bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of Water Velocity and Specific Surface Area on Filamentous Periphyton Biomass in an Artificial Stream Mesocosm
Authors: Ahn Chang , Song Ho , Lee Saeromi , Oh Ju , Ahn Hosang , Park Jae-Roh , Lee Jung , Joo Jin
Published: October 2013

To evaluate the effects of water velocity and artificial substratum characteristics on the growth rate and biomass accumulation of periphyton, an artificial stream mesocosm experiment was conducted using alternative water sources collected from the Mangwall Stream (MW), the Han River (HR), and bank filtration water (BFW) from the Han River in the Republic of Korea. The measured concentrations of organic matter and inorganic nutrients in the MW were higher than in the HR and BFW. The surface of tile is relatively smooth and nonporous, whereas the surfaces of concrete and pebble are rough with numerous isolated pores in which filamentous periphyton become immobilized against hydrodynamic shear stress and mat tensile strength. Compared with the periphyton biomass of the HR and BFW, the peak biomass in the MW was significantly higher due to higher nutrient concentrations in the MW. Reasonable linear relationships (R2 ≥ 0.69) between water velocity and total periphyton biomass/growth rate were obtained, indicating that water velocities above critical values can cause a reduction in biomass accrual. In addition, reasonable relationships (R2 ≥ 0.58) between specific surface area and total periphyton biomass were obtained for the HR and BFW, indicating that an increase in the specific surface area of the substratum can lead to an increase in periphyton biomass in a nutrient-poor water body. Principal components analysis (PCA) results indicate that nutrient concentrations were the first dominant limiting factor for the growth and accumulation of periphyton, and water velocity and the specific surface area of the substratum were determined to be potential limiting factors. Consequently, the growth rate and biomass accumulation of periphyton were considered to be a complex function of nutrient concentrations, water velocities, and substratum characteristics.
Eunome l'arien et l'exégèse néo-platonicienne du Cratyle
Authors: Daniélou Jean
Published: October 2013

L'arien Eunome affirmait qu ἀγέννητος était le nom propre de Dieu et définissait son essence. Il appuyait cette affirmation sur une théorie de l'origine révélée du langage. Or cette doctrine se retrouve dans le néo-platonisme du temps. Le système d'Eunome présente par ailleurs de nombreux points de contact avec le néo-platonisme. Lui-même a été eu rapport avec des disciples de Jamblique. Toutefois ses idées présentent surtoul des analogies avec le Commentaire sur le Cratyle de Proclus. Ceci amène à penser que le milieu avec lequel Eunome est en contact est celui des fondateurs de l'École d'Athènes, auxquels se rattachera Proclus, et dont lui-même est exactement contemporain. Son œuvre permettrait ainsi de jeter quelque lumière sur une période particulièrement obscure de l'histoire du néo-platonisme.
Vieillir en milieu rural isolé : une analyse au prisme des sociabilités
Authors: Mallon Isabelle
Published: October 2013

À partir d’une enquête auprès de personnes âgées vivant dans deux territoires ruraux aux morphologies sociales différenciées, en Creuse et en Ardèche, cet article met en évidence la manière dont s’agencent au quotidien les relations de sociabilité et de solidarité des habitants âgés du milieu rural isolé. L’intégration de la sociabilité et de la solidarité dans les mêmes relations, familiales, professionnelles ou de voisinage, caractérise les natifs n’ayant jamais quitté le pays. En revanche, les habitants venus ou revenus d’ailleurs autour de la retraite entretiennent des relations de sociabilité plus dispersées, plus segmentées, et distinctes des relations de solidarité.
Être « aidant familial » en « milieu rural » entre devoir moral et contraintes sociales, quelle place pour l'autonomie ?
Authors: Gucher Catherine
Published: October 2013

La problématique de l’aide familiale a fait l’objet de nombreux travaux se donnant pour projet d’analyser ses formes, ses motivations, ses limites et ses conséquences. Il nous paraît cependant possible d’éclairer encore autrement ces formes solidaires de soutien aux parents ou conjoints âgés, à partir des caractéristiques du milieu dans lequel elles se développent. Elles s’organisent en effet sur les fondements des liens interpersonnels et de l’histoire familiale mais également en référence à une trame d’impératifs pratiques et moraux et aux supports disponibles dans les bassins de vie. La question du choix personnel pour ce qui est de l’engagement dans l’aide en direction d’un proche dépendant se pose alors dans certains territoires ruraux où la solidarité familiale paraît socialement incontournable et où l’absence de services professionnels peut constituer une contrainte.
Le retrait des militaires avant la démocratie : enjeu d'une configuration transitionnelle. L'Égypte au regard des exemples subsahariens
Authors: Boutaleb Assia
Published: October 2013

S’il est un acquis de l’étude des changements politiques en Afrique et en Europe de l’Est à partir des années 1990 de penser les transitions politiques comme conjonctures fluides, cet article se propose de les envisager également selon une approche configurationnelle, au sens de N. Elias, à savoir de penser ensemble jeux d’acteurs et dynamiques d’élaboration des règles. En revenant de manière privilégiée sur la période allant départ du Président déchu, Hosny Moubârak (le 11 février 2011) à la veille du premier tour des élections législatives (le 28 novembre 2011), l’analyse permettra de montrer que les dynamiques de protestation et de mobilisation se focalisent bien plus sur la démilitarisation du régime que sur un enjeu de democratisation.
Stratégies en faveur de la démocratie de genre dans les syndicats
Authors: Kirton Gill , Healy Geraldine
Published: October 2013

