cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Analysis of Plant Varieties Genetic Resources in Afghanistan
Creators: name: Wasiq, Mohammad Rasikh
name: Sadat Nasiri, Sayed Mahdi
Publisher: name: figshare
Year: 2023
Subjects: Intellectual property law
Property law (excl. intellectual property law)

description: The study explains in particular the different forms of legal protection required by international IPR agreements, including the system of plant breeders' rights in the 1978 and 1991 UPOV Acts, the choice between patent and sui generis protection created by article 27.3(b) of the TRIPs Agreement and the impact of so-called "TRIPs plus" bilateral and regional treaties. It analyses the alternatives available to a state depending upon the different IPR treaties it has ratified. Each of these treaties grants national governments a different level of discretion to choose how to protect plant varieties as a form of intellectual property. Once a government has consulted this study to determine the degree of discretion it enjoys as a result of its treaty ratifications, it can then review those portions of the study that identify the mechanisms that it may adopt, consistent with its international obligations, to balance the protection of IPRs against other societal objectives. Governments interested in retaining discretion would be advised to monitor and participate in these negotiations, with a view to harmonizing their international obligations, thereby avoiding the necessity of turning to international tribunals to settle their disputes.
Amino Acid Substitutions at Position 43 of Nae I Endonuclease: EVIDENCE FOR CHANGES INNaeI STRUCTURE
Creators: name: Topal, Michael D.
name: Carrick, Kevin L.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2003

description: NaeI endonuclease contains a 10-amino acid region with sequence similarity to the active site KXDG motif of DNA ligase except for leucine (Leu-43) in NaeI ((43)LXDG(46)). Changing Leu-43 to lysine abolishes the NaeI endonuclease activity and replaces it with topoisomerase and recombinase activities. Here we report the results of substituting Leu-43 with alanine, arginine, asparagine, glutamate, and histidine. Quantitating specific activities and DNA binding values for the mutant proteins determined the range of amino acids at position 43 that alter NaeI mechanism. Substituting alanine, asparagine, glutamate, and histidine for Leu-43 maintained endonuclease activity, but at a lower level. On the other hand, substituting positively charged arginine, like lysine at position 43, converted NaeI to a topoisomerase with no observable double-strand cleavage activity. The specific activities of NaeI-43K and NaeI-43R and their relative sensitivities to salt, the topoisomerase-inhibiting drug N-[4-(9-acridinylamino)-3-methoxyphenyl]methane-sulfonamide (amsacrine) and single-stranded DNA showed that the two activities are similar. The effect of placing a positive charge at position 43 on NaeI structure was determined by measuring (for NaeI and NaeI-43K) relative susceptibilities to proteolysis, UV, circular dichroism spectra, and temperature melting transitions. The results provide evidence that a positive charge at position 43 induces dramatic changes in NaeI structure that affect both the Endo and Topo domains of NaeI. The identification of four putative DNA ligase motifs in NaeI leads us to speculate that structural changes that superimpose these motifs on the ligase structure may account for the changes in activity.
(1729) Francis Crossley
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.
Supplementary material for 'Bio-inspired periodic panels optimised for acoustic insulation' from Bioinspired periodic panels optimized for acoustic insulation
Creators: name: Dal Poggetto, Vinícius F.
name: Pugno, Nicola M.
name: Arruda, José Roberto de F.
Publisher: name: The Royal Society
Year: 2022
Subjects: Mechanics

description: The design of structures that can yield efficient sound insulation performance is a recurring topic in the acoustic engineering field. Special attention is given to panels, which can be designed using several approaches to achieve considerable sound attenuation. In a previous work, we have presented the concept of thickness-varying periodic plates with optimized profiles to inhibit flexural wave energy propagation. In this work, motivated by biological structures that present multiple locally resonant elements able to cause acoustic cloaking, we extend our shape optimization approach to design panels that achieve improved acoustic insulation performance using either thickness-varying profiles or locally resonant attachments. The optimization is performed using numerical models that combine the Kirchhoff plate theory and the plane wave expansion method. Our results indicate that panels based on locally resonant mechanisms have the advantage of being robust against variation in the incidence angle of acoustic excitation and, therefore, are preferred for single-leaf applications.This article is part of the theme issue ‘Wave generation and transmission in multi-scale complex media and structured metamaterials (part 2)’.
On Estimating the High-Energy Cutoff in the X-ray Spectra of Black Holes via Reflection Spectroscopy
Creators: name: Garcia, Javier A.
name: Dauser, Thomas
name: Steiner, James F.
name: McClintock, Jeffrey E.
name: Keck, Mason L.
name: Wilms, Joern
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: Astrophysics of Galaxies (astro-ph.GA)
subject: FOS: Physical sciences

