gebhart/patrepeval huggingface dataset:
Overexpression of the transcription factor GROWTH-REGULATING FACTOR5 improves transformation of dicot and monocot species (2020)

1 Abstract Successful regeneration of genetically modified plants from cell culture is highly dependent on the species, genotype, and tissue-type being targeted for transformation. Studies in some plant species have shown that when expression is altered, some genes regulating developmental processes are capable of triggering plant regeneration in a variety of plant cells and tissue-types previously identified as being recalcitrant to regeneration. In the present research, we report that developmental genes encoding GROWTH-REGULATING FACTORS positively enhance regeneration and transformation in both monocot and dicot species. In sugar beet ( Beta vulgaris ssp. vulgaris ), ectopic expression of Arabidopsis GRF5 ( AtGRF5 ) in callus cells accelerates shoot formation and dramatically increases transformation efficiency. More importantly, overexpression of AtGRF5 enables the production of stable transformants in recalcitrant sugar beet varieties. The introduction of AtGRF5 and GRF5 orthologs into canola ( Brassica napus L.), soybean ( Glycine max L.), and sunflower ( Helianthus annuus L.) results in significant increases in genetic transformation of the explant tissue. A positive effect on proliferation of transgenic callus cells in canola was observed upon overexpression of GRF5 genes and AtGRF6 and AtGRF9 . In soybean and sunflower, the overexpression of GRF5 genes seems to increase the proliferation of transformed cells, promoting transgenic shoot formation. In addition, the transformation of two putative AtGRF5 orthologs in maize ( Zea mays L.) significantly boosts transformation efficiency and resulted in fully fertile transgenic plants. Overall, the results suggest that overexpression of GRF genes render cells and tissues more competent to regeneration across a wide variety of crop species and regeneration processes. This sets GRFs apart from other developmental regulators and, therefore, they can potentially be applied to improve transformation of monocot and dicot plant species.
Data processing for mobile phone positioning (1999)

In this paper one aspect of mobile phone positioning will be considered. First an overview of the observed time difference (OTD) method is given. The OTD method is based on time delay measurement and is therefore highly affected by the propagation environment. To improve the measurements of the time delay, a simple postprocessing filter based on Teager-Kaiser operator is proposed and compared with other filter types.
SERCA2 regulates proinsulin processing and processing enzyme maturation in the pancreatic β cell (2022)

Abstract Increased circulating levels of incompletely processed insulin (i.e. proinsulin) are observed clinically in both type 1 and type 2 diabetes; however, the mechanisms underlying impaired proinsulin processing remain incompletely understood. Here, we identify the sarcoendoplasmic reticulum Ca 2+ ATPase-2 (SERCA2) pump and β cell ER Ca 2+ as key regulators of systemic glucose tolerance and proinsulin processing. We generated mice with a β cell-specific SERCA2 deletion (βS2KO) and SERCA2 deficient INS-1 cells to show that SERCA2 loss increases systemic and pancreatic levels of proinsulin protein and leads to aberrant localization of proinsulin within the proximal β cell secretory pathway. These defects in proinsulin processing were linked to reduced maturation of the proinsulin processing enzymes PC1/3 and PC2, suggesting a model whereby chronic ER Ca 2+ depletion in the β cell, which is observed in many pathological conditions, impairs the spatial regulation of prohormone trafficking, processing, and maturation within the β cell secretory pathway.
Exfoliation of Graphite Oxide in Propylene Carbonate and Thermal Reduction of the Resulting Graphene Oxide Platelets (2010)

Graphite oxide was exfoliated and dispersed in propylene carbonate (PC) by bath sonication. Heating the graphene oxide suspensions at 150 degrees C significantly reduced the graphene oxide platelets; paper samples comprising such reduced graphene oxide platelets had an electrical conductivity of 5230 S/m. By adding tetraethylammonium tetrafluoroborate (TEA BF(4)) to the reduced graphene oxide/PC slurry and making a two-cell ultracapacitor, specific capacitance values of about 120 F/g were obtained.
Synthesis of Superior Visible-Light-Driven Nanophotocatalyst Using High Surface Area TiO2 Nanoparticles Decorated with CuxO Particles (2020)