Cet article se propose d’exposer ce qui rapproche et sépare les responsables syndicales au Royaume-Uni et aux États-Unis face aux stratégies d’égalité des sexes mises en œuvre dans leurs syndicats pour faire avancer la démocratie de genre. Il s’appuie sur une enquête qualitative de deux ans, menée auprès de 134 représentantes syndicales des deux pays, sur de l’observation participative et sur l’analyse secondaire de données quantitatives. Entreprise à la fois dans une perspective de genre et comparatiste, cette étude souligne tant les convergences que les divergences des responsables syndicales britanniques et américaines vis-à-vis des mesures prises par leurs syndicats en faveur de l’égalité des sexes et examine l’efficacité de ces stratégies pour améliorer la représentation féminine dans les instances dirigeantes et décisionnelles. L’article évoque aussi la position de faiblesse des femmes dans les organisations syndicales et les entraves sociales et structurelles qu’elles rencontrent souvent lorsqu’elles veulent promouvoir et défendre des stratégies égalitaires réformatrices.
Tutorat en ligne et rétroactions correctives à distance – Vers un modèle de médiation pour la production en langue étrangère
Authors: Brudermann Cédric
Published: October 2013

Une expérience avec recueil et quantification de données a été conduite à l'Institut universitaire de formation des maîtres de Perpignan auprès d'étudiants Lansad (anglais B1 / B2) intégrés dans un dispositif hybride au cours de l'année universitaire 2007-2008 (Brudermann, 2010). Cette recherche visait à évaluer les besoins de ces étudiants au cours de la réalisation de tâches écrites et orales à distance, afin de réfléchir, ensuite, sur des pistes pédagogiques à considérer pour les prendre en charge, dans le cadre d'une médiation à distance. Dans cette perspective, un système de tutorat en ligne favorisant les rétroactions correctives a été élaboré pour promouvoir des expériences d'apprentissage (Bange, 1992) potentiellement favorables à l'acquisition de l'anglais langue étrangère. Afin de mesurer les effets de cette remédiation à distance sur la progression langagière des étudiants, une expérience a été mise en place auprès de trois groupes d'apprenants Lansad (B1 / B2) à l'université Pierre et Marie Curie. L'analyse du corpus CP1, collecté dans le cadre de cette deuxième étude, indique que, sous l'effet des modalités proposées, des changements qualitatifs ont pu être observés dans les productions orales et écrites des informateurs.
La prensa napoleónica en España (1808-1814). Una perspectiva.
Authors: Checa Godoy Antonio
Published: October 2013

La presse partisane du régime de José I en Espagne entre 1808 et 1814, appelée presse napoléonienne, n’a guère suscité, du moins jusqu’à il y a peu, l’attention des historiens. En effet, elle était considérée comme intruse, et ses rédacteurs étaient tenus pour des traîtres. Aujourd’hui une vision plus équilibrée s’impose. Cet article offre un tour d’horizon de cette presse, ses créateurs, ses conditions de publication, son contenu et ses obsessions. Et surtout, il décrit qui étaient ses rédacteurs et quel a été leur sort après le départ des troupes napoléoniennes de la péninsule ibérique.
Linguistic Inquiry and Word Count (LIWC)
Authors: Chung Cindy K. , Pennebaker James W.
Published: October 2013

Linguistic Inquiry and Word Count (LIWC; Pennebaker, Booth, & Francis, 2007) is a word counting software program that references a dictionary of grammatical, psychological, and content word categories. LIWC has been used to efficiently classify texts along psychological dimensions and to predict behavioral outcomes, making it a text analysis tool widely used in the social sciences. LIWC can be considered to be a tool for applied natural language processing since, beyond classification, the relative uses of various LIWC categories can reflect the underlying psychology of demographic characteristics, honesty, health, status, relationship quality, group dynamics, or social context. By using a comparison group or longitudinal information, or validation with other psychological measures, LIWC analyses can be informative of a variety of psychological states and behaviors. Combining LIWC categories using new algorithms or using the processor to assess new categories and languages further extend the potential applications of LIWC.
The Political Dimensions of Information Systems in Public Administration
Authors: Rocheleau Bruce
Published: October 2013

Many information management and generalist managers ignore the political aspects of managing information systems. But this chapter shows that political factors are often the most crucial in determining how successful information technology is. The purpose of the chapter is to provide awareness of the political context of information systems decisions. The political aspects of computing are discussed with respect to two major categories: (1) Internal, organizational politics concerning issues involving organizational members; (2) External politics concerning how the governmental organization relates to its councils or boards, external groups, and general citizenry. Several examples of internal politics are given including the structuringof the information function, the purchasing of information systems, interdepartmental sharing of information, and communication flows. External examples of politics are given concerning relationships with legislatures and citizenry such as disputes over funding, computer disasters, privatization, the Internet and telecommunications planning. 
Managing Geographic Information Systems in the Public Sector
Authors: Carr T. R.
Published: October 2013