description: The fundamental parameters describing the coronal spectrum of an accreting black hole are the slope $Γ$ of the power-law continuum and the energy $E_{cut}$ at which it rolls over. Remarkably, this parameter can be accurately measured for values as high as 1 MeV by modeling the spectrum of X-rays reflected from a black hole accretion disk at energies below 100 keV. This is possible because the details in the reflection spectrum, rich in fluorescent lines and other atomic features, are very sensitive to the spectral shape of the hardest coronal radiation illuminating the disk. We show that fitting simultaneous NuSTAR (3-79 keV) and low-energy (e.g., Suzaku) data with the most recent version of our reflection model RELXILL, one can obtain reasonable constraints on $E_{cut}$ at energies from tens of keV up to 1 MeV, for a source as faint as 1 mCrab in a 100 ks observation.
description: Accepted for publication in ApJL, 6 pages, 5 figures
An Endogenous Inhibitor of Focal Adhesion Kinase Blocks Rac1/JNK but Not Ras/ERK-dependent Signaling in Vascular Smooth Muscle Cells
Creators: name: Mack, Christopher P.
name: Galante, Lisa M.
name: Sundberg, Liisa J.
name: Taylor, Joan M.
name: Bill, Heather M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2003

description: Humoral factors and extracellular matrix are critical co-regulators of smooth muscle cell (SMC) migration and proliferation. We reported previously that focal adhesion kinase (FAK)-related non-kinase (FRNK) is expressed selectively in SMC and can inhibit platelet-derived growth factor BB homodimer (PDGF-BB)-induced proliferation and migration of SMC by attenuating FAK activity. The goal of the current studies was to identify the mechanism by which FAK/FRNK regulates SMC growth and migration in response to diverse mitogenic signals. Transient overexpression of FRNK in SMC attenuated autophosphorylation of FAK at Tyr-397, reduced Src family-dependent tyrosine phosphorylation of FAK at Tyr-576, Tyr-577, and Tyr-881, and reduced phosphorylation of the FAK/Src substrates Cas and paxillin. However, FRNK expression did not alter the magnitude or dynamics of ERK activation induced by PDGF-BB or angiotensin II. Instead, FRNK expression markedly attenuated PDGF-BB-, angiotensin II-, and integrin-stimulated Rac1 activity and attenuates downstream signaling to JNK. Importantly, constitutively active Rac1 rescued the proliferation defects in FRNK expressing cells. Based on these observations, we hypothesize that FAK activation is required to integrate integrin signals with those from receptor tyrosine kinases and G protein-coupled receptors through downstream activation of Rac1 and that in SMC, FRNK may control proliferation and migration by buffering FAK-dependent Rac1 activation.
Reevaluation of experimental data using Hedges d instead of log-transformed response ratios as a metric for effect size. from Robust quantification of fish early life CO2 sensitivities via serial experimentation.
Creators: name: Baumann, Hannes
name: Cross, Emma
name: Murray, Chris
Publisher: name: The Royal Society
Year: 2018
Subjects: Environmental Science

description: Despite the remarkable expansion of laboratory studies, robust estimates of single species CO2 sensitivities remain largely elusive. We conducted a meta-analysis of 20 CO2 exposure experiments conducted over 6 years on offspring of wild Atlantic silversides (Menidia menidia) to robustly constrain CO2 effects on early life survival and growth. We conclude that early stages of this species are generally tolerant to CO2 levels of approximately 2000 µatm, likely because they already experience these conditions on diel to seasonal timescales. Still, high CO2 conditions measurably reduced fitness in this species by significantly decreasing average embryo survival (−9%) and embryo + larval survival (−13%). Survival traits had much larger coefficients of variation (greater than 30%) than larval length or growth (3–11%). CO2 sensitivities varied seasonally and were highest at the beginning and end of the species' spawning season (April–July), likely due to the combined effects of transgenerational plasticity and maternal provisioning. Our analyses suggest that serial experimentation is a powerful, yet underused tool for robustly estimating small but true CO2 effects in fish early life stages.
Pieces of the Flavour Puzzle
Creators: name: Feruglio, Ferruccio
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: FOS: Physical sciences

description: An overview of the flavour problem is presented, with emphasis on the theoretical efforts to find a satisfactory description of fermion masses and mixing angles.
description: 26 pages, 7 figures
An SH2 Domain-dependent, Phosphotyrosine-independent Interaction between Vav1 and the Mer Receptor Tyrosine Kinase: A MECHANISM FOR LOCALIZING GUANINE NUCLEOTIDE-EXCHANGE FACTOR ACTION
Creators: name: Earp, H. Shelton
name: Mahajan, Nupam P.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2003

