gebhart/patrepeval huggingface dataset:
Leaf senescence is delayed in maize expressing the Agrobacterium IPT gene under the control of a novel maize senescence‐enhanced promoter (2004)

We have genetically modified maize plants to delay leaf senescence. A senescence-enhanced promoter from maize (P(SEE1)) was used to drive expression of the Agrobacterium cytokinin biosynthesis gene IPT in senescing leaf tissue. Three maize lines expressing IPT from P(SEE1), Sg1, Sg2 and Sg3, were analysed in detail, representing mild, intermediate and extreme expression, respectively, of the delayed-senescence phenotype. Backcross populations segregating for the presence or absence of the P(SEE1Xba)IPTNOS transgene also simultaneously segregated for the senescence phenotype. At the time of ear leaf emergence, individuals of lines Sg1 and Sg2 segregating for the presence of the transgene carried about three fewer senescing leaves than control (transgene-minus) segregants, and IPT transcript levels were higher in leaves at incipient senescence than in young leaves. Leaves of transgenic Sg3 plants were significantly greener than controls and progressed directly from fully green to bleached and dead without an intervening yellowing phase. IPT transcript abundance in this line was not related to the initiation of senescence. Extended greenness was accompanied by a delay in the loss of photosynthetic capacity with leaf age. The delayed-senescence trait was associated with relatively minor changes in morphology and development. The phenotype was particularly emphasized in plants grown in low soil nitrogen. The reduced ability of the extreme transgenic line Sg3 to recycle internal nitrogen from senescing lower leaves accounted for significant chlorosis in emerging younger leaves when plants were grown in low nutrient conditions. This study demonstrates that the agronomically important delayed-senescence ('stay-green') trait can be engineered into a monocot crop, and is the first example outside Arabidopsis of senescence modification using a homologous senescence-enhanced promoter.
Randomized benchmarking of quantum gates (2008)

A key requirement for scalable quantum computing is that elementary quantum gates can be implemented with sufficiently low error. One method for determining the error behavior of a gate implementation is to perform process tomography. However, standard process tomography is limited by errors in state preparation, measurement and one-qubit gates. It suffers from inefficient scaling with number of qubits and does not detect adverse error-compounding when gates are composed in long sequences. An additional problem is due to the fact that desirable error probabilities for scalable quantum computing are of the order of 0.0001 or lower. Experimentally proving such low errors is challenging. We describe a randomized benchmarking method that yields estimates of the computationally relevant errors without relying on accurate state preparation and measurement. Since it involves long sequences of randomly chosen gates, it also verifies that error behavior is stable when used in long computations. We implemented randomized benchmarking on trapped atomic ion qubits, establishing a one-qubit error probability per randomized $\ensuremath{\pi}/2$ pulse of 0.00482(17) in a particular experiment. We expect this error probability to be readily improved with straightforward technical modifications.
OLAP query processing for partitioned data warehouses (2003)

On-line analytical processing (OLAP) queries can take hours or even days to execute on very large data warehouses. Therefore, there is a need to employ techniques that can facilitate efficient execution of these queries. The data partitioning concept that has been studied in the context of relational databases aims to reduce query execution time and facilitate the parallel execution of queries. In this paper, we develop a framework for applying the partitioning technique on DW schema (star schema) to reduce the total query execution cost. We develop an analytical cost model for executing a set of OLAP queries on a partitioned star schema. We conduct experiments to evaluate the utility of partitioning in efficiently executing OLAP queries. Finally, we show how partitioning can be used to facilitate parallel execution of OLAP queries.
Methods for Intense Aeration, Growth, Storage, and Replication of Bacterial Strains in Microtiter Plates (2000)

