gebhart/patrepeval huggingface dataset:
The<i>Arabidopsis</i>Myb transcription factor MTF1 is a unidirectional regulator of susceptibility to<i>Agrobacterium</i> (2014)

We recently described the Arabidopsis Myb transcription factor MTF1 that negatively regulates plant susceptibility to Agrobacterium-mediated transformation. Roots of mtf1 mutant plants show increased susceptibility to several Agrobacterium strains, and complementing the mutants with a MTF1 cDNA decreases transformation susceptibility to wild-type levels. Here, we show that overexpression of MTF1 in a wild-type Arabidopsis background does not result in altered transformation susceptibility. However, MTF1 overexpressing plants show increased root length and larger and darker leaves, indicating that MTF1 plays a role in plant growth and development. MTF1 decreases Arabidopsis root susceptibility specifically to Agrobacterium but plant responses to the pathogens Alternaria brassicicola or Pseudomonas syringae pv Tomato were not altered. However, the homozygous MTF1 mutant mtf1–4 is resistant to Botrytis cinerea strain BO5–10 and is regulated through the ethylene signaling pathway mediated by upregulation of the AP2/ERF transcription factor ORA59.
Hydroprocessing catalysis by new reduced ternary molybdenum sulfides (1998)

In our research, we have investigated a new series of hydroprocessing catalysts based on our discovery of the activity of the Chevrel phases. The family of Chevrel phase compounds has characteristics structural unit based on the Mo 6 S 8 cluster : the general composition is specified as M x Mo 6 S 8 , where M (the ternary metal cation) includes over 40 different metallic elements. Previous methods for preparing Chevrel phases usually have involved solid state syntheses at high temperatures (1000-1300°C). the resulting materials have low surface areas, typically around 1m 2 /g.
Structural Origin of Selectivity in Class II-Selective Histone Deacetylase Inhibitors (2008)

The development of class- and isoform-selective histone deacetylase (HDAC) inhibitors is highly desirable for the study of the complex interactions of these proteins central to transcription regulation as well as for the development of selective HDAC inhibitors as drugs in epigenetics. To provide a structural basis for the rational design of such inhibitors, a combined computational and experimental study of inhibition of three different histone deacetylase isoforms, HDAC1, -6, and -8, with three different hydroxamate inhibitors is reported. While SAHA was found to be unselective for the inhibition of class I and class II HDACs, the other inhibitors were found to be selective toward class II HDACs. Molecular dynamics simulations indicate that this selectivity is caused by both the overall shape of the protein surface leading to the active site and specific interactions of an aspartate residue in a polar loop and two phenylalanines and a methionine in a nonpolar loop. Monitoring the specific interactions as a function of the simulation time identifies a key sulfur-pi interaction. The implications of the structural motifs for the design of class II-selective HDAC inhibitors are discussed.
A 6-month maintenance therapy with adapalene-benzoyl peroxide gel prevents relapse and continuously improves efficacy among patients with severe acne vulgaris: results of a randomized controlled trial (2011)

Adapalene-BPO not only prevents the occurrence of relapse among patients with severe acne, but also continues to reduce disease symptoms during 6 months.
Concurrent Vibrational Circular Dichroism Measurements with Infrared Spectroscopic Imaging (2020)

Vibrational circular dichroism (VCD) spectroscopy has emerged as a powerful platform to quantify chirality, a vital biological property that performs a pivotal role in the metabolism of life organisms. With a photoelastic modulator (PEM) integrated into an infrared spectrometer, the differential response of a sample to the direction of circularly polarized light can be used to infer conformation handedness. However, these optical components inherently exhibit chromatic behavior and are typically optimized at discrete spectral frequencies. Advancements of discrete frequency infrared (DFIR) spectroscopic microscopes in spectral image quality and data throughput are promising for use toward analytical VCD measurements. Utilizing the PEM advantages incorporated into a custom-built QCL microscope, we demonstrate a point scanning VCD instrument capable of acquiring spectra rapidly across all fingerprint region wavelengths in transmission configuration. Moreover, for the first time, we also demonstrate the VCD imaging performance of our instrument for site-specific chirality mapping of biological tissue samples. This study offers some insight into future possibilities of examining small, localized changes in tissue that have major implications for systemic diseases and their progression, while also laying the groundwork for additional modeling and validation in advancing the capability of VCD spectroscopy and imaging.
Synthesis and Biological Evaluation of Inhibitors of Botulinum Neurotoxin Metalloprotease (2009)

