gebhart/patrepeval huggingface dataset:
Endophytic Fungi of Pacific Yew <i>(Taxus brevifolia)</i> as a Source of Taxol, Taxanes, and Other Pharmacophores (1994)

Investigation of the bioactive components of the endophytic microbes associated with the Pacific yew tree, Taxusbrevifolia yielded a novel, hyphomycetous fungus that produces taxol and taxanes when grown in semi-synthetic liquid media. Taxomycesandreanae was isolated from the phloem (inner bark) of a Pacific yew tree, the traditional source of naturally occurring taxol. The presence of taxol in the fungal extract was confirmed by fast atom bombardment and electrospray mass spectrometry, comparative chromatographic behavior with yew taxol, reactivity with monoclonal antibodies specific for taxol, and 9KB cytotoxicity studies. Both acetate-1-14C and phenylalanine UL-14C served as precursors of taxol-14C in fungal culture labeling studies, confirming the de novo synthesis of taxol by the fungus. Immunoassay techniques are currently being used to screen extracts of Taxomycesandreanae for new taxanes, and to determine if other endophytic fungi are taxol producers.
Abstract 3768: Identification of new alternative lengthening of telomeres (ALT)-positive cancer cell lines using the C-circle assay (2015)

Abstract Alternative lengthening of telomeres (ALT) is a telomere maintenance mechanism used by approximately 10% of human cancers, including poor prognosis childhood and adult cancers for which development of better treatments is a priority. Currently there are only about ten published ALT+ cancer cell lines available for research, only four of which are available from international repositories. The development of the C-Circle Assay has made it possible to accurately and conveniently test a large number of cell lines for ALT activity. We have tested a panel of 297 cancer cell lines from the American Type Culture Collection (ATCC) with the C-Circle Assay for ALT and identified 34 new ALT+ cell lines. Importantly, we have identified for the first time ALT+ cancer cell lines derived from breast carcinoma, hepatocellular carcinoma, melanoma and leukemia. The overall proportion of ALT+ cancer cell lines was 11.4% (n = 297), which included 19.5% of leukemia (n = 46), 19.0% of melanoma (n = 21), 12.7% of non-small cell lung carcinoma (n = 53) and 3.3% of breast carcinoma (n = 37) cell lines. These results identify additional cancer cell line resources for research into the ALT mechanism, including cell lines from cancer types where ALT has not previously been studied in detail. Citation Format: Andrei G. Malykh, Jonathan R. Doyle, Fang Tian, Joyce HY Lee, Jeremy D. Henson, Roger R. Reddel. Identification of new alternative lengthening of telomeres (ALT)-positive cancer cell lines using the C-circle assay. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3768. doi:10.1158/1538-7445.AM2015-3768
Modeling and Optimal Cyclic Scheduling of Time-Constrained Single-Robot-Arm Cluster Tools via Petri Nets and Linear Programming (2017)

Scheduling a cluster tool with wafer residency time constraints is challenging and important in wafer manufacturing. With a backward strategy, the scheduling problem of such singlerobot-arm cluster tools is well-studied in the literature. It is much more challenging to schedule a more general case whose optimal scheduling strategy is not limited to the backward one. This work uses a timed Petri net (PN) to model the dynamic behavior of the system and presents a method to determine the optimal scheduling strategy for the system. Based on its PN model and the obtained strategy, it reveals that the key issue to schedule such a tool is to determine when and how long the robot should wait for. Based on this finding, this work establishes for the first time the necessary and sufficient conditions regarding the existence of an optimal and feasible one-wafer cyclic schedule for singlerobot-arm cluster tools. It then formulates a computationally efficient linear program to find it if existing, and finally gives industrial examples to show the application and power of the proposed method.
RNAi-Mediated Suppression of Laccase2 Impairs Cuticle Tanning and Molting in the Cotton Boll Weevil (Anthonomus grandis) (2020)

