gebhart/patrepeval huggingface dataset:
Production of moth sex pheromone precursors in Nicotiana spp.: a worthwhile new approach to pest control (2020)

Abstract Pheromones are environmentally friendly alternatives to traditional pesticides for pest control. They are widely applied for insect monitoring, mating disruption and mass trapping. Nicotiana benthamiana and N. tabacum are potential green biomass production platforms of moth sex pheromones. Using these two Nicotiana species as plant factories, we expressed biosynthetic genes of plant and insect origin in leaf tissue. Moth sex pheromone precursors ( E )-11-tetradecenoic acid, ( Z )-11-tetradecenoic acid and ( Z )-11-hexadecenoic acid were produced by introducing the acyl-ACP thioesterases CpuFatB1 from Cuphea pulcherrima or CpaFatB2 from C. palustris and the fatty acyl desaturases Ave∆11 from Argyrotaenia velutinana , CpaE11 from Choristoneura parallela or Atr∆11 from Amyelois transitella , under the control of CaMV-35S promoter. Among the Nicotiana spp. transformants, the best line produced ( Z )-11-hexadecenoic acid at 17.6% of total fatty acids in leaves, during flowering stage, corresponding to 335 µg of ( Z )-11-hexadecenoic acid per gram of fresh leaf. The ( Z )-11-hexadecenoic acid production lines from N. benthamiana were selected for further propagation to obtain homozygous lines. In the N. benthamiana T2 generation, the production quantity of ( Z )-11-hexadecenoic acid was stable. Our study demonstrates the feasibility of stable transformation of N. benthamiana for production of moth pheromone precursors in vegetative tissue.
Ultrahigh-Speed 0.5 V Supply Voltage $\hbox{In}_{0.7} \hbox{Ga}_{0.3}\hbox{As}$ Quantum-Well Transistors on Silicon Substrate (2007)

The direct epitaxial growth of ultrahigh-mobility InGaAs/InAlAs quantum-well (QW) device layers onto silicon substrates using metamorphic buffer layers is demonstrated for the first time. In this letter, 80 nm physical gate length depletion-mode InGaAs QW transistors with saturated transconductance <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">gm</i> of 930 muS / mum and <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">fT</i> of 260 GHz at V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">DS</sub> = 0.5 V are achieved on 3.2 mum thick buffers. We expect that compound semiconductor-based advanced QW transistors could become available in the future as very high-speed and ultralow-power device technology for heterogeneous integration with the mainstream silicon CMOS.
The influence of hydrogen bonding on the physical properties of ionic liquids (2011)

Potential applications of ionic liquids depend on the properties of this class of liquid material. To a large extent the structure and properties of these Coulomb systems are determined by the intermolecular interactions among anions and cations. In particular the subtle balance between Coulomb forces, hydrogen bonds and dispersion forces is of great importance for the understanding of ionic liquids. The purpose of the present paper is to answer three questions: Do hydrogen bonds exist in these Coulomb fluids? To what extent do hydrogen bonds contribute to the overall interaction between anions and cations? And finally, are hydrogen bonds important for the physical properties of ionic liquids? All these questions are addressed by using a suitable combination of experimental and theoretical methods including newly synthesized imidazolium-based ionic liquids, far infrared spectroscopy, terahertz spectroscopy, DFT calculations, differential scanning calorimetry (DSC), viscometry and quartz-crystal-microbalance measurements. The key statement is that although ionic liquids consist solely of anions and cations and Coulomb forces are the dominating interaction, local and directional interaction such as hydrogen bonding has significant influence on the structure and properties of ionic liquids. This is demonstrated for the case of melting points, viscosities and enthalpies of vaporization. As a consequence, a variety of important properties can be tuned towards a larger working temperature range, finally expanding the range of potential applications.
Toxic and protective constituents in pet foods (1986)

An analytical survey of mutagens, nitrosamines, polychlorinated biphenyls, toxic elements, and gamma-emission, as well as the toxicologically protective constituents zinc, selenium, and vitamin C, in 48 pet foods was conducted. Aside from high concentrations of fluoride and iodide in some samples and the expectedly higher concentrations of mercury and selenium in certain cat foods containing fish, the samples were notably free of the other toxic constituents. Direct-acting and promutagens and nitrosamines were not detectable in any of the samples. gamma-Emission was very low in all of the foods. Polychlorinated biphenyls were only detected in one cat food.
Towards Hardware Ray Tracing using Fixed Point Arithmetic (2007)

