gebhart/patrepeval huggingface dataset:
Distamycin-induced inhibition of formation of a nucleoprotein complex between the terminase small subunit G1P and the non-encapsidated end (pacL site) of Bacillus subtilis bacteriophage SPP1 (1996)

The small subunit of the Bacillus subtilis bacteriophage SPP1 terminase (G1P) forms a sequence-specific nucleoprotein complex with the SPP1 non-encapsidated end (pacL site) during initiation of DNA encapsidation. Gel mobility shift assay was used to study the G1P-pacL interaction. Distamycin, a minor groove binder that induces local distortion of the DNA, inhibits G1P-pacL complex formation. The competition of G1P with distamycin for DNA binding at the pacL site is independent of the order of addition of the reactants. Other minor groove binders, such as spermine or Hoechst 33258, which do not distort DNA, failed to compete with G1P for pacL DNA binding. Cationic metals, which generate a repertoire of DNA structures different from that caused by the minor groove binders, can partially reverse the distamycin-induced inhibition of G1P binding to pacL DNA. The major groove binder methyl green, which does not distort sequence-directed bending of pacL DNA, competes with G1P for binding at the pacL site. Our data suggest that the natural sequence-directed bend that exists within the pacL site is the architectural element that facilitates assembly of a nucleoprotein complex and hence initiation of DNA encapsidation by bacteriophage SPP1.
Introduction (2017)

Extract I recognized his face, but the image was unfamiliar. The photograph of my grandfather lay on a table with a host of letters. I was in Germany recently to visit with family, and my relatives were using the opportunity to sort through old documents, choosing which to keep and which to discard. Looking at the photograph, I felt an immediate sense of unease. My grandfather appeared to be wearing a uniform. I associated his face with the kindness he had shown me when I was a child, but his military bearing in the photograph was strangely alien. The image left me confused and unnerved. Was my grandfather uncomfortable? Or was I experiencing my own discomfort at being confronted with an unspoken family history? I was familiar with a photograph of my grandfather in the uniform of the German Luftwaffe, but this was different. He seemed younger, proud, and I imagined altogether more impressionable.
A Validated Computational Fluid Dynamics Model to Estimate Hemolysis in a Rotary Blood Pump (2005)

A major part of developing rotary blood pumps requires the optimization of hemolytic properties of the entire pump. Application of a suited computational fluid dynamics (CFD)-based hemolysis model allows approximation of blood damage in an early phase of the design process. Thus, a drastic reduction of time- and cost- intensive hemolysis experiments can be achieved. For the MicroDiagonal Pump (MDP), still under development at Helmholtz-Institute in Aachen, Germany, different pump configurations have been analyzed, both numerically and experimentally. The CFD model of the pump has been successfully validated based on the comparison of the pressure head curves (H-Q curves), as discussed in a prior publication. In the present study, the authors focus on the development of a semiempiric blood damage model using the CFD and in vitro hemolysis data. On the one hand, mean key characteristics (shear stress and exposure time) and other characteristics affecting blood damage have been calculated based on numerical data. On the other hand, in vitro hemolysis tests have been accomplished in order to determine the hemolytic curves of two different pump configurations (with the same impeller but different tip clearances). Finally, a new function based on a general power law has been defined by means of the mean key characteristics. The unknown constants of the function have been determined by multidimensional regression analysis using the hemolytic curves. For the final validation of this new blood damage model, the calculated and the in vitro obtained hemolysis indices at the specific VAD operating point have been compared for all pump configurations. The comparison showed an excellent agreement, both qualitatively and quantitatively.
Enhanced peripheral nerve regeneration by acidic fibroblast growth factor. (1993)

