gebhart/patrepeval huggingface dataset:
DNA replication <i>in vitro</i> by recombinant DNA‐polymerase‐α‐primase (1994)

DNA-polymerase-alpha--primase complex contains four subunits, p180, p68, p58, and p48, and comprises a minimum of two enzymic functions. We have cloned cDNAs encoding subunits of DNA-polymerase-alpha--primase from human and mouse. Sequence comparisons showed high amino acid conservation among the mammalian proteins. We have over-expressed the single polypeptides and co-expressed various subunit complexes using baculovirus vectors, purified the proteins and investigated their biochemical properties. The purified mouse p48 subunit (Mp48) alone had primase activity. Purification of co-expressed Mp48 and Mp58 subunits yielded stable DNA primase of high specific activity. Co-expression of all four subunits yielded large quantities of tetrameric DNA-polymerase-alpha--primase. The p180, p58 and p48 polypeptides were also co-expressed and immunoaffinity purified as a trimeric enzyme complex. The tetrameric and trimeric DNA-polymerase-alpha--primase complexes showed both DNA primase and DNA polymerase activities. The tetrameric recombinant DNA-polymerase-alpha--primase synthesized double-stranded M13 DNA and replicated polyoma viral DNA in vitro efficiently.
Sub-Surface Boron-Doped Copper for Methane Activation and Coupling: First-Principles Investigation of the Structure, Activity, and Selectivity of the Catalyst (2016)

Copper (Cu) is a commercial catalyst for the synthesis of methanol from syngas, low-temperature water gas shift reaction, oleo-chemical processing, and for the fabrication of graphene by chemical vapor deposition. However, high barriers for C–H bond activation and the ease of formation of carbon/graphene on its surface limits its application in the utilization and conversion of methane to bulk chemicals. In the present paper, using first-principles calculations, we predict that Cu catalyst doped with a monolayer of sub-surface boron (B–Cu) can efficiently activate the C–H bond of methane and can selectively facilitate the C–C coupling reaction. Boron binds strongest at the sub-surface octahedral site of Cu and the thermodynamic driving force for the diffusion of B from an on-surface to the sub-surface position in Cu is stronger than that for the experimentally synthesizable B–Ni (sub-surface boron in nickel) catalyst, providing a proof of concept for the experimental synthesis of this novel catalyst. Additionally, the first-principles computed free energy of the reaction to form B–Cu from boron precursor and Cu is also favorable. The presence of the monolayer sub-surface B in Cu creates a corrugated step-like structure on the Cu surface and significantly brings down the methane C–H activation barrier from 174 kJ/mol on Cu(111) to only 75 kJ/mol on B–Cu. The subsequent dehydrogenation of the adsorbed CH3* to CH2* is also kinetically and thermodynamically feasible. Our calculations also suggest that, unlike most of the transition metals, complete decomposition of methane to carbon would not be favored on B–Cu. The dissociation of the surface CH2* moiety on B–Cu is limited due to the high activation barrier of 161 kJ/mol and lower relative stability of the resultant CH* species, under reaction conditions. The coupling of CH2* fragments however is kinetically and thermodynamically favorable, with an activation barrier of only 92 kJ/mol; suggesting that B–Cu catalyst would have higher selectivity toward C2 hydrocarbons. Furthermore, the formation of carbon from the adsorbed CH* moiety has a very high activation barrier of 197 kJ/mol and the completely dehydrogenated C* is relatively much less stable than CH*, under reaction conditions; predicting that coking might not be an issue on the B–Cu catalyst. Evaluation of C–H activation on Cu(110) surface, which has a similar step-like surface structure as B–Cu, and Bader charge and density of states analyses of B–Cu reveal that the geometrical/corrugation effect and the charge transfer from B to Cu synergistically promote the C–H activation on B–Cu, making it as active as other expensive transition metals like Rh, Ru, Ir, and Pt.
Synthetic Studies on 2′-Substituted-4′-thiocytidine Derivatives as Antineoplastic Agents (1999)

As potential antineoplastic agents, we have synthesized 4'-thioFAC and 4'-thiocytarazid by developing an alternative synthetic method. 4'-ThioFAC showed potent antineoplastic activities in vivo as well as in vitro.
Time dependent photon mapping (2002)

