cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Aspirin Induces Platelet Receptor Shedding via ADAM17 (TACE)
Creators: name: Sunnarborg, Susan
name: Bergmeier, Wolfgang
name: Offermanns, Stefan
name: Aktas, Barsom
name: Pozgajova, Miroslava
name: Wagner, Denisa D.
name: Lee, David
name: Nieswandt, Bernhard
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: Aspirin is effective in the therapy of cardiovascular diseases, because it causes acetylation of cyclooxygenase 1 (COX-1) leading to irreversible inhibition of platelets. Additional mechanisms can be suspected, because patients treated with other platelet COX inhibitors such as indomethacin do not display an increased bleeding tendency as observed for aspirin-treated patients. Recently, aspirin and other anti-inflammatory drugs were shown to induce shedding of L-selectin in neutrophils in a metalloproteinase-dependent manner. Therefore, we investigated the effects of aspirin on the von Willebrand Factor receptor complex glycoprotein (GP) Ib-V-IX, whose lack or dysfunction causes bleeding in patients. As quantified by fluorescence-activated cell sorting analysis in whole blood, aspirin, but not its metabolite salicylic acid, induced dose-dependent shedding of human and murine GPIbalpha and GPV from the platelet surface, whereas other glycoproteins remained unaffected by this treatment. Biotinylated fragments of GPV were detected by immunoprecipitation in the supernatant of washed mouse platelets, and the expression level of GPIbalpha was decreased in these platelets as measured by Western blot analysis. Although shedding occurred normally in COX-1-deficient murine platelets, shedding was completely blocked by a broad-range metalloproteinase inhibitor and, more importantly, in mouse platelets expressing an inactive form of ADAM17. Shed fragments of GPIbalpha and GPV were elevated in the plasma of aspirin-injected mice compared with animals injected with control buffer. These data demonstrate that aspirin at high concentrations induces shedding of GPIbalpha and GPV by an ADAM17-dependent mechanism and that this process can occur in vivo.
Another deep dimming of the classical T Tauri star RW Aur A
Creators: name: Petrov, P. P.
name: Gahm, G. F.
name: Djupvik, A. A.
name: Babina, E. V.
name: Artemenko, S. A.
name: Grankin, K. N.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: Context. RW Aur A is a classical T Tauri star (CTTS) with an unusually rich emission line spectrum. In 2014 the star faded by ~ 3 magnitudes in the V band and went into a long-lasting minimum. In 2010 the star suffered from a similar fading, although less deep. These events in RW Aur A are very unusual among the CTTS, and have been attributed to occultations by passing dust clouds. Aims. We want to find out if any spectral changes took place after the last fading of RW Aur A with the intention to gather more information on the occulting body and the cause of the phenomenon. Methods. We collected spectra of the two components of RW Aur. Photometry was made before and during the minimum. Results. The overall spectral signatures reflecting emission from accretion flows from disk to star did not change after the fading. However, blue-shifted absorption components related to the stellar wind had increased in strength in certain resonance lines, and the profiles and strengths, but not fluxes, of forbidden lines had become drastically different. Conclusions. The extinction through the obscuring cloud is grey indicating the presence of large dust grains. At the same time, there are no traces of related absorbing gas. The cloud occults the star and the interior part of the stellar wind, but not the wind/jet further out. The dimming in 2014 was not accompanied by changes in the accretion flows at the stellar surface. There is evidence that the structure and velocity pattern of the stellar wind did change significantly. The dimmings could be related to passing condensations in a tidally disrupted disk, as proposed earlier, but we also speculate that large dust grains have been stirred up from the inclined disk into the line-of-sight through the interaction with an enhanced wind.
description: 5 pages, 5 figures, Accepted for publication in A&A
Few-fermion systems in one dimension: Ground- and excited-state energies and contacts
Creators: name: Rammelmüller, L.
name: Porter, W. J.
name: Loheac, A. C.
name: Drut, J. E.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: High Energy Physics - Lattice (hep-lat)
subject: FOS: Physical sciences

description: Using the lattice Monte Carlo method, we compute the energy and Tan's contact in the ground state as well as the first excited state of few- to many-fermion systems in a one-dimensional periodic box. We focus on unpolarized systems of N=4,6,...,12 particles, with a zero-range interaction, and a wide range of attractive couplings. In addition, we provide extrapolations to the infinite-volume and thermodynamic limits.
description: 8 pages, 12 figures; published version
A Comparative Analysis of Juveniles' Food Consumption Trends in Korea, China and Japan
Creators: name: Lee, Kyeiim
name: Lee, Kyeiim
Publisher: name: Unknown
Year: 2009
Subjects: subject: Food Consumption/Nutrition/Food Safety
subject: juveniles in Korea, China and Japan
subject: food consumption trend
subject: Multiple-Regression Analysis

description: This study aims to provide implications for food consumption outlook by comparing and analyzing the food consumption of juveniles in Korea, China and Japan. The important results that were found from this study are as follows: The food consumption trend of Korean juveniles showed that rice consumption fell the fastest while the consumption of bread, cookies and pork, as well as eating outs, grew fast unlike any other age groups. In Japan, however, the decreasing consumption of rice has been slowing down since 2000. During this period, the consumption of pork has changed its course to an upward trend while the consumption of beef, fruits and vegetables has been falling. In the case of China, no significant changes were seen in the food consumption of juveniles in 2007 compared to 2002, and their food consumption was relatively low compared to other age groups.
