gebhart/patrepeval huggingface dataset:
Energy applications of ionic liquids (2013)

Ionic liquids offer a unique suite of properties that make them important candidates for a number of energy related applications. Cation–anion combinations that exhibit low volatility coupled with high electrochemical and thermal stability, as well as ionic conductivity, create the possibility of designing ideal electrolytes for batteries, super-capacitors, actuators, dye sensitised solar cells and thermo-electrochemical cells. In the field of water splitting to produce hydrogen they have been used to synthesize some of the best performing water oxidation catalysts and some members of the protic ionic liquid family co-catalyse an unusual, very high energy efficiency water oxidation process. As fuel cell electrolytes, the high proton conductivity of some of the protic ionic liquid family offers the potential of fuel cells operating in the optimum temperature region above 100 °C. Beyond electrochemical applications, the low vapour pressure of these liquids, along with their ability to offer tuneable functionality, also makes them ideal as CO2 absorbents for post-combustion CO2 capture. Similarly, the tuneable phase properties of the many members of this large family of salts are also allowing the creation of phase-change thermal energy storage materials having melting points tuned to the application. This perspective article provides an overview of these developing energy related applications of ionic liquids and offers some thoughts on the emerging challenges and opportunities.
Automatic brain segmentation in rhesus monkeys (2007)

Many neuroimaging studies are applied to primates as pathologies and environmental exposures can be studied in well-controlled settings and environment. In this work, we present a framework for both the semi-automatic creation of a rhesus monkey atlas and a fully automatic segmentation of brain tissue and lobar parcellation. We determine the atlas from training images by iterative, joint deformable registration into an unbiased average image. On this atlas, probabilistic tissue maps and a lobar parcellation. The atlas is then applied via affine, followed by deformable registration. The affinely transformed atlas is employed for a joint T1/T2 based tissue classification. The deformed atlas parcellation masks the tissue segmentations to define the parcellation. Other regional definitions on the atlas can also straightforwardly be used as segmentation. We successfully built average atlas images for the T1 and T2 datasets using a developmental training datasets of 18 cases aged 16-34 months. The atlas clearly exhibits an enhanced signal-to-noise ratio compared to the original images. The results further show that the cortical folding variability in our data is highly limited. Our segmentation and parcellation procedure was successfully re-applied to all training images, as well as applied to over 100 additional images. The deformable registration was able to identify corresponding cortical sulcal borders accurately. Even though the individual methods used in this segmentation framework have been applied before on human data, their combination is novel, as is their adaptation and application to rhesus monkey MRI data. The reduced variability present in the primate data results in a segmentation pipeline that exhibits high stability and anatomical accuracy.
Cell Junctions in Development, with Particular Reference to the Neural Tube (1976)

Cell-to-cell communication by way of specialized intercellular contacts between cells in nonexcitable as well as in excitable tissues has now been shown to be an almost general phenomenon in the animal kingdom (see recent reviews by Loewenstein 1973; Bennett 1973; Sheridan 1973; Staehelin 1974). Many of the cells in chick and other embryos are linked to each other by junctions (Furshpan et al. 1966; Trelstad et al. 1967; Sheridan 1968; Furshpan and Potter 1968; Ito and Loewenstein 1969; Revel et al. 1973) that usually allow the cell-to-cell exchange of molecules at least as large as 5 × 102 daltons (Furshpan et al. 1966; Furshpan and Potter 1968; Payton et al. 1969; Slack and Palmer 1969; Sheridan 1971) and perhaps even larger (Kanno and Loewenstein 1966). The possible significance of such contacts for development has already been discussed many times (Furshpan and Potter 1968; Bennett and Trinkaus 1970; DeHaan and Sachs...
Expressions of Matrix Metalloproteinases in Early-Stage Oral Squamous Cell Carcinoma as Predictive Indicators for Tumor Metastases and Prognosis (2004)

