cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Table S1 from Drivers of spatio-temporal patterns of salinity in Spanish rivers: a nationwide assessment
Creators: name: Estévez, Edurne
name: Rodríguez-Castillo, Tamara
name: González-Ferreras, Alexia María
name: Cañedo-Argüelles, Miguel
name: Barquín, José
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Environmental Science
subject: Ecology
subject: FOS: Biological sciences

description: River typologies according to the Spanish Royal Decree, RD 817/2015, on water policy and number of river reaches in good and poor status in each river typology with water conductivity measures considered in this study. *SAICA = Automatic Water Quality Information System
Functional Analysis of Cdc42 Residues Required for Guanine Nucleotide Exchange
Creators: name: Rossman, Kent L.
name: Sondek, John
name: Whitehead, Ian P.
name: Worthylake, David K.
name: Snyder, Jason T.
name: Cheng, Li
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2002

description: Guanine nucleotide exchange factors (GEFs) directly engage small GTPases to facilitate the exchange of bound GDP for GTP, leading to GTPase activation. Several recent crystal structures of GEFs in complex with Rho family GTPases highlight the conserved interactions and conformational alterations necessary for catalyzing exchange. In the present study, functional roles were defined for specific residues within Cdc42 implicated by the crystal structures as important for physiological exchange of guanine nucleotides within Rho GTPases. In particular, this study highlights the paramount importance of the phosphate-binding loop and interactions with the magnesium co-factor as critical for proper regulation of RhoGEF-catalyzed exchange. Other conformational alterations of the GTPases affecting interactions with the sugar and base of guanine nucleotides are also important but are secondary. Of particular note, substitution of alanine for cysteine at position 18 of Cdc42 leads to a fast cycling phenotype for Cdc42 with heightened affinity for RhoGEFs and produces a dominant negative form of Cdc42 capable of inhibiting RhoGEFs both in vitro and in vivo.
Anatomy of $B\rightarrow D\bar{D}$ Decays
Creators: name: Bel, Lennaert
name: De Bruyn, Kristof
name: Fleischer, Robert
name: Mulder, Mick
name: Tuning, Niels
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Experiment (hep-ex)
subject: FOS: Physical sciences

description: The decays $B_d^0\rightarrow D_d^-D_d^+$ and $B_s^0\rightarrow D_s^-D_s^+$ probe the CP-violating mixing phases $ϕ_d$ and $ϕ_s$, respectively. The theoretical uncertainty of the corresponding determinations is limited by contributions from penguin topologies, which can be included with the help of the $U$-spin symmetry of the strong interaction. We analyse the currently available data for $B^0_{d,s}\rightarrow D_{d,s}^-D_{d,s}^+$ decays and those with similar dynamics to constrain the involved non-perturbative parameters. Using further information from semileptonic $B_d^0\rightarrow D_d^-\ell^+ν_{\ell}$ decays, we perform a test of the factorisation approximation and take non-factorisable $SU(3)$-breaking corrections into account. The branching ratios of the $B_d^0\rightarrow D_d^-D_d^+$, $B_s^0\rightarrow D_s^-D_d^+$ and $B_s^0\rightarrow D_s^-D_s^+$, $B_d^0\rightarrow D_d^-D_s^+$ decays show an interesting pattern which can be accommodated through significantly enhanced exchange and penguin annihilation topologies. This feature is also supported by data for the $B_s^0\rightarrow D_d^-D_d^+$ channel. Moreover, there are indications of potentially enhanced penguin contributions in the $B_d^0\rightarrow D_d^-D_d^+$ and $B_s^0\rightarrow D_s^-D_s^+$ decays, which would make it mandatory to control these effects in the future measurements of $ϕ_d$ and $ϕ_s$. We discuss scenarios for high-precision measurements in the era of Belle II and the LHCb upgrade.
description: 47 pages, 17 figures, matching published version
Heparan Sulfate 3- O -Sulfotransferase Isoform 5 Generates Both an Antithrombin-binding Site and an Entry Receptor for Herpes Simplex Virus, Type 1
Creators: name: Xia, Guoqing
name: Malmström, Anders
name: Ju, Wujian
name: Liu, Jian
name: Tiwari, Vaibhav
name: Chen, Jinghua
name: Li, Jin Ping
name: Shukla, Deepak
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2002

description: Heparan sulfate 3-O-sulfotransferase isoform 5 generates both anantithrombin-binding site and an entry receptor for herpes simplex virus,type 1.
Die Physikalische Sammlung (Physical Collection)
Creators: name: Schrimpf, Andreas
Publisher: name: arXiv
Year: 2015
Subjects: subject: History and Philosophy of Physics (physics.hist-ph)
subject: FOS: Physical sciences