Transection of peripheral nerves may cause permanent denervation with paralysis and disability in humans and represents a challenging problem in microsurgery. Physiologic repair at increasing intervals after the acute phase of injury results in progressively worse recovery, emphasizing the importance of rapid and timely reinnervation to optimize endorgan viability. Despite recent advances in microsurgical techniques, imperfect reinnervation results in partial return of neuromuscular function, even in the mildest neuropraxias. Axonal repair of mature neurons involves a complex interaction of molecular events, suggesting that the presence of specific neuronotropic factors might enhance the regeneration process. Recombinant human fibroblast growth factor (FGF-1) has been shown to induce both rapid angiogenesis and neurogenesis through a synthetic conduit across a 15-mm surgical gap in the peripheral nerve of the rat. Evidence of newly formed neural structures was confirmed postoperatively by histological examination in a temporal fashion over a 24-week interval. Functional motor recovery of regenerated nerves was evaluated by determining the amplitude and latency of compound muscle action potentials in treated animals. Electrophysiology studies demonstrated consistent return of motor function in 43 and 57% of animals harboring an FGF-1 conduit at 8- and 24-week intervals, respectively. None of the control animals exhibited restoration of motor function. Collectively, these data suggest that FGF may serve as an important mediator of controlled growth during peripheral nerve regeneration.
Characterization of a replication-incompetent adenovirus type 5 mutant deleted for the preterminal protein gene (1996)

An adenovirus type 5 mutant deleted for the preterminal protein (pTP) gene was constructed using cell lines that express pTP. The pTP deletion mutant virus is incapable of replicating in the absence of complementation and does not express detectable levels of viral mRNAs that are expressed only after the onset of replication. Accumulation of early-region mRNAs, including that for E1A, exhibits a lag relative to that observed from the wild-type virus. However, E1A mRNA accumulation attains a steady-state level similar to the level of expression during the early phase of infection with the wild-type virus. In 293-pTP cells (human embryonic kidney cells that express pTP in addition to high levels of adenovirus E1A and E1B proteins), the pTP deletion mutant virus replicates efficiently and yields infectious titers within 5-fold of that of the wild-type virus. The deletion of 1.2 kb of pTP-encoding sequence increases the size of foreign DNA that can be introduced into the virus and, with an absolute block to replication, makes this virus an important tool for gene therapy.
A 1.28 &amp;mu;m2 bit-line shielded memory cell technology for 64 Mb DRAMs (1990)

The technology used to fabricate high-speed and low-power 64-Mb DRAMs (dynamic random access memories) is described. The memory cell developed is a high-storage capacitance bit-line shielded stacked capacitor (STC) cell in which the storage capacitor is formed over the bit-line and a cylindrical storage node structure is used for low-voltage memory operation. The main features of the technology are low-resistance bit-line wiring to achieve short access time of the DRAM, and a simple process to fabricate the cylindrical storage node using poly-Si chemical vapor deposition (CVD) on polyimide layer to obtain large storage capacitance. The usefulness of the technology has been verified by fabricating an experimental 64-Mb DRAM
Regnase-1 in microglia negatively regulates high mobility group box 1-mediated inflammation and neuronal injury (2016)

Extracellular high mobility group box 1 (HMGB1) has been demonstrated to function as a proinflammatory cytokine and induces neuronal injury in response to various pathological stimuli in central nervous system (CNS). However, the regulatory factor involved in HMGB1-mediated inflammatory signaling is largely unclear. Regulatory RNase 1 (Regnase-1) is a potent anti-inflammation enzyme that can degrade a set of mRNAs encoding proinflammatory cytokines. The present study aims to determine the role of Regnase-1 in the regulation of HMGB1-mediated inflammatory injury in CNS. Cultured microglia and rat brain were treated with recombinant HMGB1 to examine the induction of Regnase-1 expression. Moreover, the role of Regnase-1 in modulating the expression of inflammatory cytokines and neuronal injury was then investigated in microglia by specific siRNA knockdown upon HMGB1 treatment. Results showed that HMGB1 could significantly induce the de novo synthesis of Regnase-1 in cultured microglia. Consistently, Regnase-1 was elevated and found to be co-localized with microglia marker in the brain of rat treated with HMGB1. Silencing Regnase-1 in microglia enhanced HMGB1-induced expression of proinflammatory cytokines and exacerbated neuronal toxicity. Collectively, these results suggest that Regnase-1 can be induced by HMGB1 in microglia and negatively regulates HMGB1-mediated neuroinflammation and neuronal toxicity.
Rapid Akt activation by nicotine and a tobacco carcinogen modulates the phenotype of normal human airway epithelial cells (2003)

