gebhart/patrepeval huggingface dataset:
Structural basis for the conformational adaptability of apolipophorin III, a helix-bundle exchangeable apolipoprotein (2002)

The high-resolution NMR structure of apolipophorin III from the sphinx moth, Manduca sexta, has been determined in the lipid-free state. We show that lipid-free apolipophorin III adopts a unique helix-bundle topology that has several characteristic structural features. These include a marginally stable, up-and-down helix bundle that allows for concerted opening of the bundle about "hinged" loops upon lipid interaction and buried polar/ionizable residues and buried interhelical H-bonds located in the otherwise hydrophobic interior of the bundle that adjust protein stability and facilitate lipid-induced conformational opening. We suggest that these structural features modulate the conformational adaptability of the lipid-free helix bundle upon lipid binding and control return of the open conformation to the original lipid-free helix-bundle state. Taken together, these data provide a structural rationale for the ability of exchangeable apolipoproteins to reversibly interact with circulating lipoprotein particles.
Both ionically and enzymatically crosslinkable alginate–tyramine conjugate as materials for cell encapsulation (2007)

The swelling behavior of the structural material of cell-enclosing capsules is a key factor for the successful transplantation of these capsules in the treatment of diseases. The present study aimed to develop cell-enclosing capsules displaying minimal swelling under physiological conditions. We investigated the use of an alginate-tyramine conjugate synthesized by a carbodiimide/active-ester coupling reaction. The conjugate gel crosslinked by calcium ions and peroxidase-catalyzed oxidative coupling of phenols swelled less in saline than in unmodified alginate. The degree of swelling could be controlled by conjugate preparation conditions. The conjugate gel showed no obvious cytotoxicity for cells, including the process of oxidative coupling generation. Further, encapsulated cells could be cultured for up to 2 months and achieve approximately 5.2-fold greater mitochondrial activity after 51 days of encapsulation than after 1 day. These results show that this alginate-tyramine conjugate is a promising material for use in cell-enclosing capsules for cell therapy.
Cloning and sequencing of mouse tyrosinase cDNA. (1987)

A cDNA library was constructed from poly (A)+ mRNA from mouse melanocytes and screened using anti-tyrosinase antiserum and oligonucleotide probes corresponding to amino acid sequence of tyrosinase. Sequencing of some cDNA clones positive in these screenings gave a nucleotide sequence of 1838 nucleotides including a open reading frame of 1344 nucleotides.
Peptide segment ligation strategy without use of protecting groups. (1994)

We describe the concept and the verification of a chemical ligation approach to the synthesis of proteins using peptide segments with no protecting groups and no activation of the C-terminal alpha-carboxyl group. This approach consists of three steps: (i) aldehyde introduction, in which a masked glycolaldehyde ester is linked to the carboxyl terminus of an unprotected peptide by reverse proteolysis; (ii) ring formation, in which the unmasked aldehyde reacts with the N-terminal alpha-amino group of the second unprotected peptide containing either a cysteine or a threonine residue to form a thiazolidine or oxazolidine ring at an acidic pH; and (iii) rearrangement in which O-acyl ester linkage is transferred to N-acyl amide linkage to form a peptide bond with a pseudoproline structure at higher pH. The feasibility of this scheme was verified by a model study on small compounds and its potential was demonstrated by the synthesis of a 50-residue epidermal growth factor-like peptide containing a preformed disulfide bond.
Homography-based ground plane detection for mobile robot navigation using a Modified EM algorithm (2010)

