gebhart/patrepeval huggingface dataset:
Molecular Structure of Galactokinase (2003)

Galactokinase plays a key role in normal galactose metabolism by catalyzing the ATP-dependent phosphorylation of alpha-D-galactose to galactose 1-phosphate. In humans, mutations in the galactokinase gene can lead to the diseased state referred to as Type II galactosemia. Here we describe the three-dimensional structure of galactokinase from Lactococcus lactis determined to 2.1-A resolution. As expected from amino acid sequence alignments, galactokinase adopts a similar topology to that observed for members of the GHMP superfamily. The N-terminal domain is characterized by a five-stranded mixed beta-sheet while the C-terminal motif is dominated by two distinct four-stranded anti-parallel beta-sheets. The structure was solved in the presence of alpha-D-galactose and inorganic phosphate. These ligands are wedged between the N- and C-terminal domains. Amino acid side chains responsible for anchoring the sugar ligand to the protein include Arg36, Glu42, Asp45, Asp183, and Tyr233. Both Arg36 and Asp183 are strictly conserved in the amino acid sequences available in the literature thus far for galactokinases. Interestingly, the carboxylate side chain of Asp183 is positioned within 3.5 A of the C-1 hydroxyl group of galactose, whereas the guanidinium group of Arg36 is situated between both the C-1 hydroxyl group and the inorganic phosphate. Most likely these residues play key roles in catalysis. The structure of galactokinase described here serves as a model for understanding the functional consequences of point mutations known to result in Type II galactosemia in humans.
Surface Modification of Fluoropolymers via Molecular Design (2000)

Fluoropolymer surfaces with new and specific functionalities, such as metal-free conductivity, biocompatability, and bondability to metals, can be obtained through the intelligent choice of functional monomers for graft copolymerization on pre-activated fluoropolymer surfaces, as highlighted in this review. The Figure shows a gold/fluoropolymer laminate held together by crosslinked glycidyl methacrylate polymer grafted on both surfaces.
Identification of ricin A-chain HLA class II-restricted epitopes by human T-cell clones (2001)

The identification of ricin toxin A-chain (RTA) epitopes and the molecular context in which they are recognized will allow strategies to be devised that prevent/suppress an anti-RTA immune response in patients treated with RTA-based immunotoxins. RTA-specific human T-cell lines and T-cell clones were produced by in vitro priming of PBMC. The T-cell clones used a limited set of Vbeta chains (Vbeta1, Vbeta2 and Vbeta8) to recognize RTA epitopes. The use of RTA deletion mutants demonstrated that T-cell lines and T-cell clones from three out of four donors responded to RTA epitopes within the domain D124-Q223, whereas one donor recognized the region I1-D124. The response to RTA peptides of T-cell lines and T-cell clones from two donors allowed the identification of immunogenic segments (D124-G140 and L161-T190) recognized in the context of different HLA-DRB1 alleles (HLA-DRB1*0801, and HLA-DRB1*11011 and B1*03011, respectively). The response to L161-T190 was investigated in greater detail. We found that the HLA-DRB1*03011 allele presents a minimal epitope represented by the sequence I175-Y183 of RTA, whereas the HLA-DRB1*11011 allele presents the minimal epitope M174-I184. RTA peptides and an I175A RTA point mutant allowed us to identify I175 as a crucial residue for the epitope(s) recognized by the two HLA-DRB1 alleles. Failure of T-cell clones to recognize ribosome inactivating proteins (RIPs) showing sequences similar but not identical to RTA further confirmed the role of I175 as a key residue for the epitope recognized in the context of HLA-DRB1*11011/03011 alleles.
Personalized Recommendation in Interactive Visual Analysis of Stacked Graphs (2012)

