gebhart/patrepeval huggingface dataset:
Programmable Genome Editing Tools and their Regulation for Efficient Genome Engineering (2017)

Targeted genome editing has become a powerful genetic tool for studying gene function or for modifying genomes by correcting defective genes or introducing genes. A variety of reagents have been developed in recent years that can generate targeted double-stranded DNA cuts which can be repaired by the error-prone, non-homologous end joining repair system or via the homologous recombination-based double-strand break repair pathway provided a suitable template is available. These genome editing reagents require components for recognizing a specific DNA target site and for DNA-cleavage that generates the double-stranded break. In order to reduce potential toxic effects of genome editing reagents, it might be desirable to control the in vitro or in vivo activity of these reagents by incorporating regulatory switches that can reduce off-target activities and/or allow for these reagents to be turned on or off. This review will outline the various genome editing tools that are currently available and describe the strategies that have so far been employed for regulating these editing reagents. In addition, this review will examine potential regulatory switches/strategies that can be employed in the future in order to provide temporal control for these reagents.
Interconversion among Leucomycin A<sub>3</sub>, Carbomycin A, Carbomycin B and Maridomycin II (1977)

Journal Article Interconversion among Leucomycin A3, Carbomycin A, Carbomycin B and Maridomycin II Get access Masaru Suzuki, Masaru Suzuki Microbiological Research Laboratories, Central Research Division, Takeda Chemical Industries, Ltd., Osaka, Japan Search for other works by this author on: Oxford Academic Google Scholar Tsutomu Takamaki, Tsutomu Takamaki Microbiological Research Laboratories, Central Research Division, Takeda Chemical Industries, Ltd., Osaka, Japan Search for other works by this author on: Oxford Academic Google Scholar Ken-ichiro Miyagawa, Ken-ichiro Miyagawa Microbiological Research Laboratories, Central Research Division, Takeda Chemical Industries, Ltd., Osaka, Japan Search for other works by this author on: Oxford Academic Google Scholar Hideo Ono, Hideo Ono Microbiological Research Laboratories, Central Research Division, Takeda Chemical Industries, Ltd., Osaka, Japan Search for other works by this author on: Oxford Academic Google Scholar Eijì Higashide, Eijì Higashide Microbiological Research Laboratories, Central Research Division, Takeda Chemical Industries, Ltd., Osaka, Japan Search for other works by this author on: Oxford Academic Google Scholar Mìnoru Uchida Mìnoru Uchida Microbiological Research Laboratories, Central Research Division, Takeda Chemical Industries, Ltd., Osaka, Japan Search for other works by this author on: Oxford Academic Google Scholar Agricultural and Biological Chemistry, Volume 41, Issue 2, 1 February 1977, Pages 419–421, https://doi.org/10.1080/00021369.1977.10862513 Published: 01 February 1977 Article history Received: 06 December 1976 Published: 01 February 1977
Pregnant and Nonpregnant Women in Cape Town, South Africa: Drug Use, Sexual Behavior, and the Need for Comprehensive Services (2011)

The multiple risks associated with methamphetamine use are of serious concern for women. These risks and consequences are magnified during pregnancy. This secondary analysis of a parent study compared 26 pregnant to 356 nonpregnant women in Cape Town, South Africa, on selected demographic, psychosocial, and HIV-risk domains to identify their treatment service needs. Proportionally, more pregnant than nonpregnant women are using methamphetamine, P = .01, although a very high rate of women used methamphetamine. Women reported similar monthly rates of sexual intercourse, but pregnant women were significantly less likely to report condom use, P < .0001, maintaining their risky behavior. Both groups reported elevated Center for Epidemiological Studies Depression Scale CES-D means, suggesting a need for depression treatment. Results demonstrate a pervasive need for women's comprehensive treatment, regardless of pregnancy status. Moreover, findings support the urgent need for women-focused and pregnancy-specific treatment services for methamphetamine use. Finally, a job-skills training/employment component focus is suggested.
Spectral equalization and autosweeping effects in a pulsed dye laser with an intracavity photorefractive element (1992)