In this paper, a homography-based approach for determining the ground plane using image pairs is presented. Our approach is unique in that it uses a Modified Expectation Maximization algorithm to cluster pixels on images as belonging to one of two possible classes: ground and non-ground pixels. This classification is very useful in mobile robot navigation because, by segmenting out the ground plane, we are left with all possible objects in the scene, which can then be used to implement many mobile robot navigation algorithms such as obstacle avoidance, path planning, target following, landmark detection, etc. Specifically, we demonstrate the usefulness and robustness of our approach by applying it to a target following algorithm. As the results section shows, the proposed algorithm for ground plane detection achieves an almost perfect detection rate (over 99%) despite the relatively higher number of errors in pixel correspondence from the feature matching algorithm used: SIFT.
Comparative Efficacy of Neutralizing Antibodies Elicited by Recombinant Hemagglutinin Proteins from Avian H5N1 Influenza Virus (2008)

Although the human transmission of avian H5N1 virus remains low, the prevalence of this highly pathogenic infection in avian species underscores the need for a preventive vaccine that can be made without eggs. Here, we systematically analyze various forms of recombinant hemagglutinin (HA) protein for their potential efficacy as vaccines. Monomeric, trimeric, and oligomeric H5N1 HA proteins were expressed and purified from either insect or mammalian cells. The immunogenicity of different recombinant HA proteins was evaluated by measuring the neutralizing antibody response. Neutralizing antibodies to H5N1 HA were readily generated in mice immunized with the recombinant HA proteins, but they varied in potency depending on their multimeric nature and cell source. Among the HA proteins, a high-molecular-weight oligomer elicited the strongest antibody response, followed by the trimer; the monomer showed minimal efficacy. The coexpression of another viral surface protein, neuraminidase, did not affect the immunogenicity of the HA oligomer, as expected from the immunogenicity of trimers produced from insect cells. As anticipated, HA expressed in mammalian cells without NA retained the terminal sialic acid residues and failed to bind alpha2,3-linked sialic acid receptors. Taken together, these results suggest that recombinant HA proteins as individual or oligomeric trimers can elicit potent neutralizing antibody responses to avian H5N1 influenza viruses.
Functional Characterization and Subcellular Localization of Poplar (Populus trichocarpa × Populus deltoides) Cinnamate 4-Hydroxylase (2001)

Cinnamic acid 4-hydroxylase (C4H), a member of the cytochrome P450 monooxygenase superfamily, plays a central role in phenylpropanoid metabolism and lignin biosynthesis and possibly anchors a phenylpropanoid enzyme complex to the endoplasmic reticulum (ER). A full-length cDNA encoding C4H was isolated from a hybrid poplar (Populus trichocarpa x P. deltoides) young leaf cDNA library. RNA-blot analysis detected C4H transcripts in all organs tested, but the gene was most highly expressed in developing xylem. C4H expression was also strongly induced by elicitor-treatment in poplar cell cultures. To verify the catalytic activity of the putative C4H cDNA, two constructs, C4H and C4H fused to the FLAG epitope (C4H::FLAG), were expressed in yeast. Immunoblot analysis showed that C4H was present in the microsomal fraction and microsomal preparations from strains expressing both enzymes efficiently converted cinnamic acid to p-coumaric acid with high specific activities. To investigate the subcellular localization of C4H in vivo, a chimeric C4H-green fluorescent protein (GFP) gene was engineered and stably expressed in Arabidopsis. Confocal laser microscopy analysis clearly showed that in Arabidopsis the C4H::GFP chimeric enzyme was localized to the ER. When expressed in yeast, the C4H::GFP fusion enzyme was also active but displayed significantly lower specific activity than either C4H or C4H::FLAG in in vitro and in vivo enzyme assays. These data definitively show that C4H is localized to the ER in planta.
Nanometer-Thick Yttrium Iron Garnet Films With Extremely Low Damping (2014)

