gebhart/patrepeval huggingface dataset:
Intra- and intermolecular spreading of autoimmunity involving the nuclear self-antigens La (SS-B) and Ro (SS-A). (1995)

We have tested the extent of immune self-tolerance to the ubiquitously expressed nuclear/cytoplasmic autoantigens La (SS-B) and Ro (SS-A) in healthy, nonautoimmune mice. Immunization of mice with recombinant mouse La resulted in a specific, isotype-switched autoantibody response, which was initially directed toward the La C subfragment (aa 111-242) but rapidly spread to involve the La A (aa 1-107) and La F (aa 243-345) regions of the La antigen. Intramolecular spreading of the anti-La antibody response was further demonstrated by the appearance of autoantibodies to multiple, nonoverlapping antigenic regions of La, after immunization of mice with the 107-aa La A subfragment. Moreover, immunization of mice with recombinant mouse or human La also elicited specific anti-60-kDa Ro IgG antibodies in all strains tested. Mice immunized with 60-kDa Ro produced a high titer anti-Ro antibody response, which was also associated with intermolecular spreading, resulting in the specific appearance of anti-La autoantibodies. These findings show that the development of autoantibodies to multiple components of the La/Ro ribonucleoprotein complex may follow initiation of immunity to a single component. In addition, the data reveal the incomplete nature of immune tolerance to La and Ro despite their endogenous expression in all nucleated cells. These observations are likely to account for the coexistence of anti-La/Ro antibodies in autoimmune disease and suggest a general explanation for the appearance of mixed autoantibody patterns in systemic autoimmune disorders.
Effects of receptor tyrosine kinase inhibitor A47 on estrogen and growth factor‐dependent breast cancer cell proliferation and apoptosis in vitro (2001)

Taken together, A47 blocks E2/EGF-induced activation of EGFR and therefore interferes with the proximal EGFR signaling pathway. A47 also arrests the cells at the G1-S transition of the cell cycle and induces cell death by apoptosis. Thus, a growth factor RTK may be useful in blocking hormone-dependent tumor growth in an elevated E2 environment.
A Phase I Biodistribution and Pharmacokinetic Trial of Humanized Monoclonal Antibody Hu3s193 in Patients with Advanced Epithelial Cancers that Express the Lewis-Y Antigen (2007)

Hu3S193 is well tolerated and selectively targets tumors, and the long half-life and biological function in vivo of this antibody makes it an attractive potential therapy for patients with Le(y)-expressing cancers.
Growth factor receptor interplay and resistance in cancer (2006)

Aberrant signalling through the epidermal growth factor receptor (EGFR) plays a major role in the progression and maintenance of the malignant phenotype and the receptor is therefore a rational anti-cancer target. A variety of approaches have been developed to specifically target the EGFR which include monoclonal antibodies and small molecule tyrosine kinase inhibitors, such as gefitinib (Iressa). However, the recent clinical experience across a range of cancer types is revealing that despite the anti-EGFR agents demonstrating some anti-tumour activity, there is a high level of de novo and acquired resistance to such treatments and moreover, overexpression of the EGFR is clearly not the sole determinant of response to such therapies. Such adverse phenomena, which serve to limit the overall therapeutic impact of these new agents, implies the existence of a greater complexity involved in the regulation of EGFR signalling than was previously assumed. Indeed, evidence is accumulating which demonstrates that signalling interplay occurs between the EGFR, and the IGF-1 receptor (IGF-1R) and the review will focus on the emerging concept of growth factor pathway switching between these two receptors as a means of influencing the effectiveness of anti-EGFR agents such as gefitinib.
Early Detection of Metastatic Relapse and Monitoring of Therapeutic Efficacy by Ultra-Deep Sequencing of Plasma Cell-Free DNA in Patients With Urothelial Bladder Carcinoma (2019)

ctDNA assessment for early risk stratification, therapy monitoring, and early relapse detection in bladder cancer is feasible and provides a basis for clinical studies that evaluate early therapeutic interventions.
Relationship Between Cancer Type and Impact of PET and PET/CT on Intended Management: Findings of the National Oncologic PET Registry (2008)