Based on the lead therapeutic agent NSC 240898, a new series of heterocyclic inhibitors of the BoNT serotype A metalloprotease has been generated.Highlights of the synthetic sequences include Sonogashira couplings of polysubstituted building blocks and gold-catalyzed indole formations.Preliminary structure-activity relationship studies afford detailed insights into the steric and electrostatic properties of the pharmacophore of this molecular scaffold.
Genome of the Bacterium <i>Streptococcus pneumoniae</i> Strain R6 (2001)

Streptococcus pneumoniae is among the most significant causes of bacterial disease in humans. Here we report the 2,038,615-bp genomic sequence of the gram-positive bacterium S. pneumoniae R6. Because the R6 strain is avirulent and, more importantly, because it is readily transformed with DNA from homologous species and many heterologous species, it is the principal platform for investigation of the biology of this important pathogen. It is also used as a primary vehicle for genomics-based development of antibiotics for gram-positive bacteria. In our analysis of the genome, we identified a large number of new uncharacterized genes predicted to encode proteins that either reside on the surface of the cell or are secreted. Among those proteins there may be new targets for vaccine and antibiotic development.
All-solid Photonic Bandgap Fiber with Record Mode Area (2013)

We experimentally demonstrated all-solid photonic bandgap fibers with ~50μm core diameters and excellent higher order mode suppression, which can be used for high power fiber lasers to overcome the limits of fiber nonlinearities.
Optoelectric transducer system for stringed instruments (1994)

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation Bradley W. Curtis, Bruce L. Kennedy, Christopher R. Willcox; Optoelectric transducer system for stringed instruments. J. Acoust. Soc. Am. 1 January 1994; 95 (1): 594. https://doi.org/10.1121/1.408296 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAcoustical Society of AmericaThe Journal of the Acoustical Society of America Search Advanced Search |Citation Search
Abstract LB-350: In vivo kinome screen reveals potential drivers of brain metastasis (2016)

Abstract Brain metastasis remains an unmet medical need, as its incidence continues to rise while treatment options remain palliative. Advances in targeted therapy for breast cancer have prolonged patient survival through better control of the systemic disease, but an ever-increasing number of patients later recur with brain metastasis. As no effective therapies exist for brain metastasis, the median survival of patients is less than one year. To tackle this growing clinical challenge, we sought to better understand the biological mechanism of brain metastasis and to identify novel targets for intervention. We chose to focus on kinases, as they both occupy the central nodes of cancer cell signaling pathways and structurally lend themselves to targeting by small molecules. To identify novel therapeutic targets, we performed an unbiased kinome screen in vivo for determination of brain metastasis driver kinases. We injected MDA-MB-231 human breast cancer cells overexpressing pools of 16-20 kinase ORFs into the carotid artery of nude mice to form experimental brain metastasis. Several of the kinase pools led to decreased brain metastasis-specific survival, decreasing survival time by as much as 50% relative to controls. We then performed targeted next-generation sequencing (NGS) of the pre-and post-injection tumor cells to determine those kinases most enriched in vivo, revealing 31 ORFs that were significantly increased in vivo in multiple animals. To validate the clinical relevance of these potential targets, we examined their expression in a collection of 32 human brain metastases by RNA-seq, and observed that the majority of the ORFs (29/31) were indeed expressed. One of the kinases with the highest in vivo enrichment and expression in human brain metastases was hexokinase 2 (HK2), an important glycolysis regulator that has been previously implicated in brain metastasis and served to validate our findings. Several other candidate kinases were also related to glycolysis and other metabolic pathways, suggesting that these kinases enable metastatic cancer cells to survive in the nutrient-restricted brain environment. Functional validation of these newly identified kinases as true drivers of brain metastasis will reveal whether they have potential to serve as the first targets of brain metastasis-targeted therapy. Citation Format: Frank J. Lowery, Sunil Acharya, Yong Xia, Chenyu Zhang, Jodi M. Saunus, Dihua Yu. In vivo kinome screen reveals potential drivers of brain metastasis. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-350.
Programmable frequency reference for subkilohertz laser stabilization by use of persistent spectral hole burning (1999)