Yttrium iron garnet (YIG) films that are in the nanometer thickness range and show extremely low damping are reported. The films were deposited via sputtering at room temperature and were then annealed in O <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math>$_{2}$</tex-math></inline-formula> at high temperature. A 22-nm-thick YIG film showed a Gilbert damping constant <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math>$\alpha = (8.58\pm 0.21)\times 10^{-5}$</tex-math></inline-formula> , which represents the lowest damping ever reported for nanometer-thick magnetic films. The film had a gyromagnetic ratio of <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math>$\vert\gamma \vert = 2.83$</tex-math></inline-formula> MHz/Oe and a saturation induction of <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math>$4\pi M_{\rm s} = 1766$</tex-math></inline-formula> G, which are both very close to those of single-crystal YIG bulk materials. The film had a very smooth surface, with an rms surface roughness of about 0.13 nm.
Ammonolysis of tantalum alkyls: formation of cubic tantalum nitride and a trimeric nitride, [Cp*MeTaN]3 tris[(.eta.5-pentamethylcyclopentadienyl)(methyl)nitridotantalum] (1990)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAmmonolysis of tantalum alkyls: formation of cubic tantalum nitride and a trimeric nitride, [Cp*MeTaN]3 tris[(.eta.5-pentamethylcyclopentadienyl)(methyl)nitridotantalum]Mark M. Banaszak Holl, Meinolf Kersting, Bradford D. Pendley, and Peter T. WolczanskiCite this: Inorg. Chem. 1990, 29, 8, 1518–1526Publication Date (Print):April 1, 1990Publication History Published online1 May 2002Published inissue 1 April 1990https://pubs.acs.org/doi/10.1021/ic00333a016https://doi.org/10.1021/ic00333a016research-articleACS PublicationsRequest reuse permissionsArticle Views253Altmetric-Citations48LEARN 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 Get e-Alerts
Synthesis and in Vitro Evaluation of Enzymatically Cross-Linked Elastin-Like Polypeptide Gels for Cartilaginous Tissue Repair (2005)

Genetically engineered elastin-like polypeptide (ELP) hydrogels offer unique promise as scaffolds for cartilage tissue engineering because of the potential to promote chondrogenesis and to control mechanical properties. In this study, we designed and synthesized ELPs capable of undergoing enzyme-initiated gelation via tissue transglutaminase, with the ultimate goal of creating an injectable, in situ cross-linking scaffold to promote functional cartilage repair. Addition of the enzyme promoted ELP gel formation and chondrocyte encapsulation in a biocompatible process, which resulted in cartilage matrix synthesis in vitro and the potential to contribute to cartilage mechanical function in vivo. A significant increase in the accumulation of sulfated glycosaminoglycans was observed, and histological sections revealed the accumulation of a cartilaginous matrix rich in type II collagen and lacking in type I collagen, indicative of hyaline cartilage formation. These results provide evidence of chondrocytic phenotype maintenance for cells in the ELP hydrogels in vitro. In addition, the dynamic shear moduli of ELP hydrogels seeded with chondrocytes increased from 0.28 to 1.7 kPa during a 4-week culture period. This increase in the mechanical integrity of cross-linked ELP hydrogels suggests restructuring of the ELP matrix by deposition of functional cartilage extracellular matrix components.
A direct method to extract effective geometries and series resistances of MOS transistors (2002)

A new direct method for rapid characterization of MOS transistor effective geometries and series resistances is presented. The method only requires devices of four different sizes. Also presented is a new linear regression technique that offers a natural extension of the method to any arbitrary number of devices. Finally, the channel width dependence of the mobility reduction factor is shown to be explained by the electrical broadening of the channel.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Cytokine Blockade as a New Strategy to Treat Rheumatoid Arthritis (2000)

