gebhart/patrepeval huggingface dataset:
Effect of two protein elicitors extracted from Alternaria tenuissima and Beauveria bassiana against rice leaf folder (Marasmia exigua) (2021)

The rice leaf folder, Marasmia exigua (Butler), is dangerous pests and negatively affecting the rice production worldwide. Protein elicitors are considered to be bio-factors that induce rice resistance against herbivores. The present study was performed with two protein elicitors, Hrip 1 (extracted from Alternaria tenuissima) and PebB1 (from Beauveria bassiana) to study their efficacy against the rice leaf folder. Three different concentrations of Hrip 1 (68.88, 46.69 and 28.44 µg/ml) and PebB1 (56.66, 39.76 and 32.62 µg/ml) were assigned to evaluate the developmental time, survival rate, and fecundity of M. exigua. Both elicitors were applied to the three-leaf stage of the rice plant where newly emerged adult insects were released. Bioassay results showed that after the application of protein elicitors, the life cycle and survival rate of the rice leaf folder were prolonged, while fecundity decreased. The concentration of protein had a significant (p < 0.05) influence on ontogeny. In addition to ontogeny, the expression profile of jasmonic acid, salicylic acid, and ethylene associated with signalling pathway, which indicated that exogenous application of both elicitors produced a significant up-regulation in all the genes associated in signalling pathways of the plant. The plants treated with elicitors produced resistance against M. exigua (as compared to the control). This in vitro study invites new research into Hrip 1 and PebB1 as having prophylactic potential against rice leaf folder, and suggest that both protein elicitors can be used as a novel biological control tool for M. exigua.
HPHT Well Construction with Closed-Loop Cementing Technology (2013)

Abstract Achieving successful isolation of potential flow zones during well construction in deep fault-segmented HPHT basins is often a formidable task. These wells, often drilled from floating rigs, tend to present rapid departures from more normal conditions to very high degrees of overpressure, elevated temperatures and where formation pressures often approach fracture gradient. Further, once overpressure is geologically established in isolated pressure compartments, reservoir fluids tend to migrate vertically via hydro-fracturing to shallower depths.18 Challenges associated with cementing operations include actual leak-off test value (LOT) vs. predicted, margins of error in mud weights estimated, and risk of inducing a fracture during pre-flush and slurry displacement. If the open hole was under-reamed, the actual fracture pressure may be reduced by an unknown amount. ‘Wellbore strengthening’ operations and associated procedures add additional formation fracture gradient uncertainty.4 This presentation speaks to applying the principals of Managed Pressure Drilling (MPD) and recent refinements of its practice to cementing processes. Precise flow in/out measurements in real-time, ascertainment of actual downhole pressure environment, ability to conduct frequent dynamic formation integrity tests (FIT's) without drilling interruption and use of PLC choke systems are applicable strengths.19,20,22 API Standard 65 - Part 2, Second Edition, December 2010 - Isolating Potential Flow Zones during Well Construction will be referenced to illustrate C-LC applications. Preparatory - quantify the stability of the wellbore with frequent dynamic FIT's (without exercising the BOP) and assurance of hole cleaning during pre-flush. Displacement - optimize fluid dynamics and ascertain in real-time an induced fracture. Curing - maintain more consistent annulus pressure on rigs experiencing wave heave, backpressure applications for minimizing the risk of channeling and/or help ensure the column of plug in the tubing string is balanced with the annulus Testing - Use of a rotating control device (RCD) and process logic controlled (PLC) Choke to pressure test plugs after tagging in lieu of using dedicated cementing equipment.
Dynamical Perturbations of Tetrahydroborate Anions in LiBH4 due to Nanoconfinement in Controlled-Pore Carbon Scaffolds (2013)

