gebhart/patrepeval huggingface dataset:
Human Embryonic Stem Cells: Isolation, Maintenance, and Differentiation (2006)

The isolation of pluripotent human embryonic stem (hES) cells having the capacity to differentiate in vitro to numerous cell types generated much excitement and promise in the field of regenerative medicine. However, along with great enthusiasm came hot controversy for stem cell research and researchers alike because available hES cell lines were isolated from "excess" embryos from in vitro fertilization clinics. Despite ethical and political debates, the methods and protocols to study diverse lineages are developing. Furthermore, strategies using specific growth factor combinations, cell-cell and cell-extracellular matrix induction systems are being explored for directed differentiation along a desired lineage. However, there is a great need to characterize the mechanisms that control self-renewal and differentiation and a necessity to improve methodologies and develop new purification protocols for the potential future clinical application of hES cells. After the scientific and political obstacles are overcome, it is anticipated that the hES cell field will make a tremendous difference in conditions, such as burn traumas and diabetic foot ulcers, as well a number of degenerative diseases such as Parkinson's disease, type 1 diabetes, rheumatoid arthritis, and myocardial infarction. In this introductory chapter, we will summarize and review recent progress in the field of hES cell differentiation protocols and discuss some of the current issues surrounding hES cell research.
Tandem Repeat of a Transcriptional Enhancer Upstream of the Sterol 14α-Demethylase Gene ( <i>CYP51</i> ) in <i>Penicillium digitatum</i> (2000)

We investigated the mechanism of resistance to demethylation inhibitors (DMI) in Penicillium digitatum by isolating the CYP51 gene, which encodes the target enzyme (P450(14DM)) of DMI, from three DMI-resistant and three DMI-sensitive strains. The structural genes of all six strains were identical, but in the promoter region, a unique 126-bp sequence was tandemly repeated five times in the DMI-resistant strains and was present only once in the DMI-sensitive strains. Constitutive expression of CYP51 in the resistant strains was about 100-fold higher than that in the sensitive strains. We introduced CYP51, including the promoter region, from a DMI-resistant strain into a DMI-sensitive strain, which rendered the transformants DMI resistant and increased CYP51 expression. We also found that if the number of copies of the repeat was reduced to two, resistance and CYP51 expression also decreased. These results indicate that the 126-bp unit acts as a transcriptional enhancer and that a tandem repeat of the unit enhances CYP51 expression, resulting in DMI resistance. This is a new fungicide resistance mechanism for filamentous fungi.
Nonlinear Optical Properties of Core-Shell Nanocavities for Enhanced Second-Harmonic Generation (2010)

A nonlinear optical plasmonic core-shell nanocavity is demonstrated as an efficient, subwavelength coherent light source through second-harmonic generation. The nonlinear optical plasmonic nanocavity incorporates a noncentrosymmetric medium, which utilizes the entire mode volume for even-order nonlinear optical processes. In previous plasmonic nanocavities, enhancement of such processes was only possible at the interface but symmetry prohibited in the body. We measured an enhancement of over 500 times in the second-harmonic radiation power. Calculations show that an enhancement of over 3500 times is achievable.
Phase qubits fabricated with trilayer junctions (2011)

We have developed a novel Josephson junction geometry with minimal volume of lossy isolation dielectric, suitable for higher quality trilayer junctions implemented in qubits. The junctions are based on in situ deposited trilayers with thermal tunnel oxide, have micron-sized areas and a low subgap current. In qubit spectroscopy only a few avoided level crossings are observed, and the measured relaxation time of T1≈400 ns is in good agreement with the usual phase qubit decay time, indicating low loss due to the additional isolation dielectric.
Trading Functionality for Power within Applications (2015)