description: At the end of the 17th century, the collection was established through the acquisition of Leiden instrumentmaker Musschenbroek's collection. Its aim was to demonstrate physical phenomena. Until the end of the 18th century, the collection was used and extended by a number of professors from various university departments in teaching mechanics, hydrostatics, optics and electrostatics. The foundation of the Institute for Mathematics and Physics in 1817 and the appointment of Christian Ludwig Gerling to the position of Professor for Mathematics, Physics and Astronomy strengthened the subject considerably. Gerling extended the collection mainly with devices for geodesy and astronomy, with more instruments being added in the time up to the middle of the 20th century. Today, the collection allows an insight into the history of scientific instruments as witnesses of the past.
description: 8 pages, 5 figures, in German
(1758) Anne Williams
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.
THEORY OF DEVELOPMENT THROUGH THE USE OF FICTION IN TEACHING FOREIGN LANGUAGES
Creators: name: Egamov, Erkin
Publisher: name: Zenodo
Year: 2023

description: In the process of learning a foreign language, familiarity with the culture to which the language being studied belongs plays a significant role. Culture in this case implies a set of codes that prescribe a person a certain behavior with his inherent experiences and thoughts. Therefore, knowledge of a foreign language always presupposes knowledge of these codes: the cultural traditions of the people, their material and spiritual boundaries of everyday social relations, their living conditions, realities, history, mentality (taking into account the perception of space and time, emotional state), philosophical and imaginative thinking, type of behavior, non-verbal communication, etc.
Identification of Dynein Heavy Chain 7 as an Inner Arm Component of Human Cilia That Is Synthesized but Not Assembled in a Case of Primary Ciliary Dyskinesia
Creators: name: Ostrowski, Lawrence E.
name: Moyer, Mary B.
name: Blackburn, Kevin
name: O'Neal, Wanda K.
name: Boucher, Richard C.
name: Randell, Scott H.
name: Zhang, Yan J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2002

description: Although the basic structure of the axoneme has been highly conserved throughout evolution, the varied functions of specialized axonemes require differences in structure and regulation. Cilia lining the respiratory tract propel mucus along airway surfaces, providing a critical function to the defense mechanisms of the pulmonary system, yet little is known of their molecular structure. We have identified and cloned a dynein heavy chain that is a component of the inner dynein arm. Bronchial epithelial cells were obtained from normal donors and from a patient with primary ciliary dyskinesia (PCD) whose cilia demonstrated an absence of inner dynein arms by electron microscopy. Cilia from normal and PCD cells were compared by gel electrophoresis, and mass spectrometry was used to identify DNAH7 as a protein absent in PCD cilia. The full-length DNAH7 cDNA was cloned and shares 68% similarity with an inner arm dynein heavy chain from Drosophila. DNAH7 was induced during ciliated cell differentiation, and immunohistochemistry demonstrated the presence of DNAH7 in normal cilia. In cilia from PCD cells, DNAH7 was undetectable, whereas intracellular DNAH7 was clearly present. These studies identify DNAH7 as an inner arm component of human cilia that is synthesized but not assembled in a case of PCD.
Identification of Essential Residues in the Type II Hsp40 Sis1 That Function in Polypeptide Binding
Creators: name: Ren, Hongyu
name: Michael Younger, J.
name: Lee, Soojin
name: Fan, Chun Yang
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2002

description: Sis1 is an essential yeast Type II Hsp40 protein that assists cytosolic Hsp70 Ssa1 in the facilitation of processes that include translation initiation, the prevention of protein aggregation, and proteasomal protein degradation. An essential function of Sis1 and other Hsp40 proteins is the binding and delivery of non-native polypeptides to Hsp70. How Hsp40s function as molecular chaperones is unknown. The crystal structure of a Sis1 fragment that retains peptide-binding activity suggests that Type II Hsp40s utilize hydrophobic residues located in a solvent-exposed patch on carboxyl-terminal domain I to bind non-native polypeptides. To test this model, amino acid residues Val-184, Leu-186, Lys-199, Phe-201, Ile-203, and Phe-251, which form a depression in carboxyl-terminal domain I, were mutated, and the ability of Sis1 mutants to support cell viability and function as molecular chaperones was examined. We report that Lys-199, Phe-201, and Phe-251 are essential for cell viability and required for Sis1 polypeptide binding activity. Sis1 I203T could support normal cell growth, but when purified it exhibited severe defects in chaperone function. These data identify essential residues in Sis1 that function in polypeptide binding and help define the nature of the polypeptide-binding site in Type II Hsp40 proteins.
SU(5)-inspired double beta decay
Creators: name: Fonseca, Renato M.
name: Hirsch, Martin
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: The short-range part of the neutrinoless double beta amplitude is generated via the exchange of exotic particles, such as charged scalars, leptoquarks and/or diquarks. In order to give a sizeable contribution to the total decay rate, the masses of these exotics should be of the order of (at most) a few TeV. Here, we argue that these exotics could be the "light" (i.e weak-scale) remnants of some $B-L$ violating variants of $SU(5)$. We show that unification of the standard model gauge couplings, consistent with proton decay limits, can be achieved in such a setup without the need to introduce supersymmetry. Since these non-minimal $SU(5)$-inspired models violate $B-L$, they generate Majorana neutrino masses and therefore make it possible to explain neutrino oscillation data. The "light" coloured particles of these models can potentially be observed at the LHC, and it might be possible to probe the origin of the neutrino masses with $ΔL=2$ violating signals. As particular realizations of this idea, we present two models, one for each of the two possible tree-level topologies of neutrinoless double beta decay.
description: Small changes made; matches the published version in Physical Review D
Table S2 from Drivers of spatio-temporal patterns of salinity in Spanish rivers: a nationwide assessment.
Creators: name: Estévez, Edurne
name: Rodríguez-Castillo, Tamara
name: González-Ferreras, Alexia María
name: Cañedo-Argüelles, Miguel
name: Barquín, José
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Environmental Science
subject: Ecology
subject: FOS: Biological sciences