Association of NASP with HSP90 in Mouse Spermatogenic Cells: STIMULATION OF ATPase ACTIVITY AND TRANSPORT OF LINKER HISTONES INTO NUCLEI
Creators: name: Widgren, Esther E.
name: Richardson, Richard T.
name: O'Rand, Michael G.
name: Alekseev, Oleg M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: NASP (nuclear autoantigenic sperm protein) is a linker histone-binding protein found in all dividing cells that is regulated by the cell cycle (Richardson, R. T., Batova, I. N., Widgren, E. E., Zheng, L. X., Whitfield, M., Marzluff, W. F., and O'Rand, M. G. (2000) J. Biol. Chem. 275, 30378-30386), and in the nucleus linker histones not bound to DNA are bound to NASP (Alekseev, O. M., Bencic, D. C., Richardson R. T., Widgren E. E., and O'Rand, M. G. (2003) J. Biol. Chem. 278, 8846-8852). In mouse spermatogenic cells tNASP binds the testis-specific linker histone H1t. Utilizing a cross-linker, 3,3'-dithiobissulfosuccinimidyl propionate, and mass spectrometry, we have identified HSP90 as a testis/embryo form of NASP (tNASP)-binding partner. In vitro assays demonstrate that the association of tNASP with HSP90 stimulated the ATPase activity of HSP90 and increased the binding of H1t to tNASP. HSP90 and tNASP are present in both nuclear and cytoplasmic fractions of mouse spermatogenic cells; however, HSP90 bound to NASP only in the cytoplasm. In vitro nuclear import assays on permeabilized HeLa cells demonstrate that tNASP, in the absence of any other cytoplasmic factors, transports linker histones into the nucleus in an energy and nuclear localization signal-dependent manner. Consequently we hypothesize that in the cytoplasm linker histones are bound to a complex containing NASP and HSP90 whose ATPase activity is stimulated by binding NASP. NASP-H1 is subsequently released from the complex and translocates to the nucleus where the H1 is released for binding to the DNA.
CATERPILLER 16.2 (CLR16.2), a Novel NBD/LRR Family Member That Negatively Regulates T Cell Function
Creators: name: Williams, Kristi L.
name: O'Connor Jr., William
name: Ting, Jenny P.Y.
name: Davis, Beckley K.
name: Conti, Brian J.
name: Zhang, Jinghua
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: The newly discovered mammalian CATERPILLER (NOD, NALP, PAN) family of proteins share similarities with the NBD-LRR superfamily of plant disease resistance (R) proteins and are predicted to mediate important immune regulatory function. This report describes the first cloning and characterization of a novel CATERPILLER gene, CLR16.2 that is located on human chromosome 16. The protein encoded by this gene has a typical NBD-LRR configuration. Analysis of CLR16.2 suggests the highest expression among T lymphocytes. Cellular localization studies of CLR16.2 revealed that it is a cytoplasmic protein. Querying microarray studies in the public data base showed that CLR16.2 was significantly (>90%) down-regulated 6 h after anti-CD3 and anti-CD28 stimulation of primary T lymphocytes. Its reduction upon T cell stimulation is consistent with a potential negative regulatory role. Indeed CLR16.2 decreased NF-kappaB, NFAT, and AP-1 induction of reporter gene constructs in response to T cell activation by anti-CD3 and anti-CD28 antibodies or PMA and ionomycin. Following T cell stimulation, the presence of CLR16.2 reduced the levels of the endogenous transcripts for the IL-2 and CD25 proteins that are central in maintaining T cell activation and preventing T cell anergy. This reduction was accompanied by a delay of IkappaBalpha degradation. We propose that CLR16.2 serves to attenuate T cell activation via TCR and co-stimulatory molecules, and its reduction during T cell stimulation allows the ensuing cellular activation.