The cotton boll weevil, <i>Anthonomus grandis</i>, is the most economically important pest of cotton in Brazil. Pest management programs focused on <i>A. grandis</i> are based mostly on the use of chemical insecticides, which may cause serious ecological impacts. Furthermore, <i>A. grandis</i> has developed resistance to some insecticides after their long-term use. Therefore, alternative control approaches that are more sustainable and have reduced environmental impacts are highly desirable to protect cotton crops from this destructive pest. RNA interference (RNAi) is a valuable reverse genetics tool for the investigation of gene function and has been explored for the development of strategies to control agricultural insect pests. This study aimed to evaluate the biological role of the <i>Laccase2</i> (<i>AgraLac2</i>) gene in <i>A. grandis</i> and its potential as an RNAi target for the control of this insect pest. We found that <i>AgraLac2</i> is expressed throughout the development of <i>A. grandis</i> with significantly higher expression in pupal and adult developmental stages. In addition, the immunolocalization of the AgraLac2 protein in third-instar larvae using specific antibodies revealed that AgraLac2 is distributed throughout the epithelial tissue, the cuticle and the tracheal system. We also verified that the knockdown of <i>AgraLac2</i> in <i>A. grandis</i> resulted in an altered cuticle tanning process, molting defects and arrested development. Remarkably, insects injected with ds<i>AgraLac2</i> exhibited defects in cuticle hardening and pigmentation. As a consequence, the development of ds<i>AgraLac2</i>-treated insects was compromised, and in cases of severe phenotypic defects, the insects subsequently died. On the contrary, insects subjected to control treatments did not show any visible phenotypic defects in cuticle formation and successfully molted to the pupal and adult stages. Taken together, our data indicate that <i>AgraLac2</i> is involved in the cuticle tanning process in <i>A. grandis</i> and may be a promising target for the development of RNAi-based technologies.
Luma Mapping with Chroma Scaling in Versatile Video Coding (2020)

This paper describes a new video coding tool in the Versatile Video Coding standard (VVC) named as luma mapping with chroma scaling (LMCS). Experimental compression performance results for LMCS and non-normative examples for deriving LMCS parameter values are also provided. LMCS has two main components: 1) a process for mapping input luma code values to a new set of code values for use inside the coding loop; and 2) a luma-dependent process for scaling chroma residue values. The first process, luma mapping, aims at improving the coding efficiency for standard and high dynamic range video signals by making better use of the range of luma code values allowed at a specified bit depth. The second process, chroma scaling, manages relative compression efficiency for the luma and chroma components of the video signal. The luma mapping process of LMCS is applied at the pixel sample level, and is implemented using a piecewise linear model. The chroma scaling process is applied at the chroma block level, and is implemented using a scaling factor derived from reconstructed neighboring luma samples of the chroma block.
Compact Filtering Dielectric Resonator Antenna With Quasi-Isotropic Radiation Pattern (2021)

A compact filtering dielectric resonator antenna (DRA) is proposed in this paper. The hemisphere dielectric resonator (DR) is fed by a microstrip line with two stubs. Due to the different loading effects of the two feeding stubs, the DR TE <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">111</inf> mode is excited with two adjacent resonances, showing a bandwidth of 6.8%. Two controllable radiation nulls are generated at the lower and upper edges of the passband, bring about high frequency selectivity. Also, the DR operating at TE <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">111</inf> mode is equivalent to a magnetic dipole, while a small ground plane used in the DRA radiates like an electric dipole. The combination of the two orthogonal dipoles leads to a quasi- isotropic radiation pattern. This antenna has a small size (ka = 0.88) and bandpass filtering function.
Engineering of an H<sub>2</sub>O<sub>2</sub> auto‐scavenging in vivo cascade for pinoresinol production (2017)

Pinoresinol is a natural lignan with a high market value that has potential pharmacological and food supplement applications. Pinoresinol is currently isolated from plants, which suffers from low efficiency and yield. To produce pinoresinol from inexpensive and industrially available eugenol, an in vivo enzymatic cascade composed of vanillyl alcohol oxidase and peroxidase was designed, which scavenges H<sub>2</sub> O<sub>2</sub> automatically and eliminates protein purification and cofactor addition. Two peroxidases were screened and identified from Escherichia coli BL21 (DE3), and tested in the enzymatic cascade. To balance the flux, different genetic architectures were constructed by using ePathBrick and fusion gene approaches. Scavenging H<sub>2</sub> O<sub>2</sub> alleviated by-product toxicity and enzyme inhibition, and led to efficient pinoresinol production. Optimization of the reaction conditions achieved a titer of 11.29 g/L pinoresinol. The molar yield and productivity were 52.77% and 1.03 g/(L × h), respectively. The elegant strategy developed herein utilizes the harmful by-product to drive the biosynthetic reaction forward and simultaneously detoxify cells, thereby preventing enzyme inhibition. Biotechnol. Bioeng. 2017;114: 2066-2074. © 2017 Wiley Periodicals, Inc.
Ranking the web frontier (2004)

