gebhart/patrepeval huggingface dataset:
Passive mixing in a three-dimensional serpentine microchannel (2000)

A three-dimensional serpentine microchannel design with a "C shaped" repeating unit is presented in this paper as a means of implementing chaotic advection to passively enhance fluid mixing. The device is fabricated in a silicon wafer using a double-sided KOH wet-etching technique to realize a three-dimensional channel geometry. Experiments using phenolphthalein and sodium hydroxide solutions demonstrate the ability of flow in this channel to mix faster and more uniformly than either pure molecular diffusion or flow in a "square-wave" channel for Reynolds numbers from 6 to 70. The mixing capability of the channel increases with increasing Reynolds number. At least 98% of the maximum intensity of reacted phenolphthalein is observed in the channel after five mixing segments for Reynolds numbers greater than 25. At a Reynolds number of 70, the serpentine channel produces 16 times more reacted phenolphthalein than a straight channel and 1.6 times more than the square-wave channel. Mixing rates in the serpentine channel at the higher Reynolds numbers are consistent with the occurrence of chaotic advection. Visualization of the interface formed in the channel between streams of water and ethyl alcohol indicates that the mixing is due to both diffusion and fluid stirring.
Oil and Natural Gas (2008)

This chapter contains sections titled: Genesis of Oil and Natural Gas Recovering Oil and Gas Peak Oil Reserves Properties of Hydrocarbons Oil Fields Prices Consumption Electricity Generation Impact on Environment Unconventional Oil and Gas Resources Conclusion
Long-term expression of human adenosine deaminase in mice transplanted with retrovirus-infected hematopoietic stem cells. (1989)

Long-term stable expression of foreign genetic sequences transferred into hematopoietic stem cells by using retroviral vectors constitutes a relevant model for somatic gene therapy. Such stability of expression may depend on vector design, including the presence or absence of specific sequences within the vector, in combination with the nature and efficiency of infection of the hematopoietic target cells. We have previously reported successful transfer of human DNA encoding adenosine deaminase (ADA) into CFU-S (colony-forming unit-spleen) stem cells using simplified recombinant retroviral vectors. Human ADA was expressed in CFU-S-derived spleen colonies at levels near to endogenous enzyme. However, because of the lack of an efficient dominant selectable marker and low recombinant viral titers, stability of long-term expression of human ADA was not examined. We report here the development of an efficient method of infection of hematopoietic stem cells (HSC) without reliance on in vitro selection. Peripheral blood samples of 100% of mice transplanted with HSC infected by this protocol exhibit expression of human ADA 30 days after transplantation. Some mice (6 of 13) continue to express human ADA in all lineages after complete hematopoietic reconstitution (4 months). The use of recombinant retroviral vectors that efficiently transfer human ADA cDNA into HSC leading to stable expression of functional ADA in reconstituted mice, provides an experimental framework for future development of approaches to somatic gene therapy.
Structural roles of guide RNAs in the nuclease activity of Cas9 endonuclease (2016)

The type II CRISPR-associated protein Cas9 recognizes and cleaves target DNA with the help of two guide RNAs (gRNAs; tracrRNA and crRNA). However, the detailed mechanisms and kinetics of these gRNAs in the Cas9 nuclease activity are unclear. Here, we investigate the structural roles of gRNAs in the CRISPR-Cas9 system by single-molecule spectroscopy and reveal a new conformation of inactive Cas9 that is thermodynamically more preferable than active apo-Cas9. We find that tracrRNA prevents Cas9 from changing into the inactive form and leads to the Cas9:gRNA complex. For the Cas9:gRNA complex, we identify sub-conformations of the RNA-DNA heteroduplex during R-loop expansion. Our single-molecule study indicates that the kinetics of the sub-conformations is controlled by the complementarity between crRNA and target DNA. We conclude that both tracrRNA and crRNA regulate the conformations and kinetics of the Cas9 complex, which are crucial in the DNA cleavage activity of the CRISPR-Cas9 system.
Optoelectronic oscillator for photonic systems (1996)

