gebhart/patrepeval huggingface dataset:
Metathesis of methyl oleate with a homogeneous and a heterogeneous catalyst (1985)

Abstract The cometathesis reaction of methyl oleate (MO) with unsaturated dicarboxylic acid esters has been studied using either a homogeneous catalyst system (WCl 6 ‐Me 4 Sn) or a heterogeneous catalyst system (Re 2 O 3 ‐Al 2 O 3 ‐Me 4 Sn). In the presence of the homogeneous catalyst, dimethyl‐3‐hexenedioate (DMHD) reacted with MO to give cometathesis products in 47% yield with a distribution of products that agreed with the theoretical equilibrium composition. When dipropyl‐4‐octenedioate (DPOD) was used, however, the yield of cometathesis products was less than 1%. The lower reactivity of DPOD might be due to the formation of a stable complex of DPOD with the catalyst. The cometathesis reaction of MO and DMHD was also catalyzed by the heterogeneous catalyst. However, the reaction rate decreased significantly and the distribution of products did not attain the theoretical. Similar results were obtained in the cometathesis reaction of MO and DPOD catalyzed by the heterogeneous catalyst. These results suggest that MO and DMHD are preferentially adsorbed onto the surface of this catalyst according to their polarity, and that the molar ratio of MO and DMHD at the catalytic site was different from that in the reaction medium.
Regulation of Brassinosteroid Signaling by a GSK3/SHAGGY-Like Kinase (2002)

GSK3/SHAGGY is a highly conserved serine/threonine kinase implicated in many signaling pathways in eukaryotes. Although many GSK3/SHAGGY-like kinases have been identified in plants, little is known about their functions in plant growth and development. Here we show that the Arabidopsis BRASSINOSTEROID-INSENSITIVE 2 (BIN2) gene encodes a GSK3/SHAGGY-like kinase. Gain-of-function mutations within its coding sequence or its overexpression inhibit brassinosteroid (BR) signaling, resulting in plants that resemble BR-deficient and BR-response mutants. In contrast, reduced BIN2 expression via cosuppression partially rescues a weak BR-signaling mutation. Thus, BIN2 acts as a negative regulator to control steroid signaling in plants.
Rapid sample classification using an open port sampling interface coupled with liquid introduction atmospheric pressure ionization mass spectrometry (2016)

This work illustrates that an open port sampling interface/mass spectrometer combination, with appropriate instrument control and data processing software, is a viable direct liquid extraction sampling and analysis system suitable for the non-expert user and near real-time sample classification via database matching. Published in 2016. This article is a U.S. Government work and is in the public domain in the USA.
Folding super-sized DNA origami with scaffold strands from long-range PCR (2012)

A 26 kilobase single strand DNA fragment was obtained from long-range PCR amplification and subsequent enzymatic digestion, which we folded into a super-sized DNA origami nanostructure by using ∼800 staple strands.
Glomerular mesangial cell migration in response to platelet-derived growth factor. (1990)

Platelet-derived growth factor (PDGF) is a potent mitogenic and chemotactic protein for a variety of cell types. Glomerular mesangial cells also respond to PDGF in terms of proliferation, but, to date, have not been examined for migratory behavior in response to a specific growth factor. Here, we examine the ability of isolated rat mesangial cells to migrate toward gradients of purified PDGF. Chemotaxis assays were performed in two-compartment blind well chambers, each compartment separated by a 14-microns porous filter membrane. Human PDGF was added to 200 microliters of RPMI 1640 medium in the lower compartment beneath the filters to make incremental concentrations from 2.5 to 50 units/ml. Control compartments received diluent without PDGF. Mesangial cells in RPMI 1640 medium were added to the upper compartments and the chambers were incubated for 8 hours at 37 degrees C. After fixation, the number of cells on the underside of the filter were counted by scanning electron microscopy. A linear dose response of mesangial cell migration toward increasing concentrations of PDGF was observed, achieving cell numbers of 9-fold over controls at 50 units/ml. Migratory cells were verified as mesangial cells by fluorescence expression of actin, myosin, and desmin and absence of expression of leukocyte common antigen and Ia antigen. Addition of equimolar concentrations of PDGF on both sides of the filter or addition of anti-PDGF antibody to the lower chamber containing PDGF negated the chemotactic response. These studies indicate that mesangial cells migrate in response to PDGF. This mechanism may, in part, play a role in some forms of mesangial proliferative glomerular disease.
Methanol/Gasoline Blends as Automotive Fuel (1975)