This work provides an alternate unique simple methodology to design and synthesize chemically modified nanophotocatalyst based on high surface area TiO2 nanoparticles that can be used efficiently for the photodegradation of organic pollutants under normal visible light rather than complicated UV irradiation. In this study, dual visible light and UV-driven nanophotocatalysts were synthesized via wet chemistry procedures using high surface area TiO2 nanoparticles functionalized with (3-Aminopropyl) trimethoxysilane and attached chemically to the CuXO to improve the charge separation and maintain the non-charge recombination. The successful modification of the TiO2 nanoparticles and the formation of the TiO2-NH2-CuxO nanophotocatalyst were confirmed using different characterization techniques, and the results revealed the synthesis of high surface area TiO2 nanoparticles, and their chemical modification with an amino group and further decoration with copper to produce TiO2-NH2-CuxO nanophotocatalyst. The photocatalytic activity of TiO2 and TiO2-NH2-CuxO nanophotocatalyst were evaluated using methylene blue (MB) dye; as an example of organic pollutants. The resulting TiO2-NH2-CuxO nanophotocatalyst exhibited superior photocatalytic activity for the degradation of MB dye under visible light irradiation, due to the reduction in the energy bandgap. The degradation of the MB dye using the TiO2-NH2-CuxO nanophotocatalyst was investigated using LC-MS, and the results revealed that the hydroxyl free radical is mainly responsible for the cleavage and the degradation of the MB dye.
A generalized simulation description language (2007)

Our group supports two emission tomography simulation packages: SimSET, which is in the public domain, and ASIM, which we are planning to re-engineer and release as open-source software. Currently the inputs and outputs for the two programs, though conceptually similar, have very different formats. We are creating a common input meta-language for SimSET and ASIM. We plan to make this language general enough that it will be suitable for other emission tomography simulation packages. This language will make it easier for users to use multiple simulation packages and will facilitate definition of similar simulations for various packages.
Multi-polarized multi-user Massive MIMO: Precoder design and performance analysis (2014)

Space limitation and multi-antenna channel acquisition prevent Massive multiple-input multiple-output (MIMO) from being easily deployed. The use of multi-polarized antennas can be one solution to alleviate the first obstacle. Furthermore, the dual structured precoding, in which a preprocessing based on the spatial correlation and a subsequent linear precoding based on the short-term channel state information at the transmitter (CSIT) are concatenated, can reduce the feedback overhead efficiently. To reduce the feedback overhead further, we propose a dual structured multi-user linear precoding, in which the subgrouping method based on copolarization is additionally applied to the spatially grouped mobile stations (MSs) in the preprocessing stage. By investigating the behavior of the asymptotic performance as a function of the cross-polar discrimination (XPD) parameter, we also propose a new dual structured precoding, in which the XPD, spatial correlation, and CSIT quality are jointly utilized in the precoding/feedback for the multi-polarized multi-user massive MIMO system.
Supplementary Table S3 from Gain-of-Function <i>RHOA</i> Mutations Promote Focal Adhesion Kinase Activation and Dependency in Diffuse Gastric Cancer (2023)

&lt;p&gt;Primers&lt;/p&gt;
Evaluation of Effect of Specimen-Handling Parameters for Plasma Preparation Tubes on Viral Load Measurements Obtained by Using the Abbott RealTi me HIV-1 Load Assay (2010)

HIV-1 viral load testing is essential to the management of HIV-1-infected patients, and proper specimen handling ensures accurate viral load (VL) results. This study was performed to (i) evaluate the effect of freezing plasma in situ in BD Vacutainer plasma preparation tubes (PPT) on the accuracy of HIV-1 viral load results using the Abbott RealTime HIV-1 assay and (ii) evaluate the effect of whole-blood storage in the PPT for 6 h at room temperature prior to centrifugation (PPT6H) rather than 2 h as specified in the PPT product insert. Of the 64 HIV-positive subjects evaluated, 29 had average viral load counts of >40 copies/ml in at least one of the tubes tested and 35 subjects had a result of either "undetected target" or "below the limit of quantification" (LOQ) for all or some of the tubes regardless of handling condition. For the 29 subjects with VLs that were >LOQ, the mean biases between plasma from Vacutainer K(2)EDTA tubes and plasma frozen in situ in PPT and between K(2)EDTA tube plasma and plasma from PPT6H (log(10) copies/ml) were 0.005 and -0.001, respectively, and r(2) was >0.92 for all correlations. We conclude that VLs determined from plasma frozen in situ in PPT are equivalent to VLs in K(2)EDTA tube plasma and can be used for accurate quantification of HIV-1 RNA in the Abbott RealTime HIV-1 assay. Furthermore specimens collected in PPT can be stored for 6 h at room temperature with no effect on viral load results as measured by the Abbott RealTime HIV-1 assay.
Downregulation and desensitization of A1-adenosine receptors in embryonic chicken heart (1989)