When operating systems and hardware manage power and energy, they must be conservative in order to deliver re-quested resources while maintaining an expected rate of system throughput. Application-level energy management is more flexible, because applications can choose to request fewer resources or expect less performance, effectively trad-ing accuracy or runtime for power. We propose to leverage this flexibility with energy exchanges, a C++ library exten-sion that allows software to dynamically react to measured power and energy use by reducing functionality. 1. Background and Problem Given energy’s status as a precious commodity, many have ideas about how to police its use. Solutions for power and energy management abound, from hardware to the operat-
One-pot bio-synthesis: N-acetyl-d-neuraminic acid production by a powerful engineered whole-cell catalyst (2011)

Whole cell biocatalysis is an important tool for pharmaceutical intermediates synthesis, although it is hindered by some shortcomings, such as high cost and toxicity of inducer, mass transfer resistance caused by cell membrane and side reactions. Whole-cell catalysis using N-acetyl-d-glucosamine 2-epimerase (EC 5.1.3.8) and N-acetyl-d-neuraminic acid (Neu5Ac) aldolase (EC 4.1.3.3) is a promising approach for the production of Neu5Ac, a potential precursor of many anti-viral drugs. A powerful catalyst was developed by packaging the enzymes in an engineered bacterium and using a safe temperature-induced vector. Since the mass transfer resistance and the side reactions were substantially reduced, a high Neu5Ac amount (191 mM) was achieved. An efficient method was also presented, which allows one-pot synthesis of Neu5Ac with a safe and economic manner. The results highlight the promise of large-scale Neu5Ac synthesis and point at a potential of our approach as a general strategy to improve whole-cell biocatalysis.
Pharmacological profile of TP‐680, a new cholecystokinin<sub>A</sub> receptor antagonist (1996)

1. The pharmacological characteristics of a newly developed serine derivative (R)-1-[3-(3-carboxypyridine-2-yl) thio-2-(indol-2-yl)carbonylamino]propionyl-4-diphenylmethyl- piperazine (TP-680), a cholecystokinin type A (CCKA) receptor antagonist, were studied and compared with those of MK-329 and loxiglumide. 2. TP-680 showed approximately 2 and 22 times greater selectivity for peripheral CCKA receptors relative to brain CCK (CCKB) receptors than MK-329 and loxiglumide, respectively, when IC50 values for inhibition of [125I]-CCK-8 binding in isolated acini and cerebral cortex were compared. 3. TP-680 was approximately 17 times less potent than MK-329, but was 106 times more potent than loxiglumide in inhibiting 100 pM CCK-8-stimulated amylase release from rat pancreatic acini. The antagonism produced by TP-680 was specific for CCK in that the effects of other receptor secretagogues or agents bypassing receptors were not altered. 4. TP-680 caused a parallel rightward shift of the dose-response curve for CCK-8-stimulated amylase release as did MK-329 and loxiglumide. However, in contrast to MK-329 and loxiglumide, TP-680 suppressed the maximal responses of CCK-8-induced amylase release in a concentration-dependent fashion, indicating that TP-680 is an unsurmountable antagonist. 5. Repeated washing of acini after a 30 min treatment with TP-680 restored the responsiveness but not the sensitivity, causing a residual inhibition on the action of CCK-8. 6. The addition of loxiglumide prior to or together with application of TP-680 protected CCK receptors from unsurmountable and irreversible antagonism by TP-680. 7. Our results indicate that TP-680 is a potent and the most selective CCKA receptor antagonist for the pancreas reported to date.
Optimization of the window function for digital hologram apodization in reconstructing the holographic image (2013)

In this paper, an optimal window function used for digital hologram apodization in reconstructing the holographic image is presented, which is generated by a cosine window convolving with a rectangle window and has a flat top because of the rectangle shape of the hologram. The window?s parameters are optimized using a genetic algorithm to make sure that the sidelobes of the window are minimum. Numerical simulation results show that the new window has a sidelobe lower than that of the Tukey window, and experimental results show that apodization using this window can suppress the diffraction effectively in reconstructing the holographic image.
Alkynylboronates and ‐boramides in Co<sup>I</sup>‐ and Rh<sup>I</sup>‐Catalyzed [2+2+2] Cycloadditions: Construction of Oligoaryls through Selective Suzuki Couplings (Eur. J. Org. Chem. 18/2011) (2011)