We report what is believed to be the first demonstration of laser frequency stabilization directly to persistent spectral holes in a solid-state material. The frequency reference material was deuterated CaF(2): Tm(3+) prepared with 25-MHz-wide persistent spectral holes on the H(6)(3)?H(4)(3) transition at 798 nm. The beat frequency between two lasers that were independently locked to persistent spectral holes in separate crystal samples showed typical root Allan variances of 780+/-120Hz for 20-50-ms integration times.
Resistive Susceptor Design for Uniform Heating during Induction Bonding of Composites (1998)

A novel susceptor concept for metal mesh susceptors, designed to achieve uniform in-plane temperatures during induction heating, is documented. The process involves redirecting eddy current flow patterns in the resistive mesh susceptor by specifically designed cut patterns in the mesh. A theoretical model was developed to predict heat generation in metal mesh susceptors with any prescribed network pattern. Initial results for meshes with cut patterns show significant changes in heating compared to an uncut mesh. Cut patterns can be optimized to reduce temperature gradients in the susceptor to within the processing window of the composite. Experimental results are presented for qualitative comparisons.
Surface Doping and Band Gap Tunability in Hydrogenated Graphene (2011)

We report the first observation of the n-type nature of hydrogenated graphene on SiO(2) and demonstrate the conversion of the majority carrier type from electrons to holes using surface doping. Density functional calculations indicate that the carrier type reversal is directly related to the magnitude of the hydrogenated graphene's work function relative to the substrate, which decreases when adsorbates such as water are present. Additionally, we show by temperature-dependent electronic transport measurements that hydrogenating graphene induces a band gap and that in the moderate temperature regime [220-375 K], the band gap has a maximum value at the charge neutrality point, is tunable with an electric field effect, and is higher for higher hydrogen coverage. The ability to control the majority charge carrier in hydrogenated graphene, in addition to opening a band gap, suggests potential for chemically modified graphene p-n junctions.
Enhancement of Light Extraction Through the Wave‐Guiding Effect of ZnO Sub‐microrods in InGaN Blue Light‐Emitting Diodes (2010)

Abstract The improvement of the light extraction efficiency (LEE) of a conventional InGaN blue light‐emitting diode (LED) by the incorporation of one‐dimensional ZnO sub‐microrods is reported. The LEE is improved by 31% through the wave‐guiding effect of ZnO sub‐microrods compared to LEDs without the sub‐microrods. Different types of ZnO microrods/sub‐microrods are produced using a simple non‐catalytic wet chemical growth method at a low temperature (90 °C) on an indium‐tin‐oxide (ITO) top contact layer with no seed layer. The crystal morphologies of needle‐like or flat‐top hexagonal structures, and the ZnO microrods/sub‐microrod density and size are easily modified by controlling the pH value and growth time. The wave‐guiding phenomenon within the ZnO rods is observed using confocal scanning electroluminescence microscopy and micro‐electroluminescence spectra.
Polyimides That Contain Pendent Siloxane Groups (1996)

Polyimides containing pendent siloxane groups (PISOXs) synthesized from polyimides containing hydroxy groups (PIOHs) according to either of two alternative approaches. Addition of pendent siloxane groups to polyimide decreases dielectric constant, and decreases absorption of moisture: these changes in properties advantageous in some electronic applications. Also enhance resistance to atomic oxygen in that they undergo slight degradation to form thin protective silicon oxide coats when exposed to atomic oxygen.
Binaural speech enhancement using a codebook based approach (2016)

