gebhart/patrepeval huggingface dataset:
Purification, partial characterization and plasmid‐linkage of pediocin SJ‐1, a bacteriocin produced by <i>Pediococcus acidilactici</i> (1993)

Pediococcus acidilactici SJ-1, isolated from a naturally-fermented meat product, produced an antibacterial agent active against selected strains of Lactobacillus spp., Clostridium perfringens and Listeria monocytogenes. The agent was bactericidal against sensitive indicators, and sensitive to proteolytic enzymes; it was identified as a bacteriocin, and was designated as pediocin SJ-1. It was stable over a wide pH range (3-9), and apparently most stable in the lower part of that range. At pH 3.6, pediocin SJ-1 was stable at heat-processing temperatures within the range 65-121 degrees C; its activity decreased significantly, however, when it was heated at pH 7.0. The activity of pediocin SJ-1 on sensitive indicator cells was lost in the presence of alpha-amylase, suggesting that it contains a glyco moiety, necessary for its antibacterial action. Native pediocin SJ-1 exists in the form of monomers and aggregates (with molecular weights in the range 80-150 kDa). Pediocin SJ-1 was purified 262-fold by direct application of cell-free supernatant fluids to a cation-exchange chromatography column, and was resolved by SDS-PAGE as a single peptide band with a MW of ca 4 kDa. The original pediocin SJ-1-producing strain (bac+) harbours three plasmids of 4.6, 23.5, and 45.7 MDa. Production of pediocin SJ-1, but not immunity to SJ-1, is associated with the 4.6 MDa plasmid.
Highly Functionalized Tris‐(σ)π‐Homobenzenes — Nine‐Membered Ring Compounds with Special Substitution Patterns — En Route to <i>cis,cis,cis</i>‐2,5,8‐Cyclononatriene‐1,4,7‐trione (1996)

Abstract In the pursuit of the tris‐(σ)π‐homobenzene chemistry, the synthesis of potentially tri(hexa)podal, C 3 v ‐symmetrical, polyfunctionalized 9‐membered ring systems is being explored. A rather “expensive” tris‐σ‐homobenzene ( 13b ) is the starting material for the tris‐σ‐isomer ( 14b ) from which 1,4,7‐trimethylene‐cyclononatriene ( 2 ), its tri(hexa)epoxides ( 18 , 20 ) and triepoxytriketo derivative ( 19 ) are prepared through generally highly selective transformations. An alternative approach toward the C 3 v 2,5,8‐cyclononatriene‐1,4,7‐trione [ 4 , C 6 H 6 (CO) 3 ] starts from the relatively “cheap” all‐ exo ‐1,4,7‐cyclononatriene‐trioxide ( 32 ), relies on selective epoxide opening reactions, and is complicated by typical mediumring transanular cyclizations; the rather efficient six‐step sequence does not reach the stated goal but carries attractive preparative prospects. For a central intermediate in each approach (trimethylenetrioxide 18 and bromo‐hydroxy‐diepoxycyclononane 50 ), X‐ray structural data are presented.
Clonally restricted B cells in peripheral blood of multiple sclerosis patients: Kappa/lambda staining patterns (1982)

Abstract The presence of clonally restricted B lymphocytes in the peripheral blood of patients with multiple sclerosis (MS) was investigated using a cytofluorometric technique able to detect lymphocytes having homogeneous amounts of surface immunoglobulin of one light chain class. Thirty‐five of 76 analyses (46%) performed on 63 MS patients were positive for increased numbers of clonally restricted B cells as compared with only 7 of 27 (26%) in patients with other neurological diseases ( p < 0.05) and 9 of 36 (25%) in control subjects ( p < 0.05). This B cell population expressed predominantly kappa light chain determinants in 16 of 18 MS patients (89%) but in only 6 of 11 (55%) controls ( p < 0.005). There was no correlation between the presence of abnormal B cell clones in peripheral blood and either disease activity or serum antimeasles antibody titers. The results demonstrate that there are increased numbers of clonally restricted B cells in the peripheral blood of MS patients which may be related to the oligoclonal immunoglobulin found in the serum and cerebrospinal fluid.
Improved Resistive Switching Characteristics by Al2O3 Layers Inclusion in HfO2-Based RRAM Devices (2013)

