gebhart/patrepeval huggingface dataset:
Abstract 580: The Production of a Bio-Engineered Endothelial Intima From Cultured Cells Using Whole Cardiac Cadaveric Extracellular Matrix. (2007)

Background; Bioengineered solutions to failing cardiac tissue have been difficult to achieve due partially to adverse interactions between circulating blood and the engineered surface. The aim of this study was to determine if by using naturally-derived ECM and cultured endothelial cells, a bioengineered whole-heart vascular intima could be generated. The matrix substrate for organ culture was produced by a perfusion-based detergent decelluarization of cadaveric rat heart. This process maintained ECM protein integrity as indicated by a glycosaminoglycan assay, with ~ equivalent amounts present relative to cadaveric rat heart. Its acellular nature was confirmed by loss of &gt; 96% DNA (p = 0.001) compared to normal rat heart. In vitro infusion of aqueous dye or Mercox resin suggested a complete arterial tree, with structural preservation of vascular conduits. In vivo perfusability of the ECM was demonstrated by heterotopic transplantation with anticoagulation (n=4) into RNU rats for 7 days. Recellularization of the vascular tree was attempted by In Vitro Langendorff perfusion of 2 x 107 rat aortal endothelial cells (ECs) followed by a 7d incubation with escalating pulsatile flow in a 3D bioreactor. CellTracker Green assessed EC viability and permitted visualization of engrafted cells by fluorescent microscopy. Vessels of different diameters contained “patches” of confluent endothelium with complete circumferential lining of many of the matrix conduits. ECs lining both chamber walls and trabeculae were also observed. Nuclear staining showed 537.8 +/− 67.6 ECs / mm2 on endocardial surfaces, as well as 311.7 +/− 61.8 ECs / mm2 in vessels. To enhance the delivery of cells into the ventricular walls, a microcanulization of the brachiocephalic artery with sustained aortal perfusion was undertaken. This technique diverted more cells to the vasculature and more broadly distributed the cells in each area resulting in a lower cell density; 199.8 +/− 25.0 ECs / mm2 in vessels vs 125.8 +/− 43.4 ECs / mm2 on endocardial surfaces. In conclusion, these data suggest that by using detergent prepared acellular ECM of a whole organ, generation of a complete endothelial lining of vascular structures may be possible.
GENETICS AND ULTRASTRUCTURE OF A CYTOPLASMICALLY INHERITED YELLOW MUTANT IN SOYBEANS (1980)

A chimeric plant was observed in the F(2) generation of a cross between a male-sterile line and a plant introduction homozygous for a chromosome interchange in soybeans [Glycine max (L.) Merr.]. F(3) progeny of this plant included one chimera, 36 yellow plants and 16 green plants. The yellow plants, which progressively turn green, were viable and fertile in field, greenhouse and growth-chamber environments. Reciprocal cross-pollinations were made between these yellow plants and four known nuclear yellow mutant plants, between these yellow plants and sibling green plants and between these yellow plants and unrelated green plants. Segregation data from F(1) and F(2) generations indicated cytoplasmic inheritance of the newly discovered yellow phenotype. Pollinations in which reciprocal F(1) hybrid plants were used as male or female parents were made with unrelated green plants. Observations in F(1) and F(2) generations substantiated the hypothesis of cytoplasmic inheritance. No interactions have been observed between this mutant and the various nuclear backgrounds. This is the first report of a cytoplasmically inherited mutant affecting plant color in soybeans. Exchange grafts were made between cytoplasmic yellow plants and sibling green plants and between cytoplasmic yellow plants and unrelated green plants. The phenotype was controlled by the scion, indicating that graft-transmissible agents were not involved. When grown in darkness, cytoplasmic yellow plants and normal green plants accumulated the same amount of protochlorophyllide. Cytoplasmic yellow plants grown in dim light accumulated slightly less chlorophyll than did their green siblings. Electron photomicrographs showed that the prolamellar body (a structure associated with synthesis of protochlorophyllide) and chloroplast ultrastructure were normal in the cytoplasmic yellow mutant. These observations led to the hypothesis that the synchrony involved in deposition of nuclear and cytoplasmic gene products during organelle development is impaired in this cytoplasmic mutant.
Mechanistic Study of Precursor Evolution in Colloidal Group II−VI Semiconductor Nanocrystal Synthesis (2006)

