gebhart/patrepeval huggingface dataset:
Age‐dependent transformation frequency in elite wheat varieties (2001)

Wheat is a major world crop and as such is a primary target for improvement of agronomic characteristics via genetic engineering. Optimization of transformation is essential in order to overcome the relatively low transformation frequencies encountered with wheat. Transformation of elite wheat varieties is not always successful due to variability in regeneration and transformation frequencies between varieties. In this work, two elite wheat varieties with a relatively high embryogenic capacity were transformed by particle bombardment. A strong correlation between transformation frequency and the age of wheat donor plants was observed in both varieties. The mean transformation frequency rose from 0.7% to 5% when using immature embryos from old and young donor plants, respectively. This was observed in both varieties, the best bombardments achieving up to 7.3% frequency. Using explants at an optimal developmental stage from donor plants grown under environmentally-controlled conditions has improved the reproducibility of transformation efficiency of elite wheat varieties and leads to the production of apparently phenotypically normal, fertile, transgenic plants.
Hydrogen by Catalytic Steam Reforming of Liquid Byproducts from Biomass Thermoconversion Processes (2002)

Biomass, a product of photosynthesis, is a renewable resource that can be used for sustainable production of hydrogen. We propose an approach that combines production of hydrogen with valuable coproducts and shows promising economics. The concept is based on a two-stage process: fast pyrolysis of biomass to generate bio-oil, followed by catalytic steam reforming of the bio-oil, or a fraction thereof, to produce hydrogen. The preferred option is separation of the bio-oil into a lignin-derived fraction, which could be used for producing phenolic resins or fuel-blending components, and a carbohydrate-derived material, which would be reformed to produce hydrogen. The coproduct strategy can also be applied to residual fractions derived from pulping operations or ethanol production and to effluents from other biomass conversion technologies such as transesterification of vegetable oils or food processing residues. In addition, all of the biomass-derived liquids can be coprocessed with natural gas to produce hydrogen from mixed fossil−biomass feedstocks, a strategy similar to cofiring biomass and coal for power generation. This work focuses on the second stage of the process: catalytic steam reforming of various biomass-derived liquids. We have used a commercial nickel-based naphtha reforming catalyst in a fluidized-bed reactor to produce hydrogen from the various biomass-derived liquids. Yields have approached or exceeded 80% of those theoretically possible for stoichiometric conversion.
Signals and genes induced by angiogenic growth factors in comparison to inflammatory cytokines in endothelial cells. (2007)

The evaluation of signaling pathways leading to gene induction by VEGF-A and IL-1 in endothelial cells supports the importance of the NF-kappaB pathway for the IL-1-induced gene repertoire, whereas VEGF-A is a strong and preferential trigger of signals via PLC-gamma. This leads (i) via Ca(++) to the activation of calcineurin and NFAT and (ii) via PKC and the MEK/ERK MAPK pathway to the upregulation of EGR-1. Part of the VEGF-triggered gene induction depends on a cooperation of the transcription factors NFAT and EGR-1. Gene activation via PLC-gamma provides VEGF with the potency to induce a wide spectrum of genes including many also upregulated by IL-1. A gene upregulated by VEGF and IL-1 is the DSCR-1 gene, which encodes an inhibitor of calcineurin. DSCR1 is induced by NFAT or NF-kappaB and limits Ca(++) signaling in a negative feed-back loop. Similarly, NAB2, a corepressor of EGR-1, is induced by EGR-1 and limits EGR-1 effects. Adenoviral overexpression of DSCR1 or NAB2 inhibited part of VEGF-induced gene expression and reduced sprouting in angiogenesis models.
Radioceasium activity concentrations in potatoes in Croatia after the Chernobyl accident (2006)