Abstract The cover picture shows the stepwise construction of oligoaryls, which is illustrated by three construction steps of the main tower of our University. Compounds bearing different borylated groups were constructed by Co‐ or Rh‐catalyzed [2+2+2] cycloaddition and were subjected to site‐selective Suzuki cross‐couplings. Details are discused in the article by C. Aubert, V. Gandon et al. on p. 3283 ff.
Complete nucleotide sequence of a milk-transmitted mouse mammary tumor virus: two frameshift suppression events are required for translation of gag and pol (1987)

We sequenced two recombinant DNA clones constituting a single provirus of the milk-transmitted mouse mammary tumor virus characteristic of BR6 mice. The complete provirus is 9,901 base pairs long, flanked by 6 base-pair duplications of cellular DNA at the site of integration. Five extensive blocks of open reading frame corresponding to the gag gene, the presumed protease, the pol and env genes, and the open reading frame orf within the long terminal repeat of the provirus were readily discernible. Translation of gag, protease, and pol involved three different translational reading frames to produce the three overlapping polyprotein precursors Pr77, Pr110, and Pr160 found in virus-infected cells. Synthesis of the reverse transcriptase and endonuclease therefore required two separate frameshifts to suppress the termination codons at the ends of the Pr77 and Pr110 domains. Direct evidence is presented for translational readthrough of both stop codons in an in vitro protein synthesis system.
Effect of mixed grain sizes on thermoelectric performance of Bi2Te3 compound (2009)

Coarse (about 1 μm) and fine (about 100 nm) Bi2Te3 particles were synthesized by mechanical alloying for different times, respectively. Their mixtures at different ratios were consolidated by spark plasma sintering to produce nano-/microstructured composites with the same chemical compositions. The Seebeck coefficient was significantly enhanced by addition of fine particles through the potential barrier scattering. The electrical resistivity increased rapidly when the weight fraction of fine particles exceeded about 60%, probably due to an effect similar to percolation phenomenon. However, the thermal conductivity was reduced almost linearly with increasing fraction of fine particles. Because of the combined effects of the potential barrier scattering, nonlinear change in electrical property and linear change in thermal transport property, a peak value of dimensionless figure of merit (ZT) was achieved for the sample containing 60% fine particles. This study demonstrated the possibility to enhance ZT value by introducing nonuniform microstructures even without changing chemical compositions.
Investigation of bax‐induced release of cytochrome <i>c</i> from yeast mitochondria (1999)

Recent studies that attempt to explore the action of pro- and anti-apoptotic proteins of the bcl2 family demonstrate the crucial role of relocalization of cytochrome c from the mitochondrial intermembrane space to the cytosol. This early event of apoptosis can be mimicked in the yeast Saccharomyces cerevisiae following expression of bax. In mammalian mitochondria, the mechanism of relocalization is thought to involve the opening of the so-called permeability transition pore. We show in this paper: (a) that bax-induced release of cytochrome c in yeast does not involve any permeability transition of the inner mitochondrial membrane but involves a general alteration of the permeability of the outer mitochondrial membrane to macromolecules. This suggests that a permeability transition of the inner mitochondrial membrane is not an event required for the relocalization of cytochrome c in yeast. (b) The outer-membrane voltage-dependent anion channel (VDAC), a putative component of the permeability transition pore, is not involved in bax-induced release of cytochrome c or in the prevention of this release by bcl-xL. (c) Bax devoid of its C-terminal putative hydrophobic alpha-helix is as efficient as full-length bax to allow the relocalization of cytochrome c, demonstrating this segment of the protein is not required for membrane-targeting. (d) We finally observe that the action of bax on the outer mitochondrial membrane requires the presence of ATP both in vitro and in vivo, and it is shown that ATP directly increases the amount of bax inserted to mitochondria.
Interleukin-6 Is Essential for Primary Resistance to Francisella tularensis Live Vaccine Strain Infection (2012)

