gebhart/patrepeval huggingface dataset:
The main auxin biosynthesis pathway in <i>Arabidopsis</i> (2011)

The phytohormone auxin plays critical roles in the regulation of plant growth and development. Indole-3-acetic acid (IAA) has been recognized as the major auxin for more than 70 y. Although several pathways have been proposed, how auxin is synthesized in plants is still unclear. Previous genetic and enzymatic studies demonstrated that both TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS (TAA) and YUCCA (YUC) flavin monooxygenase-like proteins are required for biosynthesis of IAA during plant development, but these enzymes were placed in two independent pathways. In this article, we demonstrate that the TAA family produces indole-3-pyruvic acid (IPA) and the YUC family functions in the conversion of IPA to IAA in Arabidopsis ( Arabidopsis thaliana ) by a quantification method of IPA using liquid chromatography–electrospray ionization–tandem MS. We further show that YUC protein expressed in Escherichia coli directly converts IPA to IAA. Indole-3-acetaldehyde is probably not a precursor of IAA in the IPA pathway. Our results indicate that YUC proteins catalyze a rate-limiting step of the IPA pathway, which is the main IAA biosynthesis pathway in Arabidopsis .
Glycaemic control in type 1 diabetes during real time continuous glucose monitoring compared with self monitoring of blood glucose: meta-analysis of randomised controlled trials using individual patient data (2011)

Continuous glucose monitoring was associated with a significant reduction in HbA(1c) percentage, which was greatest in those with the highest HbA(1c) at baseline and who most frequently used the sensors. Exposure to hypoglycaemia was also reduced during continuous glucose monitoring. The most cost effective or appropriate use of continuous glucose monitoring is likely to be when targeted at people with type 1 diabetes who have continued poor control during intensified insulin therapy and who frequently use continuous glucose monitoring.
Power efficiency oriented optimal design of high density CCP and ICP sources for semiconductor RF plasma processing equipment (2006)

This paper discusses the optimization of radio frequency (RF) power efficiency in the design of low pressure and high density capacitively coupled plasma (CCP) and inductively coupled plasma (ICP) sources for semiconductor RF plasma processing equipment, based on the analysis of the effect of stray capacitance on the RF power efficiency in the plasma reactors. Historically, RF plasma processing chambers have been designed and operated using empirical methods. The electrical analysis in this paper reveals design guidelines for both CCP and ICP sources to maximize RF power efficiency by minimizing the stray capacitance in the hardware layout. It is also shown from the external electrical analysis that at low pressure, the ICP sources are usually more efficient than the CCP sources, which is in agreement with the existing experimental results on high density RF plasma sources though the associated micromechanism in plasma physics has remained to be explored. It is further concluded that the RF frequency for an ICP source should not be too high in order to avoid the deep capacitive operating region where an ICP source is inefficient. Besides, lower frequency bias RF power on the chuck has higher RF power efficiency.
Augmented Reality Simulations on Handheld Computers (2007)

Advancements in handheld computing, particularly its portability, social interactivity, context sensitivity, connectivity, and individuality, open new opportunities for immersive learning environments. This article articulates the pedagogical potential of augmented reality simulations in environmental engineering education by immersing students in the roles of scientists conducting investigations. This design experiment examined if augmented reality simulation games can be used to help students understand science as a social practice, whereby inquiry is a process of balancing and managing resources, combining multiple data sources, and forming and revising hypotheses in situ. We provide 4 case studies of secondary environmental science students participating in the program. Positioning students in virtual investigations made apparent their beliefs about science and confronted simplistic beliefs about the nature of science. Playing the game in “real” space also triggered students' preexisting knowledge, suggesting that a powerful potential of augmented reality simulation games can be in their ability to connect academic content and practices with students' physical, lived worlds. The game structure provided students a narrative to think with, although students differed in their ability to create a coherent narrative of events. We argue that Environmental Detectives is 1 model for helping students understand the socially situated nature of scientific practice.
Overexpression of IRF9 confers resistance to antimicrotubule agents in breast cancer cells. (2001)

