cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Tumor Necrosis Factor (TNF) α Increases Collagen Accumulation and Proliferation in Intestinal Myofibroblasts via TNF Receptor 2
Creators: name: Theiss, Arianne L.
name: Lund, P. Kay
name: Simmons, James G.
name: Jobin, Christian
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: Intestinal fibrosis is an incurable complication of Crohn's disease involving increased numbers of collagen-producing myofibroblasts. Tumor necrosis factor (TNF) alpha has defined proinflammatory roles in Crohn's disease but its role in fibrosis is unclear. We tested the hypothesis that TNFalpha increases collagen accumulation and proliferation in intestinal myofibroblasts and has additive effects in combination with insulin-like growth factor (IGF) I. The mechanisms, TNF receptor isoform, and downstream signaling pathways were examined. Intestinal myofibroblasts from wild-type (WT) mice or mice homozygous for disruption of genes encoding TNFR1 (TNFR1-/-), TNFR2 (TNFR2-/-), or both (TNFR1/2-/-), were treated with TNFalpha, IGF-I, or both. In WT cells, TNFalpha and IGF-I stimulated type I collagen accumulation and DNA synthesis in an additive manner. IGF-I, but not TNFalpha, stimulated type I collagen gene activation. TNFalpha, but not IGF-I, induced tissue inhibitor of metalloproteinase-1 (TIMP-1) expression and reduced matrix metalloproteinases-2 activity and collagen degradation. TNFalpha also activated ERK1/2. These responses to TNFalpha were absent in TNFR2-/- and TNFR1/2-/- myofibroblasts, whereas TNFR1-/- cells showed similar responses to WT. Inhibition of ERK1/2 diminished TNFalpha induced DNA synthesis in WT and TNFR1-/- cells. Differences in TNFalpha-induced STAT3/DNA binding activity and not NFkappaB and AP-1 transcriptional activation correlated with impaired collagen accumulation/TIMP-1 induction in TNFR2(-/-) cells. Constitutively active STAT3 rescued TIMP-1 expression in TNFR2-/- cells. We conclude that TNFalpha and IGF-I may additively contribute to fibrosis during intestinal inflammation. TNFR2 is a primary mediator of fibrogenic actions of TNFalpha acting through ERK1/2 to stimulate proliferation and through STAT3 to stimulate TIMP-1 and inhibit collagen degradation.
(1611) Charles 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.
Figure S6d 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.
Vinculin Controls PTEN Protein Level by Maintaining the Interaction of the Adherens Junction Protein β-Catenin with the Scaffolding Protein MAGI-2
Creators: name: Nalbant, Perihan
name: Adamson, Eileen D.
name: Hahn, Klaus M.
name: Subauste, M. Cecilia
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: PTEN is a frequently mutated tumor suppressor in malignancies. Interestingly, some malignancies exhibit undetectable PTEN protein without mutations or loss of PTEN mRNA. The cause(s) for this reduction in PTEN is unknown. Cancer cells frequently exhibit loss of cadherin, beta-catenin, alpha-catenin and/or vinculin, key elements of adherens junctions. Here we show that F9 vinculin-null (vin(-/-)) cells lack PTEN protein despite normal PTEN mRNA levels. Their PTEN protein expression was restored by transfection with vinculin or by inhibition of PTEN degradation. F9 vin(-/-) cells express PTEN protein upon transfection with a vinculin fragment (amino acids 243-1066) that is capable of interacting with alpha-catenin but unable to target into focal adhesions. On the other hand, disruption of adherens junctions with an E-cadherin blocking antibody reduced PTEN protein to undetectable levels in wild-type F9 cells. PTEN protein levels were restored in F9 vin(-/-) cells upon transfection with an E-cadherin-alpha-catenin fusion protein, which targets into adherens junctions and interacts with beta-catenin in F9 vin(-/-) cells. beta-Catenin is known to interact with MAGI-2. MAGI-2 interaction with PTEN in the cell membrane is known to prevent PTEN protein degradation. Thus, MAGI-2 overexpression in F9 vin(-/-) cells restored PTEN protein levels. Moreover, expression of vinculin mutants that reinstated the disrupted interactions of beta-catenin with MAGI-2 in F9 vin(-/-) cells also restored PTEN protein levels. These studies indicate that PTEN protein levels are dependent on the maintenance of beta-catenin-MAGI-2 interaction, in which vinculin plays a critical role.
