gebhart/patrepeval huggingface dataset:
One millimeter per minute growth rates for single wall carbon nanotube forests enabled by porous metal substrates (2018)

We report an exceptionally high-efficiency synthesis of long single-wall carbon nanotube (SWCNT) forests using porous substrates (metal meshes) in place of nonporous flat substrates. This study examined the dependence of the growth efficiency on various mesh structures, including wire diameter, aperture size, and total surface area. We demonstrated that the synthesis of SWCNT forests is highly dependent on the initial porosity as well as maintaining the open pores throughout the duration of the growth. Our results show that carbon nanotubes (CNTs) can be grown on all surfaces of the mesh in high efficiency with the optimum growth efficiency observed for a mesh porosity of ∼30%. Based on these results, we demonstrated the high efficiency synthesis of SWCNT forests (height: >3.47 mm, average growth rate: 301 μm min<sup>-1</sup>, and yield: 12.7 mg cm<sup>-2</sup> in 10 min growth time). Furthermore, we showed that the initial growth rates exceeded 1 millimeter per minute (1000 μm min<sup>-1</sup>). Our results further indicate that metal meshes represent a viable alternative to nonporous flat substrates for the efficient synthesis of tall and high yielding SWCNTs.
LOX-1 deletion decreases collagen accumulation in atherosclerotic plaque in low-density lipoprotein receptor knockout mice fed a high-cholesterol diet (2008)

LOX-1 deletion reduces enhanced collagen deposition and MMP expression in atherosclerotic regions via inhibition of pro-oxidant signals.
Heavily n-Dopable π-Conjugated Redox Polymers with Ultrafast Energy Storage Capability (2015)

We report here the first successful demonstration of a "π-conjugated redox polymer" simultaneously featuring a π-conjugated backbone and integrated redox sites, which can be stably and reversibly n-doped to a high doping level of 2.0 with significantly enhanced electronic conductivity. The properties of such a heavily n-dopable polymer, poly{[N,N'-bis(2-octyldodecyl)-1,4,5,8-naphthalenedicarboximide-2,6-diyl]-alt-5,5'-(2,2'-bithiophene)} (P(NDI2OD-T2)), were compared vis-à-vis to those of the corresponding backbone-insulated poly{[N,N'-bis(2-octyldodecyl)-1,4,5,8-naphthalenedicarboximide-2,6-diyl]-alt-5,5'-[2,2'-(1,2-ethanediyl)bithiophene]} (P(NDI2OD-TET)). When evaluated as a charge storage material for rechargeable Li batteries, P(NDI2OD-T2) delivers 95% of its theoretical capacity at a high rate of 100C (72 s per charge-discharge cycle) under practical measurement conditions as well as 96% capacity retention after 3000 cycles of deep discharge-charge. Electrochemical, impedance, and charge-transport measurements unambiguously demonstrate that the ultrafast electrode kinetics of P(NDI2OD-T2) are attributed to the high electronic conductivity of the polymer in the heavily n-doped state.
How to quantitatively synthesize dynamic changes in arterial pressure from baroreflexly modulated ventricular and arterial properties (2010)

Baroreflex regulates arterial pressure by modulating ventricular and vascular properties. We investigated if the framework of circulatory equilibrium that we developed previously (Am J Physiol 2004, 2005) by extending the classic Guyton's framework is capable of predicting baroreflex induced changes in arterial pressure. In animal experiments, we estimated open loop transfer functions of baroreflexly modulated ventricular and vascular properties, synthesized baroreflex induced dynamic changes in arterial pressure using the estimated transfer functions and compared the predicted responses with measured responses. We demonstrated that the predicted baroreflex induced changes in arterial pressure matched reasonable well with those measured. We conclude that the framework of circulatory equilibrium is generalizable under the condition where baroreflex dynamically changes arterial pressure.
KRAS Engages AGO2 to Enhance Cellular Transformation (2016)