The photon map technique for global illumination does not specifically address animated scenes. In particular, prior work has not considered the problem of temporal sampling (motion blur) while using the photon map. In this paper we examine several approaches for simulating motion blur with the photon map. In particular we show that a distribution of photons in time combined with the standard photon map radiance estimate is incorrect, and we introduce a simple generalization that correctly handles photons distributed in both time and space. Our results demonstrate that this time dependent photon map extension allows fast and correct estimates of motion-blurred illumination including motion-blurred caustics.
Community Policing and the Work Routines of Street-Level Officers (2001)

Most of the literature on community policing suggests, either implicitly or explicitly, that the daily activities of community police officers will differ from the activities traditionally engaged in by police officers. The majority of studies examining officer work routines were conducted prior to the rapid proliferation of community policing throughout police departments in the United States. Any attempt to determine the nature and extent of community policing needs to include an examination of the daily activities of line-level personnel charged with its implementation. The current study, using systematic social observation data, provides a description and comparison of the work routines of both community-oriented and traditional police officers in a city implementing community-oriented policing. Many of the findings are similar to those of previous workload studies. However, the findings also indicate that community officers devoted significantly more time to nontraditional policing activities than beat officers. Further, 911 beat officers spent significantly more time engaged in traditional policing activities than community officers.
Graphene-based Composite Thin Films for Electronics (2009)

The electrical properties of solution-processed composite thin films consisting of functionalized graphene sheets (FGS) as the filler and polystyrene (PS) as the host material are described. We demonstrate that transistors from graphene-based composite thin films exhibit ambipolar field effect characteristics, suggesting transport via percolation among FGS in the insulating PS matrix. Device characteristics as a function of the FGS size are also reported. The results indicate that devices fabricated using the largest size FGS yield the highest mobility values. This simple and scaleable fabrication scheme based on a commodity plastic could be useful for low-cost, macro-scale electronics.
Optimization of Synthetic Jet Fluidic Structures in Printed Wiring Boards (2006)

The active cooling substrate in this study is a microelectromechanical system device that implements the synthetic jet concept into a printed wiring board (PWB) to enhance thermal management. Synthetic jets are oscillatory jets synthesized from the surrounding fluid using electromagnetic actuators. The jet fluid mechanics and heat transfer applications have been investigated by a variety of on-board (PWB) fluidic structures. A testbed comprising six different fluidic channels has been fabricated and characterized with a standard silicon based platinum heater. Based on the fluid mechanics measurements and cooling performance tests, an empirical correlation of synthetic jet Nusselt number with its Reynolds number, fluidic channel dimensions, and jet locations has been derived. Through a magnitude analysis, jet actuator diaphragm, fluidic channel dimension, and cooling location optimizations have been investigated.
A new class of peroxisome proliferator-activated receptor γ (PPARγ) agonists that inhibit growth of breast cancer cells: 1,1-Bis(3′-indolyl)-1-(<i>p</i>-substituted phenyl)methanes (2004)

Abstract 1,1-Bis(3′-indolyl)-1-(p-trifluoromethylphenyl)methane (DIM-C-pPhCF3) and several p-substituted phenyl analogues have been investigated as a new class of peroxisome proliferator-activated receptor γ (PPARγ) agonists. Structure-activity studies in PPARγ-dependent transactivation assays in MCF-7 breast cancer cells show that 5–20 μm concentrations of compounds containing p-trifluoromethyl, t-butyl, cyano, dimethylamino, and phenyl groups were active, whereas p-methyl, hydrogen, methoxy, hydroxyl, or halogen groups were inactive as PPARγ agonists. Induction of PPARγ-dependent transactivation by 15-deoxy-Δ12,14-prostaglandin J2 (PGJ2) and DIM-C-pPhCF3 was inhibited in MCF-7 cells cotreated with the PPARγ-specific antagonist N-(4′-aminopyridyl)-2-chloro-5-nitrobenzamide. In mammalian two-hybrid assays, DIM-C-pPhCF3 and PGJ2 (5–20 μm) induced interactions of PPARγ with steroid receptor coactivator (SRC) 1, SRC2 (TIFII), and thyroid hormone receptor-associated protein 220 but not with SRC3 (AIB1). In contrast, DIM-C-pPhCF3, but not PGJ2, induced interactions of PPARγ with PPARγ coactivator-1. C-substituted diindolylmethanes inhibit carcinogen-induced rat mammary tumor growth, induce differentiation in 3T3-L1 preadipocytes, inhibit MCF-7 cell growth and G0/G1-S phase progression, induce apoptosis, and down-regulate cyclin D1 protein and estrogen receptor α in breast cancer cells. These compounds are a novel class of synthetic PPARγ agonists that induce responses in MCF-7 cells similar to those observed for PGJ2.
Anisotropic photoluminescence in incomplete three-dimensional photonic band-gap environments (1999)