Self-organized anomalous aggregation of particles performing nonlinear and non-Markovian random walk
Creators: name: Fedotov, Sergei
name: Korabel, Nickolay
Publisher: name: arXiv
Year: 2015
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We present a nonlinear and non-Markovian random walk model for stochastic movement and the spatial aggregation of living organisms that have the ability to sense population density. We take into account social crowding effects for which the dispersal rate is a decreasing function of the population density and residence time. We perform stochastic simulations of random walk and discover the phenomenon of self-organized anomaly (SOA) which leads to a collapse of stationary aggregation pattern. This anomalous regime is self-organized and arises without the need for a heavy tailed waiting time distribution from the inception. Conditions have been found under which the nonlinear random walk evolves into anomalous state when all particles aggregate inside a tiny domain (anomalous aggregation). We obtain power-law stationary density-dependent survival function and define the critical condition for SOA as the divergence of mean residence time. The role of the initial conditions in different SOA scenarios is discussed. We observe phenomenon of transient anomalous bi-modal aggregation.
description: 7 pages, 5 figures
Figure S6c 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.
A Novel Mechanism of Tissue Inhibitor of Metalloproteinases-1 Activation by Interleukin-1 in Primary Human Astrocytes
Creators: name: Wilczynska, Katarzyna M.
name: Griswold-Prenner, Irene
name: Wright, Sarah
name: Kasza, Aneta
name: Bugno, Marcin
name: Gopalan, Sunita M.
name: Konik, Barbara S.
name: Bryan, Lauren
name: Kordula, Tomasz
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: Reactive astrogliosis is the gliotic response to brain injury with activated astrocytes and microglia being the major effector cells. These cells secrete inflammatory cytokines, proteinases, and proteinase inhibitors that influence extracellular matrix (ECM) remodeling. In astrocytes, the expression of tissue inhibitor of metalloproteinases-1 (TIMP-1) is up-regulated by interleukin-1 (IL-1), which is a major neuroinflammatory cytokine. We report that IL-1 activates TIMP-1 expression via both the IKK/NF-kappaB and MEK3/6/p38/ATF-2 pathways in astrocytes. The activation of the TIMP-1 gene can be blocked by using pharmacological inhibitors, including BAY11-7082 and SB202190, overexpression of the dominant-negative inhibitor of NF-kappaB (IkappaBalphaSR), or by the knock-down of p65 subunit of NF-kappaB. Binding of activated NF-kappaB (p50/p65 heterodimer) and ATF-2 (homodimer) to two novel regulatory elements located -2.7 and -2.2 kb upstream of the TIMP-1 transcription start site, respectively, is required for full IL-1-responsiveness. Mutational analysis of these regulatory elements and their weak activity when linked to the minimal tk promoter suggest that cooperative binding is required to activate transcription. In contrast to astrocytes, we observed that TIMP-1 is expressed at lower levels in gliomas and is not regulated by IL-1. We provide evidence that the lack of TIMP-1 activation in gliomas results from either dysfunctional IKK/NF-kappaB or MEK3/6/p38/ATF-2 activation by IL-1. In summary, we propose a novel mechanism of TIMP-1 regulation, which ensures an increased supply of the inhibitor after brain injury, and limits ECM degradation. This mechanism does not function in gliomas, and may in part explain the increased invasiveness of glioma cells.
(1612) Clara 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.
Figure S6e 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.
An Evolutionarily Conserved Function of Proliferating Cell Nuclear Antigen for Cdt1 Degradation by the Cul4-Ddb1 Ubiquitin Ligase in Response to DNA Damage
Creators: name: Hu, Jian
name: Xiong, Yue
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: The DNA replication licensing factor Cdt1 is degraded by the ubiquitin-proteasome pathway during S phase of the cell cycle, to ensure one round of DNA replication during each cell division and in response to DNA damage to halt DNA replication. Constitutive expression of Cdt1 causes DNA re-replication and is associated with the development of a subset of human non-small cell-lung carcinomas. In mammalian cells, DNA damage-induced Cdt1 degradation is catalyzed by the Cul4-Ddb1-Roc1 E3 ubiquitin ligase. We report here that overexpression of the proliferating cell nuclear antigen (PCNA) inhibitory domain from the CDK inhibitors p21 and p57, but not the CDK-cyclin inhibitory domain, blocked Cdt1 degradation in cultured mammalian cells after UV irradiation. In vivo soluble Cdt1 and PCNA co-elute by gel filtration and associate with each other physically. Silencing PCNA in cultured mammalian cells or repression of pcn1 expression in fission yeast blocked Cdt1 degradation in response to DNA damage. Unexpectedly, deletion of Ddb1 in fission yeast cells also accumulated Cdt1 in the absence of DNA damage. We suggest that the Cul4-Ddb1 ligase evolved to ubiquitinate Cdt1 during normal cell growth as well as in response to DNA damage and a separate E3 ligase, possibly SCF(Skp2), evolved to either share or take over the function of Cdt1 ubiquitination during normal cell growth and that PCNA is involved in mediating Cdt1 degradation by the Cul4-Ddb1 ligase in response to DNA damage.