In the paper are summarized the results of systematic investigations of 137Cs and 134Cs activity concentrations in potatoes (Solanum tuberosum) for the post-Chernobyl period in the Republic of Croatia. Potatoes are very important foodstuff in Croatia, the average annual consumption being about 40 kg per person. Due to a comparatively high contribution of the ingestion doses to the total dose received by population after the exposure to nuclear fallout, a reliable prognosis of the expected ingestion doses is of utmost importance. The ingestion dose strongly depends on the consumption of various types of foodstuffs, and related activity concentrations of respective radionuclides in those foodstuffs, which themselves usually depend upon the transfer from fallout. In addition, a reliable prediction of the expected ingestion dose received by consumption of a particular foodstuff requires the detailed knowledge of decreasing behaviour of activity concentrations in the environment and respective foodstuffs. The correlation between 137Cs activity concentrations in fallout and potatoes, has been found to be very good, the correlation coefficient being r2=0.88 with P(t) < 0.001 for 17 degrees of freedom. As the radiocaesium levels in potatoes decreased exponentially, the mean residence time of 137Cs in potatoes was estimated by fitting the measured activity concentrations to the exponential curve. The mean residence time was found to be 6.3 ± 0.8 years, the standard deviation being estimated by the Monte Carlo simulations. The initial observed 134Cs:137Cs activity ratio in potatoes has been found to be quite variable, but slightly lesser than theoretically predicted value of 0.5, calculated by applying the known inventory of these radionuclides in the Chernobyl reactor to the equation for the differential radioactive decay. This can be explained by presence of the pre-Chernobyl 137Cs in soil that originated from nuclear fallout. As in other environmental samples, 134Cs relatively quickly disappeared from potatoes and its activity concentrations were in 1990 under the detection limit of the instrument. The annual effective doses received by 134Cs and 137Cs intake due to consumption of potatoes estimated for an adult member of Croatian population were found to be very small, as the per caput dose for the entire 1986 – 2004 period was calculated to be about 2.5 μ Sv, 134Cs accounting approximately for 1/3 of the entire dose. Consequently, it can be argued that after the Chernobyl accident consumption of potatoes was not the critical pathway for human intake of radiocaesium from the environment in Croatia.
The IRS‐signalling system during insulin and cytokine action (1997)

The discovery of the first intracellular substrate for insulin, IRS-1, redirected the field of diabetes research and has led to many important advances in our understanding of insulin action. Detailed analysis of IRS-1 demonstrates structure/function relationships for this modular docking molecule, including mechanisms of substrate recognition and signal propagation. Recent work has also identified other structurally similar molecules, including IRS-2, the Drosophila protein, DOS, and the Grb2-binding protein, Gab1, suggesting that this intracellular signalling strategy is conserved evolutionarily and is utilized by an expanding number of receptor systems. In fact, IRS-1 itself has been shown to be important in other growth factor and cytokine signalling systems, including growth hormone and several interleukins. Analysis of mice lacking IRS-1 confirms an important physiological role for this protein in glucose metabolism and general cell growth in the intact animal. Disregulation of the signalling pathways integrated by the IRS proteins may contribute to the pathophysiology of non-insulin-dependent diabetes mellitus or other diseases.
Elimination of up to 80% of human pancreatic adenocarcinomas in athymic mice by cardiac hormones. (2007)

Four cardiac hormones eliminated up to 80% of human pancreatic adenocarcinomas in athymic mice.
Investigation of the genes for RET and its ligand complex, GDNF/GFRα‐1, in small cell lung carcinoma (1998)

RET is a receptor tyrosine kinase expressed in neuroendocrine cells and in tumors of these cell types. RET activation may be mediated by a ligand complex comprising glial cell line-derived neurotrophic factor (GDNF) and GDNF family receptor alpha-1 (GFRα-1). Activating RET mutations are found in the inherited cancer syndrome multiple endocrine neoplasia type 2 and in a subset of the related sporadic tumors, medullary thyroid carcinoma and pheochromocytoma, both being derived from neuroendocrine tissues. In one small study, mutations were identified in another tumor with neuroendocrine features, small cell lung carcinoma (SCLC). To determine whether RET mutations contribute to the pathogenesis of SCLC, we examined a panel of 54 SCLC cell lines. No mutations were identified in RET exons 10, 11, and 13–16, regions previously implicated in SCLC or other neuroendocrine tumors. We further examined the expression pattern of RET and the genes encoding the components of its ligand complex GDNF and GFRα-1, in 21 SCLC lines by using RT-PCR. Although we found no consistent pattern of expression for these three genes, RET was expressed in 57% of SCLC lines. Thus, although RET mutations appear unlikely to be an important step in the tumorigenesis of SCLC, the frequent expression of this gene suggests that RET may have a mitogenic role in a subset of SCLC cell lines. Genes Chromosomes Cancer 21:326–332, 1998. © 1998 Wiley-Liss, Inc.
Elucidation of an Archaeal Replication Protein Network to Generate Enhanced PCR Enzymes (2002)