Downregulation of cardiac A1-adenosine receptors and desensitization of the negative inotropic response to adenosine were examined 44 h after pretreatment of 15-day-old chick embryos with phenylisopropyladenosine (R-PIA) or vehicle. The number of A1-adenosine receptors, assessed by 125I-aminobenzyladenosine (125I-ABA) binding to crude cardiac membranes, was decreased by 63% (P less than 0.001) after pretreatment of embryos with 1 mumol of R-PIA, from 16.7 +/- 2.4 to 6.2 +/- 1.4 (SD) fmol/mg protein (n = 6). The KD of 125I-ABA binding to the remaining receptors did not differ significantly from control (0.71 +/- 0.45 vs. 0.79 +/- 0.57 nM). A maximally effective concentration of R-PIA (10(-5) M) decreased the developed tension of electrically paced right ventricular (RV) muscle strips from control embryos by 76 +/- 6% (mean +/- SD, n = 7) from its forskolin-stimulated plateau level, whereas the developed tension of strips from R-PIA-pretreated embryos was decreased significantly less, by 38 +/- 4% (P less than 0.001). The potency of R-PIA and the efficacy and potency of carbachol to decrease contractile tension were not changed. The data suggest that chronic exposure of the heart to R-PIA can produce downregulation of A1-adenosine receptors and homologous desensitization of the negative inotropic response to adenosine.
New DPD tracking servo method by signal processing for high-density ROM discs (2007)

Differential phase detection (DPD) is the most popular tracking error detection method for read-only optical discs (ROM discs). However, DPD tracking-error signals deteriorate for high-density discs such as over 30-GB Blu-ray discs (BDs) where zero-cross detection becomes inaccurate. To solve this problem, we propose a new zero-cross-detection-free DPD (ZF-DPD) method by applying the least-mean-square (LMS) algorithm adaptive equalizer. We experimentally confirmed its effectiveness for a high-density (33.3 GB/layer) four-layer BD-ROM disc.
Effect of Deposition Rate on Microstructure of CoCrPt-SiO2 Granular Longitudinal Media for Tape Applications (2006)

This work focuses on the effect of deposition rate in the longitudinal version of this materials system. Since two phase segregation must occur during the sputter deposition process, it is anticipated that deposition rate may be a crucial deposition parameter, and that high deposit rates may not allow this segregation to proceed to completion in each layer of the depositing film before being buried by subsequent layers.
Calculation of average molecular properties during nonlinear, living copolymerization (1991)

Abstract Describing network formation during chainwise polymerization is more complex than for stepwise (condensation) systems. The kinetics of chain growth must be combined with probability laws for random linking between chains. This approach is used to derive molecular weight averages, gel point and sol fraction during living, anionic copolymerization of vinyl with divinyl monomers. Comparison of predicted molecular weight and gel point to experimental values from Worsfold (1970), Lutz, Beinert and Rempp (1982) and others indicate that a significant amount of intramolecular linking or cyclization occurs in this system.
Resonance Raman studies and structure of a sulfide complex of methemerythrin (1979)

The complex of sulfide and methemerythrin has been characterized by resonance Raman spectroscopy. At pH 8.0 the complex contains two irons and one S2- at the active site. The resonance Raman spectrum of the sulfidomethemerythrin complex contains only one vibration, at 444 cm-1. This vibration is assigned to an iron-sulfide stretch. The possibility that sulfidomethemerythrin contains a mu-sulfido bridge. FeIII-S2-FeIII, analogous to the proposed mu-oxo bridge in azidomethemerythrin is discussed.
Chromium(V) and Chromium(VI) Nitrido Complexes of Tris(pentafluorophenyl)corrole (2003)

