gebhart/patrepeval huggingface dataset:
Synthesis of Supported Platinum Nanoparticles from Li−Pt Solid Solution (2010)

Platinum nanoparticle catalysts are essential for achieving energy-efficient and greener chemical processes that involve breaking or establishing of H-H, C-H, or O-H bonds. In this work, we report an innovative top-down strategy to prepare the supported Pt nanoparticles with an average size of approximately 2 nm, starting directly from bulk metallic Pt by metallurgical method. Bulk platinum was dissolved in liquid lithium and ruptured into nanoparticles. This Li-Pt liquid alloy was quenched into Li-Pt solid solution. The lithium content was further converted into LiOH. The resulting powder of Pt nanoparticles in LiOH can be mixed with any nonaqueous support materials. Thereafter, the LiOH can be selectively leached off by water, allowing Pt nanoparticles to be adsorbed on the desired support material. Transmission electron microscope and extended X-ray absorption fine structure analyses demonstrated that the as-formed Pt nanoparticles have an average size of around 2 nm. The carbon-supported Pt nanoparticles prepared by this method inherit more characteristics of their bulk counterparts so that high specific catalytic activity of bulk Pt is maintained, which is confirmed by a preliminary electrocatalytic characterization of oxygen reduction reaction (ORR).
Decoding the Membrane Activity of the Cyclotide Kalata B1 (2011)

Cyclotides, a large family of cyclic peptides from plants, have a broad range of biological activities, including insecticidal, cytotoxic, and anti-HIV activities. In all of these activities, cell membranes seem likely to be the primary target for cyclotides. However, the mechanistic role of lipid membranes in the activity of cyclotides remains unclear. To determine the role of lipid organization in the activity of the prototypic cyclotide, kalata B1 (kB1), and synthetic analogs, their bioactivities and affinities for model membranes were evaluated. We found that the bioactivity of kB1 is dependent on the lipid composition of target cell membranes. In particular, the activity of kB1 requires specific interactions with phospholipids containing phosphatidylethanolamine (PE) headgroups but is further modulated by nonspecific peptide-lipid hydrophobic interactions, which are favored in raft-like membranes. Negatively charged phospholipids do not favor high kB1 affinity. This lipid selectivity explains trends in antimicrobial and hemolytic activities of kB1; it does not target bacterial cell walls, which are negatively charged and lacking PE-phospholipids but can insert in the membranes of red blood cells, which have a low PE content and raft domains in their outer layer. We further show that the anti-HIV activity of kB1 is the result of its ability to target and disrupt the membranes of HIV particles, which are raft-like membranes very rich in PE-phospholipids.
Synthesis of Butene−Ethylene and Hexene−Butene−Ethylene Copolymers from Ethylene via Tandem Action of Well-Defined Homogeneous Catalysts (2000)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTSynthesis of Butene−Ethylene and Hexene−Butene−Ethylene Copolymers from Ethylene via Tandem Action of Well-Defined Homogeneous CatalystsZachary J. A. Komon, Xianhui Bu, and Guillermo C. BazanView Author Information Department of Chemistry, University of California Santa Barbara, California 93106 Cite this: J. Am. Chem. Soc. 2000, 122, 8, 1830–1831Publication Date (Web):February 10, 2000Publication History Received2 December 1999Published online10 February 2000Published inissue 1 March 2000https://pubs.acs.org/doi/10.1021/ja994222chttps://doi.org/10.1021/ja994222crapid-communicationACS PublicationsCopyright © 2000 American Chemical SocietyRequest reuse permissionsArticle Views1609Altmetric-Citations146LEARN 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 InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Catalysts,Chemical structure,Hydrocarbons,Polyethylene,Polymers Get e-Alerts
Application of fluorescence resonance energy transfer in the clinical laboratory: Routine and research (1998)