Expressions of MMP-9 and TIMP-2 have predictive value for tumor metastases and cause-specific survival. High expression of TIMP-2 is the most independent factor for worse prognosis in early-stage oral SCC.
A randomized phase 2 study of etaracizumab, a monoclonal antibody against integrin αvβ3, ± dacarbazine in patients with stage IV metastatic melanoma (2010)

The survival results in both treatment arms of this study were considered unlikely to result in clinically meaningful improvement over dacarbazine alone.
Muller's ratchet decreases fitness of a DNA-based microbe. (1996)

Muller proposed that an asexual organism will inevitably accumulate deleterious mutations, resulting in an increase of the mutational load and an inexorable, ratchet-like, loss of the least mutated class [Muller, H.J. (1964) Mutat. Res. 1, 2-9]. The operation of Muller's ratchet on real populations has been experimentally demonstrated only in RNA viruses. However, these cases are exceptional in that the mutation rates of the RNA viruses are extremely high. We have examined whether Muller's ratchet operates in Salmonella typhimurium, a DNA-based organism with a more typical genomic mutation rate. Cells were grown asexually under conditions expected to result in high genetic drift, and the increase in mutational load was determined. S. typhimurium accumulated mutations under these conditions such that after 1700 generations, 1% of the 444 lineages tested had suffered an obvious loss of fitness, as determined by decreased growth rate. These results suggest that in the absence of sex and with high genetic drift, genetic mechanisms, such as back or compensatory mutations, cannot compensate for the accumulation of deleterious mutations. In addition, we measured the appearance of auxotrophs, which allowed us to calculate an average spontaneous mutation rate of approximately 0.3-1.5 x 10(-9) mutations per base pair per generation. This rate is measured for the largest genetic target studied so far, a collection of about 200 genes.
Myeloperoxidase-dependent effect of amines on functions of isolated neutrophils. (1983)

Isolated neutrophilic leukocytes were incubated with primary amines and related nitrogenous compounds. Stimulation of neutrophil oxygen (O2) metabolism with phorbol myristate acetate or opsonized zymosan resulted in production of hydrogen peroxide (H2O2), myeloperoxidase-catalyzed oxidation of chloride (C1-) to hypochlorous acid (HOC1), and the reaction of HOC1 with the added compounds to yield nitrogen-chlorine (N-C1) derivatives. Formation of N-C1 derivatives of low lipid solubility resulted in accumulation of the derivatives in the extracellular medium. These oxidizing agents were identified and measured on the basis of their absorption spectra and their ability to oxidize 5-thio-2-nitrobenzoic acid to the disulfide form. The yield of N-Cl derivatives was in the order: taurine greater than Tris greater than spermidine greater than spermine greater than glucosamine greater than putrescine greater than guanidinoacetate. Accumulation of N-C1 derivatives was also observed in the absence of added amines, owing to the reaction of HOC1 with endogenous taurine and other amines that were released from the cells into the medium. In the presence of compounds that yield lipophilic N-C1 derivatives, little or no accumulation of oxidizing agents was observed. Instead, these compounds inhibited the accumulation of N-C1 derivatives that was obtained with taurine, and their effect was competitive with taurine. Inhibition was in the order: methylamine greater than ethanolamine greater than phenylethylamine greater than p-toluenesulfonamide greater than ammonia greater than guanidine. Formation of lipophilic N-C1 derivatives also resulted in inhibition of O2 uptake and glucose metabolism. Inhibition was prevented by adding catalase to eliminate H2O2, dapsone to inhibit myeloperoxidase, taurine to compete for reaction with HOC1, or compounds that are rapidly oxidized by HOC1 or N-C1 derivatives, to reduce these oxidizing agents. The results indicate that: (a) formation of N-C1 derivatives that do not penetrate biological membranes can protect leukocytes against the cytotoxicity of HOC1 and lipophilic N-C1 derivatives, and (b) formation of membrane-permeable N-C1 derivatives in the absence of target cells or readily oxidized substances results in oxidative attack by the N-C1 derivatives on leukocyte components and inhibition of leukocyte functions.
Are &#x0201C;Disks in the Air&#x0201D; Just Pie in the Sky? (1994)

