gebhart/patrepeval huggingface dataset:
Redox Sorting of Carbon Nanotubes (2015)

This work expands the redox chemistry of single-wall carbon nanotubes (SWCNTs) by investigating its role in a number of SWCNT sorting processes. Using a polyethylene glycol (PEG)/dextran (DX) aqueous two-phase system, we show that electron-transfer between redox molecules and SWCNTs triggers reorganization of the surfactant coating layer, leading to strong modulation of nanotube partition in the two phases. While the DX phase is thermodynamically more favored by an oxidized SWCNT mixture, the mildly reducing PEG phase is able to recover SWCNTs from oxidation and extract them successively from the DX phase. Remarkably, the extraction order follows SWCNT bandgap: semiconducting nanotubes of larger bandgap first, followed by semiconducting nanotubes of smaller bandgap, then nonarmchair metallic tubes of small but nonvanishing bandgap, and finally armchair metallic nanotubes of zero bandgap. Furthermore, we show that redox-induced surfactant reorganization is a common phenomenon, affecting nanotube buoyancy in a density gradient field, affinity to polymer matrices, and solubility in organic solvents. These findings establish redox modulation of surfactant coating structures as a general mechanism for tuning a diverse range of SWCNT sorting processes and demonstrate for the first time that armchair and nonarmchair metallic SWCNTs can be separated by their differential response to redox.
In Vitro Priming Recapitulates In Vivo HIV-1 Specific T Cell Responses, Revealing Rapid Loss of Virus Reactive CD4+ T Cells in Acute HIV-1 Infection (2009)

Our studies highlight the ability of DCs to efficiently prime naïve T cells and induce a broad repertoire of HIV-specific responses and also provide valuable insights to the pathogenesis of HIV-1 infection in vivo.
Joint encoder and channel rate control of VBR video over ATM networks (1997)

Rate control is considered an important issue in video coding, since it significantly affects video quality. We discuss joint encoder and channel rate control for variable bit-rate (VBR) video over packet-switched ATM networks. Since variable bit-rate traffic is allowed in such networks, an open-loop encoder without rate control can generate consistent quality video. However, in order to improve the statistical multiplexing gain (SMG), an encoder buffer is essential to meet traffic constraints imposed by networks and to smooth the highly variable video bitstream. Due to the finite buffer size, some forms of encoder rate control have to be enforced, and consequently, video quality varies. We argue that a rate control scheme has to balance both issues of consistent video quality on the encoder side and bitstream smoothness for the SMG on the network side. We present a joint encoder and channel rate control algorithm for ATM networks with leaky buckets as open-loop source flow control models. The algorithm considers constraints imposed by the encoder and decoder buffers, the leaky bucket control, traffic smoothing, and rate control. The encoder rate control is separated into a sustainable-rate control and a unidirectional instantaneous-rate control. It can improve the problem of leaky bucket saturation exhibited in previous works. Experimental results with MPEG video are presented. The results verify our analysis and show the effectiveness of the proposed algorithm.
Mitochondrial cytochrome c oxidase subunit IV is phosphorylated by an endogenous kinase (1997)

This study was undertaken to identify novel mitochondrial membrane proteins that are potential targets for phosphorylation. Mitochondrial membranes were incubated in the presence of [γ‐ 32 P]ATP and the Triton X‐114 extractable protein was subjected to ion‐exchange and polyacrylamide gel chromatography to purify a major phosphorylated protein of approximately 17 000 Da. The determined peptide sequence of the purified phosphoprotein corresponded to a segment of cytochrome c oxidase subunit IV, an inner membrane protein of 17 160 Da. The identity of the phosphoprotein was confirmed by two‐dimensional electrophoresis and Western blotting. The results identify mitochondrial cytochrome c oxidase subunit IV as a protein which is phosphorylated by an endogenous kinase.
Accumulation of glycinebetaine during cold acclimation and freezing tolerance in leaves of winter and spring barley plants (1994)