Fluorescence resonance energy transfer (FRET) phenomenon has been applied to a variety of scientific challenges in the past. The potential utility of this biophysical tool will be revisited in the 21st century. The rapid digital signal processing in conjunction with personal computers and the wide use of multicolor laser technology in clinical flow cytometry opened an opportunity for multiplexed assay systems. The concept is very simple. Color-coded microspheres are used as solid-phase matrix for the detection of fluorescent labeled molecules. It is the homogeneous assay methodology in which solid-phase particles behave similarly to the dynamics of a liquid environment. This approach offers a rapid cost-effective technology that harnesses a wide variety of fluorochromes and lasers. With this microsphere technology, the potential applications for clinical flow cytometry in the future are enormous. This new approach of well-established clinically proven methods sets the stage to briefly review the theoretical and practical aspects of FRET technology. The review shows various applications of FRET in research and clinical laboratories. Combination of FRET with monoclonal antibodies resulted in a boom of structural analysis of proteins in solutions and also in biological membranes. Cell surface mapping of cluster of differentiation molecules on immunocompetent cells has gained more and more interest in the last decade. Several examples for biological applications are discussed in detail. FRET can also be used to improve the spectral characteristics of fluorescent dyes and dye combinations, such as the tandem dyes in flow and image cytometry and the FRET primers in DNA sequencing and polymerase chain reactions. The advantages and disadvantages of donor-acceptor dye combinations are evaluated. In addition, the sensitivity of FRET provides the basis for establishing fast, robust, and accurate enzyme assays and immunoassays. Benefits and limitations of FRET-based assays are thoroughly scrutinized. At the end of the paper we review the future of FRET methodology. Cytometry (Comm. Clin. Cytometry) 34:159–179, 1998. © 1998 Wiley-Liss, Inc.
Porin Activity of Anaplasma phagocytophilum Outer Membrane Fraction and Purified P44 (2006)

Anaplasma phagocytophilum, an obligatory intracellular bacterium that causes human granulocytic anaplasmosis, has significantly less coding capacity for biosynthesis and central intermediary metabolism than do free-living bacteria. Thus, A. phagocytophilum needs to usurp and acquire various compounds from its host. Here we demonstrate that the isolated outer membrane of A. phagocytophilum has porin activity, as measured by a liposome swelling assay. The activity allows the diffusion of L-glutamine, the monosaccharides arabinose and glucose, the disaccharide sucrose, and even the tetrasaccharide stachyose, and this diffusion could be inhibited with an anti-P44 monoclonal antibody. P44s are the most abundant outer membrane proteins and neutralizing targets of A. phagocytophilum. The P44 protein demonstrates characteristics consistent with porins of gram-negative bacteria, including detergent solubility, heat modifiability, a predicted structure of amphipathic and antiparallel beta-strands, an abundance of polar residues, and a C-terminal phenylalanine. We purified native P44s under two different nondenaturing conditions. When reconstituted into proteoliposomes, both purified P44s exhibited porin activity. P44s are encoded by approximately 100 p44 paralogs and go through extensive antigenic variation. The 16-transmembrane-domain beta-strands consist of conserved P44 N- and C-terminal regions. By looping out the hypervariable region, the porin structure is conserved among diverse P44 proteins yet enables antigenic variation for immunoevasion. The tricarboxylic acid (TCA) cycle of A. phagocytophilum is incomplete and requires the exogenous acquisition of L-glutamine or L-glutamate for function. Efficient diffusion of L-glutamine across the outer membrane suggests that the porin feeds the Anaplasma TCA cycle and that the relatively large pore size provides Anaplasma with the necessary metabolic intermediates from the host cytoplasm.
Efficient Galerkin techniques for multipole-accelerated capacitance extraction of 3-D structures with multiple dielectrics (2002)

This paper describes an efficient implementation of a Galerkin based multipole-accelerated boundary element method for 3-D capacitance extraction of conductors in an arbitrary piecewise-constant dielectric medium. Results are presented to demonstrate that the Galerkin method is substantially more accurate than the commonly used collocation scheme for problems with dielectric interfaces. In addition, it is shown experimentally that for a given discretization, a careful implementation of the Galerkin method in a multipole-accelerated program is only slightly more computationally expensive than the collocation method.
A Hybrid Algorithm for Text Classification Problem (2012)

