gebhart/patrepeval huggingface dataset:
Oxygen-tolerant coenzyme A-acylating aldehyde dehydrogenase facilitates efficient photosynthetic n-butanol biosynthesis in cyanobacteria (2013)

Metabolic engineering of photosynthetic microorganisms such as cyanobacteria for the production of fuels or chemicals is challenging, particularly when the pathway involves oxygen-sensitive enzymes. We have previously designed a coenzyme A (CoA) dependent n-butanol biosynthesis pathway tailored to the metabolic physiology of the cyanobacterium Synechococcus elongatus PCC 7942 by incorporating an ATP driving force and a kinetically irreversible trap. However, one of the enzymes involved, CoA-acylating butyraldehyde dehydrogenase (Bldh) is oxygen sensitive, therefore hindering efficient n-butanol synthesis in cyanobacteria. To overcome this obstacle of n-butanol biosynthesis, we characterized six oxygen tolerant CoA-acylating aldehyde dehydrogenases (PduP) from the 1,2-propandiol degradation pathway for their activity toward acyl-CoA. We showed that PduP catalyzes the reversible reduction of a broad range of acyl-CoAs (C2 to C12) into corresponding aldehydes. In particular, PduP from Salmonella enterica has the highest catalytic efficiency (kcat/Km) of 292 s−1 mM−1 for butyryl-CoA, which is about 7 times higher than that for acetyl-CoA. Finally, replacing Bldh with PduP in the n-butanol synthesis pathway resulted in n-butanol production to a cumulative titer of 404 mg L−1 with peak productivity of 51 mg per L per day, exceeding the base strain by 20 fold. Thus, the oxygen sensitivity of CoA-acylating aldehyde dehydrogenase appears to be a key limiting factor for cyanobacteria to produce alcohols through the CoA-dependent route.
A and C Genome Distinction and Chromosome Identification inBrassica napusby Sequential Fluorescencein SituHybridization and Genomicin SituHybridization (2008)

The two genomes (A and C) of the allopolyploid Brassica napus have been clearly distinguished using genomic in situ hybridization (GISH) despite the fact that the two extant diploids, B. rapa (A, n = 10) and B. oleracea (C, n = 9), representing the progenitor genomes, are closely related. Using DNA from B. oleracea as the probe, with B. rapa DNA and the intergenic spacer of the B. oleracea 45S rDNA as the block, hybridization occurred on 9 of the 19 chromosome pairs along the majority of their length. The pattern of hybridization confirms that the two genomes have remained distinct in B. napus line DH12075, with no significant genome homogenization and no large-scale translocations between the genomes. Fluorescence in situ hybridization (FISH)-with 45S rDNA and a BAC that hybridizes to the pericentromeric heterochromatin of several chromosomes-followed by GISH allowed identification of six chromosomes and also three chromosome groups. Our procedure was used on the B. napus cultivar Westar, which has an interstitial reciprocal translocation. Two translocated segments were detected in pollen mother cells at the pachytene stage of meiosis. Using B. oleracea chromosome-specific BACs as FISH probes followed by GISH, the chromosomes involved were confirmed to be A7 and C6.
Neoglycophospholipids with Alkyl Spacers:  Synthesis via an Improved Reductive Amination and Monolayer Properties (1997)

An efficient synthesis of neoglycophospholipids with variable length alkyl spacer chains is described. Neoglycophospholipids tethered by alkyl chains of 3, 5, 7, 10, and 16 methylene units were synthesized in good overall yields in four steps. The key intermediates, omega-oxoalkyl glycopyranosides, were synthesized in two steps by glycosidation of chloro (or ethylthio) glycosides with a diol followed by oxidation of the remaining hydroxy group to an aldehyde functionality. Conjugation of the omega-glycoalkyl aldehyde with distearoylphosphatidylethanolamine via an improved reductive amination procedure significantly enhanced efficiency and yields with respect to those from traditional procedures. The amphiphilic properties of the neoglycophospholipids were characterized at the air-water interface. While the carbohydrate head group had relatively little effect, the length of the alkyl spacer profoundly influenced surface area-pressure isotherms.
Functionally distinct dendritic cell (DC) populations induced by physiologic stimuli: prostaglandin E2 regulates the migratory capacity of specific DC subsets (2002)