description: Environmental variables used in this study to investigate the most important drivers of the spatio-temporal patterns of water salinity and the most important drivers of salinisation. The correlation among variables (Spearman’s rank correlation coefficient > |0.7|) and the final set of variables used to perform the Random Forest and Generalized Linear Model analyses and the Generalized Linear Mixed-effect Model analyses is also shown.
Identification of Mammalian Mitochondrial Translational Initiation Factor 3 and Examination of Its Role in Initiation Complex Formation with Natural mRNAs
Creators: name: Spremulli, Linda L.
name: Koc, Emine Cavdar
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2002

description: Human mitochondrial translational initiation factor 3 (IF3(mt)) has been identified from the human expressed sequence tag data base. Using consensus sequences derived from conserved regions of the bacterial IF3, several partially sequenced cDNA clones were identified, and the complete sequence was assembled in silico from overlapping clones. IF3(mt) is 278 amino acid residues in length. MitoProt II predicts a 97% probability that this protein will be localized in mitochondria and further predicts that the mature protein will be 247 residues in length. The cDNA for the predicted mature form of IF3(mt) was cloned, and the protein was expressed in Escherichia coli in a His-tagged form. The mature form of IF3(mt) has short extensions on the N and C termini surrounding a region homologous to bacterial IF3. The region of IF3(mt) homologous to prokaryotic factors ranges between 21-26% identical to the bacterial proteins. Purified IF3(mt) promotes initiation complex formation on mitochondrial 55 S ribosomes in the presence of mitochondrial initiation factor 2 (IF2(mt)), [(35)S]fMet-tRNA, and either poly(A,U,G) or an in vitro transcript of the cytochrome oxidase subunit II gene as mRNA. IF3(mt) shifts the equilibrium between the 55 S mitochondrial ribosome and its subunits toward subunit dissociation. In addition, the ability of E. coli initiation factor 1 to stimulate initiation complex formation on E. coli 70 S and mitochondrial 55 S ribosomes was investigated in the presence of IF2(mt) and IF3(mt).
Figure S1 from Drivers of spatio-temporal patterns of salinity in Spanish rivers: a nationwide assessment
Creators: name: Estévez, Edurne
name: Rodríguez-Castillo, Tamara
name: González-Ferreras, Alexia María
name: Cañedo-Argüelles, Miguel
name: Barquín, José
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Environmental Science
subject: Ecology
subject: FOS: Biological sciences

description: Boxplots of water conductivity measured in river reaches in good and poor ecological status in each river typology. The mean conductivity (± the standard error) for each typology is indicated in brackets.
(1759) Matthew Rhodes
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.
Table S3 from Drivers of spatio-temporal patterns of salinity in Spanish rivers: a nationwide assessment.
Creators: name: Estévez, Edurne
name: Rodríguez-Castillo, Tamara
name: González-Ferreras, Alexia María
name: Cañedo-Argüelles, Miguel
name: Barquín, José
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Environmental Science
subject: Ecology
subject: FOS: Biological sciences

description: Extension of the Spanish river network and of each river typology not salinised and salinised, including the degree of salinisation (slight, moderate, heavy and extreme).
D2.2. Big data extraction module
Creators: name: Aristotle University Of Thessaloniki
name: Idener
Publisher: name: Zenodo
Year: 2022
Subjects: AGRICORE H2020

description: AGRICORE is a research project funded by the European Commission under the RUR-04-2018 call, part of the H2020 programme, which proposes an innovative way to apply agent-based modelling to improve the capacity of policymakers to evaluate the impact of agricultural-related measurements under and outside the framework of the Common Agricultural Policy (CAP). This deliverable presents the AGRICORE data extraction module (DEM), which allows the location, extraction and storage of all types of data necessary for the use of the different tools and modules of the AGRICORE platform. It also presents the main types of information that are necessary for the initialisation, calibration and use of the different AGRICORE modules, as well as the main data sources from which this information can be extracted. Among the functionalities of the data extraction module is also the statistical analysis of the variables contained in the imported datasets, as well as the detection of correlation relationships between them. This deliverable introduces the processing sequence performed on each of the variables individually, as well as on all of them to detect interdependencies. The results of these operations generate statistical metadata and forbidden directions between variables. Both outputs are arguments that are also passed as input to the data fusion module, presented in deliverable D2.3.
IKKβ and Phosphatidylinositol 3-Kinase/Akt Participate in Non-pathogenic Gram-negative Enteric Bacteria-induced RelA Phosphorylation and NF-κB Activation in Both Primary and Intestinal Epithelial Cell Lines
Creators: name: Russo, Maria P.
name: Haller, Dirk
name: Jobin, Christian
name: Balfour Sartor, R.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2002

