gebhart/patrepeval huggingface dataset:
A Rhamnogalacturonan Lyase in the <i>Clostridium cellulolyticum</i> Cellulosome (2003)

Clostridium cellulolyticum secretes large multienzymatic complexes with plant cell wall-degrading activities named cellulosomes. Most of the genes encoding cellulosomal components are located in a large gene cluster: cipC-cel48F-cel8C-cel9G-cel9E-orfX-cel9H-cel9J-man5K-cel9M. Downstream of the cel9M gene, a new open reading frame was discovered and named rgl11Y. Amino acid sequence analysis indicates that this gene encodes a multidomain pectinase, Rgl11Y, containing an N-terminal signal sequence, a catalytic domain belonging to family 11 of the polysaccharide lyases, and a C-terminal dockerin domain. The present report describes the biochemical characterization of a recombinant form of Rgl11Y. Rgl11Y cleaves the alpha-L-Rhap-(1-->4)-alpha-D-GalpA glycosidic bond in the backbone of rhamnogalacturonan I (RGI) via a beta-elimination mechanism. Its specific activity on potato pectic galactan and rhamnogalacturonan was found to be 28 and 3.6 IU/mg, respectively, indicating that Rgl11Y requires galactan decoration of the RGI backbone. The optimal pH of Rgl11Y is 8.5 and calcium is required for its activity. Rgl11Y was shown to be incorporated in the C. cellulolyticum cellulosome through a typical cohesin-dockerin interaction. Rgl11Y from C. cellulolyticum is the first cellulosomal rhamnogalacturonase characterized.
Fundamental molecular differences between alcohol dehydrogenase classes. (1994)

Two types of alcohol dehydrogenase in separate protein families are the "medium-chain" zinc enzymes (including the classical liver and yeast forms) and the "short-chain" enzymes (including the insect form). Although the medium-chain family has been characterized in prokaryotes and many eukaryotes (fungi, plants, cephalopods, and vertebrates), insects have seemed to possess only the short-chain enzyme. We have now also characterized a medium-chain alcohol dehydrogenase in Drosophila. The enzyme is identical to insect octanol dehydrogenase. It is a typical class III alcohol dehydrogenase, similar to the corresponding human form (70% residue identity), with mostly the same residues involved in substrate and coenzyme interactions. Changes that do occur are conservative, but Phe-51 is of functional interest in relation to decreased coenzyme binding and increased overall activity. Extra residues versus the human enzyme near position 250 affect the coenzyme-binding domain. Enzymatic properties are similar--i.e., very low activity toward ethanol (Km beyond measurement) and high selectivity for formaldehyde/glutathione (S-hydroxymethylglutathione; kcat/Km = 160,000 min-1.mM-1). Between the present class III and the ethanol-active class I enzymes, however, patterns of variability differ greatly, highlighting fundamentally separate molecular properties of these two alcohol dehydrogenases, with class III resembling enzymes in general and class I showing high variation. The gene coding for the Drosophila class III enzyme produces an mRNA of about 1.36 kb that is present at all developmental stages of the fly, compatible with the constitutive nature of the vertebrate enzyme. Taken together, the results bridge a previously apparent gap in the distribution of medium-chain alcohol dehydrogenases and establish a strictly conserved class III enzyme, consistent with an important role for this enzyme in cellular metabolism.
Current Trends in Rapid Diagnostics for Methicillin-Resistant <i>Staphylococcus aureus</i> and Glycopeptide-Resistant <i>Enterococcus</i> Species (2008)