Albumblatt für Paul Strauss
Creators: name: Dahn, Felix
Publisher: name: [s.n.]
Year: 1885

description: Felix Dahn
description: Antiquariat Carl Wegner Martin-Luther-Str. 113, D-10825 Berlin Kauf 26.1.2023 2023,05H Öffentliche Bibliothek der Universität Basel Kaufpreis: EUR 90.-
description: Deutsch
description: Verzeichnung=Description=Inventaire Januar 2023 HAN-Katalogisierungsregeln nni
Apop-1, a Novel Protein Inducing Cyclophilin D-dependent but Bax/Bak-related Channel-independent Apoptosis
Creators: name: Ogihara, Toshio
name: Nishitani, Masahito
name: Maeda, Nobuyo
name: Sun, Xin
name: Yasuda, Osamu
name: Fukuo, Keisuke
name: Rakugi, Hiromi
name: Yotsui, Takamori
name: Smithies, Oliver
name: Higuchi, Masayoshi
name: Suzuki, Takashi
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: In the intrinsic pathway of apoptosis, mitochondria play a crucial role by releasing cytochrome c from the intermembrane space into the cytoplasm. Cytochrome c release through Bax/Bak-dependent channels in mitochondria has been well documented. In contrast, cyclophilin D (CypD), an important component of permeability transition pore-dependent protein release, remains largely undefined, and no apoptogenic proteins that act specifically in a CypD-dependent manner have been reported to date. Here, we describe a novel and evolutionarily conserved protein, apoptogenic protein (Apop). Mouse Apop-1 expression induces apoptotic death by releasing cytochrome c from mitochondria into the cytosolic space followed by activation of caspase-9 and -3. Apop-1-induced apoptosis is not blocked by Bcl-2 or Bcl-xL, inhibitors of Bax/Bak-dependent channels, whereas it is completely blocked by cyclosporin A, an inhibitor of permeability transition pore. Cells lacking CypD were resistant to Apop-induced apoptosis. Moreover, inhibition of Apop expression prevented the cell death induced by apoptosis-inducing substances. Our findings, thus, indicate that the expression of Apop-1 induces apoptosis though CypD-dependent pathway and that Apop-1 plays roles in cell death under physiological conditions.
(1607) Thomas Stretton 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.
An Analysis of Response Lags and Asymmetric Price Transmission on Processed Grain Products
Creators: name: Kim, Taehun
name: Kim, Taehun
Publisher: name: Unknown
Year: 2009
Subjects: subject: Demand and Price Analysis
subject: International Relations/Trade
subject: world grain price
subject: response lags
subject: asymmetric price transmission

description: The aim of this paper is to analyze the response lags of world grain prices and their effects on the prices of processed grain products and to test asymmetric transmissions between grain import prices and processed grain product prices. The study result indicates that the change of global grain prices is reflected in the prices of processed grain products with 3~6month time lags. The test result of asymmetric price transmissions shows that there is a positive asymmetric price transmission for wheat flour. In the case of cooking oil price and assorted feed price, a global grain price increase affects processed grain product price, but the impact of decreasing global grain price, is not statistically significant in explaining the change of processed grain product price.
(1608) Charlotte Alicia 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.
