gebhart/patrepeval huggingface dataset:
Prevalence of gca, a gene involved in synthesis of A-band common antigen polysaccharide in Pseudomonas aeruginosa (1995)

Two distinct forms of lipopolysaccharide are expressed by Pseudomonas aeruginosa. These forms are known as the A band and the B band. In an attempt to obtain a better understanding of A-band lipopolysaccharide synthesis, a previously isolated A-band gene known as the gca gene (GDP-D-mannose conversion protein for A-band common antigen polysaccharide) was sequenced and analyzed. Previous protein expression data from our laboratory, along with nucleotide sequence analysis from the present study, suggest that the Gca protein is encoded by the open reading frame ORF36.5. Amino acid homology reveals that this protein may be functioning as a dehydratase or as a bifunctional enzyme, facilitating the conversion of GDP-D-mannose to GDP-D-rhamnose. The distribution of this gca gene among the 20 P. aeruginosa O serotypes, clinical isolates, and other Pseudomonas species was also examined. Southern hybridization results revealed that the gca gene is present and conserved on a 1.6-kb KpnI fragment among all 20 O serotypes with the exception of serotype O12. In addition, the gca gene is not universally found among all pseudomonads; however, probe-reactive profiles are similar to that of P. aeruginosa when the gca gene is present. Primers were designed from the gca nucleotide sequence, and PCR amplification of a 700-bp product was found with each of the 20 O serotypes. Because of the conservation of this gene, gca may be useful as a diagnostic tool for detecting the presence of P. aeruginosa as well as other Pseudomonas species.
Synthesis and characterization of novel glycosurfaces by ATRP (2009)

The direct synthesis of well defined sugar methacrylate-based homopolymer brushes with high grafting densities based on D-gluconamidoethyl methacrylate (GAMA) and 2-lactobionamidoethyl methacrylate (LAMA) from functionalized gold substrates was carried out using surface-initiated atom transfer radical polymerization (ATRP). A good control of the polymerization leading to an increase in the dry film thickness with reaction time was achieved in mixed methanol/water solvent media. However, grafted glycopolymer films of low thicknesses, which did not increase further with longer polymerization times were synthesized in water, suggesting the premature termination of the polymerization in the aqueous solvent. Attenuated total reflectance (ATR)-FTIR spectroscopy confirmed the successful grafting of the glycopolymer brushes on the modified gold substrates, while atomic force microscopy (AFM) verified that the anchored film covered the substrate surface completely and homogeneously. The surface roughness found by AFM was below 1 nm suggesting the preparation of very smooth glycopolymer films. The grafting of the glycopolymer chains onto the gold substrates afforded an increase in the surface hydrophilicity as confirmed by contact angle measurements. The synthesized glycopolymer films exhibited strong binding interactions with specific lectins via the “glycocluster” effect.
A Competitive Inhibitor Traps LeuT in an Open-to-Out Conformation (2008)

Secondary transporters are workhorses of cellular membranes, catalyzing the movement of small molecules and ions across the bilayer and coupling substrate passage to ion gradients. However, the conformational changes that accompany substrate transport, the mechanism by which a substrate moves through the transporter, and principles of competitive inhibition remain unclear. We used crystallographic and functional studies on the leucine transporter (LeuT), a model for neurotransmitter sodium symporters, to show that various amino acid substrates induce the same occluded conformational state and that a competitive inhibitor, tryptophan (Trp), traps LeuT in an open-to-out conformation. In the Trp complex, the extracellular gate residues arginine 30 and aspartic acid 404 define a second weak binding site for substrates or inhibitors as they permeate from the extracellular solution to the primary substrate site, which demonstrates how residues that participate in gating also mediate permeation.
Cloning and Expression of an Isovaleryl Pepstatin-Insensitive Carboxyl Proteinase Gene from Xanthomonas sp. T-22 (1996)