A pulsed dye laser with an intracavity photorefractive element is reported. It is shown that the element can be used for storage of spectral information. New effects for this system such as spectral equalization and oscillation-frequency autosweeping are demonstrated.
Translation of lymphocyte mRNA into biologically-active Interleukin 2 in oocytes. (1981)

A variant line of murine T lymphoma EL4 produces high levels of the lymphokine Interleukin 2 (IL 2) when it is stimulated with phorbol myristate acetate. We have extracted poly A+ RNA from the stimulated cells and injected it into Xenopus laevis oocytes. The injected oocytes synthesize a material with biologic and biochemical properties of murine IL 2. Namely, it stimulates the continued growth of a cloned, cytotoxic T cell line (the T cell growth factor assay) and it chromatographs on a gel filtration column (G-100) with IL 2 produced by the stimulated EL4 line. The RNA responsible for the biologic activity sediments with markers of 11 to 12S in a sucrose gradient. The IL 2 produced by injected oocytes from a given preparation of mRNA is about 1% of the amount produced by the EL4 cells stimulated originally with phorbol myristate acetate. When RNA is extracted and purified from unstimulated EL4 cells it does not induce IL 2 production in oocytes. We conclude that IL 2 is essentially protein in nature, that the protein is coded for by poly A+ mRNA, and that the amount of this mRNA increases significantly after stimulation of the variant EL4 cells with the inducer phorbol myristate acetate.
Stabilization of coordinatively unsaturated Ir<sub>4</sub>clusters with bulky ligands: a comparative study of chemical and mechanical effects (2011)

The synthesis and characterization of new cluster compounds represented by the series Ir(4)(CO)(12-x)L(x) (L = tert-butyl-calix[4]-arene(OPr)(3)(OCH(2)PPh(2)); x = 2 and 3) is reported using ESI mass spectrometry, NMR spectroscopy, IR spectroscopy and single-crystal X-ray diffraction. Thermally driven decarbonylation of the cluster compound series represented by x = 1-3 according to the formula above is followed via FTIR and NMR spectroscopies, and dynamic light scattering in toluene solution. The propensity of these clusters to decarbonylate in solution is shown to be directly correlated with number density of adsorbed calixarene phosphine ligands and controlled via Pauli repulsion between metal d and CO 5σ orbitals. The tendency for cluster aggregation unintuitively follows a trend that is exactly opposite to the cluster's propensity to decarbonylate. No cluster aggregation is observed for clusters consisting of x = 3, even after extensive decarbonylation via loss of all bridging CO ligands and coordinative unsaturation. Some of the CO lost during thermal treatment via decarbonylation can be rebound to the coordinatively unsaturated cluster consisting of x = 3. In contrast, the clusters consisting of x = 1 and x = 2 both aggregate into large nanoparticles when treated under identical conditions. Clusters in which the calixarene phosphine ligand is replaced with a sterically less demanding PPh(2)Me ligand 6 lead to significantly less coordinative unsaturation upon thermal treatment. Altogether, these data support a mechanical model of accessibility in coordinatively unsaturated metal clusters in solution, which hinges on having at least three sterically bulky organic ligands per Ir(4) core.
Effect of Microwave Pulse on the Optical Properties of Hydrogenated Amorphous Silicon Thin Films Deposited by Electron Cyclotron Resonance Plasma (1997)

Hydrogenated amorphous silicon(a-Si:H) thin films have been prepared by the electron cyclotron resonance plasma-enhanced chemical vapor deposition (ECR PECVD) method. A pulse of 27.5 kHz was applied to the microwave power of the ECR PECVD during deposition. It was found that the pulse changed the total hydrogen content, its bonding configuration, substrate temperature, and the optical properties such as the refractive index ( n ), absorption coefficient (α) and the optical energy band gap. Using the present method, better quality a-Si:H films have been obtained as compared to those obtained by the conventional ECR PECVD method. It is ascertained that the properties of these films are good enough for device application even though the films are deposited without the intentional heating of the substrate. The results show the possibility of using plastic substrates for devices such as thin film transistor-liquid crystal displays.
Physical and chemical properties of metal oxide additions to Ag-SnO/sub 2/ contact materials and predictions of electrical performance (1994)