Oncogenic mutations in RAS provide a compelling yet intractable therapeutic target. Using co-immunoprecipitation mass spectrometry, we uncovered an interaction between RAS and Argonaute 2 (AGO2). Endogenously, RAS and AGO2 co-sediment and co-localize in the endoplasmic reticulum. The AGO2 N-terminal domain directly binds the Switch II region of KRAS, agnostic of nucleotide (GDP/GTP) binding. Functionally, AGO2 knockdown attenuates cell proliferation in mutant KRAS-dependent cells and AGO2 overexpression enhances KRAS(G12V)-mediated transformation. Using AGO2-/- cells, we demonstrate that the RAS-AGO2 interaction is required for maximal mutant KRAS expression and cellular transformation. Mechanistically, oncogenic KRAS attenuates AGO2-mediated gene silencing. Overall, the functional interaction with AGO2 extends KRAS function beyond its canonical role in signaling.
Enhancement of colony formation of mouse bone marrow cells by ubenimex. (1987)

Ubenimex enhanced colony formation of bone marrow cells from CDF1 mice induced by L920 cell supernatant, which shows a macrophage-colony-stimulating activity (M-CSA), and also enhanced the colony formation induced CDF1 mouse spleen cell conditioned medium, which shows a granulocyte and macrophage-colony-stimulating activity. The maximal effect was obtained at 0.01 microgram/ml. But, ubenimex showed no effect on the nature of the colonies induced by each CSA. By preincubation of the bone marrow cells with ubenimex, M-CSA-induced colony-forming and the M-CSA-binding activities of the cells were increased. These results suggest that ubenimex enhances the CSA-induced colony formation of bone marrow progenitor cells of CDF1 mouse by increasing the amount of the CSA-binding to the cells.
Enantioselective Synthesis of Arglabin (2007)

Closing the ring: The first enantioselective synthesis of the guanianolide natural product arglabin and its dimethylamino adduct, which shows promising results in the treatment of various tumors, has been achieved. Key steps include a CuI-catalyzed asymmetric cyclopropanation, a stereoselective Sakurai allylation with a retroaldol/lactonization cascade, and a second Sakurai allylation with ring-closing metathesis (RCM).
A web-based IPTV content syndication system for personalized content guide (2015)

In this paper, we propose a web-based content syndication system in which users can easily choose Internet protocol television (IPTV) contents. This system generates personalized content guide to provide a list of IPTV contents with respect to users' interests and statistics information of their online social community. For this, IPTV contents and relevant metadata are collected from various sources and transformed. Then, the service and content metadata are processed by user metadata including audience measurement and community metadata. The metadata flows are separated from content flows of transport network. The implementation of IPTV content syndication system demonstrates how to arrange IPTV contents efficiently from content providers to the end user's screen. We also show that the user metadata including online community information are important for the system's performance and the user's satisfaction.
A RADIOSTEREOMETRIC ANALYSIS OF KNEE LAXITY, GRAFT STRETCHING AND FIXATION SLIPPAGE AFTER ANTERIOR CRUCIATE LIGAMENT RECONSTRUCTION (2009)

A recurrence of objectively measured knee laxity after anterior cruciate ligament (ACL) reconstruction has previously been reported in various papers; the purpose of this study was to accurately measure in vivo knee laxity after both bone-tendon-bone (BTB) and hamstring reconstruction using radiostereometric analysis (RSA), and to differentiate between graft fixation slippage and graft stretching and their relative contributions to any increase in laxity. Twenty patients were studied prospectively after ACL reconstruction. Ten had been operated on using BTB grafts, and ten using hamstring (four-stranded semitendinosus/gracilis) grafts. Tantalum markers were inserted in the distal femur, proximal tibia and into the graft itself. (RSA) was used to measure sagittal laxity, graft stretching and fixation slippage early post-operatively, and then at intervals up to 1 year. A steady increase in total anteroposterior laxity was found in both groups over the year. For the BTB group, total mean slippage of the bone plugs increased to 1.28 mm at 1 year. For the hamstring group, the tunnel attachments had slipped by a total of 6.82 mm. More stretching was found for the hamstrings grafts than for the BTB grafts and the amount of stretching increased significantly with time post-surgery. The hamstring grafts stretched by a mean of 4.18%, the BTB grafts by 1.18%. This is believed to be the most detailed application of RSA in analysing the performance of the two commonly used grafts in ACL reconstruction. Details such as graft stretching and fixation slippage have not been available previously; the data obtained in this study may have implications for clinical practice.
On protective buffer policies (2002)

