NetCodCCN: a Network Coding approach for Content-Centric Networks

Content-Centric Networking (CCN) naturally supports multi-path communication, as it allows the simultaneous use of multiple interfaces (e.g. LTE and WiFi). When multiple sources and multiple clients are considered, the optimal set of distribution trees should be determined in order to optimally use all the available interfaces. This is not a trivial task, as it is a computationally intense procedure that should be done centrally. The need for central coordination can be removed by employing network coding, which also offers improved resiliency to errors and large throughput gains. In this paper, we propose NetCodCCN, a protocol for integrating network coding in CCN. In comparison to previous works proposing to enable network coding in CCN, NetCodCCN permit Interest aggregation and Interest pipelining, which reduce the data retrieval times. The experimental evaluation shows that the proposed protocol leads to significant improvements in terms of content retrieval delay compared to the original CCN. Our results demonstrate that the use of network coding adds robustness to losses and permits to exploit more efficiently the available network resources. The performance gains are verified for content retrieval in various network scenarios.

3' end processing of mouse histone pre-mRNA: evidence for additional base-pairing between U7 snRNA and pre-mRNA.

We have analysed the extent of base-pairing interactions between spacer sequences of histone pre-mRNA and U7 snRNA present in the trans-acting U7 snRNP and their importance for histone RNA 3' end processing in vitro. For the efficiently processed mouse H4-12 gene, a computer analysis revealed that additional base pairs could be formed with U7 RNA outside of the previously recognised spacer element (stem II). One complementarity (stem III) is located more 3' and involves nucleotides from the very 5' end of U7 RNA. The other, more 5' located complementarity (stem I) involves nucleotides of the Sm binding site of U7 RNA, a part known to interact with snRNP structural proteins. These potential stem structures are separated from each other by short internal loops of unpaired nucleotides. Mutational analyses of the pre-mRNA indicate that stems II and III are equally important for interaction with the U7 snRNP and for processing, whereas mutations in stem I have moderate effects on processing efficiency, but do not impair complex formation with the U7 snRNP. Thus nucleotides near the processing site may be important for processing, but do not contribute to the assembly of an active complex by forming a stem I structure. The importance of stem III was confirmed by the ability of a complementary mutation in U7 RNA to suppress a stem III mutation in a complementation assay using Xenopus laevis oocytes. The main role of the factor(s) binding to the upstream hairpin loop is to stabilise the U7-pre-mRNA complex. This was shown by either stabilising (by mutation) or destabilising (by increased temperature) the U7-pre-mRNA base-pairing under conditions where hairpin factor binding was either allowed or prevented (by mutation or competition). The hairpin dependence of processing was found to be inversely related to the strength of the U7-pre-mRNA interaction.

Step by step: correcting our mental image of the mušlālu

The mušlālu, which is usually understood to be a step- or ramped gate, has so far rarely been discussed in much detail, even though the texts mentioning it have been known for a long time. This is no doubt because the evidence on which to base both philological and archaeological investigations appears sparse and scattered. Up to now, scholars have tended to focus on specific mušlālu-structures. Consequently, there are as many discussions as there are mušlālu-structures. This article attempts to get a sense of the broader picture by bringing together the philological and archaeological data hitherto available with the aim of discussing the mušlālu as term and structure, clarifying the semantics and reassessing the architectural identifications. We hope to demonstrate that it is actually possible to take the evidence one step further and correct the mušlālu image that prevails.