For realistic image synthesis and many other simulation applications, ray tracing is the only choice to achieve the desired realism and accuracy. Ray tracing has become such an important algorithm that an implementation in hardware is justified and desirable. The first ray tracing hardware realizations have been using floating point and logarithmic arithmetic. While floating point arithmetic requires considerably more logic than integer arithmetic, an implementation in logarithmic arithmetic is much simpler, but still suffers from similar problems. In analogy to rasterization hardware we therefore investigate the use of fixed point arithmetic for ray tracing. Our software implementation and comparisons provide strong evidence that an implementation of ray tracing in hardware using fixed point arithmetic is an efficient and robust choice.
Scalable, high-performance magnetoelastic tags using frame-suspended hexagonal resonators (2014)

This paper presents the analysis, design and experimental evaluation of miniaturized magnetoelastic tags using frame-suspended hexagonal resonators. Magnetoelastic tags—also known as acousto-magnetic or magnetomechanical tags-–are used in wireless detection systems—for example, electronic article surveillance and location mapping systems—that electromagnetically query the resonant response of the tags. In order to obtain a strong resonant response for miniaturized tags, a frame-suspended configuration is utilized to diminish the interaction between the vibrating portion of the tag and the substrate. The signal strength can be boosted by utilizing signal superposition with arrayed or clustered magnetoelastic tags. The hexagonal tags with a diameter of 1.3 mm are batch fabricated by photochemical machining from 27 µm thick Metglas™ 2826 MB, which is an amorphous NiFeMoB alloy. A preferred dc magnetic field bias for these tags is experimentally determined to be ≈31.5 Oe. A single frame-suspended magnetoelastic tag shows quality factors of 100–200. This design provides ≈75X improvement in signal amplitude compared to the non-suspended disc tag with similar size and resonant frequency. Across ten individual frame-suspended tags, the average resonant frequency is 2.13 MHz with a standard deviation of 0.44%, illustrating that this fabrication method provides repeatability. Linear signal superposition of the response has been experimentally measured for sets of frame-suspended tags that include as many as 500 units.
New Light-Sensitive Nucleosides for Caged DNA Strand Breaks (2002)

Phototriggered bod cleavage has found wide application in chemistry as well as in biology. Nevertheless, there are only a few methods available for site-specific photochemical induction of DNA strand scission despite numerous potential applications. In this study we report the development of new photocleavable nucleotides based on the photochemistry of o-nitrobenzyl esters. The light-sensitive moieties were generated through introduction of o-nitrophenyl groups at the 5'C position of the nucleoside sugar backbone. The newly synthesized, modified nucleosides were incorporated in oligonucleotides and are able to build stable DNA duplexes. In such a way modified oligonucleotides ca cleaved site-specifically upon irradiation with > 360 nm light with high efficiency. Furthermore, we show that these modifications can be bypassed in DNA synthesis promoted by Thermus aquaticus DNA polymerase.
The Evaluation of Micronized Barite As a Weighting Material for Completing HPHT Wells (2017)

Abstract Barite is one of the most common weighting materials for drilling and completion fluids. Its good properties (high density, less environmental impact, and low production cost) outperform the other weighting materials and make it a good candidate for drilling and completing oil and gas wells. However, some problems were encountered in the industry while using solid particles to increase fluid density, solids invasion which causes formation damage and permeability reduction in the vicinity of the wellbore, and the tendency of these solid particles to settle therefore, the loss of well control is likely. Moreover, an erosion to the surface facilities will result when these solid particles are produced. This study aims to investigate the effect of barite particle size on barite removal and completion fluids stability and how reducing barite particle size will help in resolving barite sag tendency and mitigating its effect. In this study, different samples of barite with different particle sizes were prepared using sieve analysis. Ball milling was used to reduce barite particle size to few microns. zeta potential and sag test were performed to evaluate the stability of micronized barite. Solubility test and high pressure high temperature filter press were used to study the effect of reducing barite particle size on barite removal. Solubility tests showed a good enhancement in barite removal as the particle size was reduced, with a difference of around 11 g/L (20 wt.%) between the largest and the micronized size of barite. HPHT Filtration test results confirmed the solubility results with 5 wt.% enhancement in filter cake removal efficiency. Micronized barite showed a moderate stability with zeta potential measurements for a pH range greater than 8, while sag test showed insignificant enhancement in fluid stability as barite particle size was reduced to the micronized size.
A Cell Line-Based Neutralization Assay for Primary Human Immunodeficiency Virus Type 1 Isolates That Use either the CCR5 or the CXCR4 Coreceptor (1999)