description: Pathogenic and enteroinvasive bacteria have been shown to trigger the I kappa B/NF-kappa B transcriptional system and proinflammatory gene expression in epithelial cells. In this study, we investigated the molecular mechanism of the commensal Gram-negative Bacteroides vulgatus-induced NF-kappa B signal transduction in intestinal epithelial cells (IEC). We report that B. vulgatus induced interleukin-1 receptor-associated kinase-1 degradation, I kappa B alpha phosphorylation/degradation, RelA and Akt phosphorylation, as well as NF-kappa B DNA binding and NF-kappa B transcriptional activity in rat non-transformed IEC-6 cells. B. vulgatus- but not interleukin-1 beta-mediated NF-kappa B transcriptional activity was inhibited by dominant negative (dn) toll-like receptor 4. Of importance, B. vulgatus induced I kappa B alpha phosphorylation/degradation and IKK alpha/beta and RelA phosphorylation in primary IEC derived from germ-free or mono-associated HLA-B27 transgenic and wild type rats, demonstrating the physiological relevance of non-pathogenic bacterial signaling in IEC. Adenoviral delivery of dn IKK beta or treatment with wortmannin inhibited B. vulgatus-induced endogenous RelA Ser-536 and GST-p65TAD (Ser-529/Ser-536) phosphorylation as well as NF-kappa B transcriptional activity in IEC-6 cells, suggesting a critical role of IKK beta and phosphatidylinositol 3-kinase/Akt in bacteria-induced RelA phosphorylation and NF-kappa B activation. Interestingly, B. vulgatus-induced I kappa B alpha degradation and NF-kappa B transcriptional activity in IEC transwell cultures were inhibited in the presence of lymphocytes. We propose that non-pathogenic B. vulgatus activates the NF-kappa B signaling pathway through both I kappa B degradation and RelA phosphorylation but that immune cells mediate tolerance of IEC to this commensal bacteria.
Polarized Gravitational Waves from Cosmological Phase Transitions
Creators: name: Kisslinger, Leonard
name: Kahniashvili, Tina
Publisher: name: arXiv
Year: 2015
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: FOS: Physical sciences

description: We estimate the degree of circular polarization for the gravitational waves generated during the electroweak and QCD phase transitions from the kinetic and magnetic helicity generated by bubble collisions during those cosmological phase transitions.
description: 9 pages, 1 figure
Processing and characterization of epitaxial GaAs radiation detectors
Creators: name: Wu, X.
name: Peltola, T.
name: Arsenovich, T.
name: Gädda, A.
name: Härkönen, J.
name: Junkes, A.
name: Karadzhinova, A.
name: Kostamo, P.
name: Lipsanen, H.
name: Luukka, P.
name: Mattila, M.
name: Nenonen, S.
name: Riekkinen, T.
name: Tuominen, E.
name: Winkler, A.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Instrumentation and Detectors (physics.ins-det)
subject: FOS: Physical sciences

description: GaAs devices have relatively high atomic numbers (Z=31, 33) and thus extend the X-ray absorption edge beyond that of Si (Z=14) devices. In this study, radiation detectors were processed on GaAs substrates with 110 $μ\textrm{m}$ - 130 $μ\textrm{m}$ thick epitaxial absorption volume. Thick undoped and heavily doped p$^+$ epitaxial layers were grown using a custom-made horizontal Chloride Vapor Phase Epitaxy (CVPE) reactor, the growth rate of which was about 10 $μ\textrm{m}$/h. The GaAs p$^+$/i/n$^+$ detectors were characterized by Capacitance Voltage ($CV$), Current Voltage ($IV$), Transient Current Technique (TCT) and Deep Level Transient Spectroscopy (DLTS) measurements. The full depletion voltage ($V_{\textrm{fd}}$) of the detectors with 110 $μ\textrm{m}$ epi-layer thickness is in the range of 8 V - 15 V and the leakage current density is about 10 nA/cm$^2$. The signal transit time determined by TCT is about 5 ns when the bias voltage is well above the value that produces the peak saturation drift velocity of electrons in GaAs at a given thickness. Numerical simulations with an appropriate defect model agree with the experimental results.
description: 7 pages, 10 figures, 10th International Conference on Radiation Effects on Semiconductor Materials, Detectors and Devices (RESMDD14), 8-10 October, Firenze, Italy
(1761) James Williams Scarlett
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.
Rabi-coupled Countersuperflow in Binary Bose-Einstein Condensates
Creators: name: Usui, Ayaka
name: Takeuchi, Hiromitsu
Publisher: name: arXiv
Year: 2015
Subjects: subject: Quantum Gases (cond-mat.quant-gas)
subject: FOS: Physical sciences

