gebhart/patrepeval huggingface dataset:
Comprehensive analysis of gene expression in <i>Nicotiana tabacum</i> leaves acclimated to oxidative stress (2002)

The molecular mechanisms by which plants acclimate to oxidative stress are poorly understood. To identify the processes involved in acclimation, we performed a comprehensive analysis of gene expression in Nicotiana tabacum leaves acclimated to oxidative stress. Combining mRNA differential display and cDNA array analysis, we estimated that at least 95 genes alter their expression in tobacco leaves acclimated to oxidative stress, of which 83% are induced and 17% repressed. Sequence analysis of 53 sequence tags revealed that, in addition to antioxidant genes, genes implicated in abiotic and biotic stress defenses, cellular protection and detoxification, energy and carbohydrate metabolism, de novo protein synthesis, and signal transduction showed altered expression. Expression of most of the genes was enhanced, except for genes associated with photosynthesis and light-regulated processes that were repressed. During acclimation, two distinct groups of coregulated genes ("early-" and "late-response" gene regulons) were observed, indicating the presence of at least two different gene induction pathways. These two gene regulons also showed differential expression patterns on an oxidative stress challenge. Expression of "late-response" genes was augmented in the acclimated leaf tissues, whereas expression of "early-response" genes was not. Together, our data suggest that acclimation to oxidative stress is a highly complex process associated with broad gene expression adjustments. Moreover, our data indicate that in addition to defense gene induction, sensitization of plants for potentiated gene expression might be an important factor in oxidative stress acclimation.
DEVELOPING MALAYSIAN LRT (1998)

This article describes the comprehensive programme of reconstruction of the public transport infrastructure in Kuala Lumpur, Malaysia. It includes a route map of Phases I and II of the light rail transit system (LRT). Phase I was opened in 1996, and Phase II is rapidly approaching completion. The northern part of Phase II consists entirely of elevated viaduct; the 11.8km long southern section is built partly at grade and also on four main viaducts and several major one- or two-span bridges. Phase II will also include eleven additional stations. From north to south, the main Phase II viaducts are the 3.1km long northern extension, the 0.26km long bifurcation viaduct over the Phase I line, the 0.46km and 0.34km long Mulia viaducts, the 1.23km long Seremban viaducts, and the 0.7km long Bukit Jalil viaduct. The viaducts are all made from precast concrete segments. The main influence on the superstructure design was the existence of a vocabulary of standard segment lengths, and a self-propelled launching gantry for the balanced cantilever erection method, both inherited from Phase I; as a result, the span lengths ranged from 22m to 51m. The article also describes the substructure design, construction methods and difficulties, the approvals process, the construction of the stations, and hydraulics aspects.
Recent Advances in the Discovery and Development of Direct Coagulation Factor Xa Inhibitors (2003)

Coronary heart disease (CHD) is the leading cause of mortality and morbidity in the United States. Currently, there are approximately 12 million Americans with CHD, which is most frequently caused by atherosclerosis. The thrombotic complications of atherosclerosis, such as acute coronary syndrome and ischemic stroke, can be fatal and those who survive such events have a far greater risk of future cardiovascular events. This huge medical need cries out for improved novel anticoagulants, antiplatelet agents, and profibrinolytic agents. These agents will successfully respond to the medical need by providing safe, effective, and easily administered treatments that have little, if any, drug and food interactions and that require minimal monitoring. The currently approved antiplatelet agent, clopidogrel, has satisfied some of these requirements and has played a large role in expanding the antithrombotic market over the past few years. New antithrombotics approaching the marketplace, such as the prodrug thrombin inhibitor ximelagatran, have promise in expanding the antithrombotic market further. Over the past two decades, the pharmaceutical industry has mounted a huge effort to develop antithrombotics that function by inhibiting key enzymes positioned at "higher" levels of the coagulation system. Direct inhibitors of factor Xa, which may provide a better safety and efficacy profile than currently available agents, appear to be the next major class of antithrombotic agents poised to take the pharmaceutical industry one step closer to delivering the ideal antithrombotic agent. This review focuses on recent innovations in the discovery and development of potent parenteral and oral direct factor Xa inhibitors.
The C-17 multifunction display, a building block for avionic systems (2003)