Geographic information systems emerged in the 1970s and have become significant decision-making tools as their capabilities have been enhanced. This chapter includes a brief discussion of various GIS applications and a more detailed discussion of issues that public managers should consider when evaluating implementation of a geographic information system. GIS applications provide benefits at the basic level in terms of producing maps efficiently, at the planning level through the use of database applications, and at the management decision-making level through an ability to access relational databases for policy level decisions. Issues impacting GIS implementation include: needs assessment, project planning, access to public records, liability issues, public and private partnerships, dissemination of information and privacy issues. Public managers should be aware of difficulties associated with justification of costs associated with GIS implementation and that a hesitancy exists on the part of GIS program managers to share missteps and implementation failures. 
Cutting Edge: Feed-Forward Activation of Phospholipase Cγ2 via C2 Domain–Mediated Binding to SLP65
Authors: Engelke Michael , Oellerich Thomas , Dittmann Kai , Hsiao He-Hsuan , Urlaub Henning , Serve Hubert , Griesinger Christian , Wienands Jürgen
Published: October 2013

Ag-mediated B cell stimulation relies on phospholipase Cγ2 (PLCγ2) for Ca2+ mobilization. Enzymatic activity of PLCγ2 is triggered upon Src homology 2 domain–mediated binding to the tyrosine-phosphorylated adaptor SLP65. However, SLP65 phosphorylation outlasts the elevation of cytosolic Ca2+ concentration suggesting additional levels of PLCγ2 regulation. We show in this article that the functionality of the PLCγ2/SLP65 complex is controlled by the weakly characterized C2 domain of PLCγ2. Usually C2 domains bind membrane lipids, but that of PLCγ2 docks in a Ca2+-regulated manner to a distinct phosphotyrosine of SLP65. Hence, early Ca2+ fluxing provides feed-forward signal amplification by promoting anchoring of the PLCγ2 C2 domain to phospho-SLP65. As the cellular Ca2+ resources become exhausted, the concomitant decline of Ca2+ dampens the C2-phosphotyrosine interaction so that PLCγ2 activation terminates despite sustained SLP65 phosphorylation.
Unique Features of Naive CD8+ T Cell Activation by IL-2
Authors: Cho Jae-Ho , Kim Hee-Ok , Kim Kyu-Sik , Yang Deok-Hwan , Surh Charles D. , Sprent Jonathan
Published: October 2013

IL-2 has a pervasive influence on the immune system and dictates the survival and differentiation of multiple T cell subsets, including CD4 regulatory T cells, CD4 Th cells, and CD8 memory cells. IL-2 is synthesized by T cells during the early stages of the immune response and promotes T cell expansion and effector cell generation after initial activation via TCR signaling. Based on studies with activated T cell lines maintained in vitro, IL-2 is known to activate multiple signaling pathways that show considerable overlap with the pathways elicited via the TCR. In this paper, we have examined IL-2 signaling under TCR-independent conditions, namely by culturing purified resting naive CD8 T cells with IL-2 in the absence of Ag or APC. Under these conditions, we show in this study that IL-2 elicits a unique pattern of signaling associated with strong lymphocyte-specific protein tyrosine kinase/JAK3-dependent activation of the PI3K/AKT pathway with little or no involvement of STAT5, NF-κB, or the calcineurin/NFAT pathways. Such signaling induces marked proliferation associated with rapid and selective expression of eomesodermin but not T-bet and differentiation into long-lived central memory cells after adoptive transfer.
Macro-logistics trends: Indications for a more sustainable economy
Authors: Havenga Jan H. , Simpson Zane P. , De Bod Anneke
Published: October 2013

The North American and South African logistics cost calculation-time series are the two longest-running statistical series available worldwide. These calculations indicate that transportation’s contribution to logistics costs is rising, as the key cost driver (oil price) is increasing exponentially. This is exacerbated by volatile oil prices and the inclusion of externality charges to reduce the logistics environmental footprint. Therefore, it is necessary to consider a new paradigm where material logistics requirements are reduced through localisation and consumption reduction. This, in turn, implies the consideration of new indicators for the future measurement of logistics costs. Because this article asks questions about the suitability of GDP as the primary (and often only) measurement of economic output, new measurements are required. If this position changes, the comparison of logistics costs with GDP alone will become questionable.
PhyloTreePruner: A Phylogenetic Tree-Based Approach for selection of Orthologous sequences for phylogenomics
Authors: Kocot Kevin M. , Citarella Mathew R. , Moroz Leonid L. , Halanych Kenneth M.
Published: October 2013

Molecular phylogenetics relies on accurate identification of orthologous sequences among the taxa of interest. Most orthology inference programs available for use in phylogenomics rely on small sets of pre-defined orthologs from model organisms or phenetic approaches such as all-versus-all sequence comparisons followed by Markov graph-based clustering. Such approaches have high sensitivity but may erroneously include paralogous sequences. We developed PhyloTreePruner, a software utility that uses a phylogenetic approach to refine orthology inferences made using phenetic methods. PhyloTreePruner checks single-gene trees for evidence of paralogy and generates a new alignment for each group containing only sequences inferred to be orthologs. Importantly, PhyloTreePruner takes into account support values on the tree and avoids unnecessarily deleting sequences in cases where a weakly supported tree topology incorrectly indicates paralogy. A test of PhyloTreePruner on a dataset generated from 11 completely sequenced arthropod genomes identified 2,027 orthologous groups sampled for all taxa. Phylogenetic analysis of the concatenated supermatrix yielded a generally well-supported topology that was consistent with the current understanding of arthropod phylogeny. PhyloTreePruner is freely available from http://sourceforge.net/projects/phylotreepruner /.
Impacts of cirrus clouds heterogeneities on TOA thermal infrared radiation
Authors: Fauchez T. , Cornet C. , Szczap F. , Dubuisson P. , Rosambert T.
Published: October 2013