Rheumatoid arthritis (RA) is a common, frequently severe, chronic inflammatory disease. Although the cause of RA remains unknown, recent advances in understanding its pathogenesis have been substantial. Despite the use of a variety of medications, particularly methotrexate, treatment of RA is not fully effective in most patients. Until recently, insights into inflammatory mechanisms in RA had not been successfully translated into novel classes of therapeutic agents. This gap now will likely be bridged in the form of a new strategy for treating RA-cytokine blockade. Although a variety of cytokines are important in the pathogenesis of RA, tumor necrosis factor (TNF) seems to play a pivotal role. Neutralizing TNF in patients with RA, by means of soluble TNF receptors or anti-TNF monoclonal antibodies, has proven to be a powerful means of controlling disease activity. Studies are in progress to obtain additional information regarding long-term safety of TNF blockade and its effects on disease progression.
Impact-Fatigue Response of Ultrahigh Molecular Weight Linear Polyethylene. 3. Morphological Effects (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTImpact-Fatigue Response of Ultrahigh Molecular Weight Linear Polyethylene. 3. Morphological EffectsS. Bhateja, J. Rieke, and E. AndrewsCite this: Ind. Eng. Chem. Prod. Res. Dev. 1980, 19, 4, 607–612Publication Date (Print):December 1, 1980Publication History Published online1 May 2002Published inissue 1 December 1980https://pubs.acs.org/doi/10.1021/i360076a024https://doi.org/10.1021/i360076a024research-articleACS PublicationsRequest reuse permissionsArticle Views43Altmetric-Citations5LEARN 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 options Get e-Alerts
Dynamic hash tables (1988)

Linear hashing and spiral storage are two dynamic hashing schemes originally designed for external files. This paper shows how to adapt these two methods for hash tables stored in main memory. The necessary data structures and algorithms are described, the expected performance is analyzed mathematically, and actual execution times are obtained and compared with alternative techniques. Linear hashing is found to be both faster and easier to implement than spiral storage. Two alternative techniques are considered: a simple unbalanced binary tree and double hashing with periodic rehashing into a larger table. The retrieval time of linear hashing is similar to double hashing and substantially faster than a binary tree, except for very small trees. The loading times of double hashing (with periodic reorganization), a binary tree, and linear hashing are similar. Overall, linear hashing is a simple and efficient technique for applications where the cardinality of the key set is not known in advance.
4-D blood flow in the human right ventricle (2011)

Right ventricular (RV) function is a powerful prognostic indicator in many forms of heart disease, but its assessment remains challenging and inexact. RV dysfunction may alter the normal patterns of RV blood flow, but those patterns have been incompletely characterized. We hypothesized that, based on anatomic differences, the proportions and energetics of RV flow components would differ from those identified in the left ventricle (LV) and that the portion of the RV inflow passing directly to outflow (Direct Flow) would be prepared for effective systolic ejection as a result of preserved kinetic energy (KE) compared with other RV flow components. Three-dimensional, time-resolved phase-contrast velocity, and balanced steady-state free-precession morphological data were acquired in 10 healthy subjects using MRI. A previously validated method was used to separate the RV and LV end-diastolic volumes into four flow components and measure their volume and KE over the cardiac cycle. The RV Direct Flow: 1) followed a smoothly curving route that did not extend into the apical region of the ventricle; 2) had a larger volume and possessed a larger presystolic KE (0.4 ± 0.3 mJ) than the other flow components (P < 0.001 and P < 0.01, respectively); and 3) represented a larger part of the end-diastolic blood volume compared with the LV Direct Flow (P < 0.01). These findings suggest that diastolic flow patterns distinct to the normal RV create favorable conditions for ensuing systolic ejection of the Direct Flow component. These flow-specific aspects of RV diastolic-systolic coupling provide novel perspectives on RV physiology and may add to the understanding of RV pathophysiology.
Oncogenic activation of Neu/ErbB-2 in a transgenic mouse model for breast cancer. (1998)

Recent evidence has suggested that amplification and overexpression of erbB-2/neu is an important determinant in the initiation and progression of human breast cancer. Consistent with this assertion is the observation that transgenic mice that overexpress the neu proto-oncogene heritably develop mammary adenocarcinomas. More recently, we have demonstrated that activation of neu in many of these tumours occurs as a result of somatic mutations located within the transgene itself. Indeed, careful examination of the altered neu transcripts revealed the presence of in-frame deletions that encode aberrant Neu receptors lacking 5-12 amino acids within the extracellular domain, located adjacent to the transmembrane domain. Interestingly, the majority of the deletions analysed affect one of several conserved cysteine residues present within this region. Moreover, introduction of these activating mutations into the wild-type neu cDNA results in its oncogenic conversion. These observations suggest that this cysteine-rich region plays an important role in regulating the catalytic activity of Neu.
Work system principles (2008)