Buffering policies that provide different loss priorities to packets/cells with no change in packet ordering (space priority disciplines) are studied. These policies are motivated by the possible presence, within the same connection, of packets with different loss probability requirements or guarantees. Examples of such applications are voice and video coders that generate information of unequal importance, and rate control mechanisms that mark excess traffic with a low priority rate violation tag. The focus is on the identification and evaluation of buffering policies that can guarantee performance, i.e. loss probability, to high priority packets irrespective of the traffic intensity and arrival patterns of low priority packets, while preserving the original ordering among packets. Such policies are termed protective policies.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Differential transcriptional response to antibiotics by P seudomonas putida   DOT ‐ T1E (2015)

Multi-drug resistant bacteria are a major threat to humanity, especially because the current battery of known antibiotics is not sufficient to combat infections produced by these microbes. Therefore, the study of how current antibiotics act and how bacteria defend themselves against antibiotics is of critical importance. Pseudomonas putida DOT-T1E exhibits an impressive array of RND efflux pumps, which confer this microorganism high resistance to organic solvents and antibiotics that would kill most other microorganisms. We have chosen DOT-T1E as a model microbe to study the microbial responses to a wide battery of antibiotics (chloramphenicol, rifampicin, tetracycline, ciprofloxacin, ampicillin, kanamycin, spectinomycin and gentamicin). Ribonucleic acid sequencing (RNA)-seq analyses revealed that each antibiotic provokes a unique transcriptional response profile in DOT-T1E. While many of the genes identified were related to known antibiotic targets, others were unrelated or encoded hypothetical proteins. These results indicate that our knowledge of antibiotic resistance mechanisms is still partial. We also identified 138 new small RNAs (sRNAs) in DOT-T1E, dramatically adding to the 16 that have been previously described. Importantly, our results reveal that a correlation exists between the expression of messenger RNA and sRNA, indicating that some of these sRNAs are likely involved in fine tuning the expression of antibiotic resistance genes. Taken together, these findings open new frontiers in the fight against multi-drug resistant bacteria and point to the potential use of sRNAs as novel antimicrobial targets.
Molecular recognition at the myo-inositol 1,4,5-trisphosphate receptor. 3-position substituted myo-inositol 1,4,5-trisphosphate analogues reveal the binding and Ca2+ release requirements for high affinity interaction with the myo-inositol 1,4,5-trisphosphate receptor. (1994)

Several novel D-myo-inositol 1,4,5-trisphosphate (Ins(1,4,5)P3] analogues equatorially substituted at the 3-position have been synthesized to probe the structure-activity relationship of the Ins(1,4,5)P3-receptor subsite adjacent to the native 3-hydroxy (3-OH) of Ins(1,4,5)P3. This study was prompted, in part, by our observation that myo-inositol 1,3,4,5-tetrakisphosphate (Ins(1,3,4,5)P4), the 3-position phosphorylated product of Ins(1,4,5)P3 was a full agonist at the Ca(2+)-mobilizing Ins(1,4,5)P3 receptor of SH-SY5Y cells (Wilcox, R.A., Challiss, R. A. J., Liu, C., Potter, B. V. I., and Nahorski, S. R. (1993) Mol. Pharmacol. 44, 810-817). The 3-position Ins(1,4,5)P3 analogues were equatorially substituted with groups spanning the steric range between the 3-OH of Ins(1,4,5)P3 and the 3-phosphate of Ins(1,3,4,5)P4; in order of increasing 3-position steric bulk these were: 3-fluoro-, 3-chloro-, 3-amino-, 3-bromo-, 3-methoxy-, and 3-phosphorothioate-Ins(1,4,5)P3. The analogues were assessed at the specific Ins(1,4,5)P3 binding-site of bovine adrenal cortex and for Ca2+ mobilizing activity in saponin-permeabilized SH-SY5Y human neuroblastoma cells. A correlation was observed between increasing molecular volume of the 3-position substituent and respective decreases in both affinity and Ca2+ mobilizing efficacy. Further analysis of the data also revealed that Ins(1,4,5)P3 analogues with equatorial 3-OH, 3-phosphate, and 3-phosphorothioate substituents interacted more favorably with Ins(1,4,5)P3 recognition sites than would be predicted by purely steric considerations. In contrast, 3-C-trifluoromethyl-Ins(1,4,5)P3 (which is axially substituted, but retains the native 3-OH of Ins(1,4,5)P3) interacted with Ins(1,4,5)P3 recognition sites with virtually the same potency as Ins(1,4,5)P3, indicating that the binding pocket of the Ins(1,4,5)P3-receptor was not sterically restrictive with respect to axially oriented 3-position substituents. We conclude that the Ins(1,4,5)P3 receptor has favorable non-covalent binding interactions with the equatorial 3-position substituents of Ins(1,4,5)P3 and Ins(1,3,4,5)P4 and that these interactions significantly ameliorate the steric constraints of the Ins(1,4,5)P3 receptor binding pocket.
Thermal assembly of polysilicon microstructures (2002)