Abstract. This paper presents a study on the impact of cirrus cloud heterogeneities on the thermal infrared brightness temperatures at the Top Of Atmosphere (TOA). Realistic 3-D cirrus are generated by a cloud generator based on simplified thermodynamic and dynamic equations and on the control of invariant scale properties. The 3-D thermal infrared radiative transfer is simulated with a Monte-Carlo model for three typical spectral bands in the infrared atmospheric window. Comparisons of TOA brightness temperatures resulting of 1-D and 3-D radiative transfer show significant differences for optically thick cirrus (τ > 0.3 at 532 nm) and are mainly due to the Plan-Parallel Approximation (PPA). At the spatial resolution of 1 km × 1 km, two principal parameters control the heterogeneity effects on brightness temperatures: (i) the optical thickness standard deviation inside the observation pixel, (ii) the brightness temperatures contrast between the top of the cirrus and the clear sky atmosphere. Furthermore, we show that the difference between 1-D and 3-D brightness temperatures increases with the view zenith angle from two to ten times between 0° and 60° due to the Tilted Independant Pixel Approximation (TIPA).
Freezing nucleation apparatus puts new slant on study of biological ice nucleators in precipitation
Authors: Stopelli E. , Conen F. , Zimmermann L. , Alewell C. , Morris C. E.
Published: October 2013

Abstract. Since decades, drop-freezing instruments have contributed to a better understanding of biological ice nucleation and its likely implications on cloud and precipitation development. Yet, current instruments have limitations. Drops analysed on a cold stage are subject to evaporation and potential contamination. The use of closed tubes provides a partial solution to these problems, but freezing events are still difficult to be clearly detected. Here, we present a new apparatus where freezing in closed tubes is detected automatically by a change in light transmission upon ice development, caused by the formation of air bubbles and crystal facets that scatter light. Risks of contamination and introduction of biases linked to detecting the freezing temperature of a sample are then minimized. To illustrate the performance of the new apparatus we show initial results of two assays with snow samples. In one, we repeatedly analysed the sample (208 tubes) over the course of a month with storage at +4 °C, during which evidence for biological ice nucleation activity emerged through an increase in the number of ice nucleators active around −4 °C. In the second assay, we indicate the possibility to increasingly isolate a single ice nucleator from a precipitation sample, potentially determining the nature of a particle responsible for a nucleation activity measured directly in the sample. These two seminal approaches highlight the relevance of this handy apparatus to provide new points of view in biological ice nucleation research.
Indian Ocean Dipole and El Niño/Southern Oscillation impacts on regional chlorophyll anomalies in the Indian Ocean
Authors: Currie J. C. , Lengaigne M. , Vialard J. , Kaplan D. M. , Aumont O. , Naqvi S. W. A. , Maury O.
Published: October 2013

Abstract. The Indian Ocean Dipole (IOD) and the El Niño/Southern Oscillation (ENSO) are independent climate modes, which frequently co-occur, driving significant interannual changes within the Indian Ocean. We use a four-decade hindcast from a coupled biophysical ocean general circulation model, to disentangle patterns of chlorophyll anomalies driven by these two climate modes. Comparisons with remotely sensed records show that the simulation competently reproduces the chlorophyll seasonal cycle, as well as open-ocean anomalies during the 1997/1998 ENSO and IOD event. Results suggest that anomalous surface and euphotic-layer chlorophyll blooms in the eastern equatorial Indian Ocean in fall, and southern Bay of Bengal in winter, are primarily related to IOD forcing. A negative influence of IOD on chlorophyll concentrations is shown in a region around the southern tip of India in fall. IOD also depresses depth-integrated chlorophyll in the 5–10° S thermocline ridge region, yet the signal is negligible in surface chlorophyll. The only investigated region where ENSO has a greater influence on chlorophyll than does IOD, is in the Somalia upwelling region, where it causes a decrease in fall and winter chlorophyll by reducing local upwelling winds. Yet unlike most other regions examined, the combined explanatory power of IOD and ENSO in predicting depth-integrated chlorophyll anomalies is relatively low in this region, suggestive that other drivers are important there. We show that the chlorophyll impact of climate indices is frequently asymmetric, with a general tendency for larger positive than negative chlorophyll anomalies. Our results suggest that ENSO and IOD cause significant and predictable regional re-organisation of chlorophyll via their influence on near-surface oceanography. Resolving the details of these effects should improve our understanding, and eventually gain predictability, of interannual changes in Indian Ocean productivity, fisheries, ecosystems and carbon budgets.
An Interative Grahical User Interface for Maritime Security Services
Authors: Reize T. , Müller R. , Kiefl R.
Published: October 2013