IRF9/p48/ISGF3gamma (IRF9) is an IFN regulatory factor that mediates signaling by type I IFNs (IFNalpha and IFNbeta). After single-step selection of breast adenocarcinoma cells in paclitaxel, differential display and single gene analysis demonstrated that transcriptional activation of IRF9 and other IFN-responsive genes, independent of IFN, corresponded with resistance to antimicrotubule agents. Transient overexpression of IRF9 reproduced the drug-resistance phenotype and induced expression of IFN-responsive genes. However, drug resistance was not induced by overexpression of Stat1 or Stat2, or treatment with IFNalpha per se. Using a donor-matched array of cDNA prepared from human tumor and normal tissue from a variety of organs, we observed overexpression of IRF9 in approximately one-half of breast and uterine tumors, which indicated that IRF9 may be important in signaling in these tumor types. These data identify a novel IFN-independent role for IRF9 in the development of resistance to antimicrotubule agents in breast tumor cells and may link downstream mediators of IFN signaling to drug resistance in human cancers.
Inflammation and Stem Cell Transplantation (2007)

Myoblast transplantation has been investigated as a treatment for Duchenne Muscular Dystrophy and injured myocardial tissue. Multiple groups have isolated an early myogenic precursor population, termed muscle-derived stem cells (MDSCs) that have a superior ability to regenerate dystrophin-positive myofibers and improve cardiac function following an ischemic event as compared to more differentiated myoblasts. The initial local environment of these transplantations involves a high degree of inflammation and its associated major component, oxidative stress. Here, we report that a resistance to these stresses is an important factor determining the regenerative capacity of muscle stem cells in skeletal and cardiac muscle. MDSCs have an increased antioxidant capacity that protects them from intracellular oxidative damage while myoblasts have lower levels of survival and delayed differentiation following exposure to oxidative stress. These experiments were conducted using a series of high throughput assays that combine robotic live-cell microscopy with custom image analysis software. Further, when antioxidant levels in MDSCs are lowered to values comparable to myoblasts, the regenerative capacity of MDSCs decreases to levels comparable to myoblasts in both skeletal muscle and cardiac cell therapies. These findings indicate the important role inflammation plays in cell therapies, and identifies an important new mechanism by which stem cells display a unique regenerative capacity and also a new phenotype in selecting cell populations with enhanced regeneration capacity.
Object and scene analysis by saccadic eye-movements: an investigation with higher-order statistics (2000)

Based on an information theoretical approach, we investigate feature selection processes in saccadic object and scene analysis. Saccadic eye movements of human observers are recorded for a variety of natural and artificial test images. These experimental data are used for a statistical evaluation of the fixated image regions. Analysis of second-order statistics indicates that regions with higher spatial variance have a higher probability to be fixated, but no significant differences beyond these variance effects could be found at the level of power spectra. By contrast, an investigation with higher-order statistics, as reflected in the bispectral density, yielded clear structural differences between the image regions selected by saccadic eye movements as opposed to regions selected by a random process. These results indicate that nonredundant, intrinsically two-dimensional image features like curved lines and edges, occlusions, isolated spots, etc. play an important role in the saccadic selection process which must be integrated with top-down knowledge to fully predict object and scene analysis by human observers.
Mortality and Treatment Side-Effects During Long-Term Intensified Conventional Insulin Treatment in the Stockholm Diabetes Intervention Study (1994)