We present a system which combines interactive visual analysis and recommender systems to support insight generation for the user. Our approach combines a stacked graph visualization with a content-based recommender algorithm, where promising views can be revealed to the user for further investigation. By exploiting both the current user navigational data and view properties, the system allows the user to focus on visual space in which she or he is interested. After testing with more than 30 users, we analyze the results and show that accurate user profiles can be generated based on user behavior and view property data.
Carbon fibers prepared from tailored reversible‐addition‐fragmentation transfer copolymerization‐derived poly(acrylonitrile)‐<i>co</i>‐poly(methylmethacrylate) (2014)

ABSTRACT Reversible‐addition fragmentation‐transfer (RAFT) polymerization of acrylonitrile (AN) was performed with 2‐(2‐cyano‐2‐propyl‐dodecyl)trithiocarbonate as RAFT agent and azobis(isobutyronitrile) as initiator. Linear polyacrylonitrile ( M n = 133,000 g/mol, PDI = 1.34) was prepared within 7 h in 86% isolated yield. High‐yield copolymerization with methyl methacrylate (MMA) was performed and copolymerization parameters were determined according to Kelen and Tüdös at 90 °C in ethylene carbonate yielding r AN = 0.2 and r MMA = 0.42. The molecular weights, polydispersity indices (PDIs), and MMA content of the copolymer were adjusted in a way that precursor fibers could be prepared via wet spinning. These precursor fibers had round cross‐sections and a dense morphology, showing tenacities of 40–50 cN/tex and elastic moduli of 900–1000 cN/tex at a fineness of 1 dtex and an elongation of 13–17%. Precursor fibers were oxidatively stabilized and then carbonized at different temperatures. A maximum tensile strength of 2.5 GPa was reached at 1350 °C. Thermal analysis, infrared and Raman spectroscopy, wide‐angle X‐ray scattering, scanning electron microscopy, and tensile testing were used to characterize the resulting carbon fibers. © 2014 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2014 , 52 , 1322–1333
Physicochemical properties of SARS‐CoV‐2 for drug targeting, virus inactivation and attenuation, vaccine formulation and quality control (2020)

The material properties of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its proteins are discussed. We review the viral structure, size, rigidity, lipophilicity, isoelectric point, buoyant density and centrifugation conditions, stability against pH, temperature, UV light, gamma radiation, and susceptibility to various chemical agents including solvents and detergents. Possible inactivation, downstream, and formulation conditions are given including suitable buffers and some first ideas for quality-control methods. This information supports vaccine development and discussion with competent authorities during vaccine approval and is certainly related to drug-targeting strategies and hygienics. Several instructive tables are given, including the pI and grand average of hydropathicity (GRAVY) of SARS-CoV-1 and -2 proteins in comparison. SARS-CoV-1 and SARS-CoV-2 are similar in many regards, so information can often be derived. Both are unusually stable, but sensitive at their lipophilic membranes. However, since seemingly small differences can have strong effects, for example, on immunologically relevant epitope settings, unevaluated knowledge transfer from SARS-CoV-1 to SARS-CoV-2 cannot be advised. Published knowledge regarding downstream processes, formulations and quality assuring methods is, as yet, limited. However, standard approaches employed for other viruses and vaccines seem to be feasible including virus inactivation, centrifugation conditions, and the use of adjuvants.
Synthesis of Sugar-Derived 2′- and 3′-Substituted Furans and Their Application in Diels−Alder Reactions (2001)

A convenient synthesis of 2′- and 3′-furyl sugars in which the furan and the sugar parts are directly connected is presented. The key step comprises HF·py-induced cyclization of α,β-unsaturated carbonyl compounds (ketones or aldehydes) possessing terminal hydroxymethylene groups protected as TBDPS ethers. Treatment of such furan derivatives with N-phenylmaleimide under high-pressure conditions (11 kbar) produces the corresponding [4+2] adducts, with the endo forms predominating. At p = 1 atm and T = 20 °C, however, the exo isomers are formed as the main products. The [4+2] adducts undergo retro Diels−Alder reactions at elevated temperatures at atmospheric pressure.
Improved Solubilization of Recombinant Human Growth Hormone Inclusion Body Produced in<i>Escherichia coli</i> (2008)