Abstract. In order to analyse optical satellite images for maritime security issues in Near-Real-Time (NRT) an interactive graphical user interface (GUI) based on NASA World Wind was developed and is presented in this article. Targets or activities can be detected, measured and classified with this tool simply and quickly. The service uses optical satellite images, currently taken from 6 sensors: Worldview-1 and Worldview-2, Ikonos, Quickbird, GeoEye-1 and EROS-B. The GUI can also handle SAR-images, air-borne images or UAV images. Software configurations are provided in a job-order file and thus all preparation tasks, such as image installation are performed fully automatically. The imagery can be overlaid with vessels derived by an automatic detection processor. These potential vessel layers can be zoomed in by a single click and sorted with an adapted method. Further object properties, such as vessel type or confidence level of identification, can be added by the operator manually. The heading angle can be refined by dragging the vessel's head or switching it to 180° with a single click. Further vessels or other relevant objects can be added. The objects length, width, heading and position are calculated automatically from three clicks on top, bottom and an arbitrary point at one of the object’s longer side. In case of an Activity Detection, the detected objects can be grouped in area of interests (AOI) and classified, according to the ordered activities. All relevant information is finally written to an exchange file, after quality control and necessary correction procedures are performed. If required, image thumbnails can be cut around objects or around whole areas of interest and saved as separated, geo-referenced images.
Gas por mar
Authors: Bonnefoy Pascale
Published: October 2013

La actual situación energética en Chile y Bolivia podría convertirse en una oportunidad para que ambos países retomen la fracasada iniciativa de «gas por mar» avanzada hace una década por los presidentes Ricardo Lagos y Hugo Banzer. Desde entonces, el cuadro ha cambiado: la menor demanda de gas desde Argentina y el termino del contrato de exportación de gas a Brasil dentro de algunos años obliga a Bolivia a buscar nuevos mercados y una salida más económica para su gas; Chile, en tanto, entrampado en su dependencia energética, en un costoso sustituto de las importaciones de gas argentino y paralizados dos de sus principales futuros proyectos energéticos necesita fuentes de energía más limpias y menos costosas. Ambos países tienen que despejar un conflicto centenario que mantiene la triple frontera entre Chile, Bolivia y Perú en permanente fricción, en vez de ser un polo productivo trinacional que contribuya a la integración energética de Sudamérica.
La intervención militar autorizada de las Naciones Unidas en Libia: ¿un precedente de la "responsabilidad de proteger"?
Authors: Añaños Meza María Cecilia
Published: October 2013

En febrero de 2011 surgió el conflicto libio que generó una intervención internacional intensiva y amplia de las Naciones Unidas, que impuso sanciones y autorizó el empleo de la fuerza contra el régimen de gobierno libio, en aras de la «responsabilidad de proteger». El presente trabajo examinará, desde la perspectiva del derecho internacional público, el mecanismo de sanciones de las Naciones Unidas, sus características y el concepto de la «responsabilidad de proteger» y su papel dentro del sistema de sanciones del Consejo de Seguridad y la cuestión de la conformidad de las sanciones con la Carta y el derecho internacional.
La política brasileña en materia de regionalismo. Discurso y desarrollo institucional en el Mercosur
Authors: De Almeida Medeiros Marcelo , Franzoi Dri Clarissa
Published: October 2013

En el último decenio se ha insistido en señalar que el Mercosur tiene prioridad en la política exterior del Brasil. Sin embargo, durante este tiempo la integración regional no ha aumentado ni se ha profundizado. El presente artículo procura explicar este vacío entre el discurso y la práctica mediante un examen de las características de la política brasileña en materia de regionalismo. El análisis se basa en un estudio de caso sobre la creación del Parlamento del Mercosur en 2006. En principio, sostenemos que en gran medida el institucionalismo discursivo y la teoría de los sistemas internacionales pueden explicar por qué Brasil ha mantenido distancia del Mercosur y la limitada interdependencia que se ha construido entre los países que lo componen. La conclusión apunta a que se ha producido un regionalismo débil que facilita la acción del Brasil en el plano internacional.
Engineered proteins detect spontaneous DNA breakage in human and bacterial cells
Authors: Shee Chandan , Cox Ben D , Gu Franklin , Luengas Elizabeth M , Joshi Mohan C , Chiu Li-Ya , Magnan David , Halliday Jennifer A , Frisch Ryan L , Gibson Janet L , Nehring Ralf Bernd , Do Huong G , Hernandez Marcos , Li Lei , Herman Christophe , Hastings PJ , Bates David , Harris Reuben S , Miller Kyle M , Rosenberg Susan M
Published: October 2013

Spontaneous DNA breaks instigate genomic changes that fuel cancer and evolution, yet direct quantification of double-strand breaks (DSBs) has been limited. Predominant sources of spontaneous DSBs remain elusive. We report synthetic technology for quantifying DSBs using fluorescent-protein fusions of double-strand DNA end-binding protein, Gam of bacteriophage Mu. In Escherichia coli GamGFP forms foci at chromosomal DSBs and pinpoints their subgenomic locations. Spontaneous DSBs occur mostly one per cell, and correspond with generations, supporting replicative models for spontaneous breakage, and providing the first true breakage rates. In mammalian cells GamGFP—labels laser-induced DSBs antagonized by end-binding protein Ku; co-localizes incompletely with DSB marker 53BP1 suggesting superior DSB-specificity; blocks resection; and demonstrates DNA breakage via APOBEC3A cytosine deaminase. We demonstrate directly that some spontaneous DSBs occur outside of S phase. The data illuminate spontaneous DNA breakage in E. coli and human cells and illustrate the versatility of fluorescent-Gam for interrogation of DSBs in living cells.
Reciprocal virulence and resistance polymorphism in the relationship between Toxoplasma gondii and the house mouse
Authors: Lilue Jingtao , Müller Urs Benedikt , Steinfeldt Tobias , Howard Jonathan C
Published: October 2013

