cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
The stem-loop binding protein regulates translation of histone mRNA during mammalian oogenesis
Creators: name: Marzluff, William F.
name: Clarke, Hugh J.
name: Yang, Qin
name: Allard, Patrick
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2005

description: Although messenger RNAs encoding the histone proteins are among the most abundant in mammalian oocytes, the mechanism regulating their translation has not been identified. The stem-loop binding protein (SLBP) binds to a highly conserved sequence in the 3′-untranslated region (utr) of the non-polyadenylated histone mRNAs in somatic cells and mediates their stabilization and translation. We previously showed that SLBP, which is expressed only during S-phase of proliferating cells, is expressed in growing oocytes at G2 of the cell cycle and accumulates substantially during meiotic maturation. We report here that elevating the amount of SLBP in immature (G2) oocytes is sufficient to increase translation of a reporter mRNA bearing the histone 3′-utr and endogenous histone synthesis and that this effect is not mediated through increased stability of the encoding mRNAs. We further report that translation of the reporter mRNA increases dramatically during meiotic maturation coincident with the accumulation of SLBP. Conversely, when SLBP accumulation during maturation is prevented using RNA interference, both translation of the reporter mRNA and synthesis of endogenous histones are significantly reduced. This effect is not mediated by a loss of the encoding mRNAs. Moreover, following fertilization, SLBP-depleted oocytes also show a significant decrease in pronuclear size and in the amount of acetylated histone detectable on the chromatin. These results demonstrate that histone synthesis in immature and maturing oocytes is governed by a translational control mechanism that is directly regulated by changes in the amount of SLBP.
Nonparametric modal regression
Creators: name: Chen, Yen-Chi
name: Genovese, Christopher R.
name: Tibshirani, Ryan J.
name: Wasserman, Larry
Publisher: name: arXiv
Year: 2014
Subjects: subject: Methodology (stat.ME)
subject: Statistics Theory (math.ST)
subject: Machine Learning (stat.ML)
subject: FOS: Computer and information sciences
subject: FOS: Mathematics

description: Modal regression estimates the local modes of the distribution of $Y$ given $X=x$, instead of the mean, as in the usual regression sense, and can hence reveal important structure missed by usual regression methods. We study a simple nonparametric method for modal regression, based on a kernel density estimate (KDE) of the joint distribution of $Y$ and $X$. We derive asymptotic error bounds for this method, and propose techniques for constructing confidence sets and prediction sets. The latter is used to select the smoothing bandwidth of the underlying KDE. The idea behind modal regression is connected to many others, such as mixture regression and density ridge estimation, and we discuss these ties as well.
description: Published at http://dx.doi.org/10.1214/15-AOS1373 in the Annals of Statistics (http://www.imstat.org/aos/) by the Institute of Mathematical Statistics (http://www.imstat.org)
An ethnography of environment in the Indus Delta, Sindh, Pakistan
Creators: name: Chang, Abdul Haque
name: 0000-0002-1329-2212
Publisher: name: The University of Texas at Austin
Year: 2015
Subjects: Environment
Ethnography

description: This study focuses on how the life of ordinary people living in the Indus River Delta in Pakistan has changed due to the building of the modern irrigation system, dam construction, and the development of water use infrastructure in Pakistan since 1947. The fieldwork was conducted in the Indus Delta at Baghan, Village Gul Muhammad Jat, Keti Bandar, and Kharo Chan in Sindh, Pakistan. During this fieldwork, life histories of ordinary fishermen were gathered to show how state narratives of water governance and NGO-led interventions meant to protect the environment and ecology intersect with fishermen’s everyday life. To contrast the fishermen’s ordinary lives with the narratives of national water governance and environmental initiatives, I conducted ethnographic research in carnivals held at the shrines of Sufi saints, observed political protests organized by nationalists, and held conversations with people at their otaq (male guesthouse) called kachahri. Kachahri is narrative form that allows the revealing of local sensibilities about space, place, environment, water, and ecology. Fishermen practice kachahri as a mode of sharing history and ordinary life. The research uses this form of narration as a methodological tool to understand, conceptualize, and comprehend their everyday lives in their terms. The thesis also asks how we should think about histories that are not written, archived, or narrated officially and yet are not dead, lost, or forgotten. I share ethnographic encounters in public spaces like tea-cafes, fishing jetties, shrines, and male guesthouses that become the foundation of a new understanding of how history and geography function in the Delta. The thesis also demonstrates how a lack of water in the Delta pushes fishermen beyond Pakistan’s maritime borders into Indian waters and how those arrested by the Indian Navy end up in Indian jails for years, without recourse to any legal help. Understanding the precarious lives of Pakistanis who inhabit such marginal rural spaces provides necessary insight into Pakistan’s political ecology, knowledge that is central to anthropological inquiry, particularly with ongoing discussions of climate change and its social impact.
title: Electrokinetic manipulation of micro to nano-sized objects for microfluidic application
Creators: name: Chichenkov, Aleksandr
Publisher: name: University of Liverpool Repository
Year: 2014