Mobile computers and wireless networks are emerging technologies which will soon make ubiquitous computing a reality. In the wireless environment, mobile clients may often be disconnected from stationary server machines or may have only a low-bandwidth channel for sending messages to servers. This environment raises new challenges for the support of database applications for three reasons: 1) the limited storage capacities of mobile machines, 2) the inability to accurately predict the future data needs of many data-intensive applications, and 3) the need to provide clients with new or updated data values in order to ensure consistent data access. One way (perhaps the only way) to address these challenges is to provide the stationary server machines with a relatively high bandwidth channel over which to broadcast portions of the database. Wireless networks are but one compelling example of the more general class of asymmetric cornmunication environments, which also includes CATV networks and information distribution services. We have proposed a mechanism called Broadcast Disks to provide database access in asymmetric communication environments. By appropriate organization of the broadcast program, an arbitrarlly fine-grained memory hierarchy can be created. Such a hierarchy raises fundamental new issues for pre-fetching and client cache management. In this short paper we present a brief overview of asymmetric environments, our novel approach to organizing broadcast disks and some initial simulation results.
Effect of the Fluoride/Calcium Regimen on Vertebral Fracture Occurrence in Postmenopausal Osteoporosis (1982)

We assessed the rates of vertebral fracture in patients with postmenopausal osteoporosis. Forty-five patients were not treated (91 person-years of observation); 59 were treated conventionally, with calcium (alone or combined with estrogen) or vitamin D or both (218 years); and 61 were treated with sodium fluoride combined with conventional therapy (251 years). The fracture rate (per thousand person-years) was 834 in untreated patients, 419 in those given calcium with or without vitamin D, 304 in those given fluoride and calcium with or without vitamin D, 181 in those given estrogen and calcium with or without vitamin D, and 53 in those given fluoride, estrogen, and calcium with or without vitamin D. It was reduced in all treatment groups (P less than 0.001 for calcium and P less than 1 x 10(-6) for other combinations); fluoride (one years of treatment) and estrogen (but not vitamin D) independently reduced the rate from that observed with calcium alone (P less than 0.001). The combination of calcium fluoride, and estrogen was more effective than any other combination (P less than 0.001). These results provide grounds for optimism about the efficacy of combinations of available agents with sodium fluoride for fracture in postmenopausal osteoporosis.
Future directions in quasi-phasematched semiconductors for mid-infrared lasers (2011)

Quasi-phase-matched (QPM) materials such as periodically poled lithium niobate (PPLN) and tantalate (PPLT) have led to extremely efficient frequency-shifted laser sources in the visible and near-infrared, and QPM semiconductors promise to extend this performance beyond 4um. Orientation patterned semiconductors are not only transparent far deeper into the mid-IR but also offer higher nonlinear coefficients, higher thermal conductivity, higher purity levels, and very low losses when grown from the vapor phase. We compare the properties, processing, and performance of orientationpatterned GaAs (OPGaAs) with candidate compound semiconductors being for development as the next generation QPM nonlinear optical materials in the mid-infrared, and identify gallium phosphide as the most promising material for near-term development.
Perspectives and Challenges in Tissue Engineering and Regenerative Medicine (2009)

This Essay provides a concise overview on the achievements and future challenges in regenerative medicine and tissue engineering.
PCF1 and PCF2 specifically bind to cis elements in the rice proliferating cell nuclear antigen gene. (1997)