The effect of an incomplete three-dimensional photonic band-gap structure upon the wideband photoluminescence from bare opal and opal impregnated with ZnS has been studied by means of angular-resolved photoluminescence. It has been shown that the photoluminescence becomes anisotropic in accordance with the angular dispersion of the stop band. Suppression of the spontaneous emission in the stop-band energy region and amplification of the spontaneous emission at the edge of the stop band have both been demonstrated.
Conformational changes of enzymes adsorbed at liquid– solid interface: Relevance to enzymatic activity (2002)

FTIR with attenuated total reflectance spectroscopy was used to study in situ adsorption of enzymes at water-solid interfaces to better understand how conformational changes may monitor enzymatic activity. Because the adsorption process depends on hydrophobic and electrostatic interactions, conformational changes were studied as a function of the nature of the adsorbing substrates, which are hydrophobic or hydrophilic in character. The adsorption kinetics of two examples of serine enzymes, alpha-chymotrypsin (alpha-chym) and Humicola lanuginosa lipase (HLL), were studied. The secondary structure and solvation of the adsorbed enzymes were both compared to the dissolved enzymes. The positively charged alpha-chym was adsorbed on a negatively charged hydrophilic support with minor structural changes, but the negatively charged lipase had no affinity for a similar support. Both enzymes were strongly retained on the hydrophobic support. The secondary and tertiary structures of the alpha-chym adsorbed on the hydrophobic support were strongly altered, which correlates to the inhibition of enzymatic hydrolysis. The specific solvation obtained for the adsorbed HLL is consistent with the existence of the open conformer in relation to the enhanced enzymatic activity at the water-hydrophobic interface.
Sum rate maximization in multi-operator two-way relay networks with a MIMO AF relay via POTDC (2013)

We address the beamforming problem for maximizing the sum rate of a multi-operator two-way relay (TWR) network subject to the constraint on the total relay transmit power. This scenario is also known as relay sharing for multi-way relaying or TWR for multiple operators. The relay is assumed to be equipped with multiple antennas, and it uses the amplify-and-forward relaying strategy. It is shown that the corresponding optimization problem can be represented as a difference of convex functions (DC) programming problem which is NP-hard in general. Nevertheless, we develop an efficient polynomial time algorithm to solve the problem approximately. The performance comparison of the proposed polynomial time DC (POTDC) inspired algorithm to the existing state-of-the-art algorithms demonstrate that the proposed algorithm outperforms the existing algorithms especially in the case of non-symmetric networks.
Wire + Arc Additive Manufacturing (2015)

Depositing large components (>10 kg) in titanium, aluminium, steel and other metals is possible using Wire + Arc Additive Manufacturing. This technology adopts arc welding tools and wire as feedstock for additive manufacturing purposes. High deposition rates, low material and equipment costs, and good structural integrity make Wire+Arc Additive Manufacturing a suitable candidate for replacing the current method of manufacturing from solid billets or large forgings, especially with regards to low and medium complexity parts. A variety of components have been successfully manufactured with this process, including Ti–6Al–4V spars and landing gear assemblies, aluminium wing ribs, steel wind tunnel models and cones. Strategies on how to manage residual stress, improve mechanical properties and eliminate defects such as porosity are suggested. Finally, the benefits of non-destructive testing, online monitoring and in situ machining are discussed.
Phosphorylation of the Ndc80 complex protein, HEC1, by Nek2 kinase modulates chromosome alignment and signaling of the spindle assembly checkpoint (2011)