We describe a novel photonic oscillator that converts continuous-light energy into stable and spectrally pure microwave signals. This optoelectronic oscillator (OEO) consists of a pump laser and a feedback circuit including an intensity modulator, an optical-fiber delay line, a photodetector an amplifier, and a filter. We present the results of a quasi-linear theory for describing the properties of the oscillator and their experimental verifications. Our findings indicate that the OEO can generate ultrastable, spectrally pure microwave-reference signals up to 75 GHz with a phase noise lower than -140 dBc/Hz at 10 KHz. We show that the OEO is a special voltage-controlled oscillator with an optical-output port and can be synchronized to a reference source by means of optical injection locking, electrical injection locking, and a phase-locked loop. Other OEO applications include high-frequency reference regeneration and distribution, high-gain frequency multiplication, comb frequency and pulse generation, carrier recovery, and clock recovery.
Successful Colon Cancer Eradication after Chemoimmunotherapy Is Associated with Profound Phenotypic Change of Intratumoral Myeloid Cells (2010)

IL-12 is a potent immunostimulatory cytokine, but its impact as an antitumor drug in clinical practice is limited. Upsurge of regulatory T cells (Treg) in the tumor milieu has been proposed to limit the efficacy of the treatment. In this paper, two drugs (cyclophosphamide [CPA] and anti-CD25 mAb) widely used to eliminate Treg were used in an attempt to enhance the antitumor effect of IL-12 gene therapy. Both anti-CD25 and CPA combined with IL-12 were able to deplete intratumoral Treg and myeloid-derived suppressor cells (MDSC), but only IL-12 plus CPA achieved significant antitumor activity in mice with large established s.c. colon carcinoma. This therapeutic effect was associated with the emergence of a heterogeneous population of myeloid cells within the tumor, termed inflammatory myeloid cells (IMC), composed of Ly6C(high)Ly6G(low) inflammatory monocytes and Ly6G(high)Ly6C(+) neutrophils. IMC showed a distinctive pattern of cytokine/chemokine production, and in contrast to MDSC, they did not induce conversion of naive CD4(+) T cells into Treg. The appearance of IMC coincided with intense tumor infiltration by effector T cells, which was abrogated by elimination of IMC by anti-Gr1 mAb, a maneuver that abolished the antitumor effect of the therapy. Therefore, the combination of IL-12 and CPA eliminates intratumoral Treg and MDSC, while it induces the appearance of IMC within the tumor microenvironment. The latter effect is essential to facilitate effector T cell infiltration and subsequent tumor elimination.
Identification of a human gene (HCK) that encodes a protein-tyrosine kinase and is expressed in hemopoietic cells. (1987)

We have isolated cDNAs representing a previously unrecognized human gene that apparently encodes a protein-tyrosine kinase. We have designated the gene as HCK (hemopoietic cell kinase) because its expression is prominent in the lymphoid and myeloid lineages of hemopoiesis. Expression in granulocytic and monocytic leukemia cells increases after the cells have been induced to differentiate. The 57-kilodalton protein encoded by HCK resembles the product of the proto-oncogene c-src and is therefore likely to be a peripheral membrane protein. HCK is located on human chromosome 20 at bands q11-12, a region that is affected by interstitial deletions in some acute myeloid leukemias and myeloproliferative disorders. Our findings add to the diversity of protein-tyrosine kinases that may serve specialized functions in hemopoietic cells, and they raise the possibility that damage to HCK may contribute to the pathogenesis of some human leukemias.
DARTs take aim at BiTEs (2011)

Since taken on by biotechnology and pharmaceutical companies, bispecific antibodies experience a remarkable revival. In this issue of Blood , Moore et al provide evidence that antibody engineering can push the performance envelope further. 1
Effect of 830-nm Laser Light on the Repair of Bone Defects Grafted with Inorganic Bovine Bone and Decalcified Cortical Osseus Membrane (2003)

It is concluded that LLLT had a positive effect on the repair of bone defect by graft associated or not with the use of biological membrane.
RAT XENOGRAFT SURVIVAL IN MICE TREATED WITH DONOR-SPECIFIC TRANSFUSION AND ANTI-CD154 ANTIBODY IS ENHANCED BY ELIMINATION OF HOST CD4+ CELLS1 (2001)

These data suggest that treatment with DST and anti-CD154 mAb induces a state of "functional" transplantation tolerance. They also support the hypothesis that both the induction and maintenance of graft survival based on this protocol depend on different cellular mechanisms in allogeneic and xenogeneic model systems.
Understanding the complexity of human gait dynamics (2009)