Tobacco-related diseases such as lung cancer cause over 4.2 million deaths annually, with approximately 400,000 deaths per year occurring in the US. Genotoxic effects of tobacco components have been described, but effects on signaling pathways in normal cells have not been described. Here, we show activation of the serine/threonine kinase Akt in nonimmortalized human airway epithelial cells in vitro by two components of cigarette smoke, nicotine and the tobacco-specific carcinogen 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK). Activation of Akt by nicotine or NNK occurred within minutes at concentrations achievable by smokers and depended upon α(3)-/α(4)-containing or α(7)-containing nicotinic acetylcholine receptors, respectively. Activated Akt increased phosphorylation of downstream substrates such as GSK-3, p70(S6K), 4EBP-1, and FKHR. Treatment with nicotine or NNK attenuated apoptosis caused by etoposide, ultraviolet irradiation, or hydrogen peroxide and partially induced a transformed phenotype manifest as loss of contact inhibition and loss of dependence on exogenous growth factors or adherence to ECM. In vivo, active Akt was detected in airway epithelial cells and lung tumors from NNK-treated A/J mice, and in human lung cancers derived from smokers. Redundant Akt activation by nicotine and NNK could contribute to tobacco-related carcinogenesis by regulating two processes critical for tumorigenesis, cell growth and apoptosis.
Structure of the actin-myosin complex and its implications for muscle contraction (1993)

Muscle contraction consists of a cyclical interaction between myosin and actin driven by the concomitant hydrolysis of adenosine triphosphate (ATP). A model for the rigor complex of F actin and the myosin head was obtained by combining the molecular structures of the individual proteins with the low-resolution electron density maps of the complex derived by cryo-electron microscopy and image analysis. The spatial relation between the ATP binding pocket on myosin and the major contact area on actin suggests a working hypothesis for the crossbridge cycle that is consistent with previous independent structural and biochemical studies.
Electrophoretic Deposition of Ceramic Powders-Influence of Suspension and Processing Parameters (2006)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
Chemical composition of tall oil-based cetane enhancer for diesel fuels (1993)

Tall oil is a co-product of the manufacture of kraft softwood pulp. The principal constituents of tall oil are unsaturated C{sub 18} fatty acids, resin acids and unsaponifiables such as diterpenic alcohols/aldehydes. Tall oil has been shown to be an economical feedstock for the manufacture of cetane enhancer for diesel fuels, using the proprietary CANMET (Canada Centre for Mineral and Energy Technology) technology. Under a joint R&D project between Arbokem Inc./BC Chemicals Ltd. and CANMET, pilot plant tests were conducted recently at the CANMET Energy Research Labs. in Ottawa. The results showed that tall oil could by hydroprocessed efficiently to yield a valuable fuel blending agent. When this product was mixed with conventional diesel fuel, the cetane number of the diesel fuel increased linearly with the addition of the product. Chemical analysis including chromatography-mass spectrometry has confirmed high conversion of tall oil components into straight-chain alkanes. A small amount of cyclic hydrocarbons and sulphur components were present in the tall oil-based diesel enhancer. Preliminary results indicate that this type of cetane enhancer would provide additional technical benefits. The low aromatics content of the tall oil-based cetane enhancer would significantly reduce aromatics in the final diesel fuel blend. Diesel engines operatingmore » on such fuel blends would have a lower propensity to form particulates and NO{sub x}.« less
ChemInform Abstract: Metal—Organic Framework Materials as Catalysts (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Comparative transcriptomic analysis of human and Drosophila extracellular vesicles (2016)

