gebhart/patrepeval huggingface dataset:
Time-domain study of proximity-effect induced transition shifts (1991)

An accurate time-domain technique for measuring the proximity-effect-induced nonlinear transition shift has been developed, and this technique is applied to the case of a thin-film inductive head writing on a metal-film disk of high coercivity and high coercive squareness. Significant proximity shift at high densities is shown, even when the writeability may be considered good by overwrite and hard transition shift criteria. Furthermore, many basic properties of the proximity shift have been clearly resolved by the experiments, including the attractive and long-range nature of the proximity shift, the presence of ripple structures at low densities, and the nonlinear interactions between the proximity shift and the hard transition effect. Modeling studies have also been used to obtain a good understanding of these properties, and the theoretical results show good qualitative agreement with the experimental proximity-shift behavior.
CD45 isoform expression on human haemopoietic cells at different stages of development (1994)

Alternate splicing and glycosylation produce multiple CD45 isoforms which are selectively expressed on the surface of cells of the haemopoietic system. The expression of CD45RA, CD45RB and CD45RO on CD34+ and CD34- haemopoietic cells from umbilical cord blood, bone marrow and fetal liver were studied by flow cytometry. CD34+ subpopulations defined by CD45 isoform expression were sorted from bone marrow and tested in long-term culture assays. By combining results of functional studies with phenotypic data and previously published information, the following pattern of CD45 isoform expression on early haemopoietic cells was established. The most primitive CD34+ cells are CD45RO+ CD45RB+ and express low or undetectable levels of CD45RA. Upon erythroid differentiation, CD34+ cells remain CD45RO+ CD45RB+, whereas commitment into the myeloid and lymphoid lineages coincides with down-regulation of CD45RO and up-regulation of CD45RA. As a result, the majority of CD34+ cells can be divided into two mutually exclusive populations of cells which express either CD45RO or CD45RA. This notion was confirmed in this study by three-colour immunofluorescence. The alternative expression of various CD45 isoforms on functionally distinct haemopoietic cells suggests an important role for these molecules in the proliferation and differentiation of haemopoietic cells.
RIGID POLYURETHANE FOAMS FROM LIGNIN BASED-POLYOLS (2008)

Rigid polyurethane (RPU) foams were synthesized using lignin‐based polyols obtained by an oxypropylation process. Alcell, Indulin AT, Curan 27‐11P and Sarkanda lignins have been oxypropylated using formulations deduced from an optimization study with Alcell. L/PO/C (ratio between lignin, PO and catalyst content) of 30/70/2 and 20/80/5 were used to obtain the desired polyols. The resulting RPU foams were characterized in terms of density, mechanical properties, conductivity and morphology. All Sarkanda lignin based polyols and the 30/70/2 Curan 27‐11P polyol were found inadequate for RPU formulations. Alcell and Indulin AT based polyols and the 20/80/5 Curan 27‐11P polyol resulted in RPU foams with properties very similar to those obtained from conventional commercial polyols. RPU foams produced with the 30/70/2 Alcell and the 30/70/2 Indulin AT polyols exhibited improved properties compared with those from 20/80/5 based formulations.
mprA, an Escherichia coli gene that reduces growth-phase-dependent synthesis of microcins B17 and C7 and blocks osmoinduction of proU when cloned on a high-copy-number plasmid (1990)