We have previously defined the promoter elements, sites IIa and IIb, in the rice proliferating cell nuclear antigen (PCNA) gene that are essential for meristematic tissue-specific expression. In this study, we isolated and characterized cDNAs encoding proteins that specifically bind to sites IIa and IIb. The two DNA binding proteins, designated PCF1 and PCF2, share > 70% homology in common conserved sequences at the N-terminal regions. The conserved regions are responsible for DNA binding and homodimer and heterodimer formation, and they contain a putative basic helix-loop-helix (bHLH) motif. The structure and DNA binding specificity of the bHLH motif are distinguishable from those of other known bHLH proteins that bind to the E-box. The motif is > 70% homologous to several expressed sequence tags from Arabidopsis and rice, suggesting that PCF1 and PCF2 are members of a novel family of proteins that are conserved in monocotyledons and dicotyledons. A supershift assay using an anti-PCF2 antibody showed the involvement of PCF2 in site IIa (site IIb) binding activities in rice nuclear extracts, particularly in meristematic tissues. PCF1 and PCF2 were also more likely to form heterodimers than homodimers. Our results suggest that PCF1 and PCF2 are involved in meristematic tissue-specific expression of the rice PCNA gene through binding to sites IIa and IIb and formation of homodimers or heterodimers.
Ion bombardment energy distributions in a radio frequency induction plasma (1993)

Ion bombardment energy distributions to a grounded substrate in a low pressure, rf induction plasma source are measured. The plasma source consists of a planar, spiral coil driven at 13.56 MHz which is separated from a low pressure discharge vessel by a quartz vacuum window. Ion bombardment spectra were determined using a differentially pumped retarding grid energy analyzer which samples the plasma through an 80 μm diam grounded, conducting orifice. The ion flux was found to be nearly monoenergetic for heavier ionic species such as Ar and oxygen. A double-peaked distribution was observed in water vapor plasmas where the sheath transit time of light ions is much less than the rf period. The average ion energy follows the average plasma potential and the width of the ion energy distribution correlates with the rf component of the floating probe potential, which is typically 2–6 Vp–p.
A family of hexosephosphate mutases in Saccharomyces cerevisiae (1994)

The Saccharomyces cerevisiae PGM1 and PGM2 genes encoding two phosphoglucomutase isoenzymes have been isolated and sequenced. The derived protein sequences are closely related to one another and show distinct sequence similarities to the human and rabbit phosphoglucomutases, especially in the region supposed to constitute the active site. PGM1 and PGM2 are located on chromosomes XI and XIII, respectively, just upstream of the known genes YPK1 and YKR2 coding for a pair of closely related putative protein kinases. These observations suggest that an extended region of DNA arose by the process of gene duplication. Cells deleted for both, PGM1 and PGM2, could not grow on galactose. No residual phosphoglucomutase activity could be measured in crude extracts or in permeabilized cells of pgm1/2 double mutants. Unexpectedly, growth with glucose was not impaired and the mutant cells were still able to accumulate trehalose and glycogen, although at a reduced level. Two further genes could be isolated and characterized which when over-expressed on a multi-copy plasmid could restore growth on galactose of the pgm1/2 double deletion mutant. Multi-copy complementation was due to a sharply increased level of phosphoglucomutase activity. Partial sequencing and characterization of the two genes revealed one of them to be SEC53 encoding phosphomannomutase. No extended sequence similarities could be found in the databases for the second gene. However, part of the derived amino acid sequence contained a region of high similarity to the active-site consensus sequence of hexosephosphate mutases from different organism. Further investigations suggest that a complex network of mutases exist in yeast which interact and can partially substitute for each other.
Motif‐directed redesign of enzyme specificity (2014)

Computational protein design relies on several approximations, including the use of fixed backbones and rotamers, to reduce protein design to a computationally tractable problem. However, allowing backbone and off-rotamer flexibility leads to more accurate designs and greater conformational diversity. Exhaustive sampling of this additional conformational space is challenging, and often impossible. Here, we report a computational method that utilizes a preselected library of native interactions to direct backbone flexibility to accommodate placement of these functional contacts. Using these native interaction modules, termed motifs, improves the likelihood that the interaction can be realized, provided that suitable backbone perturbations can be identified. Furthermore, it allows a directed search of the conformational space, reducing the sampling needed to find low energy conformations. We implemented the motif-based design algorithm in Rosetta, and tested the efficacy of this method by redesigning the substrate specificity of methionine aminopeptidase. In summary, native enzymes have evolved to catalyze a wide range of chemical reactions with extraordinary specificity. Computational enzyme design seeks to generate novel chemical activities by altering the target substrates of these existing enzymes. We have implemented a novel approach to redesign the specificity of an enzyme and demonstrated its effectiveness on a model system.
11 beta-hydroxysteroid dehydrogenase type 1 is a predominant 11 beta-reductase in the intact perfused rat liver (2000)