Neutron vibrational spectroscopy and quasielastic neutron scattering (QENS) were used to probe the dynamical properties of BH4– anions in both bulk LiBH4 and LiBH4 confined in nanoporous carbons (NPCs) having ≤4-nm-diameter, hexagonally arranged, cylindrical pores. The BH4– torsional band of the confined LiBH4 is significantly broadened relative to that of bulk LiBH4, reflecting a disruption of the bulk crystal lattice and thus a broader distribution of BH4– rotational potentials. QENS measurements of bulk orthorhombic LiBH4 indicate a single quasielastic component yielding an activation energy for localized BH4– jump reorientation of 19.2 ± 0.8 kJ/mol, consistent with previous QENS and NMR results. At room temperature, the measurements are in good agreement with BH4– reorientational jumps about a single C2 or C3 tetrahedral symmetry axis, with evidence for multiaxis rotations emerging as the temperature increases. In contrast, the QENS spectra of the NPC-confined LiBH4 exhibit two quasielastic components, one an order of magnitude broader than the other. The narrower component is presumably associated with more slowly reorienting BH4– anions in the interior of the pores and the broader component with much more rapidly reorienting BH4– anions in the vicinity of the pore surfaces. For 4-nm pores, these components yield two corresponding activation energies for reorientation: 16 ± 1 and 10.6 ± 0.7 kJ/mol. The data suggest that both components undergo single C2- or C3-axis reorientational jumps below 330 K, albeit with one an order of magnitude faster than the other. By 400 K (which is above the bulk phase transition temperature), both reorient more diffusively around multiple axes. These results were found to be qualitatively consistent with comparative dynamical measurements of LiBH4 confined in a 13-nm-average-pore-size carbon aerogel, which exhibited a much broader pore size distribution.
Tailored Microstructured Hyperpolarizing Matrices for Optimal Magnetic Resonance Imaging (2018)

Tailoring the physical features and the porous network architecture of silica-based hyperpolarizing solids containing TEMPO radicals, known as HYPSO (hybrid polarizing solids), enabled unprecedented performance of dissolution dynamic nuclear polarization (d-DNP). High polarization values up to P(<sup>1</sup> H)=99 % were reached for samples impregnated with a mixture of H<sub>2</sub> O/D<sub>2</sub> O and loaded in a 6.7 T polarizer at temperatures around 1.2 K. These HYPSO materials combine the best performance of homogeneous DNP formulations with the advantages of solid polarizing matrices, which provide hyperpolarized solutions free of any-potentially toxic-additives (radicals and glass-forming agents). The hyperpolarized solutions can be expelled from the porous solids, filtered, and rapidly transferred either to a nuclear magnetic resonance (NMR) spectrometer or to a magnetic resonance imaging (MRI) system.
New Materials for Si-Based Heterostructure Engineering: Synthesis of Si-Ge-C Alloys and Compounds by UHV-CVD and Molecular Chemistry (1999)

Inorganic precursors have been synthesized and used to deposit novel group IV heterostructures. Metastable SiGeC alloys offer the prospect of strain compensation in the pseudomorphic SiGe system, as well as providing the possibility of changes in the bandgap energy to values greater than those of Si and SiGe. We have demonstrated the use of the C-H free, C(SiH3)4 and C(GeH3)4, precursors to grow pseudomorphic (Si4C)xGey, (Ge4C)xSiy, and Si1-x-yGexCy alloys containing 4-7 at. % C the highest C content incorporated in crystalline SiGeC. The materials are deposited on Si by ultrahigh vacuum (UHV) CVD and characterized for structure, composition and bonding properties by RBS, high-resolution TEM, electron energy loss spectroscopy and FTIR and Raman spectroscopies, respectively. Non-stoichiometric GeC alloys are also potential candidates for bandgap engineering and lattice matching with Si. The synthetic routes involve UHV-CVD reactions of GeH4 with HC(GeH3)3 that produce Ge1-xCx alloys with up to 7 at. % C. The incorporation of C into the Ge lattice completely suppresses island like-film formation and results in 2-D layer-by-layer perfectly epitaxial growth. Synthesis of new ordered materials composed of C, Si, and Ge that incorporate carbon on a common sublattice is also described. Examples of these include new diamond-structured materials with composition Si4C, and (Si2Ge)Cx as well as a new sphalerite phase with composition GeSi3C4. Finally we present synthesis and structural analysis of the CH(GeH3)3 and C(GeH3)4 precursors utilized in these studies, as well as synthesis of corresponding halide cluster compounds C(GeBrX2)4 (X=Cl, Br).
Phase contrast imaging and tomography with hard X-rays and cold neutrons (2006)