Miniaturized growth systems for heterogeneous culture collections are not only attractive in reducing demands for incubation space and medium but also in making the parallel handling of large numbers of strains more practicable. We report here on the optimization of oxygen transfer rates in deep-well microtiter plates and the development of a replication system allowing the simultaneous and reproducible sampling of 96 frozen glycerol stock cultures while the remaining culture volume remains frozen. Oxygen transfer rates were derived from growth curves of Pseudomonas putida and from rates of oxygen disappearance due to the cobalt-catalyzed oxidation of sulfite. Maximum oxygen transfer rates (38 mmol liter(-1) h(-1), corresponding to a mass transfer coefficient of 188 h(-1)) were measured during orbital shaking at 300 rpm at a shaking diameter of 5 cm and a culture volume of 0.5 ml. A shaking diameter of 2.5 cm resulted in threefold-lower values. These high oxygen transfer rates allowed P. putida to reach a cell density of approximately 9 g (dry weight) liter(-1) during growth on a glucose mineral medium at culture volumes of up to 1 ml. The growth-and-replication system was evaluated for a culture collection consisting of aerobic strains, mainly from the genera Pseudomonas, Rhodococcus, and Alcaligenes, using mineral media and rich media. Cross-contamination and excessive evaporation during vigorous aeration were adequately prevented by the use of a sandwich cover of spongy silicone and cotton wool on top of the microtiter plates.
Design Optimization of Multigate Bulk MOSFETs (2012)

The design optimization of multigate bulk MOSFET structures is investigated for sub-20-nm gate lengths. Three-dimensional device simulations were used to optimize device design parameters such as the retrograde channel doping profile, as well as the length, width, and height of the gated channel region. Compared with the FinFET design, the results indicate that the tri-gate MOSFET design is promising for continued bulk-Si CMOS transistor scaling, because it can achieve similar on-state current performance and intrinsic delay [for the same channel stripe pitch (SP)] at a lower height/width aspect ratio (0.8 versus 2.17) and less aggressive retrograde channel doping gradient for improved manufacturability. Only by increasing the height of the channel region and/or reducing the channel SP can the FinFET bulk MOSFET design achieve better delay, but at the cost of reduced manufacturability.
Activation of internucleosomal DNA cleavage in human CEM lymphocytes by glucocorticoid and novobiocin. Evidence for a non-Ca2(+)-requiring mechanism(s). (1990)

Internucleosomal DNA cleavage is the key molecular event of the cytolytic phase of glucocorticoid-induced lymphocytolysis. We find that novobiocin, the topoisomerase II inhibitor, is a potent inducer of in vivo internucleosomal DNA cleavage in human CEM lymphocytes. This in vivo effect is very rapid, time- and dose-dependent, requires cellular integrity, and does not require de novo protein synthesis. Recently our data (Alnemri, E. S., and Litwack, G. (1989) J. Biol. Chem. 264, 4104-4111) suggested that activation of DNA cleavage in CEM-C7 lymphocytes by glucocorticoids is independent of calcium uptake. Similarly, the novobiocin effect is also independent of calcium uptake and does not occur in isolated CEM nuclei or in CEM cells treated previously with the divalent cation ionophore A23187. Internucleosomal DNA cleavage induced by novobiocin or glucocorticoid generates blunt-ended double-stranded DNA fragments possessing 3'-hydroxyls and 5'-phosphates. As demonstrated by gel retardation analysis and DNase I footprinting, novobiocin causes the disruption and unfolding of an in vitro reconstituted mononucleosome so that it becomes more susceptible to DNase I cleavage. Our data suggest that 1) novobiocin rapid activation of internucleosomal DNA cleavage and chromatin changes in CEM lymphocytes are molecular features of apoptosis or programmed cell death. 2) CEM lymphocytes apparently do not express a Ca2(+)-dependent endonuclease. 3) The mechanism(s) of glucocorticoid or novobiocin-induced DNA cleavage in CEM lymphocytes involves activation of a constitutive non Ca2(+)-dependent endonuclease. We propose that the majority of nuclear chromatin is maintained in a highly compact and charge-neutralized state and that disruption of this highly ordered structure, directly by novobiocin or indirectly by glucocorticoid, may lead to the exposure and unmasking of internucleosomal linker DNA regions which are substrates for a constitutive non-Ca2(+)-dependent endonuclease.
Fast Solid-State Li Ion Conducting Garnet-Type Structure Metal Oxides for Energy Storage (2014)