The molecular mechanism of precursor evolution in the synthesis of colloidal group II-VI semiconductor nanocrystals was studied using 1H, 13C, and 31P NMR spectroscopy and mass spectrometry. Tri-n-butylphosphine chalcogenides (TBPE; E = S, Se, Te) react with an oleic acid complex of cadmium or zinc (M-OA; M = Zn, Cd) in a noncoordinating solvent (octadecene (ODE), n-nonane-d20, or n-decane-d22), affording ME nanocrystals, tri-n-butylphosphine oxide (TBPO), and oleic acid anhydride ((OA)2O). Likewise, the reaction between trialkylphosphine selenide and cadmium n-octadecylphosphonic acid complex (Cd-ODPA) in tri-n-octylphosphine oxide (TOPO) produces CdSe nanocrystals, trialkylphosphine oxide, and anhydrides of n-octadecylphosphonic acid. The disappearance of tri-n-octylphosphine selenide in the presence of Cd-OA and Cd-ODPA can be fit to a single-exponential decay (kobs = (1.30 +/- 0.08) x 10-3 s-1, Cd-ODPA, 260 degrees C, and kobs = (1.51 +/- 0.04) x 10-3 s-1, Cd-OA, 117 degrees C). The reaction approaches completion at 70-80% conversion of TOPSe under anhydrous conditions and 100% conversion in the presence of added water. Activation parameters for the reaction between TBPSe and Cd-OA in n-nonane-d20 were determined from the temperature dependence of the TBPSe decay over the range of 358-400 K (deltaH++ = 62.0 +/- 2.8 kJ.mol-1, deltaS++ = -145 +/- 8 J.mol-1.K-1). A reaction mechanism is proposed where trialkylphsophine chalcogenides deoxygenate the oleic acid or phosphonic acid surfactant to generate trialkylphosphine oxide and oleic or phosphonic acid anhydride products. Results from kinetics experiments suggest that cleavage of the phosphorus chalcogenide double bond (TOP=E) proceeds by the nucleophilic attack of phosphonate or oleate on a (TOP=E)-M complex, generating the initial M-E bond.
Formaldehyde in the Indoor Environment (2010)

S.2536-2572
An antisense oligonucleotide complementary to a sequence in I gamma 2b increases gamma 2b germline transcripts, stimulates B cell DNA synthesis, and inhibits immunoglobulin secretion. (1992)

An antisense phosphorothioate (S)-oligonucleotide to a sequence in the intervening (I) region of the gamma 2b immunoglobulin (Ig) heavy chain gene inhibits Ig secretion by B cells stimulated with lipopolysaccharide (LPS) or LPS plus interleukin 4. It is also a striking stimulant of DNA synthesis by resting B cells. The antisense S-oligonucleotide causes a 10-20-fold increase in the expression of the gamma 2b germline transcript. Among mutants of the antisense S-oligonucleotide, some show all the effects whereas others are inactive. A similar hierarchy exists in the quantitative biological activities of mutant S-oligonucleotides and in their capacity to hybridize to the sense oligonucleotide, strongly suggesting that an I gamma 2b sequence in the RNA transcript or in the noncoding strand of the DNA is the target of the antisense S-oligonucleotide. The possible relationship of the overexpression of the germline gamma 2b transcript to the biological functions of the I gamma 2b antisense S-oligonucleotide is discussed.
Transformation and Transduction in Recombination-defective Mutants of Bacillus subtilis (1967)

The effects on transformation and transduction of an ultraviolet sensitivity (uvr(-)) and two ultraviolet sensitivity-recombination deficiency (rec-1(-) and rec-2(-)) mutations in isogenic strains of Bacillus subtilis were investigated. Transformation frequency in the rec-1(-) and rec-2(-) strains was reduced to approximately 5 and 25%, respectively, of the parental strains. Normal kinetics of deoxyribonucleic acid dose response in transformation were found for the rec-1(+) and rec-2(-) strains. Biphasic curves were obtained with the rec-1(-) strains. Transduction frequency with bacteriophage SP-10 decreased parallel to transformation frequency in the rec-1(-) and rec-2(-) strains. This result suggests that transformation and SP-10 transduction share a common mechanism for genetic recombination. It also indicates that the reduction in transformation frequency of these strains was not due to altered competence. Transduction frequency with bacteriophage PBS-1 or 3NT, on the contrary, was not diminished in rec-1(-) strains. This frequency was reduced in rec-2(-) strains but not as severely as that of transformation or SP-10 transduction. Several hypotheses to interpret these differences are presented. Recombination frequency between linked markers was reduced more than 50% in transformation by the presence of the rec-1(-) mutation. Linkage was unaffected in the rec-2(-) strains. Neither the rec-1(-) nor the rec-2(-) mutation had an effect on linkage in PBS-1 or 3NT transduction. The uvr(-) strains were transformed at a frequency equal to or greater than that of the parental strains. These strains were transduced by all bacteriophage systems at frequencies about twofold higher than those of parental strains.
Mammalian expression and secretion of functional single-chain Fv molecules (1994)