The impact of PET on physicians' intended management for patients with known cancer was consistent across cancer types.
Peptidomimetics: modifying peptides in the pursuit of better vaccines (2011)

Peptide vaccines represent a potential strategy for the prevention and treatment of pathogenic diseases, cancers and autoimmune disorders; their low cost, ease of synthesis and inherent safety are all attractive features. However, they have remained largely unsuccessful owing to low immunogenicity, predominantly stemming from reduced bioavailability due to rapid proteolytic degradation in vivo. The field of peptidomimetics, through chemical alteration of epitope structure, attempts to modify peptides to engender improved immunogenicity and stability, with the ultimate aim of rationally designing more efficacious vaccines. This article discusses the strategies employed in this process and recent advances within the field.
Altering Chemosensitivity by Modulating Translation Elongation (2009)

Our results indicate that depleting short-lived pro-survival factors by inhibiting their synthesis could achieve a therapeutic response in tumors harboring PTEN/AKT/mTOR pathway mutations.
Site-directed alkylation and the alternating access model for LacY (2006)

In a functional lactose permease mutant from Escherichia coli (LacY) devoid of native Cys residues, almost every residue was replaced individually with Cys and tested for reactivity with the permeant alkylating agent N-ethylmaleimide in right-side-out membrane vesicles. Here we present the results in the context of the crystal structure of LacY. Engineered Cys replacements located near or within the inward-facing hydrophilic cavity or at other solvent-accessible positions in LacY react well with this alkylating agent. Cys residues facing the low dielectric of the membrane or located in tightly packed regions of the structure react poorly. Remarkably, in the presence of ligand, increased reactivity is observed with Cys replacements located predominantly on the periplasmic side of the sugar-binding site. In contrast, other Cys replacements largely on the cytoplasmic side of the binding site exhibit decreased reactivity. Furthermore, both sets of Cys replacements in the putative cavities are located at the periplasmic (increased reactivity) and cytoplasmic (decreased reactivity) ends of the same helices and distributed in a pseudosymmetrical manner. The results are consistent with a model in which the single sugar-binding site in the approximate middle of the molecule is alternately exposed to either side of the membrane due to opening and closing of cytoplasmic and periplasmic hydrophilic cavities.
Variation in demersal fish species richness in the oceans surrounding New Zealand: an analysis using boosted regression trees (2006)

MEPS Marine Ecology Progress Series Contact the journal Facebook Twitter RSS Mailing List Subscribe to our mailing list via Mailchimp HomeLatest VolumeAbout the JournalEditorsTheme Sections MEPS 321:267-281 (2006) - doi:10.3354/meps321267 Variation in demersal fish species richness in the oceans surrounding New Zealand: an analysis using boosted regression trees J. R. Leathwick1,*, J. Elith2, M. P. Francis3, T. Hastie4, P. Taylor1 1National Institute of Water and Atmospheric Research, PO Box 11115, Hamilton, New Zealand 2School of Botany, University of Melbourne, Parkville 3010, Victoria, Australia 3National Institute of Water and Atmospheric Research, Private Bag 14901, Wellington, New Zealand 4Sequoia Hall, Stanford University, Stanford, California 94305-4065, USA *Email: j.leathwick@niwa.co.nz ABSTRACT: We analysed relationships between demersal fish species richness, environment and trawl characteristics using an extensive collection of trawl data from the oceans around New Zealand. Analyses were carried out using both generalised additive models and boosted regression trees (sometimes referred to as stochastic gradient boosting). Depth was the single most important environmental predictor of variation in species richness, with highest richness occurring at depths of 900 to 1000 m, and with a broad plateau of moderately high richness between 400 and 1100 m. Richness was higher both in waters with high surface concentrations of chlorophyll a and in zones of mixing of water bodies of contrasting origins. Local variation in temperature was also important, with lower richness occurring in waters that were cooler than expected given their depth. Variables describing trawl length, trawl speed, and cod-end mesh size made a substantial contribution to analysis outcomes, even though functions fitted for trawl distance and cod-end mesh size were constrained to reflect the known performance of trawl gear. Species richness declined with increasing cod-end mesh size and increasing trawl speed, but increased with increasing trawl distance, reaching a plateau once trawl distances exceed about 3 nautical miles. Boosted regression trees provided a powerful analysis tool, giving substantially superior predictive performance to generalized additive models, despite the fitting of interaction terms in the latter. KEY WORDS: Demersal fish · Species richness · Boosted regression trees · Statistical model Full text in pdf format PreviousNextExport citation RSS - Facebook - Tweet - linkedIn Cited by Published in MEPS Vol. 321. Online publication date: September 08, 2006 Print ISSN: 0171-8630; Online ISSN: 1616-1599 Copyright © 2006 Inter-Research.
trkB, a neural receptor protein-tyrosine kinase: evidence for a full-length and two truncated receptors. (1991)