description: This thesis describes experimental and numerical investigations of various electrokinetic techniques on fluorescent particles, bacteria and protein motors. The aim of this work is to extend the knowledge on the object manipulation, which is an essential part of a practical microfluidic device. The dissertation consists of three major sections that contain novel approaches to object manipulation using electric fields. The effect of dielectrophoretic force on fluorescent particles is analysed first. Using an experimental setup with a controlled switch for the input signal, the theoretical framework for amplitude modulated responce of dielectrophoretic force is developed. Also presented is the image processing software for quantitative particle motion analysis. Another analysis of various electrokinetic techniques (dielectrophoresis, AC electroosmosis, AC electrothermal flow and electrophoresis) was carried out on Pseudomonas Fluorescence bacteria in a solution that supports its growth. These bacteria usually live in geometrically restricted spaces and so spatially confined transparent channels were created to mimic their natural environment. It was noted that in these conditions the motile bacteria do not experience the effect of dielectrophoretic force. The minimum frequency that can be applied to the solution without forming bubbles is too high to distinguish AC electroosmotic effect. Using the numerical simulation, however, the experimental setup that utilises the observed effect of electrophoresis and AC electrothermal flow is designed. The final study was carried out on protein molecular motors. The novel experimental setup to investigate the effect of the electric field on the actin filament motility on five different surfaces, covered with myosin II motors, was developed. The application of higher external electric fields resulted in different velocity increases on different surfaces. Using the numerical simulation, this difference is quantitatively explained by the variation of the number of motors on surfaces. Also presented is a novel method that enables determining the forces exerted by the population of active and resistive motors without the need of expensive equipment.
Energy in density gradient
Creators: name: Vranjes, J.
name: Kono, M.
Publisher: name: arXiv
Year: 2015
Subjects: subject: Plasma Physics (physics.plasm-ph)
subject: Solar and Stellar Astrophysics (astro-ph.SR)
subject: Fluid Dynamics (physics.flu-dyn)
subject: FOS: Physical sciences

description: Inhomogeneous plasmas and fluids contain energy stored in inhomogeneity and they naturally tend to relax into lower energy states by developing instabilities or by diffusion. But the actual amount of energy in such inhomogeneities has remained unknown. In the present work the amount of energy stored in a density gradient is calculated for several specific density profiles in a cylindric configuration. This is of practical importance for drift wave instability in various plasmas, and in particular in its application in models dealing with the heating of solar corona because the instability is accompanied with stochastic heating, so the energy contained in inhomogeneity is effectively transformed into heat. It is shown that even for a rather moderate increase of the density at the axis in magnetic structures in the corona by a factor 1.5 or 3, the amount of excess energy per unit volume stored in such a density gradient becomes several orders of magnitude greater than the amount of total energy losses per unit volume (per second) in quiet regions in the corona. Consequently, within the life-time of a magnetic structure such energy losses can easily be compensated by the stochastic drift wave heating.
description: 6 pages, 6 figures
Single-cell mapping of neural and glial gene expression in the developing Drosophila CNS midline cells
Creators: name: Wheeler, Scott R.
name: Kearney, Joseph B.
name: Guardiola, Amaris R.
name: Crews, Stephen T.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: Understanding the generation of neuronal and glial diversity is one of the major goals of developmental neuroscience. The Drosophila CNS midline cells constitute a simple neurogenomic system to study neurogenesis, cell fate acquisition, and neuronal function. Previously, we identified and determined the developmental expression profiles of 224 midline-expressed genes. Here, the expression of 59 transcription factors, signaling proteins, and neural function genes was analyzed using multi-label confocal imaging, and their expression patterns mapped at the single-cell level at multiple stages of CNS development. These maps uniquely identify individual cells and predict potential regulatory events and combinatorial protein interactions that may occur in each midline cell type during their development. Analysis of neural function genes, including those encoding peptide neurotransmitters, neurotransmitter biosynthetic enzymes, transporters, and neurotransmitter receptors, allows functional characterization of each neuronal cell type. This work is essential for a comprehensive genetic analysis of midline cell development that will likely have widespread significance given the high degree of evolutionary conservation of the genes analyzed.
TBX5 is required for embryonic cardiac cell cycle progression
Creators: name: Conlon, Frank L.
name: Goetz, Sarah C.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2006