Time series of human gait stride intervals exhibit fractal and multifractal properties under several conditions. Records from subjects walking at normal, slow, and fast pace speed are analyzed to determine changes in the fractal scalings as a function of the stress condition of the system. Records from subjects with different age from children to elderly and patients suffering from neurodegenerative disease are analyzed to determine changes in the fractal scalings as a function of the physical maturation or degeneration of the system. A supercentral pattern generator model is presented to simulate the above two properties that are typically found in dynamical network performance: that is, how a dynamical network responds to stress and to evolution.
In vitro genetic reconstruction of bacterial transcription initiation by coupled synthesis and detection of RNA polymerase holoenzyme (2010)

In vitro reconstitution of a biological complex or process normally involves assembly of multiple individually purified protein components. Here we present a strategy that couples expression and assembly of multiple gene products with functional detection in an in vitro reconstituted protein synthesis system. The strategy potentially allows experimental reconstruction of a multi-component biological complex or process using only DNA templates instead of purified proteins. We applied this strategy to bacterial transcription initiation by co-expressing genes encoding Escherichia coli RNA polymerase subunits and sigma factors in the reconstituted protein synthesis system and by coupling the synthesis and assembly of a functional RNA polymerase holoenzyme with the expression of a reporter gene. Using such a system, we demonstrated sigma-factor-dependent, promoter-specific transcription initiation. Since protein synthesis, complex formation and enzyme catalysis occur in the same in vitro reaction mixture, this reconstruction process resembles natural biosynthetic pathways and avoids time-consuming expression and purification of individual proteins. The strategy can significantly reduce the time normally required by conventional reconstitution methods, allow rapid generation and detection of genetic mutations, and provide an open and designable platform for in vitro study and intervention of complex biological processes.
A Floating-Body/Gate DRAM Cell Upgraded for Long Retention Time (2011)

A novel modification of our “2T” floating-body/gate DRAM cell is described and, via numerical simulations, shown to yield very long charge data retention times under worst-case conditions, as well as good memory performance (i.e., large signal margin and low operating power). Relatively low voltage operation is enabled, thereby implying good cell reliability as well.
High-performance low-complexity wordspotting using neural networks (1997)

A high-performance low-complexity neural network wordspotter was developed using radial basis function (RBF) neutral networks in a hidden Markov model (HMM) framework. Two new complementary approaches substantially improve performance on the talker-independent Switchboard corpus. Figure of merit (FOM) training adapts wordspotter parameters to directly improve the FOM performance metric, and voice transformations generate additional training examples by warping the spectra of training data to mimic across-talker vocal tract length variability.
Surface energetics, dispersion, and nanotribomechanical behavior of POSS/PP hybrid nanocomposites (2007)

Abstract Hybrid organic–inorganic polymer nanocomposites incorporating polyhedral oligomeric silsesquioxane (POSS) nanoparticles are of increasing interest for high performance materials applications. Octaisobutyl POSS/polypropylene nanocomposites were prepared at varying POSS concentrations via melt blending. The interplay of POSS molecular geometry, composition, and concentration in relation to the tribological, nanomechanical, surface energy, and bulk properties of the nanocomposites were investigated. Ultra‐low friction and enhanced hardness, modulus, and hydrophobicity were observed for the nanocomposite surfaces, with minimal changes in the bulk thermomechanical properties. Parallel AFM, SEM, TEM, and spectroscopic analyses demonstrated significant differences in POSS distribution and aggregation in the surface and the bulk, with preferential segregation of POSS to the surface. Additionally, contact angle studies reveal significant reduction in surface energy and increase in hysteresis with incorporation of POSS nanoparticles. The differences in bulk and surface properties are largely explained by the gradient concentration of POSS in the polymer matrix, driven by POSS/POSS and POSS/polymer interactions. © 2007 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 2441–2455, 2007
Apoptosis and Autophagy in Photoreceptors Exposed to Oxidative Stress (2007)