Altogether, 102 patients were randomized to intensified conventional treatment (ICT) (n = 48) or standard treatment (ST) (n = 54). After 7.5 years, 89 patients remained, and it was shown that microangiopathy was retarded by the lower blood glucose concentrations seen in the patients in the ICT group. HbA1c was reduced from (means +/- SE) 9.5 +/- 0.2% to 7.1 +/- 0.1% in the ICT group and from 9.4 +/- 0.2% to 8.5 +/- 0.1% in the ST group (P < 0.001). Of the patients, 4 in the ICT group and 3 in the ST group died. Mortality was predicted by albuminuria, the amplitude of the sural nerve action potential, and the test of arm blood flow during contraction of the contralateral hand (sympathetic nerve function) at baseline (P < 0.05). Weight increased by 4.4 +/- 1.1 kg in the ICT group and 1.8 +/- 0.7 kg in the ST group (P = 0.05). Atherosclerosis, measured with digital pulse plethysmography, was approximately the same in the groups at baseline and after five years. In each group, 3 patients had myocardial infarctions, and 2 from each group had ketoacidosis once. There was a mean of 1.1 episodes per patient and per year of serious hypoglycemia in the ICT group and 0.4 episodes per patient and per year in the ST group. No adverse incidents or accidents were observed in either group, and there were no differences between the groups with regard to cognitive function measured with a battery of tests.(ABSTRACT TRUNCATED AT 250 WORDS)
Research Progress in the Pathogenesis of Alzheimer's Disease (2018)

This review highlights the research advances in the pathogenesis of AD. Future research has needed to fully disclose the association between multiple pathogenesis at the same time to interdict multiple signaling pathways, etc.
Induction of Glucagon Sensitivity in a Transformed Kidney Cell Line by Prostaglandin E<sub>2</sub> and Its Inhibition by Epidermal Growth Factor (1987)

A model system using a transformed dog kidney cell line (Madin-Darby canine kidney), has been established for studying the process of differentiation. Glucagon responsiveness can be restored to these transformed cells by various differentiation inducers, including prostaglandin E2. Glucagon response was measured in terms of the ability of glucagon to stimulate cAMP production. Induction of glucagon sensitivity seems to be mediated by cAMP. The ability of various prostaglandin analogs to elevate the cAMP level correlates closely with their ability to induce glucagon sensitivity. In fact, 8-Br-cAMP is also a potent inducer. To define the nature of this cAMP-mediated process, we identified several inhibitors of this induction process. These differentiation inhibitors include serum, phorbol ester, and epidermal growth factor. These inhibitors do not have a direct effect on cAMP production by cells in the presence or absence of hormones. Furthermore, induction by 8-Br-cAMP is also inhibited by these agents. Therefore, the site of inhibition is located beyond the point of cAMP production. Possible interaction between cAMP- and epidermal growth factor-dependent phosphorylations is discussed.
Shastra: multimedia collaborative design environment (1994)

A distributed environment that supports multimedia interfaces, Shastra strengthens collaboration in scientific and engineering design. Implemented on a desktop system, it provides an infrastructure for user- and application-level cooperation. We describe the Shastra architecture and tools, then walk through a scenario that shows how it enhances collaborative problem solving.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
WINEGLASS-ON-A-CHIP (2012)

This paper introduces free-standing, stem-supported silicon dioxide hemispherical shells (-wineglasses) that are thermallygrown and have high-quality-factor resonances due to unrestricted support stem diameter and low internal thermoelastic damping. The fabrication process offers a direct path to batch fabrication of hemispherical wineglass microstructures with ultra-thin conformal conductive coatings using atomic layer deposition (ALD). A novel assembly method forms capacitive electrodes for rapid electrical characterization of the silicon dioxide -wineglass resonators. A quality factor of 5,600 is measured for the m=4 resonance of a 740 m diameter, 2 m thick thermal oxide shell with 30 nm ALD TiN coating and 77 m diameter silicon support stem.
Metabolism Profiling, and Cytochrome P450 Inhibition & Induction in Drug Discovery (2001)

To reduce the high attrition rates of NCEs in preclinical and clinical development uncovering pharmacokinetics, toxicokinetics, drug metabolism, and drug-drug interactions early in drug discovery would be highly valuable. There have been many in vitro screens developed for these areas that have higher sample throughput, which is consistent with the iterative cycle of a typical drug discovery research project. We have presented the present status and given detailed descriptions of biotransformation, metabolic stability assays, identification of drug metabolizing P450 enzymes, prediction of pharmacokinetic parameters from in vitro metabolism data, structure elucidation of metabolites, CYP450 inhibition assays and CYP450 induction assays from a drug discovery perspective. Strategies for the proper sequencing of primary and secondary assays employedfor drug metabolism and CYP450 inhibition & induction is discussed.
<i>In vivo</i> dynamic light scattering microscopy of tumour blood vessels (2007)