The C-17 multifunction display (MFD) has been developed for use as the primary cockpit display system on the US Air Force C-17A military air transport. The 6-inch by 6-inch color cathode ray tube (CRT) display features a self-contained 1750 processor and vector generator (VG) capable of processing MIL-STD-1553B aircraft data and raster video into any of 10 formats as selected by the pilot or copilot. The MFD can display stroke, raster, or hybrid formats in 16 colors. Raster images are driven by sensor inputs with an RS-170 or RS-343 interface. The CRT uses a taut mask delta gun design and provides the best available brightness and line-width performance. Due to its self-contained nature and multiformat capability, reconfigurability in the aircraft is enhanced by using four identical cockpit displays. It is pointed out that its small size, low weight, low power, standard interface, and adaptable software make the C-17 MFD an attractive choice for future avionic upgrades.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
There must be a prokaryote somewhere: microbiology's search for itself (1994)

While early microbiologists showed considerable interest in the problem of the natural (evolutionary) relationships among prokaryotes, by the middle of this century that problem had largely been discarded as being unsolvable. In other words, the science of microbiology developed without an evolutionary framework, the lack of which kept it a weak discipline, defined largely by external forces. Modern technology has allowed microbiology finally to develop the needed evolutionary framework, and with this comes a sense of coherence, a sense of identity. Not only is this development radically changing microbiology itself, but also it will change microbiology's relationship to the other biological disciplines. Microbiology of the future will become the primary biological science, the base upon which our future understanding of the living world rests, and the font from which new understanding of it flows.
VIII: Meta-Analysis of the Efficacy of Vitamin D Treatment in Preventing Osteoporosis in Postmenopausal Women (2002)

Vitamin D decreases vertebral fractures and may decrease nonvertebral fractures. The available data are uninformative regarding the relative effects of standard and hydroxylated vitamin D.
Purification of the Trehalase GMTRE1 from Soybean Nodules and Cloning of Its cDNA. <i>GMTRE1</i> Is Expressed at a Low Level in Multiple Tissues1 (1999)

Trehalose (alpha-D-glucopyranosyl-1,1-alpha-D-glucopyranoside), a disaccharide widespread among microbes and lower invertebrates, is generally believed to be nonexistent in higher plants. However, the recent discovery of Arabidopsis genes whose products are involved in trehalose synthesis has renewed interest in the possibility of a function of trehalose in higher plants. We previously showed that trehalase, the enzyme that degrades trehalose, is present in nodules of soybean (Glycine max [L.] Merr.), and we characterized the enzyme as an apoplastic glycoprotein. Here we describe the purification of this trehalase to homogeneity and the cloning of a full-length cDNA encoding this enzyme, named GMTRE1 (G. max trehalase 1). The amino acid sequence derived from the open reading frame of GMTRE1 shows strong homology to known trehalases from bacteria, fungi, and animals. GMTRE1 is a single-copy gene and is expressed at a low but constant level in many tissues.
Selective laser ablation of SiN<sub><i>x</i></sub> layers on textured surfaces for low temperature front side metallizations (2008)

Abstract For an alternative front side metallization process without screen printing of metal paste the selective opening of the front surface anti‐reflection coating could be realized by laser ablation. A successful implementation of this scheme requires direct absorption of the laser light within the anti‐reflection coating, since the emitter underneath must not be damaged severely. Additionally, the ablation must be feasible on textured surfaces. In this paper, we show that laser light with a wavelength of 355 nm and a pulse length of approximately 30 ns is absorbed directly by a typical silicon nitride anti‐reflection coating. Based on lifetime measurements on ablated samples it is shown that a damage free laser ablation of SiN x layers on planar surfaces is possible. The characteristic ablation structure on textured surfaces is explained and quantified by rigorous coupled wave analysis (RCWA) simulations. Finally, high efficiency solar cells with a standard emitter ( R sh approx. 50 Ω/sq) have been processed using laser ablation of the silicon nitride anti‐reflection coating. These cells show efficiencies of up to 19·1%, comparable to the reference solar cells using photolithographically opened contact areas. Copyright © 2008 John Wiley & Sons, Ltd.
The Estimation Of Magnetotelluric Impedance Tensor Elements From Measured Data (1971)