Microcins B17 and C7 are plasmid-determined, peptide antibiotics produced by Escherichia coli when cells enter the stationary phase of growth. Microcinogenic strains are immune to the action of the microcin they synthesize. A well-characterized deficient-immunity phenotype is exhibited by microcin B17-producing cells in the absence of the immunity gene mcbG (M.C. Garrido, M. Herrero, R. Kolter, and F. Moreno, EMBO J. 7:1853-1862, 1988). A 14.6-kilobase-pair EcoRI chromosomal fragment was isolated by its ability to suppress this phenotype when cloned into a multicopy vector. This fragment was mapped to 57.5 min on the E. coli genetic map. The position of the gene responsible for suppression, designated mprA, was determined by insertional mutagenesis and deletion analysis. mprA was shown to be transcribed clockwise on the E. coli chromosome, and its product was identified as a 19-kilodalton polypeptide. Suppression was shown to be achieved by decreasing microcin B17 production. Increased mprA gene dosage also caused a decrease in microcin C7 production and blocked the osmoinduction of the proU locus in high-osmolarity media. Our results suggest that the mprA gene product could play a regulatory role on expression of several E. coli genes, this control being exerted at the transcriptional level.
MCLUST Version 3: An R Package for Normal Mixture Modeling and Model-Based Clustering (2006)

Abstract : MCLUST is a contributed R package for normal mixture modeling and model-based clustering. It provides functions for parameter estimation via the EM algorithm for normal mixture models with a variety of covariance structures, and functions for simulation from these models. Also included are functions that combine model-based hierarchical clustering, EM for mixture estimation and the Bayesian Information Criterion (BIC) in comprehensive strategies for clustering, density estimation and discriminant analysis. There is additional functionality for displaying and visualizing the models along with clustering and classification results. A number of features of the software have been changed in this version, and the functionality has been expanded to include regularization for normal mixture models via a Bayesian prior. A web page with related links including license information can be found at http://www.stat.washington.edu/mclust.
Efficient Serotype-Dependent Release of Functional Vector into the Culture Medium During Adeno-Associated Virus Manufacturing (2010)

Vectors based on adeno-associated virus (AAV) are the subject of increasing interest as research tools and agents for in vivo gene therapy. A current limitation on the technology is the versatile and scalable manufacturing of vector. On the basis of experience with AAV2-based vectors, which remain strongly cell associated, AAV vector particles are commonly harvested from cell lysates, and must be extensively purified for use. We report here that vectors based on other AAV serotypes, including AAV1, AAV8, and AAV9, are found in abundance in, and can be harvested from, the medium of production cultures carried out with or without serum. For AAV2, this difference in compartmentalization is largely due to the affinity of the AAV2 particle for heparin, because an AAV2 variant in which the heparin-binding motif has been ablated gives higher yields and is efficiently released from cells. Vector particles isolated from the culture medium appear to be functionally equivalent to those purified from cell lysates in terms of transduction efficiency in vitro and in vivo, immunogenicity, and tissue tropism. Our findings will directly lead to methods for increasing vector yields and simplifying production processes for AAV vectors, which should facilitate laboratory-scale preparation and large-scale manufacture.
Teleost B7 Expressed on Monocytes Regulates T Cell Responses, (2009)

In mammals, professional APCs induce adaptive immunity via the activation of T cells. During this process, B7 family molecules present upon APCs are known to play crucial roles in optimal T cell stimulation. In contrast, the confirmation of APCs in a nonmammalian vertebrate has yet to be achieved. To obtain further insights into the evolutionary origin of APCs, we have identified three members of the B7 family in the teleost Takifugu rubripes (fugu): B7-H1/DC, B7-H3, and B7-H4. The three fugu B7s were expressed on the surface of blood monocytes. The B7(+) monocytes, which are composed of at least two distinct populations, expressed the MHC class II component gene. The fugu B7 molecules bound to activated T cells, indicating that putative B7 receptors were expressed upon T cells. Fugu B7-H1/DC inhibited T cell proliferation concomitant with increasing levels of both IL-10 and IFN-gamma expression, whereas both B7-H3 and B7-H4 promoted T cell growth following IL-2 induction and the suppression of IL-10. These observations indicate that fugu B7s regulate T cell responses via receptors upon T cells. We suggest that fish B7(+) monocytes are APCs and that a costimulatory system has already developed in fish via the evolutionary process.
Three-dimensional images generated by quadrature interferometry (1998)