Reflection high-energy electron diffraction and scanning tunneling microscopy study of InP(001) surface reconstructions
Creators: name: LaBella, V. P.
name: Ding, Z.
name: Bullock, D. W.
name: Emery, C.
name: Thibado, P. M.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: The reconstructions of the InP(001) surface prepared by molecular beam epitaxy have been studied with in situ reflection high-energy electron diffraction (RHEED) and scanning tunneling microscopy (STM). The growth chamber contains a highly accurate temperature measurement system and uses a solid-source, cracked phosphorus, valved effusion cell. Five InP(001) reconstructions are observed with RHEED by analyzing patterns in three principal directions. Under a fixed P2 flux, decreasing the substrate temperature gives the following reconstructions: c(2x8), (2x4), (2x1), (2x2), and c(4x4). In situ STM images reveal that only two of these reconstructions yields long-range periodicity in real space. InP(001) does not form the metal rich (4x2) reconstruction, which is surprising because the (4x2) reconstruction has been coined the universal surface reconstruction since all III-V(001) surfaces were thought to favor its formation.
description: 9 pages, 4 figures
Chronic Airway Infection/Inflammation Induces a Ca 2+ i -dependent Hyperinflammatory Response in Human Cystic Fibrosis Airway Epithelia
Creators: name: O'Neal, Wanda
name: Jones, Lisa
name: Schwab, Ute
name: Paradiso, Anthony M.
name: Perez-Vilar, Juan
name: Ribeiro, Carla M.Pedrosa
name: Boucher, Richard C.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: Hyperinflammatory responses to infection have been postulated as a component of cystic fibrosis (CF) lung disease. Studies have linked intracellular calcium (Ca(2+)(i)) mobilization with inflammatory responses in several systems. We have reported that the pro-inflammatory mediator bradykinin (BK) promotes larger Ca(2+)(i) signals in CF compared with normal bronchial epithelia, a response that reflects endoplasmic reticulum (ER)/Ca(2+) store expansion induced by chronic luminal airway infection/inflammation. The present study investigated whether CF airway epithelia were hyperinflammatory and, if so, whether the hyperinflammatory CF phenotype was linked to larger Ca(2+) stores in the ER. We found that DeltaF508 CF bronchial epithelia were hyperinflammatory as defined by an increased basal and mucosal BK-induced interleukin (IL)-8 secretion. However, the CF hyperinflammation expressed in short-term (6-11-day-old) primary cultures of DeltaF508 bronchial epithelia was lost in long-term (30-40-day-old) primary cultures of DeltaF508 bronchial epithelia, indicating this response was independent of mutant cystic fibrosis transmembrane conductance regulator. Exposure of 30-40-day-old cultures of normal airway epithelia to supernatant from mucopurulent material (SMM) from CF airways reproduced the increased basal and mucosal BK-stimulated IL-8 secretion of short-term CF cultures. The BK-triggered increased IL-8 secretion in SMM-treated cultures was mediated by an increased Ca(2+)(i) mobilization consequent to an ER expansion associated with increases in protein synthesis (total, cytokines, and antimicrobial factors). The increased ER-dependent, Ca(2+)(i)-mediated hyperinflammatory epithelial response may represent a general beneficial airway epithelial adaptation to transient luminal infection. However, in CF airways, the Ca(2+)(i)-mediated hyperinflammation may be ineffective in promoting the eradication of infection in thickened mucus and, consequently, may have adverse effects in the lung.
Imperial Pandemicide
Creators: name: Van Belle, Douglas
name: Jamieson, Thomas
Publisher: name: Open Access Te Herenga Waka-Victoria University of Wellington
Year: 2023
Subjects: classificationCode: 4408
subject: Political science
subject: FOS: Political science
classificationCode: 44
subject: Human society

description: Objective: To provide a quick, in the moment analysis of the social and political aspects of the COVID-19 pandemic to preserve the possibly ephemeral aspects that might be overlooked in future historical studies. Methods: Qualitative and a statistical analyses of real time information. Results: The clustering of former imperial powers as states suffering extreme initial impacts, combined with a brief qualitative commentary on the domestic politics related to the pandemic response, suggests that colonial imperialism has lingering domestic political effects. Conclusion: The domestic political power bases that enabled colonial imperialism may be a significant and previously unrecognized factor in politics both in the context of disaster response and more broadly.
Voigt-wave propagation in active materials
Creators: name: Mackay, Tom G.
name: Lakhtakia, Akhlesh
Publisher: name: arXiv
Year: 2015
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: If a dissipative anisotropic dielectric material, characterized by the permittivity matrix $\underline{\underlineε}$, supports Voigt-wave propagation, then so too does the analogous active material characterized by the permittivity matrix $\underline{\underline{\tildeε}}$, where $\underline{\underline{\tildeε}}$ is the hermitian conjugate of $\underline{\underlineε}$. Consequently, a dissipative material that supports Voigt-wave propagation can give rise to a material that supports the propagation of Voigt waves with attendant linear gain in amplitude with propagation distance, by infiltration with an active dye.
Figure S1 from Expansion in geographical and morphological space drives continued lineage diversification in a global passerine radiation.