description: Despite the critical importance of TBX5 in normal development and disease, relatively little is known about the mechanisms by which TBX5 functions in the embryonic heart. Our present studies demonstrate that TBX5 is necessary to control the length of the embryonic cardiac cell cycle, with depletion of TBX5 leading to cardiac cell cycle arrest in late G1- or early S-phase. Blocking cell cycle progression by TBX5 depletion leads to a decrease in cardiac cell number, an alteration in the timing of the cardiac differentiation program, defects in cardiac sarcomere formation, and ultimately, to cardiac programmed cell death. In these studies we have also established that terminally differentiated cardiomyocytes retain the capacity to undergo cell division. We further show that TBX5 is sufficient to determine the length of the embryonic cardiac cell cycle and the timing of the cardiac differentiation program. Thus, these studies establish a role for TBX5 in regulating the progression of the cardiac cell cycle.
Polarizable atomic multipole-based force field for cholesterol
Creators: name: Li, Yan
name: Liu, Ye
name: Yang, Boya
name: Li, Guohui
name: Chu, Huiying
Publisher: name: Taylor & Francis
Year: 2023
Subjects: Biophysics
Physical Sciences not elsewhere classified
Medicine
Chemical Sciences not elsewhere classified
Biological Sciences not elsewhere classified
Information Systems not elsewhere classified
Cancer
Computational Biology

description: Cholesterol is one of the essential component of lipid in membrane. We present a polarizable atomic multipole force field (FF) for the molecular dynamic simulation of cholesterol. The FF building process follows the computational framework as the atomic multipole optimized energetics for biomolecular applications (AMOEBA) model. In this framework, the electronics parameters, including atomic monopole moments, dipole moments, and quadrupole moments calculated from ab initio calculations in the gas phase, are applied to represent the charge distribution. Furthermore, the many-body polarization is modeled by following the same pattern of distributed atomic polarizabilities. Then, the bilayers composed of two typical phospholipid molecules, 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC), and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), in a range of different cholesterol concentrations are built and implemented by molecular dynamics (MD) simulations based on the proposed polarizable FF. The simulation results are statistically analyzed to validate the feasibility of the proposed FF. The structural properties of the bilayers are calculated to compare with the related experimental values. The MD values show the same trend of experimental values changes. Communicated by Ramaswamy H. Sarma
Differential rotation of the unstable nonlinear r-modes
Creators: name: Friedman, John L.
name: Lindblom, Lee
name: Lockitch, Keith H.
Publisher: name: arXiv
Year: 2015
Subjects: subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: At second order in perturbation theory, the $r$-modes of uniformly rotating stars include an axisymmetric part that can be identified with differential rotation of the background star. If one does not include radiation-reaction, the differential rotation is constant in time and has been computed by Sá. It has a gauge dependence associated with the family of time-independent perturbations that add differential rotation to the unperturbed equilibrium star: For stars with a barotropic equation of state, one can add to the time-independent second-order solution arbitrary differential rotation that is stratified on cylinders (that is a function of distance $\varpi$ to the axis of rotation). We show here that the gravitational radiation-reaction force that drives the $r$-mode instability removes this gauge freedom: The expontially growing differential rotation of the unstable second-order $r$-mode is unique. We derive a general expression for this rotation law for Newtonian models and evaluate it explicitly for slowly rotating models with polytropic equations of state.
description: Published (2016) version, but with two updated references
van der Waals-corrected Density Functional Theory simulation of adsorption processes on transition-metal surfaces: Xe and graphene on Ni(111)
Creators: name: Silvestrelli, Pier Luigi
name: Ambrosetti, Alberto
Publisher: name: arXiv
Year: 2015
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: Chemical Physics (physics.chem-ph)
subject: FOS: Physical sciences

description: The DFT/vdW-WF2s1 method, recently developed to include the van der Waals interactions in the Density Functional Theory and describe adsorption processes on metal surfaces by taking metal-screening effects into account, is applied to the case of the interaction of Xe and graphene with a transition-metal surface, namely Ni(111). In general the adsorption of rare-gas atoms on metal surfaces is important because is prototypical for physisorption processes. Moreover, the interaction of graphene with Ni(111) is of particular interest for practical applications (efficient and large-scale production of high-quality graphene) and, from a theoretical point of view, is particularly challenging, since it can be described by a delicate interplay between chemisorption and physisorption processes. The first-principles simulation of transition metals require particular care also because they can be viewed as intermediate systems between simple metals and insulating crystals. Even in these cases the method performs well as demonstrated by comparing our results with available experimental data and other theoretical investigations. We confirm that the rare gas Xe atom is preferentially adsorbed on the top-site configuration on the Ni(111) surface too. Our approach based on the use of the Maximally Localized Wannier Functions also allow us to well characterize the bonds between graphene and Ni(111).
description: 3 figures
title: Aspects of the Gribov-Zwanziger Lagrangian in relation to gluon confinement
Creators: name: Thelan, David
Publisher: name: University of Liverpool Repository
Year: 2014