Extracellular vesicles (EVs) are membrane-enclosed nanoparticles containing specific repertoires of genetic material. In mammals, EVs can mediate the horizontal transfer of various cargos and signaling molecules, notably miRNA and mRNA species. Whether this form of intercellular communication prevails in other metazoans remains unclear. Here, we report the first parallel comparative morphologic and transcriptomic characterization of EVs from Drosophila and human cellular models. Electronic microscopy revealed that human and Drosophila cells release similar EVs with diameters ranging from 30 to 200 nm, which contain complex populations of transcripts. RNA-seq identified abundant ribosomal RNAs, related pseudogenes and retrotransposons in human and Drosophila EVs. Vault RNAs and Y RNAs abounded in human samples, whereas small nucleolar RNAs involved in pseudouridylation were most prevalent in Drosophila EVs. Numerous mRNAs were identified, largely consisting of exonic sequences displaying full-length read coverage and enriched for translation and electronic transport chain functions. By analogy with human systems, these sizeable similarities suggest that EVs could potentially enable RNA-mediated intercellular communication in Drosophila.
Structure prediction for CASP8 with all‐atom refinement using Rosetta (2009)

We describe predictions made using the Rosetta structure prediction methodology for the Eighth Critical Assessment of Techniques for Protein Structure Prediction. Aggressive sampling and all-atom refinement were carried out for nearly all targets. A combination of alignment methodologies was used to generate starting models from a range of templates, and the models were then subjected to Rosetta all atom refinement. For the 64 domains with readily identified templates, the best submitted model was better than the best alignment to the best template in the Protein Data Bank for 24 cases, and improved over the best starting model for 43 cases. For 13 targets where only very distant sequence relationships to proteins of known structure were detected, models were generated using the Rosetta de novo structure prediction methodology followed by all-atom refinement; in several cases the submitted models were better than those based on the available templates. Of the 12 refinement challenges, the best submitted model improved on the starting model in seven cases. These improvements over the starting template-based models and refinement tests demonstrate the power of Rosetta structure refinement in improving model accuracy.
Determination of glass thickness using laser-based ultrasound (2001)

Thickness measurements of glass plates and glass bottles using laser-based ultrasound (LBU) are described. Ultrasound in the glass specimens was generated thermoelastically with either a pulsed CO2 laser, or a Q-switched Nd:YAG laser in the case of colored glass filters. The detection of ultrasound was accomplished by one of the following methods; a spherical Fabry-Pérot interferometer system or a photo-refractive interferometer based on two-wave mixing. A self-interference effect, utilizing the partial reflection from the front and back faces of a glass plate was also demonstrated to have sufficient sensitivity under certain conditions. The thickness of the glass plates and colored glass bottles was determined using the fundamental reverberation frequency obtained from the time-domain waveform data. LBU results were compared to physical thickness measurements and showed excellent agreement.
Programmed Hydrolysis in Designing Paclitaxel Prodrug for Nanocarrier Assembly (2015)

Nanocarriers delivering prodrugs are a way of improving in vivo effectiveness and efficiency. For therapeutic efficacy, the prodrug must hydrolyze to its parent drug after administration. Based on the fact that the hydrolysis is impeded by steric hindrance and improved by sufficient polarity, in this study, we proposed the PTX-S-S-VE, the conjugation of paclitaxel (PTX) to vitamin E (VE) through a disulfide bridge. This conjugate possessed the following advantages: first, it can be encapsulated in the VE/VE2-PEG2000/water nanoemulsions because of favorable hydrophobic interactions; second, the nanoemulsions had a long blood circulation time; finally, the concentrated glutathione in the tumor microenvironment could cleave the disulfide bond to weaken the steric hindrance and increase the polarity, promoting the hydrolysis to PTX and increasing the anticancer activity. It was demonstrated in vitro that the hydrolysis of PTX-S-S-VE was enhanced and the cytotoxicity was increased. In addition, PTX-S-S-VE had greater anticancer activity against the KB-3-1 cell line tumor xenograft and the tumor size was smaller after the 4(th) injection. The present result suggests a new way, use of reduction, to improve the in vivo anticancer activity of a prodrug for nanocarrier delivery by unshielding the ester bond and taking off the steric block.
Crystal Gazing: Structure Prediction and Polymorphism (1997)