Thermal microassembly techniques are demonstrated which extend the capabilities of surface micromachining technology. Bridges are cleanly severed by application of a single 30 mA, 100 mu s pulse. Delicately suspended microstructures are supported by tee bridges during wet etching of phosphosilicate glass, in order to reduce yield loss due to breakage and stiction to the substrate during rinsing and drying. The supports are subsequently severed to release the structure. Mechanical contacts are welded together with 30 mA of current, with a microprobe used to force together the contacts. Qualitative destructive tests indicate that the welded contact is robust. Electrostatic force applied by interdigitated electrodes is insufficient to initiate welding of polysilicon, possibly because the native oxide film must be penetrated to allow current to pass through the contact. Current vs. voltage measurements of polysilicon microbridges agree well with a first-order model, in which heat conduction and convection in air are neglected. Values of the voltage needed to melt the bridge are found to vary with bridge dimensions, because the bridge anchors are not perfect heat sinks.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Change of Conductivity with Salt Content, Solvent Composition, and Temperature for Electrolytes of LiPF[sub 6] in Ethylene Carbonate-Ethyl Methyl Carbonate (2001)

We measured the electrolytic conductivities of the electrolytes of in ethylene carbonate-ethyl methyl carbonate at different salt contents, solvent compositions, and temperatures in the ranges of their practical values. To these data, we fitted a fourth degree trivariate polynomial and obtained a close fit. We then plotted this function as surface and contour plots in the coordinates of salt content and solvent composition for a series of temperatures. These plots showed the change of conductivity with the simultaneous changes of salt content and solvent composition and the influence of temperature on this change, thus mapping the locations for the optimal combinations of salt content and solvent composition for maximum conductivity of the electrolytes at desired temperatures. Here we also discuss and interpret qualitatively the trends found in the change of conductivity with salt content, solvent composition, and temperature, based on the dependency on the same variables of these three factors: the number of dissociated ions in the electrolyte, the dielectric constant of the solvent, and the viscosity of the electrolyte. © 2001 The Electrochemical Society. All rights reserved.
Aminoacyl-tRNA Synthetase : Structural Basis for the Substrate Recognition and the Molecular Evolution (1996)

Aminoacyl-tRNA synthetases (aaRS's) play key roles in the correct protein biosynthesis through strict recognition/ligation of the cognate amino acid and tRNA. Twenty aaRS's were evolutionally devided into two classes (class I and class II) based on the architecture of the ATP-binding domain. Our recent result on the crystal structure of class-I aaRS (glutamyl-tRNA synthetase) delineates that aaRS's accomplish their strict recognition of the tRNA through a combination of insertions and deletions of modular structures in the class/subclass-defining domains and a total exchange of the non-conserved anticodon-binding domains. In contrast, structure of ternary complex of aaRS ·ATP ·amino-acid suggests that the strict amino-acid recognition is accomplished through evolutionary accumulation of mutation of the amino acid residues in the amino-acid binding site.
Dependence of secondary-electron yield on aspect ratio of several trench patterns (2014)