Recombinant human growth hormone (r-hGH) overexpressed in Escherichia coli forms inactive and insoluble aggregates as inclusion bodies in the cytoplasm. The efficient solubilization of inclusion bodies is critical for cost-effective production. Contrary to a previous report, in our production system, the solubilization method by alkaline treatment including 2 M urea was ineffective. Hence various buffers containing different concentrations of urea or guanidine hydrochloride (GnHCl) at neutral and alkaline pH were attempted. Efficient solubilization (about 90%) was observed in 100 mM Tris buffer, pH 8.0, with more than 4 M GnHCl, and at pH 12.5 with more than 2 M GnHCl, but not with about 8 M of urea. The r-hGH solubilized at pH 12.5 containing 2 M GnHCl was refolded by simple dilution and purified by DEAE Sepharose anion-exchange chromatography. The biological activity of the resulting r-hGH was comparable with commercially available r-hGH in in vitro cell proliferation assay using the hGH-dependent cell line.
A rat cerebellar protein containing the cdc10/SWI6 motif (1992)

Systematic analysis of soluble proteins in developing rat cerebellum by an automated two-dimensional liquid-chromatography system detected a number of proteins which increased transiently during the initial stage of postnatal development. One of the proteins, V-1, was isolated using a liquid-chromatography system, and its amino acid sequence was determined by analysis of the purified protein. The sequence showed that the V-1 protein consists of 117 amino acids with an acetylated N-terminus, and has 2.5 internal sequence repeats of 33 amino acids. Computer retrieval of the sequence indicated that the repeated sequences have a structural characteristics of the cdc10/SWI6 motif, which is found in a series of proteins, including those involved in cell-cycle control and cell-fate determination in yeast, Drosophila melanogaster and Caenorhabditis elegans. The structure of V-1, coupled with its controlled expression in early postnatal development, implies a potential role for V-1 in cerebellar morphogenesis.
Flow cytometric analysis of the early phases of apoptosis by cellular and nuclear techniques (1996)

The early events occurring during apoptosis at the plasma membrane, chromatin, and mitochondrial levels were investigated in freshly isolated irradiated human lymphocytes, growth factor-deprived cultured human lymphocytes, and dexamethasone (DEX)-treated murine thymocytes. In intact, unfixed cells, evaluation of the light scatter properties and of DNA stainability with ethidium bromide (EB) allowed a cell subset suggestive for initial apoptosis to be identified. The apoptotic nature of these cells was confirmed by cell sorting in irradiated human lymphocyte model. EB could not be substituted for by propidium iodide, indicating that the nature of DNA probe used is of major importance for detecting initial apoptotic changes. Because mitochondria are thought to represent a primary target during apoptosis, we measured the uptake of mitochondria transmembrane potential sensitive (Rhodamine 123) and nonsensitive (10-nonyl-acridine-orange) probes concomitantly with EB uptake. Cells starting apoptosis had an enhanced incorporation of both mitochondria dyes, which in combination with EB identified several cell subsets. This suggests that complex alterations in mitochondrial structure and functioning occur in the early stages of apoptosis. To investigate phenomena occurring at the chromatin level in similar phases of apoptosis, irradiated human lymphocytes and DEX-treated murine thymocytes were disrupted and DNA stainability assessed in nuclear suspensions. A transient increase in DNA stainability, i.e., the appearance of distinct hyperdiploid peaks in the human model and a generalised upward shift of the G0/1 peak in the murine model, was observed in the early phases of apoptosis concomitantly with specific alterations in light scattering properties. These findings suggest that chromatin texture is altered in early apoptosis and affects DNA stainability.
Connected Consumption: The Hidden Networks of Consumption (2009)