We present a study investigating the use of dynamic light scattering microscopy based on the temporal laser speckle's contrast that is produced over time by red blood cells (RBCs) flowing inside tumour blood vessels. The proposed noninvasive methodology is capable of producing high-resolution images of tumour vasculature. The technique is effective at producing images from tissue at a significant depth, as well as potentially having the ability to monitor tumour perfusion. An advantage of this methodology is that it has improved depth penetration compared with conventional imaging techniques (such as reflected-light microscopy), and one can avoid the use of any fluorescent or artificial chemicals for labeling. This is advantageous since labeling materials can affect imaging and animal welfare with respect to experiments that require continuous and repetitive monitoring.
The <i>bgI1</i> gene encoding extracellular β‐glucosidase from <i>Trichoderma reesei</i> is required for rapid induction of the cellulase complex (1992)

We have used a targeted gene deletion event to remove the coding region for the bgl1 gene encoding an extracellular beta-glucosidase from the genome of the cellulolytic fungus Trichoderma reesei. The bgl1 null mutants were used to investigate the role of beta-glucosidase in the hydrolysis of cellulose and induction of the other cellulolytic enzyme components. In the absence of extracellular beta-glucosidase, growth of bgl1 null strains on several carbon sources was the same as that of the parent (as measured by mycelial dry weight). However, levels of extracellular protein and total endoglucanase production were seen to lag relative to those levels observed in the control strain. The mRNA levels of the CBHI, CBHII, EGI, and EGII cellulase genes (cbh1, cbh2, egl1 and egl3) showed a corresponding lag in induction, suggesting that the absence of extracellular beta-glucosidase has an effect on the co-ordinate regulation of the other cellulase genes at the level of transcription. The addition of a potent inducer of the cellulase complex (sophorose) resulted in normal rates of cellulase gene mRNA production and extracellular protein release. This indicates that the absence of beta-glucosidase is not affecting some intrinsic cellular ability to produce mRNA or secrete protein. These data suggest that a functional beta-glucosidase is at least partially responsible for the efficient induction of the depolymerase enzymes of the cellulase complex. The observation that the cellulase complex is induced, albeit after a lag, suggests that other enzymes are present that can substitute for the function of beta-glucosidase during induction.
Latched domino CMOS logic (1985)

A new gate configuration: the latched domino (Idomino) CMOS gate is described in the letter. It can be used to alleviate the inversion problem inherent in domino CMOS logic. It retains the speed advantages of domino logic while improving logic flexibility and reducing area. The gate is compatible with standard domino logic.
It is time to test low level laser therapy in Great Britain (2005)

Low level laser therapy (LLLT) has been used in Eastern Europe and Asia for the treatment of a wide range of conditions for many years. Its continued acceptance in these populations reflects the efficacy with which it is regarded both by clinicians and their patients. Although there have been a substantial number of reports on its clinical benefit and some practitioners have used the technique in North America and Australasia it has yet to be subjected to detailed assessment through randomised clinical trials. The purpose of this review is to stimulate interest in the technique and to encourage rigorous research into its potential value.
Energy Technology 2016: Carbon Dioxide Management and Other Technologies (2016)