A series of complex HfO2/Al2O3 layer by layer resistive random access memory(RRAM) structure grown by atomic layer deposition are investigated. The modulation of forming voltage can be achieved by controlling the number of Al2O3 layers in HfO2 devices. In addition, the crystallization temperature of HfO2 based RRAM devices can also be improved by insetting Al2O3 layers in HfO2 film. Compared with pure HfO2 device, a significant improvement in resistive switching properties such as forming voltage variation and the distribution of HRS/LRS during resistance switching is demonstrated in the HfO2/Al2O3 layer by layer devices. Moreover, good endurance characteristic and highly reliable multibit operation are also achieved in this device structure.
WE-E-330D-05: Investigation of Imaging Performance and Acquisition Technique for a New Dual-Energy Chest Imaging System (2006)

Purpose: A novel, high-performance, cardiac-gated dual-energy (DE) chest system is under development in our lab. This paper investigates the influence of key image acquisition technique parameters (viz., selection of kVp, filtration, and dose) on DE imaging performance. Method and Materials: Experiments were conducted on a DE imaging bench with a custom-built phantom containing simulated lung nodules of varying contrast. Performance was quantified in terms of nodule contrast-noise ratio (CNRDE) in DE ‘tissue-only’ images. Low- and high-kVp were varied from 60–90 kVp and 120–150 kVp, respectively. Differential added filtration in low- and high-kVp projections was analyzed in terms of soft-tissue CNRDE both theoretically across the entire Periodic Table (Z=1−92) and experimentally for specific material types (Al, Ce, Cu, and Ag). Allocation of dose (defined A=ESDlow/ESDhigh) between low- and high-energy projections was analyzed at various levels of total entrance surface dose, ESD, over a broad range of allocation. Results: The results provide valuable guidance of technique selection for high-performance DE imaging. Optimal performance was achieved at a technique of [60/130] kVp, increasing soft-tissue CNRDE by 32% compared to [90/120] kVp. Differential added filtration [0.2 mm Ce / 0.6 mm Ag] increased soft-tissue CNRDE by 21% compared to the undifferentiated case ([1 mm Al / 1 mm Al]). Dose allocation was found to have significant influence on performance, with CNRDE increasing by more than ∼30% for A<1 compared to higher A>3 (with optima suggested in the range A∼0.3–0.5). Conclusion: Knowledgeable selection of kVp pairs, differential added filtration, and dose allocation provide significant increase in the soft-tissue CNR of DE images compared to conventional or sub-optimal techniques. Quantitative theoretical and experimental evaluation demonstrates the importance of optimized acquisition techniques for high-performance DE imaging and guides the implementation of a novel DE imaging system under development for pre-clinical imaging trials.
Engagement-based user attention distribution on web article pages (2013)

The main monetization vehicle of many Web media sites are display ads located on article pages. Those ads are typically displayed either as banners on top of the page, or on the page's side bar. Advertiser ROI depends on the quality of ad targeting, as well as on how noticeable those ads are to users reading the article. Focusing on the latter issue, previous work has studied which ad positions are, on aggregate, more noticed by users.
Different rheumatoid factors in the serum of one patient with rheumatoid arthritis. (1961)

Abstract The occurrence of a number of unusual macroglobulins has been noted in the serum of a patient with rheumatoid arthritis. On examination in the analytic ultracentrifuge small amounts of macroglobulin, sedimenting either more rapidly or more slowly than the normal 19S macroglobulin were noted. A scheme for the isolation of rheumatoid factors was devised that resulted in the recovery of four distinct serum fractions. Each fraction was free of low molecular weight contaminants and possessed serologic activities characteristic of the rheumatoid factor. The first fraction, eluted after its adsorption onto the antigen-antibody complex, sheep erythrocyte stroma-raibbit antisheep serum, contained a main component sedimenting at 19.7S, which on electrophoresis migrated ahead of gamma globulin. The minor component sedimented at approximately 27S. The fraction was highly reactive with serologic reagents employing cells sensitized with rabbit antibody as well as with latex particles coated with human gamma globulin. Three additional macroglobular fractions were obtained from that portion of the serum which failed to adsorb onto the sheep erythrocyte stromarabbit antisheep serum complex. These fractions were obtained on step-wise elution of a euglobulin preparation applied onto DEAE cellulose. The fractions contained either a 19.5S, a 22.2S, or a 17.5S macroglobulin as the major component. The macroglobulins with such sedimentation coefficients were eventually isolated. The macroglobulins reacted with latex particles coated with human gamma globulin, but not with sheep cells sensitized with rabbit antibody. The heterogencity of the rheumatoid factors seems to be a characteristic feature of sera of individuals with rheumatoid arthritis.
The leftward promoter of bacteriophage lambda. Structure, biological activity, and influence by adjacent regions. (1981)