Creators: name: Kennedy, Jonathan D.
name: Borregaard, Michael K.
name: Marki, Petter Z.
name: Machac, Antonin
name: Fjeldså, Jon
name: Rahbek, Carsten
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology

description: Why diversification rates vary so extensively across the tree of life remains an important yet unresolved issue in biology. Two prominent and potentially independent factors proposed to explain these trends reflect the capacity of lineages to expand into new areas of (i) geographical or (ii) ecological space. Here, we present the first global assessment of how diversification rates vary as a consequence of geographical and ecological expansion, studying these trends among 15 speciose passerine families (together approximately 750 species) using phylogenetic path analysis. We find that relative slowdowns in diversification rates characterize families that have accumulated large numbers of co-occurring species (at the 1° scale) within restricted geographical areas. Conversely, more constant diversification through time is prevalent among families in which species show limited range overlap. Relative co-occurrence is itself also a strong predictor of ecological divergence (here approximated by morphological divergence among species); however, once the relationship between co-occurrence and diversification rates have been accounted for, increased ecological divergence is an additional explanatory factor accounting for why some lineages continue to diversify towards the present. We conclude that opportunities for prolonged diversification are predominantly determined by continued geographical range expansion and to a lesser degree by ecological divergence among lineages.
Towards FAIRer EPR data – a toolset for fully reproducible data analysis
Creators: name: Schröder, Mirjam
name: Popp, Jara
name: Biskup, Till
Publisher: name: Zenodo
Year: 2022
Subjects: spectroscopy
data processing and analysis
FAIR data
reproducible science
reproducible research
good scientific practice
recipe-driven data analysis
electron paramagnetic resonance spectroscopy
EPR spectroscopy
magnetic resonance

description: As Newton famously stated, we’re all standing on the shoulders of giants: The progress of science rests on the published work of others. In the digital age, we are confronted with an exponential growth of available data. Hence, appropriate research data management is urgently needed and data need to be findable, accessible, interoperable, and reusable (FAIR), prompting initiatives such as the German NFDI. However, a necessary though often underrepresented prerequisite for FAIR data is a gapless record of their provenance. We therefore need tools that automatically record each step from the raw/primary data to their final shareable representation and take care of the respective metadata of each step starting with the data acquisition. Here, we present both, a general framework for the reproducible analysis of spectral data (ASpecD) as well as concrete packages for working with continuous-wave and time-resolved EPR data. Key features are an automatic and gapless record of each processing and analysis step as well as an intuitive yet powerful user interface requiring no programming skills. Additional packages actively being developed demonstrate the potential of the underlying ASpecD framework, dealing with optical absorption and NMR data. Furthermore, the FitPy package allows for advanced fitting of models to spectroscopic data. Together, these tools fill a crucial gap. In context of a larger infrastructure for research data management – including an electronic lab notebook (ELN), wiki-based knowledge management and data stores providing unique IDs, i.e. a laboratory information and management system (LIMS) – they allow for actually thinking about FAIRer EPR
 (and other spectroscopic) data.
(1633) Francis Edwin Armstrong
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
(1634) Lucy Rosamund Wicksteed
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
(1630) Frances [Armstrong]
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
(1632) Richard Harold Armstrong
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
Crystal Structure of the Bovine Mitochondrial Elongation Factor Tu·Ts Complex
Creators: name: Navratil, Tomas
name: Jeppesen, Mads Gravers
name: Nyborg, Jens
name: Spremulli, Linda Lucy
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: The three-dimensional structure of the bovine mitochondrial elongation factor (EF)-Tu.Ts complex (EF-Tumt.Tsmt) has been determined to 2.2-A resolution using the multi-wavelength anomalous dispersion experimental method. This complex provides the first insight into the structure of EF-Tsmt. EF-Tsmt is similar to Escherichia coli and Thermus thermophilus EF-Ts in the amino-terminal domain. However, the structure of EF-Tsmt deviates considerably in the core domain with a five-stranded beta-sheet forming a portion of subdomain N of the core. In E. coli EF-Ts, this region is composed of a three-stranded sheet. The coiled-coil domain of the E. coli EF-Ts is largely eroded in EF-Tsmt, in which it consists of a large loop packed against subdomain C of the core. The conformation of bovine EF-Tumt in complex with EF-Tsmt is distinct from its conformation in the EF-Tumt.GDP complex. When domain III of bovine EF-Tumt.GDP is superimposed on domain III of EF-Tumt in the EF-Tumt.Tsmt complex, helix B from domain I is also almost superimposed. However, the rest of domain I is rotated relative to this helix toward domain II, which itself is rotated toward domain I relative to domain III. Extensive contacts are observed between the amino-terminal domain of EF-Tsmt and domain I of EF-Tumt. Furthermore, the conserved TDFV sequence of EF-Tsmt also contacts domain I with the side chain of Asp139 contacting helix B of EF-Tumt and inserting the side chain of Phe140 between helices B and C. The structure of the EF-Tumt.Tsmt complex provides new insights into the nucleotide exchange mechanism and provides a framework for explaining much of the mutational data obtained for this complex.