We have screened an adult rat cerebellar cDNA library in search of novel protein tyrosine-kinase (PTK) cDNAs. A cDNA for a putative PTK, trkB, was cloned, and its sequence indicates that it is likely to be derived from a gene for a ligand-regulated receptor closely related to the human trk oncogene. Northern (RNA) analysis showed that the trkB gene is expressed predominantly in the brain and that trkB expresses multiple mRNAs, ranging from 0.7 to 9 kb. Hybridization of cerebral mRNAs with a variety of probes indicates that there are mRNAs encoding truncated trkB receptors. Two additional types of cDNA were isolated, and their sequences are predicted to encode two distinct C-terminally truncated receptors which have the complete extracellular region and transmembrane domain, but which differ in their short cytoplasmic tails.
Mutational analysis of the adeno-associated virus rep gene (1992)

The replication (rep) gene of the human parvovirus adeno-associated virus (AAV) is a pleiotropic effector of numerous viral functions and experts profound effects on cellular transformation. Of the four Rep proteins, the primarily nuclear Rep78 and Rep68 direct AAV DNA replication, trans activation of the capsid (cap) gene promoter, and inhibition of cellular proliferation mediated by various oncogenes. In an initial attempt to define functional domains in Rep78, we have constructed a comprehensive set of XhoI linker insertion and deletion mutations in the rep gene. Each of the mutant genes has been expressed in cell culture and assayed for the following functions: (i) nuclear localization, (ii) AAV DNA replication, (iii) trans activation of the AAV capsid gene transcription promoter, and (iv) suppression of cellular transformation mediated by the adenovirus E1a and an activated ras oncogene pair. Modest disruptions in the normal conformation of Rep78 inactivated its AAV DNA replication function and trans activation of the cap gene promoter. Linker insertion mutations in the amino-terminal one-third of the protein inactivated Rep78's ability to suppress oncogene-mediated cellular transformation. The transformation suppression domains are not limited to the amino-terminal regions, however, since deletions throughout the protein altered its suppression capabilities. A putative nuclear localization signal that is essential for each of the above functions was found in the Rep proteins. These results provide a preliminary screening of the functional domains in the AAV Rep proteins and pave the way for more subtle mutational analysis.
Scoring Genes for Relevance (2000)

Recent molecular level studies that compare different classes of disease conditions produce labeled gene expression data. We examine scoring methods that are useful in mining such gene expression data for genes that have biological relevance to the condition studied. Relevance information is useful in identifying genes driving the biological process, in selecting small subsets of genes with diagnostic potential, and in better understanding the condition studied and its relationship to known or hypothesized biochemical pathways. We present the scoring methods; describe a process for computing the corresponding p-values; and finally, present results from application to actual cancer gene expression data. These include applying classification techniques employing varying relevance based selected sets of genes.
MSiReader: An Open-Source Interface to View and Analyze High Resolving Power MS Imaging Files on Matlab Platform (2013)