The effect of regions adjacent to the lambda PL promoter was studied using a sequence deleted in an A/T-rich segment immediately upstream from the promoter. High resolution thermal denaturation analysis showed that the undeleted sequence, as isolated on a 360-bp restriction fragment (360-PL) melted in two distinct steps. Since the deleted sequence (230-PL) melts at a higher temperature than any portion of 360-PL, the deleted promoter is more stable to denaturation. This increased stability was also suggested by a transcription assay in which the strong binding of RNA polymerase is inhibited at low temperature. The deleted promoter fragment required a higher temperature to become functional than did the 360-PL fragment. Furthermore, RNA polymerase bound to the 230-PL fragment is displaced by heparin at a faster rate than from 360-PL, and the deleted fragment initiates transcription at a reduced rate. Thus, by several criteria the deleted promoter is less active than the parent sequence. Evidence is presented arguing that the deletion does not alter the sequence directly recognized by RNA polymerase. Therefore, the altered sequence is reducing promoter activity by changing some other level of overall promoter structure. These results suggest that regions outside of the sequence directly recognized by a regulatory protein can affect genetic expression from the site.
Effect of Deoxyribonucleic Acid Length on the Adenosine Triphosphatase Activity of Escherichia coli Restriction Endonuclease B (1974)

Abstract Restriction endonuclease B possesses a DNA-dependent ATPase activity. The ATP hydrolysis can continue for hours after the DNA hydrolysis has stopped and is due to a stable DNA-enzyme complex. RFI of bacteriophage f1 is much more active than its full length linear form (RFIII) in stimulating the ATP hydrolysis. Experiments with λ phage DNA sheared into various size molecules indicate that the ATPase activity is a direct function of the molecular weight of linear DNA in a range between 0.9 to 13 x 106 daltons. While sonicated, unmodified λ DNA molecules (5 x 105 daltons) fail to stimulate the ATPase activity, they do inhibit the intact DNA-stimulated ATP hydrolysis. The results can be interpreted as follows. (a) Endonuclease R-B recognizes DNA at the SB sites; this recognition step is independent of DNA length. (b) The probability that a linear DNA molecule is cleaved by an enzyme molecule bound to the DNA depends upon the length of the DNA: the greater the number of nucleotide pairs the higher the probability of cleavage. Circularization of a small DNA duplex also increases the probability of cleavage. One possible explanation is that the enzyme travels along the DNA molecule before cleaving the DNA. If the enzyme reaches an end of the DNA molecule before cleavage occurs, the enzyme molecule is inactivated. (c) After DNA hydrolysis has occurred, the enzyme (or one of its components) remains on the DNA molecule and causes the massive ATP hydrolysis.
Single-molecule transport kinetics of a glutamate transporter homolog shows static disorder (2020)

Kinetic properties of membrane transporters are typically poorly defined because high-resolution functional assays analogous to single-channel recordings are lacking. Here, we measure single-molecule transport kinetics of a glutamate transporter homolog from <i>Pyrococcus horikoshii</i>, Glt<sub>Ph</sub>, using fluorescently labeled periplasmic amino acid binding protein as a fluorescence resonance energy transfer-based sensor. We show that individual transporters can function at rates varying by at least two orders of magnitude that persist for multiple turnovers. A gain-of-function mutant shows increased population of the fast-acting transporters, leading to a 10-fold increase in the mean transport rate. These findings, which are broadly consistent with earlier single-molecule measurements of Glt<sub>Ph</sub> conformational dynamics, suggest that Glt<sub>Ph</sub> transport is defined by kinetically distinct populations that exhibit long-lasting "molecular memory."
Cross-Section Molecular Imaging of Supramolecular Microtubes with Contact Atomic Force Microscopy (1998)

Bent molecules, distorted layers, columnar domains, and tube membranes (shown schematically in the picture): These hierarchical layers were directly visualized by contact atomic force microscopy along the long axes of the molecules aligned within microtubes made up of bolaamphiphile 1 by self-assembly.
Lipid metabolism during encystment of Azotobacter vinelandii (1981)