In this paper, we present the Connected Consumption Network (CCN) that allows a community of consumers to collaboratively sense the market from a mobile device, enabling more informed financial decisions in geo-local context. The mobile application allows one to log one's wish list and itemized list of transactions to form a social network around the list of interests. Individuals can share this data to inform and guide others in a timely, personal and contextual manner when they are shopping for a product or seeking a service. It can also help people connect opportunistically in a local area to make group purchases, to pick up an item for a friend, and to perform reverse auctions. We present the design, architecture and concept prototype. We simulate a social network with three months of existing credit/debit card transaction data in various geographical areas to analyze the mutual information and recommendations that can be shared among networked consumers.
Internal ribosomal entry site substitution eliminates neurovirulence in intergeneric poliovirus recombinants. (1996)

Neuropathogenicity of poliovirus can be attenuated by mutations in the internal ribosomal entry site (IRES) within the 5' nontranslated region of its genome. The Sabin vaccine strains used in prevention of poliomyelitis carry such mutations in their IRES elements. In addition, mutations within the structural and nonstructural proteins of Sabin strains may equally contribute to the attenuation phenotype. Despite their effectiveness as vaccines, the Sabin strains retain a neuropathogenic potential in animal models for poliomyelitis and, at a very low rate, they can cause poliomyelitis in vaccine recipients. The elimination of the neurocytopathic phenotype was achieved through the exchange of the entire poliovirus IRES with its counterpart from human rhinovirus type 2 without affecting growth properties in nonneuronal cells. The attenuating effect of the human rhinovirus type 2 IRES within the context of a poliovirus genome has been mapped to the 3' portion of this genetic element.
Paracellular route of aqueous outflow in the trabecular meshwork and canal of Schlemm. A freeze-fracture study of the endothelial junctions in the sclerocorneal angel of the macaque monkey eye. (1981)

The intercellular junctions of the endothelial cells of the trabecular meshwork and canal of Schlemm were examined with the electron microscope in the macaque monkey eye by both thin-sectioned specimens and the freeze-fracturing technique. The endothelial cells that line the beams of the meshwork are joined by gap junctions and short, isolated strands of tight junction; zonulae occludentes are absent. Thus aqueous humor can freely traverse the patent endothelial clefts of the trabecular meshwork. The endothelial cells of the canal of Schlemm are joined by zonulae occludentes and a small number of minute gap junctions. In 57% of their length, the tight junctions consist of one or two strands; the strands are rarely more than four. They remain preferentially associated with the E-face of the membrane, run parallel to one another, and only exceptionally branch or anastomose. Thus they are provided with free endings and do not form a bidimensional network. As a result of this organization, the zonula occludens is traversed by meandering channels of extracellular space or split pores, which connect the open endothelial clefts on the luminal and tissue fronts of the junction. The frequency of slit pores is 0.134 per micrometer of zonula occludens. They occupy 0.87% of the intercellular boundary and 0.0015% of the area of the endothelium. Estimates of the fluid conductance of the zonulae occludentes indicate that the intercellular clefts of the endothelium of Schlemm's canal filter but a small fraction of the amount of aqueous humor that leaves the anterior chamber through the conventional route.
Decomposition of trimethylgallium in the downstream region of a near afterglow plasma (1989)

The downstream region of a near afterglow plasma (Δt=100 μs) has been used to decompose trimethylgallium (TMGa) and the products analyzed using a mass spectrometer. The major TMGa dissociation products with a hydrogen plasma were identified as methane and ethane while with a helium plasma ethane, ethylene, and acetylene were the main dissociation species. Time-resolved optical emission originating from the downstream reaction zone shows that decomposition of TMGa occurs primarily via photodissociation with the hydrogen plasma while both photon and metastable species (He 21 S and 23 S) contributed to the TMGa decomposition with the helium plasma. VUV transmitting and VUV absorbing windows placed between the upstream hydrogen plasma and the downstream TMGa source provided further direct evidence of the role of VUV photodissociation in the TMGa decomposition.
Effect of ten quaternary ammonium cations on tetrachloromethane sorption to clay from water (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEffect of ten quaternary ammonium cations on tetrachloromethane sorption to clay from waterJames A. Smith, Peter R. Jaffe, and Cary T. ChiouCite this: Environ. Sci. Technol. 1990, 24, 8, 1167–1172Publication Date (Print):August 1, 1990Publication History Published online1 May 2002Published inissue 1 August 1990https://doi.org/10.1021/es00078a003RIGHTS & PERMISSIONSArticle Views872Altmetric-Citations237LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (790 KB) Get e-Alerts Get e-Alerts
Is endoscopic harvesting bad for saphenous vein graft patency in coronary surgery? (2011)