We describe here a cell line-based assay for the evaluation of human immunodeficiency virus type 1 (HIV-1) neutralization. The assay is based on CEM.NKR cells, transfected to express the HIV-1 coreceptor CCR5 to supplement the endogenous expression of CD4 and the CXCR4 coreceptor. The resulting CEM.NKR-CCR5 cells efficiently replicate primary HIV-1 isolates of both R5 and X4 phenotypes. A comparison of the CEM.NKR-CCR5 cells with mitogen-activated peripheral blood mononuclear cells (PBMC) in neutralization assays with sera from HIV-1-infected individuals or specific anti-HIV-1 monoclonal antibodies shows that the sensitivity of HIV-1 neutralization is similar in the two cell types. The CEM.NKR-CCR5 cell assay, however, is more convenient to perform and eliminates the donor-to-donor variation in HIV-1 replication efficiency, which is one of the principal drawbacks of the PBMC-based neutralization assay. We suggest that this new assay is suitable for the general measurement of HIV-1 neutralization by antibodies.
Preparation and Characterization of Temperature-Sensitive Poly(N-isopropylacrylamide)-b-poly(d,l-lactide) Microspheres for Protein Delivery (2003)

Temperature-sensitive diblock copolymers, poly(N-isopropylacrylamide)-b-poly(D,L-lactide) (PNIPAAm-b-PLA) with different PNIPAAm contents were synthesized and utilized to fabricate microspheres containing bovine serum albumin (BSA, as a model protein) by a water-in-oil-in-water double emulsion solvent evaporation process. XPS analysis showed that PNIPAAm was a dominant component of the microspheres surface. BSA was well entrapped within the microspheres, and more than 90% encapsulation efficiency was achieved. The in vitro degradation behavior of microspheres was investigated using SEM, NMR, FTIR, and GPC. It was found that the microspheres were erodible, and polymer degradation occurred in the PLA block. Degradation of PLA was completed after 5 months incubation in PBS (pH 7.4) at 37 degrees C. A PVA concentration of 0.2% (w/v) in the internal aqueous phase yielded the microspheres with an interconnected porous structure, resulting in fast matrix erosion and sustained BSA release. However, 0.05% PVA produced the microspheres with a multivesicular internal structure wrapped with a dense skin layer, resulting in lower erosion rate and a biphasic release pattern of BSA that was characterized with an initial burst followed by a nonrelease phase. The microspheres made from PNIPAAm-b-PLA with a higher portion of PNIPAAm provided faster BSA release. In addition, BSA release from the microspheres responded to the external temperature changes. BSA release was slower at 37 degrees C (above the LCST) than at a temperature below the LCST. The microspheres fabricated with PNIPAAm-b-PLA having a 1:5 molar ratio of PNIPAAm to PLA and 0.2% (w/v) PVA in the internal aqueous phase provided a sustained release of BSA over 3 weeks in PBS (pH 7.4) at 37 degrees C.
Poly(l‐lysine)‐modified silica nanoparticles for the delivery of antisense oligonucleotides (2004)