The spindle assemble checkpoint (SAC) is critical for accurate chromosome segregation. Hec1 contributes to chromosome segregation in part by mediating SAC signaling and chromosome alignment. However, the molecular mechanism by which Hec1 modulates checkpoint signaling and alignment remains poorly understood. We found that Hec1 serine 165 (S165) is preferentially phosphorylated at kinetochores. Phosphorylated Hec1 serine 165 (pS165) specifically localized to kinetochores of misaligned chromosomes, showing a spatiotemporal distribution characteristic of SAC molecules. Expressing an RNA interference (RNAi)-resistant S165A mutant in Hec1-depleted cells permitted normal progression to metaphase, but accelerated the metaphase-to-anaphase transition. The S165A cells were defective in Mad1 and Mad2 localization to kinetochores, regardless of attachment status. These cells often entered anaphase with lagging chromosomes and elicited increased segregation errors and cell death. In contrast, expressing S165E mutant in Hec1-depleted cells triggered defective chromosome alignment and severe mitotic arrest associated with increased Mad1/Mad2 signals at prometaphase kinetochores. A small portion of S165E cells eventually bypassed the SAC but showed severe segregation errors. Nek2 is the primary kinase responsible for kinetochore pS165, while PP1 phosphatase may dephosphorylate pS165 during SAC silencing. Taken together, these results suggest that modifications of Hec1 S165 serve as an important mechanism in modulating SAC signaling and chromosome alignment.
Event-based low-frequency impedance modeling using well logs and seismic attributes (2008)

Acoustic impedance is a rock property that, under specific conditions, can be derived from seismic data and can provide important insights into reservoir parameters—such as porosity, lithology, fluid content, etc. Direct measurements of acoustic impedance are available from sonic and density well logs. Seismic inversion, a process of converting seismic data into relative impedance, provides estimates of relative acoustic impedance away from the well locations. Because absolute acoustic impedance can be related to other rock properties, the inverted relative seismic impedance could be used to predict these properties away from the wells if the missing low frequencies could be reliably calculated and compensated for. In chalk, seismic inversion finds its most significant application in porosity prediction.
A New Method for Chemical Vapor Deposition of Silicon Dioxide (1974)

A new method for the deposition of films prepared by the oxidation of alkyl‐silane vapors is reported. It is found that the oxidation of tripropyl‐silane in oxygen at a temperature of about 650°C yields transparent adhesive and uniform films of grown on silicon substrates. The growth rate of the films as a function of various growth parameters is studied. The films have been characterized using IR absorption, spark source mass spectrometry, and emission spectroscopy. The structure of the films has been studied by optical microscopy and scanning electron microscopy and the index of refraction by ellipsometry. The applicability of these films to the planar MOS technology in microelectronics is evaluated by the following properties: etch rate, masking efficiency, flatband voltage, and electrical stability. Finally, the characteristics of MOS field effect transistors built with these oxides are given and shown to be almost comparable to those built with thermally grown .
Niche-Dependent Gene Expression Profile of Intratumoral Heterogeneous Ovarian Cancer Stem Cell Populations (2013)

Intratumoral heterogeneity challenges existing paradigms for anti-cancer therapy. We have previously demonstrated that the human embryonic stem cells (hESC)-derived cellular microenvironment in immunocompromised mice, enables functional distinction of heterogeneous tumor cells, including cells which do not grow into a tumor in a conventional direct tumor xenograft platform. We have identified and characterized six cancer cell subpopulations each clonally expanded from a single cell, derived from human ovarian clear cell carcinoma of a single tumor, to demonstrate striking intratumoral phenotypic heterogeneity that is dynamically dependent on the tumor growth microenvironment. These cancer cell subpopulations, characterized as cancer stem cell subpopulations, faithfully recapitulate the full spectrum of histological phenotypic heterogeneity known for human ovarian clear cell carcinoma. Each of the six subpopulations displays a different level of morphologic and tumorigenic differentiation wherein growth in the hESC-derived microenvironment favors growth of CD44+/aldehyde dehydrogenase positive pockets of self-renewing cells that sustain tumor growth through a process of tumorigenic differentiation into CD44-/aldehyde dehydrogenase negative derivatives. Strikingly, these derivative cells display microenvironment-dependent plasticity with the capacity to restore self-renewal markers and CD44 expression. In the current study, we delineate the distinct gene expression and epigenetic profiles of two such subpopulations, representing extremes of phenotypic heterogeneity in terms of niche-dependent self-renewal and tumorigenic differentiation. By combining Gene Set Enrichment, Gene Ontology and Pathway-focused array analyses with methylation status, we propose a suite of robust differences in tumor self-renewal and differentiation pathways that underlie the striking intratumoral phenotypic heterogeneity which characterize this and other solid tumor malignancies.
Rituximab induces phenotypical and functional changes of NK cells in a non-malignant experimental setting (2016)