Single-chain Fv (sFv) proteins are genetically engineered molecules that consist of the two variable domains of an antibody connected by a polypeptide linker; they contain the antigen binding function of the parental protein in a single 30-kDa polypeptide chain. sFvs are usually produced in bacteria where they are insoluble and therefore require extensive refolding in vitro. In this report we followed the processing of three antibody sFvs (145-2C11 directed against murine CD3 epsilon chain, OKT9 against the human transferrin receptor, and U7.6 against dinitrophenyl groups) by transfected mammalian (COS-7) cells to determine whether the mammalian protein folding machinery can produce and secrete active sFv with high efficiency. The sFvs contained an immunoglobulin light chain leader sequence, which directed them to the endoplasmic reticulum and allowed secretion into the medium. We found that the sFvs were secreted at different rates, with the rate-limiting step of secretion being their exit from the endoplasmic reticulum. We increased the secretion rate of one of the sFvs by introducing an asparagine-linked glycosylation site in FR1 of the heavy chain, and by using tunicamycin (an inhibitor of glycosylation) we found that glycosylated antibody sFvs were secreted faster than their nonglycosylated counterparts. All secreted sFvs specifically bound their antigens; where tested, at least 90% of the secreted sFv was functional. Therefore, mammalian cells can effectively fold and secrete sFv antibody and can provide a convenient system for testing and producing sFv proteins.
Synthesis of 1-Substituted 3-(Chloromethyl)-6-aminoindoline (6-Amino-seco-CI) DNA Minor Groove Alkylating Agents and Structure−Activity Relationships for Their Cytotoxicity (1999)

A series of racemic 6-amino-seco-cyclopropylindole (seco-CI) compounds was prepared by coupling 1-(tert-butyloxycarbonyl)-3-(chloromethyl)-6-nitroindoline with appropriate acids, followed by nitro group reduction, and evaluated for cytotoxicity in AA8, UV4, EMT6, and SKOV3 cell lines. These compounds are of interest due to their close structural relationship to known AT-specific alkylating agents and cytotoxins and also for the possible construction of stable amine-based prodrugs designed for tumor-specific release. Variations included indole or furan side chains with different substituents, sulfonamide or carboxamide linkers, extension of the minor groove binding side chain to two subunits, and the use of a pyrroylacryloyl unit previously reported to give extremely potent analogues. The parent compound, with a trimethoxyindole side chain, was a moderately potent cytotoxin (IC50 = 0.34 microM in AA8 cells, 4 h exposure). A single 5-methoxy group on the indole minor groove binding unit was sufficient to maintain potency, and a series of dimethylaminoethoxy-substituted analogues retained the cytotoxicity of the parent compound, while providing increased aqueous solubility.
Rheology and Transport of Improved EOR Polymers under Harsh Reservoir Conditions (2012)

Abstract New polymers that are stable in harsh environments (high salinity/hardness and high temperature) are in high demand because of the need for chemical EOR in oil reservoirs with these conditions. Commonly used partially hydrolyzed polyacrylamides (HPAM) have been successfully used in the field for decades, but they hydrolyze at high temperature and eventually precipitate in the presence of high concentrations of divalent cations. This paper mainly focuses on rheology and transport behavior of scleroglucan (non-ionic polysaccharide) and N-vinylpyrrolidone (NVP)-polyacrylamide (AM) co-polymer. The rigid, rod-like, triple helical structure of scleroglucan imparts exceptional stability and its non-ionic functionality makes it insensitivity to salinity and hardness. By a different mechanism, NVP in modified HPAM protects the polymer's amide group against thermal hydrolysis, i.e., by sterically hindering the amide group. This allows maintaining high viscosity even in high salinity brines at high temperature. Both scleroglucan and NVP co- or ter-polymers show good filterability and transport properties in sandstone and carbonate cores at high temperature and in brine with high salinity and hardness. Therefore, both polymers are promising candidates for polymer flooding, surfactant-polymer flooding and alkali-surfactant-polymer flooding in hard brine at high temperature, but must be evaluated under specific reservoir conditions.
Safety Assessment of Citric Acid, Inorganic Citrate Salts, and Alkyl Citrate Esters as Used in Cosmetics (2014)