A given molecular structure can lead to more than one crystallized form, a phenomenon known as polymorphism. As discussed in the Perspective by Desiraju, polymorphism is an important scientific and technological question as more effort is brought to bear on the problem of designing materials. Moreover, polymorphism can have legal ramifications, as demonstrated in the litigation surrounding the ulcer drug Zantac.
On Dykstra's Iterative Fitting Procedure (1990)

This paper shows that Dykstra's procedure for finding the $I$-projection onto the intersection of closed convex sets holds in general. It does this by first showing that each of the $I$-projections onto individual convex sets defined in Dykstra's iterative procedure exists and that no condition such as imposed by Dykstra is required to prove the convergence of the iterative procedure to a unique $I$-projection.
Thrombospondin 2 Inhibits Microvascular Endothelial Cell Proliferation by a Caspase-independent Mechanism (2002)

The matricellular protein thrombospondin 2 (TSP2) regulates a variety of cell-matrix interactions. A prominent feature of TSP2-null mice is increased microvascular density, particularly in connective tissues synthesized after injury. We investigated the cellular basis for the regulation of angiogenesis by TSP2 in cultures of murine and human fibroblasts and endothelial cells. Fibroblasts isolated from murine and human dermis synthesize TSP2 mRNA and secrete significant amounts of immunoreactive TSP2, whereas endothelial cells from mouse lung and human dermis did not synthesize TSP2 mRNA or protein. Recombinant mouse TSP2 inhibited growth of human microvascular endothelial cells (HMVECs) mediated by basic fibroblast growth factor, insulin-like growth factor-1, epidermal growth factor, and vascular endothelial growth factor (VEGF). HMVECs exposed to TSP2 in the presence of these growth factors had a decreased proportion of cells in S and G2/M phases. HMVECs cultured with a combination of basic fibroblast growth factor, insulin-like growth factor-1, and epidermal growth factor displayed an increased proportion of nonviable cells in the presence of TSP2, but the addition of VEGF blocked this TSP2-mediated impairment of cell viability. TSP2-mediated inhibition of DNA synthesis by HMVECs in the presence of VEGF was not affected by the broad-spectrum caspase inhibitor zVAD-fmk. Similar findings were obtained with TSP1. Taken together, these observations indicate that either TSP2 or TSP1 can inhibit HMVEC proliferation by inhibition of cell cycle progression and induction of cell death, but the mechanisms responsible for TSP2-mediated inhibition of cell cycle progression are independent from those leading to cell death.
ABCB11 gene mutations in Chinese children with progressive intrahepatic cholestasis and low γ glutamyltransferase (2009)

ABCB11 gene mutations play an important role in Chinese patients with progressive intrahepatic cholestasis and low GGT. The characteristics of ABCB11 gene mutations in Chinese are different from other population groups. Histological examination may be helpful in diagnosis of PFIC2.
Efficacy of Castor Oil in the Control of Throat, Skin and Enteric Bacteria (2017)

The potential of using castor oil as an antibacterial agent was investigated on three species of bacteria chiefly responsible for throat, skin and enteric infections. Staphylococcus aureus was used as the test organism for skin bacteria, the throat bacteria used was Streptococcus viridans, while for enteric bacteria, Shigella dysenteriae was used. Castor oil was extracted by cold pressing of seed kernels. The extract obtained was assayed for antimicrobial activity on the in-vitro growth of test organism using direct inoculation, paper disc method. These were soaked in the castor oil for 1 hour. The soaked discs were then placed on prepared plates each containing the test bacteria, the antimicrobial effect of the castor oil was observed by measuring the zone of inhibition of the agent against the test bacteria. The result showed that castor oil is highly effective against all the bacteria species tested; the zone of inhibition measured, showed that Staphylococcus aureus is more susceptible to the oil than the other bacteria with a range of 11-13mm while Streptococcus viridans had a range of 8-10mm and the least was Shigella dysenteriae which had a range of 3-6mm. The result obtained implies that castor oil can be used in the control of wounds, skin infections, throat infections and in the treatment of stomach unrest caused by these bacteria species.