Clear clinical advantages over traditional open vein harvest have allowed EVH to rapidly become the standard-of-care for harvesting of one or more vein grafts during CABG. The quality of these conduits, suggested to be equivalent by early studies, has come into question as groups with varying levels of experience have adopted the endoscopic technique. Elucidating the principles of 'best practice' for vein harvest will likely help shorten the learning curve and improve the safety of EVH.
Flexible waveguide coupling probe for wafer-level optical characterization of planar lightwave circuits (2007)

A probe that enables optical coupling to planar lightwave circuits (PLCs) is described. A flexible waveguide is used to form a variable length directional coupler that extracts light from a waveguide in the wafer to the probe. Varying the length enables optimal coupling to be achieved for a wide range of probe-to-waveguide gap, materials, widths and cladding thicknesses present on a chip. In this paper we consider the use of SU-8 polymer as waveguide test probe and polydimethylsiloxane (PDMS) as cladding for the probe. The results indicate that this approach is ideal for characterizing PLC's as the 3dB bandwidth of the probe covers the whole 1300 - 1700 nm fiber-optic telecommunication range. Coupling length control in the range of 50 - 200 mm leads to maximum coupling in excess of 80% for the range of conditions investigated.
Towards a Definition and Classification of Acute Kidney Injury (2005)

Chertow and colleagues ([1][1]) have an interesting and provocative paper in this issue of JASN that brings a pragmatic approach to bear on the issue of defining acute renal failure. This area is rapidly gaining prominence and was the theme of one of the American Society of Nephrology’s research
Constructing Ordered Sensitized Heterojunctions: Bottom-Up Electrochemical Synthesis of p-Type Semiconductors in Oriented n-TiO<sub>2</sub> Nanotube Arrays (2009)

Fabrication of efficient semiconductor-sensitized bulk heterojunction solar cells requires the complete filling of the pore system of one semiconductor (host) material with nanoscale dimensions (<100 nm) with a different semiconductor (guest) material. Because of the small pore size and electrical conductivity of the host material, it is challenging to employ electrochemical approaches to fill the entire pore network. Typically, during the electrochemical deposition process, the guest material blocks the pores of the host, precluding complete pore filling. We describe a general synthetic strategy for spatially controlling the growth of p-type semiconductors in the nanopores of electrically conducting n-type materials. As an illustration of this strategy, we report on the facile electrochemical deposition of p-CuInSe(2) in nanoporous anatase n-TiO(2) oriented nanotube arrays and nanoparticle films. We show that by controlling the ambipolar diffusion length the p-type semiconductors can be deposited from the bottom-up, resulting in complete pore filling.
Structures of two novel toxins from Protogonyaulax (1981)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTStructures of two novel toxins from ProtogonyaulaxCarol Fix Wichmann, Walter P. Niemczura, Heinrich K. Schnoes, Sherwood Hall, Paul B. Reichardt, and Stephen D. DarlingCite this: J. Am. Chem. Soc. 1981, 103, 23, 6977–6978Publication Date (Print):November 1, 1981Publication History Published online1 May 2002Published inissue 1 November 1981https://pubs.acs.org/doi/10.1021/ja00413a042https://doi.org/10.1021/ja00413a042research-articleACS PublicationsRequest reuse permissionsArticle Views88Altmetric-Citations41LEARN 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-Alertsclose Get e-Alerts