Rare earth elements from the Atlantic Sector

We present a Rare Earth Elements (REE) record at decadal resolution determined in the EPICA ice core drilled in Dronning Maud Land (EDML) in the Atlantic Sector of the East Antarctic Plateau, covering the transition from the last glacial age (LGA) to the early Holocene (26 600-7500 yr BP). Additionally, samples from potential source areas (PSAs) for Antarctic dust were analysed for their REE characteristics. The dust provenance is discussed by comparing the REE fingerprints in the ice core and the PSAs samples. We find a shift in REE composition at 15 200 yr BP in the ice core samples. Before 15 200 yr BP, the dust composition is very uniform and its provenance was likely to be dominated by a South American source. After 15 200 yr BP, multiple sources such as Australia and New Zealand become relatively more important, albeit South America is possibly still an important dust supplier. A similar change in the dust characteristics was observed in the EPICA Dome C ice core at around ~15 000 yr BP. A return to more glacial dust characteristics between ~8300 and ~7500 yr BP, as observed in the EPICA Dome C core, could not be observed in the EDML core. Consequently, the dust provenance at the two sites must have been different at that time.

Tab. 1: Mineralogical composition and chemical analyses of major and trace elements of Ameghino Formation rocks

As a result of a petrographical, mineralogical and geochemical characterization of the Ameghino Formation mudstones (Upper Jurassic- Lower Cretaceous, Antarctic Peninsula), "epiclastic" radiolaria-rich and mixed (radiolaria-rich + tuff) mudstone types were recognized. Contents of clastic material in the mudstones generally increase with younger paleontological age, but local exceptions to this trend have been found. The anoxic environment of the lower part of the sequence changes to more oxidizing conditions towards the top, in transition to the Hauterivian - Barrêmian conglomerates. Element to element correlations show good agreement with the normal differentiation trends of volcanic (andesite-rhyolite) rocks, suggesting that the overall sequence is mainly volcanic in origin with various grade of reworking. For example, the radiolaria-rich mudstone matrix could have been originated from very fine touffaceous suspensions deposited very slowly after the main fall of the tuffs. However, in the upper part of the sequence, some epiclastic supply is revealed by petrographic evidence and illite crystallinity index. The clay mineral association (illite, chlorite and illite-smectite mixed layers) is mainly of diagenetic origin in the stratigraphically lower sections. Low percentages of expandable layers in the illite-smectite mixed layers, as well as the general mineralogical association, suggest a late mesodiagenetic stage, and together with geological evidence, a relatively deep burial (> 1000 m - probably > 2500 m) and temperatures exceeding 100°C.

Concentrations of rare earth elements in pore waters of IODP Holes 323-U1345A and 323-U1345B

We studied the diagenetic behavior of rare earth elements (REEs) in a highly productive passive margin setting of the Bering Sea Slope. Site U1345 was drilled during the Integrated Ocean Drilling Program Expedition 323 at a water depth of 1008 m currently in the center of an oxygen minimum zone. Pore water concentrations of fourteen REEs were determined down to ~ 140 meters below the seafloor (mbsf). The REE concentrations were higher in the pore water than the deep seawater, indicating that there was significant liberation from the sediments during diagenesis. There was a major peak at ~ 10 mbsf that was more pronounced for the heavy REE (HREE); this peak occurred below the sulfate-methane transition zone (6.3 mbsf) and coincided with high concentrations of dissolved iron and manganese. At ~ 2 mbsf, there was a minor peak in REE and Mn contents. Below ~ 40 mbsf, the REE concentration profiles remained constant. The Ce anomaly was insignificant and relatively constant (PAAS-normalized Ce/Ce = 1.1 ± 0.2) throughout the depth profile, showing that the Ce depleted in seawater was restored in the pore water. HREE-enrichment was observed over the entire 140 m except for the upper ~ 1 m, where a middle REE (MREE)-bulge was apparent. REE release in shallow depths (2-4 mbsf) is attributed to the release of light REEs (LREEs) and MREEs during the organoclastic reduction of Mn oxides in anoxic sediments. The high HREE concentrations observed at ~ 10 mbsf can be attributed to the reduction of Fe and Mn minerals tied to anaerobic oxidation of methane or, less significantly, to ferromagnesian silicate mineral weathering. The upward diffusion flux across the sediment-water interface was between 3 (for Tm) and 290 (for Ce) pmol/m**2/y.