Using phase information present in a beam after transmission through a sample offers the possibility of reducing the delivered dose while maintaining the visible contrast.Several phase sensivitive imaging techniques have been developed in recent years, among them in-line holography [1], which is now used on a routine base, and analyser based techniques[2] whose feasibility for medical imaging is currently under investigation.Although known for a long time imaging with asymmetric Bragg reflection as magnification optics[3] may be regarded as a further development of analyser based imaging providing two dimensional phase contrast while its two dimensional magnification yields the possibility of using thick fluorescence screens as x-ray to visual photon converter (i.e.commercial CCD-area detectors) thus enhancing detection efficiency at submicrometer resolution.Furthermore, imaging with asymmetric Bragg reflection provides a strong phase contrast and a large field of view on the sample.Recently, our group developed a full theoretical description of the imaging process (including the influences of Bragg reflection and free-space propagation) [4].This enabled us to verify that a submicrometer resolution limit is achievable, to estimate the minimum detectable phase gradient present in the beam corresponding directly to the minimum detectable density variation in the sample and to understand the influences of beam divergence and dispersion effects.It also provides crucial information about future improvements of the experimental setup.In order to avoid artefacts during tomographic reconstructions phase retrieval algorithms have to be applied to the measured images.Several of these algorithms have been reported in literature differing in the underlying model of contrast formation (i.e. the presence of coherence, absorption or small angle scattering) and thus producing different kinds of quantative information about the sample.Our latest measurements at the ID-19/ESRF beamline will help to identify the most appropriate algorithm in case of magnifying analyser based imaging.Furthermore, we expect to directly measure the maximum achievable resolution limit in experiment for both two dimensional imaging and three dimensional reconstruction.
Incoherent self-accelerating beams (2015)

Self-accelerating optical beams form as a direct outcome of interference, initiated by a predesigned initial condition. In a similar fashion, quantum mechanical particles exhibit force-free acceleration as a result of interference effects following proper preparation of the initial Schrodinger wave function. Indeed, interference is at the heart of such wave packets, and hence it is implied that self-accelerating wave packets must be coherent entities. Counter to that, we demonstrate theoretically and experimentally spatially incoherent self-accelerating beams, in both the paraxial and the nonparaxial domains. We show that in principle, the transverse correlation distance can be as short as a single wavelength, while a properly designed initial beam will give rise to shape-preserving acceleration for the same distance as a coherent accelerating beam propagating on the same trajectory. These findings expand the understanding of the relation between coherence and accelerating beams, and may have implications for the design of self-accelerating quantum wave packets with limited quantum coherence.
Predictive Genes in Adjacent Normal Tissue Are Preferentially Altered by sCNV during Tumorigenesis in Liver Cancer and May Rate Limiting (2011)

This suggests that the process of tumor evolution involves rate-limiting steps related to the background from which the tumor evolved where these were frequently predictive of clinical outcome. Additionally treatments that alter the likelihood of tumorigenesis occurring may act by altering AN-survival genes, suggesting that the process can be manipulated. Further sCNV explains a substantial fraction of tumor specific expression and may therefore be a causal driver of tumor evolution in HCC and perhaps many solid tumor types.
A Study on the Dynamic Characteristics of Hydraulic Engine Mount. (2002)

This paper describes an identification method of the dynamic characteristics in consideration of the dependency of amplitude and frequency, followed by the vibration analysis of rigid body supported with hydraulic engine mounts. At first the parameters to describe the dynamic characteristics of hydraulic engine mount, unable to be measured directly, are predicted. The identified results agree well with measured values. The amplitude range which hydraulic mount features high damping coefficient was investigated. Secondary, the steady-state response analysis of rigid body supported by the hydraulic mounts was performed. The validity was confirmed by the excitation experiment.
Solid‐Phase Synthesis of Natural Products and Natural Product‐Like Libraries (2002)

This chapter contains sections titled: Introduction Solid-phase Derivatization of Natural Product Scaffolds – Combinatorial Semisynthesis Solid-phase Semisynthesis of Rauwolfa Alkaloids Solid-phase Synthesis of Purine Derivatives Solid-phase Semisynthesis of a Taxoid Library Solid-phase Semisynthesis of Sarcodictyns A and B and Libraries Thereof Solid-phase Semisynthesis of Vancomycin Solid-phase Total Synthesis of Natural Products – Combinatorial Total Synthesis Solid-phase Synthesis of Prostaglandins and Libraries Thereof Solid-phase Synthesis of Epothilone A and Libraries Thereof Solid-phase Synthesis of (S)-Zearalenone Solid-phase Synthesis of (DL)-Muscone and Libraries Thereof Solid-phase Synthesis of the Vitamin D3 System Solid-phase Synthesis of Carpanone-like Molecules Combinatorial Solid-phase Synthesis of Natural Product-like Libraries Conclusion Addendum References
Cell-dependent influence on the phagocytosis induced by non-ionic contrast medium injection (2008)

