gebhart/patrepeval huggingface dataset:
Coarse-Grained Brownian Dynamics Simulations of Electrophoresis of DNA Molecules from Generalized Reptation Models (2006)

We derive a course-grained Brownian dynamics simulation algorithm for the motion of DNA chains under an external electric field. We generalize a model for bulk rheological response of entangled polymers by Schieber et al. [J. Rheol. 2003, 47, 213], allowing both rheology and electrophoresis to be modeled under the same theoretical framework. The effect of the external electric field is included by modifying the strand free energy, which then influences both the monomer sliding dynamics between entanglements and the renewal of entanglements at the chain ends. We also modify the free energy to include the finite extensibility of the chain segments and account for changes in local chain mobility with chain configuration. The resulting model gives a detailed account of the chain dynamics on length scales above the tube diameter and is suitable to model a wide range of field conditions. Simulation results for a constant-field mobility are presented, which fully characterize the model under these conditions. We ensure that the model captures known scaling regimes from analytic theory and compare the predictions to a set of experimental data for constant-field mobility of double-stranded DNA in agarose gels at a range of gel concentrations. This data comparison provides a method to characterize DNA−matrix systems, providing possibilities for modeling of more general field conditions.
Induced pluripotent stem cells derived from mouse models of lysosomal storage disorders (2010)

Most lysosomal storage diseases (LSDs) are life-threatening genetic diseases. The pathogenesis of these diseases is poorly understood. Induced pluripotent stem (iPS) cell technology offers new opportunities for both mechanistic studies and development of stem cell- based therapies. Here we report the generation of disease-specific iPS cells from mouse models of Fabry disease, globoid cell leukodystrophy (GLD), and mucopolysaccharidosis VII (MPSVII). These mouse model-derived iPS cells showed defects in disease-specific enzyme activities and significant accumulation of substrates for these enzymes. In the lineage-directed differentiation studies, Fabry-iPS and GLD-iPS cells were efficiently differentiated into disease-relevant cell types, such as cardiomyocytes and neural stem cells, which might be useful in mechanistic and therapeutic studies. Notably, MPSVII-iPS cells demonstrated a markedly impaired ability to form embryoid bodies (EBs) in vitro. MPSVII-EBs exibited elevated levels of hyaluronan and its receptor CD44, and markedly reduced expression levels of E-cadherin and cell-proliferating marker. Partial correction of enzyme deficiency in MSPVII-iPS cells led to improved EB formation and reversal of aberrant protein expression. These data indicate a potential mechanism for the partial lethality of MPSVII mice in utero, and suggest a possible abnormality of embryonic development in MPSVII patients. Thus, our study demonstrates the unique promise of iPS cells for studying the pathogenesis and treatment of LSDs.
Oxygen Minimum Layer: Vertical Distribution and Respiration of the Mysid Gnathophausia ingens (1968)

The large mysid crustacean Gnathophausia ingens (between 35 and 125 millimeters long) lives at oxygen concentrations between 1.25 and 0.20 milliliter per liter along the coast of California. It lives aerobically at these low oxygen concentrations by regulating its rate of oxygen consumption in water having down to and below 0.26 milliliter of oxygen per liter.
Genetic and Epigenetic Alterations of Familial Pancreatic Cancers (2008)

The prevalence of mutant KRAS2, inactivation of TP53 and SMAD4, and aberrant DNA methylation of a seven-gene panel is similar in familial pancreatic adenocarcinomas as in sporadic pancreatic adenocarcinomas. These findings support the use of markers of sporadic pancreatic adenocarcinomas to detect familial pancreatic adenocarcinomas.
Modulation of the voltage-sensitive Na+/H+ exchange in sea urchin spermatozoa through membrane potential changes induced by the egg peptide speract. (1986)