description: Over the years there have been many developments in the field of Quantum Chromodynamics, however there still remains some unresolved issues with the theory. Central to these is the principle of gauge copies arising from the Gribov problem. In this work we shall try and address some these issues, in recent years there has been a shift in the lattice data for the low momentum behaviour of the propagators for the gluon and ghost. This change suggests there may now be disagreement with the Lagrangian proposed by Gribov and Zwanziger and the lattice data. It is possible to modify the Gribov-Zwanziger Lagrangian so that it fits the lattice data but these modifications are not unique. The aim of this work is to investigate what effect these modified solutions have to our understanding of the low momentum behaviour of QCD and to see which if any of these solutions is favourable. Further to see we shall explore many of the methods and techniques used in this work by performing a calculation involving polarized deep inelastic scattering operators in QCD, this work while not related to the Gribov problem will help provide a strong understanding of many of the problems we shall encounter while considering the low momentum behaviour in the Gribov case.
Quantum correlations of light and matter through environmental transitions
Creators: name: Iles-Smith, Jake
name: Nazir, Ahsan
Publisher: name: arXiv
Year: 2014
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: One aspect of solid-state photonic devices that distinguishes them from their atomic counterparts is the unavoidable interaction between system excitations and lattice vibrations of the host material. This coupling may lead to surprising departures in emission properties between solid-state and atomic systems. Here we predict a striking and important example of such an effect. We show that in solid-state cavity quantum electrodynamics, interactions with the host vibrational environment can generate quantum cavity-emitter correlations in regimes that are semiclassical for atomic systems. This behaviour, which can be probed experimentally through the cavity emission properties, heralds a failure of the semiclassical approach in the solid-state, and challenges the notion that coupling to a thermal bath supports a more classical description of the system. Furthermore, it does not rely on the spectral details of the host environment under consideration and is robust to changes in temperature. It should thus be of relevance to a wide variety of photonic devices.
description: 8 pages, 7 figures. v2 - minor edits. v3 - more substantial edits to the text. Title changed and new results on correlations added in Fig. 3. v4 - close to published version, presentation clarified
Novel roles for APC family members and Wingless/Wnt signaling during Drosophila brain development
Creators: name: Akong, Kathryn
name: Hayden, Melissa A.
name: Peifer, Mark
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2007

description: Construction of the brain is one of the most complex developmental challenges. Wnt signals shape all tissues, including the brain, and the tumor suppressor Adenomatous Polyposis Coli (APC) is a key negative regulator of Wnt/Wingless (Wg) signaling. We carried out the first assessment of the role of APC proteins in brain development, simultaneously inactivating both APC1 and APC2 in clones of cells in the Drosophila larval optic lobe. We focused on the medulla, where epithelial neural progenitors shift from symmetric to asymmetric divisions across the lateral-medial axis. Loss of both APCs triggers dramatic defects in optic lobe development. Double mutant cells segregate from wild-type neighbors, while double mutant neurons form tangled axonal knots, suggesting changes in cell adhesion. Strikingly, phenotypes are graded along the anterior-posterior axis. Activation of Wg signaling downstream of APC mimics these phenotypes, a dominant-negative TCF blocks them, and a known Wg target, decapentaplegic, is activated in double mutant clones, strongly suggesting that the phenotypes result from activated Wg signaling. We also explored the roles of classic cadherins in differential adhesion. Finally, we propose a model suggesting that Wg signaling regulates fine scale cell fates along the anterior-posterior axis, in part by creating an adhesion gradient, and consider possible alternate explanations for our observations.
title: Can Patience Account for Subnational Differences in Student Achievement?
title: Regional Analysis with Facebook Interests
titleType: Subtitle
Creators: name: Hanushek, Eric A.
name: Kinne, Lavinia
name: Sancassani, Pietro
name: Woessmann, Ludger
Publisher: name: Universitätsbibliothek der Ludwig-Maximilians-Universität München
Year: 2023

description: Decisions to invest in human capital depend on people’s time preferences. We show that differences in patience are closely related to substantial subnational differences in educational achievement, leading to new perspectives on longstanding within-country disparities. We use social-media data – Facebook interests – to construct novel regional measures of patience within Italy and the United States. Patience is strongly positively associated with student achievement in both countries, accounting for two-thirds of the achievement variation across Italian regions and one-third across U.S. states. Results also hold for six other countries with more limited regional achievement data.
Total cost of operating an information engine
Creators: name: Um, Jaegon
name: Hinrichsen, Haye
name: Kwon, Chulan
name: Park, Hyunggyu
Publisher: name: arXiv
Year: 2015
Subjects: subject: Statistical Mechanics (cond-mat.stat-mech)
subject: FOS: Physical sciences