<div class="htmlview paragraph">An experimental program was conducted by the Energy Research &amp; Development Administration's Bartlesville (Okla.) Energy Research Center to determine the effect on exhaust emissions and fuel economy when methanol is added to conventional motor fuel, that is, gasoline. Ten 1974 and 1975 model vehicles were used in the study. Ambient temperature was varied from 20° to 100°F to determine temperature effects while using methanol/gasoline blends. Emissions were generally modified as a consequence of the fact that the addition of methanol to gasoline alters both the fuel vapor pressure and the stoichiometry of the air-fuel mixture. Fuel economy was generally decreased by methanol addition.</div> <div class="htmlview paragraph">Moderate mileage accumulation using 10% methanol fuel showed no deterioration either in emissions control or of fuel-related engine components. Driveability differences between methanol 10% blends and gasoline were detectable but were judged not to be objectionable.</div>
Tensegrity, cellular biophysics, and the mechanics of living systems (2014)

The recent convergence between physics and biology has led many physicists to enter the fields of cell and developmental biology. One of the most exciting areas of interest has been the emerging field of mechanobiology that centers on how cells control their mechanical properties, and how physical forces regulate cellular biochemical responses, a process that is known as mechanotransduction. In this article, we review the central role that tensegrity (tensional integrity) architecture, which depends on tensile prestress for its mechanical stability, plays in biology. We describe how tensional prestress is a critical governor of cell mechanics and function, and how use of tensegrity by cells contributes to mechanotransduction. Theoretical tensegrity models are also described that predict both quantitative and qualitative behaviors of living cells, and these theoretical descriptions are placed in context of other physical models of the cell. In addition, we describe how tensegrity is used at multiple size scales in the hierarchy of life—from individual molecules to whole living organisms—to both stabilize three-dimensional form and to channel forces from the macroscale to the nanoscale, thereby facilitating mechanochemical conversion at the molecular level.
Characterization of Phenolic Composition in Lamiaceae Spices by LC-ESI-MS/MS (2010)

A total of 38 phenolic compounds in the solid/liquid extracts of five Lamiaceae spices, rosemary, oregano, sage, basil, and thyme, were identified in the present study using LC-ESI-MS/MS. These compounds were distributed in four major categories, namely, hydroxycinnamic acid derivatives, hydroxybenzoic acid derivatives, flavonoids, and phenolic terpenes. Among them, the category of flavonoids was the largest, with 17 compounds. Identification of the phenolic compounds was carried out by comparing retention times and mass spectra with those of authentic standards. If standards were unavailable, phenolic compounds were identified on the basis of accurate mass of pseudomolecular [M - H](-) ions and tandem mass spectrometry (MS/MS) data. The results of accurate mass measurements fit well with the elemental composition of the compounds. The diagnostic fragmentation patterns of the compounds during collision-induced dissociation (CID) elucidated the structural information of the compounds analyzed.
Crystal structure of [Leu1]zervamicin, a membrane ion-channel peptide: implications for gating mechanisms. (1991)

Structures in four different crystal forms of [Leu1]zervamicin (zervamicin Z-L, Ac-Leu-Ile-Gln-Iva-Ile5-Thr-Aib-Leu-Aib-Hyp10-Gln-Aib-Hyp-Aib-P ro15-Phol, where Iva is isovaline, Aib is alpha-amino isobutyric acid, Hyp is 4-hydroxyproline, and Phol is phenylalaninol), a membrane channel-forming polypeptide from Emericellopsis salmosynnemata, have been determined by x-ray diffraction. The helical structure is amphiphilic with all the polar moieties on the convex side of the bent helix. Helices are bent at Hyp10 from approximately 30 degrees to approximately 45 degrees in the different crystal forms. In all crystal forms, the peptide helices aggregate in a similar fashion to form water channels that are interrupted by hydrogen bonds between N epsilon H(Gln11) and O delta (Hyp10) of adjacent helices. The Gln11 side chain is folded in an unusual fashion in order to close the channel. Space is available for an extended conformation for Gln11, in which case the channel would be open, suggesting a gating mechanism for cation transport. Structural details are presented for one crystal form derived from methanol/water solution: C85H140N18O22. 10H2O, space group P21, a = 23.068(6) A, b = 9.162(3) A, c = 26.727(9) A, beta = 108.69(2) degrees (standard deviation of last digit is given in parentheses); overall agreement factor R = 10.1% for 5322 observed relfections [magnitude of Fo greater than 3 sigma (F)]; resolution, 0.93 A.
A Human RNA Viral Cysteine Proteinase That Depends upon a Unique Zn2+-binding Finger Connecting the Two Domains of a Papain-like Fold (1999)