The celebrated PageRank algorithm has proved to be a very effective paradigm for ranking results of web search algorithms. In this paper we refine this basic paradigm to take into account several evolving prominent features of the web, and propose several algorithmic innovations. First, we analyze features of the rapidly growing frontier of the web, namely the part of the web that crawlers are unable to cover for one reason or another. We analyze the effect of these pages and find it to be significant. We suggest ways to improve the quality of ranking by modeling the growing presence of link rot on the web as more sites and pages fall out of maintenance. Finally we suggest new methods of ranking that are motivated by the hierarchical structure of the web, are more efficient than PageRank, and may be more resistant to direct manipulation.
Advanced modulation and coding technologies for ultra-high-speed optical communications (2008)

We introduce two important technologies for development of next generation ultra-high-speed optical communications: (i) polarization multiplexing, phase modulation with digital coherent detection, and (ii) OFDM-based optical fiber transmission. In both schemes, digital signal processing plays a key role in recovering the signal and mitigating the detrimental effects from optical signal transmission. We further describe a novel three dimensional low-density parity check (LDPC) coded modulation scheme, including its principle and system performance.
Dynamic modeling of nonlinear SRM drive with Pspice (2002)

In this paper, a comprehensive nonlinear dynamic model for a switched reluctance motor (SRM) drive using Pspice is presented. The SRM is represented by its nonlinear dynamic equations and the magnetic model of SRM includes the representation of inductance-current-position characteristics which closely match those obtained experimentally. The variation of the phase inductance with rotor position is expressed by a limited number of Fourier series terms. The coefficients of the Fourier series are determined by the values of the inductance at the aligned position, unaligned position and a position midway between the two. The nonlinear relationship between the phase inductance and the current is represented by polynomial functions whose coefficients are derived by static characteristics obtained from finite element analysis or experimental results. Since Pspice is a circuit oriented package, any type of converter and control scheme can be modeled with ease and hence the component ratings can be selected based on simulation results. Further, any type of converter/motor faults as well as phase asymmetries can also be simulated. It is also possible to simulate various control strategies for low and higher speed operations and obtain optimum control angles. The details of the developed model and the simulation results obtained for a 300 W, 12 V, 8/6 SRM drive in various operating regions are presented in this paper. To validate the model, the simulation results are compared with experimental and finite element analysis results.
Conditionals by inversion provide a universal method for the generation of conditional alleles (2013)

Conditional mutagenesis is becoming a method of choice for studying gene function, but constructing conditional alleles is often laborious, limited by target gene structure, and at times, prone to incomplete conditional ablation. To address these issues, we developed a technology termed conditionals by inversion (COIN). Before activation, COINs contain an inverted module (COIN module) that lies inertly within the antisense strand of a resident gene. When inverted into the sense strand by a site-specific recombinase, the COIN module causes termination of the target gene's transcription and simultaneously provides a reporter for tracking this event. COIN modules can be inserted into natural introns (intronic COINs) or directly into coding exons as part of an artificial intron (exonic COINs), greatly simplifying allele design and increasing flexibility over previous conditional KO approaches. Detailed analysis of over 20 COIN alleles establishes the reliability of the method and its broad applicability to any gene, regardless of exon-intron structure. Our extensive testing provides rules that help ensure success of this approach and also explains why other currently available conditional approaches often fail to function optimally. Finally, the ability to split exons using the COIN's artificial intron opens up engineering modalities for the generation of multifunctional alleles.
OP15 Discovery of new liver fibrosis markers in hepatitis C patients using proteomics (2011)