description: We study a two-level system controlled in a discrete feedback loop, modeling both the system and the controller in terms of stochastic Markov processes. We find that the extracted work, which is known to be bounded from above by the mutual information acquired during measurement, has to be compensated by an additional energy supply during the measurement process itself, which is bounded by the same mutual information from below. Our results confirm that the total cost of operating an information engine is in full agreement with the conventional second law of thermodynamics. We also consider the efficiency of the information engine as function of the cycle time and discuss the operating condition for maximal power generation. Moreover, we find that the entropy production of our information engine is maximal for maximal efficiency, in sharp contrast to conventional reversible heat engines.
description: PDFLaTeX, 12 pages, 11 figures
Comparative docking and molecular dynamics studies of molnupiravir (EIDD-2801): implications for novel mechanisms of action on influenza and SARS-CoV-2 protein targets
Creators: name: Istifli, Erman Salih
name: Okumus, Nurullah
name: Sarikurkcu, Cengiz
name: Kuhn, Eduardo Ramires
name: Netz, Paulo A.
name: Tepe, Arzuhan Sihoglu
Publisher: name: Taylor & Francis
Year: 2023
Subjects: subject: Biophysics
subject: Biochemistry
subject: Medicine
subject: Chemical Sciences not elsewhere classified
subject: Sociology
subject: FOS: Sociology
subject: Biological Sciences not elsewhere classified
subject: Cancer
subject: Infectious Diseases
subject: FOS: Health sciences
subject: Virology

description: Molnupiravir (EIDD-2801) (MLN) is an oral antiviral drug for COVID-19 treatment, being integrated into viral RNA through RNA-dependent RNA polymerase (RdRp). Upon ingestion, MLN is transformed into two active metabolites: β-d-N4-hydroxycytidine (NHC) (EIDD-1931) in the host plasma, and EIDD-1931-triphosphate (MTP) within the host cells. However, recent studies provide increasing evidence of MLN’s interactions with off-target proteins beyond the viral genome, suggesting that the complete mechanisms of action of MLN remain unclear. The aim of this study was therefore to investigate the molecular interactions of MLN in the form of NHC and MTP with the non-RNA structural components of avian influenza (hemagglutinin, neuraminidase) and SARS-CoV-2 (spike glycoprotein, Mpro, and RdRp) viruses and to elucidate whether these two metabolites possess the ability to form stable complexes with these major viral components. Molecular docking of NHC and MTP was performed using AutoDock 4.2.6 and the obtained protein-drug complexes were submitted to 200-ns molecular dynamics simulations in triplicate with subsequent free energy calculations using GROMACS. Docking scores, molecular dynamics and MM/GBSA results showed that MTP was tightly bound within the active site of SARS-CoV-2 RdRp and remained highly stable throughout the 200-ns simulations. Besides, it was also shown that NHC and MTP formed moderately-to-highly stable molecular complexes with off-target receptors hemagglutinin, neuraminidase and Mpro, but rather weak interactions with spike glycoprotein. Our computational findings suggest that NHC and MTP may directly inhibit these receptors, and propose that additional studies on the off-target effects of MLN, i.e. real-time protein binding assays, should be performed. Communicated by Ramaswamy H. Sarma
The Drosophila Dead end Arf-like3 GTPase controls vesicle trafficking during tracheal fusion cell morphogenesis
Creators: name: Rogers, Stephen L.
name: Jiang, Lan
name: Crews, Stephen T.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2007

description: The Drosophila larval tracheal system consists of a highly branched tubular organ that becomes interconnected by migration-fusion events during embryonic development. Fusion cells at the tip of each branch guide migration, adhere, and then undergo extensive remodeling as the tracheal lumen extends between the two branches. The Drosophila dead end gene is expressed in fusion cells, and encodes an Arf-like3 GTPase. Analyses of dead end RNAi and mutant embryos reveals that the lumen fails to connect between the two branches. Expression of a constitutively active form of Dead end in S2 cells reveal that it influences the state of actin polymerization, and is present on particles that traffic along actin/microtubule-containing processes. Imaging experiments in vivo reveal that Dead end-containing vesicles are associated with recycling endosomes and the exocyst, and control exocyst localization in fusion cells. These results indicate that the Dead end GTPase plays an important role in trafficking membrane components involved in tracheal fusion cell morphogenesis and lumenal development.
Transgenic over-expression of the microRNA miR-17-92 cluster promotes proliferation and inhibits differentiation of lung epithelial progenitor cells
Creators: name: Thomson, J. Michael
name: Hammond, Scott M.
name: Lu, Yun
name: Wong, Ho Yuen Frank
name: Hogan, Brigid L.M.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2007

description: The miR-17-92 locus encodes a cluster of 7 microRNAs transcribed as a single primary transcript. It can accelerate c-Myc induced B cell lymphoma development and is highly expressed in many tumors, including lung tumors. However, the role of miR-17-92 in development has not been well studied. From analysis of microRNAs during lung development, expression of the miR-17-92 cluster is high at early stages, but declines as development proceeds. We used the mouse surfactant protein C (Sftpc) promoter to over-express the cluster in embryonic lung epithelium. Transgenic lungs have a very abnormal lethal phenotype. They contain numerous proliferative epithelial cells that retain high levels of Sox9, a marker of distal progenitors. The differentiation of proximal epithelial cells was also inhibited. Furthermore, a significant increase in the number of neuroendocrine cell clusters was observed in the lungs of dead transgenic pups. We identify a tumor suppressor, Rbl2 which belongs to the Rb family, as a new target for miR-17-5p. Together, these studies suggest that mir-17-92 normally promotes the high proliferation and undifferentiated phenotype of lung epithelial progenitor cells.
Septate junctions are required for ommatidial integrity and blood–eye barrier function in Drosophila
Creators: name: Beckstead, Robert
name: Bainton, Roland J.
name: Mayer, Nasima
name: Banerjee, Swati
name: Bhat, Manzoor A.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2008