description: Mer belongs to the Mer/Axl/Tyro3 receptor tyrosine kinase family, which regulates immune homeostasis in part by triggering monocyte ingestion of apoptotic cells. Mutations in Mer can also cause retinitis pigmentosa, again due to defective phagocytosis of apoptotic material. Although, some functional aspects of Mer have been deciphered, how receptor activation lead to the physiological consequences is not understood. By using yeast two-hybrid assays, we identified the carboxyl-terminal region of the guanine nucleotide-exchange factor (GEF) Vav1 as a Mer-binding partner. Unlike similar (related) receptors, Mer interacted with Vav1 constitutively and independently of phosphotyrosine, yet the site of binding localized to the Vav1 SH2 domain. Mer activation resulted in tyrosine phosphorylation of Vav1 and release from Mer, whereas Vav1 was neither phosphorylated nor released from kinase-dead Mer. Mutation of the Vav1 SH2 domain phosphotyrosine coordinating Arg-696 did not alter Mer/Vav1 constitutive binding or Vav1 tyrosine phosphorylation but did retard Vav1 release from autophosphorylated Mer. Ligand-dependent activation of Mer in human monocytes led to Vav1 release and stimulated GDP replacement by GTP on RhoA family members. This unusual constitutive, SH2 domain-dependent, but phosphotyrosine-independent, interaction and its regulated local release and subsequent activation of Rac1, Cdc42, and RhoA may explain how Mer coordinates precise cytoskeletal changes governing the ingestion of apoptotic material by macrophages and pigmented retinal epithelial cells.
Association of the Kinesin Motor KIF1A with the Multimodular Protein Liprin-α
Creators: name: Kim, Eunjoon
name: Huh, Kyung Hye
name: Ko, Jaewon
name: Streuli, Michel
name: Lee, Jae Ran
name: Wyszynski, Michael
name: Valtschanoff, Juli G.
name: Shin, Hyewon
name: Sheng, Morgan
name: Weinberg, Richard J.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2003

description: Liprin-alpha/SYD-2 is a multimodular scaffolding protein important for presynaptic differentiation and postsynaptic targeting of alpha-amino-3-hydroxy-5-methyl-4-isoxazoleproprionic acid glutamate receptors. However, the molecular mechanisms underlying these functions remain largely unknown. Here we report that liprin-alpha interacts with the neuron-specific kinesin motor KIF1A. KIF1A colocalizes with liprin-alpha in various subcellular regions of neurons. KIF1A coaccumulates with liprin-alpha in ligated sciatic nerves. KIF1A cofractionates and coimmunopreciptates with liprin-alpha and various liprin-alpha-associated membrane, signaling, and scaffolding proteins including alpha-amino-3-hydroxy-5-methyl-4-isoxazoleproprionic acid receptors, GRIP/ABP, RIM, GIT1, and beta PIX. These results suggest that liprin-alpha functions as a KIF1A receptor, linking KIF1A to various liprin-alpha-associated proteins for their transport in neurons.
(1731) Hilda Blackburn Baines
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.
What do we not know? Quantifying data gaps and biases in knowledge of bat co-roosting
Creators: name: Sherman, Aja C.
name: Geiselman, Cullen
name: Simons, Nancy B.
name: Upham, Nathan S.
name: Poelen, Jorrit H.
name: Reeder, DeeAnn  M.
name: Bertolino, Sandro
name: Groom, Quentin
name: Phelps, Kendra
name: Agosti, Donat
name: Willoughby, Anna R.
Publisher: name: Zenodo
Year: 2022
Subjects: biodiversity, chiroptera, viral spillover

description: Improved understanding of co-habitation of roosts by multiple species of bats is essential for estimating the risks of zoonotic disease transmission. However, ecological data on roosting environments, species richness, bat-bat interactions, viral infections, and other species interactions are scattered throughout the literature, making them difficult to study on a global scale. The research scope for most roost studies has been narrow, focusing on roost type, bat abundance, and locality data while failing to investigate interspecific roosting interactions. To meet this need, we have collaboratively built an open-access dataset of ecological interactions (including co-roosting, trophic, anthropogenic, and parasitic) extracted from the literature to improve our understanding of roost dynamics on a global scale, and to elucidate the role of shared roosts in disease transmission. As of April 2022, >11,500 interaction records involving >360 bat species from >137 countries encompassing a variety of habitats have been extracted from >175 publications spanning from 1860-2020, all accessible via the Coronavirus-Host community at Zenodo. With this benchmark dataset of open-access digitized interaction data, tools, and workflows, we provide evidence of co-roosting events that we aligned with multiple ontologies (interaction terms, taxonomies, administrative regions) and phylogenies suitable for high-throughput analysis We followed open access and FAIR (Findable, Accessible, Interoperable, and Reusable) data principles for extracting data and choosing methodologies. We identify biases in the coverage of bat interaction records, suggest new tools for biodiversity informatics, and explore obstacles and opportunities in the mining of eco-interactions previously lost in the annals of scientific literature.
A Bayesian Approach to Longevity Risk Management
Creators: name: MELVERN  LEUNG
Publisher: name: Monash University
Year: 2020
Subjects: subject: 140302 Econometric and Statistical Methods
subject: FOS: Economics and business
subject: 150202 Financial Econometrics