in Environmental Technologies: Recycling and Sustainability Joint Session Symposium.The Energy Technologies Symposium was open to the participants from both industry and academia and focused on energy-efficient technologies, including innovative ore beneficiation, smelting technologies, recycling, and waste heat recovery.This volume also covers various technological aspects of sustainable energy ecosystems, processes that improve energy efficiency, reduce thermal emissions, and reduce carbon dioxide and other greenhouse emissions.Papers addressing renewable energy resources for metals and materials production, waste heat recovery and other industrial energy efficient technologies, new concepts or devices for energy generation and conversion, energy efficiency improvement in process engineering, sustainability and life cycle assessment of energy systems, as well as the thermodynamics and modeling for sustainable metallurgical processes are included.This volume also includes topics on CO 2 sequestration and reduction in greenhouse gas emissions from process engineering, sustainable technologies in extractive metallurgy, as well as the materials processing and manufacturing industries with reduced energy consumption and CO 2 emission.Contributions from all areas of non-nuclear and non-traditional energy sources, such as solar, wind, and biomass, are also included in this volume.We hope this volume will provide a reference for the materials scientists and engineers as well as metallurgists for exploring innovative energy technologies and novel energy materials processing.We would like to acknowledge the contributions from the authors of the papers in this volume, the efforts of the reviewers dedicated to the manuscripts review v process, and the help received from the publisher.We
Formation of palladium(0) nanoparticles at microbial surfaces (2010)

The increasing demand and limited natural resources for industrially important platinum-group metal (PGM) catalysts render the recovery from secondary sources such as industrial waste economically interesting. In the process of palladium (Pd) recovery, microorganisms have revealed a strong potential. Hitherto, bacteria with the property of dissimilatory metal reduction have been in focus, although the biochemical reactions linking enzymatic Pd(II) reduction and Pd(0) deposition have not yet been identified. In this study we investigated Pd(II) reduction with formate as the electron donor in the presence of Gram-negative bacteria with no documented capacity for reducing metals for energy production: Cupriavidus necator, Pseudomonas putida, and Paracoccus denitrificans. Only large and close-packed Pd(0) aggregates were formed in cell-free buffer solutions. Pd(II) reduction in the presence of bacteria resulted in smaller, well-suspended Pd(0) particles that were associated with the cells (called "bioPd(0)" in the following). Nanosize Pd(0) particles (3-30 nm) were only observed in the presence of bacteria, and particles in this size range were located in the periplasmic space. Pd(0) nanoparticles were still deposited on autoclaved cells of C. necator that had no hydrogenase activity, suggesting a hydrogenase-independent formation mechanism. The catalytic properties of Pd(0) and bioPd(0) were determined by the amount of hydrogen released in a reaction with hypophosphite. Generally, bioPd(0) demonstrated a lower level of activity than the Pd(0) control, possibly due to the inaccessibility of the Pd(0) fraction embedded in the cell envelope. Our results demonstrate the suitability of bacterial cells for the recovery of Pd(0), and formation and immobilization of Pd(0) nanoparticles inside the cell envelope. However, procedures to make periplasmic Pd(0) catalytically accessible need to be developed for future nanobiotechnological applications.
Studies on the Pathway of Incorporation of 2-Aminopurine into the Deoxyribonucleic Acid of <i>Escherichia coli</i> (1970)

A pathway for the incorporation of 2-aminopurine into deoxyribonucleic acid (DNA) was studied in cell-free extracts of Escherichia coli. It was demonstrated that the free base can be converted to the deoxynucleoside, and that the deoxynucleotide can be phosphorylated to the di- and triphosphates and then incorporated into the DNA. From a consideration of the individual reactions in crude extracts, it is likely that the rate-limiting step in this pathway is the formation of the deoxynucleotide. Of especial interest is the observation that 2-aminopurine may be viewed as an analogue of either guanine or adenine, depending on which enzymatic step is being considered. On the one hand, it resembles guanine in that it is specifically converted from the mono- to the diphosphate by guanylate kinase and not by adenylate kinase. On the other hand, it replaces adenine rather than guanine in the DNA synthesized with purified DNA polymerases. E. coli DNA polymerase utilizes aminopurine deoxynucleoside triphosphate as a substrate for DNA synthesis much better than does purified phage T5-induced DNA polymerase and is also much less inhibited by this analogue than the T5 enzyme. These experiments in vitro correlate with known differential effects of 2-aminopurine on E. coli and phage in vivo.