The aim of the paper is to explore a possible theoretical foundation for the `work system approach'. The concept of work systems has been suggested as the core object of study in the field of information systems. The scope of the work system approach is determined by pragmatic relevance and high comprehensibility, with the goal of being applicable for professionals in both IT and business as well as IS researchers. This approach has, however, been criticized for having theoretical shortcomings. In this paper, a theoretical foundation is suggested and explored by relating it to work practice theory and its roots in socio-instrumental pragmatism. The results show that it is both possible and fruitful to ground the work system approach theoretically in socio-instrumental actions.
The Sarcin/Ricin Loop, a Modular RNA (1995)

The conformation of a 29 base oligonucleotide called E73 has been determined in solution by NMR. E73 includes a 23 nucleotide sequence that is identical with that of a the alpha-sarcin and ricin-sensitive loop (SRL) from rat 28 S rRNA, and like the SRL in intact ribosomes, E73 is a substrate for both toxins. The SRL includes a long, conserved sequence found in the RNA of all large ribosomal subunits, which plays a critical role in the factor-dependent steps of protein synthesis. The spectroscopic observations and analysis that led to the determination of the conformation of E73 are presented. The SRL in E73 has a highly structured conformation, which is stabilized by several non-Watson-Crick base-pairs, and many properties of the SRL in the ribosome can be understood assuming that the conformation of E73 and that of the SRL in the ribosome are the same. The role of the SRL in protein synthesis is discussed in light of the conformation of E73, as is the modular relationship that exists between the conformation of the SRL and other smaller RNAs.
Effect of phosphorylation and S–S bond-induced dimerization on DNA binding and transcriptional activation by C/EBPβ (2007)

CCAAT enhancer binding protein beta (C/EBPbeta) plays an essential role in the cascade that triggers adipocyte differentiation. C/EBPbeta activates transcription of C/EBPalpha and peroxisome proliferator-activated receptor-gamma, transcriptional activators of genes that give rise to the adipocyte phenotype. Sequential phosphorylation of C/EBPbeta/liver activating protein (LAP) on Thr(188) by MAPK and on Ser(184) or Thr(179) by glycogen synthase kinase beta (GSK3beta) is required for acquisition of DNA binding activity and transcriptional activation. To investigate how phosphorylation and dimerization of C/EBPbeta/LAP alter these activities, wild-type (Wt) and mutant rC/EBPbetas were prepared and purified to assess DNA binding and transcription in cell-free systems. rC/EBPbeta/LAP, phosphorylated by MAPK and GSK3beta in vitro, produced a >100-fold increase in DNA binding activity. Mutation of the phosphorylation to Glu increased DNA binding activity. Using a cell-free transcription system with nuclear extract from 3T3-L1 preadipocytes and rC/EBPbeta/LAP, only doubly phosphorylated rC/EBPbeta/LAP (by MAPK and GSK3beta) activated transcription driven by Wt C/EBPalpha, 422/aP2, and SCD1 promoters. Oxidation-induced dimerization of doubly phosphorylated Wt rC/EBPbeta/LAP increased DNA binding, whereas unphosphorylated Wt rC/EBPbeta/LAP lacked DNA binding activity. Mutation of the C-terminal Cys(296) adjacent to the leucine zipper and Cys(143) just upstream of the DNA binding domain eliminated phosphorylation-, oxidation-, and dimerization-dependent DNA binding activity, whereas mutation of Cys(201) within the basic DNA binding domain had little effect on DNA binding. These findings indicate that dual phosphorylation of C/EBPbeta/LAP caused a conformational change that facilitates S-S bond formation and dimerization, rendering the basic region accessible to the C/EBP regulatory element.