Xanthomonas carboxyl proteinase (XCP), isolated from Xanthomonas sp. T-22, is the second example of the unique carboxyl proteinases [EC 3.4.23.33] which are insensitive to the classical aspartic proteinase inhibitor. The gene coding for XCP was cloned, sequenced, and expressed in Escherichia coli. The XCP gene contains an open reading frame of 2,481 base pairs encoding a protein of 827 amino acid residues with a M(r) of 83,677. The XCP was synthesized as a large precursor consisting of three regions: NH2-terminal prepro (N-Prepro) (237 amino acid residues); mature XCP (398 a.a.residues); and COOH-terminal pro (C-Pro) (192 a.a. residues). The N-Prepro and mature XCP regions had no sequence similarity to any other proteins reported so far, except the carboxyl proteinase from Pseudomonas sp. 101 [Oda, K., Takahashi, T., Tokuda, Y., Shibano, Y., and Takahashi, S. (1994) J. Biol. Chem. 269, 26518-26524]. The C-Pro region showed high similarity to COOH-terminal regions of other microbial proteinase precursors. E. coli carrying a plasmid containing the cloned wild-type XCP gene produced an 84-kDa protein. This protein was processed into a mature, active form under acidic conditions. This process was completely blocked by tyrostatin, an XCP-specific inhibitor from Kitasatosporia sp. 55, indicating an autocatalytic processing. The purified recombinant XCP had the same characteristics as authentic XCP except for the NH2-terminal amino acid sequence. When the mutant XCP gene truncated in the C-Pro region was expressed in E. coli, an expected 64-kDa protein was detected in the cells, and also processed into the 42-kDa active form under the acidic conditions. Thus, the C-Pro region was not essential for the formation of active mature XCP.
Optimal vector transform for vector quantization (1994)

The vector transform has previously been proposed for vector quantization image coding. It is intended for decorrelating intervector dependency and preserving intravector dependency. The present authors study optimally such a transform. It is found that the optimal vector transform in the above senses, with the first-order Gaussian Markov model, does not exist unless the overall correlation matrix has an intervector and intravector decomposition structure. This is especially true for vectors formed by blocks of pixels. Then, a necessary and sufficient condition is derived for general vectors on the existence of their optimal vector transforms.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Biofabrication with Chitosan (2005)

The traditional motivation for integrating biological components into microfabricated devices has been to create biosensors that meld the molecular recognition capabilities of biology with the signal processing capabilities of electronic devices. However, a different motivation is emerging; biological components are being explored to radically change how fabrication is achieved at the micro- and nanoscales. Here we review biofabrication, the use of biological materials for fabrication, and focus on three specific biofabrication approaches: directed assembly, where localized external stimuli are employed to guide assembly; enzymatic assembly, where selective biocatalysts are enlisted to build macromolecular structure; and self-assembly, where information internal to the biological material guides its own assembly. Also reviewed are recent results with the aminopolysaccharide chitosan, a material that offers a combination of properties uniquely suited for biofabrication. In particular, chitosan can be directed to assemble in response to locally applied electrical signals, and the chitosan backbone provides sites that can be employed for the assembly of proteins, nucleic acids, and virus particles.
A surgical model for studying biliary bile acid and cholesterol metabolism in swine. (1991)

Techniques were developed in young growing pigs to simultaneously collect and reinfuse bile. Silastic cannulae were designed and surgically implanted in the common bile duct and the duodenum. Direct sampling of the hepatic bile was achieved by bypassing the gallbladder. The techniques allowed for steady-state studies of hepatic function to be conducted in conscious swine in two different studies. Pigs, thus surgically modified, can serve as an appropriate model for physiologic, pharmacologic, and nutritional research that involves bile sampling.
Physiological Adaptation to the Environment (1989)