description: We show theoretically that periodic density patterns are stabilized in two counter-propagating Bose-Einstein condensates of atoms in different hyperfine states under Rabi coupling. In the presence of coupling, the relative velocity between two components is localized around density depressions in quasi-one-dimensional systems. When the relative velocity is sufficiently small, the periodic pattern reduces to a periodic array of topological solitons as kinks of relative phase. According to our variational and numerical analyses, the soliton solution is well characterized by the soliton width and density depression. We demonstrate the dependence of the depression and width on the Rabi frequency and the coupling constant of inter-component density-density interactions. The periodic pattern of the relative phase transforms continuously from a soliton array to a sinusoidal pattern as the period becomes smaller than the soliton width. These patterns become unstable when the localized relative velocity exceeds a critical value. The stability-phase diagram of this system is evaluated with a stability analysis of countersuperflow, by taking into account the finite-size-effect owing to the density depression.
description: 9 pages, 8 figures
Figure S3 from Drivers of spatio-temporal patterns of salinity in Spanish rivers: a nationwide assessment
Creators: name: Estévez, Edurne
name: Rodríguez-Castillo, Tamara
name: González-Ferreras, Alexia María
name: Cañedo-Argüelles, Miguel
name: Barquín, José
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Environmental Science
subject: Ecology
subject: FOS: Biological sciences

description: Partial dependence plots showing the fitted functions for the most important environmental factors driving spatial water salinity patterns (MN = in the draining catchment to the river reach, LC = in the hillslopes adjacent to the river reach). Codes according to Table S2: (a) MN_PRE, (b) MN_AGR, (c) LC_TEM, (d) MN_CON, (e) ELE, (f) MN_HAR.
Supplementary Figures and Tables from Quantifying phenology and migratory behaviours of hummingbirds using single-site dynamics and mark-detection analyses
Creators: name: English, Simon G.
name: Wilson, Scott
name: Bandivadekar, Ruta R.
name: Graves, Emily E.
name: Holyoak, Marcel
name: Brown, Jennifer C.
name: Tell, Lisa A.
Publisher: name: The Royal Society
Year: 2022
Subjects: subject: Ecology
subject: FOS: Biological sciences

description: Nuanced understanding of seasonal movements of partially migratory birds is paramount to species and habitat conservation. Using nascent statistical methods, we identified migratory strategies of birds outfitted with radio-frequency identification (RFID) tags detected at RFID feeders in two sites in California, USA. We quantified proportions of migrants and residents and the seasonal phenology for each movement strategy in Allen’s and Anna’s hummingbirds; we also validated our methodology by fitting our model to obligate migratory black-chinned hummingbirds. Allen’s and Anna’s hummingbirds exhibited characteristics of facultative migratory behaviour. We also quantified apparent annual survival for each migratory strategy and found that residents had significantly higher probabilities of apparent survival. Low survival estimates for migrants suggest that a high proportion of birds in the migrant group permanently emigrated from our study sites. Considered together, our analyses suggest that hummingbirds in both northern and southern California sites partake in diverse and highly plastic migratory behaviours. Our assessment elucidates the dynamics underlying idiosyncratic migratory behaviours of two species of hummingbirds, in addition to describing a framework for similar assessments of migratory behaviours using the multi-state open robust design with state uncertainty model and single-site dynamics.
Increased Basal cAMP-dependent Protein Kinase Activity Inhibits the Formation of Mesoderm-derived Structures in the Developing Mouse Embryo
Creators: name: Amieux, Paul S.
name: Laszlo, George S.
name: Knickerbocker, Heidi
name: Idzerda, Rejean L.
name: Lee, David C.
name: Su, Thomas
name: Stanley McKnight, G.
name: Howe, Douglas G.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2002

description: A targeted disruption of the RIalpha isoform of protein kinase A (PKA) was created by using homologous recombination in embryonic stem cells. Unlike the other regulatory and catalytic subunits of PKA, RIalpha is the only isoform that is essential for early embryonic development. RIalpha homozygous mutant embryos fail to develop a functional heart tube at E8.5 and are resorbed at approximately E10.5. Mutant embryos show significant growth retardation and developmental delay compared with wild type littermates from E7.5 to E10.5. The anterior-posterior axis of RIalpha mutants is well developed, with a prominent head structure but a reduced trunk. PKA activity measurements reveal an increased basal PKA activity in these embryos. Brachyury mRNA expression in the primitive streak of RIalpha mutants is significantly reduced, consistent with later deficits in axial, paraxial, and lateral plate mesodermal derivatives. This defect in the production and migration of mesoderm can be completely rescued by crossing RIalpha mutants to mice carrying a targeted disruption in the Calpha catalytic subunit, demonstrating that unregulated PKA activity rather than a specific loss of RIalpha is responsible for the phenotype. Primary embryonic fibroblasts from RIalpha mutant embryos display an abnormal cytoskeleton and an altered ability to migrate in cell culture. Our results demonstrate that unregulated PKA activity negatively affects growth factor-mediated mesoderm formation during early mouse development.
Inhibition of Nucleoside Transport by p38 MAPK Inhibitors
Creators: name: Mitchell, Beverly S.
name: Graves, Lee M.
name: Huang, Min
name: Jing, Jin Gu
name: Wang, Yanhong
name: Collins, Matthew
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2002