Abstract Six different estimates of the magnetotelluric impedance tensor elements may be computed from measured data by use of auto-power and cross-power density spectra. We show that each of the estimates satisfies a mean-square error criterion. Two of the six estimates are relatively unstable in the one-dimensional case when the incident fields are unpolarized. For the remaining four estimates, it is shown that two are unaffected by random noise on the H signal, but are biased upward by random noise on the E signal. The remaining two estimates are unaffected by random noise on the E signal, but are biased downward by random noise on the H signal. Computation of all of the estimates provides a measure of the total amount of noise present, as indicated by a stability coefficient for the estimates. In the absence of additional information as to the relative signal-to-noise ratios of the E and H signals, we suggest that a mean estimate be used. A numerical example is included.
Synthetic small interfering RNA targeting heat shock protein 105 induces apoptosis of various cancer cells both <i>in vitro</i> and <i>in vivo</i> (2006)

We previously reported that heat shock protein 105 (HSP105), identified by serological analysis of a recombinant cDNA expression library (SEREX) using serum from a pancreatic cancer patient, was overexpressed in various human tumors and in the testis of adult men by immunohistochemical analysis. In the present study, to elucidate the biological function of the HSP105 protein in cancer cells, we first established NIH3T3 cells overexpressing murine HSP105 (NIH3T3-HSP105). The NIH3T3-HSP105 cells acquired resistance to apoptosis induced by heat shock or doxorubicin. The small interfering RNA (siRNA)-mediated suppression of HSP105 protein expression induced apoptosis in human cancer cells but not in fibroblasts. By a combination of siRNA introduction and doxorubicin or heat shock treatment, apoptosis was induced synergistically in a human colon cancer cell line, HCT116. In vivo, siRNA inoculation into the human gastric cancer cell line KATO-3 established in the flank of an NOD SCID mouse suppressed the tumor growth. This siRNA-induced apoptosis was mediated through caspases, but not the p53 tumor suppressor protein, even though the HSP105 protein was bound to wild-type p53 protein in HCT116 cells. These findings suggest that the constitutive overexpression of HSP105 in cancer cells is involved in malignant transformation by protecting tumor cells from apoptosis. HSP105 may thus be a novel target molecule for cancer therapy and a treatment regimen using synthetic siRNA to suppress the expression of HSP105 protein may provide a new strategy for cancer therapy.
Perfect Thermal Emission by Nanoscale Transmission Line Resonators (2017)

Thermal radiation with a narrow-band emission spectrum is of great importance in a variety of applications such as infrared sensing, thermophotovoltaics, radiation cooling, and thermal circuits. Although resonant nanophotonic structures such as metamaterials and nanocavities have been demonstrated to achieve the narrow-band thermal emission, maximizing their radiation power toward perfect emission still remains challenging. Here, based on the recently developed quasi-normal mode theory, we prove that thermal emission from a nanoscale transmission line resonator can always be maximized by tuning the waveguiding loss of the resonator or bending the structure. By use of nanoscale transmission line resonators as basic building blocks, we experimentally demonstrate a new type of macroscopic perfect and tunable thermal emitters. Our experimental demonstration in conjunction with the general theoretical framework from the quasi-normal mode theory lays the foundation for designing tunable narrow-band thermal emitters with applications in thermal infrared light sources, thermal management, and infrared sensing and imaging.
NUMBERS: A collection of utilities for pre- and postprocessing two- and three-dimensional EXODUS finite element models (1989)