Sea urchin sperm motility can be activated by alkalinization of the internal pH, and previous studies have shown that the internal pH can be regulated by a voltage-sensitive Na+/H+ exchanger present in the flagellar plasma membrane. In this study, the effects of speract, a peptide purified from egg conditioned media, on the Na+/H+ exchange were investigated. Evidence presented indicates that speract activates K+ channels in the flagellar membrane and modulates the Na+/H+ exchange activity through resultant changes in membrane potential. In the presence of tetraphenylphosphonium, a lipophilic ion, or high external Na+, the isolated flagella were depolarized, and Na+/H+ exchanger was inhibited. Speract and valinomycin, a K+ ionophore, were able to reactivate 22Na+ uptake, H+ efflux, and alkalinization of intraflagellar pH under either of the depolarizing conditions. Membrane potential measurements using 3,3'-dipropylthiodicarbocyanide iodide indicated repolarization by either speract or valinomycin. The speract-induced voltage changes did not require Na+ but were sensitive to [K+]. Thus, speract induced a slight depolarization in Na+-free seawater with 10 mM K+ but a hyperpolarization with 2 mM K+. Further support for the activation of K+ channels in the flagella was the 2-5-fold stimulation of K+ efflux induced by speract as measured with a K+ electrode. The ionic selectivity of the speract-activated channel assessed by voltage measurements was K+ greater than Rb+ greater than Cs+. The half-maximally effective concentration of speract was about 0.2 nM. That the H+ and K+ efflux in response to peptide was receptor-mediated was confirmed by the use of speract or resact on intact sea urchin spermatozoa, where the peptides were found to stimulate K+ efflux and to reverse the tetraphenylphosphonium inhibition on H+ efflux only in the homologous spermatozoa. Modulation of the voltage-sensitive Na+/H+ exchange by egg peptides, therefore, appears to be indirect and is coupled through its action on membrane potential.
Transfer Hydrogenation of Organic Formates and Cyclic Carbonates: An Alternative Route to Methanol from Carbon Dioxide (2014)

Transfer hydrogenation of organic formates and cyclic carbonates was achieved for the first time using a readily available ruthenium catalyst. Nontoxic and economical 2-propanol was used, both as a solvent and hydrogen source, without the need of using flammable H2 gas under high pressure. This method provides an indirect strategy to produce methanol from carbon dioxide under mild conditions as well as an operationally simple and environmentally benign way to reduce formates and carbonates.
Transformation of mono‐ and dichlorinated phenoxybenzoates by phenoxybenzoate‐dioxygenase in Pseudomonas pseudoalcaligenes POB310 and a modified diarylether‐metabolizing bacterium (2000)

Pseudomonas pseudoalcaligenes POB310 contains genes that encode phenoxybenzoate dioxygenase. The enzyme transforms mono- and dichlorinated phenoxybenzoates to yield protocatechuate that is used as a growth substrate and chlorophenols that are nonmetabolizable. Mass spectral analysis of 18O metabolites obtained from the protocatechuate 3,4-dioxygenase-deficient mutant, POB310-B1, suggested that the reaction mechanism is a regioselective angular dioxygenation. A cloning vector containing reaction relevant genes (pD30.9) was transferred into Pseudomonas sp. strain B13 containing a modified ortho-cleavage pathway for aromatic compounds. The resultant Pseudomonas sp. strain B13-D5 (pD30.9) completely metabolized 3-(4-chlorophenoxy)benzoate. During growth on 3-phenoxybenzoate, strain B13-D5 (pD30.9) (Ks = 0.70 ± 0.04 mM, μmax = 0.45 ± 0.03 h−1, td = 1.5 h, Y = 0.45 ± 0.03 g bio- mass · g substrate−1) was better adapted to low substrate concentrations, had a faster rate of growth, and a greater yield than POB310 (Ks = 1.13 ± 0.06 mM, μmax = 0.31 ± 0.02 h−1, td = 2.2 h, Y = 0.39 ± 0.02 g biomass · g substrate−1). © 2000 John Wiley & Sons, Inc. Biotechnol Bioeng 69: 107–112, 2000.
Adenocarcinoma of duodenum and ampulla of Vater: Clinicopathology study and expression of p53, c-neu, TGF-α, CEA, and EMA (1996)

Oncogenes, tumor suppressor genes, and growth factors are being explored as to their role in the initiation and progression of most neoplasms, but little information exists on the expression of oncoproteins or growth factors in adenocarcinoma of the duodenum or ampulla of Vater. This report covers expressions of p53, c-neu, TGF-alpha, CEA, and EMA in duodenal adenocarcinoma and ampullary adenocarcinoma, as well as correlations between expressions and tumor stage, histological grade and patient survival. The expression of p53, c-neu, TGF-alpha, CEA, and EMA has been studied in 15 duodenal adenocarcinomas and in eight ampullary adenocarcinomas by avidin-biotin-peroxidase complex indirect immunoperoxidase technique. The positive reaction for p53, c-neu, TGF-alpha, CEA, and EMA in duodenal adenocarcinoma was 20%, 60%, 60%, 73%, and 100%, respectively, and in ampullary adenocarcinoma, 13%, 100%, 50%, 63%, and 100%. Among the duodenal tumors, C-neu and p53 expression was noted more frequently in groups with high histological grades. Patients with c-neu positive duodenal adenocarcinoma had a shorter survival than the patients with c-neu negative duodenal adenocarcinoma (P < 0.01). C-neu product may serve as an unfavorable prognostic indicator in duodenal adenocarcinoma. No statistically significant correlation was found between the expressions of CEA, EMA, p53, and TGF-alpha and patient survival, tumor stage, or histological grade in either duodenal or ampullary adenocarcinomas.
Effective Octadecylamine System for Nanocrystal Synthesis (2011)