ABSTRACT A study was performed to examine whether or not betaine (glycinebetaine), a compatible solute, is accumulated in response to cold stress and is involved in mechanisms that protect plants from freezing injury. For this purpose, we used near‐isogenic lines of barley, with each line differing only in a single gene for the spring type of growth habit; the various lines were produced by back‐crosses to a recurrent cultivar of the winter type. The winter type of growth habit requires a low temperature for triggering of flower development (vernalization), whereas the spring type does not. Betaine was accumulated to five times the basal level over the course of 3 weeks at low temperature (5 °C) in the winter‐type cultivar and in a spring‐sh line having the sh gene for the spring‐type growth habit, but the level was only doubled in the spring‐Sh3 line, which carried the Sh 3 gene for the spring‐type growth habit. Among near‐isogenic lines of the same cultivar, the levels of betaine accumulated in leaves at low temperature were well correlated with the percentages (on a dry weight basis) of green leaves that survived freezing injury (‐5 °C). This observation indicates the possibility, separate from the recognized role of betaine in the response to salinity and/or drought, that betaine accumulates in response to cold stress and that the accumulation of betaine during cold acclimation is associated to some extent with freezing tolerance in leaves of barley plants.
PI3K inhibitors in inflammation, autoimmunity and cancer (2015)

The healthy immune system protects against infection and malignant transformation without causing significant damage to host tissues. Immune dysregulation results in diverse pathologies including autoimmune disease, chronic inflammatory disorders, allergies as well as immune deficiencies and cancer. Phosphoinositide 3-kinase (PI3K) signalling has been shown to be a key pathway in the regulation of the immune response and continues to be the focus of intense research. In recent years we have gained detailed understanding of PI3K signalling, and saw the development of potent and highly selective small molecule inhibitors, of which several are currently in clinical trials for the treatment of immune-related disorders and cancer. The role of PI3K signalling in the immune response has been the subject of detailed reviews; here we focus on relevant recent progress in pre-clinical and clinical development of PI3K inhibitors.
Summarizing and correcting the GC content bias in high-throughput sequencing (2012)

GC content bias describes the dependence between fragment count (read coverage) and GC content found in Illumina sequencing data. This bias can dominate the signal of interest for analyses that focus on measuring fragment abundance within a genome, such as copy number estimation (DNA-seq). The bias is not consistent between samples; and there is no consensus as to the best methods to remove it in a single sample. We analyze regularities in the GC bias patterns, and find a compact description for this unimodal curve family. It is the GC content of the full DNA fragment, not only the sequenced read, that most influences fragment count. This GC effect is unimodal: both GC-rich fragments and AT-rich fragments are underrepresented in the sequencing results. This empirical evidence strengthens the hypothesis that PCR is the most important cause of the GC bias. We propose a model that produces predictions at the base pair level, allowing strand-specific GC-effect correction regardless of the downstream smoothing or binning. These GC modeling considerations can inform other high-throughput sequencing analyses such as ChIP-seq and RNA-seq.
Finding the K Shortest Loopless Paths in a Network (1971)

This paper presents an algorithm for finding the K loopless paths that have the shortest lengths from one node to another node in a network. The significance of the new algorithm is that its computational upper bound increases only linearly with the value of K. Consequently, in general, the new algorithm is extremely efficient as compared with the algorithms proposed by Bock, Kantner, and Haynes [2], Pollack [7], [8], Clarke, Krikorian, and Rausan [3], Sakarovitch [9] and others. This paper first reviews the algorithms presently available for finding the K shortest loopless paths in terms of the computational effort and memory addresses they require. This is followed by the presentation of the new algorithm and its justification. Finally, the efficiency of the new algorithm is examined and compared with that of other algorithms.
Highly sensitive ZnO nanowire CO sensors with the adsorption of Au nanoparticles (2008)

In this study, the growth of high density single-crystalline ZnO nanowires on patterned ZnO:Ga/SiO(2)/Si templates was reported. We also adsorbed Au nanoparticles onto nanowire surfaces and fabricated ZnO nanowire CO sensors. With 50 ppm CO gas, it was found that we could enhance the device sensitivities at 350 °C from 4.2% to 46.5% by the adsorption of Au nanoparticles. It was also found that measured sensitivities were around 30%, 37%, 46.5% and 53% when concentration of the injected CO gas was 5, 20, 50 and 100 ppm, respectively.
Single-molecule detection and DNA sequencing-by-synthesis (2004)