Numbers is a shell program which reads and stores data from a finite element model described in the EXODUS database format. Within this shell program are several utility routines which generate information about the finite element model. The utilities currently implemented in Numbers allows the analyst to determine information such as the volume and coordinate limits of each of the materials in the model; the mass properties of the model; the minimum, maximum, and average element volumes for each material; the volume and change in volume of a cavity; the nodes or elements that are within a specified distance from a user-defined point, line, or plane; an estimate of the explicit central-difference timestep for each material; the validity of contact surfaces or slidelines, that is, whether two surfaces overlap at any point; and, the distance between two surfaces. 10 refs., 11 figs., 1 tab.
Update on Fusidic Acid (CEM-102) Tested against <i>Neisseria gonorrhoeae</i> and <i>Chlamydia trachomatis</i> (2010)

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A new modified cytosine base capable of base pairing with guanine using four hydrogen bonds (2014)

Oligonucleotides, containing 4-N-(1H-pyrrol-2-ylcarbonyl)deoxycytidine (dC(Pyc)) and related derivatives, were synthesized via deprotection using 1.5 M NaOMe/MeOH. Among them, oligodeoxynucleotides containing dC(Pyc) exhibited a higher hybridization affinity for DNA and RNA than the unmodified oligodeoxynucleotides. Comparative analysis between dC(Pyc) and its derivatives by molecular dynamic simulation indicated that the C(Pyc) residue could form four hydrogen bonds with the opposite G nucleobase keeping a more planar structure than the C(Inc) residue where the Pyc group was replaced with a 1H-indol-2-ylcarbonyl group.
<title>Grating line shape characterization using scatterometry</title> (1991)

Identification of dimensional parameters of an arbitrarily shaped grating using scatter characteristics is presented. A rigorous diffraction model is used to predict the scatter from a known grating structure, and utilizing this information we perform the inverse problem of predicting line shape from a measurement of the scatter.
Low Glass Transition Temperature (<i>T</i><sub>g</sub>) Rubber Latex Film Formation Studied by Atomic Force Microscopy (2000)

Latex with very low glass transition temperature (Tg) polymers forms a continuous film on drying. The physical and mechanical properties of the film are dependent on the extent the latex particles are able to coalesce and fuse into each other. Any hindrance to the film formation process would result in a poorly formed film and a drop in performance. The film formation process of natural rubber (Tg ∼ −65 °C) latexes and synthetic latexes with low Tg are monitored as a function of time using atomic force microscopy (AFM). The influence of the leaching method of the film, the presence of additives (some added after preparation) and nonrubber materials [specific for natural rubber (NR) latex only], and gel content on film morphology and flattening of the particles in the film is studied. The influence of the leaching procedure on the effectiveness of nonrubber removal from NR latex films and their effect on film formation is highlighted. The effects of nonrubbers and high gel content of NR latex in slowing down the NR film formation is discussed and contrasted with the synthetic polyisoprene and chloroprene latexes. The change of the surface mean roughness, Ra, with time provides a convenient means of comparing the rate of flattening of the polydisperse particles in these films.
Model-Driven Engineering of Composite Service Oriented Applications (2011)

Composite applications integrate web services with other business applications and components to implement business processes. Model-driven approaches tackle the complexity of composite applications caused by domain and technology heterogeneity and integration requirements. The method and framework described in this paper generate all artefacts (workflow, data, user interfaces, etc.), required for a composite application from high level service oriented descriptions of the composite application, using model transformation and code generation techniques.
The relationship between a polymorphism in CYP17 with plasma hormone levels and prostate cancer. (2001)

The A2 allele of the CYP17 gene has been thought to be associated with increased functional activity of this steroidogenic enzyme. Consequently, the A2 allele has been examined as a biomarker of individual susceptibility to hormone-related diseases among men and women. We prospectively assessed the association between the A2 allele of CYP17 and prostate cancer risk among 590 cases and 782 controls in a case-control study nested within the Physicians' Health Study cohort. We also evaluated associations between CYP17 genotype and plasma steroid hormones among controls and the potential interaction between CYP17 and SRD5A2 V89L polymorphisms in relationship with prostate cancer risk and circulating steroid hormone levels. We observed a borderline significant association between the A2 allele and prostate cancer risk (odds ratio, 1.23; 95% confidence interval, 0.99-1.54), however, we did not observe evidence of a gene-dosage effect (versus A1/A1 genotype: A1/A2 genotype; odds ratio, 1.26; 95% confidence interval, 0.99-1.59; A2/A2 genotype: odds ratio, 1.17; 95% confidence interval, 0.85-1.61). The A2 allele was not overrepresented among cases with advanced prostate cancer. Among controls, carriers of the A2 allele had steroid hormone levels similar to noncarriers. We also found no evidence of a gene-gene interaction between CYP17 and SRD5A2 V89L polymorphisms on prostate cancer risk or endogenous steroid hormone levels. These results suggest that CYP17 genotype may possibly confer a small increased susceptibility to prostate cancer but is not a strong predictor of endogenous steroid hormone levels in men.
Drilling with force feedback (2009)