A cysteine proteinase, papain-like proteinase (PL1pro), of the human coronavirus 229E (HCoV) regulates the expression of the replicase polyproteins, pp1a and ppa1ab, by cleavage between Gly111 and Asn112, far upstream of its own catalytic residue Cys1054. In this report, using bioinformatics tools, we predict that, unlike its distant cellular homologues, HCoV PL1pro and its coronaviral relatives have a poorly conserved Zn2+ finger connecting the left and right hand domains of a papain-like fold. Optical emission spectrometry has been used to confirm the presence of Zn2+ in a purified and proteolytically active form of the HCoV PL1pro fused with the Escherichia coli maltose-binding protein. In denaturation/renaturation experiments using the recombinant protein, its activity was shown to be strongly dependent upon Zn2+, which could be partly substituted by Co2+ during renaturation. The reconstituted, Zn2+-containing PL1pro was not sensitive to 1,10-phenanthroline, and the Zn2+-depleted protein was not reactivated by adding Zn2+ after renaturation. Consistent with the proposed essential structural role of Zn2+, PL1pro was selectively inactivated by mutations in the Zn2+ finger, including replacements of any of four conserved Cys residues predicted to co-ordinate Zn2+. The unique domain organization of HCoV PL1pro provides a potential framework for regulatory processes and may be indicative of a nonproteolytic activity of this enzyme.
Evidence that senescent human prostate epithelial cells enhance tumorigenicity: Cell fusion as a potential mechanism and inhibition by p16INK4a and hTERT (2007)

Normal human prostate (NHP) epithelial cells undergo senescence in vitro and in vivo but the potential role of senescent NHP cells in prostate tumorigenesis remain unclear. Here we show that senescent NHP cells enhance the in vivo tumorigenicity of low-tumorigenic LNCaP prostate cancer and low/non-tumorigenic subset of cells (called L cells) isolated from multiple bulk-cultured prostate (and other) cancer cell lines. Subsequent studies suggest cell-cell fusion as a potential mechanism for senescent NHP cell-enhanced tumor development. Using fluorescently tagged tumor cells and/or NHP cells, we find that NHP cells, like fibroblasts, can undergo fusion with unfractionated tumor cells or the L cells. Using 293T-L cells as the model cell system, we verify NHP and 293T-L cell fusion by using differential RT-PCR, karyotyping, and gene expression analyses. Further experiments demonstrate that senescent NHP cells that have lost progenitor markers, accumulated p16INK4a (p16) protein expression, and acquired the AR mRNA expression, appear to be the preferential fusion targets. Strikingly, the tumorigenicity of the NHP/293T-L hybrid cells was inhibited by exogenous p16 as well as hTERT. Chromosomal analyses revealed that hTERT probably inhibited the in vivo tumorigenicity by maintaining genomic stability. These results suggest that senescent NHP cells, like senescent fibroblasts, may promote tumor development and that one of the mechanisms underlying the senescent NHP cell-enhanced tumorigenicity could be through cell fusion.
Multi-function Technology for FAX / MFP Devices (1998)

We released DOCIT in 1992 as an MFP (Multi-Function Peripheral) which integrates PC peripherals such as printers and scanners. We have been consecutively developing FAX / MFP as PC peripherals integrating the accumulated printer technology and FAX technology while reexamining DOCIT. This paper describes the technology on each functional element of MFP, and the combining technology that allows these multiple functions to coexist on one equipment. An example of a PC application for utilizing FAX / MFP is also introduced.
Protein Synthesis during Natural and Precocious Soybean Seed (<i>Glycine max</i> [L.] Merr.) Maturation (1988)

