gebhart/patrepeval huggingface dataset:
CAD-guided automated nanoassembly using atomic force microscopy-based nonrobotics (2006)

Nanoassembly using atomic force microscopy (AFM) is a promising technique for nanomanufacturing. Most AFM-based nanoassembly schemes are implemented either manually using haptic devices or in an interactive way between the users and the atomic force microscope images. These schemes are time consuming and inefficient. Therefore, the computer-aided design (CAD)-guided automated nanoassembly using AFM is desirable for nanomanufacturing. In this paper, a general framework for CAD-guided automated nanoassembly using AFM is developed. Based on the CAD model of a nanostructure, the manipulation paths for both nanoparticles and nanorods are generated automatically. A local scanning method is developed to compensate for the random drift that may cause the failure of the nanoassembly. The experimental results demonstrate that the developed general framework can be employed to manufacture nanostructures efficiently. The research work opens a door to the CAD-guided automated nanomanufacturing using AFM. Note to Practitioners-Atomic force microscope (AFM)-based nanoassembly will lead to potential breakthroughs in manufacturing new revolutionary industrial products because many potential nanostructures and nanodevices are asymmetric, which cannot be manufactured using self-assembly only. In order to increase the efficiency and accuracy of AFM-based nanoassembly, automated computer-aided-design (CAD)-guided nanoassembly is desirable to manufacture nanostructures and nanodevices. Based on the CAD model, the environment model and the model of the nanoobjects, collision-free paths are generated to control the AFM tip to manipulate nanoobjects. A local scanning method is developed to obtain the actual position of each nanoobject to compensate for the random drift. Since the building materials of nanostructures and nanodevices may include nanoparticles, nanorods, nanowires, nanotubes, etc., automated path planning algorithms are developed for both nanoparticles and nanorods. The experimental results show that the developed general framework can be used to manufacture nanostructures more efficiently.
Biodegradation of Atrazine byAgrobacterium radiobacterJ14a and Use of This Strain in Bioremediation of Contaminated Soil (1998)

We examined the ability of a soil bacterium, Agrobacterium radiobacter J14a, to degrade the herbicide atrazine under a variety of cultural conditions, and we used this bacterium to increase the biodegradation of atrazine in soils from agricultural chemical distribution sites. J14a cells grown in nitrogen-free medium with citrate and sucrose as carbon sources mineralized 94% of 50 microgram of [14C-U-ring]atrazine ml-1 in 72 h with a concurrent increase in the population size from 7.9 x 10(5) to 5.0 x 10(7) cells ml-1. Under these conditions cells mineralized the [ethyl-14C]atrazine and incorporated approximately 30% of the 14C into the J14a biomass. Cells grown in medium without additional carbon and nitrogen sources degraded atrazine, but the cell numbers did not increase. Metabolites produced by J14a during atrazine degradation include hydroxyatrazine, deethylatrazine, and deethyl-hydroxyatrazine. The addition of 10(5) J14a cells g-1 into soil with a low indigenous population of atrazine degraders treated with 50 and 200 microgram of atrazine g-1 soil resulted in two to five times higher mineralization than in the noninoculated soil. Sucrose addition did not result in significantly faster mineralization rates or shorten degradation lag times. However, J14a introduction (10(5) cells g-1) into another soil with a larger indigenous atrazine-mineralizing population reduced the atrazine degradation lag times below those in noninoculated treatments but did not generally increase total atrazine mineralization.
Tyrosine 222, a Member of the YXDD Motif of MuLV RT, Is Catalytically Essential and Is a Major Component of the Fidelity Center (1999)