description: While investigating the ability of p38 MAPK to regulate cytarabine (Ara C)-dependent differentiation of erythroleukemia K562 cells, we observed effects that indicated that the imidazoline class of p38 MAPK inhibitors prevented nucleoside transport. Incubation of K562 cells with SB203580, SB203580-iodo, or SB202474, an analogue of SB203580 that does not inhibit p38 MAPK activity, inhibited the uptake of [3H]Ara C or [3H]uridine and the differentiation of K562 cells. Consistent with the effects of these compounds on the nitrobenzylthioinosine (NBMPR)-sensitive equilibrative nucleoside transporter (ENT1), incubation with SB203580 or SB203580-iodo eliminated the binding of [3H]NBMPR to K562 cells or membranes isolated from human erythrocytes. Furthermore, using a uridine-dependent cell type (G9c), we observed that SB203580 or SB203580-iodo efficiently inhibited the salvage synthesis of pyrimidine nucleotides in vivo. Thus these studies demonstrate that the NBMPR-sensitive equilibrative nucleoside transporters are novel and unexpected targets for the p38 MAPK inhibitors at concentrations typically used to inhibit protein kinases.
(1752) Charlotte Brown
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.
Insulin-like Growth Factor I Increases α V β 3 Affinity by Increasing the Amount of Integrin-associated Protein That Is Associated with Non-raft Domains of the Cellular Membrane
Creators: name: Maile, Laura A.
name: Imai, Yumi
name: Clemmons, David R.
name: Clarke, Jane Badley
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2002

description: Insulin-like growth factor I (IGF-I) stimulates an increase in alpha(V)beta(3) ligand binding. Stimulation of smooth muscle cells by IGF-I requires alpha(V)beta(3) ligand occupancy, and enhanced alpha(V)beta(3) ligand occupancy augments IGF-I actions. Therefore, IGF-I-induced changes in alpha(V)beta(3) ligand binding may act to further enhance IGF-I actions. Integrin-associated protein (IAP) has been shown to be associated with alpha(V)beta(3) and is required for the binding of alpha(V)beta(3) to vitronectin-coated beads. We therefore investigated whether IGF-I could stimulate IAP-alpha(V)beta(3) association resulting in enhanced ligand binding. IGF-I stimulated an increase in IAP-alpha(V)beta(3) association. This was due, at least in part, to an IGF-I-stimulated redistribution of IAP from the Triton-insoluble fraction of the cell to the Triton-soluble fraction of the cell, where most of the alpha(V)beta(3) was located. Inhibition of the phosphatidylinositol 3-kinase pathway blocked both the redistribution of IAP and the increase in IAP-alpha(V)beta(3) association, providing further evidence that the redistribution of IAP is essential for the increase in association. An anti-IAP monoclonal antibody, blocked both the IGF-I-stimulated increase in IAP-alpha(V)beta(3) complex formation and cell migration. IGF-I-stimulated translocation of IAP and increase in IAP-alpha(V)beta(3) association represent an important process by which IGF-I modulates alpha(V)beta(3) ligand binding and cellular responses.
Table S2 from Drivers of spatio-temporal patterns of salinity in Spanish rivers: a nationwide assessment
Creators: name: Estévez, Edurne
name: Rodríguez-Castillo, Tamara
name: González-Ferreras, Alexia María
name: Cañedo-Argüelles, Miguel
name: Barquín, José
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Environmental Science
subject: Ecology
subject: FOS: Biological sciences

description: Environmental variables used in this study to investigate the most important drivers of the spatio-temporal patterns of water salinity and the most important drivers of salinisation. The correlation among variables (Spearman’s rank correlation coefficient > |0.7|) and the final set of variables used to perform the Random Forest and Generalized Linear Model analyses and the Generalized Linear Mixed-effect Model analyses is also shown.
Liganded Androgen Receptor Interaction with β-Catenin: NUCLEAR CO-LOCALIZATION AND MODULATION OF TRANSCRIPTIONAL ACTIVITY IN NEURONAL CELLS
Creators: name: Wierman, Margaret E.
name: Pawlowski, John E.
name: Allen, Melissa P.
name: Ertel, Jessica R.
name: Xu, Mei
name: Butler, Cheryl
name: Wilson, Elizabeth M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2002