Lithium ion batteries are the most promising energy storage system on the market today; however, safety issues associated with the use of flammable organic polymer-based electrolytes with poor electrochemical and chemical stabilities prevent this technology from reaching maturity. Solid lithium ion electrolytes (SLIEs) are being considered as potential replacements for the organic electrolytes to develop all-solid-state Li ion batteries. Out of the recently discovered SLIEs, the garnet-related structured Li-stuffed metal oxides are the most promising electrolytes due to their high total (bulk + grain boundary) Li ion conductivity, high electrochemical stability window (∼6 V versus Li(+)/Li at room temperature), and chemical stability against reaction with an elemental Li anode and high-voltage metal oxide Li cathodes. This Perspective discusses the structural-chemical composition-ionic conductivity relationship of Li-stuffed garnets, followed by a discussion on the Li ion conduction mechanism, as well as the electrochemical and chemical stability of these materials. The performance of a number of all-solid-state batteries employing garnet-type Li ion electrolytes is also discussed.
Industrial polysaccharides : genetic engineering, structure/property relations and applications : proceedings of the Symposium on the Applications and Modifications of Industrial Polysaccharides, held during the 193rd American Chemical Society National Meeting, Denver, Colorado, U.S.A., 5-10 April 1987 (1987)

Introduction: Synthesis and Characterization of Polysaccharides (M. Yalpani). Part 1. Genetic Engineering and Enzymatic Modifications. Developments and prospects in enzymatic biopolymer modifications (M. Yalpani, M.J. Desrochers). Genetically engineered polymers: Manipulation of xanthan biosynthesis (M.R. Betlach et al.). Polyhydroxybutyrate (PHB): A model system for biopolymer engineering (O.P. Peoples, A.J. Sinskey). Controlled biosynthesis of yeast glucan particles (S. Jamas et al.). Polysaccharide modification - A physiological approach (I.W. Sutherland). Production and characterization of a thermostable bacterial cyclodextrin glycosyltransferase (H. Aoki et al.). Bacterial degradation of xanthan gum (M.C. Cadmus, M.E. Slodki). Hydrolysis products of Pichia (Hansenula) holstii O-phosphomannan and uses in phosphomannosyl receptor characterization (M.E. Slodki). Part 2. Chemical Modifications. Progress in chemical modifications of polysaccharides (M. Yalpani). Glycol-modified polysaccharides (G.L. Brode et al.). Natural and synthetic derivatives of agarose and their use in biochemical separations (K.B. Guisely). Chemically-modified group B meningococcal polysaccharides as human vaccines (H.J. Jennings et al.). Calcium complexation by oxidized maltodextrins in water (M.S. Nieuwenhuizen et al.). Part 3. Structure/Property Relations. Effect of mono-O-acetyl groups on the conformation and interaction of microbial polysaccharides (E.T. Atkins). Structure/property relations of a family of microbial polysaccharides (R. Moorehouse). The role of structural modification in controlling polysaccharide functionality (I.C.M. Dea). On the properties of polysaccharides: Relation between chemical structure and physical properties (M. Rinaudo, M. Milas). Organoleptic properties of food polysaccharides in thickened systems (E.R. Morris). Part 4. Characterization. Rheological characterization of high viscosity polysaccharides (B.-D. Kwon et al.). Conformations of chitosan, its metal complexes, and acid salts revealed by high-resolution solid-state 13 C-NMR (H. Saito et al.). CP/MAS 13 C-NMR studies on aqueous polysaccharide gels (A.J. Stipanovic, P.J. Giammatteo). Polysaccharide structure from circular dichroism (I. Tobias). Part 5. Novel Applications. Commercial polysaccharides: Recent trends and developments (M. Yalpani, P.A. Sandford). Binding of metal cations by chitin derivatives: Improvement of adsorption ability through chemical modifications (K. Kurita). Immunological aspects of chitin derivatives (S. Tokura et al.). Chitosan-A natural, cationic biopolymer: Commercial applications (P.A. Sandford, G.P. Hutchings). Modification of dextran and application in prodrug design (E.H. Schacht). Author Index. Subject Index.
Comparison of boron diffusion in Si and strained Si1−xGex epitaxial layers (1993)