Hospital-acquired (HA) infections are an increasing global problem. Methicillin-resistant Staphylococcus aureus (MRSA) and glycopeptide-resistant Enterococcus (GRE) are multidrugresistant organisms and are particularly frequent causes of HA infections that often prove difficult and expensive to treat. Major sources of MRSA and GRE causing infections are either the patient’s own floras (endogenous infection), those acquired from another person (cross-infection), or those from substances recently contaminated by a human source (environmental infection). Active surveillance cultures from patients for carriage of MRSA and GRE facilitate an early contact isolation (and even treatment), thus preventing spread in the hospital and reducing costs (42). However, the time to result with conventional cultures is 2 to 3 days, which allows these organisms a sizeable time window for potential spread prior to the institution of contact precautions. Recently, several “rapid” diagnostic tests have been introduced that would be very beneficial in decreasing the time to detection, therefore reducing the risk of nosocomial transmission and infections, especially in high-risk patients. This review discusses the current state of the art on rapid and direct detection methods for MRSA and GRE from patient material and hopes to facilitate the infectious disease specialist or microbiologist in choosing an appropriate diagnostic test.
Properties and non-food potential of gluten (1996)

The physicochemical properties of wheat gluten, and how these may be utilized for non-food applications, are discussed. Aspects considered include: an overview of past gluten research; isolation and characterization of gluten proteins (using electrophoresis and chromatography, wheat protein sequences and structures, functional properties); production and current uses of vital gluten; and possibilities for gluten utilization.
Site-specific mutations in the COOH-terminus of placental alkaline phosphatase: a single amino acid change converts a phosphatidylinositol-glycan-anchored protein to a secreted protein. (1992)

Placental alkaline phosphatase (PLAP) is anchored in the plasma membrane by a phosphatidylinositol-glycan moiety (PI-glycan). PI-glycan is added posttranslationally to the nascent peptide chain after the removal of 29 amino acids from the COOH-terminus. The contribution of selected COOH-terminal amino acids to the signal for PI-glycan addition was tested by creating a fusion protein with the COOH-terminus of PLAP and a secreted protein and by mutagenesis of specific PLAP COOH-terminal amino acids. The cDNA encoding the COOH-terminus of PLAP was fused in frame to the cDNA for human clotting Factor X and expressed in transfected COS-1 cells. Fusion proteins containing 32 amino acids of the PLAP COOH-terminus were modified by PI-glycan addition. Thus, the signal for PI-glycan modification must reside in these amino acids. Next, the region between the hydrophobic domain and the cleavage site was examined for additional determinants. Mutations of the hydrophilic residues in the spacer region demonstrated that these amino acids do not contribute to the signal for PI-glycan addition. Deletion of amino acids in the spacer region prevented the addition of PI-glycan suggesting that the length of the spacer domain or the amino acids around the cleavage site are important determinants. Finally, we demonstrated that interruption of the hydrophobic domain by a charged residue prevents PI-glycan addition and results in a protein that is secreted into the medium. The finding that a single Leu to Arg substitution in the hydrophobic domain converts a PI-glycan anchored, membrane protein to a secreted protein suggests that an essential signal for the correct sorting of PI-glycan anchored proteins versus secreted proteins resides in the hydrophobic domain. Substitution of a charged amino acid for a hydrophobic amino acid may be a mechanism for producing membrane bound and secreted forms of the same protein.
Micropatterning of Biomolecules on Polymer Substrates (1998)

UV−excimer laser photoablation was used, in combination with surface blocking techniques, to pattern proteins on the surfaces of polyimide and poly(ethylene terephthalate). This technique involves physical adsorption of avidin through laser-defined openings in low-temperature laminates or adsorbed protein blocking layers. Visualization of biomolecular patterns were monitored using avidin and fluorescein-labeled biotin as a model receptor−ligand couple. Adsorbed proteins could be shown to bind to UV-laser-treated polymer surfaces up to three times higher than on commercially available polymers. UV-laser photoablation was also used for the generation of three-dimensional structure, which leads to the possibility of biomolecule patterning within polymer-based microanalytical systems. The simplicity and easy handling of the described technique facilitate its application in microdiagnostic devices.
Collapsible Underwater Docking Station Design and Evaluation (2018)