PM2.5, PM10, and PM10-associated elements in the air in Bamako, Mali (2012-2013)

Saharan dust incursions and particulates emitted from human activities degrade air quality throughout West Africa, especially in the rapidly expanding urban centers in the region. Particulate matter (PM) that can be inhaled is strongly associated with increased incidence of and mortality from cardiovascular and respiratory diseases and cancer. Air samples collected in the capital of a Saharan-Sahelian country (Bamako, Mali) between September 2012 - July 2013 were found to contain inhalable PM concentrations that exceeded World Health Organization (WHO) and US Environmental Protection Agency (USEPA) PM2.5 and PM10 24-h limits 58 - 98% of days and European Union (EU) PM10 24-h limit 98% of days. Mean concentrations were 1.2-to-4.5 fold greater than existing limits. Inhalable PM was enriched in transition metals, known to produce reactive oxygen species and initiate the inflammatory reaction, and other potentially bioactive and biotoxic metals/metalloids. Eroded mineral dust composed the bulk of inhalable PM, whereas most enriched metals/metalloids were likely emitted from oil combustion, biomass burning, refuse incineration, vehicle traffic, and mining activities. Human exposure to inhalable PM and associated metals/metalloids over 24-h was estimated. The findings indicate that inhalable PM in the Sahara-Sahel region may present a threat to human health, especially in urban areas with greater inhalable PM and transition metal exposure.

Genomic analyses of flowering transition and inflorescence development in grapevine = Análisis genómicos de la transición floral y del desarrollo de la inflorescencia en la vid