description: In this thesis, we apply three Bayesian econometric tools in the area of longevity risk management. Firstly, we develop an algorithm to Mortality modelling under the Bayesian state-space framework. Our framework allows for efficient and fast estimation of model parameters. Secondly, we provide a new hypothesis testing method using Bayesian Decision Theory applied in annuity liabilities, which is a more robust approach to the standard Null Hypothesis Significance Testing. Lastly, we provide a Bayesian risk premium analysis for longevity derivatives.
Developmental time windows for axon growth influence neuronal network topology
Creators: name: Lim, Sol
name: Kaiser, Marcus
Publisher: name: arXiv
Year: 2015
Subjects: subject: Neurons and Cognition (q-bio.NC)
subject: Biological Physics (physics.bio-ph)
subject: Physics and Society (physics.soc-ph)
subject: FOS: Biological sciences
subject: FOS: Physical sciences

description: Early brain connectivity development consists of multiple stages: birth of neurons, their migration and the subsequent growth of axons and dendrites. Each stage occurs within a certain period of time depending on types of neurons and cortical layers. Forming synapses between neurons either by growing axons starting at similar times for all neurons (much-overlapped time windows) or at different time points (less-overlapped) may affect the topological and spatial properties of neuronal networks. Here, we explore the extreme cases of axon formation especially concerning short-distance connectivity during early development, either starting at the same time for all neurons (parallel, i.e. maximally-overlapped time windows) or occurring for each neuron separately one neuron after another (serial, i.e. no overlaps in time windows). For both cases, the number of potential and established synapses remained comparable. Topological and spatial properties, however, differed: neurons that started axon growth early on in serial growth achieved higher out-degrees, higher local efficiency, and longer axon lengths while neurons demonstrated more homogeneous connectivity patterns for parallel growth. Second, connection probability decreased more rapidly with distance between neurons for parallel growth than for serial growth. Third, bidirectional connections were more numerous for parallel growth. Finally, we tested our predictions with C. elegans data. Together, this indicates that time windows for axon growth influence the topological and spatial properties of neuronal networks opening the possibility to a posteriori estimate developmental mechanisms based on network properties of a developed network.
description: Biol Cybern. 2015 Jan 30. [Epub ahead of print]
(1726) Harold Crossley Salt
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.
Dynamics of social contagions with limited contact capacity
Creators: name: Wang, Wei
name: Shu, Panpan
name: Zhu, Yu-Xiao
name: Tang, Ming
name: Zhang, Yi-Cheng
Publisher: name: arXiv
Year: 2015
Subjects: subject: Physics and Society (physics.soc-ph)
subject: Social and Information Networks (cs.SI)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences

description: Individuals are always limited by some inelastic resources, such as time and energy, which restrict them to dedicate to social interaction and limit their contact capacity. Contact capacity plays an important role in dynamics of social contagions, which so far has eluded theoretical analysis. In this paper, we first propose a non-Markovian model to understand the effects of contact capacity on social contagions, in which each individual can only contact and transmit the information to a finite number of neighbors. We then develop a heterogeneous edge-based compartmental theory for this model, and a remarkable agreement with simulations is obtained. Through theory and simulations, we find that enlarging the contact capacity makes the network more fragile to behavior spreading. Interestingly, we find that both the continuous and discontinuous dependence of the final adoption size on the information transmission probability can arise. And there is a crossover phenomenon between the two types of dependence. More specifically, the crossover phenomenon can be induced by enlarging the contact capacity only when the degree exponent is above a critical degree exponent, while the the final behavior adoption size always grows continuously for any contact capacity when degree exponent is below the critical degree exponent.
description: 8 pages, 6 figures
Chaperone-dependent Regulation of Endothelial Nitric-oxide Synthase Intracellular Trafficking by the Co-chaperone/Ubiquitin Ligase CHIP
Creators: name: Babbitt, Roger W.
name: Sessa, William C.
name: Cyr, Douglas
name: Patterson, Cam
name: Jiang, Jihong
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2003

description: Endothelial nitric-oxide synthase (eNOS), the enzyme responsible for production of endothelial NO, is under tight and complex regulation. Proper cellular localization of eNOS is critical for optimal coupling of extracellular stimulation with NO production. In addition, the molecular chaperone Hsp90 interacts with eNOS and positively regulates eNOS activity. Hsp90 is modulated by physical interaction with its co-chaperones. CHIP (carboxyl terminus of Hsp70-interacting protein) is such a co-chaperone that remodels the Hsp90 heterocomplex and causes protein degradation of some Hsp90 substrates through the ubiquitin-protein isopeptide ligase activity of CHIP. Here we show that CHIP incorporated into the eNOS.Hsp90 complex and specifically decreased soluble eNOS levels in transiently transfected COS cells. Surprisingly, in contrast to the effects of the Hsp90 inhibitor geldanamycin, which induces eNOS ubiquitylation and its subsequent protein degradation, CHIP did not target eNOS for ubiquitylation and proteasome-dependent degradation. Instead, CHIP partitioned soluble eNOS into an insoluble and inactive cellular compartment, presumably through its co-chaperone activity. This effect seems to be due to displacement of eNOS from the Golgi apparatus, which is otherwise required for trafficking of eNOS to the plasmalemma and subsequent activation. Consistent with observations from overexpression studies, eNOS localization to the membrane and activity were increased in mouse lung endothelial cells lacking CHIP. Taken together, these results demonstrate a novel co-chaperone-dependent mechanism through which eNOS trafficking is regulated and suggest a potentially generalized role for CHIP in protein trafficking through the Golgi compartment.
Supplemental Information from Neural differences between internal and external episodic counterfactual thoughts
Creators: name: Khoudary, Maria
name: O'Neill, Kevin
name: Faul, Leonard
name: Murray, Samuel
name: Smallman, Rachel
name: De Brigard, Felipe
Publisher: name: The Royal Society
Year: 2022
Subjects: subject: Neuroscience
subject: 170299 Cognitive Science not elsewhere classified
subject: FOS: Psychology