Enhancement of speech in non stationary noise environments has been a major research topic due to its wide range of applications, e.g., in hearing aids. This paper proposes a method for performing dual channel speech enhancement. The proposed method involves the estimation of speech and noise short term predictor (STP) parameters using a codebook based approach, when we have access to binaural noisy signals. The estimated STP parameters are subsequently used for enhancement in a dual channel scenario. Objective measures indicate, that the proposed method is able to improve the speech intelligibility and quality.
Enhancement of Cardiac Function and Suppression of Heart Failure Progression By Inhibition of Protein Phosphatase 1 (2005)

Abnormal calcium cycling, characteristic of experimental and human heart failure, is associated with impaired sarcoplasmic reticulum calcium uptake activity. This reflects decreases in the cAMP-pathway signaling and increases in type 1 phosphatase activity. The increased protein phosphatase 1 activity is partially due to dephosphorylation and inactivation of its inhibitor-1, promoting dephosphorylation of phospholamban and inhibition of the sarcoplasmic reticulum calcium-pump. Indeed, cardiac-specific expression of a constitutively active inhibitor-1 results in selective enhancement of phospholamban phosphorylation and augmented cardiac contractility at the cellular and intact animal levels. Furthermore, the beta-adrenergic response is enhanced in the transgenic hearts compared with wild types. On aortic constriction, the hypercontractile cardiac function is maintained, hypertrophy is attenuated and there is no decompensation in the transgenics compared with wild-type controls. Notably, acute adenoviral gene delivery of the active inhibitor-1, completely restores function and partially reverses remodeling, including normalization of the hyperactivated p38, in the setting of pre-existing heart failure. Thus, the inhibitor 1 of the type 1 phosphatase may represent an attractive new therapeutic target.
Ultrasonic imaging and characterization of objects submerged in highly attenuating fluids. (2010)

An ultrasonic scanning tool to image objects with high-spatial resolution submerged in highly attenuating fluids is described. The attenuation coefficient of the fluids used range over two orders of magnitude. For deeper penetration into the attenuating fluids, a parametric array with a difference frequency between 200 and 500 kHz was used. The primary frequencies that generated this difference frequency varied between 2 and 8 MHz. This parametric array provides a collimated beam for imaging. Both simple tone burst and frequency chirp signals were used for the measurement. Using this apparatus, the quality and accuracy of the image as a function of frequency, fluid attenuation coefficient, and fluid type (clear and suspensions) were investigated. It was found that imaging was possible over a wide range of attenuating coefficients and fluid types.
A Rapid and Direct Approach to Identify Promoters That Confer High Levels of Gene Expression in Monocots (2003)

Direct screening of genomic libraries for highly expressed genes is an efficient way to identify promoters that confer high levels of gene expression. To test the efficacy of this approach to isolate promoters for directing high levels of gene expression in sugarcane, 11 genomic clones were isolated after screening a sugarcane genomic library with radioactively labeled first strand cDNA probes synthesized from sugarcane leaf mRNA. Hybridization analysis with pooled first strand cDNA indicated that eight of the clones probably contain genes with expression levels similar to or higher than ubiquitin (which was also isolated in this screen). The coding regions of these 11 genomic clones were isolated from a cDNA library, sequenced, and found to represent parts of five different genes including elongation factor 1α, α‐tubulin, an aquaporin, a proline‐rich protein, and one novel gene. Southern and Northern results showed that the sugarcane proline‐rich protein‐encoding gene (SPRP1) was the best candidate to isolate a promoter that would direct high levels of expression, although the other four are also good candidates. Two genomic clones of the sugarcane proline‐rich gene and a sugarcane elongation factor 1α (SEF1α) gene, which contain both the promoter and coding regions, were subcloned, sequenced, and promoter regions defined by comparison of cDNA and genomic DNA sequences. Both the SEF1α and SPRP1 promoter/β‐glucuronidase (GUS) fusions resulted in high levels of GUS expression when reintroduced into embryogenic sugarcane callus, and also resulted in high levels of transient GUS expression in wheat embryos. This approach has value as an efficient technique to find promoters that confer high‐level gene expression in monocots.
NFV orchestrator placement for geo-distributed systems (2017)