This paper investigates a novel algorithm-EGA-SVM for text classification problem by combining support vector machines (SVM) with elitist genetic algorithm (GA). The new algorithm uses EGA, which is based on elite survival strategy, to optimize the parameters of SVM. Iris dataset and one hundred pieces of news reports in Chinese news are chosen to compare EGA-SVM, GA-SVM and traditional SVM. The results of numerical experiments show that EGA-SVM can improve classification performance effectively than the other algorithms. This text classification algorithm can be extended easily to apply to literatures in the field of electrical engineering. Streszczenie. W artykule przedstawiono nowy algorytm klasyfikacji tekstu bazujący na mechanizmie SVM (support vector machine) I algorytmie genetycznym. Algorytm zbadano na podstawie bazy danych Iris i setek innych chinskich przykladow. Algorytm wykazal swoją skutecznośc. Moze byc on latwo rozszerzony na analize tekstow w inzynierii elektrycznej (Hybrydowy algorytm do klasyfikacji tekstu)
Controlled/“Living” Radical Polymerization. Atom Transfer Radical Polymerization Catalyzed by Copper(I) and Picolylamine Complexes (1999)

Two picolyl structure based amines, the tridentate N,N-bis(2-pyridylmethyl)octylamine (BPMOA) and the tetradentate tris[(2-pyridyl)methyl]amine, have been successfully synthesized and employed as new ligands in the copper-mediated atom transfer radical polymerization (ATRP) of styrene, methyl acrylate, and methyl methacrylate. Polymerizations showed a linear increase in molecular weight with conversion and relatively low polydispersities throughout the reactions. Compared with the structurally related N,N,N‘,N‘ ‘,N‘ ‘-pentamethyldiethylenetriamine, different kinetic behavior was observed when BPMOA was used as the ligand for the copper-mediated ATRP of methyl methacrylate. This is mainly attributed to the solubility difference of the catalyst in these systems. The ready availability of ligands based on the picolyl structure and their easily tunable solubilities as well as steric and electronic properties make them very attractive as new ligands in copper-mediated ATRP.
Plasmids as Epidemiologic Markers in Nosocomial Gram-Negative Bacilli: Experience at a University and Review of the Literature (1986)

Bacterial plasmids have become valuable markers for the comparison of strains of nosocomial gram-negative bacilli. The importance of plasmids in nosocomial infections is primarily due to their transferable antibiotic resistance genes (R plasmids), but other plasmid-mediated traits may eventually serve as potential markers. Stable cryptic plasmids have also served to relate outbreak strains, particularly nonfermenting strains of gram-negative bacteria. Klebsiella pneumoniae and Serratia marcescens have been the major plasmid-containing species in outbreaks involving single or multiple species. Outbreaks of single species with common plasmid patterns have included the Enterobacteriaceae, Pseudomonas aeruginosa, Pseudomonas cepacia, Ewingella americana, and Legionella pneumophila. Intrageneric spread of the same or similar R plasmids has nearly always occurred within the Enterobacteriaceae in large medical centers or Veterans Administration hospitals. High-risk nurseries and burn units have been conspicuous foci for R plasmid evolution. Hospital epidemiologists and clinical microbiologists will likely have an ever-increasing need to determine the plasmid content of gram-negative bacilli producing endemic and epidemic nosocomial infections.
Engineering Redox Cofactor Regeneration for Improved Pentose Fermentation in Saccharomyces cerevisiae (2003)