Silica nanoparticles were prepared in a microemulsion system, using polyoxyethylene nonylphenyl ether/cyclohexane/ammonium hydroxide. The surface charge of the particle was modified with PLL [poly(L-lysine)]. PAGE demonstrated the ability of PMS-NP (PLL-modified silica nanoparticles) to bind and protect antisense ODNs (oligonucleotides). The intracellular localization of FITC-labelled ODN was investigated by fluorescence microscopy. The results demonstrated that ODN could be delivered to cytoplasm. Flow-cytometry analysis showed a 20-fold enhancement of ODN delivered by PMS-NP compared with free ODN for a serum-free medium. Blocking efficacy of c- myc antisense ODN, delivered by PMS-NP, was examined in HNE1 and HeLa cell lines. Significant down-regulation of c- myc mRNA levels was observed in both the cell lines. However, the cellular uptake efficiency and antisense effects on target gene decreased in the presence of serum-containing medium. The analysis of the filtration assay showed that PMS-NP interacted with serum proteins. These results indicated that PMS-NP was a suitable delivery vector for antisense ODN, although its delivery efficiency decreased in the presence of a serum-containing medium.
Notch Signaling (1995)

The Notch/Lin-12/Glp-1 receptor family mediates the specification of numerous cell fates during development in Drosophila and Caenorhabditis elegans. Studies on the expression, mutant phenotypes, and developmental consequences of unregulated receptor activation have implicated these proteins in a general mechanism of local cell signaling, which includes interactions between equivalent cells and between different cell types. Genetic approaches in flies and worms have identified putative components of the signaling cascade, including a conserved family of extracellular ligands and two cellular factors that may associate with the Notch Intracellular domain. One factor, the Drosophila Suppressor of Hairless protein, is a DNA-binding protein, which suggests that Notch signaling may involve relatively direct signal transmission from the cell surface to the nucleus. Several vertebrate Notch receptors have also been discovered recently and play important roles in normal development and tumorigenesis.
Worldwide innovations in the development of carbon capture technologies and the utilization of CO2 (2012)

While Carbon Capture and Storage (CCS) technologies are being developed with the focus of capturing and storing CO2 in huge quantities, new methods for the chemical exploitation of carbon dioxide (CCU) are being developed in parallel. The intensified chemical or physical utilization of CO2 is targeted at generating value from a limited part of the CO2 stream and developing better and more efficient chemical processes with reduced CO2 footprint. Here, we compare the status of the three main lines of CCS technologies with respect to efficiency, energy consumption, and technical feasibility as well as the implications of CCS on the efficiency and structure of the energy supply chain.
Vesicular Stomatitis Virus (VSV) Therapy of Tumors (2000)

Vesicular stomatitis virus (VSV) is an essentially nonpathogenic negative-stranded RNA virus, the replication of which is extremely sensitive to the antiviral effects of interferon (IFN). We demonstrate here that VSV selectively induces the cytolysis of numerous transformed human cell lines in vitro, with all the morphological characteristics of apoptotic cell death. Importantly, VSV can also potently inhibit the growth of p53-null C6 glioblastoma tumors in vivo without infecting and replicating in normal tissue. With our previous findings demonstrating that primary cells containing the double-stranded RNA-activated protein kinase PKR and a functional IFN system are not permissive to VSV replication, these results suggest that signaling by IFN may be defective in many malignancies. Thus VSV might be useful in novel therapeutic strategies for targeting neoplastic disease.
Hydroxychloroquine Reverses Thrombogenic Properties of Antiphospholipid Antibodies in Mice (1997)

Background Previous studies have demonstrated that human monoclonal and polyclonal anticardiolipin antibodies have thrombogenic properties in vivo. Using such a model in which these antibodies have been shown to increase both the size of an induced thrombus and the duration of time in which such a clot lasts, we investigated whether hydroxychloroquine alters the dynamics of such thrombus formation. Methods and Results Three groups of nine mice were injected with purified immunoglobulin G (IgG) from a patient with the antiphospholipid syndrome (IgG-APS) and then fed with hydroxychloroquine at various doses (100, 6, and 3 mg/kg body wt). Three control groups of mice were also studied, including mice injected with IgG-APS and then fed with placebo, as well as two other groups injected with IgG from normal human serum and fed either hydroxychloroquine or placebo. A standardized thrombogenic injury was subsequently induced in the femoral vein of each mouse and the area (size) of thrombus measured as well as the total period of time that thrombus was present. Mice treated with hydroxychloroquine and IgG-APS showed significantly smaller thrombi that persisted for a shorter period of time compared with animals treated with IgG-APS and placebo. Conclusions Hydroxychloroquine significantly diminished both thrombus size and total time of thrombus formation in mice previously injected with IgG-APS.
Distinguishing Rational from Irrational Applications of Pharmacogenetic Synergies from the Bench to Clinical Trials (2007)