Persistent undersea operation is dependent on effective and accessible underwater docking and charging mechanisms for autonomous underwater vehicles (AUVs). Existing docking stations are able to support extended operations with one specific AUV and generally require extensive modification to the AUV to function. This paper presents a new underwater docking station that can support a wide range of AUVs with minimal modification required. Key aspects of the docking station design are the simplified funnel design that reduces manufacturing and deployment complexity and the docking adapter. The adapter can be used as a drop-in replacement for a more traditional AUV antenna with the addition of recharging electronics. It is the only component that contacts the docking station meaning that one station can support AUVs over a wide range of designs and sizes. This work is focused on optimization of the terminal homing stage for docking. Specifically, the effect of impact velocity relative to capture envelope and impact force is studied. Based on the initial optimization of the docking system, a target impact velocity of 1.0m/sresults in the largest effective capture envelope and the minimum impact force when using a Dolphin II AUV.
A Built-In Redundancy-Analysis Scheme for Self-Repairable RAMs with Two-Level Redundancy (2006)

With the increasing demand of memories in system-on-chip (SOC) designs, developing efficient yield-improvement techniques for memories becomes an important issue. Built-in self-repair (BISR) technique has become a popular method for repairing defective embedded memories. To allocate redundancy efficiently, built-in redundancy-analysis (BIRA) function is usually needed for designing a BISR scheme. This paper presents an efficient BIRA scheme for RAMs with two-level redundancy (i.e., spare rows, spare columns, and spare words). Experimental results show that the repair rate of the proposed BIRA scheme approximates to that of the exhaustive search with the same redundancy organization. Furthermore, the repair rate of the proposed BIRA scheme with two-level redundancy is higher than that of the exhaustive search scheme with one-level redundancy (i.e., spare rows and spare columns). The area cost of the proposed BIRA scheme is low. For example, the hardware overhead of the proposed BIRA scheme for an 8Ktimes64-bit RAM with three spare rows, three spare columns, and two spare words is only about 2%
The Three-Dimensional Structure of Peptide-MHC Complexes (1995)

The ability of MHC molecules to present a broad spectrum of peptide antigens for T cell recognition requires a compromise between high affinity and broad specificity. Three-dimensional atomic structures of several class I and class II MHC molecules reveal a unique structural solution to this problem: Tight binding to the peptide main chain is supplemented by more or less restrictive interactions with peptide side chains. In spite of these contacts, peptide side-chain and conformational variability ensures that the resulting peptide-MHC complex presents an antigenically unique surface to T cell receptors. Extension of this understanding to other peptide-MHC complexes, including agonist/antagonist peptides and the identification of antigenic peptides within protein sequences, however, requires a detailed analysis of the interactions that determine both peptide-MHC binding affinity and the conformations of bound peptides. While many of these interactions can be modeled by homology with known structures, their specificity can depend sensitively on subtle and long-range structural effects. Structurally and immunologically important distinctions are also found between the class I and class II peptide-binding strategies. Taken together, these interactions ultimately determine the ability of an individual to respond successfully to immune challenges.
Support Vector Machines for ADME Property Classification (2003)

Abstract This work describes the application of a recent addition to the data analysis toolbox, Support Vector Machines (SVMs) [1], to a classification task involved in contemporary drug discovery.
Working Forum on Manifold Method of Material Analysis, Volume 2. The Numerical Manifold Method and Simplex Integration (1997)

Abstract : Aiming at global analysis, the well known mathematical manifold is perhaps the most important subject of modern mathematics. Based upon mathematical manifold, this numerical manifold method is a newly developed general numerical method. This method computes the movements and deformations of structures or materials. The meshes of the numerical manifold method are finite covers. As the material domains, the finite covers overlapped each other and covered the entire material volume. On each cover, the manifold method defines an independent cover displacement function. The cover displacement functions on individual covers are connected to form a global displacement function on the entire material volume. The global displacement function are the weighted averages of local independent cover functions on the common part of several covers. Using the entire finite cover systems, continuous, jointed, or blocky materials can be computed in a mathematically consistent manner. For a manifold computation, the mathematical mesh and physical mesh are independent.
Characterization of Intravacuolar Pigmented Structures in Anthocyanin-Containing Cells of Sweet Potato Suspension Cultures (1993)