Thermostable DNA polymerases are an important tool in molecular biology. To exploit the archaeal repertoire of proteins involved in DNA replication for use in PCR, we elucidated the network of proteins implicated in this process in Archaeoglobus fulgidus. To this end, we performed extensive yeast two-hybrid screens using putative archaeal replication factors as starting points. This approach yielded a protein network involving 30 proteins potentially implicated in archaeal DNA replication including several novel factors. Based on these results, we were able to improve PCR reactions catalyzed by archaeal DNA polymerases by supplementing the reaction with predicted polymerase co-factors. In this approach we concentrated on the archaeal proliferating cell nuclear antigen (PCNA) homologue. This protein is known to encircle DNA as a ring in eukaryotes, tethering other proteins to DNA. Indeed, addition of A. fulgidus PCNA resulted in marked stimulation of PCR product generation. The PCNA-binding domain was determined, and a hybrid DNA polymerase was constructed by grafting this domain onto the classical PCR enzyme from Thermus aquaticus, Taq DNA polymerase. Addition of PCNA to PCR reactions catalyzed by the fusion protein greatly stimulated product generation, most likely by tethering the enzyme to DNA. This sliding clamp-induced increase of PCR performance implies a promising novel micromechanical principle for the development of PCR enzymes with enhanced processivity.
Effect of sacral neuromodulation on female sexual function and quality of life: Are they correlated? (2014)

SNM may improve female sexual function and quality of life, yet there is no correlation between the improvement in FSFI and quality of life.
Chemotherapy of Chagas Disease (2002)

In this article we review the current status of chemotherapeutic approaches for the specific treatment of Chagas disease or American Trypanosomiasis, as well as new rational approaches being developed as a consequence on the increased understanding of the biochemistry and physiology of its causative agent, the protozoan parasite Trypanosoma cruzi. Currently available drugs (nitrofurans and nitroimidazoles), developed empirically over three decades ago, are unsatisfactory due to frequent toxic side effects and limited efficacy, particularly in the prevalent chronic form of the disease. Furthermore, studies of their mechanism of action have shown that their antiparasitic activity is inextricably linked to mammalian host toxicity. Recent advances in this field include the demonstration that new triazole derivatives, with selective inhibitory activity on the parasite's de novo sterol biosynthesis and special pharmacokinetic properties, can induce radical parasitological cure of both acute and chronic Chagas experimental disease. These compounds are active against nitrofuran- and nitroimidazole-resistant T.cruzi strains and maintain their activity even if the hosts are immunosuppressed and are thus logical candidates for clinical trials with Chagas disease patients. Inhibitors of cruzipain, a cathepsin L-like protease responsible for the major proteolytic activity in all stages of the life cycle of the parasite, can selectively block the proliferation of T.cruzi, both in vitro and in vivo and have curative activity in murine models of acute Chagas disease; a significant effort is being devoted to their development as antiparasitic drugs. Alkyl-lysophospholipids, which selectively block phosphatidyl-choline biosynthesis in T.cruzi, are promising antiparasitic agents with good oral activity and low toxicity. Other biochemical pathways have been identified as potential chemotherapeutic targets, including hypoxanthine-guanine phosphoribosyl transferase and the enzymes involved in the synthesis and metabolism of trypanothione and inorganic pyrophosphate.
Waves of early transcriptional activation and pluripotency program initiation during human preimplantation development (2011)