Studies on human and animal models of retinal dystrophy have suggested that apoptosis may be the common pathway of photoreceptor cell death. Autophagy, the major cellular degradation process in animal cells, is important in normal development and tissue remodeling, as well as under pathological conditions. Previously we provided evidence that genes, whose products are involved in apoptosis and autophagy, may be coexpressed in photoreceptors undergoing degeneration. Here, we investigated autophagy in oxidative stress-mediated cell death in photoreceptors, analyzing the light-damage mouse model and 661W photoreceptor cells challenged with H(2)O(2). In the in vivo model, we demonstrated a time-dependent increase in the number of TUNEL-positive cells, concomitant with the formation of autophagosomes. In vitro, oxidative stress increased mRNA levels of apoptotic and autophagic marker genes. H(2)O(2) treatment resulted in the accumulation of TUNEL-positive cells, the majority of which contain autophagosomes. To determine whether autophagy and apoptosis might precede each other or co-occur, we performed inhibitor studies. The autophagy inhibitor 3-methyladenine (3-MA), silencing RNA (siRNA) against two genes whose products are required for autophagy (autophagy-related (ATG) gene 5 and beclin 1), as well as the pan-caspase-3 inhibitor, Zvad-fmk, were both found to partially block cell death. Blocking autophagy also significantly decreased caspase-3 activity, whereas blocking apoptosis increased the formation of autophagosomes. The survival effects of 3?MA and zVAD-fmk were not additive; rather treatment with both inhibitors lead to increased cell death by necrosis. In summary, the study first suggests that autophagy participates in photoreceptor cell death possibly by initiating apoptosis. Second, it confirms that cells that normally die by apoptosis will execute cell death by necrosis if the normal pathway is blocked. And third, these results argue that the up-stream regulators of autophagy need to be identified as potential therapeutic targets in photoreceptor degeneration.
High-efficiency module-integrated photovoltaic power conditioning system (2009)

A module-integrated, photovoltaic (PV) power conditioning system with a high-efficiency, high step-up DC–DC converter is proposed. The step-up DC–DC converter employs an active-clamp circuit for soft switching of the power semiconductor switches. Also, a dual series-resonant rectifier is employed in order to remove the reverse-recovery problem of the output-rectifying diodes and to provide a much higher voltage conversion ratio. The PV current is estimated without using a DC current sensor, and the PV current ripple reduction technique is suggested to reduce the current ripple without an external component. A 1 kW prototype for the PV voltage range of 30–60 V is implemented, and all algorithms and controllers are implemented on a single-chip microcontroller. Experimental results show that the power efficiency is 92.5–94% and the ripple current is 3.5% of the rated input current.
The anthracyclines: will we ever find a better doxorubicin? (1992)

The anthracyclines are the class of antitumor drugs with the widest spectrum of activity in human cancers, and only a few cancers (eg, colon cancer) are unresponsive to them. The first two anthracyclines were developed in the 1960s. Doxorubicin (DOX) differs from daunorubicin (DNR) only by a single hydroxyl group. This fact has spurred researchers worldwide to find analogs of DOX that have less acute toxicity, cause less cardiomyopathy, can be administered orally, and/or have different, or greater, antitumor efficacy. Five DOX/DNR analogs are marketed in other countries, and one (idarubicin) is available in the United States. None of these analogs have stronger antitumor efficacy than the original two anthracyclines, but there are some differences in toxicity. Methods have been fashioned to keep the peak plasma level of DOX muted to minimize cardiotoxicity, but the only apparently effective method available so far (prolonged drug infusion) is cumbersome. The bisoxopiperazine class of drugs (especially dexrazoxane) provides protection against anthracycline-induced cardiomyopathy and has much promise for helping mitigate this major obstacle to prolonged use of the anthracyclines. The DOX analogs being evaluated in the 1990s have been selected for their ability to overcome multidrug resistance in cancer cells. Thirty years after discovery of the anticancer activity of the first anthracycline, some means of reducing anthracycline toxicity have been devised. Current studies are evaluating increased doses of epirubicin to improve anthracycline cytotoxicity, while limiting cardiotoxicity, but at present DOX still reigns in this drug class as the one having the most proven cancerocidal effect.
Localization of Cellular Retinol‐binding Protein and Cellular Retinoic Acid‐binding Protein in the Rat Testis and Epididymis (1985)