The general objective of this work is to analyze the regulatory processes underlying flowering transition and inflorescence and flower development in grapevine. Most of these crucial developmental events take place within buds growing during two seasons in two consecutive years. During the first season, the shoot apical meristem within the bud differentiates all the basic elements of the shoot including flowering transition in lateral primordia and development of inflorescence primordia. These events practically end with bud dormancy. The second season, buds resume shoot growth associated to flower formation and development. In grapevine, the lateral meristems can give rise either to tendril or inflorescence primordia that are homologous organs. With this purpose, we performed global transcriptome analyses along the bud annual cycle and during inflorescence and tendril development. In addition, we approach the genomic analysis of the MIKC type MADS-box gene family in grapevine to identify all its members and assign them putative biological functions. Regarding buds developmental cycle, the results indicate that the main factors explaining the global gene expression differences were the processes of bud dormancy and active growth as well as stress responses. Non dormant buds exhibited up-regulation in functional categories typical of actively proliferating and growing cells (photosynthesis, cell cycle regulation, chromatin assembly) whereas in dormant ones the main functional categories up-regulated were associated to stress response pathways together with transcripts related to starch catabolism. Major transcriptional changes during the dormancy period were associated to the para/endodormancy, endo/ecodormancy and ecodormancy/bud break transitions. Global transcriptional analyses along tendril and inflorescence development suggested that these two homologous organs share a common transcriptional program related to cell proliferation functions. Both structures showed a progressive decrease in the expression of categories such as cell-cycle, auxin metabolism/signaling, DNA metabolism, chromatin assembly and a cluster of five transcripts belonging to the GROWTH-REGULATING FACTOR (GRF) transcription factor family, that are known to control cell proliferation in other species and determine the size of lateral organs. However, they also showed organ specific transcriptional programs that can be related to their differential organ structure and function. Tendrils showed higher transcription of genes related to photosynthesis, hormone signaling and secondary metabolism than inflorescences, while inflorescences have higher transcriptional activity for genes encoding transcription factors (especially those belonging to the MADS-box gene family). Further analysis along inflorescence development evidenced the relevance of additional functions likely related to processes of flower development such as fatty acid and lipid metabolism, jasmonate signaling and oxylipin biosynthesis. The transcriptional analyses performed highlighted the relevance of several groups of transcriptional regulators in the developmental processes studied. The expression profiles along bud development revealed significant differences for some MADS-box subfamilies in relation to other plant species, like the members of the FLC and SVP subfamilies suggesting new roles for these groups in grapevine. In this way, it was found that VvFLC2 and VvAGL15.1 could participate, together with some members of the SPL-L family, in dormancy regulation, as was shown for some of them in other woody plants. Similarly, the expression patterns of the VvFLC1, VvFUL, VvSOC1.1 (together with VvFT, VvMFT1 and VFL) genes could indicate that they play a role in flowering transition in grapevine, in parallel to their roles in other plant systems. The expression levels of VFL, the grapevine LEAFY homolog, could be crucial to specify the development of inflorescence and flower meristems instead of tendril meristems. MADS-box genes VvAP3.1 and 2, VvPI, VvAG1 and 3, VvSEP1-4, as well as VvBS1 and 2 are likely associated with the events of flower meristems and flower organs differentiation, while VvAP1 and VvFUL-L (together with VvSOC1.1, VvAGL6.2) could be involved on tendril development given their expression patterns. In addition, the biological function ofVvAP1 and VvTFL1A was analyzed using a gene silencing approach in transgenic grapevine plants. Our preliminary results suggested a possible role for both genes in the initiation and differentiation of tendrils. Finally, the genomic analysis of the MADS-box gene family in grapevine revealed differential features regarding number and expression pattern of genes putatively involved in the flowering transition process as compared to those involved in the specification of flower and fruit organ identity. Altogether, the results obtained allow identifying putative candidate genes and pathways regulating grapevine reproductive developmental processes paving the way to future experiments demonstrating specific gene biological functions. RESUMEN El objetivo general de este trabajo es analizar los procesos regulatorios subyacentes a la inducción floral así como al desarrollo de la inflorescencia y la flor en la vid. La mayor parte de estos eventos cruciales tienen lugar en las yemas a lo largo de dos estaciones de crecimiento consecutivas. Durante la primera estación, el meristemo apical contenido en la yema diferencia los elementos básicos del pámpano, lo cual incluye la inducción