Systematic understanding of the mechanism of secondary-electron (SE) emission is important to simulate an SEM image of a high-aspect-ratio (AR) structure. The simulation technique for a high-AR structure is useful for optimizing the observation conditions of SEM. Trench patterns with AR between 0.5 and 8 were fabricated on the same substrate, and dependence of SE yield on AR of the trench patterns was determined from SEM images for several landing energies of primary electrons. In addition, to understand the SE emission inside a trench, Monte-Carlo simulation of the signal intensity for Si was performed. The SEM observations and simulation results indicate that SEM image contrast at the bottom of a trench improves with decreasing landing energy (owing to a positive charging effect) and that reflection of SEs at the sidewall of a trench is essential for accurately estimating SE emission for the high-AR structure with AR over eight.
Investigation of monotherapy and combined anticoronaviral therapies against feline coronavirus serotype II in vitro (2021)

Although evidence of compound synergy was identified for several combinations of antiviral agents, monotherapies were ultimately determined to be the most effective in the inhibition of viral transcription.
Peroxisomal Import Reduces the Proapoptotic Activity of Deubiquitinating Enzyme USP2 (2015)

The human deubiquitinating enzyme ubiquitin-specific protease 2 (USP2) regulates multiple cellular pathways, including cell proliferation and apoptosis. As a result of alternative splicing four USP2 isoenzymes are expressed in human cells of which all contain a weak peroxisome targeting signal of type 1 (PTS1) at their C-termini. Here, we systematically analyzed apoptotic effects induced by overexpression and intracellular localization for each isoform. All isoforms exhibit proapoptotic activity and are post-translationally imported into the matrix of peroxisomes in a PEX5-dependent manner. However, a significant fraction of the USP2 pool resides in the cytosol due to a weaker PTS1 and thus low affinity to the PTS receptor PEX5. Blocking of peroxisomal import did not interfere with the proapoptotic activity of USP2, suggesting that the enzyme performs its critical function outside of this compartment. Instead, increase of the efficiency of USP2 import into peroxisomes either by optimization of its peroxisomal targeting signal or by overexpression of the PTS1 receptor did result in a reduction of the apoptotic rate of transfected cells. Our studies suggest that peroxisomal import of USP2 provides additional control over the proapoptotic activity of cytosolic USP2 by spatial separation of the deubiquitinating enzymes from their interaction partners in the cytosol and nucleus.
Interaction of Volatiles, Sugars, and Acids on Perception of Tomato Aroma and Flavor Descriptors (2008)

To better understand the effect of sugars and acid levels on perception of aroma volatiles, intensity of tomato earthy/medicinal/musty, green/grassy/viney, and fruity/floral aroma and flavor descriptors were evaluated using coarsely chopped partially deodorized tomato puree. This puree was spiked with 1.5% to 3% sugar (glucose/fructose combinations), 0.1% to 0.2% acid (citric/malic acid combinations), or water and 2 levels of 12 individual food-grade volatiles reported to contribute to tomato flavor. A panel consisting of 6 to 8 trained members rated 9 aroma, 8 taste, and 1 aftertaste descriptors of the spiked and nonspiked purees. The panelists detected significant differences (P < or = 0.1) for various individual aroma compound/sugar/acid combinations for a range of descriptors. Adding 0.2% acids alone to bland tomato puree decreased green and floral aromas as well as sweet taste. Adding 3% sugars alone increased green and musty aromas and decreased floral aroma as well as sour, citrus, and bitter tastes. Principal component analysis (PCA) explained 56.5% of the variation in the first 3 principal components (PCs) for added acids and volatiles to bland tomato puree. The effect of added acids with the various aroma compounds generally increased perception of overall and ripe tomato taste and aroma, tropical aroma, and sour taste, and decreased sweet, fruity, and bitter tastes. PCA for added sugars with volatiles explained 67.8% of the variation in first 3 PCs, and sugars generally decreased perception of sour, bitter, and citrus tastes and green aroma, while enhancing perception of flavors associated with ripe, tropical, and aromatic tomatoes. Adding sugars, acids, and volatiles together had a similar effect to addition of sugars alone.