The events regulating human preimplantation development are still largely unknown owing to a scarcity of material, ethical and legal limitations and a lack of reliable techniques to faithfully amplify the transcriptome of a single cell. Nonetheless, human embryology is gathering renewed interest due to its close relationship with both stem cell biology and epigenetic reprogramming to pluripotency and their importance in regenerative medicine. Carefully timed genome-wide transcript analyses of single oocytes and embryos uncovered a series of successive waves of embryonic transcriptional initiation that start as early as the 2-cell stage. In addition, we identified the hierarchical activation of genes involved in the regulation of pluripotency. Finally, we developed HumER, a database of human preimplantation gene expression, to serve the scientific community. Importantly, our work links early transcription in the human embryo with the correct execution of the pluripotency program later in development and paves the way for the identification of factors to improve epigenetic reprogramming.
In Vivo VEGF Imaging with Radiolabeled Bevacizumab in a Human Ovarian Tumor Xenograft (2007)

Radiolabeled bevacizumab showed higher uptake compared with radiolabeled human IgG in a human SKOV-3 ovarian tumor xenograft. Noninvasive quantitative small-animal PET was similar to invasive ex vivo biodistribution. Radiolabeled bevacizumab is a new tracer for noninvasive in vivo imaging of VEGF in the tumor microenvironment.
Mobility and transverse flow visualization using phase variance contrast with spectral domain optical coherence tomography (2007)

Phase variance-based motion contrast is demonstrated using two phase analysis methods in a spectral domain optical coherence tomography system. Mobility contrast is demonstrated for an intensity matched Intralipid solution placed without flow within agarose wells. Vasculature oriented transversely to the imaging direction has been imaged for 3-4 dpf in vivo zebrafish using the phase variance contrast methods. 2D phase variance contrast images are demonstrated with imaging times only 25% higher than a Doppler flow image with comparable statistics. En face images created by integrating depth regions of 3D zebrafish intensity and phase variance contrast data demonstrate vasculature consistent with expected images.
Pharmacodynamics, pharmacokinetics, and safety of multiple doses of FTY720 in stable renal transplant patients: a multicenter, randomized, placebo-controlled, phase I study (2003)

At doses up to 5.0 mg/day for 28 days, stable renal transplant patients treated with FTY720 in combination with CsA and prednisone displayed a dose-dependent, reversible decline in peripheral blood lymphocytes without an enhanced incidence of collateral toxicities, except possibly bradycardia.
Xenon Difluoride Exchanges Fluoride under Mild Conditions: A Simple Preparation of [18F]Xenon Difluoride for PET and Mechanistic Studies (2001)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTXenon Difluoride Exchanges Fluoride under Mild Conditions: A Simple Preparation of [18F]Xenon Difluoride for PET and Mechanistic StudiesMaria Constantinou, Franklin I. Aigbirhio, Rachel G. Smith, Christopher A. Ramsden, and Victor W. PikeView Author Information Chemistry and Engineering Group, MRC Cyclotron Unit Imperial College School of Medicine Hammersmith Hospital, Ducane Road London W12 ONN, UK School of Chemistry and Physics, Keele University Keele, Staffordshire, ST5 5 BG, UK Cite this: J. Am. Chem. Soc. 2001, 123, 8, 1780–1781Publication Date (Web):February 2, 2001Publication History Received11 September 2000Published online2 February 2001Published inissue 1 February 2001https://pubs.acs.org/doi/10.1021/ja003321jhttps://doi.org/10.1021/ja003321jrapid-communicationACS PublicationsCopyright © 2001 American Chemical SocietyRequest reuse permissionsArticle Views611Altmetric-Citations26LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Amorphous materials,Anions,Catalysts,Lewis acids,Solvents Get e-Alerts
Tim-3 marks human natural killer cell maturation and suppresses cell-mediated cytotoxicity (2012)