We have investigated boron diffusion in Si and strained Si1−xGex, in situ doped, epitaxial layers. During inert ambient annealing at 860 °C, boron diffusion is observed to be slower in Si0.83Ge0.17 than in Si for boron concentration levels between 5×1016 and 2.5×1019 cm−3. Computer simulations of the measured boron profiles for annealed samples indicate that the effective boron diffusivity Deff in Si0.83Ge0.17 is approximately an order of magnitude lower than that in Si. This disparity is found to increase with increasing boron concentration.
Differential EphA2 epitope display on normal versus malignant cells. (2003)

The EphA2 receptor tyrosine kinase is overexpressed in many different types of human cancers where it functions as a powerful oncoprotein. Dramatic changes in the subcellular localization and function of EphA2 have also been linked with cancer, and in particular, unstable cancer cell-cell contacts prevent EphA2 from stably binding its ligand on the surface of adjoining cells. This change is important in light of evidence that ligand binding causes EphA2 to transmit signals that negatively regulate tumor cell growth and invasiveness and also induce EphA2 degradation. On the basis of these properties, we have begun to target EphA2 on tumor cells using agonistic antibodies, which mimic the consequences of ligand binding. In our present study, we show that a subset of agonistic EphA2 antibodies selectively bind epitopes on malignant cells, which are not available on nontransformed epithelial cells. We also show that such epitopes arise from differential cell-cell adhesions and that the stable intercellular junctions of nontransformed epithelial cells occlude the binding site for ligand, as well as this subset of EphA2 antibodies. Finally, we demonstrate that antibody targeting of EphA2 decreases tumor cell growth as measured using xenograft tumor models and found that the mechanism of antibody action relates to EphA2 protein degradation in vivo. Taken together, these results suggest new opportunities for therapeutic targeting of the large number of different cancers that express EphA2 in a manner that could minimize potential toxicities to normal cells.
RETRACTED: Collagen Prolyl Hydroxylases Are Essential for Breast Cancer Metastasis (2013)

The presence of hypoxia and fibrosis within the primary tumor are two major risk factors for metastasis of human breast cancer. In this study, we demonstrate that hypoxia-inducible factor 1 activates the transcription of genes encoding collagen prolyl hydroxylases that are critical for collagen deposition by breast cancer cells. We show that expression of collagen prolyl hydroxylases promotes cancer cell alignment along collagen fibers, resulting in enhanced invasion and metastasis to lymph nodes and lungs. Finally, we establish the prognostic significance of collagen prolyl hydroxylase mRNA expression in human breast cancer biopsies and show that ethyl 3,4-dihydroxybenzoate, a prolyl hydroxylase inhibitor, decreases tumor fibrosis and metastasis in a mouse model of breast cancer.
Zinc Chelation by a Small-Molecule Adjuvant Potentiates Meropenem Activity in Vivo against NDM-1-Producing Klebsiella pneumoniae (2015)

The widespread emergence of antibiotic drug resistance has resulted in a worldwide healthcare crisis. In particular, the extensive use of β-lactams, a highly effective class of antibiotics, has been a driver for pervasive β-lactam resistance. Among the most important resistance determinants are the metallo-β-lactamases (MBL), which are zinc-requiring enzymes that inactivate nearly all classes of β-lactams, including the last-resort carbapenem antibiotics. The urgent need for new compounds targeting MBL resistance mechanisms has been widely acknowledged; however, the development of certain types of compounds-namely metal chelators-is actively avoided due to host toxicity concerns. The work herein reports the identification of a series of zinc-selective spiro-indoline-thiadiazole analogues that, in vitro, potentiate β-lactam antibiotics against an MBL-carrying pathogen by withholding zinc availability. This study demonstrates the ability of one such analogue to inhibit NDM-1 in vitro and, using a mouse model of infection, shows that combination treatment of the respective analogue with meropenem results in a significant decrease in bacterial burden in contrast to animals that received antibiotic treatment alone. These results support the therapeutic potential of these chelators in overcoming antibiotic resistance.
Annular Structures as Intermediates in Fibril Formation of Alzheimer Aβ17−42 (2008)