The European Telecommunications Standards Institute (ETSI) developed Network Functions Virtualization (NFV) Management and Orchestration (MANO) framework. Within that framework, NFV orchestrator (NFVO) and Virtualized Network Function (VNF) Manager (VNFM) functional blocks are responsible for managing the lifecycle of network services and their associated VNFs. However, they face significant scalability and performance challenges in large-scale and geo-distributed NFV systems. Their number and location have major implications for the number of VNFs that can be accommodated and also for the overall system performance. NFVO and VNFM placement is therefore a key challenge due to its potential impact on the system scalability and performance. In this paper, we address the placement of NFVO and VNFM in large-scale and geo-distributed NFV infrastructure. We provide an integer linear programming formulation of the problem and propose a two-step placement algorithm to solve it. We also conduct a set of experiments to evaluate the proposed algorithm.
GEN-SLAM: Generative Modeling for Monocular Simultaneous Localization\n and Mapping (2019)

We present a Deep Learning based system for the twin tasks of localization\nand obstacle avoidance essential to any mobile robot. Our system learns from\nconventional geometric SLAM, and outputs, using a single camera, the\ntopological pose of the camera in an environment, and the depth map of\nobstacles around it. We use a CNN to localize in a topological map, and a\nconditional VAE to output depth for a camera image, conditional on this\ntopological location estimation. We demonstrate the effectiveness of our\nmonocular localization and depth estimation system on simulated and real\ndatasets.\n
<title>Green fluorescent protein: new light to visualize metastasis and angiogenesis in cancer</title> (1999)

Green fluorescent protein (GFP)-expressing cell-lines have been established by our laboratory that permit the visualization and imaging of primary tumors and micrometastases in live tissue and live animals. Hamster and human cancer cell-lines were transfected with vectors containing the humanized GFP cDNA. Stable high-level expression of GFP was maintained in subcutaneously and orthotopically growing tumors in nude or SCID mice. Subsequent micro-metastases were visualized by GFP fluorescence in live tissue of systematic organs down to the single-cell level. GFP-expressing lung and prostate cancer were visualized to metastasize widely throughout the skeleton when implanted orthotopically in nude mice. With these GFP-cell lines, we have developed models that closely mimic the clinic situation. We have now developed a mean to visualize the onset and progression of angiogenesis of growing and spreading tumors by injecting a fluorescent rhodamine dye to the GFP-tumor-bearing mice indicate that the onset and extent of tumor angiogenesis depends on the site and type of tumor growing in the animal. These models are ideal for studying the mechanisms of cancer metastasis and for discovery of angiogenesis and metastasis inhibitors.
Methional as an antioxidant for vegetable oils (1977)

Abstract and summary Brief heating of safflower oil with 1% by weight of DL‐methionine at 200 C stabilized the oil to subse‐quent autoxidation. Since this treatment also caused development of a strong cabbage‐like aroma, it was difficult to follow the oxidation organoleptically. Measurements of oxygen absorption rate and per‐oxide development confirmed that the heated oil was quite stable. The major product of the reaction between methionine and safflower oil, N(3‐methyl‐thiopropyl) linoleic amide, was found to be a pro‐oxidant. There was evidence that methional (β‐methylmercaptopropionaldehyde), formed by de‐gradation of methionine, is the active antioxidant. Commercial methional contains significant quantities of a dimer and trimer, both of which were also found to have antioxidant activity. The dimer is a de‐hydrated aldol condensation product whereas the trimer is cyclic, a substituted trioxymethylene. Meth‐ional and its polymers have such strong objectionable odors, even at low concentrations in oil, that their usefulness as antioxidants may be very limited.