Natural killer (NK) cells are innate lymphocytes that play an important role against viral infections and cancer. This effect is achieved through a complex mosaic of inhibitory and activating receptors expressed by NK cells that ultimately determine the magnitude of the NK-cell response. The T-cell immunoglobulin- and mucin domain-containing (Tim)-3 receptor was initially identified as a T-helper 1-specific type I membrane protein involved in regulating T-cell responses. Human NK cells transcribe the highest amounts of Tim-3 among lymphocytes. Tim-3 protein is expressed on essentially all mature CD56(dim)CD16(+) NK cells and is expressed heterogeneously in the immature CD56(bright)CD16(-) NK-cell subset in blood from healthy adults and in cord blood. Tim-3 expression was induced on CD56(bright)CD16(-) NK cells after stimulation with IL-15 or IL-12 and IL-18 in vitro, suggesting that Tim-3 is a maturation marker on NK cells. Whereas Tim-3 has been used to identify dysfunctional T cells, NK cells expressing high amounts of Tim-3 are fully responsive with respect to cytokine production and cytotoxicity. However, when Tim-3 was cross-linked with antibodies it suppressed NK cell-mediated cytotoxicity. These findings suggest that NK-cell responses may be negatively regulated when NK cells encounter target cells expressing cognate ligands of Tim-3.
Type inference with polymorphic recursion (1993)

The Damas-Milner Calculus is the typed A-calculus underlying the type system for ML and several other strongly typed polymorphic functional languages such as Mirandal and Haskell. Mycroft has extended its problematic monomorphic typing rule for recursive definitions with a polymorphic typing rule. He proved the resulting type system, which we call the Milner-Mycroft Calculus, sound with respect to Milner's semantics, and showed that it preserves the principal typing property of the Damas-Milner
Calibration of Dynamic Molecular Rulers Based on Plasmon Coupling between Gold Nanoparticles (2005)

Pairs of noble metal nanoparticles can be used to measure distances via the distance dependence of their plasmon coupling. These "plasmon rulers" offer exceptional photostability and brightness; however, the advantages and limitations of this approach remain to be explored. Here we report detailed plasmon peak versus separation calibration curves for 42- and 87-nm-diameter particle pairs, determine their measurement errors, and describe experimental procedures to improve their performance in biology, nanotechnology, and materials sciences.
Intermittent Hypoxia Research in the Former Soviet Union and the Commonwealth of Independent States: History and Review of the Concept and Selected Applications (2002)

This review aims to summarize the basic research in the field of intermittent hypoxia in the Soviet Union and the Commonwealth of Independent States (CIS) that scientists in other Western countries may not be familiar with, since Soviet scientists were essentially cut off from the global scientific community for about 60 years. In the 1930s the concept of repeated hypoxic training was developed and the following induction methods were utilized: repeated stays at high-mountain camps for several weeks, regular high altitude flights by plane, training in altitude chambers, and training by inhalation of low-oxygen-gas mixtures. To the present day, intermittent hypoxic training (IHT) has been used extensively for altitude preacclimatization; for the treatment of a variety of clinical disorders, including chronic lung diseases, bronchial asthma, hypertension, diabetes mellitus, Parkinson's disease, emotional disorders, and radiation toxicity, in prophylaxis of certain occupational diseases; and in sports. The basic mechanisms underlying the beneficial effects of IHT are mainly in three areas: regulation of respiration, free-radical production, and mitochondrial respiration. It was found that IHT induces increased ventilatory sensitivity to hypoxia, as well as other hypoxia-related physiological changes, such as increased hematopoiesis, alveolar ventilation and lung diffusion capacity, and alterations in the autonomic nervous system. Due to IHT, antioxidant defense mechanisms are stimulated, cellular membranes become more stable, Ca(2+) elimination from the cytoplasm is increased, and O(2) transport in tissues is improved. IHT induces changes within mitochondria, involving NAD-dependent metabolism, that increase the efficiency of oxygen utilization in ATP production. These effects are mediated partly by NO-dependent reactions. The marked individual variability both in animals and humans in the response to, and tolerance of, hypoxia is described. Studies from the Soviet Union and the CIS significantly contributed to the understanding of intermittent hypoxia and its possible beneficial effects and should stimulate further research in this direction in other countries.