Iodinated contrast media (CM) can inhibit phagocytosis. To better understand the importance of this effect upon the elementary defence mechanism, the aim of the study was to compare the in vivo effect of non-ionic CM on the engulfing ability of peripheral blood phagocytic cells from patients undergoing CM-enhanced CT. Neutrophil granulocytes and monocytes from patients' peripheral blood obtained before and 30 min after CM injection were incubated with fluorescent-labelled Escherichia coli bacteria. Both the percentage of cells that engulfed bacteria and the phagocytic activity per cell has been determined by flow cytometry. We found that phagocytosis was greater in neutrophils than in monocytes. CM decreased the percentage of monocytes phagocyting bacteria, both at 4 degrees C (20.3%+/-3.3% versus 16.1%+/-2.0%; p<0.03) and at 37 degrees C (51.6%+/-4.1% versus 47.5%+/-2.6%; p>0.05), and increased the percentage of neutrophils at 4 degrees C (11.8%+/-2.1% versus 14.3%+/-2.2%; p<0.002) and at 37 degrees C (83.1%+/-3.6% versus 85.1%+/-3.2%; p>0.05). The phagocytic activity decreased significantly at 37 degrees C in monocytes (p<0.02), and was not affected in neutrophils. CM injection has different effects on both the percentage of phagocytosing cells and the phagocytic activity in monocytes and neutrophils. The inhibitory effect on monocyte phagocytosis seems to be compensated by neutrophils.
A FAST AND ACCURATE ISOTACHOPHORESIS SIMULATION CODE (2008)

We developed a numerical code which allows fast and accurate simulation of isotachophoresis (ITP). The multi-species code accounts for equilibrium chemistry, non-uniform electroosmotic flow, and dispersion. Our modeling efforts for the latter are also presented. The goal of our work is to create an efficient, accurate, validated, and uniquely-capable electrophoresis simulation code available for free via the web to the microfluidics community.
Circuit design, transistor sizing and wire layout of FPGA interconnect (2003)

This paper examines the electrical design of FPGA interconnect circuitry. We explore the circuit design of pass transistor and tri-state buffer routing switches, determine which transistor sizing, metal width and metal spacing are best for FPGA interconnect, and show that FPGA interconnect should be electrically heterogeneous-some (/spl sim/20%) of the routing tracks should be designed for maximum speed while the remainder should be more area-efficient.
Data from Phase I/II Multicenter Trial of a Novel Therapeutic Cancer Vaccine, HepaVac-101, for Hepatocellular Carcinoma (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;Immunotherapy for hepatocellular carcinoma (HCC) shows considerable promise in improving clinical outcomes. HepaVac-101 represents a single-arm, first-in-human phase I/II multicenter cancer vaccine trial for HCC (NCT03203005). It combines multipeptide antigens (IMA970A) with the TLR7/8/RIG I agonist CV8102. IMA970A includes 5 HLA-A*24 and 7 HLA-A*02 as well as 4 HLA-DR restricted peptides selected after mass spectrometric identification in human HCC tissues or cell lines. CV8102 is an RNA-based immunostimulator inducing a balanced Th1/Th2 immune response.&lt;/p&gt;Patients and Methods:&lt;p&gt;A total of 82 patients with very early- to intermediate-stage HCCs were enrolled and screened for suitable HLA haplotypes and 22 put on study treatment. This consisted in a single infusion of low-dose cyclophosphamide followed by nine intradermal coadministrations of IMA970A and CV8102. Only patients with no disease relapse after standard-of-care treatments were vaccinated. The primary endpoints of the HepaVac-101 clinical trial were safety, tolerability, and antigen-specific T-cell responses. Secondary or exploratory endpoints included additional immunologic parameters and survival endpoints.&lt;/p&gt;Results:&lt;p&gt;The vaccination showed a good safety profile. Transient mild-to-moderate injection-site reactions were the most frequent IMA970A/CV8102-related side effects. Immune responses against ≥1 vaccinated HLA class I tumor-associated peptide (TAA) and ≥1 vaccinated HLA class II TAA were respectively induced in 37% and 53% of the vaccinees.&lt;/p&gt;Conclusions:&lt;p&gt;Immunotherapy may provide a great improvement in treatment options for HCC. HepaVac-101 is a first-in-human clinical vaccine trial with multiple novel HLA class I– and class II–restricted TAAs against HCC. The results are initial evidence for the safety and immunogenicity of the vaccine. Further clinical evaluations are warranted.&lt;/p&gt;&lt;/div&gt;
In silicoanalysis of trypanosomatids' helicases (2012)