description: A yeast two-hybrid assay was employed to identify androgen receptor (AR) protein partners in gonadotropin-releasing hormone neuronal cells. By using an AR deletion construct (AR-(Delta371-485)) as a bait, beta-catenin was identified as an AR-interacting protein from a gonadotropin-releasing hormone neuronal cell library. Immunolocalization of co-transfected AR and FLAG-beta-catenin demonstrated that FLAG-beta-catenin was predominantly cytoplasmic in the absence of androgen. In the presence of 5alpha-dihydrotestosterone, FLAG-beta-catenin completely co-localized to the nucleus with AR. This effect was specific to AR because liganded progesterone, glucocorticoid, or estrogen alpha receptors did not translocate FLAG-beta-catenin to the nucleus. Agonist-bound AR was required because the AR antagonists casodex and hydroxyflutamide failed to translocate beta-catenin. Time course experiments demonstrated that co-translocation occurred with similar kinetics. Nuclear co-localization was independent of the glycogen synthase kinase-3beta, p42/44 ERK mitogen-activated protein kinase, and phosphatidylinositol 3-kinase pathways because inhibitors of these pathways had no effect. Transcription assays demonstrated that liganded AR repressed beta-catenin/T cell factor-responsive reporter gene activity. Conversely, co-expression of beta-catenin/T cell factor repressed AR stimulation of AR-responsive reporter gene activity. Our data suggest that liganded AR shuttles beta-catenin to the nucleus and that nuclear interaction of AR with beta-catenin may modulate transcriptional activity in androgen target tissues.
Supplementary table and figures from Pectoral girdle and forelimb musculoskeletal function in the echidna (Tachyglossus aculeatus): insights into mammalian locomotor evolution.
Creators: name: Regnault, Sophie
name: Pierce, Stephanie E.
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: 110601 Biomechanics
subject: FOS: Health sciences

description: File contains supplementary Table S1 and Figures S1-S6
Localization of Phosphatidylserine Binding Sites to Structural Domains of Factor X a
Creators: name: Esmon, Charles T.
name: Srivastava, Arvind
name: Rezaie, Alireza R.
name: Majumder, Rinku
name: Lentz, Barry R.
name: Wang, Jianfang
name: Stenflo, Johan
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2002

description: Binding of short chain phosphatidylserine (C6PS) enhances the proteolytic activity of factor X(a) by 60-fold (Koppaka, V., Wang, J., Banerjee, M., and Lentz, B. R. (1996) Biochemistry 35, 7482-7491). In the present study, we locate three C6PS binding sites to different domains of factor X(a) using a combination of activity, circular dichroism, fluorescence, and equilibrium dialysis measurements on proteolytic and biosynthetic fragments of factor X(a). Our results demonstrate that the structural responses of human and bovine factor X(a) to C6PS binding are somewhat different. Despite this difference, data obtained with fragments from both human and bovine factor X(a) are consistent with a common hypothesis for the location of C6PS binding sites to different structural domains. First, the gamma-carboxyglutamic acid (Gla) domain binds C6PS only in the absence of Ca(2+) (k(d) approximately 1 mm), although this PS site does not influence the functional response of factor X(a). Second, a Ca(2+)-dependent binding site is in the epidermal growth factor domains (EGF(NC)) that are linked by Ca(2+) and C6PS binding to the Gla domain. This site appears to be the lipid regulatory site of factor X(a). Third, a Ca(2+)-requiring site seems to be in the EGF(C)-catalytic domain. This site appears not to be a lipid regulatory site but rather to share residues with the substrate recognition site. Finally, the full functional response to C6PS requires linkage of the Gla, EGF(NC), and catalytic domains in the presence of Ca(2+), meaning that PS regulation of factor X(a) involves linkage between widely separated parts of the protein.
(1754) Richard Streatfield
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.
The strong reflecting property and Harrington's Principle
Creators: name: Cheng, Yong
Publisher: name: arXiv
Year: 2015
Subjects: subject: Logic (math.LO)
subject: FOS: Mathematics

description: In this paper we characterize the strong reflecting property for $L$-cardinals for all $ω_n$, characterize Harrington's Principle $HP(L)$ and its generalization and discuss the relationship between the strong reflecting property for $L$-cardinals and Harrington's Principle $HP(L)$.
description: 15 pages, to appear in MLQ
Table S3 from Drivers of spatio-temporal patterns of salinity in Spanish rivers: a nationwide assessment
Creators: name: Estévez, Edurne
name: Rodríguez-Castillo, Tamara
name: González-Ferreras, Alexia María
name: Cañedo-Argüelles, Miguel
name: Barquín, José
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Environmental Science
subject: Ecology
subject: FOS: Biological sciences

description: Extension of the Spanish river network and of each river typology not salinised and salinised, including the degree of salinisation (slight, moderate, heavy and extreme).
Loss of Transgelin in Breast and Colon Tumors and in RIE-1 Cells by Ras Deregulation of Gene Expression through Raf-independent Pathways
Creators: name: Der, Channing J.
name: Rogers-Graham, Kelley
name: Shields, Janiel M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2002