de la floración en los meristemos laterales y el subsiguiente desarrollo de primordios de inflorescencia. Estos procesos prácticamente cesan con la entrada en dormición de la yema. En la segunda estación, se reanuda el crecimiento del pámpano acompañado por la formación y desarrollo de las flores. En la vid, los meristemos laterales pueden dar lugar a primordios de inflorescencia o de zarcillo que son considerados órganos homólogos. Con este objetivo llevamos a cabo un estudio a nivel del transcriptoma de la yema a lo largo de su ciclo anual, así como a lo largo del desarrollo de la inflorescencia y del zarcillo. Además realizamos un análisis genómico de la familia MADS de factores transcripcionales (concretamente aquellos del tipo MIKC) para identificar todos sus miembros y tratar de asignarles posibles funciones biológicas. En cuanto al ciclo de desarrollo de la yema, los resultados indican que los principales factores que explican las diferencias globales en la expresión génica fueron los procesos de dormición de la yema y el crecimiento activo junto con las respuestas a diversos tipos de estrés. Las yemas no durmientes mostraron un incremento en la expresión de genes contenidos en categorías funcionales típicas de células en proliferación y crecimiento activo (como fotosíntesis, regulación del ciclo celular, ensamblaje de cromatina), mientras que en las yemas durmientes, las principales categorías funcionales activadas estaban asociadas a respuestas a estrés, así como con el catabolismo de almidón. Los mayores cambios observados a nivel de transcriptoma en la yema coincidieron con las transiciones de para/endodormición, endo/ecodormición y ecodormición/brotación. Los análisis transcripcionales globales a lo largo del desarrollo del zarcillo y de la inflorescencia sugirieron que estos dos órganos homólogos comparten un programa transcripcional común, relacionado con funciones de proliferación celular. Ambas estructuras mostraron un descenso progresivo en la expresión de genes pertenecientes a categorías funcionales como regulación del ciclo celular, metabolismo/señalización por auxinas, metabolismo de ADN, ensamblaje de cromatina y un grupo de cinco tránscritos pertenecientes a la familia de factores transcripcionales GROWTH-REGULATING FACTOR (GRF), que han sido asociados con el control de la proliferación celular y en determinar el tamaño de los órganos laterales en otras especies. Sin embargo, también pusieron de manifiesto programas transcripcionales que podrían estar relacionados con la diferente estructura y función de dichos órganos. Los zarcillos mostraron mayor actividad transcripcional de genes relacionados con fotosíntesis, señalización hormonal y metabolismo secundario que las inflorescencias, mientras que éstas presentaron mayor actividad transcripcional de genes codificantes de factores de transcripción (especialmente los pertenecientes a la familia MADS-box). Análisis adicionales a lo largo del desarrollo de la inflorescencia evidenciaron la relevancia de otras funciones posiblemente relacionadas con el desarrollo floral, como el metabolismo de lípidos y ácidos grasos, la señalización mediada por jasmonato y la biosíntesis de oxilipinas. Los análisis transcripcionales llevados a cabo pusieron de manifiesto la relevancia de varios grupos de factores transcripcionales en los procesos estudiados. Los perfiles de expresión estudiados a lo largo del desarrollo de la yema mostraron diferencias significativas en algunas de las subfamilias de genes MADS con respecto a otras especies vegetales, como las observadas en los miembros de las subfamilias FLC y SVP, lo cual sugiere que podrían desempeñar nuevas funciones en la vid. En este sentido, se encontró que los genes VvFLC2 y VvAGL15.1 podrían participar, junto con algunos miembros de la familia SPL-L, en la regulación de la dormición. De un modo similar, los patrones de expresión de los genes VvFLC1, VvFUL, VvSOC1.1 (junto con VvFT, VvMFT1 y VFL) podría indicar que desempeñan un papel en la regulación de la inducción de la floración en la vid, como se ha observado en otros sistemas vegetales. Los niveles de expresión de VFL, el homólogo en vid del gen LEAFY de A. thaliana podrían ser cruciales para la especificación del desarrollo de meristemos de inflorescencia y flor en lugar de meristemos de zarcillo. Los genes VvAP3.1 y 2, VvPI, VvAG1 y 3, VvSEP1-4, así como VvBS1 y 2 parecen estar asociados con los eventos de diferenciación de meristemos y órganos florales, mientras que VvAP1 y VvFUL-L (junto con VvSOC1.1 y VvAGL6.2) podrían estar implicados en el desarrollo del zarcillo dados sus patrones de expresión. Adicionalmente, se analizó la función biológica de los genes VvAP1 y VvTFL1A por medio de una estrategia de silenciamiento génico. Los datos preliminares sugieren un posible papel para ambos genes en la iniciación y diferenciación de los zarcillos. Finalmente, el análisis genómico de la familia MADS en vid evidenció diferencias con respecto a otras especies vegetales en cuanto a número de miembros y patrón de expresión en genes supuestamente implicados en la inducción de la floración, en comparación con aquellos relacionados con la especificación de identidad de órganos florales y desarrollo del fruto. En conjunto, los resultados obtenidos han permitido identificar posibles rutas y genes candidatos a participar en la regulación de los procesos de desarrollo reproductivo de la vid, sentando las bases de futuros experimentos encaminados a conocer la funciones biológicas de genes específicos.