Virulence in the ubiquitous intracellular protozoon Toxoplasma gondii for its natural intermediate host, the mouse, appears paradoxical from an evolutionary standpoint because death of the mouse before encystment interrupts the parasite life cycle. Virulent T. gondii strains secrete kinases and pseudokinases that inactivate the immunity-related GTPases (IRG proteins) responsible for mouse resistance to avirulent strains. Such considerations stimulated a search for IRG alleles unknown in laboratory mice that might confer resistance to virulent strains of T. gondii. We report that the mouse IRG system shows extraordinary polymorphic complexity in the wild. We describe an IRG haplotype from a wild-derived mouse strain that confers resistance against virulent parasites by interference with the virulent kinase complex. In such hosts virulent strains can encyst, hinting at an explanation for the evolution of virulence polymorphism in T. gondii.
Structure and function of the Smoothened extracellular domain in vertebrate Hedgehog signaling
Authors: Nachtergaele Sigrid , Whalen Daniel M , Mydock Laurel K , Zhao Zhonghua , Malinauskas Tomas , Krishnan Kathiresan , Ingham Philip W , Covey Douglas F , Siebold Christian , Rohatgi Rajat
Published: October 2013

The Hedgehog (Hh) signal is transduced across the membrane by the heptahelical protein Smoothened (Smo), a developmental regulator, oncoprotein and drug target in oncology. We present the 2.3 Å crystal structure of the extracellular cysteine rich domain (CRD) of vertebrate Smo and show that it binds to oxysterols, endogenous lipids that activate Hh signaling. The oxysterol-binding groove in the Smo CRD is analogous to that used by Frizzled 8 to bind to the palmitoleyl group of Wnt ligands and to similar pockets used by other Frizzled-like CRDs to bind hydrophobic ligands. The CRD is required for signaling in response to native Hh ligands, showing that it is an important regulatory module for Smo activation. Indeed, targeting of the Smo CRD by oxysterol-inspired small molecules can block signaling by all known classes of Hh activators and by clinically relevant Smo mutants.
Receptor–Ligand Interactions: Binding Affinities Studied by Single‐Molecule and Super‐Resolution Microscopy on Intact Cells
Authors: Dietz Marina S. , Fricke Franziska , Krüger Carmen L. , Niemann Hartmut H. , Heilemann Mike
Published: October 2013

Protein–ligand interactions play an important role in many biological processes. Notably, membrane receptors are the starting point for a huge variety of cellular signal transduction pathways. Quantifying the binding affinity of a ligand for its transmembrane receptor is of great importance as it provides information on the potency of the ligand. We developed a new experimental procedure to determine binding affinities of ligands for their membrane receptors directly on intact single cells using super‐resolution imaging. Dissociation constants were determined by titrating fluorophore‐labelled ligand against cells expressing the target protein and applying single‐molecule imaging.
Large‐Sized Fabrication of Tunable Plasmonic Electrodes Via Electrodeposition
Authors: Chen Wei‐Hung , Chen Ying‐Shiou , Fu Shu‐Juan , Ko Wen‐Yin , Lin Kuan‐Jiuh
Published: October 2013

Electrodeposition method, a simple, cheap, and flexible approach, to fabricate gold nanoparticle (Au NPs) films with an area larger than 1 cm2 on indium tin oxide (ITO) electrodes modified with (3‐mercaptopropyl) trimethoxysilane (MPTMS) was presented. Size‐controllable and high loading Au NPs were obtained, which were characterized by field‐emission scanning electron microscopic (FESEM) and UV‐vis spectroscopy. Our current method provides a versatile and facile pathway to fabricate large‐scale metal nanoparticles thin film, enhancing alternatives for academic investigation and industrial application.
Electrochemical Determination of Cu(II) Ions in Chloride‐Rich Environment Using Polyviologen‐Modified Glassy Carbon Electrodes
Authors: Hsu Pei‐Fen , Ciou Wan‐Lun , Chen Po‐Yu
Published: October 2013

Polyviologen was formed on glassy carbon electrodes using potentiostatic electropolymerization in pH 4.2 Britton‐Robinson buffer solution. The polyviologen‐modified glassy carbon electrode (PVGCE) was employed to determine Cu(II) in chloride‐rich solutions in order to demonstrate the electroanalytical application of polyviologen. The PVGCE was found capable of enhancing the detection limit of Cu(II) in chloride‐rich environment because of the anion‐exchange feature of the polymer film. Cathodic stripping square‐wave voltammetry (CSSWV) was employed to determine Cu(II). The dependence of the cathodic stripping current on the concentration of Cu(II) was linear from 0.06 ppm to 9.53 ppm with a regression coefficient of 0.999. The detection limit is 0.02 ppm (σ = 3). Regeneration of the PVGCE can be achieved by simply immersing the electrode in a stirred 0.5 M NaCl solution.
Adhesion properties of potentially probioticLactobacillus kefirito gastrointestinal mucus
Authors: Carasi Paula , Ambrosis Nicolás M. , De Antoni Graciela L. , Bressollier Philippe , Urdaci María C. , Serradell María de los Angeles
Published: October 2013