Migration of antigen (Ag)-loaded dendritic cells (DCs) from sites of infection into draining lymphoid tissues is fundamental to the priming of T-cell immune responses. We evaluated monocyte-derived DCs (MoDCs) and peripheral blood DCs (PBDCs) to respond to proinflammatory mediators, CD40L, and intact bacteria. All classes of stimuli induced DC phenotypic maturation. However, for MoDCs, only prostaglandin E(2) (PGE(2))-containing stimuli induced migratory-type DCs. Thus, immature MoDCs that encountered proinflammatory cytokines or CD40L or intact bacteria in the presence of PGE(2) acquired migratory capacity but secreted low levels of cytokines. Conversely, MoDCs that encountered pathogens or CD40L alone become nonmigratory cytokine-secreting cells (proinflammatory type). Interestingly, both migratory- and proinflammatory-type DCs expressed equivalent levels of chemokine receptors, suggesting that the role of PGE(2) was to switch on migratory function. We demonstrate that PGE(2) induces migration via the E-prostanoid 2/E-prostanoid 4 (EP(2)/EP(4)) receptors and the cAMP pathway. Finally, migratory-type MoDCs stimulated T-cell proliferation and predominantly IL-2 secretion, whereas proinflammatory-type MoDCs induced IFN-gamma production. In contrast, CD1b/c(+) PBDC rapidly acquired migratory capacity irrespective of the class of stimulus encountered and secreted low levels of cytokines. This suggests that not all mature stages of DCs are destined to migrate to lymphoid organs and that the sequence in which stimuli are encountered significantly affects which functions are expressed. Thus, certain immature DC subsets recruited from the resting precursor pool may have multiple functional fates that play distinct roles during the induction and effector phases of the immune response. These findings have important implications for the clinical utility of DCs in immunotherapy.
The Mechanism of Ethylene Perception (1996)

Almost one century ago, Anton Nicolyovitch Neljubov determined that the gaseous olefin ethylene was capable of altering the development of higher plants in a variety of ways. In the ensuing decades, the involvement of endogenously produced ethylene in plant growth and development was firmly established (reviewed by Abeles et al., 1992). Ethylene has been implicated as a factor that controls the timing of seed germination, the rate and dimensions of etiolated seedling growth and leaf expansion, the initiation and progression of abscission and fruit ripening, and the expression of a number of stress-related responses in plants (Abeles et al., 1992). More recently, the biochemical and molecular characterization of the biosynthetic pathway for ethylene has provided insights into the mechanisms by which plants control the interna1 concentrations of this hormone (reviewed by Kende, 1993). Understanding the mechanisms by which plant cells perceive and transduce the ethylene signal has been a more daunting problem. Physiochemical considerations have prompted a number of researchers to postulate that ethylene might interact with a receptor through a protein-bound transition metal such as Cu(1) (Burg and Burg, 1967; Kovacic et al., 1991; Sisler, 1991). High-affinity, saturable binding sites for ethylene have been detected in plant tissues and extracts (reviewed by Sisler, 1991). However, the physiological relevance of these sites with respect to ethylene responses has never been demonstrated, nor have the biochemical agents responsible for binding been isolated and characterized from plants. Recent advances in understanding ethylene signal transduction have come from pursuing a genetic approach with Arabidopsis thaliana. A number of mutants affecting ethylene responses in Arabidopsis have been identified (reviewed by Ecker, 1995), and these define a common initial pathway for all recognized ethylene-induced changes in the plant. In this Update, we will describe the initial pathway for ethylene signal transduction as it is currently understood and emphasize, in particular, evidence that the ETRZ gene codes for an ethylene receptor. We will also
Accuracy of devices for self-monitoring of blood glucose: A stochastic error model (2015)