Crack mechanical failure in lithium niobate crystal under ion irradiation; novel simulation by extended finite elements

Swift heavy ion irradiation (ions with mass heavier than 15 and energy exceeding MeV/amu) transfer their energy mainly to the electronic system with small momentum transfer per collision. Therefore, they produce linear regions (columnar nano-tracks) around the straight ion trajectory, with marked modifications with respect to the virgin material, e.g., phase transition, amorphization, compaction, changes in physical or chemical properties. In the case of crystalline materials the most distinctive feature of swift heavy ion irradiation is the production of amorphous tracks embedded in the crystal. Lithium niobate is a relevant optical material that presents birefringence due to its anysotropic trigonal structure. The amorphous phase is certainly isotropic. In addition, its refractive index exhibits high contrast with those of the crystalline phase. This allows one to fabricate waveguides by swift ion irradiation with important technological relevance. From the mechanical point of view, the inclusion of an amorphous nano-track (with a density 15% lower than that of the crystal) leads to the generation of important stress/strain fields around the track. Eventually these fields are the origin of crack formation with fatal consequences for the integrity of the samples and the viability of the method for nano-track formation. For certain crystal cuts (X and Y), these fields are clearly anisotropic due to the crystal anisotropy. We have used finite element methods to calculate the stress/strain fields that appear around the ion-generated amorphous nano-tracks for a variety of ion energies and doses. A very remarkable feature for X cut-samples is that the maximum shear stress appears on preferential planes that form +/-45º with respect to the crystallographic planes. This leads to the generation of oriented surface cracks when the dose increases. The growth of the cracks along the anisotropic crystal has been studied by means of novel extended finite element methods, which include cracks as discontinuities. In this way we can study how the length and depth of a crack evolves as function of the ion dose. In this work we will show how the simulations compare with experiments and their application in materials modification by ion irradiation.