The distribution of cellular retinol-binding protein (CRBP) and cellular retinoic acid-binding protein (CRABP) in rat testis and epididymis was examined by the peroxidase-antiperoxidase immunolocalization technique. In the testis, cellular retinol-binding protein was localized exclusively in the Sertoli cells. Staining varied with the stages of the seminiferous epithelium cycle and was maximal prior to the maturation divisions. Cellular retinoic acid-binding protein was localized exclusively in the germinal cells in the adluminal compartment. The results suggest that retinoic acid may be the retinoid form used by the germinal cells, and that Sertoli cells may use the cellular retinol-binding protein to transfer retinol from the basal to the adluminal compartment. In the epididymis, cellular retinol-binding protein was localized in the cytoplasm and stereocilia of the principal cells in the proximal caput epididymidis, while cellular retinoic acid-binding protein was localized in the spermatozoa and the stereocilia of the principal cells throughout the epididymis and in the epithelial cells of the distal vas deferens. Sperm staining intensity decreased from the initial segment to the cauda. The presence of high levels of cellular retinol-binding protein in the epithelial cells and high levels of cellular retinoic acid-binding protein in the spermatozoa of the caput epididymidis, known to be involved in the synthesis and secretion of factors necessary for sperm maturation, suggests that vitamin A may have a role in this process.
d10 Cations within triple-helical cryptand hosts; a structural and modelling study (2000)

Dicopper(I) analogues of disilver(I) iminocryptates show intercationic separations substantially larger, by as much as 1.5 Å, than do their disilver(I) analogues. This has been confirmed via X-ray crystallography of the tris(ethylene)-capped cryptate [Cu2L3][BPh4]2, 1, and the tris(trimethylene)-capped cryptate [Cu2L2][ClO4]2, 2, for comparison with structurally characterised disilver analogues. A heterobinuclear AgI–CuI cryptate [CuAgL2][ClO4]2, 3, with an intermediate M⋯M′ internuclear distance has also been synthesized. These cryptates have been studied by solution 1H NMR and solid state MAS CP 13C and 15N spectroscopy, and compared with the disilver analogues of these and related cryptand hosts. Although both copper(I) and silver(I) cations are formally closed shell systems, density functional calculations show non-zero bond order between the silver cations. The 1H NMR solution spectra reveal the presence of only one conformer for all dicopper cryptates studied, as well as for the tris(ethylene)-capped disilver analogues, while in the tris(trimethylene)-capped disilver systems several conformers coexist in solution.
Mechanism of suppressive action of TJ114 upon murine type II collagen-induced arthritis. (1995)

Sairei-to (TJ114) is an extract with a multitude of constituents, prepared from 12 mixed raw herbs, i.e., Bupleurum Root, Alisma Rhizome, Pinellia Tuber, Scutellaria Root, Atractylodes Lancea Rhizome, Jujube Fruit, Chuling, Ginseng Root, Hoelen, Glycyrrhiza Root, Cinnamon Bark and Ginger Rhizome. The pharmacological actions of TJ114 include promotion of endogenous steroid secretion and enhancement of steroid effects. Type II collagen induced arthritis was generated in DBA/ 1J mice. Mice were immunized with a series of subcutaneous injections of type II collagen with complete Freund's adjuvant. Three weeks later, incomplete Freund's adjuvant and an equal quantity of type II collagen were injected at the same site as a booster, thereby creating a mouse with type II collagen induced arthritis.TJ114 was effective in delaying and mitigating the development of type II collagen-induced arthritis after both the intial immunization and the booster immunization. As regards the optimal dosage of TJ114, 500 mg/kg/day appeared most effective with respect to mitigation of swelling in the extremities as well as improvement in the inflammation score. The latter is a severity of bone lesions. The special characteristic which emerged in the present study was the significant inhibitory effect of TJ114 with respect to the blast transformation of splenic cells in response to type II collagen as well as inhibition of anti-type II collagen antibody production in the blood serum.
Defining the Incidence of Cardiorespiratory Instability in Patients in Step-down Units Using an Electronic Integrated Monitoring System (2008)

Cardiorespiratory instability, while uncommon and often unrecognized, was preceded by elevation of the IMS index. Continuous noninvasive monitoring augmented by IMS provides sensitive detection of early instability in patients in SDUs.