Tyrosine 222 of MuLV RT is an invariant residue of the highly conserved YXDD motif in the reverse transcriptase class of enzymes. The residue X is Met 184 in HIV-1 RT and Val 223 in MuLV RT. This residue has been implicated in the fidelity of DNA synthesis, whereas the role of the preceding tyrosine in this aspect, as well as in the catalytic mechanism of MuLV RT, remains to be elucidated. We have substituted Tyr 222 with Phe, Ser, and Ala by site-directed mutagenesis and have characterized the properties of the individual mutant enzymes. The results show that Tyr-->Phe substitution did not affect the polymerase activity of the enzyme, while Tyr-->Ser and Tyr-->Ala substitutions significantly reduced the polymerase activity. The pyrophosphorolysis activities of these mutants showed the same trend as the polymerase activities, suggesting an essential role for Y222 in the catalytic mechanism of MuLV RT. One of the most interesting observations of Y-->F substitution was the significantly increased fidelity of DNA synthesis on RNA templates. In addition, a limited extent of ribonucleotide incorporation on RNA template that was consistently noted with the wild-type enzyme was reduced with the Y222F mutant. The resistance to all four ddNTPs, however, persisted in the wild type and Y222 mutants on the RNA template. A ternary complex model of MuLV RT shows that (a) the aromatic ring of Tyr/Phe is positioned between the terminal and penultimate primer bases and (b) the phenolic OH group is seen within hydrogen bonding distance with the base moieties of two template and penultimate primer nucleotides. We propose that the base stacking interaction of Tyr 222 stabilizes the primer terminus position which is essential for the catalytic reaction. However, the weaker stacking interaction of Y compared to F, due to polarization of the pi-charge toward the phenoxyl-OH as well as the resonating character of its H-bond center, may provide slight flexibility to the position of the template base which may be responsible for the error-proneness of MuLV RT.
Flip-chip assembly for Si-based RF MEMS (1999)

MEMS-based RF components are being developed for various microwave and millimeter-wave applications. However, most RF MEMS have to be fabricated using GaAs, ceramics, high-resistivity silicon or other RF-compatible materials; such fabrication techniques are not commonly used by mainstream silicon-based MEMS manufacturing infrastructure. As a result, the complexity of these MEMS is limited. Using flip-chip assembly and silicon removal techniques, there is an opportunity to integrate MEMS onto any RF compatible substrate without the silicon semiconductor effects. Thus, it is possible to manufacture complex MEMS cost-effectively for a new generation of RF MEMS with superior functionality, e.g. tunable capacitors, multi-way switches and arrays of hundreds of these or other RF components. This new technology is described with an emphasis on four issues: warpage, actuators, release and flip-chip bonding.
Design of Narrow-Bandgap Polymers. Syntheses and Properties of Monomers and Polymers Containing Aromatic-Donor and o-Quinoid-Acceptor Units (1996)

A series of novel monomers and polymers containing aromatic-donor and o-quinoid-acceptor units was prepared, and the relationship between their spectral and electrochemical properties and their structures was investigated. X-ray structure analyses of the monomers possessing thiophene units revealed coplanar conformations, whereas calculations of the monomers containing N-methylpyrrole showed torsional conformations. Cyclic voltammetry showed amphoteric properties for all the monomers and p- and n-doping processes for most of the polymers. The reduction potentials were primarily dependent on the electron-accepting character of the o-quinoid-acceptor units. The electrochemical behavior of the polymers was characterized by cyclic voltammetry and suggested narrow-bandgap systems. The bandgaps determined from optical absorption spectra range from 0.5 to 1.4 eV. The polymer composed of thiophenes and benzo[1,2-c;3,4-c‘]bis[1,2,5]thiadiazole exhibited the narrowest bandgap.
Precipitation of Magnesium Hydroxide from Brine (1995)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPrecipitation of Magnesium Hydroxide from BrineMarian Turek and Witold GnotCite this: Ind. Eng. Chem. Res. 1995, 34, 1, 244–250Publication Date (Print):January 1, 1995Publication History Published online1 May 2002Published inissue 1 January 1995https://pubs.acs.org/doi/10.1021/ie00040a025https://doi.org/10.1021/ie00040a025research-articleACS PublicationsRequest reuse permissionsArticle Views1801Altmetric-Citations75LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Digital Single-Nucleotide Polymorphism Analysis for Allelic Imbalance (2004)