New chemical reactions and synthetic systems are of key importance for materials fabrication. In this work, we reported a facile and effective octadecylamine (ODA) synthetic system for various nanocrystals including metals, mixed metal oxides, metal/metal oxide heterostructured nanocrystals, intermetallics, and alloys. We found that the products were mainly determined by metal ions used in our synthetic system: noble metal ions led to the formation of metals; two kinds of non-noble metal ions led to the formation of mixed metal oxides; silver ions and non-noble metal ions led to the formation of metal/metal oxide heterostructured nanocrystals; non-noble metal ions and noble metal (excluding Ag) ions led to the formation of intermetallics and alloys. The difference was attributed to different ability to attract electrons from ODA solvent among these metal ions. This effective system provides a general strategy for various nanocrystals which would find potential applications in many significant fields.
The 1,629-nucleotide open reading frame located downstream of the Autographa californica nuclear polyhedrosis virus polyhedrin gene encodes a nucleocapsid-associated phosphoprotein (1993)

A 78-kDa protein was produced in bacteria from a clone of the 1,629-nucleotide open reading frame located immediately downstream from the polyhedrin gene of Autographa californica nuclear polyhedrosis virus. The identity of this protein was confirmed by its reactivity with peptide antiserum and amino terminal peptide sequencing after purification from transformed bacteria. The polypeptide was used to produce polyclonal antisera in rabbits. Immunoblot analysis of insect cells infected with the baculovirus indicated that two related proteins with molecular masses of 78 and 83 kDa were synthesized late in infection. Biochemical fractionation studies indicated that both of these proteins were present in purified nucleocapsids from budded and occluded virus preparations. Immunoprecipitation of 32P-labeled proteins and treatment of purified nucleocapsids with alkaline phosphatase demonstrated that the 83-kDa protein was a phosphorylated derivative of the 78-kDa protein. Furthermore, immunoelectron microscopy revealed that the proteins were localized to regions of nucleocapsid assembly within the infected cell and appeared to be associated with the end structures of mature nucleocapsids.
Metabolism of poly(3-hydroxyalkanoates) (PHAs) by Pseudomonas oleovorans. Identification and sequences of genes and function of the encoded proteins in the synthesis and degradation of PHA (1991)

Pseudomonas oleovorans accumulates poly(3-hydroxyalkanoates) (PHAs) after growth on medium chain length hydrocarbons. Large amounts of this polyester are synthesized when cells are grown under nitrogen-limiting conditions. When nitrogen is resupplied in the medium, the accumulated PHA is degraded. In this paper, we describe mutants which are defective in the synthesis or in the degradation of PHA. These mutants were used to select DNA fragments which encode PHA polymerases and a PHA depolymerase. A 25-kilobase (kb) DNA fragment was isolated from P. oleovorans that complements a Pseudomonas putida mutant unable to accumulate PHA. Subcloning resulted in the assignment of a 6.4-kb EcoRI fragment as the pha locus, containing genetic information for PHA synthesis. Mutants in the PHA degradation pathway were also complemented by this fragment, indicating that genes encoding PHA biosynthetic and degradative enzymes are clustered. Analysis of the DNA sequence of the 6.4-kb fragment revealed the presence of two open reading frames encoding PHA polymerases based on homology to the poly(3-hydroxybutyrate) polymerase from Alcaligenes eutrophus. A third open reading frame complemented the PHA degradation mutation and is likely to encode a PHA depolymerase. The presence of two PHA polymerases is due to a 2098-base pair DNA duplication. The PHA polymerases are 53% identical and show 35-40% identity to the poly(3-hydroxybutyrate) polymerase. No clear difference in specificity was found for the PHA polymerases. However, with the pha locus cloned on a multicopy vector, a polymer was accumulated that contains a significantly higher amount of substrate-derived monomers. An increase in the rate of polyester synthesis versus oxidation of the monomers in the beta-oxidation explains these findings.
Control of neurite outgrowth by RhoA inactivation (2011)