The new contact material AgSnO/sub 2/, which is replacing AgCdO in many applications, requires the addition of doping agents to improve electrical contact performance. These additions effect thermodynamic stability, the wettability of the SnO/sub 2/ surface by liquid silver, as well as the microstructure of the area melted by the electric arc. This work considers the frequently used dopants WO/sub 3/, MoO/sub 3/, Bi/sub 2/O/sub 3/, CuO and RuO/sub 2/, as well as others: ZnO, Ta/sub 2/O/sub 5/, HgO, RuO/sub 2/, Sb/sub 2/O/sub 3/, TeO/sub 2/ and TaC. DTA and TGA analyses are performed on mixtures of these metal oxides with SnO/sub 2/, Ag, and AgSnO/sub 2/. Reactions products, if present, are characterized by x-ray diffraction. The wetting angles of molten silver on surfaces of these mixtures are established. The results are used to interpret the microstructures found in the molten regions of AgSnO/sub 2/ materials doped with these substances. These structures are interpreted and related to performance in arcing contact applications.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Compact Wideband Equivalent-Circuit Model for Electrical Modeling of Through-Silicon Via (2011)

This paper presents a compact wideband equivalent circuit model for electrical modeling of through-silicon vias (TSVs) in 3-D stacked integrated circuits and packaging. Rigorous closed form formulas for the resistance and inductance of TSVs are de rived from the magneto-quasi-static theory with a Fourier-Bessel expansion approach, whereas analytical formulas from static solutions are used to compute the capacitance and conductance. The equivalent-circuit model can capture the important parasitic effects of TSVs, including the skin effect, proximity effect, lossy effect of silicon, and semiconductor effect. Therefore, it yields accurate results comparable to those with 3-D full-wave solvers.
Hypermutation of Immunoglobulin Genes in Memory B Cells of DNA Repair–deficient Mice (1998)

To investigate the possible involvement of DNA repair in the process of somatic hypermutation of rearranged immunoglobulin variable (V) region genes, we have analyzed the occurrence, frequency, distribution, and pattern of mutations in rearranged Vlambda1 light chain genes from naive and memory B cells in DNA repair-deficient mutant mouse strains. Hypermutation was found unaffected in mice carrying mutations in either of the following DNA repair genes: xeroderma pigmentosum complementation group (XP)A and XPD, Cockayne syndrome complementation group B (CSB), mutS homologue 2 (MSH2), radiation sensitivity 54 (RAD54), poly (ADP-ribose) polymerase (PARP), and 3-alkyladenine DNA-glycosylase (AAG). These results indicate that both subpathways of nucleotide excision repair, global genome repair, and transcription-coupled repair are not required for somatic hypermutation. This appears also to be true for mismatch repair, RAD54-dependent double-strand-break repair, and AAG-mediated base excision repair.
Comparative Evaluation of Chlamydiazyme, PACE 2, and AMP-CT Assays for Detection of <i>Chlamydia trachomatis</i> in Endocervical Specimens (1998)

We conducted a comparative evaluation of the Chlamydiazyme (Abbott Laboratories), PACE 2 (Gen-Probe), and AMP-CT (Gen-Probe) assays for the detection of Chlamydia trachomatis in endocervical samples. Specimens from 787 females were included in the study. The sensitivities of the PACE 2 and Chlamydiazyme assays in comparison to the results of the AMP-CT assay were 79.3 and 63.4%, respectively. The specificities of the Chlamydiazyme and PACE 2 assays were 100%. All of the positive specimens detected in this study were positive by the AMP-CT assay. On the basis of the final results of the comparison, the prevalence of C. trachomatis in the population was 10.4%. Retesting of specimens whose results were in the intermediate zone by the PACE 2 assay by a probe competition assay identified some additional true-positive specimens. Amplification assay testing of such specimens did not significantly increase the yield. The majority of specimens which tested positive by the AMP-CT assay only were not in the intermediate zone by the PACE 2 assay. We were unable to identify demographic or clinical factors which could predict those individuals who tested positive by amplified tests but not by nonamplified tests. The Gen-Probe PACE 2 assay proved to be superior to the Chlamydiazyme assay for the screening and diagnosis of C. trachomatis infections in female endocervical specimens.
Zinc Is a Potent Inhibitor of the Apoptotic Protease, Caspase-3 (1997)