Recent Results in Galactic Cosmic Ray Physics and Their Interpretation
Creators: name: Evoli, Carmelo
Publisher: name: Zenodo
Year: 2022
Subjects: cosmic rays
astroparticle physics

description: Slides of the talk I gave at the NOW 2022 Conference: https://agenda.infn.it/event/30418/
description: {"references": ["Evoli et al., 2021, Physical Review D, Volume 103, Issue 8, article id.083010, arXiv:2010.11955", "Evoli et al., 2020, Physical Review Letters, Volume 125, Issue 5, article id.051101, arXiv:2007.01302", "Evoli et al., 2020, Physical Review D, Volume 101, Issue 2, article id.023013, arXiv:1910.04113", "Evoli et al., 2019, Physical Review D, Volume 99, Issue 10, id.103023, arXiv:1904.10220"]}
To Apply or Not to Apply: A Survey Analysis of Grant Writing Costs and Benefits
Creators: name: von Hippel, Ted
name: von Hippel, Courtney
Publisher: name: arXiv
Year: 2015
Subjects: subject: Physics and Society (physics.soc-ph)
subject: Instrumentation and Methods for Astrophysics (astro-ph.IM)
subject: FOS: Physical sciences

description: We surveyed 113 astronomers and 82 psychologists active in applying for federally funded research on their grant-writing history between January, 2009 and November, 2012. We collected demographic data, effort levels, success rates, and perceived non-financial benefits from writing grant proposals. We find that the average proposal takes 116 PI hours and 55 CI hours to write; although time spent writing was not related to whether the grant was funded. Effort did translate into success, however, as academics who wrote more grants received more funding. Participants indicated modest non-monetary benefits from grant writing, with psychologists reporting a somewhat greater benefit overall than astronomers. These perceptions of non-financial benefits were unrelated to how many grants investigators applied for, the number of grants they received, or the amount of time they devoted to writing their proposals. We also explored the number of years an investigator can afford to apply unsuccessfully for research grants and our analyses suggest that funding rates below approximately 20%, commensurate with current NIH and NSF funding, are likely to drive at least half of the active researchers away from federally funded research. We conclude with recommendations and suggestions for individual investigators and for department heads.
description: Full paper plus three tables not included here and supplemental material available at journals.plos.org/plosone/article?id=10.1371/journal.pone.0118494, PLOS ONE, March 4, 2015
Characterization of 3′hExo, a 3′ Exonuclease Specifically Interacting with the 3′ End of Histone mRNA
Creators: name: Purdy, Matthew
name: Yang, Xiao Cui
name: Dominski, Zbigniew
name: Marzluff, William F.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: The 3' end of mammalian histone mRNAs consisting of a conserved stem-loop and a terminal ACCCA interacts with a recently identified human 3' exonuclease designated 3'hExo. The sequence-specific interaction suggests that 3'hExo may participate in the degradation of histone mRNAs. ERI-1, a Caenorhabditis elegans homologue of 3'hExo, has been implicated in degradation of small interfering RNAs. We introduced a number of mutations to 3'hExo to identify residues required for RNA binding and catalysis. To assure that the introduced mutations specifically target one of these two activities of 3'hExo rather than cause global structural defects, the mutant proteins were tested in parallel for the ability both to bind the stem-loop RNA and to degrade RNA substrates. Our analysis confirms that 3'hExo is a member of the DEDDh family of 3' exonucleases. Specific binding to the RNA requires the SAP domain and two lysines located immediately to its C terminus. 3'hExo binds with the highest affinity to the wild-type 3' end of histone mRNA, and any changes to this sequence reduce efficiency of binding. 3'hExo has only residual, if any, 3' exonuclease activity on DNA substrates and localizes mostly to the cytoplasm, suggesting that in vivo it performs exclusively RNA-specific functions. Efficient degradation of RNA substrates by 3'hExo requires 2' and 3' hydroxyl groups at the last nucleotide. 3'hExo removes 3' overhangs of small interfering RNAs, whereas the double-stranded region is resistant to the enzymatic activity.
Figure S6f 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.
Cholesterol-induced Apoptotic Macrophages Elicit an Inflammatory Response in Phagocytes, Which Is Partially Attenuated by the Mer Receptor
Creators: name: Thorp, Edward
name: Matsushima, Glenn K.