The CIR Expert Panel (Panel) assessed the safety of citric acid, 12 inorganic citrate salts, and 20 alkyl citrate esters as used in cosmetics, concluding that these ingredients are safe in the present practices of use and concentration. Citric acid is reported to function as a pH adjuster, chelating agent, or fragrance ingredient. Some of the salts are also reported to function as chelating agents, and a number of the citrates are reported to function as skin-conditioning agents but other functions are also reported. The Panel reviewed available animal and clinical data, but because citric acid, calcium citrate, ferric citrate, manganese citrate, potassium citrate, sodium citrate, diammonium citrate, isopropyl citrate, stearyl citrate, and triethyl citrate are generally recognized as safe direct food additives, dermal exposure was the focus for these ingredients in this cosmetic ingredient safety assessment.
THE PATHOGENESIS OF EXPERIMENTAL TOXIC SHOCK SYNDROME: THE ROLE OF INTERLEUKIN-2 IN THE INDUCTION OF HYPOTENSION AND RELEASE OF CYTOKINES (1995)

Toxic shock syndrome (TSS) is a multisystem disorder characterized by fever, hypotension, and involvement of three other organ systems. The etiologic agent is a toxigenic strain of Staphylococcus aureus which secretes the exotoxin, TSST-1. The toxin is a superantigen which stimulates the immune system to produce interleukin-1 (IL-1), interleukin-2, and tumor necrosis factor (TNF). We hypothesized that TSST-1 induces the release of IL-2 which in turn is either directly involved or acts via an additional mediator to produce hypotension. We submitted four pairs of normal anesthetized adult female baboons to intravenous boluses of TSST-1. One baboon in each pair received anti-IL-2 intravenously and anti-IL-2 receptor intrathyroidally 15 min prior to TSST-1. The other baboon received the same dose and placement of anti-sheep red blood cell antibody. Systolic and diastolic blood pressure was recorded continuously and mean arterial pressure was calculated and plotted. IL-1, IL-2, IL-6, and TNF were measured in serum at varying times before and after toxin administration. Systolic, diastolic, and mean arterial pressure were significantly lower in the sham-treated group versus the experimental (anti-IL-2/IL-2R) group (p < .05 for all variables). In addition no differences were seen in any of the measurements between experimentally treated baboons and those receiving no TSST-1.(ABSTRACT TRUNCATED AT 250 WORDS)
Message Passing for Dynamic Network Energy Management (2012)

We consider a network of devices, such as generators, fixed loads, deferrable loads, and storage devices, each with its own dynamic constraints and objective, connected by lossy capacitated lines. The problem is to minimize the total network objective subject to the device and line constraints, over a given time horizon. This is a large optimization problem, with variables for consumption or generation in each time period for each device. In this paper we develop a decentralized method for solving this problem. The method is iterative: At each step, each device exchanges simple messages with its neighbors in the network and then solves its own optimization problem, minimizing its own objective function, augmented by a term determined by the messages it has received. We show that this message passing method converges to a solution when the device objective and constraints are convex. The method is completely decentralized, and needs no global coordination other than synchronizing iterations; the problems to be solved by each device can typically be solved extremely efficiently and in parallel. The method is fast enough that even a serial implementation can solve substantial problems in reasonable time frames. We report results for several numerical experiments, demonstrating the method's speed and scaling, including the solution of a problem instance with over 30 million variables in 52 minutes for a serial implementation; with decentralized computing, the solve time would be less than one second.
Structure and function of plant cell wall proteins. (1993)