description: Supplementary Figures and Tables; Section S10: fMRI preprocessing; Section S15: Autobiographical memory prompts; References
Reevaluation of experimental data using Hedges d instead of log-transformed response ratios as a metric for effect size. from Robust quantification of fish early life CO2 sensitivities via serial experimentation
Creators: name: Baumann, Hannes
name: Cross, Emma
name: Murray, Chris
Publisher: name: The Royal Society
Year: 2018
Subjects: Environmental Science

description: Despite the remarkable expansion of laboratory studies, robust estimates of single species CO2 sensitivities remain largely elusive. We conducted a meta-analysis of 20 CO2 exposure experiments conducted over 6 years on offspring of wild Atlantic silversides (Menidia menidia) to robustly constrain CO2 effects on early life survival and growth. We conclude that early stages of this species are generally tolerant to CO2 levels of approximately 2000 µatm, likely because they already experience these conditions on diel to seasonal time scales. Still, high CO2 conditions measurably reduced fitness in this species by significantly decreasing average embryo survival (−9%) and embryo + larval survival (−13%). Survival traits had much larger coefficients of variation (greater than 30%) than larval length or growth (3–11%). CO2 sensitivities varied seasonally and were highest at the beginning and end of the species' spawning season (April–July), likely due to the combined effects of transgenerational plasticity and maternal provisioning. Our analyses suggest that serial experimentation is a powerful, yet underused tool for robustly estimating small but true CO2 effects in fish early life stages.
Citron Kinase Is a Cell Cycle-dependent, Nuclear Protein Required for G 2 /M Transition of Hepatocytes
Creators: name: Reid, Lola M.
name: Di Cunto, Ferdinando
name: Liu, Huifei
name: Imarisio, Sara
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2003

description: Citron Kinase (Citron-K) is a cell cycle-dependent protein regulating the G(2)/M transition in hepatocytes. Synchronization studies demonstrated that expression of the Citron-K protein starts at the late S and/or the early G(2) phase after that of cyclin B1. Expression of Citron-K is developmentally regulated. Levels of Citron-K mRNA and protein are highest in embryonic liver and gradually decrease after birth. Citron-K exists in interphase nuclei and begins to disperse into the cytoplasm at prophase. It concentrates at the cleavage furrow and midbody during anaphase, telophase, and cytokinesis, implicating a role in the control of cytokinesis. However, studies with knockouts show that Citron-K is not essential for cytokinesis in hepatocytes. Instead, loss of Citron-K causes a significant increase of G(2) tetraploid nuclei in one-week-old rat and mouse liver. In addition, Citron-K deficiency triggers apoptosis in a small subset of embryonic liver cells. In summary, our data demonstrate that Citron-K has a distinct cell cycle-dependent expression pattern and cellular localization as a downstream target of Rho-GTPase and functions in the control of G(2)/M transition in the hepatocyte cell cycle.
Supplementary material Quiroga et al. from Niche squeeze induced by climate change of the cold-tolerant subtropical montane Podocarpus parlatorei.
Creators: name: Quiroga, María Paula
name: Premoli, Andrea C.
name: Kitzberger, Thomas
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Genetics
subject: FOS: Biological sciences
subject: Ecology
subject: Plant Biology

description: Tables S1, S2 and S3 and figure 1S
Lattice Boltzmann Model for Numerical Relativity
Creators: name: Ilseven, E.
name: Mendoza, M.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Computational Physics (physics.comp-ph)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: Fluid Dynamics (physics.flu-dyn)
subject: FOS: Physical sciences