Journal Article Characterization of Intravacuolar Pigmented Structures in Anthocyanin-Containing Cells of Sweet Potato Suspension Cultures Get access Masayuki Nozue, Masayuki Nozue 2 1Department of Biology, Faculty of Science, Shinshu UniversityAsahi 3-1-1, Matsumoto, 390 Japan 2To whom all correspondence should be addressed. Search for other works by this author on: Oxford Academic Google Scholar Hiroyoshi Kubo, Hiroyoshi Kubo 1Department of Biology, Faculty of Science, Shinshu UniversityAsahi 3-1-1, Matsumoto, 390 Japan Search for other works by this author on: Oxford Academic Google Scholar Mikio Nishimura, Mikio Nishimura 3Department of Cell Biology, National Institute for Basic BiologyMyodaijicho, Okazaki, 444 Japan Search for other works by this author on: Oxford Academic Google Scholar Akira Katou, Akira Katou 1Department of Biology, Faculty of Science, Shinshu UniversityAsahi 3-1-1, Matsumoto, 390 Japan Search for other works by this author on: Oxford Academic Google Scholar Chiho Hattori, Chiho Hattori 1Department of Biology, Faculty of Science, Shinshu UniversityAsahi 3-1-1, Matsumoto, 390 Japan Search for other works by this author on: Oxford Academic Google Scholar Nobuteru Usuda, Nobuteru Usuda 5Department of Anatomy and Cell Biology, School of Medicine, Shinshu UniversityAsahi 3-1-1, Matsumoto, 390 Japan Search for other works by this author on: Oxford Academic Google Scholar Tetsuji Nagata, Tetsuji Nagata 5Department of Anatomy and Cell Biology, School of Medicine, Shinshu UniversityAsahi 3-1-1, Matsumoto, 390 Japan Search for other works by this author on: Oxford Academic Google Scholar Hitosi Yasuda Hitosi Yasuda 1Department of Biology, Faculty of Science, Shinshu UniversityAsahi 3-1-1, Matsumoto, 390 Japan Search for other works by this author on: Oxford Academic Google Scholar Plant and Cell Physiology, Volume 34, Issue 6, September 1993, Pages 803–808, https://doi.org/10.1093/oxfordjournals.pcp.a078487 Published: 01 September 1993 Article history Received: 24 December 1992 Accepted: 24 May 1993 Published: 01 September 1993
Transthyretin and cystatin C are catabolized in proximal tubular epithelial cells and the proteins are not useful as markers for renal cell carcinomas (1995)

Ten human kidney specimens and thirty-two renal cell carcinomas were investigated for the presence of transthyretin mRNA and cystatin C mRNA using Northern blot analysis. Five of ten kidney specimens and 15 of 32 renal carcinomas were also immunohistochemically investigated for the presence of the corresponding proteins. Transthyretin mRNA could not be detected in any of the normal or neoplastic tissue preparations, whereas low amounts of cystatin C mRNA were found in nine of ten normal kidneys and in 24 of 32 renal cell carcinomas. Immunoreactive transthyretin and cystatin C were present in proximal tubular epithelial cells of all kidney specimens, whereas neither of the proteins was detected the tumour cells of the renal carcinomas. Immunoreactive cystatin C was, however, demonstrated in scattered monocyte/macrophage-like cells. We conclude that the presence of immunoreactive transthyretin and cystatin C in proximal tubular cells of the kidney is most likely due to reabsorption of the proteins from the primary urine. The small amounts of cystatin C mRNA in some of the normal and neoplastic renal preparations are probably due to cystatin C synthesis in macrophages. Transthyretin has been recommended as an immunohistochemical marker for renal cell carcinomas. Our results, however, clearly indicate that neither transthyretin nor cystatin C constitutes a useful marker for such neoplasms.
Constructing finite state machines for fast gesture recognition (2002)