Protein synthesis was studied during precocious and natural soybean seed (Glycine max [L.] Merr.) maturation. Developing seeds harvested 35 days after flowering were precociously matured through controlled dehydration. Total soluble proteins and proteins labeled with [(35)S]methionine were extracted from control, developing seeds and from precociously and naturally matured seeds and were analyzed by one-dimensional PAGE and fluorography. The results demonstrated that several polypeptides which were designated "mature polypeptides," were synthesized de novo during precocious and natural seed maturation. Two of these polypeptides, 31 and 128 kilodalton in mass, also stained intensely with Coomassie blue, suggesting their abundant accumulation during seed maturation. Results from in vitro translation experiments showed that the mRNAs corresponding to these "maturation polypeptides" accumulated during precocious maturation and in naturally matured seeds, but not in seeds freshly harvested 35 days after flowering (control). The role of the "maturation polypeptides" is currently unknown; however, their presence and that of their corresponding mRNAs was coincident with the ability of matured seeds to establish seedling growth. This study has demonstrated that precocious seed maturation treatments may be extremely useful for investigations of metabolic events and molecular control mechanisms affecting soybean seed maturation.
A Clonal Selection Algorithm for the container stacking problem (2011)

Due to increasing demand, container terminals face the challenges of increasing its service capacity and minimize the time of ships loading and unloading. The assignment of storage locations for reshuffled containers is a problem to the efficiency of container terminals operations, as a wrong assignment may result in several future reshuffles. This paper proposes a meta-heuristic based on the Clonal Selection Algorithm to minimize reshuffle when retrieving containers from a stack. The model competitiveness in accuracy and time are established by extensive numerical experiments comparing with an existing Integer Program model. The preliminary results obtained here suggest the proposed model is a promising optimization tool for the container stacking problem.
Tachykinin receptors in the circular muscle of the guinea‐pig ileum (1990)

1. We have studied the mechanical response of circular strips of the guinea-pig ileum to tachykinins and characterized the receptors involved by means of receptor-selective agonists. 2. The strips responded to both substance P (SP) and neurokinin A (NKA), as well as to [Pro9]-SP sulphone (selective NK1-receptor agonist), [beta Ala8]-NKA(4-10) (selective NK2-receptor agonist) and [MePhe7]-neurokinin B (selective NK3-receptor agonist). The ED50s of the various peptides (calculated as the concentration of agonist which produced 50% of the response to 10 microM carbachol) were similar, in the range of 40-200 nM, i.e. no clearcut rank order of potency was evident. 3. The response to a submaximal (10 nM) concentration of SP or NKA was unaffected in the presence of peptidase inhibitors (thiorphan, captopril and bestatin, 1 microM each). 4. The response to the NK1-agonist was totally atropine-resistant, but was reduced (about 30% inhibition) by tetrodotoxin. The response to the NK3-receptor agonist was halved by atropine and abolished by tetrodotoxin. The response to the NK2-agonist was unaffected by either atropine or tetrodotoxin. 5. The response to the selective NK2-agonist was unchanged after desensitization of NK1- or NK3-receptors. 6. The response to the NK2-selective agonist was strongly inhibited by [Tyr5, D-Trp6,8,9, Arg10]-NKA(4-10) (MEN 10,207) a selective NK2-receptor antagonist which did not modify the response to the NK1-selective agonist. 7. Our findings indicate that all the three known types of tachykinin receptors mediate the contractile response of the circular muscle of the guinea-pig ileum to peptides of this family. The response to activation of NK3-receptors is totally neurogenic and partially mediated by endogenous acetylcholine, the response to activation of NK1-receptors is partly neurogenic and largely myogenic and the response to activation of NK2-receptors is totally myogenic.
The Role of Acetate in CO2 Corrosion: the Double Whammy (1999)