11 beta-Hydroxysteroid dehydrogenase type 1 (11 beta-HSD-1), a regulator of intrahepatocellular glucocorticoid activity, is bidirectional in homogenates but catalyses 11 beta-reduction (regenerating glucocorticoid) in intact primary hepatocytes in culture. To examine this discrepancy at the whole-organ level, we examined 11 beta-HSD-1 activity in the intact bivascularly perfused rat liver. On a single pass through male rat liver, 44+/-5% of 11-dehydrocorticosterone (11-DHC) recovered was 11 beta-reduced to corticosterone, whereas 10+/-1% of corticosterone was 11 beta-dehydrogenated to 11-DHC. 11 beta-Reduction was less in female liver (21+/-2%, P<0.01) and was significantly greater with perfusion of all substrate via the portal vein (50+/-3%) than via the hepatic artery (30+/-2%, P<0.05). 11 beta-Reductase activity was not saturated by 11-DHC (10(-)(9)-10(-)(6) M). Perfusion with carbenoxolone (CBX, 10(-)(6)-10(-)(3 )M) did not alter 11 beta-reduction of 11-DHC. In contrast, pretreatment with CBX in vivo (10 mg/day) for 7 days inhibited 11 beta-reductase (19+/-4% conversion, P<0.01). Concentrations of 11-DHC in male rat plasma were 44+/-6 nM. Thus 11 beta-HSD-1 is predominantly an 11 beta-reductase in the intact rat liver and is only inhibited by chronic administration of CBX. The substantial concentrations of plasma 11-DHC as substrate suggest that 11 beta-HSD-1 activity and its potential selective inhibition could modify glucocorticoid action in vivo.
The microcosm link service (1993)

Article Free Access Share on The microcosm link service Authors: Wendy Hall Department of Electronics and Computer Science, University of Southampton, Highfield, Hampshire, UK, SO9 5NH Department of Electronics and Computer Science, University of Southampton, Highfield, Hampshire, UK, SO9 5NHView Profile , Gary Hill Department of Electronics and Computer Science, University of Southampton, Highfield, Hampshire, UK, SO9 5NH Department of Electronics and Computer Science, University of Southampton, Highfield, Hampshire, UK, SO9 5NHView Profile , Hugh Davis Department of Electronics and Computer Science, University of Southampton, Highfield, Hampshire, UK, SO9 5NH Department of Electronics and Computer Science, University of Southampton, Highfield, Hampshire, UK, SO9 5NHView Profile Authors Info & Claims HYPERTEXT '93: Proceedings of the fifth ACM conference on HypertextDecember 1993 Pages 256–259https://doi.org/10.1145/168750.168842Online:01 December 1993Publication History 9citation330DownloadsMetricsTotal Citations9Total Downloads330Last 12 Months10Last 6 weeks1 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my Alerts New Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Microspheres with pH modulated release: Design and characterization of formulation variables for colonic delivery (2008)

The aim of this study was to design and develop microspheres of indomethacin with pH and transit time dependent release properties for achieving targeted delivery to the colon. Microspheres containing varying proportions of ethyl cellulose and Eudragit (L100 or S100) either alone or in combination were prepared using an oil-in-oil emulsion-based solvent evaporation technique. System comprising of acetone (internal phase) and liquid paraffin (external phase) in the ratio of 1 : 1 and 1 : 9 yielded microspheres with good physical properties (spherical and discrete), high drug loading (70-80%) and entrapment efficiency (70-85%). The lag time in the initial release depended on the proportion of pH-sensitive polymer Eudragit, while the duration of indomethacin release from microspheres was found to be directly proportional to proportion of the total polymer. Thus, a pH- and time-modulated sigmoidal release pattern could be observed in optimized formulations with less than 10% drug release in 4-6 h followed by controlled release extending up to 14-16 h.