description: In the Bona-Masso formulation, Einstein equations are written as a set of flux conservative first order hyperbolic equations that resemble fluid dynamics equations. Based on this formulation, we construct a lattice Boltzmann model for Numerical Relativity. Our model is validated with well-established tests, showing good agreement with analytical solutions. Furthermore, we show that by increasing the relaxation time, we gain stability at the cost of losing accuracy, and by decreasing the lattice spacings while keeping a constant numerical diffusivity, the accuracy and stability of our simulations improves. Finally, in order to show the potential of our approach a linear scaling law for parallelisation with respect to number of CPU cores is demonstrated. Our model represents the first step in using lattice kinetic theory to solve gravitational problems.
description: 9 pages, 11 figures
(1727) John Crossley Wright
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.
(1728) Arthur Andrews
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.
Various samples from Algorithm for a particle-based growth model for plant tissues.
Creators: name: Opheusden, Joost H. J. Van
name: Molenaar, Jaap
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Plant Biology
subject: FOS: Biological sciences
subject: Computational Biology

description: Results for similar samples with different random seeds
Close Homolog of L1 Is an Enhancer of Integrin-mediated Cell Migration
Creators: name: Buhusi, Mona
name: Gates, Amanda M.
name: Maness, Patricia F.
name: Midkiff, Bentley R.
name: Richter, Melanie
name: Schachner, Melitta
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2003

description: Close homolog of L1 (CHL1) is a member of the L1 family of cell adhesion molecules expressed by subpopulations of neurons and glia in the central and peripheral nervous system. It promotes neurite outgrowth and neuronal survival in vitro. This study describes a novel function for CHL1 in potentiating integrin-dependent cell migration toward extracellular matrix proteins. Expression of CHL1 in HEK293 cells stimulated their haptotactic migration toward collagen I, fibronectin, laminin, and vitronectin substrates in Transwell assays. CHL1-potentiated cell migration to collagen I was dependent on alpha1beta1 and alpha2beta1 integrins, as shown with function blocking antibodies. Potentiated migration relied on the early integrin signaling intermediates c-Src, phosphatidylinositol 3-kinase, and mitogen-activated protein kinase. Enhancement of migration was disrupted by mutation of a potential integrin interaction motif Asp-Gly-Glu-Ala (DGEA) in the sixth immunoglobulin domain of CHL1, suggesting that CHL1 functionally interacts with beta1 integrins through this domain. CHL1 was shown to associate with beta1 integrins on the cell surface by antibody-induced co-capping. Through a cytoplasmic domain sequence containing a conserved tyrosine residue (Phe-Ile-Gly-Ala-Tyr), CHL1 recruited the actin cytoskeletal adapter protein ankyrin to the plasma membrane, and this sequence was necessary for promoting integrin-dependent migration to extracellular matrix proteins. These results support a role for CHL1 in integrin-dependent cell migration that may be physiologically important in regulating cell migration in nerve regeneration and cortical development.
Various samples from Algorithm for a particle-based growth model for plant tissues
Creators: name: Opheusden, Joost H. J. Van
name: Molenaar, Jaap
Publisher: name: The Royal Society
Year: 2018
Subjects: subject: Plant Biology
subject: FOS: Biological sciences
subject: Computational Biology

description: Results for similar samples with different random seeds
(1725) Gordon Locksley Salt
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 Wild-type Penicillin-binding Protein 5 from Escherichia coli: IMPLICATIONS FOR DEACYLATION OF THE ACYL-ENZYME COMPLEX
Creators: name: Davies, Christopher
name: Nicola, George
name: Krings, Sandra
name: Tomberg, Joshua
name: Nicholas, Robert A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2003

description: Penicillin-binding protein 5 (PBP 5) of Escherichia coli functions as a d-alanine carboxypeptidase (CPase), cleaving d-alanine from the C terminus of cell wall peptides. Like all PBPs, PBP 5 forms a covalent acyl-enzyme complex with beta-lactam antibiotics; however, PBP 5 is distinguished by its high rate of deacylation of the acylenzyme complex (t(1/2) approximately 10 min). A Gly105 --> Asp mutation in PBP 5 markedly impairs deacylation with only minor effects on acylation, and abolishes CPase activity. We have determined the three-dimensional structure of a soluble form of wild-type PBP 5 at 1.85-A resolution and have also refined the structure of the G105D mutant form of PBP 5 to 1.9-A resolution. Comparison of the two structures reveals that the major effect of the mutation is to disorder a loop comprising residues 74-90 that sits atop the SXN motif of the active site. Deletion of the 74-90 loop in wild-type PBP 5 markedly diminished the deacylation rate of penicillin G with a minimal impact on acylation, and abolished CPase activity. These effects were very similar to those observed in the G105D mutant, reinforcing the idea that this mutation causes disordering of the 74-90 loop. Mutation of two consecutive serines within this loop, which hydrogen bond to Ser110 and Asn112 in the SXN motif, had marked effects on CPase activity, but not beta-lactam antibiotic binding or hydrolysis. These data suggest a direct role for the SXN motif in deacylation of the acyl-enzyme complex and imply that the functioning of this motif is modulated by the 74-90 loop.
Dentin Sialophosphoprotein Knockout Mouse Teeth Display Widened Predentin Zone and Develop Defective Dentin Mineralization Similar to Human Dentinogenesis Imperfecta Type III
Creators: name: Wright, J. Tim
name: Longenecker, Glenn
name: Thyagarajan, Tamizchelvi
name: Hall, Bradford
name: Kulkarni, Ashok B.
name: D'Souza, Rena
name: Sreenath, Taduru
name: Hong, Sung
name: MacDougall, Mary
name: Sauk, John
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2003