Ab initio calculations of Ca III Stark broadening parameters,transition probabilities and radiative lifetimes

We have determined matrix elements for all experimental configurations of Ca III, including the 3s3p63d configuration. These values have been obtained using intermediate coupling (IC). For these IC calculations, we have used the standard method of least-squares fitting from the experimental energy levels, using the computer code developed by Robert Cowan. In this paper, using these matrix elements, we report the calculated values of the Ca III Stark widths and shifts for 148 spectral lines, of 56 Ca III spectral line transition probabilities and of eight radiative lifetimes of Ca III levels. The Stark widths and shifts, calculated using the Griem semi-empirical approach, correspond to the spectral lines of Ca III and are presented for an electron density of 1017 cm?3 and temperatures T = 1.0?10.0 (×104 K). The theoretical trends of the Stark broadening parameter versus the temperature are presented for transitions that are of astrophysical interest. There is good agreement between our calculations, for transition probabilities and radiative lifetimes, and the experimental values presented in the literature. We have not been able to find any values for the Stark parameters in the references.

Analysis of the problems associated with dynamic interaction between train, track and structure at transition zones

El gran desarrollo experimentado por la alta velocidad en los principales países de la Unión Europea, en los últimos 30 años, hace que este campo haya sido y aún sea uno de los principales referentes en lo que a investigación se refiere. Por otra parte, la aparición del concepto super − alta velocidad hace que la investigación en el campo de la ingeniería ferroviaria siga adquiriendo importancia en los principales centros de investigación de los países en los que se desea implantar este modo de transporte, o en los que habiendo sido ya implantado, se pretenda mejorar. Las premisas de eficacia, eficiencia, seguridad y confort, que este medio de transporte tiene como razón de ser pueden verse comprometidas por diversos factores. Las zonas de transición, definidas en la ingeniería ferroviaria como aquellas secciones en las que se produce un cambio en las condiciones de soporte de la vía, pueden afectar al normal comportamiento para el que fue diseñada la infraestructura, comprometiendo seriamente los estándares de eficiencia en el tiempo de viaje, confort de los pasajeros y aumentando considerablemente los costes de mantenimiento de la vía, si no se toman las medidas oportunas. En esta tesis se realiza un estudio detallado de la zonas de transición, concretamente de aquellas en las que existe una cambio en la rigidez vertical de la vía debido a la presencia de un marco hidráulico. Para realizar dicho estudio se lleva a cabo un análisis numérico de interacción entre el vehículo y la estructura, con un modelo bidimensional de elemento finitos, calibrado experimentalmente, en estado de tensión plana. En este análisis se tiene en cuenta el efecto de las irregularidades de la vía y el comportamiento mecánico de la interfaz suelo-estructura, con el objetivo de reproducir de la forma más real posible el efecto de interacción entre el vehículo, la vía y la estructura. Otros efectos como la influencia de la velocidad del tren y los asientos diferenciales, debidos a deformaciones por consolidación de los terraplenes a ambos lados el marco hidráulico, son también analizados en este trabajo. En esta tesis, los cálculos de interacción se han llevado a cabo en dos fases diferentes. En la primera, se ha considerado una interacción sencilla debida al paso de un bogie de un tren Eurostar. Los cálculos derivados de esta fase se han denominado cálculos a corto plazo. En la segunda, se ha realizado un análisis considerando múltiples pasos de bogie del tren Eurostar, conformando un análisis de degradación en el que se tiene en cuenta, en cada ciclo, la deformación de la capa de balasto. Los cálculos derivados de esta fase, son denominados en el texto como cálculos a largo plazo. Los resultados analizados muestran que la utilización de los denominados elementos de contacto es fundamental cuando se desea estudiar la influencia de asientos diferenciales, especialmente en transiciones terraplén-estructura en las que la cuña de cimentación no llega hasta la base de cimentación de la estructura. Por otra parte, tener en cuenta los asientos del terraplén, es sumamente importante, cuando se desea realizar un análisis de degradación de la vía ya que su influencia en la interacción entre el vehículo y la vía es muy elevada, especialmente para valores altos de velocidad del tren. En cuanto a la influencia de las irregularidades de la vía, en los cálculos efectuados, se revela que su importancia es muy notable, siendo su influencia muy destacada cuanto mayor sea la velocidad del tren. En este punto cabe destacar la diferencia de resultados derivada de la consideración de perfiles de irregularidades de distinta naturaleza. Los resultados provenientes de considerar perfiles artificiales son en general muy elevados, siendo estos más apropiados para realizar estudios de otra índole, como por ejemplo de seguridad al descarrilamiento. Los resultados provenientes de perfiles reales, dados por diferentes Administradores ferroviarios, presentan resultados menos elevados y más propios del problema analizar. Su influencia en la interacción dinámica entre el vehículo y la vía es muy importante, especialmente para velocidades elevadas del tren. Además el fenómeno de degradación conocido como danza de traviesas, asociado a zonas de transición, es muy susceptible a la consideración de irregularidades de la vía, tal y como se desprende de los cálculos efectuados a largo plazo. The major development experienced by high speed in the main countries of the European Union, in the last 30 years, makes railway research one of the main references in the research field. It should also be mentioned that the emergence of the concept superhigh − speed makes research in the field of Railway Engineering continues to gain importance in major research centers in the countries in which this mode of transportation is already implemented or planned to be implemented. The characteristics that this transport has as rationale such as: effectiveness, efficiency, safety and comfort, may be compromised by several factors. The transition zones are defined in railway engineering as a region in which there is an abrupt change of track stiffness. This stiffness variation can affect the normal behavior for which the infrastructure has been designed, seriously compromising efficiency standards in the travel time, passenger comfort and significantly increasing the costs of track maintenance, if appropriate measures are not taken. In this thesis a detailed study of the transition zones has been performed, particularly of those in which there is a change in vertical stiffness of the track due to the presence of a reinforced concrete culvert. To perform such a study a numerical interaction analysis between the vehicle, the track and the structure has been developed. With this purpose a two-dimensional finite element model, experimentally calibrated, in a state of plane stress, has been used. The implemented numerical models have considered the effects of track irregularities and mechanical behavior of soil-structure interface, with the objective of reproducing as accurately as possible the dynamic interaction between the vehicle the track and the structure. Other effects such as the influence of train speed and differential settlement, due to secondary consolidation of the embankments on both sides of culvert, have also been analyzed. In this work, the interaction analysis has been carried out in two different phases. In the first part a simple interaction due to the passage of a bogie of a Eurostar train has been considered. Calculations derived from this phase have been named short-term analysis. In the second part, a multi-load assessment considering an Eurostar train bogie moving along the transition zone, has been performed. The objective here is to simulate a degradation process in which vertical deformation of the ballast layer was considered. Calculations derived from this phase have been named long-term analysis. The analyzed results show that the use of so-called contact elements is essential when one wants to analyze the influence of differential settlements, especially in embankment-structure transitions in which the wedge-shaped backfill does not reach the foundation base of the structure. Moreover, considering embankment settlement is extremely important when it is desired to perform an analysis of track degradation. In these cases the influence on the interaction behaviour between the vehicle and the track is very high, especially for higher values of speed train. Regarding the influence of the track irregularities, this study has proven that the track’s dynamic response is heavily influenced by the irregularity profile and that this influence is more important for higher train velocities. It should also be noted that the difference in results derived from consideration of irregularities profiles of different nature. The results coming from artificial profiles are generally very high, these might be more appropriate in order to study other effects, such as derailment safety. Results from real profiles, given by the monitoring works of different rail Managers, are softer and they fit better to the context of this thesis. The influence of irregularity profiles on the dynamic interaction between the train and the track is very important, especially for high-speeds of the train. Furthermore, the degradation phenomenon known as hanging sleepers, associated with transition zones, is very susceptible to the consideration of track irregularities, as it can be concluded from the long-term analysis.