<h3>Introduction</h3> Liver biopsy is the reference standard for assessing liver fibrosis, and no reliable non-invasive diagnostic approach is available to discriminate between the intermediate stages of fibrosis. Therefore suitable serological biomarkers of liver fibrosis are urgently needed. <h3>Aim</h3> The objective of this study was to use proteomics to identify novel fibrosis biomarkers in hepatitis C patients with different degrees of liver fibrosis. <h3>Method</h3> Proteins in plasma samples from healthy control individuals and patients with hepatitis C virus (HCV) induced cirrhosis were analysed using a proteomics technique—two dimensional gel electrophoresis (2-DE). This technique separated the proteins in plasma samples of control and cirrhotic patients and by visualising the separated proteins we were able to identify proteins which were increasing or decreasing in hepatic cirrhosis. Identified markers were validated across all Ishak stages and compared to the markers used in FibroTest, Enhanced Liver Fibrosis (ELF) test, Hepascore and FIBROSpect by western blotting. <h3>Results</h3> 44 candidate biomarkers for hepatic fibrosis were identified of which 20 were novel. western blot validation of all candidate markers using plasma samples from patients across all Ishak fibrosis scores showed that the markers which changed with increasing fibrosis most consistently included lipid transfer inhibitor protein, complement C3d, corticosteroid-binding globulin, apolipoprotein J and apolipoprotein L1. These five novel markers which are secreted in blood showed a promising consistent change with increasing fibrosis stage when compared to the markers used for the FibroTest, ELF test, Hepascore and FIBROSpect. <h3>Conclusion</h3> This study identifies 20 novel fibrosis biomarker candidates. The proteins identified by these improved approaches may help to assess hepatic fibrosis and eliminate the need for invasive liver biopsies.
Design and testing of the Series III AMTEC cell (1999)

This paper describes the design and testing of the Series III (S3) Alkali Metal Thermal to Electric Converter (AMTEC) cell which is capable of high efficiency (15--25%) and high power density (100--150 W/kg). Compared to the Series 2 cell which is being developed primarily for space power systems, the Series III cell design provides a significantly higher beta{double_prime}-alumina solid electrolyte (BASE) tube packing density around the heat source thereby increasing cell power and minimizing heat loss. The prototype S3 cell will have 96 BASE tubes and is expected to produce about 150 We. In this cell design the BASE tube assemblies are mounted on a cylindrical tube support plate. The BASE tubes are arranged like spokes on a wheel. The inner cylinder, concentric to the tube support plate, is the hot side of the cell and the outer cylinder is the condenser. Since the prototype S3 cell will be the first of its kind, an engineering cell with same dimensions as the prototype but with 24 BASE tubes was built first. The purpose of this cell was to identify and resolve structural, thermal, manufacturing and sodium management issues before launching into the build of a complete 96 BASE tube cell.more » The engineering cell has been successfully built and tested. The data of the engineering cells have been used to calibrate the SINDA/FLUINT code to predict the prototype cell performance more accurately. The build of the prototype 96 BASE tube cells is now in progress. This paper presents the design and development of the prototype S3 cell. The fabrication and testing of the first S3 engineering cell is discussed next. Based on the test data of the engineering cell, the anticipated thermal performance of the prototype cells predicted by the calibrated SINDA model are also presented.« less
A first catch, non-DRE urine exosome gene signature to predict Gleason 7 prostate cancer on an initial prostate needle biopsy. (2015)