(1627) Henry Sheen Solly
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
Cytochrome b Mutations That Modify the Ubiquinol-binding Pocket of the Cytochrome bc 1 Complex and Confer Anti-malarial Drug Resistance in Saccharomyces cerevisiae
Creators: name: Meunier, Brigitte
name: Trumpower, Bernard L.
name: Merritt, Anne K.
name: Hill, Philip
name: Lange, Benjamin B.
name: Meshnick, Steven R.
name: Ha, Kevin H.
name: Kessl, Jacques J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: Atovaquone is a new anti-malarial agent that specifically targets the cytochrome bc1 complex and inhibits parasite respiration. A growing number of failures of this drug in the treatment of malaria have been genetically linked to point mutations in the mitochondrial cytochrome b gene. To better understand the molecular basis of atovaquone resistance in malaria, we introduced five of these mutations, including the most prevalent variant found in Plasmodium falciparum (Y268S), into the cytochrome b gene of the budding yeast Saccharomyces cerevisiae and thus obtained cytochrome bc1 complexes resistant to inhibition by atovaquone. By modeling the variations in cytochrome b structure and atovaquone binding with the mutated bc1 complexes, we obtained the first quantitative explanation for the molecular basis of atovaquone resistance in malaria parasites.
Desmosome Signaling: INHIBITION OF p38MAPK PREVENTS PEMPHIGUS VULGARIS IgG-INDUCED CYTOSKELETON REORGANIZATION
Creators: name: Enghild, Jan J.
name: Diaz, Luis A.
name: Berkowitz, Paula
name: Chua, Michael P.
name: Rubenstein, David S.
name: Liu, Zhi
name: Hu, Peiqi
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: In the human autoimmune blistering disease pemphigus vulgaris (PV) pathogenic antibodies bind the desmosomal cadherin desmoglein-3 (dsg3), causing epidermal cell-cell detachment (acantholysis). Pathogenic PV dsg3 autoantibodies were used to initiate desmosome signaling in human keratinocyte cell cultures. Heat shock protein 27 (HSP27) and p38MAPK were identified as proteins rapidly phosphorylated in response to PV IgG. Inhibition of p38MAPK activity prevented PV IgG-induced HSP27 phosphorylation, keratin filament retraction, and actin reorganization. These observations suggest that PV IgG binding to dsg3 activates desmosomal signal transduction cascades leading to (i) p38MAPK and HSP27 phosphorylation and (ii) cytoskeletal reorganization, supporting a mechanistic role for signaling in PV IgG-induced acantholysis. Targeting desmosome signaling via inhibition of p38MAPK and HSP27 phosphorylation may provide novel treatments for PV and other desmosome-associated blistering diseases.
(1629) George Armstrong
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
Differential Regulation of G Protein α Subunit Trafficking by Mono- and Polyubiquitination
Creators: name: Marotti Jr., Louis A.
name: Wang, Yuqi
name: Dohlman, Henrik G.
name: Lee, Michael J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: Previously we used mass spectrometry to show that the yeast G protein alpha subunit Gpa1 is ubiquitinated at Lys-165, located within a subdomain not present in other G alpha proteins (Marotti, L. A., Jr., Newitt, R., Wang, Y., Aebersold, R., and Dohlman, H. G. (2002) Biochemistry 41, 5067-5074). Here we describe the functional role of Gpa1 ubiquitination. We find that Gpa1 expression is elevated in mutants deficient in either proteasomal or vacuolar protease function. Vacuolar protease pep4 mutants accumulate monoubiquitinated Gpa1, and much of the protein is localized within the vacuolar compartment. In contrast, proteasome-defective rpt6/cim3 mutants accumulate polyubiquitinated Gpa1, and in this case the protein exhibits cytoplasmic localization. Cells that lack Ubp12 ubiquitin-processing protease activity accumulate both mono- and polyubiquitinated forms of Gpa1. In this case, Gpa1 accumulates in both the cytoplasm and vacuole. Finally, a Gpa1 mutant that lacks the ubiquitinated subdomain remains unmodified and is predominantly localized at the plasma membrane. These data reveal a strong relationship between the extent of ubiquitination and trafficking of the G protein alpha subunit to its site of degradation.