Industrial robots have been used for a long time in the industry. Despite this thedevelopment of advanced force control system using industrial robots is relativelylimited. Using force controlled robot systems expands the possibility of what canbe done with industrial robots.Previously a force feedback system for a standard industrial robot from ABBhas been developed. The system is developed towards the aircraft industry, where amounted drill machine on the robot has to fulfill the requirements in robot drillingin aircraft structures. This thesis presents experimental results and improvementsof this industrial robot system. Mechanical modifications and tests of a new endeffector are analyzed.
The Fanconi anemia protein, FANCE, promotes the nuclear accumulation of FANCC (2002)

Fanconi anemia is an autosomal recessive disorder characterized by aplastic anemia, cancer susceptibility, and cellular sensitivity to mitomycin C. The 6 known Fanconi anemia gene products (FANCA, FANCC, FANCD2, FANCE, FANCF, and FANCG proteins) interact in a common pathway. The monoubiquitination and nuclear foci formation of FANCD2 are essential for the function of this pathway. FANCA, FANCC, FANCG, and FANCF proteins form a multisubunit nuclear complex (FA complex) required for FANCD2 monoubiquitination. Because FANCE and FANCC interact in vitro and FANCE is required for FANCD2 monoubiquitination, we reasoned that FANCE is a component of the FA complex in vivo. Here we demonstrate that retroviral transduction of Fanconi anemia subtype E (FA-E) cells with the FANCE cDNA restores the nuclear accumulation of FANCC protein, FANCA-FANCC complex formation, monoubiquitination and nuclear foci formation of FANCD2, and mitomycin C resistance. Hemagglutinin (HA)-tagged FANCE protein localizes diffusely in the nucleus. In normal cells, HA-tagged FANCE protein coimmunoprecipitates with FANCA, FANCC, and FANCG but not with FANCD2. Our data indicate that FANCE is a component of the nuclear FA complex in vivo and is required for the monoubiquitination of FANCD2 and the downstream events in the FA pathway.
A New Method of Photothermal Displacement Measurement by Laser Interferometric Probe -Its Mechanism and Applications to Evaluation of Lattice Damage in Semiconductors (1992)

A new, highly sensitive technique for measuring photothermal displacement using a laser heterodyne interferometric probe has been developed. This technique is based on the detection of phase changes in the probe beam and is very sensitive to the presence of lattice damage in semiconductors. It has been found that the phase change is caused by the thermal expansion of a sample surface induced by absorption of a modulated pump beam. The displacements of metals and semiconductors measured by this technique coincided with the results predicted by a thermal diffusion model. These displacements simply depended upon the ratio of the thermal expansion coefficient to the thermal conductlvity of a sample.
Design issues for interactive television systems (1995)

Computing, communication, and relevant standards are on the brink of enabling thousands of people to enjoy the services offered by large, distributed multimedia systems in their own homes. Collectively, these services will include TV (basic, subscription, and pay-per-view), service navigator, interactive entertainment, digital audio, video-on-demand, home shopping, financial transactions, interactive single- and multiuser games, digital multimedia libraries, and electronic versions of newspapers, magazines, TV program guides, and yellow pages. It is obvious that current TV systems and architectures must be redesigned to support such services. In this article, we propose potential solutions to modify existing systems to support these new functions, and we discuss related matters.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>