Pentose fermentation to ethanol with recombinant Saccharomyces cerevisiae is slow and has a low yield. A likely reason for this is that the catabolism of the pentoses D-xylose and L-arabinose through the corresponding fungal pathways creates an imbalance of redox cofactors. The process, although redox neutral, requires NADPH and NAD+, which have to be regenerated in separate processes. NADPH is normally generated through the oxidative part of the pentose phosphate pathway by the action of glucose-6-phosphate dehydrogenase (ZWF1). To facilitate NADPH regeneration, we expressed the recently discovered gene GDP1, which codes for a fungal NADP+-dependent D-glyceraldehyde-3-phosphate dehydrogenase (NADP-GAPDH) (EC 1.2.1.13), in an S. cerevisiae strain with the D-xylose pathway. NADPH regeneration through an NADP-GAPDH is not linked to CO2 production. The resulting strain fermented D-xylose to ethanol with a higher rate and yield than the corresponding strain without GDP1; i.e., the levels of the unwanted side products xylitol and CO2 were lowered. The oxidative part of the pentose phosphate pathway is the main natural path for NADPH regeneration. However, use of this pathway causes wasteful CO2 production and creates a redox imbalance on the path of anaerobic pentose fermentation to ethanol because it does not regenerate NAD+. The deletion of the gene ZWF1 (which codes for glucose-6-phosphate dehydrogenase), in combination with overexpression of GDP1 further stimulated D-xylose fermentation with respect to rate and yield. Through genetic engineering of the redox reactions, the yeast strain was converted from a strain that produced mainly xylitol and CO2 from D-xylose to a strain that produced mainly ethanol under anaerobic conditions.
Biotype, serotype, and pathogenicity of attaching and effacing enteropathogenic Escherichia coli strains isolated from diarrheic commercial rabbits (1988)

A total of 568 strains of Escherichia coli isolated from healthy and diarrheic rabbits were separated into 11 different biotypes according to the fermentation patterns of four carbohydrates. Strains belonging to biotypes 1 to 3, 6, and 8 induced lesions characteristic for attaching and effacing E. coli (AEEC). They attached to the intestinal epithelium of the terminal small intestine and the large intestine of 5-week-old rabbits after experimental infection and caused effacement of the microvillous brush border. However, pathogenicity for weaned rabbits, as judged by diarrhea score, anorexia, and reduced weight gain, varied according to the biotypes of the strains. Strains belonging to biotypes 1 and 6 produced only discrete clinical signs, strains belonging to biotypes 2 and 3+ (motile) induced diarrhea and growth depression, whereas strains belonging to biotypes 3- (immotile) and 8 caused severe clinical signs and high mortality. This confirms evidence from the field. Biotypes 3- and 8, accounting for 35.5 and 7.1% of AEEC strains in weaned diarrheic rabbits, respectively, were not detected in weaned healthy rabbits, while biotype 2 was the predominant strain in weaned healthy rabbits (62.3%). Finally, serotyping showed a close relationship between biotype and serotype of the AEEC examined. Most strains of biotypes 1+ and 2+ tested were O109:K-:H2 and O132:K-:H2, respectively, whereas all strains tested of biotype 3- were O15:K-:H- and those of biotype 8 were O103:K-:H2. These data indicate that specific clones of AEEC might be involved in juvenile rabbit enteritis. It was concluded that determination of biotypes allows the screening of highly pathogenic AEEC in weaned rabbits (biotypes 3- and 8).
C-Terminal Fluorescent Labeling Impairs Functionality of DNA Mismatch Repair Proteins (2012)

The human DNA mismatch repair (MMR) process is crucial to maintain the integrity of the genome and requires many different proteins which interact perfectly and coordinated. Germline mutations in MMR genes are responsible for the development of the hereditary form of colorectal cancer called Lynch syndrome. Various mutations mainly in two MMR proteins, MLH1 and MSH2, have been identified so far, whereas 55% are detected within MLH1, the essential component of the heterodimer MutLα (MLH1 and PMS2). Most of those MLH1 variants are pathogenic but the relevance of missense mutations often remains unclear. Many different recombinant systems are applied to filter out disease-associated proteins whereby fluorescent tagged proteins are frequently used. However, dye labeling might have deleterious effects on MutLα's functionality. Therefore, we analyzed the consequences of N- and C-terminal fluorescent labeling on expression level, cellular localization and MMR activity of MutLα. Besides significant influence of GFP- or Red-fusion on protein expression we detected incorrect shuttling of single expressed C-terminal GFP-tagged PMS2 into the nucleus and found that C-terminal dye labeling impaired MMR function of MutLα. In contrast, N-terminal tagged MutLαs retained correct functionality and can be recommended both for the analysis of cellular localization and MMR efficiency.
The Proteoglycan Brevican Binds to Fibronectin after Proteolytic Cleavage and Promotes Glioma Cell Motility (2008)