Fluorescence detection has established itself as one of the main techniques of interrogation of biological systems. Extending those techniques to decrease the sample size to single molecules provides an absolute standard for bulk sample calibrations, as well as better insights since individual behavior is observed instead of population averages. We observed a number of fluorophores, including GFP, at the single-molecule level at room temperature. Calibrations gave a correct estimate of bulk surface densities over four orders of magnitude, through an optical, non-invasive, non-destructive means. Novel surface chemistry enabled visualization of single tagged nucleotide incorporations inside DNA immobilized on a glass surface at the single-molecule level. This technology was later extended to successful single-molecule DNA sequencing.

At the same time, PDMS microfluidics was developed to provide the plumbing control, speed, and economy of scale for a broad range of applications. Novel surface chemistry anchored DNA to the PDMS microchannels, which allowed sequencing-by-synthesis to be conducted in the microfluidic environment using optical techniques. Materials, device, and architecture problems were also solved. Finally, all technology was put together and successful microfluidic bulk-fluorescence DNA sequencing was demonstrated. The same technology is applicable to any DNA studies in microfluidic environments and can eventually be extended to close the circle to single-molecule detection.
New Australian fishes. Part 4. A new species of Steeneichthys (Plesiopidae) (1987)

A new species of plesiopid, Steeneichthys nativitalis, is described from Christmas Island. In- dian Ocean, on the basis of a single specimen. It is similar to 5. plesiopsus Allen & Randall from north-western Australia and the western Pacific, but differs in pectoral ray and gill raker counts, and also in coloration.
Antitrinitrophenyl (TNP) Plaque Assay. Primary Response of Balb/c Mice to Soluble and Particulate Immunogen (1969)

A technique was developed for the detection of individual cells producing anti-TNP antibody by the hemolytic plaque technique. Conjugation of TNP directly to the erythrocyte surface by use of TNBS resulted in a stable reagent that permitted a study of the antihapten response to TNP-KLH. It was possible to induce a primary anti-TNP response with soluble TNP-KLH but the response was greater when the immunogen was made particulate by coating it onto bentonite. Both primary and secondary responding cells (those brought out by antiglobulin serum) were inhibited by TNP-BSA added to the plating medium but at an equivalent concentration of hapten only the secondary cells were completely inhibited. This was interpreted to indicate the higher binding affinity of secondary antibody.
A Controlled Trial of Amantadine and Rimantadine in the Prophylaxis of Influenza a Infection (1982)

Four hundred fifty volunteers participated in a placebo-controlled, double-blind, randomized trial of the prophylactic effects of rimantadine and amantadine during an outbreak of influenza A. The subjects received drugs orally at a dose of 100 mg twice a day for six weeks. Influenza-like illness occurred in 41 per cent of the subjects receiving placebo but in only 14 per cent of those receiving rimantadine and 9 per cent of these receiving amantadine (P less than 0.001 for either drug vs. placebo). Laboratory-documented influenza occurred in 21 per cent of placebo recipients, 3 per cent of rimantadine recipients, and 2 per cent of amantadine recipients (P less than 0.001). These findings represent efficacy rates of 85 per cent for rimantadine and 91 per cent for amantadine, as compared with placebo. More recipients of amantadine (13 per cent) than recipients of rimantadine (6 per cent; P less than 0.05) or placebo (4 per cent; P less than 0.01) withdrew from the study because of central-nervous-system side effects. On the basis of this study, rimantadine appears to be the drug of choice for the prophylaxis of influenza A.
Treatment of Factor VII Deficiency with Recombinant Factor VIla (1996)

Factor VII deficiency is a relatively infrequent hereditary bleeding disorder. Recombinant factor VIIa has been used to treat patients with factor VII deficiency with bleeding episodes or undergoing surgery. The drug has shown a high efficacy rate and will provide factor VII-deficient patients with a therapeutic agent that is not derived from human plasma.
Tailoring interfacial oxide for polysilicon bit-cell contacts and emitters with in situ vapor HF interface cleaning and polysilicon deposition in a 4 Mbit BiCMOS fast static RAM (2003)