We investigated the mucus-binding properties of aggregating and non-aggregating potentially probiotic strains of kefir-isolatedLactobacillus kefiri, using different substrates. All the strains were able to adhere to commercial gastric mucin (MUCIN) and extracted mucus from small intestine (SIM) and colon (CM). The extraction of surface proteins from bacteria using LiCl or NaOH significantly reduced the adhesion of three selected strains (CIDCA 8348, CIDCA 83115 and JCM 5818); although a significant proportion (up to 50%) of S-layer proteins were not completely eliminated after treatments. The surface (S-layer) protein extracts from all the strains ofLb. kefiriwere capable of binding to MUCIN, SIM or CM, and no differences were observed among them. The addition of their own surface protein extract increased adhesion of CIDCA 8348 and 83115 to MUCIN and SIM, meanwhile no changes in adhesion were observed for JCM 5818. None of the seven sugars tested had the ability to inhibit the adhesion of whole bacteria to the three mucus extracts. Noteworthy, the degree of bacterial adhesion reached in the presence of their own surface protein (S-layer) extract decreased to basal levels in the presence of some sugars, suggesting an interaction between the added sugar and the surface proteins. In conclusion, the ability of these food-isolated bacteria to adhere to gastrointestinal mucus becomes an essential issue regarding the biotechnological potentiality ofLb. kefirifor the food industry.
Introduction: the essential role of the Pteridophyta in the study of land plants
Authors: Bell P. R.
Published: October 2013

Synopsis

Arguments based on their technical advantages, undoubted antiquity and lack of evolutionary extravagances are advanced for promoting the study of the Pteridophyta. Sound interpretations of fundamental aspects of the land plants, together with useful knowledge, are likely to follow, and grievous errors arising from too great a concentration on the flowering plants can be avoided.
The Occurrence of a Human Skeleton in a Glacial Deposit at Ipswich
Authors: Moir J. Reid
Published: October 2013

On Friday, October 6th, 1911, I received a message from Mr. Laughlin, of Messrs. Bolton & Laughlin, brickmakers, Ipswich, to the effect that one of his workmen, while removing some surface clay to get at the underlying glacial gravel, had turned out some human bones. I at once went down to the pit where the discovery had been made and found that a portion of a human skull attached to an almost complete cranial cast had been recovered. The workmen pointed out that two bones were protruding from the spot whence the skull had been derived, and so it was arranged for the remainder of the skeleton to be dug up on the following day. Messrs. Woolnough, Canton, and Snell accompanied me, and we afterwards drew up a short report of our observations. This report is as follows:—

“We, the undersigned, were present at, and superintended, the digging out of the human remains found at Messrs. Bolton & Laughlin's pit, Ipswich, on Saturday, October 7th, 1911. We all most carefully examined the section of decalcified Boulder Clay, under which the bones lay, before any digging commenced, and were absolutely convinced that no grave had ever been dug on the spot before.
Flint Implements of Man from the Middle Glacial Gravel and the Chalky Boulder Clay of Suffolk
Authors: Moir J. Reid
Published: October 2013

The Middle Glacial Sands and Gravel which occur over such a large portion of East Anglia are somewhat difficult to explain, and various opinions have been put forward to account for them. In Suffolk they generally occur under the Chalky Boulder Clay, and in some parts of Norfolk between that deposit and the older Contorted Drift. In the neighbourhood of Ipswich these deposits generally rest upon Red Crag, and are covered by the Chalky Boulder Clay. They are best seen where pits have been sunk upon the plateau or where streams have cut into the plateau and exposed the various beds composing it.

Having discovered six years ago that the Middle Glacial Gravel is implementiferous, I have continually searched these deposits, and am led to the following views regarding them.
The Stone Age in Beechamwell
Authors: Nightingale R. C.
Published: October 2013

The greater part of the northern side of the parish of Beechamwell consists of marl and chalk with a top-soil of from one to eighteen feet of gravelly sand. The average depth of this is about eight feet. On the top of it there is a layer of turf or of cultivable soil from three-quarters of a foot to a foot and a-half in depth. There is a narrow strip of boulder clay deposit on which ice-scratched, worked flints are found. There is also a tongue of gravel one and a-half-mile long and half-a-mile wide at its widest part. On this, generally, very few worked flints have been found; fragments of pottery in some numbers have been found all over it however. On the edge of this strip, adjacent on the west to the boulder clay, several worked flints have been picked up, and a hoard of about 200 splinters and flakes was found lying between the sand and the turf, a foot deep here.

The greater part of the worked flints are found in an area of about half-a-mile square. The axes, whole or in fragments, are found scattered over the whole of the northern half of the parish. The first axe, however, I found was lying beside a path through the old fen that lies on the south side of Beechamwell. The worked flints found near the moraine are of a peculiar grey colour, and nearly all scimitar-shaped.