Quadrature detection techniques have been applied to images obtained from a Mach-Zehnder interferometer with differently polarized beams to yield the real and the imaginary parts of the diffracted fields simultaneously. This approach eliminates the need for phase retrieval by providing complete information on the complex amplitude of the diffracted signal. We present results in which we demonstrate our ability to reconstruct two- and three-dimensional microscopic objects from their complex diffraction patterns.
Crystal Structure of (1→3)-α-D-Glucan (1980)

A linear (1→3)-α-D-glucan (sample A) was prepared by mild Smith degradation from a bacterial α-glucan elaborated by a strain of S. salivarius TTL-LP1. The oriented glucan film (sample B) was obtained by acetylating the glucan, followed by stretching in glycerine at 150°C and deacetylation. Annealing the oriented film in water at 140°C, under tension in a sealed bomb, improved the crystallinity. All the 29 reflections on the equator and four layer lines were indexed with an orthorhombic unit cell with a = 1.646 nm, b = 0.955 nm, and c (fiber axis) = 0.844 nm. P212121 seemed to be the best space group. The crystal structure of sample A and another bacterial (1→3)-α-D-glucan (sample D) prepared from S. mutans fell in two of three polymorphs I-III of fungal (1→3)-α-D-glucan reported by Jelsma and Kreger; the crystal structure of sample B might be named as polymorph IV. All polymorphs of (l→3)-α-D-glucan observed to date have almost identical helix parameters n = 2 and h = 0.422 nm. These h values are close to the virtual bond length of 0.428 nm determined for α-D-glucose, suggesting that the typical chain conformation is an extended, ribbon-like structure. The similarities of (1→3)-α-D-glucan to cellulose are discussed.
Protein aggregation and degradation mechanisms in neurodegenerative diseases. (2013)

Neurodegenerative diseases are characterized by selective neuronal vulnerability and neurodegeneration in specific brain regions. The pathogenesis of these disorders centrally involves abnormal accumulation and aggregation of specific proteins, which are deposited in intracellular inclusions or extracellular aggregates that are characteristic for each disease. Increasing evidence suggests that genetic mutations or environmental factors can instigate protein misfolding and aggregation in these diseases. Consequently, neurodegenerative diseases are often considered as conformational diseases. This idea is further supported by studies implicating that impairment of the protein quality control (PQC) and clearance systems, such as the ubiquitin-proteasome system and autophagosome-lysosome pathway, may lead to the abnormal accumulation of disease-specific proteins. This suggests that similar pathological mechanisms may underlie the pathogenesis of the different neurodegenerative disorders. Interestingly, several proteins that are known to associate with neurodegenerative diseases have been identified as important regulators of PQC and clearance systems. In this review, we summarize the central features of abnormal protein accumulation in different common neurodegenerative diseases and discuss some aspects of specific disease-associated proteins regulating the PQC and clearance mechanisms, such as ubiquilin-1.
PERSONALITY DISORDERS AND POSTTRAUMATIC STRESS DISORDER IN MOTOR VEHICLE ACCIDENT SURVIVORS (2002)

This study examined the impact of a co-occurring personality disorder on the development and remission of posttraumatic stress disorder (PTSD) in 158 motor vehicle accident (MVA) survivors followed prospectively for 1 year. Participants were assessed 1 to 4 months after trauma and at 6-month and 1-year follow-up evaluations during 1991 through 1993. These archival data were analyzed in the present study. The prevalence of at least one personality disorder was 13.3%, with the majority (52.4%) presenting with obsessive-compulsive personality disorder. Persons with a personality disorder were significantly more likely to be diagnosed with PTSD at 1-year follow-up evaluation. For persons diagnosed with PTSD at the initial assessment, those with a personality disorder were significantly less likely to remit by 1 year. The presence of a preexisting personality disorder may increase the risk of chronic PTSD and impede remission.
A 275 basepair fragment at the 5' end of the interleukin 2 gene enhances expression from a heterologous promoter in response to signals from the T cell antigen receptor. (1987)