description: The anatomical organization of the Drosophila ommatidia is achieved by specification and contextual placement of photoreceptors, cone and pigment cells. The photoreceptors must be sealed from high ionic concentrations of the hemolymph by a barrier to allow phototransduction. In vertebrates, a blood-retinal barrier (BRB) is established by tight junctions (TJs) present in the retinal pigment epithelium and endothelial membrane of the retinal vessels. In Drosophila ommatidia, the junctional organization and barrier formation is poorly understood. Here we report that septate junctions (SJs), the vertebrate analogs of TJs, are present in the adult ommatidia and are formed between and among the cone and pigment cells. We show that the localization of Neurexin IV (Nrx IV), a SJ-specific protein, coincides with the location of SJs in the cone and pigment cells. Somatic mosaic analysis of nrx IV null mutants shows that loss of Nrx IV leads to defects in ommatidial morphology and integrity. nrx IV hypomorphic allelic combinations generated viable adults with defective SJs and displayed a compromised blood-eye barrier (BEB) function. These findings establish that SJs are essential for ommatidial integrity and in creating a BEB around the ion and light sensitive photoreceptors. Our studies may provide clues towards understanding the vertebrate BEB formation and function.
Geometric transitions and SYZ mirror symmetry
Creators: name: Kanazawa, Atsushi
name: Lau, Siu-Cheong
Publisher: name: arXiv
Year: 2015
Subjects: subject: Symplectic Geometry (math.SG)
subject: Algebraic Geometry (math.AG)
subject: FOS: Mathematics
subject: 53D37, 14J33, 14J32

description: We prove that the punctured generalized conifolds and punctured orbifolded conifolds are mirror symmetric under the SYZ program with quantum corrections. This mathematically confirms the gauge-theoretic prediction by Aganagic-Karch-Lüst-Miemiec, and also provides a supportive evidence to Morrison's conjecture that geometric transitions are reversed under mirror symmetry.
description: v3: one compact example added. 25 pages, 12 figures
Test ideals in rings with finitely generated anti-canonical algebras
Creators: name: Chiecchio, Alberto
name: Enescu, Florian
name: Miller, Lance Edward
name: Schwede, Karl
Publisher: name: arXiv
Year: 2014
Subjects: subject: Algebraic Geometry (math.AG)
subject: Commutative Algebra (math.AC)
subject: FOS: Mathematics
subject: 14J17, 13A35, 14B05

description: Many results are known about test ideals and $F$-singularities for ${\bf Q}$-Gorenstein rings. In this paper we generalize many of these results to the case when the symbolic Rees algebra $O_X \oplus O_X(-K_X) \oplus O_X(-2K_X) \oplus ...$ is finitely generated (or more generally, in the log setting for $-K_X - Δ$). In particular, we show that the $F$-jumping numbers of $τ(X, a^t)$ are discrete and rational. We show that test ideals $τ(X)$ can be described by alterations as in Blickle-Schwede-Tucker (and hence show that splinters are strongly $F$-regular in this setting -- recovering a result of Singh). We demonstrate that multiplier ideals reduce to test ideals under reduction modulo $p$ when the symbolic Rees algebra is finitely generated. We prove that Hartshorne-Speiser-Lyubeznik-Gabber type stabilization still holds. We also show that test ideals satisfy global generation properties in this setting.
description: Lemma 2.10 was incorrect, it stated something that was too strong. We have restated Lemma 2.10 correctly we believe. Fortunately, we only needed the new weaker statement. This also corrects the published version
title: Carbon emission policies impact in logistics supply chain networks
Creators: name: Hanafi, Zurina
Publisher: name: University of Liverpool Repository
Year: 2013