The ability of an animal to cope with new environments arises from its capacity to respond to environmental variables and maintain body equilibrium (homeostasis). Each compensating mechanism depends on, and is a part of, a physiological feedback process. The severity (intensity and duration) of an environmental change relative to the animal's capacity to respond determines the potential disruption to the animal's equilibrium and the resources that must be invested to regain homeostasis. However, an environmental change sufficient to seriously challenge one individual may be insufficient to produce a measurable response in another. The principles behind the responses occurring in animals as a consequence of a change in their physical environment are illustrated in this review by examples drawn from responses of animals to cold stress. Behavioral opportunities sometimes are constrained in farm animals, and internal metabolic responses tend to become more prominent in such situations. Furthermore, as a disturbing factor persists, the immediate defensive responses are replaced by longer-term and adaptive mechanisms that reduce the burden on the animal. As we gain greater understanding of the environment-animal interface and the sensitivity and response of animals to disruption, we will be better able to establish and maintain suitable environments for our farm animals.
Molecular Weight Distribution of Polyethylene Produced by Ziegler-Natta Catalysts (1971)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMolecular Weight Distribution of Polyethylene Produced by Ziegler-Natta CatalystsDaljit Singh and R. P. MerrillCite this: Macromolecules 1971, 4, 5, 599–604Publication Date (Print):September 1, 1971Publication History Published online1 May 2002Published inissue 1 September 1971https://pubs.acs.org/doi/10.1021/ma60023a017https://doi.org/10.1021/ma60023a017research-articleACS PublicationsRequest reuse permissionsArticle Views948Altmetric-Citations95LEARN 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
Hyaluronidase enhancement of TNF-mediated cell death is reversed by TGF-β1 (1997)

Both hyaluronidase and transforming growth factor (TGF)-beta 1 play a significant role in the development of prostate cancer. In this study, the regulation of tumor necrosis factor (TNF)-mediated cell death by hyaluronidase and TGF-beta 1 was investigated. Preexposure of L929 fibroblasts, prostate LNCaP cells, and epithelial Mv 1 Lu cells to hyaluronidase for a minimum of 12 h resulted in significant enhancement of cell death by TNF. Phosphorylation of p42 and p44 mitogen-activated-protein (MAP) kinases was found by stimulation of L929 cells with hyaluronidase for 30 min, indicating that the Raf/MAP kinase-extracellular signal-regulating protein kinase (MEK)/ MAP kinase pathway was activated. However, blocking the activation of upstream MAP kinase kinase (MEK 1 and 2 kinase) by PD-98059 failed to inhibit the hyaluronidase-enhanced TNF killing of cells, suggesting that hyaluronidase-mediated degradation of extracellular matrix and membrane components may elicit multiple signaling pathways. As a potent stimulator of extracellular matrix protein synthesis, TGF-beta 1 blocked the hyaluronidase-enhanced death of L929 and LNCaP cells mediated by TNF. TGF-beta 1 activated protein-tyrosine kinases in L929 cells, in which the tyrosine kinase inhibitors lavendustin A and tyrphostin blocked the activation as well as the TGF-beta 1 inhibition of hyaluronidase effects. Functional antagonism was also observed between hyaluronidase and TGF-beta 1 in cell growth regulation. For example, TGF-beta 1-mediated suppression of epithelial Mv 1 Lu cell growth was abolished by hyaluronidase. Overall, it is demonstrated in this study that hyaluronidase reciprocally antagonized TGF-beta 1 in the modulation of cell proliferation and TNF-mediated death.
Crystal Structures of the Soluble Methane Monooxygenase Hydroxylase from <i>Methylococcus </i><i>capsulatus</i> (Bath) Demonstrating Geometrical Variability at the Dinuclear Iron Active Site (2001)