Plant cell walls are amazingly complex amalgams of carbohy? drates, proteins, lignin, water, and incrusting substances such as cutin, suberin, and certain inorganic compounds that vary among plant species, cell types, and even neighboring cells. Developmental events and exposure to any of a number of abiotic and biotic stresses further increase this compositional and structural variation. Moreover, the dynamic nature and func? tions of plant cell walls in terms of growth and development, environmental sensing and signaling, plant defense, intercel? lular communication, and selective exchange interfaces are reflected in these variations. Much is currently known about the structure and metabolic regulation of the various cell wall components, but relatively little is known about their precise functions and intermolecular interactions. In this review, I will discuss the accumulated structural and regulatory data and the much more limited functional and in? termolecular interaction information on five plant cell wall protein classes. These five protein classes, listed in Table 1, include the extensins, the glycine-rich proteins (GRPs), the proline-rich proteins (PRPs), the solanaceous lectins, and the arabinogalactan proteins (AGPs). These five proteins may be evolutionarily related to one another, most obviously because each of them, with the exception of the GRPs, contains hydroxyproline, and less obviously in the case of the GRPs because this class has nucleotide sequence similarity to the extensins. For completeness, I should mention that these are not the only cell wall proteins that are known. Others exist, such as cysteine-rich thionins, 28and 70-kD water-regulated proteins, a histidine-tryptophan-rich protein, and many cell wall enzymes such as peroxidases, phosphatases, invertases, a-mannosidases, P-mannosidases, p-1,3-glucanases, (3-1,4glucanases, polygalacturonase, pectin methylesterases, malate dehydrogenase, arabinosidases, a-galactosidases, (3-galactosidases, |3-glucuronosidases, p-xylosidases, proteases, and ascorbic acid oxidase (Varner and Lin, 1989). However, the above five classes generally represent the most abundant, and to date, the most well-studied and widely documented, plant cell wall proteins. Before describing these five wall protein classes, I should point out that research on these individual proteins has oc? curred in several plant species, but relatively few examples exist where these cell wall proteins have been studied together in one plant, let alone in one particular plant organ or type of cell. Thus, data from one plant species are often extrapolated to represent the situation in other plant species. Although such extrapolations are usually valid, enough variations are now known that caution should be exercised in making or believing such claims.
Platform Engineering of Corynebacterium glutamicum with Reduced Pyruvate Dehydrogenase Complex Activity for Improved Production of l -Lysine, l -Valine, and 2-Ketoisovalerate (2013)

Exchange of the native Corynebacterium glutamicum promoter of the aceE gene, encoding the E1p subunit of the pyruvate dehydrogenase complex (PDHC), with mutated dapA promoter variants led to a series of C. glutamicum strains with gradually reduced growth rates and PDHC activities. Upon overexpression of the l-valine biosynthetic genes ilvBNCE, all strains produced l-valine. Among these strains, C. glutamicum aceE A16 (pJC4 ilvBNCE) showed the highest biomass and product yields, and thus it was further improved by additional deletion of the pqo and ppc genes, encoding pyruvate:quinone oxidoreductase and phosphoenolpyruvate carboxylase, respectively. In fed-batch fermentations at high cell densities, C. glutamicum aceE A16 Δpqo Δppc (pJC4 ilvBNCE) produced up to 738 mM (i.e., 86.5 g/liter) l-valine with an overall yield (YP/S) of 0.36 mol per mol of glucose and a volumetric productivity (QP) of 13.6 mM per h [1.6 g/(liter × h)]. Additional inactivation of the transaminase B gene (ilvE) and overexpression of ilvBNCD instead of ilvBNCE transformed the l-valine-producing strain into a 2-ketoisovalerate producer, excreting up to 303 mM (35 g/liter) 2-ketoisovalerate with a YP/S of 0.24 mol per mol of glucose and a QP of 6.9 mM per h [0.8 g/(liter × h)]. The replacement of the aceE promoter by the dapA-A16 promoter in the two C. glutamicum l-lysine producers DM1800 and DM1933 improved the production by 100% and 44%, respectively. These results demonstrate that C. glutamicum strains with reduced PDHC activity are an excellent platform for the production of pyruvate-derived products.
Flexible fabric keyboard with conductive polymer-coated fibers (2011)

We proposed flexible fabric keyboard which consists of conductive polymer of PEDOT:PSS-coated fibers, standard Micro Control Unit (MCU) with capacitance measurement circuits and personal computer (PC). In the sensor structure, PEDOT:PSS and UltraViolet(UV) -curable adhesive-coated fibers were woven as wefts and warps. The conductive polymer and insulating polymer coating technique was developed to form functional material on enough long fibers to weave fabric with. The weaving with automatic looming machine was employed, forming 1.2 m × 3 m sensor fabric. The sensors could detect human touch by measuring capacitance change between human fingers. The values of capacitance change under touch input ranges from 1.0 to 2.0 pF which is able to be detected by conventional capacitance meters that were integrated in MCUs. By using 9 by 3 touch sensors, keyboard was constructed and the demonstration of inputting character was made.