Single therapeutic agents very often fail in unselected patients. It is therefore commonplace to combine an agent specifically with a selected patient subgroup or with another agent. To support such efforts, it is useful to clarify the distinctions between the terms and the mathematical models used in analyzing combinations. To incorporate molecular disease classifications, the familiar concept of the therapeutic window is modified to define a pharmacogenetic window, which is an unambiguous numerical measure of the magnitude of interaction produced by a combination, and to define a test of pharmacogenetic synergy. In contrast, certain common comparative methods, such as vertical windows (comparing effects at a given dose) and animal models of mutational targets may be dominated by undesirable features. Although this discussion is oriented towards cancer therapy, an extension of these concepts to other comparative biologic assays is feasible and advisable.
FastMap (1995)

A very promising idea for fast searching in traditional and multimedia databases is to map objects into points in k -d space, using k feature-extraction functions, provided by a domain expert [25]. Thus, we can subsequently use highly fine-tuned spatial access methods (SAMs), to answer several types of queries, including the 'Query By Example' type (which translates to a range query); the 'all pairs' query (which translates to a spatial join [8]); the nearest-neighbor or best-match query, etc.However, designing feature extraction functions can be hard. It is relatively easier for a domain expert to assess the similarity/distance of two objects. Given only the distance information though, it is not obvious how to map objects into points.This is exactly the topic of this paper. We describe a fast algorithm to map objects into points in some k -dimensional space ( k is user-defined), such that the dis-similarities are preserved. There are two benefits from this mapping: (a) efficient retrieval, in conjunction with a SAM, as discussed before and (b) visualization and data-mining: the objects can now be plotted as points in 2-d or 3-d space, revealing potential clusters, correlations among attributes and other regularities that data-mining is looking for.We introduce an older method from pattern recognition, namely, Multi-Dimensional Scaling (MDS) [51]; although unsuitable for indexing, we use it as yardstick for our method. Then, we propose a much faster algorithm to solve the problem in hand, while in addition it allows for indexing. Experiments on real and synthetic data indeed show that the proposed algorithm is significantly faster than MDS, (being linear, as opposed to quadratic, on the database size N ), while it manages to preserve distances and the overall structure of the data-set.
VEGFR-1 Overexpression Identifies a Small Subgroup of Aggressive Prostate Cancers in Patients Treated by Prostatectomy (2015)

The VEGFR-1 is suggested to promote tumor progression. In the current study we analyzed prevalence and prognostic impact of the VEGFR-1 by immunohistochemistry on a tissue microarray containing more than 3000 prostate cancer specimens. Results were compared to tumor phenotype, ETS-related gene (ERG) status, and biochemical recurrence. Membranous VEGFR-1 expression was detectable in 32.6% of 2669 interpretable cancers and considered strong in 1.7%, moderate in 6.7% and weak in 24.2% of cases. Strong VEGFR-1 expression was associated with TMPRSS2:ERG fusion status as determined by fluorescence in situ hybridization (FISH) and immunohistochemistry (p < 0.0001 each). Elevated VEGFR-1 expression was linked to high Gleason grade and advanced pT stage in TMPRSS2:ERG negative cancers (p = 0.0008 and p = 0.001), while these associations were absent in TMPRSS2:ERG positive cancers. VEGFR-1 expression was also linked to phosphatase and tensin homolog (PTEN) deletions. A comparison with prostate specific antigen (PSA) recurrence revealed that the 1.7% of prostate cancers with the highest VEGFR-1 levels had a strikingly unfavorable prognosis. This could be seen in all cancers, in the subsets of TMPRSS2:ERG positive or negative, PTEN deleted or undeleted carcinomas (p < 0.0001 each). High level VEGFR-1 expression is infrequent in prostate cancer, but identifies a subgroup of aggressive cancers, which may be candidates for anti-VEGFR-1 targeted therapy.