The oxidation of methane to methanol is performed at carboxylate-bridged dinuclear iron centers in the soluble methane monooxygenase hydroxylase (MMOH). Previous structural studies of MMOH, and the related R2 subunit of ribonucleotide reductase, have demonstrated the occurrence of carboxylate shifts involving glutamate residues that ligate the catalytic iron atoms. These shifts are thought to have important mechanistic implications. Recent kinetic and theoretical studies have also emphasized the importance of hydrogen bonding and pH effects at the active site. We report here crystal structures of MMOH from Methylococcus capsulatus (Bath) in the diiron(II), diiron(III), and mixed-valent Fe(II)Fe(III) oxidation states, and at pH values of 6.2, 7.0, and 8.5. These structures were investigated in an effort to delineate the range of possible motions at the MMOH active site and to identify hydrogen-bonding interactions that may be important in understanding catalysis by the enzyme. Our results present the first view of the diiron center in the mixed-valent state, and they indicate an increased lability for ferrous ions in the enzyme. Alternate conformations of Asn214 near the active site according to redox state and a distortion in one of the alpha-helices adjacent to the metal center in the diiron(II) state have also been identified. These changes alter the surface of the protein in the vicinity of the catalytic core and may have implications for small-molecule accessibility to the active site and for protein component interactions in the methane monooxygenase system. Collectively, these results help to explain previous spectroscopic observations and provide new insight into catalysis by the enzyme.
Acetyldiarylamines by arylation of acetanilides. Some applications and limitations (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAcetyldiarylamines by arylation of acetanilides. Some applications and limitationsHarold S. Freeman, Jack R. Butler, and Leon D. FreedmanCite this: J. Org. Chem. 1978, 43, 26, 4975–4978Publication Date (Print):December 1, 1978Publication History Published online1 May 2002Published inissue 1 December 1978https://pubs.acs.org/doi/10.1021/jo00420a018https://doi.org/10.1021/jo00420a018research-articleACS PublicationsRequest reuse permissionsArticle Views653Altmetric-Citations50LEARN 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
An enhancer sequence from bovine papilloma virus DNA consists of two essential regions (1984)

A comprehensive structural analysis of an enhancer sequence from bovine papilloma virus DNA is presented based on the construction and functional analysis of 20 mutant derivatives. The results, obtained in CV-1 tissue culture cells, show that this enhancer is a small genetic element--only 40 bp in length--that contains two essential regions. The two regions exhibit homology to each other and to DNA fragments from other viral genomes that also act as enhancers in the assay used. However, there is a certain latitude in the sequences that have enhancer activity in CV-1 cells, even within the critical regions. The results are discussed with respect to the model that enhancers are binding sites for tissue specific transcription factors. The formation of Z-DNA might be involved in the enhancement process. However, single base pair transitions in an 8 base pair stretch of alternating purines and pyrimidines within the BPV enhancer which conserve this pattern destroy enhancer function.
Dielectric Relaxation of Aqueous Solution with Low-molecular-weight Nonelectrolytes and Its Relationship with Solution Structure (1997)

Dielectric relaxation of water molecules was measured in the frequency range from 0.2 to 20 GHz for aqueous solutions of urea, formamide, alcohols, and saccharides. The relaxation behavior was described well by the Debye equation with a single relaxation process in most cases. The static permittivity of solution and relaxation time of water in solution changed linearly with solute concentration. The relaxation time shift of water molecules through the existence of solute was correlated well to the first virial coefficient of the activity coefficient of water suggesting the close relationship between dielectric relaxation time and aqueous solution structure.
The relationship between perceived religious discrimination and self‐esteem for Muslim Australians (2014)