Flints are found in beds in the chalk and are still plentiful on the surface of the soil, although many have been picked off it for building and road-mending. The small area on which the worked flints are so numerous is the highest ground in Beechamwell.
Roman Interments at Scole
Authors: Dutt W. A.
Published: October 2013

About ten years ago some labourers engaged in excavating gravel from a pit on the estate of Mr. A. Wood Crawshay, J.P., in the parish of Scole, Norfolk, brought to light a number of iron spear-heads, a quantity of fragmentary pottery, a small ornamented object of bronze, and several bones. No effort was made to discover the positions these various objects occupied in relation to each ether, but it was ascertained that they were all deposited in some trenches about six feet long and three feet wide, cut in the surface soil of the ground bordering the pit. Through the kindness of Mr. Crawshay, I was able to exhibit some of these relics at a meeting of the Prehistoric Society of East Anglia, held at Norwich, on March 22nd, 1909, and the conclusion come to concerning them was that they represented interments of the Roman period. Six spear-heads were found, two being uninjured apart from corrosion, while the remaining four were broken, one having lost the whole of its blade.
Surface Changes Since the Palæolithic Period in Kent and Surrey
Authors: Dewey Henry
Published: October 2013

A series of implements were collected during the summer and autumn of 1914 from an area of some twenty square miles lying between the Cray Valley and Kingsdown in North Kent. The specimens were not distributed uniformly over this area, but confined more or less to a few localities where they occurred in considerable numbers. It is, moreover, significant that these localities are on high land commanding extensive views of the surrounding country, and especially of the river valleys. The sites were presumably chosen for this and another reason—the local abundance of green-coated flint, a material which was largely employed in the manufacture of implements.

The sites had been inhabited by a succession of peoples who left their implements behind them. Among these the commonest are assignable to the Neolithic period, but Palæolithic implements are by no means rare. There are, moreover, localities where only Palæolithic forms are found, and these all of one pattern, namely, the pointed ovate. Many possess the familiar reversed S twist, and all are deeply patinated, either pure white, pinkish-yellow, or cream.
A Prehistoric Flint-Pit at Ringland
Authors: Clarke W. G.
Published: October 2013

In 1906 I described a “Cissbury type” station at Ringland, Norfolk, the implements lying abundantly on the surface of two fields and covering an area of about 440 yards in length by 90 yards in width. The fields are at the foot of a steep tree-clad ridge known as Cobb's Hills, and slope gently to the river Wensum which is but a few yards distant from the lower part of the fields and is here about 34 feet above O.D. Some of the implements were described and figured in our “Proceedings,” and the site has yielded about 900 implements and several thousand flakes.
The Norfolk Sub-Crag Implements
Authors: Clarke W. G.
Published: October 2013

In his able article on “The Chipping of Flint by Natural Agencies,” Mr. F. N. Haward endeavoured to prove that certain flints found in the basement-bed of the Red and Norwich Crags and supposed by some archæologists to have been chipped by man, were really the product of natural forces, evidence of the working of which he considered that he had found in the Eaton Pit, Norwich. He argued that the flints were chipped either before the deposition of the gravels above by forces moving over the surface, probably stones moved by snow or ice or by currents of water (p. 188), or during or after the deposition of the gravels above, by lateral or vertical movements in the gravels. This point of view was elaborated at considerable length and supported by an excellent series of illustrations.
Some “Flat-Faced” Palæoliths from Farnham
Authors: Bury Henry
Published: October 2013

In his chapter on the forms of implements from the River Drift, Sir J. Evans mentions certain specimens which, are “flat on one face and convex on the other,” and among these he recognises one type with a thick butt (“shoe-shaped”) and another thinner one, for which he proposes the term “flat-faced.” As however, the thick specimens are by no means always typically shoe-shaped, and the one characteristic which binds the two groups together is the comparative flatness of one face, there seems to be no sufficient reason for limiting the term “flat-faced,” and in the following pages it is applied to the whole series, whether thick or thin.
Foreign Relations in the Neolithic Period
Authors: Smith Reginald A.
Published: October 2013

In discussing the points of contact between Neolithic Britain and the Continent, it is desirable from many points of view to begin at the beginning, and to conclude with the introduction of metal. I prefer this to the method adopted in our leading text-book, even though it brings us at once into an area of conflict, where nothing should be taken for granted, and general agreement is not yet in sight. In Scandinavia there seems to be a definite terminus a quo, though even there some elements of doubt can be detected. It is generally assumed that human life began in the peninsula soon after the last or Baltic glaciation came to an end; and the first question is whether the same holds good for Britain, and if so, to what extent, for an ice-free area in the south of England is recognised by most authorities even during the severe glaciation that accounted for boulder-clay at Finchley, only three miles north of the Thames.

As will be seen later, intercourse with Scandinavia was lively during two phases of the Megalithic period, but there is nothing to shew that the Neolithic civilisations east and west of the North Sea had a common origin or began at the same date.
Man and the Ice Age
Authors: Marr J. E.
Published: October 2013

Highly as I feel the honour of having been asked to occupy this Presidential chair, I accepted that honour with some diffidence, for I recognise that my studies in Pre-history.have not been carried very far. As, however, these studies have convinced me that the application of geology to prehistoric problems is even yet fraught with many difficulties, it appears to me desirable in this address to call special attention to some of these difficulties.

Having devoted nearly half a century to geological researches of various kinds, I can state with confidence that those geological problems with which we are concerned are among the most difficult with which the geologist is confronted, and their investigation cannot be lightly undertaken.

At present, what we above all require is the collection of facts, and I therefore hailed with pleasure the foundation of this Society, and congratulate its members upon the amount of valuable work which they have already performed. Among these members the name of Dr. Allen Sturge stands out pre-eminent. He may be regarded as the Father of the Society, and all members must deeply deplore the loss which the Society has sustained by his death.