Self-monitoring of blood glucose (SMBG) devices are portable systems that allow measuring glucose concentration in a small drop of blood obtained via finger-prick. SMBG measurements are key in type 1 diabetes (T1D) management, e.g. for tuning insulin dosing. A reliable model of SMBG accuracy would be important in several applications, e.g. in in silico design and optimization of insulin therapy. In the literature, the most used model to describe SMBG error is the Gaussian distribution, which however is simplistic to properly account for the observed variability. Here, a methodology to derive a stochastic model of SMBG accuracy is presented. The method consists in dividing the glucose range into zones in which absolute/relative error presents constant standard deviation (SD) and, then, fitting by maximum-likelihood a skew-normal distribution model to absolute/relative error distribution in each zone. The method was tested on a database of SMBG measurements collected by the One Touch Ultra 2 (Lifescan Inc., Milpitas, CA). In particular, two zones were identified: zone 1 (BG≤75 mg/dl) with constant-SD absolute error and zone 2 (BG>75mg/dl) with constant-SD relative error. Mean and SD of the identified skew-normal distributions are, respectively, 2.03 and 6.51 in zone 1, 4.78% and 10.09% in zone 2. Visual predictive check validation showed that the derived two-zone model accurately reproduces SMBG measurement error distribution, performing significantly better than the single-zone Gaussian model used previously in the literature. This stochastic model allows a more realistic SMBG scenario for in silico design and optimization of T1D insulin therapy.
EPIDEMIOLOGY OF RHEUMATOID ARTHRITIS: UPDATE (1990)

We have highlighted advances and new developments in the epidemiology of rheumatoid arthritis in four major areas. Further research, as suggested by us and others (48) should focus on understanding the mechanisms which underlie the association of etiologic and protective factors with rheumatoid arthritis, and on identifying and modifying prognostic factors associated with long-term morbidity and mortality among patients with rheumatoid arthritis. Major increases in funding provided by the National Institute of Arthritis and Musculoskeletal and Skin Diseases and the Arthritis Foundation will be needed to realize such efforts in the United States.
Dietary chromium effects on tissue chromium concentrations and chromium absorption in rats (1996)

Chromium (Cr) absorption is low (<1%) and there is a need to find Cr compounds that are absorbed better than inorganic Cr salts. Therefore, the incorporation of nine different chromium (Cr) compounds on tissue Cr concentration of 6-week male Wistar rats was investigated. Chromium compounds tested were Cr chloride (Cr chloride), Cr acetate (Cr acetate), Cr potassium sulfate (CrAlum), Cr trihistidine (Cr histidine), Cr triglycine (Cr glycine), Cr trinicotinic acid (CrNA), Cr dinicotinic acid dihistidine (CrNA-HIS), Cr tripicolinic acid (Cr picolinate), and Cr dinicotinic acid diglycine cysteine glutamic acid (CrNA-AA). Complexes were fed to weanling rats for 3 weeks at 5,000 ng of Cr/g of diet. Basal control diet was a cornstarch-based diet containing 30 ng Cr/g. Chromium incorporation into the kidney was greatest for CrNA-AA complex (850 ng/g dry wt) followed by CrAlum (407 ng/g), Cr acetate (397), CrNA-HIS (394), Cr picolinate (368), Cr glycine (343), Cr nicotinate (166), Cr chloride (74), CrHIS (49), and control (23 ng/g). Chromium concentration of the liver was greatest for the Cr picolinate compound (50 ng/g) followed by CrNA-AA and Cr acetate. Liver Cr concentrations of remaining complexes were not significantly different from those of the control animals that received no added Cr. Chromium concentrations were significantly greater in the kidney than those for the liver, spleen, heart, lungs, and gastrocnemius muscle. Supplemental Cr did not affect tissue zinc and copper but did alter tissue iron concentrations. Absorption of radioactive forms of Cr did not explain the differences in tissue Cr concentrations. Chromium absorption after 4 hours and retention after 24 hours were not significantly different for the forms of Cr tested. These data demonstrate that Cr concentrations are greatest in the kidney and that the form of dietary Cr significantly affects tissue Cr concentrations. Absorption of Cr does not correlate with tissue Cr concentrations and blood Cr is not in equilibrium with tissue Cr stores. © 1996 Wiley-Liss, Inc. This article is a U.S. Government work and, as such, is in the public domain in the United States of America.
Calculation of the electrostatic forces that act on carbon nanotubes placed in the vicinity of metallic protrusions (2005)