Figure S6m from Expansion in geographical and morphological space drives continued lineage diversification in a global passerine radiation
Creators: name: Kennedy, Jonathan D.
name: Borregaard, Michael K.
name: Marki, Petter Z.
name: Machac, Antonin
name: Fjeldså, Jon
name: Rahbek, Carsten
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology

description: Why diversification rates vary so extensively across the tree of life remains an important yet unresolved issue in biology. Two prominent and potentially independent factors proposed to explain these trends reflect the capacity of lineages to expand into new areas of (i) geographical or (ii) ecological space. Here, we present the first global assessment of how diversification rates vary as a consequence of geographical and ecological expansion, studying these trends among 15 speciose passerine families (together approximately 750 species) using phylogenetic path analysis. We find that relative slowdowns in diversification rates characterize families that have accumulated large numbers of co-occurring species (at the 1° scale) within restricted geographical areas. Conversely, more constant diversification through time is prevalent among families in which species show limited range overlap. Relative co-occurrence is itself also a strong predictor of ecological divergence (here approximated by morphological divergence among species); however, once the relationship between co-occurrence and diversification rates have been accounted for, increased ecological divergence is an additional explanatory factor accounting for why some lineages continue to diversify towards the present. We conclude that opportunities for prolonged diversification are predominantly determined by continued geographical range expansion and to a lesser degree by ecological divergence among lineages.
Appendix B from Expansion in geographical and morphological space drives continued lineage diversification in a global passerine radiation.
Creators: name: Kennedy, Jonathan D.
name: Borregaard, Michael K.
name: Marki, Petter Z.
name: Machac, Antonin
name: Fjeldså, Jon
name: Rahbek, Carsten
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology

description: Sensitivity analyses
Appendix A from Expansion in geographical and morphological space drives continued lineage diversification in a global passerine radiation.
Creators: name: Kennedy, Jonathan D.
name: Borregaard, Michael K.
name: Marki, Petter Z.
name: Machac, Antonin
name: Fjeldså, Jon
name: Rahbek, Carsten
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Evolutionary Biology
subject: FOS: Biological sciences
subject: Ecology

description: Details of morphological measurements
(1628) Richard Acland Armstrong
Creators: name: Professions, Victorian
Publisher: name: University of Oxford
Year: 2022
Subjects: subject: 220201 Business and Labour History
subject: FOS: Philosophy, ethics and religion
subject: History
subject: 140203 Economic History
subject: FOS: Economics and business

description: This three-year research project began in January 2014 and investigated whether, during the Victorian period, the professions formed a distinct self-sustaining social group with its own mores and values. The project looked at 16,000 individuals drawn from census data for Alnwick, Brighton, Bristol, Dundee, Greenock, Leeds, Merthyr Tydfil, Morpeth, and Winchester. The research project was funded by the UK Economic & Social Research Council and was based at the Universities of Oxford and Northumbria.
Differential Single-stranded DNA Binding Properties of the Paralogous SsbA and SsbB Proteins from Streptococcus pneumoniae
Creators: name: Bryant, Floyd R.
name: Grove, Diane E.
name: Willcox, Smaranda
name: Griffith, Jack D.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: The naturally transformable Gram-positive bacterium Streptococcus pneumoniae has two single-stranded DNA-binding (SSB) proteins, designated SsbA and SsbB. The SsbA protein is similar in size to the well characterized SSB protein from Escherichia coli (SsbEc). The SsbB protein, in contrast, is a smaller protein that is specifically induced during natural transformation and has no counterpart in E. coli. In this report, the single-stranded DNA (ssDNA) binding properties of the SsbA and SsbB proteins were examined and compared with those of the SsbEc protein. The ssDNA binding characteristics of the SsbA protein were similar to those of the SsbEc protein in every ssDNA binding assay used in this study. The SsbB protein differed from the SsbA and SsbEc proteins, however, both in its binding to short homopolymeric dT(n) oligomers (as judged by polyacrylamide gel-shift assays) and in its binding to the longer naturally occurring X and M13 ssDNAs (as judged by agarose gel-shift assays and electron microscopic analysis). The results indicate that an individual SsbB protein binds to ssDNA with an affinity that is similar or higher than that of the SsbA and SsbEc proteins. However, the manner in which multiple SsbB proteins assemble onto a ssDNA molecule differs from that observed with the SsbA and SsbEc proteins. These results represent the first analysis of paralogous SSB proteins from any bacterial species and provide a foundation for further investigations into the biological roles of these proteins.
Candidate hypervelocity stars of spectral type G and K revisited
Creators: name: Ziegerer, E.
name: Volkert, M.
name: Heber, U.
name: Irrgang, A.
name: Gaensicke, B. T.
name: Geier, S.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: FOS: Physical sciences

description: Hypervelocity stars (HVS) move so fast that they are unbound to the Galaxy. When they were first discovered in 2005, dynamical ejection from the supermassive black hole (SMBH) in the Galactic Centre (GC) was suggested as their origin. The two dozen HVSs known today are young massive B stars, mostly of 3-4 solar masses. Recently, 20 HVS candidates of low mass were discovered in the Segue G and K dwarf sample, but none of them originates from the GC. We embarked on a kinematic analysis of the Segue HVS candidate sample using the full 6D phase space information based on new proper motion measurements. Their orbital properties can then be derived by tracing back their trajectories in different mass models of our Galaxy. We present the results for 14 candidate HVSs, for which proper motion measurements were possible. Significantly lower proper motions than found in the previous study were derived. Considering three different Galactic mass models we find that all stars are bound to the Galaxy. We confirm that the stars do not originate from the GC. The distribution of their proper motions and radial velocities is consistent with predictions for runaway stars ejected from the Galactic disk by the binary supernova mechanism. However, their kinematics are also consistent with old disk membership. Moreover, most stars have rather low metallicities and strong $α$-element enrichment as typical for thick disk and halo stars, whereas the metallicity of the three most metal-rich stars could possibly indicate that they are runaway stars from the thin disk. One star shows halo kinematics.