A cluster-tool-based technique for in situ vapor HF cleaning, ultrathin oxide growth and polysilicon deposition is compared to conventional processing in forming polysilicon emitters and polysilicon bit-cell contacts in a 4-Mb/0.5- mu m BiCMOS fast static RAM (FSRAM) process. The in situ processing techniques involve removing native oxide with vapor HF, optionally growing several monolayers of thermal interfacial oxide and depositing a polysilicon film using a load-locked multichamber cluster tool. The authors have examined the capability of this process for producing low bit-cell contact resistance while tailoring bipolar gain through the use of a thin interfacial oxide. Results are reported which indicate that the control achieved with cluster tool processing provides greater flexibility in simultaneously optimizing the performance of the polysilicon emitters and bit-cell contacts.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The endocytic receptor megalin binds the iron transporting neutrophil‐gelatinase‐associated lipocalin with high affinity and mediates its cellular uptake (2004)

Neutrophil-gelatinase-associated lipocalin (NGAL) is a prominent protein of specific granules of human neutrophils also synthesized by epithelial cells during inflammation. NGAL binds bacterial siderophores preventing bacteria from retrieving iron from this source. Also, NGAL may be important in delivering iron to cells during formation of the tubular epithelial cells of the primordial kidney. No cellular receptor for NGAL has been described. We show here that megalin, a member of the low-density lipoprotein receptor family expressed in polarized epithelia, binds NGAL with high affinity, as shown by surface plasmon resonance analysis. Furthermore, a rat yolk sac cell line known to express high levels of megalin, endocytosed NGAL by a mechanism completely blocked by an antibody against megalin.
Strand Displacement Binding of a Duplex-Forming Homopurine PNA to a Homopyrimidine Duplex DNA Target (1996)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTStrand Displacement Binding of a Duplex-Forming Homopurine PNA to a Homopyrimidine Duplex DNA TargetPeter E. Nielsen and Leif ChristensenView Author Information Center for Biomolecular Recognition Department of Medical Biochemistry and Genetics Biochemistry Laboratory B, The Panum Institute Blegdamsvej 3c, DK-2200 N Copenhagen, Denmark Cite this: J. Am. Chem. Soc. 1996, 118, 9, 2287–2288Publication Date (Web):March 6, 1996Publication History Received11 September 1995Published online6 March 1996Published inissue 1 January 1996https://doi.org/10.1021/ja953125qCopyright © 1996 American Chemical SocietyRIGHTS & PERMISSIONSArticle Views847Altmetric-Citations74LEARN 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 InReddit Read OnlinePDF (77 KB) Get e-AlertsSUBJECTS:Biopolymers,Genetics,Thermal stability Get e-Alerts
Molecular Cloning of Human GDP-mannose 4,6-Dehydratase and Reconstitution of GDP-fucose Biosynthesis in Vitro (1998)

We have cloned the cDNA encoding human GDP-mannose 4,6-dehydratase, the first enzyme in the pathway converting GDP-mannose to GDP-fucose. The message is expressed in all tissues and cell lines examined, and the cDNA complements Lec13, a Chinese Hamster Ovary cell line deficient in GDP-mannose 4,6-dehydratase activity. The human GDP-mannose 4,6-dehydratase polypeptide shares 61% identity with the enzyme from Escherichia coli, suggesting broad evolutionary conservation. Purified recombinant enzyme utilizes NADP+ as a cofactor and, like its E. coli counterpart, is inhibited by GDP-fucose, suggesting that this aspect of regulation is also conserved. We have isolated the product of the dehydratase reaction, GDP-4-keto-6-deoxymannose, and confirmed its structure by electrospray ionization-mass spectrometry and high field NMR. Using purified recombinant human GDP-mannose 4,6-dehydratase and FX protein (GDP-keto-6-deoxymannose 3,5-epimerase, 4-reductase), we show that the two proteins alone are sufficient to convert GDP-mannose to GDP-fucose in vitro. This unequivocally demonstrates that the epimerase and reductase activities are on a single polypeptide. Finally, we show that the two homologous enzymes from E. coli are sufficient to carry out the same enzymatic pathway in bacteria.
Hemodynamic and Antiadrenergic Effects of Dronedarone and Amiodarone in Animals with a Healed Myocardial Infarction (2000)