\nDielectrophoresis has appeared recently as a non-destructive means to manipulate and sort carbon nanotubes. In order to compute the electrostatic forces that act on carbon nanotubes when subjected to an external field and placed in the vicinity of metallic protrusions, we develop a technique that relies on a monopole-dipole description of the nanotubes and on a dielectric-function model of the metallic elements. The technique proceeds iteratively between these two descriptions in order to determine the nanotube polarization and the resulting counter-polarization of the metallic elements. Specific differentiation schemes as well as a finite-difference formulation of Poisson's equation are given in cartesian and cylindrical coordinates. As an application, we compute the polarization and forces that act on a metallic (5, 5) and a semiconducting (10, 0) nanotube, when placed in the vicinity of a flat metallic support with either a conical or semi-elliptical protrusion. The results quantify the relevant electrostatic forces as well as the contribution of the image interaction to these forces. It is shown that the nanotubes get more polarized and attracted to the protrusion when the latter has a semi-elliptical shape. The differences in the polarization and forces that act on the metallic (5, 5) and semiconducting (10, 0) nanotubes support the idea that dielectrophoresis may be used to separate them.\n
Dose-dependent killing of leukemia cells by low-temperature plasma (2012)

Abstract The effect of low-temperature atmospheric pressure plasma towards the progression of cancerous human T-cell leukemia cells was investigated. The plasma pencil, which utilizes short duration high voltage pulses, was used to generate a low-temperature plasma (LTP) plume in ambient air. Our data showed that cell morphology and cell viability were affected in a dose-dependent manner after treatment with LTP. The outcome of this study revealed that the effect of plasma exposure was not immediate, but had a delayed effect and increasing the time of plasma exposure resulted in increased leukemia cell death.
Enantiomeric resolution and chiral recognition of racemic nicotine and nicotine analogs by .beta.-cyclodextrin complexation. Structure-enantiomeric resolution relationships in host-guest interactions (1988)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEnantiomeric resolution and chiral recognition of racemic nicotine and nicotine analogs by .beta.-cyclodextrin complexation. Structure-enantiomeric resolution relationships in host-guest interactionsJeffrey I. Seeman, Henry V. Secor, Daniel W. Armstrong, Karen D. Timmons, and Timothy J. WardCite this: Anal. Chem. 1988, 60, 19, 2120–2127Publication Date (Print):October 1, 1988Publication History Published online1 May 2002Published inissue 1 October 1988https://doi.org/10.1021/ac00170a027RIGHTS & PERMISSIONSArticle Views469Altmetric-Citations71LEARN 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 PDF (789 KB) Get e-AlertsSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Blockade of reflex venous capacitance responses in liver and spleen by hexamethonium, atropine, and surgical section (1991)

Since hexamethonium and surgical section have been used to prevent reflex splanchnic capacitance responses, we examined the effectiveness of these procedures in blocking responses to direct stimulation of preganglionic fibres in the splanchnic nerves. Liver blood volume was measured by plethysmography and splenic blood volume by weighing in cats anesthetized by pentobarbital. The cats were adrenalectomized to prevent adrenal catecholamine secretion in response to splanchnic nerve stimulation. Hexamethonium (10 and 20 mg/kg) alone or atropine (1 mg/kg) alone caused only a small variable block of the responses to preganglionic nerve stimulation. A combination of the two drugs essentially produced a complete block of the liver capacitance response, but a significant response still persisted in the spleen. Surgical section of the postganglionic nerve bundles around the hepatic and splenic arteries completely abolished the responses to preganglionic stimulation. It is concluded that a relatively complete block of reflex splanchnic capacitance responses requires either a combination of hexamethonium and atropine or surgical section of the postganglionic nerves.
THE EFFECTIVENESS OF ANTI-Ia-IMMUNOTOXINS IN THE SUPPRESSION OF MLR (1986)

The potential use of a mouse anti-Ia monoclonal antibody conjugated with a plant toxin as an immunosuppressive agent for organ transplantation was examined by studying the mixed lymphocyte reaction (MLR). In initial observations in a murine system utilizing strains A/J and C57B1/6 (B6), it was shown that a rich-toxin-conjugated anti-I-Ek monoclonal antibody (13.4-immunotoxin) would kill Ia-bearing cells of strain A/J (I-Ek)--but not of strain B6, the cells of which lack I-E determinants. Studies reported here demonstrated that 13.4-immunotoxin effectively removed stimulatory cells from the I-E-bearing spleen cells but had no effect on spleen cells lacking I-E determinants or responder lymph node cells (I-E+ or I-E-) similarly treated (i.e., 1 microgram/10(6) cells). Taking advantage of the finding that such anti-I-E antibodies react with rat spleen cells bearing class II major histocompatibility complex molecules, we utilized these toxin-conjugated antibodies to inhibit MLR in rats. Assuming that the MLR is an in vitro representative of graft rejection, we suggest that such immunotoxins might be useful for pretreatment of organ allografts for transplantation across major histocompatibility barriers.
Molecular Computation of Solutions to Combinatorial Problems (1994)