Using a transient transfection assay, we have defined the sequences required for the activation of the IL-2 gene in response to signals from the T cell antigen receptor. To do so we have transfected the human T cell line Jurkat with hybrid DNA constructs in which fragments from the IL-2 gene are linked to an indicator gene. The indicator gene product, as well as IL-2 production from the endogenous IL-2 gene were assayed after activation of the transfected Jurkat cells by various stimuli. We have demonstrated that a 275 bp fragment stretching from 52 to 326 bp upstream of the IL-2 gene transcription initiation site is required for expression of the linked indicator gene. This IL-2 gene fragment has several of the characteristics of a transcriptional enhancer element, in that it functions in both orientations and will enhance the expression from the promoter of an unrelated gene. Such enhancement occurred only after activation of Jurkat cells through the T cell antigen receptor. More specifically, this 275 bp fragment activated the expression of a linked gene after binding of a monoclonal antibody to the Jurkat T cell antigen receptor in the presence of PMA. In addition, calcium ionophore, which circumvents antigen receptor binding in T cell activation, induced the expression of the linked gene through this 275 bp sequence, in the presence of PMA. Finally, in a mutant Jurkat cell line lacking T3/antigen receptor complexes at the cell surface, no expression due to the IL-2 5' flanking region was seen after exposure to antibody to the T cell antigen receptor plus PMA or to PHA plus PMA. In contrast, calcium ionophore plus PMA did induce the expression of a linked gene through the IL-2 5' flanking region in the mutant Jurkat cell line. The responsiveness of the transfected hybrid genes containing the IL-2 regulatory region paralleled the expression of the endogenous IL-2 gene, as determined by IL-2 bioassays. We conclude that the 275 bp IL-2 sequence (-326 to -52 bp) is a target for the signal pathway originating at the T cell antigen receptor. Definition of this 275 bp target sequence should now permit the isolation of the molecules that bind to and activate the IL-2 gene.
Recent Progress of the Synthetic Studies of Biologically Active Marine Cyclic Peptides and Depsipeptides (2005)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRecent Progress of the Synthetic Studies of Biologically Active Marine Cyclic Peptides and DepsipeptidesYasumasa Hamada and Takayuki ShioiriView Author Information Graduate School of Pharmaceutical Sciences, Chiba University, Yayoi-cho, Inage-ku, Chiba 263-8522, Japan, and Graduate School of Environmental and Human Sciences, Meijo University, Shiogamaguchi, Tempaku, Nagoya 468-8502, Japan Cite this: Chem. Rev. 2005, 105, 12, 4441–4482Publication Date (Web):October 11, 2005Publication History Received22 March 2005Published online11 October 2005Published inissue 1 December 2005https://pubs.acs.org/doi/10.1021/cr0406312https://doi.org/10.1021/cr0406312research-articleACS PublicationsCopyright © 2005 American Chemical SocietyRequest reuse permissionsArticle Views4536Altmetric-Citations239LEARN 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 SUBJECTS:Chemical structure,Monomers,Organic compounds,Peptides and proteins,Reaction products Get e-Alerts
Aminoglycoside and Nephrotoxicity (1987)

The effect of three aminoglycosides--gentamicin, netilmicin and amikacin--on renal acid excretion was studied in male rats treated with doses equivalent to those clinically used. The amikacin and netilmicin groups showed no important changes in the values of glomerular filtration rate (GFR), effective renal plasma flow (ERPF) and U/P inulin ratio during normal and acidotic conditions. The gentamicin group, however, showed a clear tendency to decreases in these functional parameters even in normal conditions, a finding that reinforces the concept that gentamicin is more nephrotoxic than other aminoglycosides. During normal conditions net acid excretion (BH) did not change with any of the three tested drugs. However, after an acute acid load BH markedly fell regardless of the antibiotic used. The capacity to elevate the urine-blood pCO2 was preserved after an alcaline overload, suggesting that the distal tubule was not significantly affected by aminoglycoside treatment. These data suggest that the clinical use of aminoglycosides during metabolic acidosis deserves close attention due to the possible deleterious effect that can emerge as the result of an inappropriate retention of acid loads.
Identification of Residues within the 727–767 Segment of Human Complement Component C3 Important for Its Interaction with Factor H and with Complement Receptor 1 (CR1, CD35) (1999)