description: Environmental issue is becoming a serious global concern. Human activities associate with industrial activities and households produce a great amount of greenhouse gases, particularly carbon dioxide, and gives significant impact on the environment. The legislation on carbon emissions has become an important agenda in order to control the amount of carbon emissions that might affect the world for future generations. In conjunction to this issue, therefore, the research was conducted to investigate the impact of the carbon emission policies on reverse and forward logistics strategies and operations and propose optimisation models for the paper recycling and fresh produce industry with cases in the UK. The optimal network design approach for both cases under carbon emission control is formulated. The research concluded that exporting the waste paper to Asia is a better option when pollution from the recycling is not charged. However, when considering the carbon emission in both the UK and the Asian country, the best strategy would depend on the amount of recycling and the differences between the costs of the recycling locally and overseas. For fresh produce case, with no carbon policies, road is a better transportation option. However, if the industry has to pay for carbon emission, consideration of multimodal transportation has to be made in order to remain optimal. The analysis of business strategies and configuration of reverse and forward logistics networks are carried out with quantitative optimisation modelling. The analysis for paper recycling and the fresh produce industry consider contributions to the environment and costs in relation to carbon emission. Mixed integer linear programming models were developed for both cases to obtain the optimal choice in strategic and operational decision making. Transportation industry is a main contributor of greenhouse gases that give direct impact to the environment. Multimodal transportation planning is important because it can help to reduce impact on the environment, by using a combination of at least two modes of transportation in a single transport chain, without a change of container for the goods, with most of the route travelled by road, rail, inland waterway or ocean-going vessel and with the shortest possible initial and final journeys by road. Multimodal transportation planning is proposed in the fresh produce industry with another variable which is time. The analytical result derived from sensitivity analysis is discussed to draw academic and practical findings for carbon control policy making and logistics network configuration. The research outcome has a good generic contribution to eco-logistics management of other recycling materials and to generic logistics network configuration issues. The research is also significantly contributed to government policy making in carbon emission control.
Enabled and Capping protein play important roles in shaping cell behavior during Drosophila oogenesis
Creators: name: Mahaffey, James P.
name: Herrera, Cristina
name: Homem, Catarina C.F.
name: Yin, Hongyan
name: Montell, Denise J.
name: Gates, Julie
name: Nowotarski, Stephanie H.
name: Peifer, Mark
name: Janody, Florence
name: Bridges, Tina
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: During development, cells craft an impressive array of actin-based structures, mediating events as diverse as cytokinesis, apical constriction, and cell migration. One challenge is to determine how cells regulate actin assembly and disassembly to carry out these cell behaviors. During Drosophila oogenesis diverse cell behaviors are seen in the soma and germline. We used oogenesis to explore developmental roles of two important actin regulators: Enabled/VASP proteins and Capping protein. We found that Enabled plays an important role in cortical integrity of nurse cells, formation of robust bundled actin filaments in late nurse cells that facilitate nurse cell dumping, and migration of somatic border cells. During nurse cell dumping, Enabled localizes to barbed ends of the nurse cell actin filaments, suggesting its mechanism of action. We further pursued this mechanism using mutant Enabled proteins, each affecting one of its protein domains. These data suggest critical roles for the EVH2 domain and its tetramerization subdomain, while the EVH1 domain appears less critical. Enabled appears to be negatively regulated during oogenesis by Abelson kinase. We also explored the function of Capping protein. This revealed important roles in oocyte determination, nurse cell cortical integrity and nurse cell dumping, and support the idea that Capping protein and Enabled act antagonistically during dumping. Together these data reveal places these actin regulators shape oogenesis.
title: Structural studies of the adsorption of molecules on Cu(110)
Creators: name: Thomas, Geoffrey
Publisher: name: University of Liverpool Repository
Year: 2013

description: The adsorption of thymine and melamine on Cu(110) has been investigated using a combination of experimental and theoretical techniques. These techniques have allowed the development of an extensive picture of how these molecules may orient on this surface. Many Density Functional Theory (DFT) calculations using the latest version of the Vienna Ab-Initio Simulation Package (VASP) have allowed the production of a series of models which have, in general, corroborated the experimental data. The additional utilisation of semi-empirical techniques (like those used by Grimme), which seek to simulate long-range inter-molecular vdW interactions, have allowed the creation of a firm foundation of, not only how the individual molecules bond to the Cu(110) surface, but of how they arrange themselves into long-range structures. With thymine, two long-range phases were observed; a room temperature structure, which aligned along the [001] direction in 1-D chains, one molecule thick and with the cyclic plane roughly parallel to the [110] direction. The higher temperature phase occurred after annealing between 350-400K and consisted of two distinct 1-D chains, two molecules thick and angled at ~±20o to the [001] direction. In both cases the thymine was deprotonated at the N(1) atom. With melamine, only the room temperature phase is discussed and this consisted of a 2-D “hexagonal” structure arranged on a (6x2) unit cell. Although structural relaxation techniques give good indications of the stability of the models, the technique of Scanning Tunneling Microscopy (STM) simulation has been used extensively with both thymine and melamine systems in order to verify their validity. Although it is not yet possible to directly observe individual atoms in such small molecules it is possible (with STM) to observe their electronic “footprint” and to then re-create this observed image. The similarity of this “simulated STM” to the “experimental STM” combined with a relaxed stable model is a strong indication that the model is in good accordance with the observed (static) system. Combining this analysis technique with experimental data, models are proposed for both the room temperature thymine and melamine phases as well as the annealed thymine phase.
title: A systems biology approach to explore the dynamics and interactions of the NF-κB signalling pathway
Creators: name: Boyd, James
Publisher: name: University of Liverpool Repository
Year: 2013