The adult neural parenchyma contains a distinctive extracellular matrix that acts as a barrier to cell and neurite motility. Nonneural tumors that metastasize to the central nervous system almost never infiltrate it and instead displace the neural tissue as they grow. In contrast, invasive gliomas disrupt the extracellular matrix and disperse within the neural tissue. A major inhibitory component of the neural matrix is the lectican family of chondroitin sulfate proteoglycans, of which brevican is the most abundant member in the adult brain. Interestingly, brevican is also highly up-regulated in gliomas and promotes glioma dispersion by unknown mechanisms. Here we show that brevican secreted by glioma cells enhances cell adhesion and motility only after proteolytic cleavage. At the molecular level, brevican promotes epidermal growth factor receptor activation, increases the expression of cell adhesion molecules, and promotes the secretion of fibronectin and accumulation of fibronectin microfibrils on the cell surface. Moreover, the N-terminal cleavage product of brevican, but not the full-length protein, associates with fibronectin in cultured cells and in surgical samples of glioma. Taken together, our results provide the first evidence of the cellular and molecular mechanisms that may underlie the motility-promoting role of brevican in primary brain tumors. In addition, these results underscore the important functional implications of brevican processing in glioma progression.
Lymphangiogenesis and tumor metastasis (2003)

In several human cancers, increased expression in primary tumors of vascular endothelial growth factor-C (VEGF-C) is correlated with regional lymph node metastasis. Studies using transgenic mice overexpressing VEGF-C, or xenotransplantation of VEGF-C-expressing tumor cells into immunodeficient mice, have demonstrated a role for VEGF-C in tumor lymphangiogenesis and the subsequent formation of lymph node metastasis. However, at variance with data obtained in animal models, there is at present very little evidence for lymphangiogenesis in human tumors. Nonetheless, the striking correlation between levels of VEGF-C in primary human tumors and lymph node metastases exists, which suggests that VEGF-C may serve functions other than lymphangiogenesis. Thus, VEGF-C may activate pre-existing lymphatics which in turn become directly involved in tumor cell chemotaxis, intralymphatic intravasation and distal dissemination. A reciprocal dialogue is therefore likely to exist between tumor and lymphatic endothelial cells which results in the formation of lymph node metastases.
Studies on Search of New Antimicrobial Active Compound for Food Preservation (1966)

A search was made for new antimicrobial compounds which are effective in preserving foods, particularly in inhibiting the growth of microorganisms.In this paper, straight-chain unsaturated fatty acids, aromatic ones, pinonic acid and their esters and fatty aminocarboxylic acids were synthesized and their antimicrobial activities were investigated. It was found that straight-chain unsaturated fatty acids, such as octatrienoic and decatetraenoic acids, show antimicrobial action, and fatty aminocarboxylic acids possessing cationic structure exhibit the action considerablly.
A new model for random X chromosome inactivation (2008)

X chromosome inactivation (XCI) reduces the number of actively transcribed X chromosomes to one per diploid set of autosomes, allowing for dosage equality between the sexes. In eutherians, the inactive X chromosome in XX females is randomly selected. The mechanisms for determining both how many X chromosomes are present and which to inactivate are unknown. To understand these mechanisms, researchers have created X chromosome mutations and transgenes. Here, we introduce a new model of X chromosome inactivation that aims to account for the findings in recent studies, to promote a re-interpretation of existing data and to direct future experiments.
TECHNOLOGIES FOR LARGE DATA MANAGEMENT IN SCIENTIFIC COMPUTING (2013)

In recent years, intense usage of computing has been the main strategy of investigations in several scientific research projects. The progress in computing technology has opened unprecedented opportunities for systematic collection of experimental data and the associated analysis that were considered impossible only few years ago. This paper focuses on the strategies in use: it reviews the various components that are necessary for an effective solution that ensures the storage, the long term preservation, and the worldwide distribution of large quantities of data that are necessary in a large scientific research project. The paper also mentions several examples of data management solutions used in High Energy Physics for the CERN Large Hadron Collider (LHC) experiments in Geneva, Switzerland which generate more than 30,000 terabytes of data every year that need to be preserved, analyzed, and made available to a community of several tenth of thousands scientists worldwide.