gebhart/patrepeval huggingface dataset:
Isoprenoid modification of rab proteins terminating in CC or CXC motifs. (1991)

Mevalonate starvation of hamster fibroblasts resulted in a shift of rab1b from the membrane to the cytosolic fraction, suggesting that rab1b depends upon an isoprenoid modification for its membrane localization. rab1b and rab3a proteins expressed in insect cells incorporated a product of [3H]mevalonate, and gas chromatography analysis of material released by Raney nickel cleavage demonstrated that rab1b and rab3a are modified by geranylgeranyl groups. Additionally, in vitro prenylation analysis demonstrated farnesyl modification of H-ras but geranylgeranyl modification of five rab proteins (1a, 1b, 2, 3a, and 6). Together, these results suggest that the carboxyl-terminal CC/CXC motifs (X = any amino acid) specifically signal for addition of geranylgeranyl, but not farnesyl, groups. A rab1b mutant protein lacking the two carboxyl-terminal cysteine residues was not prenylated in vitro. However, since a mutant H-ras protein that terminates with tandem cysteine residues was also not modified, the CC motif may be essential, but not sufficient, to signal prenylation of rab1b. Finally, rab1b and rab3a proteins were not efficient substrates for either farnesyl- or geranylgeranyltransferase activities that modify CAAX-containing proteins (A = any aliphatic amino acid). Therefore, rab proteins may be modified by a prenyltransferase(s) distinct from the prenyltransferases that modify carboxyl-terminal CAAX proteins.
Thermodynamics of Energy Production from Biomass (2005)

With high quality petroleum running out in the next 50 years, the world governments and petrochemical industry alike are looking at biomass as a substitute refinery feedstock for liquid fuels and other bulk chemicals. New large plantations are being established in many countries, mostly in the tropics, but also in China, North America, Northern Europe, and in Russia. These industrial plantations will impact the global carbon, nitrogen, phosphorus, and water cycles in complex ways. The purpose of this paper is to use thermodynamics to quantify a few of the many global problems created by industrial forestry and agriculture. It is assumed that a typical tree biomass-for-energy plantation is combined with an efficient local pelleting facility to produce wood pellets for overseas export. The highest biomass-to-energy conversion efficiency is afforded by an efficient electrical power plant, followed by a combination of the FISCHER-TROPSCH diesel fuel burned in a 35%-efficient car, plus electricity. Wood pellet conversion to ethanol fuel is always the worst option. It is then shown that neither a prolific acacia stand in Indonesia nor an adjacent eucalypt stand is “sustainable.” The acacia stand can be made “sustainable” in a limited sense if the cumulative free energy consumption in wood drying and chipping is cut by a factor of two by increased reliance on sun-drying of raw wood. The average industrial sugarcane-for-ethanol plantation in Brazil could be “sustainable” if the cane ethanol powered a 60%-efficient fuel cell that, we show, does not exist. With some differences (ethanol distillation vs. pellet production), this sugarcane plantation performs very similarly to the acacia plantation, and is unsustainable in conjunction with efficient internal combustion engines.
Cannabinoid receptors in microglia of the central nervous system: immune functional relevance (2005)

Microglia, resident macrophages of the brain, function as immune effector and accessory cells. Paradoxically, they not only play a role in host defense and tissue repair but also have been implicated in a variety of neuropathological processes. Microglia, in addition to exhibiting phenotypic markers for macrophages, express CB1 and CB2 cannabinoid receptors. Recent studies suggest the existence of a third, yet-to-be cloned, non-CB1, non-CB2 cannabinoid receptor. These receptors appear to be functionally relevant within defined windows of microglial activation state and have been implicated as linked to cannabinoid modulation of chemokine and cytokine expression. The recognition that microglia express cannabinoid receptors and that their activation results in modulation of select cellular activities suggests that they may be amenable to therapeutic manipulation for ablating untoward inflammatory responses in the central nervous system.
Neuropilin-1 as Therapeutic Target for Malignant Melanoma (2015)