NK cells mediate rituximab-induced B cell depletion. Rituximab induces altered NK cell phenotype and function.
Antitumor activity of monomeric and polymeric cyclophosphamide derivatives compared with in vitro hydrolysis. (1980)

Relatively stable sulfhydryl derivatives of 4-hydroxycyclophosphamide and these same derivatives covalently bound to a polymeric carrier were studied in vitro and in vivo. The rate of release of 4-hydroxycyclophosphamide from monomeric and polymeric derivatives was examined under physiological conditions (pH 7.0, 37.0 degrees) in vitro. Hydrophobicity and length of alkyl chain of substituents at the 4-position of the phosphamide ring decreased the rate of hydrolysis. The polymeric derivatives were more slowly hydrolyzed than were their corresponding monomers. Toxicity in mice indicated that the rate of hydrolysis in vitro is related to toxicity in vivo. The optimal antitumor activity (maximum 270% increase in life span in L1210-bearing mice) and effective dose range of each derivative of low molecular weight were similar to cyclophosphamide. The polymeric derivatives exhibited much less antitumor activity (maximum 50% increase in the life span) than did cyclophosphamide. The short-alkyl-chain monomeric derivatives such as propanol and propionic acid caused acute lethal toxicity, which limited the upper dose usable for antitumor activity. Polymeric derivatives, when compared on a molar basis to their corresponding monomers, were relatively more toxic to the mice which limited their maximum dose.
Silicon-Neuron Design: A Dynamical Systems Approach (2010)

We present an approach to design spiking silicon neurons based on dynamical systems theory. Dynamical systems theory aids in choosing the appropriate level of abstraction, prescribing a neuron model with the desired dynamics while maintaining simplicity. Further, we provide a procedure to transform the prescribed equations into subthreshold current-mode circuits. We present a circuit design example, a positive-feedback integrate-and-fire neuron, fabricated in 0.25 μm CMOS. We analyze and characterize the circuit, and demonstrate that it can be configured to exhibit desired behaviors, including spike-frequency adaptation and two forms of bursting.
[Studies on polymer-support drug: synthesis of PEG-estrogen compounds]. (1987)

Estrogen denotes a kind of steroidal hormone and has strong physiological activity. PEG is a polymer with good solubility both in water and in organic solvents. We hope to change the solubility and drug metabolism kinetic behavior of estrogen by connecting PEG to estrogen in order to apply polymer in medical chemistry. In the present paper, four new PEG-estrogen compounds were prepared and their structures determined by UV, IR, and ~(13)CNMR. Estrodiol(E) and Ethinyl Estrodiol(EE)were selected as low-molecular weight drugs. The procedure for synthesis reported in this paper: first the terminal hydroxyl groups in PEG were substituted by chlorine-atom; then the chlorinated PEG reacted with E-3-Na and EE-3-Na to form the title compounds. Initial pharmacological tests indicated that the new compounds retain the some estrogenic action.
Adsorption and absorption of boron, nitrogen, aluminum, and phosphorus on silicene: Stability and electronic and phonon properties (2013)

Ab initio calculations within the density-functional theory formalism are performed to investigate the chemical functionalization of a graphene-like monolayer of silicon---silicene---with B, N, Al, or P atoms. The structural, electronic, magnetic, and vibrational properties are reported. The most preferable adsorption sites are found to be valley, bridge, valley and hill sites for B, N, Al, and P adatoms, respectively. All the relaxed systems with adsorbed/substituted atoms exhibit metallic behavior with strongly bonded B, N, Al, and P atoms accompanied by an appreciable electron transfer from silicene to the B, N, and P adatom/substituent. The Al atoms exhibit opposite charge transfer, with $n$-type doping of silicene and weaker bonding. The adatoms/substituents induce characteristic branches in the phonon spectrum of silicene, which can be probed by Raman measurements. Using molecular dynamics, we found that the systems under study are stable up to at least $T=500$ K. Our results demonstrate that silicene has a very reactive and functionalizable surface.