During the past decade, the field of mass spectrometry imaging (MSI) has greatly evolved, to a point where it has now been fully integrated by most vendors as an optional or dedicated platform that can be purchased with their instruments. However, the technology is not mature and multiple research groups in both academia and industry are still very actively studying the fundamentals of imaging techniques, adapting the technology to new ionization sources, and developing new applications. As a result, there important varieties of data file formats used to store mass spectrometry imaging data and, concurrent to the development of MSi, collaborative efforts have been undertaken to introduce common imaging data file formats. However, few free software packages to read and analyze files of these different formats are readily available. We introduce here MSiReader, a free open source application to read and analyze high resolution MSI data from the most common MSi data formats. The application is built on the Matlab platform (Mathworks, Natick, MA, USA) and includes a large selection of data analysis tools and features. People who are unfamiliar with the Matlab language will have little difficult navigating the user-friendly interface, and users with Matlab programming experience can adapt and customize MSiReader for their own needs.
RENAL 1,25‐DIHYDROXYVITAMIN D, PHOSPHATURIC, AND CYCLIC‐AMP RESPONSES TO INTRAVENOUS SYNTHETIC HUMAN PARATHYROID HORMONE‐(1‐34) ADMINISTRATION IN NORMAL SUBJECTS (1984)

The exogenous administration of bovine parathyroid hormone or parathyroid extract has been used to differentiate states of parathyroid hormone resistance and parathyroid gland secretory failure, and in recent years to test renal 1,25-dihydroxyvitamin D (1,25-(OH)2-D) secretion. We evaluated the effect of synthetic human parathyroid hormone (hPTH-(1-34] administration on the renal 1,25-(OH)2-D, phosphaturic and cyclic-AMP responses in eleven normal young adults. The intravenous administration of 200 units of hPTH-(1-34) over 10 min produced a 1.3-5.4 fold increase (P less than 0.01) in renal phosphate clearance and a 19-75 fold increase (P less than 0.0001) in urinary cyclic-AMP excretion. Serum 1,25-(OH)2-D levels showed a small and insignificant change at 2.5 h and a significant (P less than 0.05) but small (21 +/- 24 pmol/l) increase at 7 h after the first injection. In eight subjects a second injection of hPTH-(1-34) was given at 7 h. In these individuals serum 1,25-(OH)2-D levels at 24 h were 40 +/- 14 pmol/l (44%) higher than baseline (P less than 0.01), but were variable over the 24 h period. The present study shows that hPTH-(1-34) produces renal phosphaturic and cyclic-AMP responses in normals similar to those produced by bovine PTH preparations. However, the serum 1,25-(OH)2-D response to one or two intravenous injections of hPTH-(1-34) is small, variable, and inconsistent and, therefore, will not provide a consistent way of stimulating renal 1,25-(OH)2-D secretion.
Tunable grating coupled surface-emitting tapered laser (1999)

We report on the design and fabrication of a wavelength-tunable grating coupled surface-emitting laser. A curved second-order grating is used at the end of a tapered gain section to provide feedback as well as collimated surface out-coupling. Wavelength tuning is achieved by current injection into the grating section through a film of indium-tin oxide deposited on the grating surface. Low divergence single-frequency surface emission with /spl sim/1-nm wavelength tuning is demonstrated.
Cryptographic Message Syntax (CMS) (2004)

CMS).This syntax is used to digitally sign, digest, authenticate, or encrypt arbitrary message content.
Central role of α7 nicotinic receptor in differentiation of the stratified squamous epithelium (2002)

Several ganglionic nicotinic acetylcholine receptor (nAChR) types are abundantly expressed in nonneuronal locations, but their functions remain unknown. We found that keratinocyte alpha7 nAChR controls homeostasis and terminal differentiation of epidermal keratinocytes required for formation of the skin barrier. The effects of functional inactivation of alpha7 nAChR on keratinocyte cell cycle progression, differentiation, and apoptosis were studied in cell monolayers treated with alpha-bungarotoxin or antisense oligonucleotides and in the skin of Acra7 homozygous mice lacking alpha7 nAChR channels. Elimination of the alpha7 signaling pathway blocked nicotine-induced influx of 45Ca2+ and also inhibited terminal differentiation of these cells at the transcriptional and/or translational level. On the other hand, inhibition of the alpha7 nAChR pathway favored cell cycle progression. In the epidermis of alpha7-/- mice, the abnormalities in keratinocyte gene expression were associated with phenotypic changes characteristic of delayed epidermal turnover. The lack of alpha7 was associated with up-regulated expression of the alpha3 containing nAChR channels that lack alpha5 subunit, and both homomeric alpha9- and heteromeric alpha9alpha10-made nAChRs. Thus, this study demonstrates that ACh signaling through alpha7 nAChR channels controls late stages of keratinocyte development in the epidermis by regulating expression of the cell cycle progression, apoptosis, and terminal differentiation genes and that these effects are mediated, at least in part, by alterations in transmembrane Ca2+ influx.
THE EARLY STAGES OF GASTRIDIOTA ADOXIMA (TURNER) (LEPIDOPTERA: BOMBYCOIDEA) AND ITS FAMILY PLACEMENT (1991)