Information-centric communication in mobile and wireless networks

Information-centric networking (ICN) is a new communication paradigm that has been proposed to cope with drawbacks of host-based communication protocols, namely scalability and security. In this thesis, we base our work on Named Data Networking (NDN), which is a popular ICN architecture, and investigate NDN in the context of wireless and mobile ad hoc networks. In a first part, we focus on NDN efficiency (and potential improvements) in wireless environments by investigating NDN in wireless one-hop communication, i.e., without any routing protocols. A basic requirement to initiate informationcentric communication is the knowledge of existing and available content names. Therefore, we develop three opportunistic content discovery algorithms and evaluate them in diverse scenarios for different node densities and content distributions. After content names are known, requesters can retrieve content opportunistically from any neighbor node that provides the content. However, in case of short contact times to content sources, content retrieval may be disrupted. Therefore, we develop a requester application that keeps meta information of disrupted content retrievals and enables resume operations when a new content source has been found. Besides message efficiency, we also evaluate power consumption of information-centric broadcast and unicast communication. Based on our findings, we develop two mechanisms to increase efficiency of information-centric wireless one-hop communication. The first approach called Dynamic Unicast (DU) avoids broadcast communication whenever possible since broadcast transmissions result in more duplicate Data transmissions, lower data rates and higher energy consumption on mobile nodes, which are not interested in overheard Data, compared to unicast communication. Hence, DU uses broadcast communication only until a content source has been found and then retrieves content directly via unicast from the same source. The second approach called RC-NDN targets efficiency of wireless broadcast communication by reducing the number of duplicate Data transmissions. In particular, RC-NDN is a Data encoding scheme for content sources that increases diversity in wireless broadcast transmissions such that multiple concurrent requesters can profit from each others’ (overheard) message transmissions. If requesters and content sources are not in one-hop distance to each other, requests need to be forwarded via multi-hop routing. Therefore, in a second part of this thesis, we investigate information-centric wireless multi-hop communication. First, we consider multi-hop broadcast communication in the context of rather static community networks. We introduce the concept of preferred forwarders, which relay Interest messages slightly faster than non-preferred forwarders to reduce redundant duplicate message transmissions. While this approach works well in static networks, the performance may degrade in mobile networks if preferred forwarders may regularly move away. Thus, to enable routing in mobile ad hoc networks, we extend DU for multi-hop communication. Compared to one-hop communication, multi-hop DU requires efficient path update mechanisms (since multi-hop paths may expire quickly) and new forwarding strategies to maintain NDN benefits (request aggregation and caching) such that only a few messages need to be transmitted over the entire end-to-end path even in case of multiple concurrent requesters. To perform quick retransmission in case of collisions or other transmission errors, we implement and evaluate retransmission timers from related work and compare them to CCNTimer, which is a new algorithm that enables shorter content retrieval times in information-centric wireless multi-hop communication. Yet, in case of intermittent connectivity between requesters and content sources, multi-hop routing protocols may not work because they require continuous end-to-end paths. Therefore, we present agent-based content retrieval (ACR) for delay-tolerant networks. In ACR, requester nodes can delegate content retrieval to mobile agent nodes, which move closer to content sources, can retrieve content and return it to requesters. Thus, ACR exploits the mobility of agent nodes to retrieve content from remote locations. To enable delay-tolerant communication via agents, retrieved content needs to be stored persistently such that requesters can verify its authenticity via original publisher signatures. To achieve this, we develop a persistent caching concept that maintains received popular content in repositories and deletes unpopular content if free space is required. Since our persistent caching concept can complement regular short-term caching in the content store, it can also be used for network caching to store popular delay-tolerant content at edge routers (to reduce network traffic and improve network performance) while real-time traffic can still be maintained and served from the content store.

STUDIES ON THE PATTERNS OF NUCLEOTIDE AND AMINO ACID SUBSTITUTION (ELECTROPHORESIS, MUTATION RATE, SELECTION, BASE, COMPOSITION)