Nitrogen-atom transfer from a (nitrido)manganese(V) complex to a CrIII complex of the 5,10,15-tris(pentafluorophenyl)corrole trianion gave the stable CrV nitrido complex 1 (Ar=C6F5). In contrast, treatment of the same CrIII starting material with ammonia/sodium hypochlorite gave the CrVI analogue of 1.
Hierarchical Super-Resolution-Based Inpainting (2013)

This paper introduces a novel framework for examplar-based inpainting. It consists in performing first the inpainting on a coarse version of the input image. A hierarchical super-resolution algorithm is then used to recover details on the missing areas. The advantage of this approach is that it is easier to inpaint low-resolution pictures than high-resolution ones. The gain is both in terms of computational complexity and visual quality. However, to be less sensitive to the parameter setting of the inpainting method, the low-resolution input picture is inpainted several times with different configurations. Results are efficiently combined with a loopy belief propagation and details are recovered by a single-image super-resolution algorithm. Experimental results in a context of image editing and texture synthesis demonstrate the effectiveness of the proposed method. Results are compared to five state-of-the-art inpainting methods.
Novel Perspectives on Mucormycosis: Pathophysiology, Presentation, and Management (2005)

Mucormycosis is a life-threatening fungal infection that occurs in immunocompromised patients. These infections are becoming increasingly common, yet survival remains very poor. A greater understanding of the pathogenesis of the disease may lead to future therapies. For example, it is now clear that iron metabolism plays a central role in regulating mucormycosis infections and that deferoxamine predisposes patients to mucormycosis by inappropriately supplying the fungus with iron. These findings raise the possibility that iron chelator therapy may be useful to treat the infection as long as the chelator does not inappropriately supply the fungus with iron. Recent data support the concept that high-dose liposomal amphotericin is the preferred monotherapy for mucormycosis. However, several novel therapeutic strategies are available. These options include combination therapy using lipid-based amphotericin with an echinocandin or with an azole (largely itraconazole or posaconazole) or with all three. The underlying principles of therapy for this disease remain rapid diagnosis, reversal of underlying predisposition, and urgent surgical debridement.
Sequential Gene Expression Analysis of Coagulation Factors and Proteaseactivated Receptors in Hematopoietic Lineage Development (2014)

The hematopoietic lineage is derived from pre-mesodermal cells and differentiates into hematopoietic and endothelial cells. The hematopoietic lineage cells play a key role in vasculogenesis during fetal development. Coagulation factors are essential for embryonic development and may also contribute to hematopoietic differentiation. The role of these factors and their corresponding protease-activated receptors (PARs) in the differentiation of hematopoietic lineage is not well characterized. PAR1 can be activated by activated factors VII and X as well as thrombin, and PAR4 by thrombin. We performed real-time reverse transcription PCR to assess the mRNA expression of prothrombin, tissue factor, factor V, VII, and X, and PAR1, 2, and 4 during murine-induced pluripotent stem cell differentiation into hematopoietic and hepatic lineages. PAR2 expression did not show significant changes. However, PAR1 expression increased from day 4 of hematopoietic cell differentiation. The increase was concomitant with the increase in expression of prothrombin and factor VII in the hepatic lineage from day 5–6, and with the transient upregulation of factor X in both lineages from day 7–8. PAR4 expression increased on day 4 for both lineages and peaked (>3000-fold higher than baseline level) on days 6 and 7 in hepatic and hematopoietic lineages, respectively. The increase in PAR4 levels was concomitant with an increase in prothrombin expression in hepatic lineage. These results indicate that there may be potential crosstalk between hematopoietic and hepatic lineages through a coagulation factor–PAR axis in vasculogenesis. Keywords: Coagulation factor, hematopoietic lineage, protease-activated receptor, real-time reverse transcription PCR, sequential gene expression analysis, vasculogenesis.
Simultaneous Quantitation of 2-Hydroxy-4-Methoxybenzophenone, a Sunscreen Ingredient, and its Metabolites in Harlan Sprague Dawley Rat Plasma Following Perinatal Dietary Exposure (2017)