Digital single-nucleotide polymorphism (SNP) analysis is developed to amplify a single template from a pool of DNA samples, thereby generating the amplicons that are homogeneous in sequence. Different fluorophores are then applied as probes to detect and discriminate different alleles (paternal vs maternal alleles or wild-type vs mutant), which can be readily counted. In this way, digital SNP analysis transforms the exponential and analog signals from conventional polymerase chain reaction (PCR) to linear and digital ones. Digital SNP analysis has the following advantages. First, statistical analysis of the PCR products becomes available as the alleles can be directly counted. Second, this technology is designed to generate PCR products of the same size; therefore, DNA degradation would not be a problem as it commonly occurs when microsatellite markers are used to assess allelic status in clinical samples. Last, digital SNP analysis is designed to amplify a relatively small amount of DNA samples, which is available in some clinical samples. Digital SNP analysis has been applied in quantification of mutant alleles and detection of allelic imbalance in clinical specimens and it represents another example of the power of PCR and provides unprecedented opportunities for molecular genetic analysis.
Interphase exchange coupling in Fe∕Sm–Co bilayers with gradient Fe thickness (2005)

We have fabricated Fe∕Sm–Co bilayers with gradient Fe thicknesses in order to systematically study the dependence of exchange coupling on the thickness of the Fe layer. The Fe layer was deposited at two different temperatures (150 and 300°C) to study the effect of deposition temperature on the exchange coupling. Magneto-optical Kerr effect and x-ray magnetic circular dichroism (XMCD) have been employed as nondestructive rapid characterization tools to map the magnetic properties of the gradient samples. Systematic enhancement in exchange coupling between the soft layer and the hard layer is observed as the soft layer thickness is decreased. Separate exchange couplings of the Fe layer with Co and Sm in the hard layer are revealed through measuring the element-specific hysteresis curves using XMCD. The single-phase-like magnetization reversal critical thickness increases from 12nm for Fe deposited at 150°Cto24nm for Fe deposited at 300°C, indicating an important role of the state of the interface in the exchange coupling.
Cosmetic and Drug Microbiology (2016)

Introduction. A History of Cosmetic Microbiology in the USA. A History of Pharmaceutical Preservation in the UK. A History of Cosmetic and Drug Microbiology in Japan. Factors in Selecting and Testing Preservatives. Preservative Efficacy Testing during Formula Development and Stability Testing. Introduction to the Preservation of Make-up Type Products. Risk Factor Assessment of Anhydrous/Atypical Cosmetic Products. Global Preservative Systems. Safety and Toxicological Properties of Preservatives. Hurdle Technology for Cosmetic and Drug Preservation. Cosmetic Preservation Using Enzymes. Plant Products as Antimicrobial Agents. Microbiological Limit Testing: Microbial Specifications for Finished Products. Raw Material and Water Microbial Bioburden. Nanotechnology: Tools Microbiologists Can Use to Refine Their Research. Microbiology of the Skin. Microbiological Testing During Clinical Trials. Evolution of Cosmetic Microbiology Beyond Agar Plating. New Developments and Opportunities in Cosmetic Microbiology.
Characterization of response to radiation mediated gene therapy by means of multimodality imaging (2009)

Imaging techniques are under development to facilitate early analysis of spatial patterns of tumor response to combined radiation and antivascular gene therapy. A genetically modified, replication defective adenoviral vector (Ad.EGR-TNFalpha), injected intratumorally, mediates infected cells to express tumor necrosis factor alpha (TNFalpha), which is increased after exposure to radiation. The goal of this study was to characterize an image based "signature" for response to this combined radiation and gene therapy in mice with human prostate xenografts. This study is part of an imaged guided therapy project where such a signature would be useful in guiding subsequent treatments. Changes in the tumor micro-environment were assessed using MRI registered with electron paramagnetic resonance imaging which provides images of tissue oxygenation. Dynamic contrast-enhanced MRI was used to assess tissue perfusion. When compared with null vector (control) treatment, the ratio of contrast agent (Gd-DTPA-BMA) washout rate to uptake rate was lower (P = 0.001) after treatment, suggesting a more balanced perfusion. Concomitantly, oxygenation significantly increased in the treated animals and decreased or did not change in the control animals (P < 0.025). This is the first report of minimally invasive, quantitative, absolute oxygen measurements correlated with tissue perfusion in vivo.
A critical role for neutralizing-antibody-producing B cells, CD4+T cells, and interferons in persistent and acute infections of mice with lymphocytic choriomeningitis virus: Implications for adoptive immunotherapy of virus carriers (1997)