Neuropilin-1 (NRP-1) is a transmembrane glycoprotein that acts as a co-receptor for various members of the vascular endothelial growth factor (VEGF) family. Its ability to bind or modulate the activity of a number of other extracellular ligands, such as class 3 semaphorins, TGF-β, HGF, FGF, and PDGF, has suggested the involvement of NRP-1 in a variety of physiological and pathological processes. Actually, this co-receptor has been implicated in axon guidance, angiogenesis, and immune responses. NRP-1 is also expressed in a variety of cancers (prostate, lung, pancreatic, or colon carcinoma, melanoma, astrocytoma, glioblastoma, and neuroblastoma), suggesting a critical role in tumor progression. Moreover, a growing amount of evidence indicates that NRP-1 might display important functions independently of other VEGF receptors. In particular, in the absence of VEGFR-1/2, NRP-1 promotes melanoma invasiveness, through the activation of selected integrins, by stimulating VEGF-A and metalloproteinases secretion and modulating specific signal transduction pathways. This review is focused on the role of NRP-1 in melanoma aggressiveness and on the evidence supporting its use as target of therapies for metastatic melanoma.
Overexpression, Solubization and Purification of Rat and Human Olfactory Receptors (1996)

The superfamily of olfactory receptor genes, whose products are thought to be activated by odorant ligands, is critical for odor recognition. Two olfactory receptors, olp4 from rat and OR17-4 from human, were overexpressed in Sf9 insect cells. The presence of the proteins in cell membranes was monitored by immunoblotting with peptide-specific polyclonal antibodies directed against the C-terminal sequences of these receptors and with a mAb against an N-terminal octapeptide epitope tag. A DNA sequence that codes for a His6 tag, which binds tightly to a Ni2+-chelate-affinity column, was incorporated into the N-termini of both genes. The expressed olfactory receptors were found mainly in the cell-membrane fraction. The proteins were difficult to solubilize by many detergents and only lysophosphatidylcholine was found to be both suitable for efficient solubilization of the overexpressed olfactory receptors and compatible with the purification system used. After solubilization, the olfactory receptors were purified to near homogeneity by affinity chromatography on nickel nitrilotriacetic acid resin and by cation-exchange chromatography. Electrophoresis of the purified proteins and visualization with Coomassie Blue staining or by immunoblotting with specific antibodies, revealed bands of 32, 69 and 94 kDa, which were identified as the monomeric, dimeric and trimeric forms of the receptor proteins. The oligomeric forms were resistant to reduction and alkylation, and are therefore thought to be held together by non-covalent hydrophobic interactions that are resistant to SDS. This finding is similar to previous observations for other guanine-nucleotide-binding-regulatory-protein-coupled receptors. Reconstitution in phospholipid vesicles showed that the purified olfactory receptors insert specifically into the lipid bilayer. This provides a means to study functional reconstitution with putative transduction components such as olfactory guanine-nucleotide-binding-regulatory protein.
Improving selection performance on pen-based systems (2000)

Two experiments were conducted to compare pen-based selection strategies and their characteristics. Two state transition models were also formulated which provide new vocabulary that will help in investigating interactions related to target selection issues. Six strategies, which can be described by the state transition models, were used in the experiments. We determined the best strategy of the six to be the "Slide Touch" strategy, where the target is selected at the moment the pen-tip touches the target for the first time after landing on the screen surface. The six strategies were also classified into strategy groups according to their characteristics. We determined the best strategy group to be the "In-Out" strategy group, where the target is selected by contact either inside or outside the target. Analyses show that differences between strategies are influenced by variations in target size; however, the differences between strategies are not affected by the distance to the target (i.e., pen-movement-distance) or the direction of pen movement (i.e., pen-movement-direction). We also found "the smallest maximum size" of five pixels, i.e., the boundary value for the target size below which there are significant differences, and above which there are no significant differences between the strategies in error rate. Relationships between interaction states, routes, and strategy efficiency were also investigated.
FISH characterization of head and neck carcinomas reveals that amplification of band 11q13 is associated with deletion of distal 11q (1998)