The tools of molecular biology were used to solve an instance of the directed Hamiltonian path problem. A small graph was encoded in molecules of DNA, and the "operations" of the computation were performed with standard protocols and enzymes. This experiment demonstrates the feasibility of carrying out computations at the molecular level.
B Cells Turn Off Virgin But Not Memory T Cells (1992)

There are three possible outcomes when a T cell recognizes a cell bearing a self or foreign antigen. (i) The T cell is not sufficiently signaled and is unaffected. (ii) The T cell is activated. (iii) The T cell is turned off. The differentiation state of the T cell is critical to the outcome. Although both virgin and memory T cells can be activated by antigens presented by "professional" antigen-presenting cells such as dendritic cells, they differ in their responses to B cells. Experienced T cells respond to antigen presented by B cells, whereas virgin T cells are rendered tolerant. These findings may relate to the phenomena of low- and high-zone tolerance, neonatal tolerance, and the beneficial effect of blood transfusions on allograft survival.
Echo planar spectroscopic imaging (2001)

Abstract Echo planar spectroscopic imaging (EPSI) allows for mapping one spatial dimension and the spectroscopic dimension in a single readout. Modern clinical magnetic resonance imaging scanners are becoming widely equipped with echo planar imaging gradient capabilities. Thus there exists an enormous potential for EPSI to facilitate clinical magnetic resonance spectroscopy. Here, a pedagogical analysis of how the spectral and spatial encoding occur within EPSI is provided along with demonstrations of the technique and a discussion of the inherent signal‐to‐noise limitations. © 2001 John Wiley &amp; Sons, Inc. Concepts Magn Reson 13: 213–237, 2001
Self-assembly of noble metal monolayers on transition metal carbide nanoparticle catalysts (2016)

Tough core-shell catalysts One approach for increasing the activity of precious metals in catalysis is to coat them onto less expensive earth-abundant transition metal cores such as nickel, but often these structures alloy and deactivate during reactions. Hunt et al. synthesized several types of transition metal carbide nanoparticles coated with atomically thin precious-metal shells. Titanium-doped tungsten carbide nanoparticles with platinum-ruthenium shells were highly active for methanol electrooxidation, stable over 10,000 cycles, and resistant to CO deactivation. Science , this issue p. 974
15N MAS NMR Studies of Cph1 Phytochrome:  Chromophore Dynamics and Intramolecular Signal Transduction (2006)

Solid-state nuclear magnetic resonance (NMR) is applied for the first time to the photoreceptor phytochrome. The two stable states, Pr and Pfr, of the 59-kDa N-terminal module of the cyanobacterial phytochrome Cph1 from Synechocystis sp. PCC 6803 containing a uniformly 15N-labeled phycocyanobilin cofactor are explored by 15N cross-polarization (CP) magic-angle spinning (MAS) NMR. As recently shown by 15N solution-state NMR using chemical shifts [Strauss, H. M.; Hughes, J.; Schmieder, P. Biochemistry 2005, 44, 8244], all four nitrogens are protonated in both states. CP/MAS NMR provides two additional independent lines of evidence for the protonation of the nitrogens. Apparent loss of mobility during photoactivation, indicated by the decrease of line width, demonstrates strong tension of the entire chromophore in the Pfr state, which is in clear contrast to a more relaxed Pr state. The outer rings (A and D) of the chromophore are significantly affected by the phototransformation, as indicated by both change of chemical shift and line width. On the other hand, on the inner rings (B and C) only minor changes of chemical shifts are detected, providing evidence for a conserved environment during phototransformation. In a mechanical model, the phototransformation is understood in terms of rotations between the A-B and C-D methine bridges, allowing for intramolecular signal transduction to the protein surface by a unit composed of the central rings B and C and its tightly linked protein surroundings during the highly energetic Pfr state.