This study demonstrates that neutralizing-antibody-producing B cells, CD4(+) T cells, and interferons (IFNs) are of key importance in virus control both in adoptive immunotherapy of persistent infection and in the late phase of acute infection with the WE strain of lymphocytic choriomeningitis virus (LCMV). We report the following results. (i) Clearance of LCMV-WE from C57BL/6 carrier mice by adoptive transfer of memory spleen cells requires B cells and CD4(+) T cells but not necessarily CD8(+) T cells. (ii) At the doses examined, CD8(+) T cells contribute to the initial reduction of viral titers but are alone not sufficient to clear the virus because they are exhausted. (iii) In the presence of functional IFN-gamma, virus clearance correlates well with the generation of neutralizing antibodies in the treated carrier mice. (iv) In the absence of receptors for IFN-gamma, virus clearance is not achieved. (v) Adoptive immunotherapy of mice persistently infected with a distinct virus isolate, LCMV-Armstrong, revealed only low levels of neutralizing antibodies; in this case, CD8(+) T cells were needed for virus clearance in addition to B and CD4(+) T cells. (vi) After low dose infection of C57BL/6 mice with LCMV-WE, virus is eliminated below detectable levels by CD8(+) T cells, but long-term (>2 months) virus control is usually not achieved in the absence of B cells or CD4(+) T cells; reappearance of the virus is paralleled either by exhaustion of virus-specific cytotoxic T lymphocytes or lethal immunopathology. These findings are of importance for adoptive immunotherapy strategies against persistent virus infections in humans.
Energy Balance, Metabolic Hormones, and Early Postpartum Follicular Development in Dairy Cows Fed Prilled Lipid (1998)

The objectives of this study were to relate energy balance and metabolic hormones during the early postpartum period in dairy cows with dominant follicle development before first ovulation and to evaluate the effects of prilled lipid on follicular development during the first follicular wave after parturition and the postpartum anovulatory interval. At parturition, 42 cows received a control diet (4.8% fat) or a diet supplemented with prilled fatty acids (7.0% fat). Energy balance was determined daily. Ovarian follicular development was monitored by ultrasonography, and blood plasma or serum was analyzed for estradiol, progesterone, and metabolic hormones. Dry matter intake was lower in cows supplemented with dietary lipids during the first 4 wk of lactation, but energy intake, energy balance, and the postpartum anovulatory interval were similar between diets. A wave of follicular development occurred in all cows during the 2nd wk postpartum, and 50% of all cows ovulated their first dominant follicle. Numbers of follicles that were 3 to 5 mm, 6 to 9 mm, and 10 to 15 mm on d 8 postpartum were similar between diets and unrelated to energy balance or metabolic hormones. Diameter of the dominant follicle during d 8 to 14 postpartum and maximum diameter of the first-wave ovulatory follicle did not differ between diets. Cows with nonovulatory first-wave dominant follicles had lower mean plasma concentrations of estradiol during d 8 to 14 postpartum, a longer interval to the day of the energy balance nadir, lower serum concentrations of IGF-I, and higher 4% FCM yield than did cows with ovulatory first-wave dominant follicles. Serum IGF-I during d 1 to 13 was positively correlated with plasma estradiol during d 8 to 14 postpartum. Possibly because of reductions in dry matter intake, the consumption of prilled lipid by dairy cows during early lactation may be ineffective in altering energy balance, follicular development, and the postpartum anovulatory interval. Ovulation failure of dominant follicles early in the postpartum period is associated with greater production of 4% fat-corrected milk, a delayed energy balance nadir, and reduced concentrations of peripheral IGF-I.
Kinetic Analysis of the Binding of Human Matrix Metalloproteinase-2 and -9 to Tissue Inhibitor of Metalloproteinase (TIMP)-1 and TIMP-2 (1997)