Abstract The role of acetate (Ac−) ion on the rate of CO2 corrosion has been investigated. The presence of Ac− in oilfield brines can significantly increase the rate of corrosion of carbon steel. In the presence of Ac−, the corrosion rate can increase even if the pH increases. Many corrosion prediction models cannot accommodate this observation. On a ppm basis, Ac− increases the corrosion rate more than the HCO3− decreases it. The presence of Ac− only affects the corrosion rate and not the corrosion mechanism. The mechanism by which HAc increases the corrosion rate may be explained by its ability to both decrease the pH and solubilise Fe2+, thus reducing the iron carbonate film thickness. Ac− has been shown to attack existing iron carbonate films and make them thinner. If local film thinning were to occur this would result in localised corrosion. Nitrate, another small anion, did not increase the corrosion rate. Brines containing Ac− can be inhibited using conventional oilfield inhibitors. The presence of Ac− can result in positive errors in the determination ofHCO3−. The routine analysis of HCO3− and Ac− need to be undertaken carefully otherwise significant errors can result. Some commercial laboratories have been shown to be incapable of these ‘routine’ procedures. All of the above could result in the corrosion rate being significantly underestimated and consequently the specification of too low a corrosion allowance and/or the implementation of an insufficient inspection and corrosion control strategy. This is the acetate double whammy: Acetate may lead to an overestimation of the HCO3− and thus an underestimation of the corrosion rate for CO2 only.Acetate will cause the corrosion rate to be higher than for CO2 only.
Fast delta evaluation for the Vehicle Routing Problem with Multiple Time Windows (2019)

In many applications of vehicle routing, a set of time windows are feasible for each visit, giving rise to the Vehicle Routing Problem with Multiple Time Windows (VRPMTW). We argue that such disjunctions are problematic for many solution methods, and exemplify this using a state of the art Adaptive Large Neighbourhood Search heuristic. VRPMTW comes in two variants depending on whether the time used en route must be minimised. A more compact and corrected mathematical formulation for both variants of the problem is presented, and new best solutions for all but six benchmark instances of VRPMTW without time minimisation is found. A new solution representation for VRPMTW with time minimisation is presented, its importance is demonstrated and it is used to find new best solutions for all but one benchmark instance of VRPMTW with time minimisation.
Computational Disclosure Control for Medical Microdata (2018)

We present a computer program named Datafly that uses computational disclosure techniques to maintain anonymity in medical data by automatically generalizing, substituting and removing information as appropriate without losing many of the details found within the data. Decisions are made at the field and record level at the time of database access, so the approach can be used on the fly in role-based security within an institution, and in batch mode for exporting data from an institution. Often organizations release and receive medical data with all explicit identifiers, such as name, address, phone number, and social security number, removed in the incorrect belief that patient confidentiality is maintained because the resulting data look anonymous; however, we show that in most of these cases, the remaining data can be used to re-identify individuals by linking or matching the data to other databases or by looking at unique characteristics found in the fields and records of the database itself. When these less apparent aspects are taken into account, each released record can be made to ambiguously map to many possible people, providing a level of anonymity which the user determines.
A laminin 511 matrix is regulated by TAZ and functions as the ligand for the α6Bβ1 integrin to sustain breast cancer stem cells (2015)

Understanding how the extracellular matrix impacts the function of cancer stem cells (CSCs) is a significant but poorly understood problem. We report that breast CSCs produce a laminin (LM) 511 matrix that promotes self-renewal and tumor initiation by engaging the α6Bβ1 integrin and activating the Hippo transducer TAZ. Although TAZ is important for the function of breast CSCs, the mechanism is unknown. We observed that TAZ regulates the transcription of the α5 subunit of LM511 and the formation of a LM511 matrix. These data establish a positive feedback loop involving TAZ and LM511 that contributes to stemness in breast cancer.
Transforming behavioral specifications to facilitate synthesis of testable designs (2002)

Recently, several high level synthesis approaches have been proposed to synthesize testable data paths from behavioral specifications. This paper introduces a novel technique to transform behavioral specifications, such that an existing behavioral test synthesis system can generate area-efficient, testable designs with significantly lower partial scan overhead. Experimental results demonstrate the significant savings in partial scan overhead when the transformation is applied before using the behavioral test synthesis system to synthesize 100% test-efficient designs.