description: Dentin sialophosphoprotein (Dspp) is mainly expressed in teeth by the odontoblasts and preameloblasts. The Dspp mRNA is translated into a single protein, Dspp, and cleaved into two peptides, dentin sialoprotein and dentin phosphoprotein, that are localized within the dentin matrix. Recently, mutations in this gene were identified in human dentinogenesis imperfecta II (Online Mendelian Inheritance in Man (OMIM) accession number 125490) and in dentin dysplasia II (OMIM accession number 125420) syndromes. Herein, we report the generation of Dspp-null mice that develop tooth defects similar to human dentinogenesis imperfecta III with enlarged pulp chambers, increased width of predentin zone, hypomineralization, and pulp exposure. Electron microscopy revealed an irregular mineralization front and a lack of calcospherites coalescence in the dentin. Interestingly, the levels of biglycan and decorin, small leucine-rich proteoglycans, were increased in the widened predentin zone and in void spaces among the calcospherites in the dentin of null teeth. These enhanced levels correlate well with the defective regions in mineralization and further indicate that these molecules may adversely affect the dentin mineralization process by interfering with coalescence of calcospherites. Overall, our results identify a crucial role for Dspp in orchestrating the events essential during dentin mineralization, including potential regulation of proteoglycan levels.
Ramanujan Cayley graphs of Frobenius groups
Creators: name: Hirano, Miki
name: Katata, Kohei
name: Yamasaki, Yoshinori
Publisher: name: arXiv
Year: 2015
Subjects: subject: Number Theory (math.NT)
subject: Combinatorics (math.CO)
subject: FOS: Mathematics
subject: 05C50 (Primary), 05C25 (Secondary), 11M41, 11N32

description: In this paper, we determine the bound of the valency of Cayley graphs of Frobenius groups with respect to normal Cayley subsets which guarantees to be Ramanujan. We see that if the ratio between the orders of the Frobenius kernel and complement is not so small, then this bound coincides with the trivial one coming from the trivial estimate of the largest non-trivial eigenvalue of the graphs. Moreover, in the cases of the dihedral groups of order twice odd primes, which are special cases of the Frobenius groups, we determine the same bound for the Cayley graphs of the groups with respect to not only normal but also all Cayley subsets. As is the case of abelian groups which we have treated in the previous papers, such a bound is equal to the trivial one in the above sense or, as exceptional cases, exceeds one from it. We then clarify that the latter occurs if and only if the corresponding prime is represented by a quadratic polynomial in a finite family.
description: 12 pages
Session II: Future Directions for Open Force Field Initiative
Creators: name: Chodera, J. D.
Publisher: name: Zenodo
Year: 2020
Subjects: Open Force Field Initiative
force fields
machine learning
biomolecules
Bayesian inference

description: This presentation is a part of the Open Force Field Virtual Meeting 2020. Abstract: This talk provides an overview of potential future directions in force field development within the Open Force Field Initiative. These include self-consistent parameterization of biopolymers and other biomolecules, Bayesian inference modelling and machine learning applications. The latter include accelerating partial charge and torsion assignment, integrating machine learning potentials and differential typing.
Causal Fermion Systems -- An Overview
Creators: name: Finster, Felix
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mathematical Physics (math-ph)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: The theory of causal fermion systems is an approach to describe fundamental physics. We here introduce the mathematical framework and give an overview of the objectives and current results.
description: 54 pages, LaTeX, 1 figure, minor improvements (published version)
DIZAYNERLIKDA PEDAGOGIK TEXNOLOGIYALAR
Creators: name: To'xtayeva, Zebo
name: Rahmatova, Barnogul
Publisher: name: Zenodo
Year: 2023