Proposes an approach to 2D gesture recognition that models each gesture as a finite state machine (FSM) in the spatial-temporal space. The model construction works in a semi-automatic way. The structure of the model is first manually decided based on the observation of the spatial topology of the data. The model is refined iteratively between two stages: data segmentation and model training. We incorporate a modified Knuth-Morris-Pratt algorithm recognition procedure to speed up recognition. The computational efficiency of the FSM recognizers allows real-time online performance to be achieved.
Footballene: a theoretical prediction for the stable, truncated icosahedral molecule C60 (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTFootballene: a theoretical prediction for the stable, truncated icosahedral molecule C60A. D. J. HaymetCite this: J. Am. Chem. Soc. 1986, 108, 2, 319–321Publication Date (Print):January 1, 1986Publication History Published online1 May 2002Published inissue 1 January 1986https://pubs.acs.org/doi/10.1021/ja00262a035https://doi.org/10.1021/ja00262a035research-articleACS PublicationsRequest reuse permissionsArticle Views313Altmetric-Citations128LEARN 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
A low-complexity waveform interpolation coder (2002)

A recent independent survey found a 2.4 kbit/s waveform-interpolation (WI) algorithm to perform better than other state-of-the-art speech coders. However, this coder had a very high level of computational complexity. The introduction of various techniques, including a time-varying waveform sampling rate and a cubic B-spline waveform representation, has reduced the computational complexity by an order of magnitude. The new implementation allows full-duplex real-time operation on a single DSP device and on an average workstation (the latter using non-optimized compiled C source code). The new coder also contains a number of new features which improve the quality of the reconstructed speech signal.
A Single Mms2 “Key” Residue Insertion into a Ubc13 Pocket Determines the Interface Specificity of a Human Lys63 Ubiquitin Conjugation Complex (2005)

Human Ubc13 and Mms2 (or its homolog, Uev1) form a unique ubiquitin-conjugating enzyme (Ubc) complex that generates atypical Lys(63)-linked ubiquitin conjugates. Such conjugates are attached to specific targets that modulate the activity of various cellular processes including DNA repair, mitotic progression, and nuclear factor-kappaB signaling. Whereas Ubc13 is a typical Ubc, Mms2 is a non-catalytic Ubc variant. Substantial biochemical evidence has revealed a mechanism whereby Mms2 properly orients ubiquitin to allow for Lys(63) conjugation by Ubc13; however, how this specific Ubc13-Mms2 complex is formed and why Mms2 does not form a complex with other Ubcs have not been reported. In order to address these questions, we used a structure-based approach to design mutations and characterize the human Ubc13-Mms2 interface. We used the yeast two-hybrid assay, glutathione S-transferase pull-downs, and surface plasmon resonance to test in vivo and in vitro binding. These experiments were paired with functional complementation and ubiquitin conjugation studies to provide in vivo and in vitro functional data. The results in this study allowed us to identify important residues of the Ubc13-Mms2 interface, determine a correlation between heterodimer formation and function, and conclude why Mms2 forms a specific complex with Ubc13 but not other Ubc proteins.
MAOA methylation is associated with nicotine and alcohol dependence in women (2008)

In recent years, the role of epigenetic phenomenon, such as methylation, in mediating vulnerability to behavioral illness has become increasingly appreciated. One prominent locus at which epigenetic phenomena are thought to be in play is the monoamine oxidase A (MAOA) locus. In order to examine the role of methylation at this locus, we performed quantitative methylation analysis across the promoter region of this gene in lymphoblast lines derived from 191 subjects participating in the Iowa Adoption Studies (IAS). We analyzed the resulting data with respect to genotype and lifetime symptom counts for the more common major behavioral disorders in the IAS, antisocial personality disorder (ASPD), and substance use disorders (alcohol (AD) and nicotine dependence (ND)). We found that methylation status was significantly associated with lifetime symptom counts for ND (P < 0.001) and AD (P < 0.008) in women, but not men. Furthermore, a trend was found for women homozygous for the 3,3 allele to have a higher degree of overall methylation than women homozygous for the 4,4 allele (P < 0.10). We conclude that methylation of MAOA may play a significant role in common psychiatric illness and that further examination of epigenetic processes at this locus is in order.