description: A&A letter accepted
Direct Observation of Protein Folding, Aggregation, and a Prion-like Conformational Conversion
Creators: name: Ding, Feng
name: LaRocque, Joshua J.
name: Dokholyan, Nikolay V.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: Protein conformational transition from alpha-helices to beta-sheets precedes aggregation of proteins implicated in many diseases, including Alzheimer and prion diseases. Direct characterization of such transitions is often hindered by the complicated nature of the interaction network among amino acids. A recently engineered small protein-like peptide with a simple amino acid composition features a temperature-driven alpha-helix to beta-sheet conformational change. Here we studied the conformational transition of this peptide by molecular dynamics simulations. We observed a critical temperature, below which the peptide folds into an alpha-helical coiled-coil state and above which the peptide misfolds into beta-rich structures with a high propensity to aggregate. The structures adopted by this peptide during low temperature simulations have a backbone root mean square deviation less than 2 A from the crystal structure. At high temperatures, this peptide adopts an amyloid-like structure, which is mainly composed of coiled anti-parallel beta-sheets with the cross-beta-signature of amyloid fibrils. Most strikingly, we observed conformational conversions in which an alpha-helix is converted into a beta-strand by proximate stable beta-sheets with exposed hydrophobic surfaces and unsaturated hydrogen bonds. Our study suggested a possible generic molecular mechanism of the template-mediated aggregation process, originally proposed by Prusiner (Prusiner, S. B. (1998) Proc. Natl. Acad. Sci. U. S. A. 95, 13363-13383) to account for prion infectivity.
Heparin-binding Epidermal Growth Factor-like Growth Factor Links Hepatocyte Priming with Cell Cycle Progression during Liver Regeneration
Creators: name: Mitchell, Claudia
name: Campbell, Jean S.
name: Fausto, Nelson
name: Fox, Richard
name: Nivison, Mary
name: Jackson, Leslie F.
name: Lee, David C.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: The mechanisms that regulate the transition between the initial priming phase and DNA replication in liver regeneration are poorly understood. To study this transition, we compared events occurring after standard two-thirds partial hepatectomy, which elicits full regeneration, with response to a reduced hepatectomy, one-third partial hepatectomy (1/3PH), which leads to little DNA replication. Although the initial response to partial hepatectomy at the priming phase appeared to be similar between the two procedures, cell cycle progression was significantly blunted in 1/3PH mice. Among the main defects observed in 1/3PH mice were an almost complete deficiency in retinoblastoma phosphorylation and the lack of increase in kinase activity associated with cyclin E. We report that, in two-thirds partial hepatectomy mice, the expression of heparin-binding epidermal growth factor-like growth factor (HB-EGF) preceded the start of DNA replication and was not detectable in 1/3PH animals. Injection of HB-EGF into 1/3PH mice resulted in a >15-fold increase in DNA replication. Moreover, we show that hepatocyte DNA replication was delayed in HB-EGF knock-out mice. In summary, we show that HB-EGF is a key factor for hepatocyte progression through G(1)/S transition during liver regeneration.
Oscillation and collective conveyor of water-in-oil droplets by microfluidic bolus flow
Creators: name: Ohmura, Takuya
name: Ichikawa, Masatoshi
name: Kamei, Ken-ichiro
name: Maeda, Yusuke T.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Fluid Dynamics (physics.flu-dyn)
subject: Pattern Formation and Solitons (nlin.PS)
subject: Biological Physics (physics.bio-ph)
subject: FOS: Physical sciences

description: Microfluidic techniques have been extensively developed to realize micro-total analysis systems in a small chip. For microanalysis, electro-magnetic forces have generally been utilized for the trapping of objects, but hydrodynamics has been little explored despite its relevance to pattern formation. Here, we report that water-in-oil (W/O) droplets can be transported in the grid of an array of other large W/O droplets. As each droplet approaches an interspace of the large droplet array, while exhibiting persistent back-and-forth motion, it is conveyed at a velocity equal to the droplet array. We confirm the appearance of closed streamlines in a numerical simulation, suggesting that a vortex-like stream is involved in trapping the droplet. Furthermore, more than one droplet is also conveyed as an ordered cluster with dynamic reposition.