cAMP induces neurite outgrowth in the rat pheochromocytoma cell line 12 (PC12). In particular, di-butyric cAMP (db-cAMP) induces a greater number of primary processes with shorter length than the number induced by nerve growth factor (NGF). db-cAMP up- and down-regulates GTP-RhoA levels in PC12 cells in a time-dependent manner. Tat-C3 toxin stimulates neurite outgrowth, whereas lysophosphatidic acid (LPA) and constitutively active (CA)-RhoA reduce neurite outgrowth, suggesting that RhoA inactivation is essential for the neurite outgrowth from PC12 cells stimulated by cAMP. In this study, the mechanism by which RhoA is inactivated in response to cAMP was examined. db-cAMP induces phosphorylation of RhoA and augments the binding of RhoA with Rho guanine nucleotide dissociation inhibitor (GDI). Moreover, RhoA (S188D) mimicking phosphorylated RhoA induces greater neurite outgrowth than RhoA (S188A) mimicking dephosphorylated form does. Additionally, db-cAMP increases GTP-Rap1 levels, and dominant negative (DN)-Rap1 and DN-Rap-dependent RhoGAP (ARAP3) block neurite outgrowth induced by db-cAMP. DN-p190RhoGAP and the Src inhibitor PP2 suppress neurite outgrowth, whereas transfection of c-Src and p190RhoGAP cDNAs synergistically stimulate neurite outgrowth. Taken together, RhoA is inactivated by phosphorylation of itself, by p190RhoGAP which is activated by Src, and by ARAP3 which is activated by Rap1 during neurite outgrowth from PC12 cells in response to db-cAMP.
Novel vitamin E analogue decreases syngeneic mouse mammary tumor burden and reduces lung metastasis. (2003)

A nonhydrolyzable ether analogue of RRR-alpha-tocopherol, 2,5,7,8-tetramethyl-2R-(4R, 8R, 12-trimethyltridecyl)chroman-6-yloxyacetic acid, called RRR-alpha-tocopheryloxyacetic acid or RRR-alpha-tocopherol ether-linked acetic acid analogue (alpha-TEA), exhibits antitumor activity in vitro and in vivo using a syngeneic BALB/c mouse mammary tumor model (line 66 clone 4 stably transfected with green fluorescent protein). Treatment of cells with 5, 10, and 20 micro g/ml alpha-TEA for 3 days produced 6, 34, and 50% apoptosis, respectively, and treatment of cells with 10 micro g/ml for 2, 3, 4, and 5 days produced 20, 35, 47, and 58% apoptosis, respectively. A liposomal formulation of alpha-TEA administered by aerosol reduced s.c. tumor growth and lung metastasis. Alpha-TEA-treated animals showed a significant decrease in tumor volumes over 17 days of aerosol treatment (P < 0.001). Forty percent of aerosol as well as untreated control mice had visible, macroscopic lung metastases versus none (0%) of the alpha-TEA-treated mice. On the basis of fluorescence microscopic examination of the surface (top and bottom) of flattened whole left lung lobes, an average of 60 +/- 15 and 102 +/- 17 versus 11 +/- 4 fluorescent microscopic metastases was observed in aerosol control and untreated control versus alpha-TEA-treated animals, respectively. Alpha-TEA formulated in ethanol + peanut oil (5 mg/mouse/day) delivered by gavage did not reduce s.c. primary tumor burden; however, fluorescent microscopic lung metastases were significantly reduced (P < 0.0021). In summary, alpha-TEA formulated in liposomes and delivered by aerosol is a potent antitumor agent and reduces lung metastasis.
Impact of microstructure on local carrier lifetime in perovskite solar cells (2015)

The remarkable performance of hybrid perovskite photovoltaics is attributed to their long carrier lifetimes and high photoluminescence (PL) efficiencies. High-quality films are associated with slower PL decays, and it has been claimed that grain boundaries have a negligible impact on performance. We used confocal fluorescence microscopy correlated with scanning electron microscopy to spatially resolve the PL decay dynamics from films of nonstoichiometric organic-inorganic perovskites, CH3NH3PbI3(Cl). The PL intensities and lifetimes varied between different grains in the same film, even for films that exhibited long bulk lifetimes. The grain boundaries were dimmer and exhibited faster nonradiative decay. Energy-dispersive x-ray spectroscopy showed a positive correlation between chlorine concentration and regions of brighter PL, whereas PL imaging revealed that chemical treatment with pyridine could activate previously dark grains.
Activation of the Native 45-kDa Precursor Form of Interleukin-1-converting Enzyme (1996)