Theoretical and empirical studies were conducted on the pattern of nucleotide and amino acid substitution in evolution, taking into account the effects of mutation at the nucleotide level and purifying selection at the amino acid level. A theoretical model for predicting the evolutionary change in electrophoretic mobility of a protein was also developed by using information on the pattern of amino acid substitution. The specific problems studied and the main results obtained are as follows: (1) Estimation of the pattern of nucleotide substitution in DNA nuclear genomes. The pattern of point mutations and nucleotide substitutions among the four different nucleotides are inferred from the evolutionary changes of pseudogenes and functional genes, respectively. Both patterns are non-random, the rate of change varying considerably with nucleotide pair, and that in both cases transitions occur somewhat more frequently than transversions. In protein evolution, substitution occurs more often between amino acids with similar physico-chemical properties than between dissimilar amino acids. (2) Estimation of the pattern of nucleotide substitution in RNA genomes. The majority of mutations in retroviruses accumulate at the reverse transcription stage. Selection at the amino acid level is very weak, and almost non-existent between synonymous codons. The pattern of mutation is very different from that in DNA genomes. Nevertheless, the pattern of purifying selection at the amino acid level is similar to that in DNA genomes, although selection intensity is much weaker. (3) Evaluation of the determinants of molecular evolutionary rates in protein-coding genes. Based on rates of nucleotide substitution for mammalian genes, the rate of amino acid substitution of a protein is determined by its amino acid composition. The content of glycine is shown to correlate strongly and negatively with the rate of substitution. Empirical formulae, called indices of mutability, are developed in order to predict the rate of molecular evolution of a protein from data on its amino acid sequence. (4) Studies on the evolutionary patterns of electrophoretic mobility of proteins. A theoretical model was constructed that predicts the electric charge of a protein at any given pH and its isoelectric point from data on its primary and quaternary structures. Using this model, the evolutionary change in electrophoretic mobilities of different proteins and the expected amount of electrophoretically hidden genetic variation were studied. In the absence of selection for the pI value, proteins will on the average evolve toward a mildly basic pI. (Abstract shortened with permission of author.) ^

Emotional Content in Autobiographical Memory through an Attachment Theory Framework

The current study investigates the relationship between individual differences in attachment style and the recall of autobiographical memories. According to attachment theory, affect regulation strategies employed by individuals high in attachment anxiety and high in attachment avoidance are likely to influence how information about the past is recalled. This study examines how attachment anxiety and attachment avoidance relate to the presence of negative emotions in autobiographical memories of upsetting events with important relationship figures (i.e., mother, father, or roommate). Participants included 248 undergraduate students ranging from ages 18-22 that attend a public university in the northeast. As hypothesized, individuals with an avoidant attachment expressed less sadness in their responses to the written narrative task, especially when prompted for memories involving their primary caregiver. Contrary to the hypothesis, anxiously attached individuals did not display higher levels of worry/fear emotions in their responses to the written narrative. Attachment anxiety was related to some differences in emotional content; however, this varied by relationship partner. The results provide evidence linking attachment style to emotion selection and retrieval in autobiographical memories of ‘upsetting’ events. Implications for close relationships and therapy are discussed.

Age analysis, aragonite and high magnesium calcite content from different IODP Holes from Exp 310

The widespread occurrence of microbialites in the last deglacial reef frameworks (16-6 Ka BP) implies that the accurate study of their development patterns is of prime importance to unravel the evolution of reef architecture through time and to reconstruct the reef response to sea-level variations and environmental changes. The present study is based on the sedimentological and chronological analysis (14C AMS dating) of drill cores obtained during the IODP Expedition #310 "Tahiti Sea Level" on the successive terraces which typify the modern reef slopes from Tahiti. It provides a comprehensive data base to investigate the microbialite growth patterns (i.e. growth rates and habitats), to analyze their roles in reef frameworks and to reconstruct the evolution of the reef framework architecture during sea-level rise. The last deglacial reefs from Tahiti are composed of two distinctive biological communities: (1) the coralgal communities including seven assemblages characterized by various growth forms (branching, robust branching, massive, tabular and encrusting) that form the initial frameworks and (2) the microbial communities developed in the primary cavities of those frameworks, a few meters (1.5 to 6 m) below the living coral reef surface, where they heavily encrusted the coralgal assemblages to form microbialite crusts. The dating results demonstrate the occurrence of two distinctive generations of microbialites: the "reefal microbialites" which developed a few hundred years after coralgal communities in shallow-water environments, whereas the "slope microbialites" grew a few thousands of years later in significantly deeper water conditions after the demise of coralgal communities. The development of microbialites was controlled by the volume and the shape of the primary cavities of the initial reef frameworks determined by the morphology and the packing of coral colonies. The most widespread microbialite development occurred in frameworks dominated by branching, thin encrusting, tabular and robust branching coral colonies which built loose and open frameworks typified by a high porosity (> 50%). In contrast, their growth was minimal in compact coral frameworks formed by massive and thick encrusting corals where primary cavities yielded a low porosity (~ 30%) and could not host a significant microbialite expansion.