description: 11 pages, 5 figures
Identification of the Ankyrin Repeat Proteins ANKRA and RFXANK as Novel Partners of Class IIa Histone Deacetylases
Creators: name: Zika, Eleni
name: Grégoirei, Serge
name: Wright, Kenneth L.
name: Yang, Xiang Jiao
name: Li, Hongwei
name: Xiao, Lin
name: Li, Cathy S.
name: Wangi, Audrey H.
name: Ting, Jenny P.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: Eighteen human histone deacetylases (HDACs) have been identified, and according to their sequence similarity to yeast homologs, these enzymes are grouped into distinct classes. Within class II, HDAC4, HDAC5, HDAC7, and HDAC9 share similar domain organization both within the N-terminal extension and the C-terminal catalytic domain, thus forming a subclass known as class IIa. These HDACs function as signal-responsive transcriptional corepressors. To gain further insight into their function and regulation, we utilized an N-terminal fragment of HDAC4 as bait in yeast two-hybrid screens, which uncovered myocyte enhancer factor 2C, 14-3-3zeta, and ankyrin repeat family A protein (ANKRA). ANKRA is a poorly characterized protein with an ankyrin repeat domain similar to RFXANK, a subunit of the trimeric transcription factor RFX. Mutations on genes of the RFX subunits and the coactivator CIITA are responsible for the bare lymphocyte syndrome, an immunodeficiency disorder attributed to the lack of major histocompatibility complex class II (MHCII) antigens. Through its ankyrin repeat domain, RFXANK interacted with HDAC4. Two RFXANK-binding sites were found on HDAC4 with one located within residues 118-279 and another within residues 448-666. Interestingly, this deacetylase also interacted with CIITA. Consistent with the physical interaction with RFXANK and CIITA, HDAC4 and homologs repressed MHCII expression. These results identify ANKRA, RFXANK, and CIITA as novel targets of class IIa HDACs and suggest that these deacetylases play a role in regulating MHCII expression.
In Situ Photoactivation of a Caged Phosphotyrosine Peptide Derived from Focal Adhesion Kinase Temporarily Halts Lamellar Extension of Single Migrating Tumor Cells
Creators: name: Humphrey, David
name: Imperiali, Barbara
name: Rajfur, Zenon
name: Schaller, Michael D.
name: Scheswohl, Danielle
name: Jacobson, Ken
name: Vazquez, M. Eugenio
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: Focal adhesion kinase (FAK), a non-receptor tyrosine kinase, mediates integrin-based cell signaling by transferring signals regulating cell migration, adhesion, and survival from the extracellular matrix to the cytoplasm. Following autophosphorylation at tyrosine 397, FAK binds the Src homology 2 domains of Src and phosphoinositide 3-kinase, among several other possible binding partners. To further investigate the role of phosphorylated FAK in cell migration in situ, peptides comprising residues 391-406 of human FAK with caged phosphotyrosine 397 were synthesized. Although the caged phosphopeptides were stable to phosphatase activity, the free phosphopeptides showed a half-life of approximately 10-15 min in cell lysates. Migrating NBT-II cells (a rat bladder tumor cell line) were microinjected with the caged FAK peptide and locally photoactivated using a focused laser beam. The photoactivation of caged FAK peptide in 8-microm diameter spots over the cell body led to the temporary arrest of the leading edge migration within approximately 1 min of irradiation. In contrast, cell body migration was not inhibited. Microinjection of a non-caged phosphorylated tyrosine 397 FAK peptide into migrating NBT-II cells also led to lamellar arrest; however, this approach lacks the temporal control afforded by the caged phosphopeptides. Photoactivation of related phosphotyrosine peptides with altered sequences did not result in transient lamellar arrest. We hypothesize that the phosphorylated FAK peptide competes with the endogenous FAK for binding to FAK effectors including, but not limited to, Src and phosphoinositide 3-kinase, causing spatiotemporal misregulation and subsequent lamellar arrest.
Inositol Diphosphate Signaling Regulates Telomere Length
Creators: name: York, John D.
name: Armbruster, Blaine N.
name: Greenwell, Patricia
name: York, Sally J.
name: Petes, Thomas D.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: Activation of phospholipase C-dependent inositol polyphosphate signaling pathways generates distinct messengers derived from inositol 1,4,5-trisphosphate that control gene expression and mRNA export. Here we report the regulation of telomere length by production of a diphosphorylinositol tetrakisphosphate, PP-IP4, synthesized by the KCS1 gene product. Loss of PP-IP4 production results in lengthening of telomeres, whereas overproduction leads to their shortening. This effect requires the presence of Tel1, the yeast homologue of ATM, the protein mutated in the human disease ataxia telangiectasia. Our data provide in vivo evidence of a regulatory link between inositol polyphosphate signaling and the checkpoint kinase family and describe a third nuclear process modulated by phospholipase C activation.