We employed Francisella tularensis live vaccine strain (LVS) to study mechanisms of protective immunity against intracellular pathogens and, specifically, to understand protective correlates. One potential molecular correlate identified previously was interleukin-6 (IL-6), a cytokine with pleotropic roles in immunity, including influences on T and B cell functions. Given its role as an immune modulator and the correlation with successful anti-LVS vaccination, we examined the role IL-6 plays in the host response to LVS. IL-6-deficient (IL-6 knockout [KO]) mice infected with LVS intradermally or intranasally or anti-IL-6-treated mice, showed greatly reduced 50% lethal doses compared to wild-type (WT) mice. Increased susceptibility was not due to altered splenic immune cell populations during infection or decreased serum antibody production, as IL-6 KO mice had similar compositions of each compared to WT mice. Although LVS-infected IL-6 KO mice produced much less serum amyloid A and haptoglobin (two acute-phase proteins) than WT mice, there were no other obvious pathophysiological differences between LVS-infected WT and IL-6 KO mice. IL-6 KO or WT mice that survived primary LVS infection also survived a high-dose LVS secondary challenge. Using an in vitro overlay assay that measured T cell activation, cytokine production, and abilities of primed splenocytes to control intracellular LVS growth, we found that IL-6 KO total splenocytes or purified T cells were slightly defective in controlling intracellular LVS growth but were equivalent in cytokine production. Taken together, IL-6 is an integral part of a successful immune response to primary LVS infection, but its exact role in precipitating adaptive immunity remains elusive.
Design of a feedback-feedforward steering controller for accurate path tracking and stability at the limits of handling (2015)

This paper presents a feedback-feedforward steering controller that simultaneously maintains vehicle stability at the limits of handling while minimising lateral path tracking deviation. The design begins by considering the performance of a baseline controller with a lookahead feedback scheme and a feedforward algorithm based on a nonlinear vehicle handling diagram. While this initial design exhibits desirable stability properties at the limits of handling, the steady-state path deviation increases significantly at highway speeds. Results from both linear and nonlinear analyses indicate that lateral path tracking deviations are minimised when vehicle sideslip is held tangent to the desired path at all times. Analytical results show that directly incorporating this sideslip tangency condition into the steering feedback dramatically improves lateral path tracking, but at the expense of poor closed-loop stability margins. However, incorporating the desired sideslip behaviour into the feedforward loop creates a robust steering controller capable of accurate path tracking and oversteer correction at the physical limits of tyre friction. Experimental data collected from an Audi TTS test vehicle driving at the handling limits on a full length race circuit demonstrates the improved performance of the final controller design.
Driver identification and driver's emotion verification using KDE and MLP neural networks (2010)

A Driver's behavior is a major factor that contributes to the high accidents rates. However, if we are able to identify their behavior, it may be possible for us to detect driving idiosyncrasies that may prevent accidents. Therefore, this paper presents some simple and effective methods for an in-car data acquisition in collecting real time driving data. The data has been classified into three different driver's condition which leads into accident. They are happy expression, talking on the phone and normal driving. These data will be used to investigate the effectiveness of a driver's behavior which focusing on the driver's response towards the brake and gas pedals as well as its rate of change. From these data we will demonstrate simple yet effective technique in driver identification and driver verification. We use the kernel density estimation (KDE) as tools to extract features. Then, we use these features to recognize the emotion of the driver by using multi layer perceptron (MLP) as classifiers. The enhancement of driver's security, safety and comfort driving can be derived trough the performances of the driver's emotion verification which contribute to the development in the area of intelligent vehicle driver verification system.
S-Nitroso-N-Acetylcysteine (SNAC) Prevents Myocardial Alterations in Hypercholesterolemic LDL Receptor Knockout Mice by Antiinflammatory Action (2008)