description: Mazkur maqolada dizaynerlik yo'nalishida tahsil oluvchi talabalar bilimini yanada yaxshilash uchun ijodkorlik va dizayn ta'limi sohasida qo'llaniladigan o'qitish usullari va tadqiqotchilarning asl dizayn ta'limi sohasidagi natijalari an'anaviy dizayn ta'limi va yangi dizayn ta'lim usullarini o'zaro qiyoslash orqali atroflicha tahlil qilingan. Shuningdek ular sun'iy intellekt ya'ni AI texnologiyasi (inglizcha artificial intelligence) bilan uyg'unlashtirilgan. Qolaversa, dizaynerlikda zamonaviy pedogogik texnalogiyalarning mohiyati yoritib berilgan.
Test of the Atiyah-Singer Index Theorem for Fullerene with a Superconducting Microwave Resonator
Creators: name: Dietz, B.
name: Klaus, T.
name: Miski-Oglu, M.
name: Richter, A.
name: Bischoff, M.
name: von Smekal, L.
name: Wambach, J.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Nuclear Experiment (nucl-ex)
subject: Nuclear Theory (nucl-th)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: Experiments have been performed using a spherical superconducting microwave resonator that simulates the geometric structure of the C60 fullerene molecule. The objective was to study with very high resolution the exceptional spectral properties emerging from the symmetries of the icosahedral structure of the carbon lattice. In particular, the number of zero modes has been determined to test the predictions of the Atiyah-Singer index theorem, which relates it to the topology of the curved carbon lattice. This is, to the best of our knowledge, the first experimental verification of the index theorem.
Supplementary document for Flat-optics generation of broadband photon pairs with tunable polarization entanglement - 5794237.pdf
Creators: name: Sultanov, Vitaliy
name: Santiago, Tomas
name: Chekhova, Maria
Publisher: name: Optica Publishing Group
Year: 2022
Subjects: Uncategorized

description: The supplement contains the results of nonlinear characterization of the GaP thin film, the details about quantum polarization tomography, and clarifications about the Bell inequalitiy
Dependence of Peroxisome Proliferator-activated Receptor Ligand-induced Mitogen-activated Protein Kinase Signaling on Epidermal Growth Factor Receptor Transactivation
Creators: name: Dewar, Brian J.
name: Gardner, Olivia S.
name: Earp, H. Shelton
name: Samet, James M.
name: Graves, Lee M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2003

description: Peroxisome proliferator-activated receptors (PPARs) are nuclear hormone receptors that function as ligand-activated transcription factors regulating lipid metabolism and homeostasis. In addition to their ability to regulate PPAR-mediated gene transcription, PPARalpha and gamma ligands have recently been shown to induce activation of mitogen-activated protein kinases (MAPKs), which in turn phosphorylate PPARs, thereby affecting transcriptional activity. However, the mechanism for PPAR ligand-dependent MAPK activation is unclear. In the current study, we demonstrate that various PPARalpha (nafenopin) and gamma (ciglitazone and troglitazone) agonists rapidly induced extracellular signal-regulated kinase (Erk) and/or p38 phosphorylation in rat liver epithelial cells (GN4). The selective epidermal growth factor receptor (EGFR) kinase inhibitors, PD153035 and ZD1839 (Iressa), abolished PPARalpha and gamma agonist-dependent Erk activation. Consistent with this, PPAR agonists increased tyrosine autophosphorylation of the EGFR as well as phosphorylation at a putative Src-specific site, Tyr845. Experiments with the Src inhibitor, PP2, and the antioxidant N-acetyl-L-cysteine revealed critical roles for Src and reactive oxygen species as upstream mediators of EGFR transactivation in response to PPAR ligands. Moreover, PPARalpha and gamma ligands increased Src autophosphorylation as well as kinase activity. EGFR phosphorylation, in turn, led to Ras-dependent Erk activation. In contrast, p38 activation by PPARalpha and gamma ligands occurred independently of Src, oxidative stress, the EGFR, and Ras. Interestingly, PPARalpha and gamma agonists caused rapid activation of proline-rich tyrosine kinase or Pyk2; Pyk2 as well as p38 phosphorylation was reduced by intracellular Ca2+ chelation without an observable effect on EGFR and Erk activation, suggesting a possible role for Pyk2 as an upstream activator of p38. In summary, PPARalpha and gamma ligands activate two distinct signaling cascades in GN4 cells leading to MAPK activation.
Downstream DNA Sequence Effects on Transcription Elongation: ALLOSTERIC BINDING OF NUCLEOSIDE TRIPHOSPHATES FACILITATES TRANSLOCATION VIA A RATCHET MOTION
Creators: name: Holmes, Shannon F.
name: Erie, Dorothy A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2003

description: The ability of RNA polymerase (RNAP) to adopt multiple conformations is central to transcriptional regulation. In previous work, we demonstrated that RNAP can exist in an unactivated state that catalyzes synthesis slowly and an activated state that catalyzes synthesis rapidly, with the transition from the unactivated to the activated state being induced by the templated NTP binding to an allosteric site on the RNAP. In this work, we investigate the effects of downstream DNA sequences on the kinetics of single nucleotide incorporation. We demonstrate that changing the identity of the DNA base 1 bp downstream (+2) from the site of incorporation (+1) can regulate the catalytic activity of RNAP. Combining these data with sequence and structural analyses and molecular modeling, we identify the streptolydigin-binding region (Escherichia coli beta residues 543-546), which lies across from the downstream DNA, as the putative allosteric NTP binding site. We present a structural model in which the NTP binds to the streptolydigin loop and upon pairing with the +1 DNA base in the unactivated state or the +2 DNA base in the activated state facilitates translocation via a ratchet motion. This model provides an alternative mechanism for pausing as well as a structural explanation not only for our kinetic data but also for data from elongation studies on yeast RNAP II.