Mapping approaches employing blocking antibodies and synthetic peptides have implicated the 727-767 segment at the NH2 terminus of C3b alpha'-chain as contributing to the interactions with factor B, factor H, and CR1. Our previous mutagenesis study on the NH2-terminal acidic cluster of this segment identified residues Glu-736 and Glu-737 as contributing to the binding of C3b to factor B and CR1 but not factor H. We have now extended the charged residue mutagenic scan to cover the remainder of the segment (738-767) and have assessed the ability of the C3b-like C3(H2O) form of the mutant molecules to interact with factor H, CR1, and membrane cofactor protein (MCP) using a cofactor-dependent factor I cleavage assay as a surrogate binding assay. We have found that the negatively charged side chains of Glu-744 and Glu-747 are important for the interaction between C3(H2O) and factor H, a result in general agreement with an earlier synthetic peptide study (Fishelson, Z. (1991) Mol. Immunol. 28, 545-552) which implicated residues within the 744-754 segment in H binding. The interactions of the mutants with soluble CR1 (sCR1) revealed two classes of residues. The first are residues required for sCR1 to be an I cofactor for the first two cleavages of alpha-chain. These are all acidic residues and include the Glu-736/Glu-737 pair, Glu-747, and the Glu-754/Asp-755 pairing. The second class affects only the ability of sCR1 to be a cofactor for the third factor I cleavage and include Glu-744 and the Lys-757/Glu-758 pairing. The dominance of acidic residues in the loss-of-function mutants is striking and suggests that H and CR1 contribute basic residues to the interface. Additionally, although there is partial overlap, the contacts required for CR1 binding appear to extend over a wider portion of the 727-767 segment than is the case for factor H. Finally, none of the mutations had any effect on the interaction between soluble MCP and C3(H2O), indicating that despite its functional homology to H and CR1, MCP differs in its mode of binding to C3b/C3(H2O).
Established and emerging biological activity markers of inflammatory bowel disease (2000)

Assessment of disease activity in inflammatory bowel disease (IBD), i.e., ulcerative colitis (UC) and Crohn's disease (CD), is done using clinical parameters and various biological disease markers. Ideally, a disease marker must: be able to identify individuals at risk of a given disorder, be disease specific, mirror the disease activity and, finally, be easily applicable for routine clinical purposes. However, no such disease markers have yet been identified for IBD. In this article, classical disease markers including erythrocyte sedimentation rate, acute phase proteins (especially orosomucoid and CRP), leukocyte and platelet counts, albumin, neopterin, and beta2-microglobulin will be reviewed together with emerging disease markers such as antibodies of the ANCA/ASCA type, cytokines (e.g., IL-1, IL-2Ralpha, IL-6, IL-8, TNF-alpha, and TNF-alpha receptors) and with various adhesion molecules. It is concluded that none of the pertinent laboratory surrogate markers of disease activity in IBD are specific or sensitive enough to replace basic clinical observation such as the number of daily bowel movements, general well-being, and other parameters in parallel. Further studies are highly warranted to identify and assess the clinical importance and applicability of new laboratory markers for the diagnosis or the disease activity of IBD.
Advances in Corrosion Resistant Steels (1988)

A survey is presented of advances which have occurred over the past ten years in corrosion resistant steels, particularly those at the lower cost end of the range. Typical applications are given, but also special attention is drawn to applications for which the materials have been found unsuitable and therefore an alternative needs to be found.