Transition-state structure as a unifying basis in protein-folding mechanisms: Contact order, chain topology, stability, and the extended nucleus mechanism

I attempt to reconcile apparently conflicting factors and mechanisms that have been proposed to determine the rate constant for two-state folding of small proteins, on the basis of general features of the structures of transition states. Φ-Value analysis implies a transition state for folding that resembles an expanded and distorted native structure, which is built around an extended nucleus. The nucleus is composed predominantly of elements of partly or well-formed native secondary structure that are stabilized by local and long-range tertiary interactions. These long-range interactions give rise to connecting loops, frequently containing the native loops that are poorly structured. I derive an equation that relates differences in the contact order of a protein to changes in the length of linking loops, which, in turn, is directly related to the unfavorable free energy of the loops in the transition state. Kinetic data on loop extension mutants of CI2 and α-spectrin SH3 domain fit the equation qualitatively. The rate of folding depends primarily on the interactions that directly stabilize the nucleus, especially those in native-like secondary structure and those resulting from the entropy loss from the connecting loops, which vary with contact order. This partitioning of energy accounts for the success of some algorithms that predict folding rates, because they use these principles either explicitly or implicitly. The extended nucleus model thus unifies the observations of rate depending on both stability and topology.

CDP/cut is the DNA-binding subunit of histone gene transcription factor HiNF-D: a mechanism for gene regulation at the G1/S phase cell cycle transition point independent of transcription factor E2F.

Transcription of the genes for the human histone proteins H4, H3, H2A, H2B, and H1 is activated at the G1/S phase transition of the cell cycle. We have previously shown that the promoter complex HiNF-D, which interacts with cell cycle control elements in multiple histone genes, contains the key cell cycle factors cyclin A, CDC2, and a retinoblastoma (pRB) protein-related protein. However, an intrinsic DNA-binding subunit for HiNF-D was not identified. Many genes that are up-regulated at the G1/S phase boundary are controlled by E2F, a transcription factor that associates with cyclin-, cyclin-dependent kinase-, and pRB-related proteins. Using gel-shift immunoassays, DNase I protection, and oligonucleotide competition analyses, we show that the homeodomain protein CDP/cut, not E2F, is the DNA-binding subunit of the HiNF-D complex. The HiNF-D (CDP/cut) complex with the H4 promoter is immunoreactive with antibodies against CDP/cut and pRB but not p107, whereas the CDP/cut complex with a nonhistone promoter (gp91-phox) reacts only with CDP and p107 antibodies. Thus, CDP/cut complexes at different gene promoters can associate with distinct pRB-related proteins. Transient coexpression assays show that CDP/cut modulates H4 promoter activity via the HiNF-D-binding site. Hence, DNA replication-dependent histone H4 genes are regulated by an E2F-independent mechanism involving a complex of CDP/cut with cyclin A/CDC2/ RB-related proteins.

Lithology and approximate sub-bottom depths and ages of the transition of soft to firm ooze and of firm ooze to chalk at DSDP Leg 89 and 90 Sites