description: Activated Ras but not Raf can transform RIE-1 and other epithelial cells, indicating the critical importance of Raf-independent effector function in Ras transformation of epithelial cells. To elucidate the nature of these Raf-independent activities, we utilized representational difference analysis to identify genes aberrantly expressed by Ras through Raf-independent mechanisms in RIE-1 cells. We identified a total of 22 genes, both known and novel, whose expression was either activated or abolished by Ras but not Raf. The genes up-regulated encode proteins involved in protein or DNA synthesis, regulation of protease activity, or ligand binding, whereas those genes down-regulated encode actin cytoskeletal-, extracellular matrix-, and gap junction-associated proteins, and transmembrane receptor- or cytokine-like proteins. These results suggest that a key function of Raf-independent signaling involves deregulation of gene expression. We further characterized transgelin as a gene whose expression was abolished by Ras. Transgelin was identified previously as a protein whose expression was lost in virally transformed cell lines. We show that this loss is regulated at the level of gene expression and that both Raf-dependent and Raf-independent pathways are required to cause Ras down-regulation of transgelin in RIE-1 cells, whereas Raf alone is sufficient to cause its loss in NIH 3T3 fibroblasts. We also found that Ras-dependent and Ras-independent mechanisms can cause the down-regulation of transgelin in human breast and colon carcinoma cells lines and patient-derived tumor samples. We conclude that loss of transgelin gene expression may be an important early event in tumor progression and a diagnostic marker for breast and colon cancer development.
R Notebook of S1 from Quantitative characterization of iridescent colours in biological studies: a novel method using optical theory.
Creators: name: Gruson, Hugo
name: Andraud, Christine
name: WillyDaney DeMarcillac
name: Berthier, Serge
name: Elias, Marianne
name: Gomez, Doris
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Biophysics
subject: Environmental Science
subject: 90301 Biomaterials
subject: FOS: Medical engineering

description: R Notebook containing the code used in our worked example presented in S1. All necessary data to run the code and test the method yourself is provided as well.
(1755) Mary Williams Scarlett
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.
Mer Receptor Tyrosine Kinase Signaling: PREVENTION OF APOPTOSIS AND ALTERATION OF CYTOSKELETAL ARCHITECTURE WITHOUT STIMULATION OR PROLIFERATION
Creators: name: Shelton Earp, H.
name: Kozlowska, Eva
name: Dawson, Thomas L.
name: Guttridge, Katherine L.
name: Christopher Luft, J.
name: Mahajan, Nupam P.
name: Varnum, Brian
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2002

description: Mer is a member of the Axl/Mer/Tyro3 receptor tyrosine kinase family, a family whose physiological function is not well defined. We constructed a Mer chimera using the epidermal growth factor receptor (EGFR) extracellular and transmembrane domains and the Mer cytoplasmic domain. Stable transfection of the Mer chimera into interleukin 3 (IL-3)-dependent murine 32D cells resulted in ligand-activable surface receptor that tyrosine autophosphorylated, stimulated intracellular signaling, and dramatically reduced apoptosis initiated by IL-3 withdrawal. However, unlike multiple other ectopically expressed receptor tyrosine kinases including full-length EGFR or an EGFR/Axl chimera, the Mer chimera did not stimulate proliferation. Moreover, and in contrast to EGFR, Mer chimera activation induced adherence and cell flattening in the normally suspension-growing 32D cells. The Mer chimera signal also blocked IL-3-dependent proliferation leading to G(1)/S arrest, dephosphorylation of retinoblastoma protein, and elongation of cellular processes. Unlike other agonists that lead to a slow (4-8 days) ligand-dependent differentiation of 32D cells, the combined Mer and IL-3 signal resulted in differentiated morphology and growth cessation in the first 24 h. Thus the Mer chimera blocks apoptosis without stimulating growth and produces cytoskeletal alterations; this outcome is clearly separable from the proliferative signal produced by most receptor tyrosine kinases.
Unveiling hidden topological phases of a one-dimensional Hadamard quantum walk
Creators: name: Obuse, Hideaki
name: Asboth, Janos K.
name: Nishimura, Yuki
name: Kawakami, Norio
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Quantum walks, whose dynamics is prescribed by alternating unitary coin and shift operators, possess topological phases akin to those of Floquet topological insulators, driven by a time-periodic field. While there is ample theoretical work on topological phases of quantum walks where the coin operators are spin rotations, in experiments a different coin, the Hadamard operator is often used instead. This was the case in a recent photonic quantum walk experiment, where protected edge states were observed between two bulks whose topological invariants, as calculated by the standard theory, were the same. This hints at a hidden topological invariant in the Hadamard quantum walk. We establish a relation between the Hadamard and the spin rotation operator, which allows us to apply the recently developed theory of topological phases of quantum walks to the one-dimensional Hadamard quantum walk. The topological invariants we derive account for the edge state observed in the experiment, we thus reveal the hidden topological invariant of the one-dimensional Hadamard quantum walk.
description: 11 pages, 4 figures