The prevention of apoptosis by Zn2+ has generally been attributed to its inhibition of an endonuclease acting in the late phase of apoptosis. In this study we investigated the effect of Zn2+ on an earlier event in the apoptotic process, the proteolysis of the "death substrate" poly(ADP-ribose) polymerase (PARP). Pretreatment of intact Molt4 leukemia cells with micromolar concentrations of Zn2+ caused an inhibition of PARP proteolysis induced by the chemotherapeutic agent etoposide. Using a cell-free system consisting of purified bovine PARP as a substrate and an apoptotic extract or recombinant caspase-3 as the PARP protease, Zn2+ inhibited PARP proteolysis in the low micromolar range. To rule out an effect of Zn2+ on PARP, a protein with two zinc finger domains, we used recombinant caspase-3 and a chromogenic tetrapeptide substrate containing the caspase-3 cleavage site. In this system, Zn2+ inhibited caspase-3 with an IC50 of 0.1 microM. These results identify caspase-3 as a novel target of Zn2+ inhibition in apoptosis and suggest a regulatory role for Zn2+ in modulating the upstream apoptotic machinery.
A New RAKE Receiver Structure for the Forward-Link of W-CDMA Systems (2002)

We propose a new receiver structure to mitigate interpath interference (IPI) in W-CDMA systems. We model IPI in RAKE combining as intersymbol interference (ISI) and use a two-stage receiver structure. The first stage is a RAKE receiver and the second stage is an equalizer. In cases of multicode transmission, interference among code channels causes extra impairments which can not be modelled as ISI. Under these circumstances, they are estimated by using decisions from the first stage and then subtracted from the input of the equalizer. The residual interference is equivalent to ISI and can be mitigated by the equalizer. Simulation results show that the proposed receiver provides very promising performance in low spreading factor W-CDMA.
Direct Biological Sample Analyses by Laserspray Ionization Miniature Mass Spectrometry (2018)

With improved performances, miniature mass spectrometers are becoming suitable for more practical applications. At the same time, the coupling of an approximate ionization source is essential in terms of minimizing sample preparation and broadening the range of samples that could be analyzed. In this study, an atmospheric pressure laserspray ionization (AP-LSI) source was coupled with our home developed miniature ion trap mass spectrometer. The whole system is compact in size, and biological samples could be directly analyzed with minimum sample preparation. Direct detections of peptides, proteins, drugs in whole blood, and urine could be achieved with high sensitivity. The analyses of tissue sections were demonstrated, and different regions in a tissue section could be differentiated based on their lipid profiles. Results suggest that the coupling of AP-LSI with miniature mass spectrometer is a powerful technique, which could potentially benefit target molecule analysis in biological and medical applications.
Overexpression of RNase H partially complements the growth defect of an Escherichia coli delta topA mutant: R-loop formation is a major problem in the absence of DNA topoisomerase I. (1995)

Previous biochemical studies have suggested a role for bacterial DNA topoisomerase (TOPO) I in the suppression of R-loop formation during transcription. In this report, we present several pieces of genetic evidence to support a model in which R-loop formation is dynamically regulated during transcription by activities of multiple DNA TOPOs and RNase H. In addition, our results suggest that events leading to the serious growth problems in the absence of DNA TOPO I are linked to R-loop formation. We show that the overexpression of RNase H, an enzyme that degrades the RNA moiety of an R loop, can partially compensate for the absence of DNA TOPO I. We also note that a defect in DNA gyrase can correct several phenotypes associated with a mutation in the rnhA gene, which encodes the major RNase H activity. In addition, we found that a combination of topA and rnhA mutations is lethal.
Dynamic microarchitecture adaptation via co-designed virtual machines (2003)