Carbonate content in lower Cretaceous sediments of ODP Hole 123-765C

Sediments recovered during Ocean Drilling Program (ODP) Leg 123 from the Argo Abyssal Plain (AAP) consist largely of turbidites derived from the adjacent Australian continental margin. The oldest abundant turbidites are Valanginian-Aptian in age and have a mixed (smarl) composition; they contain subequal amounts of calcareous and siliceous biogenic components, as well as clay and lesser quartz. Most are thin-bedded, fine sand- to mud-sized, and best described by Stow and Piper's model (1984) for fine-grained biogenic turbidites. Thicker (to 3 m), coarser-grained (medium-to-coarse sand-sized) turbidites fit Bouma's model (1962) for sandy turbidites; these generally are base-cut-out (BCDE, BDE) sequences, with B-division parallel lamination as the dominant structure. Parallel laminae most commonly concentrate quartz and/or calcispheres vs. lithic clasts or clay, but distinctive millimeter- to centimeter-thick, radiolarian-rich laminae occur in both fine- and coarse-grained Valanginian-Hauterivian turbidites. AAP turbidites were derived from relatively deep parts of the continental margin (outer shelf, slope, or rise) that lay below the photic zone, but above the calcite compensation depth (CCD). Biogenic components are largely pelagic (calcispheres, foraminifers, radiolarians, nannofossils); lesser benthic foraminifers are characteristic of deep-water (abyssal to bathyal) environments. Abundant nonbiogenic components are mostly clay and clay clasts; smectite is the dominant clay species, and indicates a volcanogenic provenance, most likely the Triassic-Jurassic volcanic suite exposed along the northern Exmouth Plateau. Lower Cretaceous smarl turbidites were generated during eustatic lowstands and may have reached the abyssal plain via Swan Canyon, a submarine canyon thought to have formed during the Late Jurassic. In contrast to younger AAP turbidites, however, Lower Cretaceous turbidites are relatively fine-grained and do not contain notably older reworked fossils. Early in its history, the northwest Australian margin provided mainly contemporaneous slope sediment to the AAP; marginal basins adjacent to the continent trapped most terrigenous detritus, and pronounced canyon incisement did not occur until Late Cretaceous and, especially, Cenozoic time.

Total organic carbon content and isorenieratene concentrations from three holes of ODP Leg 160

Carotenoids were analysed in ca. 1-cm thick subsamples of three laterally time-equivalent sapropels from a west-east transect of the eastern Mediterranean Basin to study euxinic periods during Pliocene sapropel formation. The amount of intact isorenieratene (summed all-trans and cis isomers), ranged from non-detectable at the base and top of a sapropel up to 140 µg/g sediment in the central parts. Isorenieratene accumulation rates at the central and western site are remarkably similar and increase sharply to levels of up to 3.0 mg/m**2/ yr in the central part of the sapropel and then drop to low levels. This pattern indicates an expansion of euxinic conditions reaching into the photic zone, followed by deepening of the chemocline during deposition of this Pliocene sapropel. The sapropel from the easternmost site of the basin, which contains less organic carbon, shows much lower isorenieratene accumulation rates and even absence of isorenieratene in the central part of the sapropel. Ba/Al ratios indicate enhanced palaeoproductivity during sapropel formation, supporting previously proposed models, according to which increased productivity is the driving force for the generation of euxinic conditions.

Potential of RapidEye image data for sediment monitoring of the German tidal flats