Leg 90 recovered approximately 3705 m of core at eight sites lying at middle bathyal depths (1000-2200 m) (Sites 587 to 594) in a traverse from subtropical to subantarctic latitudes in the southwest Pacific region, chiefly on Lord Howe Rise in the Tasman Sea. This chapter summarizes some preliminary lithostratigraphic results of the leg and includes data from Site 586, drilled during DSDP Leg 89 on the Ontong-Java Plateau that forms the northern equatorial point of the latitudinal traverse. The lithofacies consist almost exclusively of continuous sections of very pure (>95% CaCO3) pelagic calcareous sediment, typically foraminifer-bearing nannofossil ooze (or chalk) and nannofossil ooze (or chalk), which is mainly of Neogene age but extends back into the Eocene at Sites 588, 592, and 593. Only at Site 594 off southeastern New Zealand is there local development of hemipelagic sediments and several late Neogene unconformities. Increased contents of foraminifers in Leg 90 sediments, notably in the Quaternary interval, correspond to periods of enhanced winnowing by bottom currents. Significant changes in the rates of sediment accumulation and in the character and intensity of sediment bioturbation within and between sites probably reflect changes in calcareous biogenic productivity as a result of fundamental paleoceanographic events in the region during the Neogene. Burial lithification is expressed by a decrease in sediment porosity from about 70 to 45% with depth. Concomitantly, microfossil preservation slowly deteriorates as a result of selective dissolution or recrystallization of some skeletons and the progressive appearance of secondary calcite overgrowths, first about discoasters and sphenoliths, and ultimately on portions of coccoliths. The ooze/chalk transition occurs at about 270 m sub-bottom depth at each of the northern sites (Sites 586 to 592) but is delayed until about twice this depth at the two southern sites (Sites 593 and 594). A possible explanation for this difference between geographic areas is the paucity of discoasters and sphenoliths at the southern sites; these nannofossil elements provide ideal nucleation sites for calcite overgrowths. Toward the bottom of some holes, dissolution seams and flasers appear in recrystallized chalks. The very minor terrigenous fraction of the sediment consists of silt- through clay-sized quartz, feldspar, mica, and clay minerals (smectite, illite, kaolinite, and chlorite), supplied as eolian dust from the Australian continent and by wind and ocean currents from erosion on South Island, New Zealand. Changes in the mass accumulation rates of terrigenous sediment and in clay mineral assemblages through time are related to various external controls, such as the continued northward drift of the Indo-Australian Plate, the development of Antarctic ice sheets, the increased desertification of the Australian continent after 14 m.y. ago, and the progressive increase in tectonic relief of New Zealand through the late Cenozoic. Disseminated glass shards and (altered) tephra layers occur in Leg 90 cores. They were derived from major silicic eruptions in North Island, New Zealand, and from basic to intermediate explosive volcanism along the Melanesian island chains. The tephrostratigraphic record suggests episodes of increased volcanicity in the southwest Pacific centered near 17, 13, 10, 5 and 1 m.y. ago, especially in the middle and early late Miocene. In addition, submarine basaltic volcanism was widespread in the southeast Tasman Sea around the Eocene/Oligocene boundary, possibly related to the propagation of the Southeast Indian Ridge through western New Zealand as a continental rift system.

The role of trust in the transition from traditional to electronic B2B relationships in agri-food chains

E-business adoption rates in the agri-food sector are rather low, despite the fact that technical barriers have been mostly overcome during the last years and a large number of sophisticated offers are available. However, concerns about trust seem to impede the development of electronic relationships in the agri-food chains as trust is of particular importance in any exchange of agri-food products along the value chain. Drawing on existing research, characteristics and dimensions of trust are initially identified both in traditional and in electronic B2B relationships and a typology of trust is proposed. The aim of the paper is to provide an overview of the implementation and use of trust elements that e-commerce offers dedicated to agri-food sector. This assessment will show the current situation and discuss gaps for further improvement with the objective to facilitate the uptake of e-commerce in agri-food chains. © 2009 Elsevier B.V. All rights reserved.

Tackling transition! Peer mentoring in engineering education:a UK perspective

This paper builds on previous work (Clark, 2009; Clark & Andrews 2011, 2014) to continue the debate around a seemingly universal question…“How can educational theory be applied to engineering education in such a way so as to make the subject more accessible and attractive to students? It argues that there are three key elements to student success; Relationships, Variety & Synergy (RVS). By further examining the purposefully developed bespoke learning and teaching approach constructed around these three elements (RVS) the discourse in this paper links educational theory to engineering education and in doing so further develops arguments for the introduction of a purposefully designed pedagogic approach for use in engineering education.

A Circuit Implementing Massive Parallelism in Transition P Systems

ransition P-systems are based on biological membranes and try to emulate cell behavior and its evolution due to the presence of chemical elements. These systems perform computation through transition between two consecutive configurations, which consist in a m-tuple of multisets present at any moment in the existing m regions of the system. Transition between two configurations is performed by using evolution rules also present in each region. Among main Transition P-systems characteristics are massive parallelism and non determinism. This work is part of a very large project and tries to determine the design of a hardware circuit that can improve remarkably the process involved in the evolution of a membrane. Process in biological cells has two different levels of parallelism: the first one, obviously, is the evolution of each cell inside the whole set, and the second one is the application of the rules inside one membrane. This paper presents an evolution of the work done previously and includes an improvement that uses massive parallelism to do transition between two states. To achieve this, the initial set of rules is transformed into a new set that consists in all their possible combinations, and each of them is treated like a new rule (participant antecedents are added to generate a new multiset), converting an unique rule application in a way of parallelism in the means that several rules are applied at the same time. In this paper, we present a circuit that is able to process this kind of rules and to decode the result, taking advantage of all the potential that hardware has to implement P Systems versus previously proposed sequential solutions.