We report all-atom molecular dynamics simulations of annular beta-amyloid (17-42) structures, single- and double-layered, in solution. We assess the structural stability and association force of Abeta annular oligomers associated through different interfaces, with a mutated sequence (M35A), and with the oxidation state (M35O). Simulation results show that single-layered annular models display inherent structural instability: one is broken down into linear-like oligomers, and the other collapses. On the other hand, a double-layered annular structure where the two layers interact through their C-termini to form an NC-CN interface (where N and C are the N and C termini, respectively) exhibits high structural stability over the simulation time due to strong hydrophobic interactions and geometrical constraints induced by the closed circular shape. The observed dimensions and molecular weight of the oligomers from atomic force microscopy (AFM) experiments are found to correspond well to our stable double-layered model with the NC-CN interface. Comparison with K3 annular structures derived from the beta 2-microglobulin suggests that the driving force for amyloid formation is sequence specific, strongly dependent on side-chain packing arrangements, structural morphologies, sequence composition, and residue positions. Combined with our previous simulations of linear-like Abeta, K3 peptide, and sup35-derived GNNQQNY peptide, the annular structures provide useful insight into oligomeric structures and driving forces that are critical in amyloid fibril formation.
The growing catalog of small RNAs and their association with distinct Argonaute/Piwi family members (2008)

Several distinct classes of small RNAs, some newly identified, have been discovered to play important regulatory roles in diverse cellular processes. These classes include siRNAs, miRNAs, rasiRNAs and piRNAs. Each class binds to distinct members of the Argonaute/Piwi protein family to form ribonucleoprotein complexes that recognize partially, or nearly perfect, complementary nucleic acid targets, and that mediate a variety of regulatory processes, including transcriptional and post-transcriptional gene silencing. Based on the known relationship of Argonaute/Piwi proteins with distinct classes of small RNAs, we can now predict how many new classes of small RNAs or silencing processes remain to be discovered.
Mesenchymal Stem Cells and Tooth Engineering (2009)

Tooth loss compromises human oral health. Although several prosthetic methods, such as artificial denture and dental implants, are clinical therapies to tooth loss problems, they are thought to have safety and usage time issues. Recently, tooth tissue engineering has attracted more and more attention. Stem cell based tissue engineering is thought to be a promising way to replace the missing tooth. Mesenchymal stem cells (MSCs) are multipotent stem cells which can differentiate into a variety of cell types. The potential MSCs for tooth regeneration mainly include stem cells from human exfoliated deciduous teeth (SHEDs), adult dental pulp stem cells (DPSCs), stem cells from the apical part of the papilla (SCAPs), stem cells from the dental follicle (DFSCs), periodontal ligament stem cells (PDLSCs) and bone marrow derived mesenchymal stem cells (BMSCs). This review outlines the recent progress in the mesenchymal stem cells used in tooth regeneration.
The BAFF/APRIL System: An Important Player in Systemic Rheumatic Diseases (2004)

Many rheumatic diseases have an autoimmune basis, characterized by organ-specific inflammation and tissue destruction. Diseases such as rheumatoid arthritis, systemic lupus erythematosus or Sjögren's syndrome often associate with abnormal B cell function and the production of various autoantibodies. B cell activating factor belonging to the TNF family (BAFF) is a B cell survival factor essential for B cell maturation, but also contributes to autoimmunity when overexpressed in mice. In addition, elevated levels of BAFF have been detected in the serum of patients with various rheumatic diseases, suggesting a role for this factor in these pathologies. BAFF has additional functions that may be important in rheumatic diseases. For instance, excess BAFF leads to the expansion of a subset of B cells named marginal zone (MZ) B cells, a cell type able to activate naïve T cells. In addition, expansion of the MZ B cell population correlates with certain autoimmune diseases, and these cells have been detected in inflamed tissues in mice and humans. Recently, BAFF was shown to also stimulate T cell activation, an aspect that may also contribute to autoimmunity. Finally, BAFF has emerged as a potent survival factor for B cell lymphomas and as such may be involved in promoting B cell cancers. This result possibly offers an explanation for the occasional lymphoma complication observed in a subset of patients with certain rheumatic diseases, particularly Sjögren's syndrome. New elements about BAFF biology indicate that this factor may be involved in a wider range of pathologies than first anticipated, and inhibitors of this factor are likely to provide attractive new treatments for rheumatic diseases and B cell lymphomas.