The formation of cysts by Azotobacter vinelandii involves the synthesis of lipids as major metabolic products. Cells which encyst at low levels in aging glucose cultures undergo the same pattern of lipid synthesis as cells which undergo reasonably synchronous encystment in beta-hydroxybutyrate or n-butanol. The accumulation of poly-beta-hydroxybutyrate (PHB) precedes the synthesis of 5-n-heneicosylresorcinol and 5-n-tricosylresorcinol (AR1), which is then followed in about 6 h by the synthesis of the 5-n-alkylresorcinol galactosides (AR2). In the mature cyst, PHB, AR1, and AR2 account for 8, 5.6, and 4.5%, respectively, of the dry weight. Phospholipid formation levels off 4 h postinduction, which coincides with the final cell division, but fatty acids synthesis continues at a very low level throughout encystment, suggesting some turnover of fatty acid. Distribution studies show that AR1 and AR2 are found in roughly equal amounts in the exine and central body of the cysts, with only trace amounts recovered from the intine. Studies of cysts labeled during encystment with [14C]beta-hydroxybutyrate or during vegetative growth with [14C]glucose suggest that the exine structure is synthesized during encystment, but that the intine is composed largely of vegetative cell components.
Nonenzymatic-Gravimetric Determination of Total Dietary Fiber in Fruits and Vegetables (1992)

Abstract Most gravimetric methods for total dietary fiber (TDF) determination require the complete removal of starch and the partial removal of protein with various combination of enzymes In buffers at different pH values and at temperatures much above ambient condition. A hydrolysis step Is crucial In dietary fiber analysis of samples, such as cereals and legumes, which contain appreciable amounts of starch. However, many vegetables and most fruits contain very little or no starch, and they are often eaten uncooked. It would be unnecessary to use high temperatures and enzymes on these types of samples. Initially, we found that hexane and dilute alcohol extractions of a few selected fruits and vegetables gave residue weights comparable to those after enzymatic treatments. We were able to show later that simply suspending the samples in delonized water for 90 mln at 37°C and then adding 95% ethanol also yields TDF values similar to those obtained from other published methods. Comparison data obtained by using variations of the AOAC/TDF method are presented for 10 fruits and vegetables.
ChemInform Abstract: A CONVENIENT ROUTE TO VINYLLITHIUM REAGENTS (1976)

Abstract Aus den Sulfonylhydrazonen (I) erhält man mit Butyllithium die Vinyllithium‐Verbindungen (II), die mit Oxo‐Verbindung (III) zu Allylalkoholen (IV), mit Kohlendioxid zu Acrylsäuren (V) oder mit Alkylbromiden (VI) zu Olefinen (VII) umgesetzt werden können.
1H NMR Database of Lignin Model Compounds in Different Solvents (2016)

The attached pdf-files contain 1H NMR data of a number of lignin model compounds in different solvents (CD3SOCD3, CD3COCD3, CDCl3 etc.). All the data are based on earlier research by K. Lundquist and co-workers. A few obvious misprints are corrected. The files start with a formula collection where all substances analyzed in the topical solvent can be found. The substances are sorted by molecular formula according to the Hill convention, i.e. firstly by the number of carbons, secondly by the number of hydrogen atoms and then by increasing numbers of other elements in alphabetical order. To find the spectrum of a certain substance calculate the molecular formula, locate the substance in the formula section and go to the corresponding data sheet.
A well‐defined amphipathic conformation for the calcium‐free cyclic lipopeptide antibiotic, daptomycin, in aqueous solution (2005)

Daptomycin is a 13-residue cyclic lipopeptide with Ca2+-dependent bactericidal activity against a variety of high-risk pathogens. Ring closure in daptomycin is via an ester linkage between the side chain of Thr4 and the C-terminal carboxyl of the main chain; the N-terminal residue is capped by a decanoyl aliphatic chain. Extensive NMR data obtained under solution conditions that minimize aggregation have provided constraints for a detailed conformational analysis of daptomycin in aqueous solution, which should facilitate the rational design of improved analogs and enhance understanding of its mode of action. Transannular and shorter-range nuclear Overhauser effects (NOEs) as well as amide temperature shifts and 3J(NH alpha) coupling constants indicate that daptomycin adopts a well-defined conformation containing a distorted hairpin formed by Gly5-D-Ala6 type II' beta-turn. A number of hydrophobic moieties (the lipid N-cap and the Trp1 and Kyn13 side chains) are clustered at one end of the hairpin, while neutral polar and anionic residues are localized on the other end, leading to amphipathicity in the molecule. These features suggest a mode of action in which the large hydrophobic cluster of the peptide interacts with the acyl chain region of a membrane. This interaction may be facilitated by Ca2+ ions, both by neutralizing the anionic charges and by favoring association with the membrane head groups. Interestingly, our findings differ from two recent articles in which the aqueous conformation of Ca2+-free daptomycin is reported to lack a well-defined conformation (D. Jung, A. Rozek, M. Okron, and R. E. W. Hancock, Chemistry & Biology, 2004, Vol. 11, pp. 949-957) or is suggested to populate an alternate conformation (L.-J. Ball, C. M. Goult, J. A. Donarski, J. Micklefield, and V. Ramesh, Organic & Biomolecular Chemistry, 2004, Vol. 2, pp. 1872-1878).
Development of General Antisera for Trichothecanes (1986)