name: Gerbod-Giannone, Marie Christine
name: Tabas, Ira
name: Seitz, Heather
name: Li, Yankun
name: Cui, Dongying
name: Tall, Alan R.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: Macrophage apoptosis and the ability of phagocytes to clear these apoptotic cells are important processes in advanced atherosclerosis. Phagocytic clearance not only disposes of dead cells but usually elicits an anti-inflammatory response. To study this process in a model of advanced lesional macrophage death, macrophages rendered apoptotic by free cholesterol loading (FC-AMs) were incubated briefly with fresh macrophages ("phagocytes"). FC-AMs were promptly ingested by the phagocytes, which was dependent upon actin polymerization and the phagocyte Mer receptor. Surprisingly, this brief exposure to FC-AMs triggered a modest proinflammatory response in the phagocytes: tumor necrosis factor-[alpha] (TNF-[alpha]) and interleukin (IL)-1[beta] were induced, whereas the levels of transforming growth factor-[beta] and IL-10 were not increased. This response required cell contact between the FC-AMs and phagocytes but not FC-AM ingestion. TNF-[alpha] and IL-1[beta] induction required one or more proteins on the FC-AM surface and was dependent on signaling through extracellular signal-regulated kinase-1/2 mitogen-activated protein kinase and nuclear factor-[kappa]B in the phagocytes. TNF-[alpha] production was markedly greater when Mer-defective phagocytes were used, indicating that Mer attenuated the inflammatory response. Interestingly, a more typical anti-inflammatory response was elicited when phagocytes were exposed to macrophages rendered apoptotic by oxidized
(1609) John Hamilton 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.
Crystal Structure of the FERM Domain of Focal Adhesion Kinase
Creators: name: Poy, Florence
name: Ceccarelli, Derek F.J.
name: Schaller, Michael D.
name: Eck, Michael J.
name: Hyun, Kyu Song
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: Focal adhesion kinase (FAK) is a non-receptor tyrosine kinase that localizes to focal adhesions in adherent cells. Through phosphorylation of proteins assembled at the cytoplasmic tails of integrins, FAK promotes signaling events that modulate cellular growth, survival, and migration. The amino-terminal region of FAK contains a region of sequence homology with band 4.1 and ezrin/radixin/moesin (ERM) proteins termed a FERM domain. FERM domains are found in a variety of signaling and cytoskeletal proteins and are thought to mediate intermolecular interactions with partner proteins and phospholipids at the plasma membrane and intramolecular regulatory interactions. Here we report two crystal structures of an NH2-terminal fragment of avian FAK containing the FERM domain and a portion of the regulatory linker that connects the FERM and kinase domains. The tertiary folds of the three subdomains (F1, F2, and F3) are similar to those of known FERM structures despite low sequence conservation. Differences in the sequence and relative orientation of the F3 subdomain alters the nature of the interdomain interface, and the phosphoinositide binding site found in ERM family FERM domains is not present in FAK. A putative protein interaction site on the F3 lobe is masked by the proximal region of the linker. Additionally, in one structure the adjacent Src SH3 and SH2 binding sites in the linker associate with the surfaces of the F3 and F1 lobes, respectively. These structural features suggest the possibility that protein interactions of the FAK FERM domain can be regulated by binding of Src kinases to the linker segment.
Dimerization of the Scaffolding Protein ZO-1 through the Second PDZ Domain
Creators: name: Fanning, Alan S.
name: Utepbergenov, Darkhan I.
name: Anderson, James M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: The tight junction protein ZO-1 is known to link the transmembrane proteins occludin, claudins, and JAMs to many cytoplasmic proteins and the actin cytoskeleton. Although specific roles for ZO-1 at the tight junction are unknown, it is widely assumed that ZO-1, together with its homologs ZO-2 and ZO-3, serves as a platform to scaffold various transmembrane and cytoplasmic tight junction proteins. Thus the manner in which the zonula occludens (ZO) proteins multimerize has implications for the protein networks they can coordinate. The purpose of our study was to determine whether ZO-1 forms homodimers and to determine the protein interaction region. Using laser light scattering and analytical centrifugation, we show that protein sequences corresponding to the NH(2)-terminal half of ZO-1 form stable homodimers with a submicromolar equilibrium dissociation constant. Analysis of the molecular weight of different truncated forms of ZO-1 revealed that the second PDZ domain is both necessary and sufficient for dimerization. This interaction does not use the beta-finger motif described for other PDZ dimers. Furthermore, ZO-1 does not dimerize via an Src homology 3 to Guk domain interaction as was demonstrated previously for MAGUKs, like PSD-95. Results from immunoprecipitation experiments with polarized Madin-Darby canine kidney epithelial cells stably transfected with full-length GFP-ZO-1 indicate that a substantial portion of ZO-1 forms homodimers in vivo. As described previously, ZO-1 also forms heterodimers with ZO-2 and ZO-3. We conclude that the dimerization of ZO proteins is unlike that of other MAGUKs and that the previously unrecognized ZO-1 homodimers may allow formation of protein networks distinct from those of heterodimers with ZO-2 and ZO-3.