45 Background: There is a critical need to reduce initial prostate biopsies (PB) in the PSA ‘gray zone’ of 2-10 ng/mL. Non-invasive screening tools that add predictive value for identifying high-grade, Gleason score (GS) ≥7 should impact on the current diagnostic paradigm. We have developed standardized processes to isolate exosomal-RNA from first-catch urine specimens and sought to identify a gene signature that reliably differentiates GS7+ from GS6 and benign disease. Methods: First-catch non-DRE urine specimens were collected at six sites in standard collection vessels without preservative, stored at 2-8C (up to two weeks) and shipped on ice to a central laboratory (Exosome Diagnostics, St. Paul, MN). Upon receipt, samples were filtered (0.8um), and exosome isolation and RNA extraction performed. RT-qPCR RNA copy numbers of ERG and PCA3, normalized to SPDEF, were measured to generate a three-gene signature, defined to yield a score S between 0 and 30, where S>10 predicts GS7+ vs. GS6 and benign lesions with optimal NPV, Sensitivity and Specificity. Results: Urine samples from 170 men (PSA 2-10 ng/mL, first biopsy,40 mL; median age 62 years, median PSA 5.1 ng/mL, 70% negative DRE, 77%, no family history, 82% Caucasian) of 453 total, with comparable demographics, were evaluated. With 46% and 21% prevalence of positive biopsy for any cancer or GS7+ disease, respectively, a dichotomous gene signature demonstrated good clinical performance in predicting biopsy result. For GS7+, the NPV and PPV were 98.6% and 34.7%, respectively. A continuous score alone had an AUC of 0.76 for discriminating GS7+ from GS6 and benign disease and the results were significantly better than the prostate cancer prevention trial risk calculator (PCPTRC), AUC 0.60. Conclusions: A novel, non-invasive urine exosome gene signature demonstrated independent, negative predictive value for the diagnosis of GS7+ from first biopsy patients with ‘gray zone’ serum PSA. Its use in the biopsy decision process could result in fewer prostate biopsies once validated on an expanded prospective cohort.
Isolation and properties of soybean [ <i>Glycine max</i> (L.) Merr.] mutants that nodulate in the presence of high nitrate concentrations (1985)

Soybean seeds [Glycine max (L.) Merr. ev. Bragg] were mutagenized with ethyl methanesulfonate. The M(2) progeny (i.e., the first generation after mutagenesis) of these seeds were screened for increased nodulation under high nitrate culture conditions. Fifteen independent nitrate-tolerant symbiotic (nts) mutants were obtained from 2500 M(2) families. In culture on sand with KNO(3), nodule mass and nodule number in mutant lines were several-fold those of the wild type cultured under the same conditions. Inheritance of the nts character through to subsequent generations was observed in the 10 mutants tested. Mutant nts382 also nodulated more than the wild type in the absence of nitrate. Furthermore, nitrate stimulated growth in both the wild type and nts382, and these lines had similar nitrate reductase activity. These results indicate that nts382 is affected in a nodule-development regulatory gene and not in a gene related to nitrate assimilation.
Development and properties of duplex MgF2/PCL coatings on biodegradable magnesium alloy for biomedical applications (2018)

The present work addresses the performance of polycaprolactone (PCL) coating on fluoride treated (MgF2) biodegradable ZK60 magnesium alloy (Mg) for biomedical application. MgF2 conversion layer was first produced by immersing Mg alloy substrate in hydrofluoric acid solution. The outer PCL coating was then prepared using dip coating technique. Morphology, elements profile, phase structure, roughness, mechanical properties, invitro corrosion, and biocompatibility of duplex MgF2/PCL coating were then characterized and compared to those of fluoride coated and uncoated Mg samples. The invivo degradation behavior and biocompatibility of duplex MgF2/PCL coating with respect to ZK60 Mg alloy were also studied using rabbit model for 2 weeks. SEM and TEM analysis showed that the duplex coating was uniform and comprised of porous PCL film (~3.3 μm) as upper layer with compact MgF2 (~2.2 μm) as inner layer. No significant change in microhardness was found on duplex coating compared with uncoated ZK60 Mg alloy. The duplex coating showed improved invitro corrosion resistance than single layered MgF2 or uncoated alloy samples. The duplex coating also resulted in better cell viability, cell adhesion, and cell proliferation compared to fluoride coated or uncoated alloy. Preliminary invivo studies indicated that duplex MgF2/PCL coating reduced the degradation rate of ZK60 Mg alloy and exhibited good biocompatibility. These results suggested that duplex MgF2/PCL coating on magnesium alloy might have great potential for orthopedic applications.
Subharmonic driving: a new concept to drive piezoelectric transformers in power converters (2002)

A new concept to drive piezoelectric transformers (PT) is presented and validated in this paper. The subharmonic driving consists on applying a voltage waveform to the PT whose fundamental frequency (f/sub PT//n) contains the resonance harmonic (f/sub PT/) at which the PT transfers the energy. It is important to highlight that this solution is proposed in order to improve the whole power converter, even if the PT performance is not as good as it could be with sinusoidal excitation. The PT should be specifically designed to handle more energy.