In order to characterize homogeneously staining regions (HSR) and other 11q13 rearrangements identified cytogenetically, we performed fluorescence in situ hybridization (FISH) using a CCND1cosmid and five YAC clones spanning chromosomal bands 11q13–14 on metaphase cells from 14 primary and one metastatic head and neck carcinomas. At the cytogenetic level, a total of 17 HSR were detected in ten cases: five were in derivative chromosomes 11 in band 11q13, and 12 were located in other derivative chromosomes. Other forms of 11q13 rearrangements were observed in five cases, whereas two cases had normal chromosomes 11. FISH analysis demonstrated that all HSR but two were derived from the 11q13 band. The size of the amplicon varied from case to case, but the amplification always included the region covered by YAC 55G7, which contains the CCND1 locus. The amplification of CCND1was confirmed by use of a CCND1cosmid. We also showed that most of the cases (9 of 11) with 11q13 amplification had lost material from distal 11q. The breakpoints were mapped by FISH and were shown to cluster to the region between YACs 55G7 and 749G2. We conclude that loss of gene(s) in distal 11q may be as important as amplification of genes in 11q13 for the biological aggressiveness of head and neck carcinomas. Genes Chromosomes Cancer 22:312–320, 1998. © 1998 Wiley-Liss, Inc.
Debye Screening in Single-Molecule Carbon Nanotube Field-Effect Sensors (2011)

Point-functionalized carbon nanotube field-effect transistors can serve as highly sensitive detectors for biomolecules. With a probe molecule covalently bound to a defect in the nanotube sidewall, two-level random telegraph noise (RTN) in the conductance of the device is observed as a result of a charged target biomolecule binding and unbinding at the defect site. Charge in proximity to the defect modulates the potential (and transmission) of the conductance-limiting barrier created by the defect. In this Letter, we study how these single-molecule electronic sensors are affected by ionic screening. Both charge in proximity to the defect site and buffer concentration are found to affect RTN amplitude in a manner that follows from simple Debye length considerations. RTN amplitude is also dependent on the potential of the electrolyte gate as applied to the reference electrode; at high enough gate potentials, the target DNA is completely repelled and RTN is suppressed.
Gene targeting, genome editing: from Dolly to editors (2016)

One of the most powerful strategies to investigate biology we have as scientists, is the ability to transfer genetic material in a controlled and deliberate manner between organisms. When applied to livestock, applications worthy of commercial venture can be devised. Although initial methods used to generate transgenic livestock resulted in random transgene insertion, the development of SCNT technology enabled homologous recombination gene targeting strategies to be used in livestock. Much has been accomplished using this approach. However, now we have the ability to change a specific base in the genome without leaving any other DNA mark, with no need for a transgene. With the advent of the genome editors this is now possible and like other significant technological leaps, the result is an even greater diversity of possible applications. Indeed, in merely 5 years, these 'molecular scissors' have enabled the production of more than 300 differently edited pigs, cattle, sheep and goats. The advent of genome editors has brought genetic engineering of livestock to a position where industry, the public and politicians are all eager to see real use of genetically engineered livestock to address societal needs. Since the first transgenic livestock reported just over three decades ago the field of livestock biotechnology has come a long way-but the most exciting period is just starting.
Push-push oscillators for 94 and 140 GHz applications using standard pseudomorphic GaAs HEMTs (2002)