Abstract : Antibodies with narrow structural requirements of binding are useful in specific assays. Antibodies which bind a variety of structurally related compounds could be used in detection of classes of compounds. This project is exploring the relationship between immunogen (hapten) structure and the selectivity of resulting antibodies to various of the trichothencenes. Immunogens are synthesized and used to immunize rabbits. The polyclonal sera are then examined for their selectivity for various trichothecene compounds before attempts are made to prepare monoclonal antibodies. The first position examined for linkage to protein was the 8-position of the trichothecene molecule. Two simple syntheses of T-2 toxin from readily available anguidine were developed. The synthesis of the 4-keto analog of HT-2 toxin was achieved. Keywords: Mycotoxins; Trichothecanes; Synthesis; Radioisotope; Immunoassay; EIA(Enzyme Immunoassay), RIA(Radioimmunoassay).
Organic/Inorganic Hybrid Nanostructured Materials for Thermoelectric Energy Conversion (2018)

Thermoelectric (TE) materials can directly convert heat into electricity. This chapter investigates the organic thermoelectric (TE) materials and hybrid nanostructured TE composites. It reviews the hybrid TE nanostructured composites are fabricated by physical mixing, solution mixing, or in situ polymerization. The chapter summarizes many key advances on polymer/inorganic TE nanocomposites. Embedding inorganic TE nanostructures into polymer matrices is one of the most promising approaches to combine the advantages of organic TE materials and inorganic TE materials. Therefore, one could design a new category of hybrid organic-inorganic TE materials with enhanced TE performance based on surface transfer doping. In order to enhance the TE performance of hybrid inorganic/organic nanocomposites, other carrier transport mechanisms, such as modulation doping and energy filtering, could be employed to enhance electrical conductivity and the Seebeck coefficient while reducing the thermal conductivity of the hybrid nanocomposites.
Bipolar, anastral spindle development in artificially activated sea urchin eggs (2008)

The mitotic apparatus of the early sea urchin embryo is the archetype example of a centrosome-dominated, large aster spindle organized by means of the centriole of the fertilizing sperm. In this study, we tested the hypothesis that artificially activated sea urchin eggs possess the capacity to assemble the anastral, bipolar spindles present in many acentrosomal systems. Control fertilized Lytechinus pictus embryos and ammonia-activated eggs were immunolabeled for tubulin, centrosomal material, the spindle pole structuring protein NuMA and the mitotic kinesins MKLP1/Kinesin-6, Eg5/Kinesin-5, and KinI/Kinesin-13. Confocal imaging showed that a subset of ammonia-activated eggs contained bipolar "mini-spindles" that were anastral; displayed metaphase and anaphase-like stages; labeled for centrosomal material, NuMA, and the three mitotic kinesins; and were observed in living eggs using polarization optics. These results suggest that spindle structural and motor proteins have the ability to organize bipolar, anastral spindles in sea urchin eggs activated in the absence of the paternal centriole.
THE BENEFICIAL ACTIONS OF BEPRIDIL IN ACUTE MYOCARDIAL INFARCTION IN ANAESTHETIZED DOGS (1981)

1 When administered intravenously shortly before acute coronary ligation in dogs anaesthetized with chloralose, bepridil (5 mg/kg) produced immediate and transient falls in coronary and systemic vascular resistance which were accompanied by marked decreases in myocardial oxygen extraction. These effects were followed by sustained decreases in heart rate and myocardial oxygen consumption. 2 This dose of bepridil reduced the number of premature ventricular beats and abolished fibrillation induced by coronary artery ligation without modifying the haemodynamic or metabolic consequences (lactate production) of myocardial ischaemia. 3 When administered 1.5-2 h after ligation, bepridil did not compromise the critical perfusion of the acutely ischaemic zone but reduced the lactate production and ST-segment elevation in the ischaemic zone. 4 These results suggest that bepridil may be a useful drug in the chronic treatment of angina pectoris and in this respect may possess advantages over beta-adrenoceptor antagonists.