We investigated the ability of S-nitroso-N-acetylcyseine (SNAC) to prevent structural and functional myocardial alterations in hypercholesterolemic mice. C57BL6 wild-type (WT) and LDL-R-/- male mice (S) were fed a standard diet for 15 days. LDL-R-/- mice (S) showed an 11% increase in blood pressure, 62% decrease in left atrial contractility, and lower CD40L and eNOS expression relative to WT. LDL-R-/- mice fed an atherogenic diet for 15 days (Chol) showed significant increased left ventricular mass compared to S, which was characterized by: (1) 1.25-fold increase in the LV weight/body weight ratio and cardiomyocyte diameter; (2) enhanced expression of the NOS isoforms, CD40L, and collagen amount; and (3) no alteration in the atrial contractile performance. Administration of SNAC to Chol mice (Chol + SNAC) (0.51 micromol/kg/day for 15 day, IP) prevented increased left ventricular mass, collagen deposit, NOS isoforms, and CD40L overexpression, but it had no effect on the increased blood pressure or atrial basal hypocontractility. Deletion of the LDL receptor gene in mice resulted in hypertension and a marked left atrial contractile deficit, which may be related to eNOS underexpression. Our data show that SNAC treatment has an antiinflammatory action that might contribute to prevention of structural and functional myocardial alterations in atherosclerotic mice independently of changes in blood pressure.
Induction of Aggressive Breast Cancer in p53 Wild Type Cells by BRCA1-IRIS Overexpression. (2009)

Abstract Background: Agents that introduce genotoxic stresses in mammalian cells, such as paclitaxel (Taxol) or ionizing radiation activate a complex array of cellular responses, including p53 activation. As a component of the response to acute stress, p53 has a well-established role in protecting against cancer development. It is not surprising that half of all human tumors have mutated p53. We asked how then tumors are initiated in the cells that carry wild-type p53 allele?Material and Methods: Here we report the identification of a potential novel mechanism that induces tumor formation in p53 wild-type cells. Overexpression of the proto-oncogene, BRCA1-IRIS in human mammary epithelial (HME) cells not only upregulates the expression of the serine/threonine phosphatase; Wild-type p53-Induced Phosphatase (WIP1) through induction of p53 expression but also increases the WIP1 gene copy number in these cells. WIP1 is a negative regulator of p53 as well as p38MAPK. Both proteins are involved in arresting and/or killing cells with extensive genotoxic stresses. Failure to arrest or die in response to massive genotoxic stress leads to the propagation of damaged cells and the development of cancer. BRCA1-IRIS overexpressing cells failed to arrest or die when exposed to UV radiation or Taxol. In fact, treatment of normal HME cells with UV or Taxol upregulated the expression of BRCA1-IRIS and thus WIP-1, prevented p53 and p38MAPK activation and their death.Results: This data suggest that BRCA1-IRIS is perhaps involved in the acquisition of cellular resistance to these agents upon prolonged exposure. On the other hand, depletion of BRCA1-IRIS from tumor cell lines induced apoptosis even in cells with functional p53 and p38MAPK.Discussion: We propose that in p53 wild type cells, whether endogenous or UV- or chemotherapy-induced BRCA1-IRIS overexpression leads to the survival and proliferation of what most likely are severely damaged cells, leading to the transformation of mammary cells in vitro and the induction of breast tumors in vivo. We also propose that BRCA1-IRIS and WIP1 overexpression abrogates the homeostatic balance maintained by p38-p53-WIP1 pathway. Together with the ability of BRCA1-IRIS to upregulate Cyclin D1 expression increases the likelihood that BRCA1-IRIS is an oncogene that induces breast cancer progression when overexpressed, hence making it an attractive target for novel breast cancer therapy. Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 3154.
Generating EDI message translations from visual specifications (2005)

Electronic data interchange (EDI) systems are used in many domains to support inter-organisational information exchange. To get systems using different EDI message formats to communicate, complex message translations (where data must be transformed from one EDI message format into another), are required. We describe a visual language and support environment which greatly simplify the task of the systems integrator by using a domain-specific visual language to express data formats and format translations. Complex message translations are automated by an underlying transformation engine. We describe the motivation for this system, its key visual language and transformation engine features, a prototype environment, and experience translating it into a commercial product.