Co-designed virtual machines provide hardware designers with a hidden layer of software that can be used to manage configurable hardware units. A reconfiguration algorithm based on a mechanism for identifying recurring program phases provides power savings in caches and predictors up to 60%, without significantly affecting performance.
Mild Elevation of Body Temperature Reduces Tumor Interstitial Fluid Pressure and Hypoxia and Enhances Efficacy of Radiotherapy in Murine Tumor Models (2011)

Human and rodent solid tumors often exhibit elevated interstitial fluid pressure (IFP). This condition is recognized as a prognostic indicator for reduced responses to therapy and decreased disease-free survival rate. In the present study, we tested whether induction of a thermoregulatory-mediated increase in tissue blood flow, induced by exposure of mice to mild environmental heat stress, could influence IFP and other vascular parameters within tumors. Using several murine tumor models, we found that heating results in a sustained reduction in tumor IFP correlating with increased tumor vascular perfusion (measured by fluorescent imaging of perfused vessels, laser Doppler flowmetry, and MRI) as well as a sustained reduction in tumor hypoxia. Furthermore, when radiation therapy was administered 24 hours postheating, we observed a significant improvement in efficacy that may be a result of the sustained reduction in tumor hypoxia. These data suggest, for the first time, that environmental manipulation of normal vasomotor function is capable of achieving therapeutically beneficial changes in IFP and microvascular function in the tumor microenvironment.
Optical functions and electronic structure of<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">CuInSe</mml:mi></mml:mrow><mml:mrow><mml:mn>2</mml:mn></mml:mrow></mml:msub></mml:mrow><mml:mo>,</mml:mo></mml:math><mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">CuGaSe</mml:mi></mml:mrow><mml:mrow><mml:mn>2</mml:mn></mml:mrow></mml:msub></mml:mrow><mml:mo>,</mml:mo></mml:math><mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">CuInS</mml:mi></mml:mrow><mml:mrow><mml:mn>2</mml:mn></mml:mrow></mml:msub></mml:mrow><mml:mo>,</mml:mo></mml:math>and<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">CuGaS</mml:mi></mml:mrow><mml:mrow><mml:mn>2</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math> (2001)

We report on the complex dielectric tensor components of four chalcopyrite semiconductors in an optical energy range (1.4--5.2 eV, from 0.9 eV for ${\mathrm{CuInSe}}_{2})$ determined at room temperature by spectroscopic ellipsometry. Our results were obtained on single crystals of ${\mathrm{CuInSe}}_{2},$ ${\mathrm{CuGaSe}}_{2},$ ${\mathrm{CuInS}}_{2},$ and ${\mathrm{CuGaS}}_{2}.$ Values of refractive indices n, extinction coefficients k, and normal-incidence reflectivity R in the two different polarizations are given and compared with earlier data where available. We analyze in detail the structures of the dielectric function observed in the studied energy region. Critical-point parameters of electronic transitions are obtained from a fitting of numerically calculated second-derivative spectra ${d}^{2}\ensuremath{\varepsilon}(\ensuremath{\omega})/d{\ensuremath{\omega}}^{2}.$ Experimental energies and polarizations are discussed on the basis of published band-structure calculations.
Chemotherapy of cell-line-derived human colon carcinomas in mice immunosuppressed with antithymocyte serum (1977)

An in vivo model is described for assessing the antitumor activity of chemotherapeutic agents. Tumors derived from human colon carcinoma cell lines injected into antithymocyte serum (ATS) immunosuppressed mice were used. In this system, both antitumor effects and host toxicity can be quantitated, permitting calculation of a Therapeutic Index. Compared with other xenograft models, the present system is simple, experiments are completed in less than 2 weeks, and the use of cultured cell lines allows in vitro studies to be performed. The in vitro sensitivities of one colon cell line to 22 chemotherapeutic agents and of four cell lines to three agents is reported. Four drugs used in treating colon cancer (Mitomycin C, 5-FU, BCNU, and methyl-CCNU) show antitumor activity in vivo in this system. Each has a low therapeutic index. Further work with this model is indicated, with the goal of finding new drugs with high Therapeutic Indices.