description: The family of nuclear factor kappa B (NF-κB) transcription factors controls diverse mammalian signalling responses that mediate cell survival, inflammation, and immune response. Complex spatial and temporal dynamics observed in the NF-κB pathway are believed to determine gene expression profiles, which confer different physiological responses. The intricate and non-linear nature of the NF-κB system has benefited from the application of mathematical modelling methods which provide non-intuitive insights into the mechanism of cellular regulation. It has become apparent that responses in signalling networks are influenced by complex spatial and temporal dynamics, which arise from a diverse range of competitive and combinatorial interactions. The systematic collection of quantitative data allows the application of a systems biology approaches to investigate and model complex biological systems. Through reiterative cycles of experimental and mathematical analysis it is possible to make predictions which generate testable hypotheses and guide future research. The primary aim of this work is to consider ways in which understanding of the core NF-κB system can be expanded to include a wider array of dynamic interactions using both theoretical and experimental approaches. From a modelling perspective, the goal of the project was to consider methods of how the network presented by Ashall et al. could be adapted and expanded to incorporate new data on the interactions of NF-κB with other signalling pathways. The main technique was to explore different network topologies and parameter set spaces in order to elucidate key features of the system structure. In experimental terms the goal was to consider methods and techniques of observing molecular dynamics and interactions in live cells and to define the potential and limitations of these tools for studying the NF-κB signalling pathway. In particular, fluorescence fluctuation microscopy approaches are explored. By combining both experimental and theoretical approaches, a new model of NF-κB signalling is proposed, with statements on the dynamics of protein complex formation in live cells made.
Pastorale 2. Handreichung für den pastoralen Dienst, hrsg. v. d. Konferenz der deutschsprachigen Pastoraltheologen
Creators: name: Bayer, Niklaus
Publisher: name: Diakonia
Year: 1970

description: Diakonia, Bd. 6 Nr. 1 (1975): Diakonia, Band 6, Heft 1
Shox2 is essential for the differentiation of cardiac pacemaker cells by repressing Nkx2-5
Creators: name: Tang, Ruhang
name: Martin, James F.
name: Sun, Xiaoxiao
name: Yang, Jing
name: Chen, YiPing
name: Liu, Hongbing
name: Wang, Dazhi
name: He, Fenglei
name: Shi, Jiangli
name: Espinoza-Lewis, Ramón A.
name: Yu, Ling
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2009

description: The pacemaker is composed of specialized cardiomyocytes located within the sinoatrial node (SAN), and is responsible for originating and regulating the heart beat. Recent advances towards understanding the SAN development have been made on the genetic control and gene interaction within this structure. Here we report that the Shox2 homeodomain transcription factor is restrictedly expressed in the sinus venosus region including the SAN and the sinus valves during embryonic heart development. Shox2 null mutation results in embryonic lethality due to cardiovascular defects, including an abnormal low heart beat rate (bradycardia) and severely hypoplastic SAN and sinus valves attributed to a significantly decreased level of cell proliferation. Genetically, the lack of Tbx3 and Hcn4 expression, along with ectopic activation of Nppa, Cx40, and Nkx2-5 in the Shox2−/− SAN region, indicates a failure in SAN differentiation. Furthermore, Shox2 overexpression in Xenopus embryos results in extensive repression of Nkx2-5 in the developing heart, leading to a reduced cardiac field and aberrant heart formation. Reporter gene expression assays provide additional evidence for the repression of Nkx2-5 promoter activity by Shox2. Taken together our results demonstrate that Shox2 plays an essential role in the SAN and pacemaker development by controlling a genetic cascade through the repression of Nkx2-5.
Apical constriction: A cell shape change that can drive morphogenesis
Creators: name: Shemer, Gidi
name: Roh-Johnson, Minna
name: Sullivan-Brown, Jessica
name: Goldstein, Bob
name: Sawyer, Jacob M.
name: Harrell, Jessica R.
Publisher: name: The University of North Carolina at Chapel Hill University Libraries
Year: 2010

description: Biologists have long recognized that dramatic bending of a cell sheet may be driven by even modest shrinking of the apical sides of cells. Cell shape changes and tissue movements like these are at the core of many of the morphogenetic movements that shape animal form during development, driving processes such as gastrulation, tube formation and neurulation. The mechanisms of such cell shape changes must integrate developmental patterning information in order to spatially and temporally control force production -- issues that touch on fundamental aspects of both cell and developmental biology and on birth defects research. How does developmental patterning regulate force-producing mechanisms, and what roles do such mechanisms play in development? Work on apical constriction from multiple systems including Drosophila, C. elegans, sea urchin, Xenopus, chick and mouse has begun to illuminate these issues. Here, we review this effort to explore the diversity of mechanisms of apical constriction, the diversity of roles that apical constriction plays in development, and the common themes that emerge from comparing systems.