Figure S6d 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.
DNA Unwinding by Escherichia coli DNA Helicase I (TraI) Provides Evidence for a Processive Monomeric Molecular Motor
Creators: name: Sikora, Bartek
name: Matson, Steven W.
name: Raney, Kevin D.
name: Eoff, Robert L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: The F plasmid TraI protein (DNA helicase I) plays an essential role in conjugative DNA transfer as both a transesterase and a helicase. Previous work has shown that the 192-kDa TraI protein is a highly processive helicase, catalytically separating >850 bp under steady-state conditions. In this report, we examine the kinetic mechanism describing DNA unwinding of TraI. The kinetic step size of TraI was measured under both single turnover and pre-steady-state conditions. The resulting kinetic step-size estimate was approximately 6-8 bp step(-1). TraI can separate double-stranded DNA at a rate of approximately 1100 bp s(-1), similar to the measured unwinding rate of the RecBCD helicase, and appears to dissociate very slowly from the 3' terminus following translocation and strand-separation events. Analyses of pre-steady-state burst amplitudes indicate that TraI can function as a monomer, similar to the bacteriophage T4 helicase, Dda. However, unlike Dda, TraI is a highly processive monomeric helicase, making it unique among the DNA helicases characterized thus far.
Figure S6g 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.
Optical spectroscopic observations of gamma-ray blazar candidates II. The 2013 KPNO campaign in the Northern Hemisphere
Creators: name: Massaro, F.
name: Landoni, M.
name: D'Abrusco, R.
name: Milisavljevic, D.
name: Paggi, A.
name: Masetti, N.
name: Smith, Howard A.
name: Tosti, G.
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: We recently started a systematic search of low-energy counterparts of the unidentified gamma-ray sources (UGSs) listed in the Fermi-Large Area Telescope (LAT) First Source Catalog (1FGL) and the Fermi-LAT 2-Year Source Catalog (2FGL).} The main goal of our investigation is to find active galaxies belonging to the blazar class that lie within the positional uncertainty region of the UGSs and thus could be their potential low-energy counterparts. To achieve our aims, we first adopted several procedures based on the peculiar observational properties of blazars in the radio and in the IR. Then we carried out a follow-up spectroscopic campaign in the optical band to verify the nature of the candidates selected as potential counterparts of the UGSs. Here we present the results of the observations carried out in 2013 in the Northern Hemisphere at Kitt Peak National Observatory (KPNO). Optical spectroscopy is crucial to confirm the nature of the sources and can be used to estimate their redshifts; it will also allow us to test the robustness of our methods when the whole campaign is completed. Here we present the optical spectroscopic observations of 39 sources. Within our sample we found that 6 sources are blazars, candidates to be low-energy counterparts of the UGSs listed in the 2FGL. We confirm that an additional 8 sources, previously classified as active galaxies of uncertain type and associated in the 2FGL, are also all BL Lac objects. Moreover, we also present 20 new spectra for known blazars listed in the Multi-frequency Catalogue of Blazars as having an uncertain redshift and/or being classified as BL Lac candidates. We conclude that our methods for selecting gamma-ray blazar candidates allows us to discover new blazars and increase the list of potential low-energy counterparts for the Fermi UGSs.
description: 27 pages, 39 figures, 1 table, A&A accepted for publication (pre-proof version)
Figure S6e 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.
(1604) Ann [Lupton]
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.
Quantum Heat Baths satisfying the eigenstate thermalization hypothesis
Creators: name: Fialko, O.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Physics (quant-ph)
subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: A class of autonomous quantum heat baths satisfying the eigenstate thermalization hypothesis (ETH) criteria is proposed. We show that such systems are expected to cause thermal relaxation of much smaller quantum systems coupled to one of the baths local observables. The process of thermalization is examined through residual fluctuations of local observables of the bath around their thermal values predicted by ETH. It is shown that such fluctuations perturb the small quantum system causing its decoherence to the thermal state. As an example, we investigate theoretically and numerically thermalization of a qubit coupled to a realistic ETH quantum heat bath.
description: 6 pages, 5 figures
(1606) Anne 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.