The hemodynamic and antiadrenergic effects of dronedarone, a noniodinated compound structurally related to amiodarone, were compared with those of amiodarone after prolonged oral administration, both at rest and during sympathetic stimulation in conscious dogs with a healed myocardial infarction. All dogs (n = 6) randomly received orally dronedarone (10 and 30 mg/kg), amiodarone (10 and 30 mg/kg), and placebo twice daily for 7 days, with a 3-week washout between consecutive treatments. Heart rate (HR), mean arterial pressure (MBP), positive rate of increase of left ventricular pressure (+LVdP/dt), echocardiographically assessed left ventricular ejection fraction (LVEF), and fractional shortening (FS), as well as chronotropic response to isoproterenol and exercise-induced sympathetic stimulation were evaluated under baseline and posttreatment conditions. Resting values of LVEF, FS, +LVdP/dt, and MBP remained unchanged whatever the drug and the dosing regimen, whereas resting HR was significantly and dose-dependently lowered after dronedarone and to a lesser extent after amiodarone. Both dronedarone and amiodarone significantly reduced the exercise-induced tachycardia and, at the highest dose, decreased the isoproterenol-induced tachycardia. Thus, dronedarone and amiodarone displayed a similar level of antiadrenergic effect and did not impair the resting left ventricular function. Consequently, dronedarone might be particularly suitable for the treatment and prevention of various clinical arrhythmias, without compromising the left ventricular function.
Deep-submicrometer BiCMOS circuit technology for sub-10-ns ECL 4-Mb DRAM's (1992)

A 0.3- mu m sub-10-ns ECL 4-Mb BiCMOS DRAM design is described. The results obtained are: (1) a V/sub cc/ connection limiter with a BiCMOS output circuit is chosen due to ease of design, excellent device reliability and layout area; (2) a mostly CMOS periphery with a specific bipolar use provides better performances at high speed and low power; (3) the direct sensing scheme of a single-stage MOS preamplifier combined with a bipolar main amplifier offers high speed; and (4) the strict control of MOS transistor parameters has been proven to be more important in obtaining high speed DRAMs, based on the 4-Mb design.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A redirected proton pathway in the bacteriorhodopsin mutant Tyr-57–>Asp. Evidence for proton translocation without Schiff base deprotonation. (1994)

Light-driven proton pumping in bacteriorhodopsin involves deprotonation of the retinylidene Schiff base during M formation and reprotonation during N formation as key steps. This study reports on the spectroscopic characterization of the bacteriorhodopsin mutant Tyr-57-->Asp (Y57D). The results reveal that although formation of the M intermediate and Schiff base deprotonation is blocked, the mutant still exhibits a significant level of light-driven proton translocation. The photocycle of Y57D involves formation of K and L intermediates accompanied by the normal chromophore isomerization and changes in the hydrogen bonding of Asp-96 and Asp-115. However, an additional Asp residue deprotonates during formation of the L intermediate along with a transmembrane alpha-helical structural change that normally occurs upon N formation. We postulate that proton transport in Y57D occurs through a redirected pathway that does not involve the deprotonation of the Schiff base. Chromophore isomerization, which normally results in the transfer of a proton from the Schiff base to Asp-85, instead causes the deprotonation of Asp-57 in Y57D, most likely through an interaction involving Asp-212. This deprotonation of Asp-57 causes the release of a proton into the extracellular medium. Reprotonation of Asp-57 occurs through the Schiff base reprotonation pathway, which consists of a hydrogen-bonded network of residues spanning from Asp-96 to Asp-212. The results also indicate that the transmembrane alpha-helical structural changes observed during N formation (Rothschild, K.J., Marti, T., Sonar, S., He, Y.W., Rath, P., Fischer, W., Bousche, O., and Khorana, H. G. (1993) J. Biol. Chem. 268, 27046-27052) do not require deprotonation of Asp-96 or of the Schiff base.
Incidence of chemotherapy‐induced nausea and emesis after modern antiemetics (2004)

Physicians and nurses markedly underestimated the incidence of delayed nausea and emesis after both HEC and MEC. Delayed nausea and emesis, which may appear even in the absence of acute nausea and emesis, remain important targets for improved therapeutic intervention.