Muslim Australians represent one of the fastest growing migrant groups in Australia. They are also the group who, after Indigenous Australians, experience the most discrimination. Previous research on the minority stress model confirms a link between such discrimination and mental health. However, in relation to self‐esteem and discrimination, the results are mixed, potentially reflecting whether people reject or identify with prejudiced views of them and also the type of discrimination being measured. To explore this issue further in an Australian context, we asked 49 Australian Muslims to complete Rosenberg's Self‐esteem Scale and the Perceived Religious Discrimination Scale. In support of both the minority stress model and the rejection‐identification model, we found that perceived interpersonal and systemic discrimination accounts for a small but significant variation in self‐esteem. Interpersonal discrimination was negatively related to self‐esteem, and systemic discrimination positively related. The effects of interpersonal discrimination on self‐esteem can guide therapists to interventions that help clients resist internalising discrimination experiences. The effects of institutional discrimination support therapists becoming part of the resistance to and challenging of discrimination and inequality.
Reactivation of γHV68 induces neointimal lesions in pulmonary arteries of S100A4/Mts1-overexpressing mice in association with degradation of elastin (2007)

S100A4/Mts-overexpressing mice have thick elastic laminae and mild pulmonary arterial hypertension (PAH), and the occasional older mouse develops occlusive neointimal lesions and perivascular inflammation. We hypothesized that a vasculotropic virus could induce neointimal lesions in the S100A4/Mts1 mouse by facilitating breakdown of elastin and migration and proliferation of smooth muscle cells. To test this hypothesis, we infected S100A4/Mts1 mice with gammaherpesvirus 68 (gammaHV68). We observed, 6 mo after gammaHV68 [4 x 10(3) plaque-forming units (PFU)], perivascular inflammation in 10/15 S100A4/Mts1 mice and occlusive neointimal formation in 3/10 mice, accompanied by striking degradation of elastin. We then compared the early response after high-dose gammaHV68 (4 x 10(6) PFU) in C57Bl/6 and S100A4/Mts1 mice. In S100A4/Mts1 mice only, significant PAH, muscularization of distal vessels, and elastase activity were observed 6 wk after gammaHV68. These features resolved by 3 mo without neointimal formation. We therefore infected mice with the M1-gammaHV68 strain that reactivates from latency with higher efficiency and observed neointimal lesions at 3 mo in 2/5 C57Bl/6 (5-9% of vessels) and in 5/5 S100A4/Mts1 mice (13-40% of vessels) accompanied by mild PAH, heightened lung elastase activity, and intravascular viral expression. This suggested that enhanced generation of elastin peptides in S100A4/Mts1 mice may promote increased viral entry in the vessel wall. Using S100A4/Mts1 PA organ culture, we showed, in response to elastase activity, heightened production of elastin peptides associated with invasion of inflammatory cells and intravascular viral antigen. We therefore propose that early viral access to the vessel wall may be a critical determinant of the extent of vascular pathology following reactivation.
Employing Nodal Generalized Perturbation Theory for the Minimization of Feed Enrichment during Pressurized Water Reactor In-Core Nuclear Fuel Management Optimization (1995)

The computer code FORMOSA-P (Fuel Optimization for Reloads Multiple Objectives by Simulated Annealing—PWR) has been developed to address pressurized water reactor (PWR) in-core nuclear fuel management optimization. Until recently, the optimization objectives available to the user included minimization of relative power peaking throughout the cycle, maximization of the end-of-cycle reactivity, and maximization of region-average discharge burnup. In addition, during an optimization, various core attributes (including the preceding objectives) can be optionally activated as constraints via penalty functions or to directly reject sampled loading patterns that violate established design limits. The underlying theoretical framework that enables the accurate and efficient calculation of objective and constraint values within the FORMOSA-P code is its higher order, nodal generalized perturbation theory (GPT) neutronics model. The utility of the FORMOSA-P code has been extended to include a traditionally out-of-core decision variable, namely, the fresh (i.e., feed) reload fuel enrichment. This is accomplished by formulating the feed enrichment as a GPT variable that can be adjusted concurrently with changes in the core loading pattern to enforce a target cycle length. This provides a reload designer with the capability to minimize feed enrichment during an in-core optimization while enforcing all other constraints (e.g., power peaking limit, cycle energy requirement, degree of eighth-core power tilt, discharge burnup limit, and moderator temperature coefficient limit).