Millimeter wave harmonic oscillators taking advantage of the push-push principle are demonstrated, allowing the use of the second harmonic of the oscillators to extend the applicable frequency range of standard pseudomorphic HEMTs to 94 and 140 GHz. Two configuration schemes are realized. An improved approach using a drain-connected pair of oscillators for efficient and compact circuit design and high output power is presented. Using this approach, oscillators at 94 GHz and 135 GHz were developed, with more than 0 dBm and -2 dBm output power and a high suppression of the fundamental signal of 38 dBc and 20 dBc, respectively. All MMICs were realized in a standard 0.13 /spl mu/m pHEMT technology using optical stepper lithography.
On-the-fly sharing for streamed aggregation (2006)

Data streaming systems are becoming essential for monitoring applications such as financial analysis and network intrusion detection. These systems often have to process many similar but different queries over common data. Since executing each query separately can lead to significant scalability and performance problems, it is vital to share resources by exploiting similarities in the queries. In this paper we present ways to efficiently share streaming aggregate queries with differing periodic windows and arbitrary selection predicates. A major contribution is our sharing technique that does not require any up-front multiple query optimization. This is a significant departure from existing techniques that rely on complex static analyses of fixed query workloads. Our approach is particularly vital in streaming systems where queries can join and leave the system at any point. We present a detailed performance study that evaluates our strategies with an implementation and real data. In these experiments, our approach gives us as much as an order of magnitude performance improvement over the state of the art.
Human cerebral venous outflow pathway depends on posture and central venous pressure (2004)

Internal jugular veins are the major cerebral venous outflow pathway in supine humans. In upright humans the positioning of these veins above heart level causes them to collapse. An alternative cerebral outflow pathway is the vertebral venous plexus. We set out to determine the effect of posture and central venous pressure (CVP) on the distribution of cerebral outflow over the internal jugular veins and the vertebral plexus, using a mathematical model. Input to the model was a data set of beat-to-beat cerebral blood flow velocity and CVP measurements in 10 healthy subjects, during baseline rest and a Valsalva manoeuvre in the supine and standing position. The model, consisting of 2 jugular veins, each a chain of 10 units containing nonlinear resistances and capacitors, and a vertebral plexus containing a resistance, showed blood flow mainly through the internal jugular veins in the supine position, but mainly through the vertebral plexus in the upright position. A Valsalva manoeuvre while standing completely re-opened the jugular veins. Results of ultrasound imaging of the right internal jugular vein cross-sectional area at the level of the laryngeal prominence in six healthy subjects, before and during a Valsalva manoeuvre in both body positions, correlate highly with model simulation of the jugular cross-sectional area (R(2) = 0.97). The results suggest that the cerebral venous flow distribution depends on posture and CVP: in supine humans the internal jugular veins are the primary pathway. The internal jugular veins are collapsed in the standing position and blood is shunted to an alternative venous pathway, but a marked increase in CVP while standing completely re-opens the jugular veins.
Comparison of 16S rRNA and protein-coding genes as molecular markers for assessing microbial diversity (Bacteria and Archaea) in ecosystems (2011)

PCR amplification of the rRNA gene is the most popular method for assessing microbial diversity. However, this molecular marker is often present in multiple copies in cells presenting, in addition, an intragenomic heterogeneity. In this context, housekeeping genes may be used as taxonomic markers for ecological studies. However, the efficiency of these protein-coding genes compared to 16S rRNA genes has not been tested on environmental data. For this purpose, five protein marker genes for which primer sets are available, were selected (rplB, pyrG, fusA, leuS and rpoB) and compared with 16S rRNA gene results from PCR amplification or metagenomic data from aquatic ecosystems. Analysis of the major groups found in these ecosystems, such as Actinobacteria, Bacteroides, Proteobacteria and Cyanobacteria, showed good agreement between the protein markers and the results given by 16S rRNA genes from metagenomic reads. However, with the markers it was possible to detect minor groups among the microbial assemblages, providing more details compared to 16S rRNA results from PCR amplification. In addition, the use of a set of protein markers made it possible to deduce a mean copy number of rRNA operons. This average estimate is essentially lower than the one estimated in sequenced genomes.
Synthesis of Carrier‐Transporting Dendrimers with Perylenebis(dicarboximide)s as a Luminescent Core (2005)