The dissociation constants (Kd) of tissue inhibitor of metalloproteinase (TIMP)-1 and TIMP-2 for the active and latent forms of matrix metalloproteinase (MMP)-2 and MMP-9 were evaluated using surface plasmon resonance (SPR) and enzyme inhibition studies. SPR analysis shows biphasic kinetics with high (nM) and low (microM) affinity binding sites of TIMP-2 and TIMP-1 for MMP-2 (72- and 62-kDa species) and MMP-9 (92- and 82-kDa species), respectively. In contrast, binding data of TIMP-2 to an MMP-2 45-kDa active form lacking the C-terminal domain and to an MMP-2 C-terminal domain (CTD) fragment displays monophasic kinetics with Kd values of 315 and 60 nM, respectively. This suggests that the CTD contains the high affinity binding site, whereas the catalytic domain contains the low affinity site. Also, binding of TIMP-2 to pro-MMP-2 is stronger at both the high and low affinity sites than the corresponding binding of TIMP-2 to the MMP-2 62-kDa form demonstrating the importance of the N-terminal prodomain. In addition, the Kd value of TIMP-1 for the MMP-2 62-kDa species is 28. 6 nM at the high affinity site, yet neither the MMP-2 45-kDa species nor the CTD interacts with TIMP-1. Enzyme inhibition studies demonstrate that TIMPs are slow binding inhibitors with monophasic inhibition kinetics. This suggests that a single binding event results in enzyme inhibition. The kinetic parameters for the onset of inhibition are fast (kon approximately 10(5) M-1 s-1) with slow off rates (koff approximately 10(-3) s-1). The inhibition constants (Ki) are in the 10(-7)-10(-9) M range and correlate with the values determined by SPR.
A coupled knowledge based system using fuzzy optimization for advisory control (1992)

Abstract A knowledge based system is described that is designed to generate on‐line advice for operators regarding the proper distribution of hydrogen resources in a refinery. The system uses a coupled architecture incorporating numerical computing in a knowledge based system environment. This arrangement allows for powerful and flexible problem solving. One portion of the coupled system formulates an optimization problem that is subsequently solved by an external routine. This application is particularly concerned with uncertainty that is present in some of the constraints. To deal with this uncertainty, a fuzzy approach to the optimization is taken. A method is presented that solves the fuzzy optimization problem using standard mathematical programming techniques. The results of the fuzzy optimization allow the crisp solution to be expanded into a neighborhood of solutions that is considered acceptable. Although this work examines a specific problem, the concepts presented are general.
Tn10-encoded tet repressor can regulate an operator-containing plant promoter. (1988)

The Tn10-encoded tet repressor-operator system was used to regulate transcription from the cauliflower mosaic virus (CaMV) 35S promoter. Expression was monitored in a transient assay system by using electric field-mediated gene transfer ("electroporation") into tobacco protoplasts. The tet repressor, being expressed in the plant cells under the control of eukaryotic transcription signals, blocks transcription of a CaMV 35S promoter chloramphenicol acetyltransferase (cat) fusion gene when the two tet operators flank the "TATA" box. In the presence of the inducer tetracycline, expression is restored to full activity. Location of the operators 21 base pairs downstream of the transcription start site does not significantly affect transcription in the presence of the repressor. These experiments show that a prokaryotic regulatory protein can function in plant cells. The tet repressor-operator complex may be useful for specifically inducing transferred genes at different stages of plant development.
Molecular biology and biochemistry of the natriuretic peptide system. II: Natriuretic peptide receptors (1992)

From the Second Division, Department of Medicine, Kyoto University School of Medicine, Kyoto, Japan