The Wadden Sea is located in the southeastern part of the North Sea forming an extended intertidal area along the Dutch, German and Danish coast. It is a highly dynamic and largely natural ecosystem influenced by climatic changes and anthropogenic use of the North Sea. Changes in the environment of the Wadden Sea, natural or anthropogenic origin, cannot be monitored by the standard measurement methods alone, because large-area surveys of the intertidal flats are often difficult due to tides, tidal channels and unstable underground. For this reason, remote sensing offers effective monitoring tools. In this study a multi-sensor concept for classification of intertidal areas in the Wadden Sea has been developed. Basis for this method is a combined analysis of RapidEye (RE) and TerraSAR-X (TSX) satellite data coupled with ancillary vector data about the distribution of vegetation, mussel beds and sediments. The classification of the vegetation and mussel beds is based on a decision tree and a set of hierarchically structured algorithms which use object and texture features. The sediments are classified by an algorithm which uses thresholds and a majority filter. Further improvements focus on radiometric enhancement and atmospheric correction. First results show that we are able to identify vegetation and mussel beds with the use of multi-sensor remote sensing. The classification of the sediments in the tidal flats is a challenge compared to vegetation and mussel beds. The results demonstrate that the sediments cannot be classified with high accuracy by their spectral properties alone due to their similarity which is predominately caused by their water content.

Stable organic carbon isotope record and total organic carbon content from the Cenomanian-Turonian boundary

Ocean Drilling Program (ODP) Leg 207 recovered expanded sections of organic-carbon-rich laminated shales on Demerara Rise (western tropical Atlantic). High-resolution organic carbon isotope and total organic carbon (TOC) records are presented, which span the Cenomanian-Turonian boundary interval (CTBI), including the Oceanic Anoxic Event (OAE) 2, from four sites oriented along a NW striking depth transect. These records represent the first high-resolution carbon isotope records across OAE 2 from the South American margin of the tropical Atlantic. Due to the scarcity of age significant fossils, the main purpose of this study was to develop a detailed carbon isotope stratigraphy in order to correlate the CTBI across the depth transect and to tie this to biostratigraphically well-defined sections in the Western Interior Basin (Pueblo, USA), boreal shelf seas (Eastbourne, England), and western Tethys (Oued Mellegue, Tunisia). All four sections studied document a 6 per mil increase of d13Corg values at the base of the CTBI, which is followed by an interval of elevated d13Corg values and a subsequent decrease. Our results supply an important stratigraphic base for subsequent paleoceanographic studies on Late Cenomanian to Early Turonian sediments from Demerara Rise and elsewhere.

The CLIMATE data base of monthly normals for globally gridded climatic variables (version 2.1)

This database (Leemans & Cramer 1991) contains monthly averages of mean temperature, temperature range, precipitation, rain days and sunshine hours for the terrestrial surface of the globe, gridded at 0.5 degree longitude/latitude resolution. All grd-files contain the same 62483 pixels in the same order, with 30' latitude and longitude resolution. The coordinates are in degree-decimals and indicate the SW corner of each pixel. Topography is from ETOPO5 and indicates modal elevation. Data were generated from a large data base, using the partial thin-plate splining algorithm (Hutchinson & Bischof 1983). This version is widely used around the globe, notably by all groups participating in the IGBP NPP model intercomparison.

Data base on heterotrophic dinoflagellates grazing and growth rate as a function of size, prey size and type compiled from the literature

Microzooplankton (the 20 to 200 µm size class of zooplankton) is recognised as an important part of marine pelagic ecosystems. In terms of biomass and abundance heterotrophic dinoflagellates are one of the important groups of organism in microzooplankton. However, their rates - grazing and growth - , feeding behaviour and prey preferences are poorly known and understood. A set of data was assembled in order to derive a better understanding of heterotrophic dinoflagellates rates, in response to parameters such as prey concentration, prey type (size and species), temperature and their own size. With these objectives, literature was searched for laboratory experiments with information on one or more of these parameters effect studied. The criteria for selection and inclusion in the database included: (i) controlled laboratory experiment with a known dinoflagellate feeding on a known prey; (ii) presence of ancillary information about experimental conditions, used organisms - cell volume, cell dimensions, and carbon content. Rates and ancillary information were measured in units that meet the experimenter need, creating a need to harmonize the data units after collection. In addition different units can link to different mechanisms (carbon to nutritive quality of the prey, volume to size limits). As a result, grazing rates are thus available as pg C dinoflagellate-1 h-1, µm3 dinoflagellate-1 h-1 and prey cell dinoflagellate-1 h-1; clearance rate was calculated if not given and growth rate is expressed as the growth rate per day.