Abstract Well‐defined, modular dendrimers enable processing techniques and electronic properties to be tuned independently. Moreover, the dendritic topology can isolate the core chromophore, thus reducing or eliminating strong intermolecular interactions. This paper presents the synthesis of three series of flexible, dendron‐functionalized dendrimers as red‐light‐emitting materials by a convergent approach: (1) carbazole (CZ) or oxadiazole (OXZ) terminated imide‐type dendrimers, (2) cascade energy‐transferring imide‐type dendrimers, and (3) CZ‐terminated perylene bay‐type dendrimers. They all consist of the luminescent core of perylenebis(dicarboximide)s with specific functional groups of CZ or OXZ at the periphery and are constructed from flexible Fréchet‐type poly(aryl ether) dendrons. The chemical structures of the dendrons and dendrimers were determined by standard spectroscopic techniques including 1 H and 13 C NMR spectroscopy and low/high‐resolution mass spectrometry (ESI or MALDI‐TOF). The dendrimers are designed on the basis of the following considerations: (1) dendron functionalization to incorporate CZ or OXZ units to realize the carrier‐injection adjustment, (2) tuning or improving solubility, functionality, glass‐transition temperature ( T g ) with well‐defined dendrons, and (3) avoiding luminescence quenching with the help of high site‐isolation of dendrons to enhance core luminescence. DSC results indicate that the incorporation of Fréchet‐type poly(aryl ether) dendrons can improve the amorphous properties and increase T g . (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2006)
Enhanced Bonding of Organometallics to Titanium via a Titanium(III) Phosphate Interface (2001)

ADVERTISEMENT RETURN TO ISSUEPREVNoteNEXTEnhanced Bonding of Organometallics to Titanium via a Titanium(III) Phosphate InterfaceEllen S. Gawalt, Kristina Brault-Rios, Mark S. Dixon, David C. Tang, and Jeffrey SchwartzView Author Information Department of Chemistry, Princeton University, Princeton, New Jersey 08544-1009 Cite this: Langmuir 2001, 17, 21, 6743–6745Publication Date (Web):September 20, 2001Publication History Received23 April 2001Revised23 July 2001Published online20 September 2001Published inissue 1 October 2001https://pubs.acs.org/doi/10.1021/la010595rhttps://doi.org/10.1021/la010595rbrief-reportACS PublicationsCopyright © 2001 American Chemical SocietyRequest reuse permissionsArticle Views518Altmetric-Citations18LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Deposition,Layers,Metals,Oxides,Titanium Get e-Alerts
High Pressure and Temperature Conversion of Lignin and Black Liquor to Liquid Fuels (2010)

A project aiming to find a method for conversion of lignin or black liquor to liquid fuels has been initiated. The conversion is supposed to take place in a high pressure and temperature reactor at near supercritical water conditions. A pilot scale autoclave station, acquired for this purpose, has been evaluated considering the heat transfer in three different units; the storage tank, the preheater and the reactor. Experiments with water have been carried out at different pressures and temperatures near the supercritical region. The temperatures of the heaters and the corresponding heated units have been measured and the results have been evaluated with mathematical models for the heat transfer. Heat transfer coefficients have been calculated both theoretically and experimentally. A difference between the theoretical and experimental overall heat transfer coefficient was found for the preheater. This difference has been investigated and the most likely cause is a small passage of air in the preheater which reduces the heat transfer from the preheater material to the water pipe. The water experiments showed that the heaters can supply enough heat to reach water temperatures near the supercritical point. Pump trials with lignin slurry at different lignin concentrations have been conducted. Slurries at higher concentrations than 10 wt% lignin could not be pumped easily with the current pump components. At these higher concentrations, the pump valves were contaminated and the flow interrupted. The results will be used in further research within the project for obtaining liquid fuels from lignin or black liquor.