2-Hydroxy-4-methoxybenzophenone (HMB) is a common ingredient in sunscreens and other personal care products and thus significant potential exists for human exposure. HMB was nominated to the National Toxicology Program (NTP) for testing due to its high exposure through consumer products and inadequate toxicological data at the time, which also included increasing concern for the potential effects of HMB on reproduction and development. HMB is metabolized to numerous metabolites in vivo and in vitro including 2,4-dihydroxybenzophenone (DHB), 2,3,4-trihydroxybenzophenone (THB) and 2,5-dihydroxy-4-methoxybenzophenone (2,5-DHMB) as well as their corresponding glucuronide and/or sulfate conjugates. In this study, we have developed and validated a liquid chromatography-tandem mass spectrometry method to quantitate free (unconjugated) HMB and DHB, and total (combined conjugated and unconjugated) HMB, DHB, THB and 2,5-DHMB. The method was successfully applied to quantitate these analytes in plasma from postnatal day 28 and 56 male and female Harlan Sprague Dawley rat pups following perinatal dietary exposure to 0 (control), 3,000, 10,000 and 30,000 ppm HMB beginning on gestational Day 6. All determined analyte concentrations increased with increasing dose and were significantly higher than the controls at both timepoints. All the total analytes were quantified in all plasma samples and total concentrations were considerably higher than free, suggesting extensive conjugation. Mean concentrations of total HMB and DHB were higher (~100-300-fold) than the free HMB and DHB concentrations, and total concentrations in plasma were approximately HMB≈DHB > 2,5-DHMB»THB. Free and total analyte plasma concentrations were not sex-dependent and in general, both free and total analytes were detected in the control samples. Comparison of our rat data, using the internal dose, with human data available in the literature suggests that the rat doses used in our studies were within 4-fold of the human dose.
Supplementary Table S2 from The Bromodomain Inhibitor JQ1 and the Histone Deacetylase Inhibitor Panobinostat Synergistically Reduce N-Myc Expression and Induce Anticancer Effects (2023)

&lt;p&gt;JQ1 and panobinostat synergistically modulate gene expression.&lt;/p&gt;
Characterization of LiNbO3 thin films grown on Al2O3 by RF sputtering (1995)

Abstract We describe our work on LiNbO3 thin films grown on Al2O3-c by rf sputtering. X-ray diffraction shows that we grow single phase, epitaxial films in which the lithium content can be varied. Optical measurements and surface morphology characterization show that the optical loss increases with the surface roughness and that the presence of large crystalline outgrowths is a limiting factor for low loss waveguides.
70 nm Seamless Band Transmission of 17.3 Tb/s over 40×100km of Fiber using Complementary Raman/EDFA (2015)

We demonstrated 70nm seamless band transmission of 173×128Gb/s QPSK signals over 40×100km of TeraWaveTM fiber. The complementary Raman/EDFAs and wide-band single-stage discrete Raman amplifiers were used to achieve this 17.3Tb/s capacity ultra-wide single-band transmission.
Arginyl-glycyl-aspartic acid sequences and fibrinogen binding to platelets (1987)

Human fibrinogen has an Arg-Gly-Asp-Ser (RGDS) sequence at residues 572-575 of its A alpha-chain. Although RGDS-containing peptides inhibit fibrinogen binding to stimulated platelets, these peptides also inhibit platelet binding of human fibrinogen fragment X and rat fibrinogen, which lack RGDS sequences corresponding to A alpha 572-575. Thus competition between free RGD-containing peptides and internal RGDS sequence at A alpha 572-575 is not the basis for their inhibition of fibrinogen binding to platelets. Addition of a Thr to the carboxy-terminus and an Asn to the amino-terminus of the RGDS sequence, the amino acids corresponding to A alpha 576 and 571 respectively, reduced the inhibitory potency of RGDS-containing peptides by fourfold to tenfold. Arg-Gly-Asp-Phe (RGDF) corresponds to A alpha 95-98, and the RGDF peptide was an effective inhibitor of fibrinogen binding, fourfold to fivefold more potent than RGDS. Thus, local primary structure may play an important role in regulating the capacity of RGD sequences in proteins to interact with specific adhesion receptors.
ChemInform Abstract: Photochemistry of Iron Atoms and Dimers with Ethylene in Cryogenic Matrices. (1986)

Abstract IR studies show that atomic and molecular iron interact with ethylene in two distinct ways.
Expedient Approach to Novel N-Unprotected Bicyclic Azapyrimidine and Pyridine Structures (2012)

A direct route to novel bicyclic N-unprotected azapyrimidine structures including fused five-, six-, and seven-membered rings is described involving radical addition and cyclization of xanthates; this approach could be partially extended to pyridines.