Active interleukin-1beta-converting enzyme (ICE) is composed of 20- and 10-kDa polypeptides (p20 and p10) derived from the processing of a cytosolic 45-kDa precursor protein (p45). The cleavage and activation of the native p45 ICE precursor have been characterized by use of specific inhibitors and antibodies recognizing various regions of ICE. The processing of p45 in vitro in THP.1 monocytic cell cytoplasmic extracts is inhibited only by protease inhibitors that inhibit ICE and not by inhibitors of other protease classes. The addition of L-742,395, a biotinylated irreversible ICE inhibitor, to these extracts labels only p45 and simultaneously inhibits p45 processing, demonstrating that the p45 has catalytic activity. Following a cleavage of p45 at a site that becomes the COOH terminus of p20, a more active intermediate is formed which migrates on SDS-polyacrylamide gel electrophoresis with an molecular mass of 35 kDa (ED50 of approximately 0.1 microM L-742,395 labeling versus 5 microM for p45). This new more active ICE form serves both as an intermediate enzyme to cleave p45 as well as a substrate for the formation of the final active ICE (ED50 of 1 nM L-742,395 labeling of p20 and for p22, an NH2-terminally extended form of p20). While initial cleavage of p45 can be found at the sites corresponding to both the NH2 termini of p22 and p20, these fragments cannot be labeled by L-742,395 and are hence inactive. p45 is not processed at the site corresponding to the NH2 terminus of the p10. Less than 50% of the p45 is cleaved down to active p20 or p22 ICE as determined by band shift on SDS-polyacrylamide gel electrophoresis of the biotinylated fragments, indicating that the in vitro activation is highly inefficient. The ICE fragmentation occurs by an intermolecular process and is highly dilution sensitive. Cleavage of p45 by exogenous p20/p10 ICE differs from that of the endogenous p45 cleavage activity in that the p20/p10 activity is more salt sensitive, and it produces a different pattern of cleavage fragments, principally 35- and 12-kDa fragments. These results indicate that the nature of the ICE activity changes as p45 is processed down to the p20/p10 form of the enzyme.
A single amino acid substitution strongly modulates the activity and substrate specificity of the mouse mdr1 and mdr3 drug efflux pumps. (1991)

Specific protein domains and amino acids responsible for the apparent capacity of P-glycoprotein (mdr) to recognize and transport a large group of structurally unrelated drugs have not been identified. We have introduced a single Ser----Phe substitution within the predicted TM11 domain of mdr1 (position 941) and mdr3 (position 939) and analyzed the effect of these substitutions on the drug-resistance profiles of these two proteins. Mutations at this residue drastically altered the overall degree of drug resistance conveyed by mdr1 and mdr3. The modulating effect of this mutation on mdr1 and mdr3 varied for the drugs tested: it was very strong for colchicine and adriamycin and moderate for vinblastine. For mdr1, the Ser941----Phe941 substitution produced a unique mutant protein that retained the capacity to confer vinblastine resistance but lost the ability to confer adriamycin and colchicine resistance. These results strongly suggest that the predicted TM11 domain of proteins encoded by mdr and mdr-like genes plays an important role in the recognition and transport of their specific substrates.
NBBS traffic management overview (1995)

In this paper, we describe an integrated set of procedures used for bandwidth management and congestion control in high-speed packet-switched networks such as asynchronous transfer mode (ATM), which are part of IBM's Networking BroadBand Services (NBBS) architecture. These controls are designed to support a wide variety of services with different characteristics in the network and operate at different time scales: connection-level controls such as path selection, admission control and bandwidth allocation, and packet-level controls that discriminate between packets from different connections to support multiple levels of service guarantees. Connection-level controls are applied at connection setup time and are based on the connection characterization and the network state at that time. They perform efficient allocation of resources to ensure performance guarantees for connections while achieving high utilization of network resources. Various packet-level controls developed include access or rate control and intermediate node buffer management and scheduling. For connections that do not require explicit service guarantees, NBBS offers an available bit rate service. This service mostly relies on packet-level control in the form of an end-to-end rate-based flow control algorithm that regulates the flow of traffic into the network. This paper, in addition to providing an overview of the different mechanisms used for traffic management in NBBS, highlights how they interact to ensure efficient network operation.
A design for a smartphone-based head mounted display (2011)

Thin computing clients, such as smartphones and tablets, have experienced recent growth in display resolutions and graphics processing power. In this poster, we show how to leverage these trends to create an experimental wide field of view, 3D stereoscopic head mounted display (HMD), based on two high resolution smart-phones. This HMD prototype is unique in that the graphics system is entirely onboard, allowing it to be lightweight, wireless, and convenient to use.