Abstract The monotypic genus Gastridiota Turner is transferred from the Eupterotidae to the Bombycidae. The immature stages of G. adoxima (Turner), here described and figured, provide characters in addition to those of wing venation, which support the transfer. The characters include the presence in the final instar larva of minute scattered secondary setae, paired extensible filaments on some abdominal segments and a dorsal horn on abdominal segment 8. The food plant family, Moraceae, is shared with many other Bombycidae. The native species of Bombycidae in Australia are briefly discussed.
Cyclization Reactions of Dianions in Organic Synthesis (2004)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTCyclization Reactions of Dianions in Organic Synthesis†Peter Langer and Walter FreibergView Author Information Institut für Chemie und Biochemie der Ernst-Moritz-Arndt Universität Greifswald, Soldmannstrasse 16, 17487 Greifswald, Germany Cite this: Chem. Rev. 2004, 104, 9, 4125–4150Publication Date (Web):August 21, 2004Publication History Received17 February 2004Published online21 August 2004Published inissue 1 September 2004https://pubs.acs.org/doi/10.1021/cr010203lhttps://doi.org/10.1021/cr010203lresearch-articleACS PublicationsCopyright © 2004 American Chemical SocietyRequest reuse permissionsArticle Views2898Altmetric-Citations133LEARN 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:Anions,Cyclization,Ethyl groups,Hydrocarbons,Ketones Get e-Alerts
Metal Bisporphyrinate Double-Decker Complexes as Redox-Responsive Rotating Modules. Studies on Ligand Rotation Activities of the Reduced and Oxidized Forms Using Chirality as a Probe (2000)

Reduction of a chiral cerium bisporphyrinate double-decker complex Ce(MOFPP)2 (MOFPP = 5,15-bis(3,5-dimethoxyphenyl)- 10,20-bis(pentafluorophenyl)porphyrin dianion) with sodium anthracenide in dioxane at 20 °C resulted in acceleration of the porphyrin ligand rotation (= racemization) by a factor of more than 300. Photoreduction of Ce(MOFPP)2 in dioxane also resulted in enhancing the ligand rotation activity of the complex. On the other hand, oxidation of a chiral zirconium complex Zr(DTP)2 (DTP = 5,15-ditolylporphyrin dianion) with phenoxathiinylium hexachloroantimonate (Phen•+SbCl6-) or FeCl3 resulted in deceleration of the acid-induced racemization in tetrahydrofuran (THF), where monocationic and dicationic forms of the complex racemized 21 and 99 times more slowly than the neutral complex, respectively.
Microwave Bandwidth Active Transversal Filter Concept With MESFETs (1971)

An active transversal filter concept for microwave frequencies is proposed. Silicon metal semiconductor field-effect transistors (MESFETs) with high impedances are used as active coupling elements. A hardware implementation yields a minimum interval between equalized pulses of 1.5 ns. Simulations with improved MESFETs predict equalization for smaller pulse intervals than 400 ps.
Navigating the New World of Private Equity-A Conference Summary (2008)

The Federal Reserve System's Private Equity Merchant Banking Knowledge Center, formed at the Chicago Fed in 2000 shortly after the passage of the Gramm?Leach?Bliley Act, sponsors an annual conference on new industry developments. This article summarizes the 2008 conference held on July 9 - 10.