Trypanosomatids are unicellular protozoan parasites that cause many diseases in animals, including humans, and plants. These early divergent eukaryotes have many singular structures and processes, including the hyper-modified 'base J', a mitochondrial DNA network, RNA editing, and trans-splicing; all of these unique features involve a wide variety of specific DNA/RNA helicases. In this work, the genomes of trypanosomatids were analyzed by data mining, searching for genes coding for DNA/RNA helicases. Specific motifs and full-length sequences from all families present in the helicase's superfamilies (SFs) 1 and 2 were used as baits for genome analyses. A total of 328 putative helicases were identified; 204 genes were assigned to the SF2, 42 genes to the SF1, and 76 genes remain unclassified. Eight species-specific SF2 helicases were also found; Trypanosoma cruzi has three DEAD-box and one DEAH/RHA-specific helicases, while Leishmania major has three Swi2/Snf2 and Trypanosoma brucei has only one RigI helicase. Finally, to identify helicases that could be used as future therapeutic targets, all obtained genes were compared with those present in the human genome. Forty-two helicases underrepresented in the human genome were identified; constituting 16 orthologs groups from L. major, T. brucei, and T. cruzi.
Wortmannin-C20 Conjugates Generate Wortmannin (2005)

We report on C20-6-(N-methylamino)hexanoic conjugates of wortmannin featuring a tertiary enamine attached to the C20 that inhibit phosphoinositol-3-OH kinase (PI3K) by producing wortmannin (Wm) through an intramolecular attack. The generation of Wm by these conjugates permits the design of Wm based PI3K inhibitors that need not fit into the ATP pocket of PI3K, including Wm conjugates of BSA, IgG, or beads. Wm generating WmC20-N(Me)-hexanoate conjugates offer an approach to the design of targeted or slow release forms of Wm which may inhibit PI3K in tissues more selectively than the parent Wm, a compound which has desirable anti-inflammatory and anti-proliferative activities but which also has a variety of toxic effects.
Treatment strategies for thymic carcinoma in a real-life setting: Insights from the rythmic network. (2020)

9072 Background: Thymic carcinomas are an aggressive and difficult to treat subset of thymic epithelial tumors (TETs) that represent a heterogeneous group of rare intrathoracic malignancies. Most of the current knowledge and guidelines tumors rely on surgically-oriented databases focusing on early-stage disease, and small prospective, single-arm trials conducted in metastatic thymic carcinomas, mostly in a refractory, late-line setting. “Réseau tumeurs THYMiques et Cancer” (RYTHMIC) is the nationwide network for TETs in France. The management of any patient has to be systematically discussed on a real-time basis at a national multidisciplinary tumor board; a database is hosted by the French Thoracic Cancer Intergroup (IFCT). Methods: We took advantage of the RYTHMIC prospective database to describe baseline characteristics, analyze treatment strategies, and provide landmark outcomes in a cohort of consecutive patients with thymic carcinoma. The inclusion period was January 2012 to April 2017. Results: A total of 213 patients were analyzed. Overall, 60 (28%) patients were considered as surgical candidates upfront, 91 (43%) received primary chemotherapy, and 62 (29%) received exclusive chemotherapy. Median OS was 49.2 months (IC95%: 34.8-63.6); OS was significantly longer in patients with a lower stage at diagnosis (p &lt; 0.001), who were operated on upfront, as opposed to patients who received primary or exclusive chemotherapy (p &lt; 0.001). Surgery, conducted upfront or after primary chemotherapy, was significantly associated with more prolonged OS (p &lt; 0.001); complete resection and postoperative radiotherapy were also predictors of better outcome (p = 0.018 and p = 0.081, respectively). Exclusive chemotherapy was delivered to 62 patients with advanced disease, who all received platinum-based regimen as first-line treatment; PAC regimen was delivered to 66% of patients. Best objective response to first-line chemotherapy was partial response in 33 (53%) patients. Median PFS was 8.0 months (IC95%: 5.0-11.1). Median OS was 32.9 months (IC95%: 20.6-45.1). Response to first-line chemotherapy and squamous histology were the only significant predictors of OS (p = 0.002 and p = 0.040, respectively). Conclusions: Our cohort is the first to analyze in depth outcomes and treatment strategies in a prospective cohort of consecutive patients with thymic carcinoma. While we confirm the major prognostic impact of surgery, our data highlight the need for optimized multidisciplinary management and innovative therapies as the survival of patients remains limited.