various attempts to cryopreserve human oocytes have been performed with contrasting results. Therefore the effect of some factors, such as the presence or absence of the cumulus oophorus, the sucrose concentration in the freezing solution and the exposure time to cryoprotectants, on human oocyte survival after thawing were investigated. The oocytes were cryopreserved in 1,2-propanediol added with sucrose, using a slow-freezing-rapid-thawing programme. After thawing, the oocytes were inseminated by intracytoplasmic sperm injection (ICSI) and the outcomes of insemination and subsequent embryo development were also recorded. The post-thaw cryosurvival rate was not different for the oocytes cryopreserved with their cumuli partially removed mechanically (56%) when compared with those cryopreserved with their cumuli totally removed enzymatically (53%). On the contrary, a significantly higher survival rate was obtained when the oocytes were cryopreserved in the presence of a doubled sucrose concentration (0.2 mol/l) in the freezing solution and the survival rate was even higher when the sucrose concentration was tripled (0.3 mol/l) (60 versus 82% P < 0.001). Furthermore, a longer exposure time (from 10.5 to 15 min) to cryoprotectants, before lowering the temperature, significantly increased the oocyte survival rate (P < 0.005). Intracytoplasmic sperm injection produced a good fertilization rate (57%) of thawed oocytes and a high embryo cleavage rate (91%) and a satisfactory embryo morphology was observed (14 and 34% for grade I and grade II embryos respectively).
Chirp-controlled EA-modulator/SOA/widely-tunable laser transmitter (2005)

We report on chirp-controlled optical modulation realized using a semiconductor optical amplifier and an electroabsorption modulator monolithically integrated with a widely-tunable laser. The chirp parameter can be adjusted from +1.0 to -0.7 across 30 nm tuning range.
Very virulent Marek's disease viruses: importance and control (1989)

The emergence of viral strains of increased virulence has been associated with increased Marek's disease losses in certain vaccinated flocks. Methods are described for the isolation and typing of these strains, and for their control by means of improved vaccines.
Annoyance perception and modeling for hearing-impaired listeners (2012)

Perceptual annoyance of environmental sounds is measured for normal-hearing and hearing-impaired listeners under iso-level and iso-loudness conditions. Data from the hearing-impaired listeners shows similar trends to that from normal-hearing listeners, but with greater variability across individuals. A regression model based on the statistics of specific loudness and other perceptual features is fit to the data from the normal-hearing listeners, and is used to predict annoyance for the hearing-impaired listeners. Differences across the subject populations are discussed.