Linking the High-Resolution Architecture of Modern and Ancient Wave-Dominated Deltas : Processes, Products and Forcing Factors

Many thoughts and concepts used in this paper were initially developed as a result of work conducted with funding provided to the WAVE Consortium at the Australian School of Petroleum, University of Adelaide (RBA, BKV and JB). The consortium sponsors (Apache, BAPETCO, BHPBP, BG, BP, Chevron, ConocoPhillips, Nexen, OMV, Shell, Statoil, Todd Energy, and Woodside Energy) are thus thanked for making this work possible. We are indebted to journal reviewers Cornel Olariu and Howard Feldman, and to Associate Editor Janok Bhattacharya for numerous comments and suggestions that improved the clarity of the manuscript.Peer reviewedPostprin

Prussian Blue to reduce radiocaesium accumulation in fish in lakes affected by the Chornobyl accident

publishedVersio

BAKTRAK: Backtracking drifting objects using an iterative algorithm with a forward trajectory model

The task of determining the origin of a drifting object after it has been located is highly complex due to the uncertainties in drift properties and environmental forcing (wind, waves and surface currents). Usually the origin is inferred by running a trajectory model (stochastic or deterministic) in reverse. However, this approach has some severe drawbacks, most notably the fact that many drifting objects go through nonlinear state changes underway (e.g., evaporating oil or a capsizing lifeboat). This makes it difficult to naively construct a reverse-time trajectory model which realistically predicts the earliest possible time the object may have started drifting. We propose instead a different approach where the original (forward) trajectory model is kept unaltered while an iterative seeding and selection process allows us to retain only those particles that end up within a certain time-space radius of the observation. An iterative refinement process named BAKTRAK is employed where those trajectories that do not make it to the goal are rejected and new trajectories are spawned from successful trajectories. This allows the model to be run in the forward direction to determine the point of origin of a drifting object. The method is demonstrated using the Leeway stochastic trajectory model for drifting objects due to its relative simplicity and the practical importance of being able to identify the origin of drifting objects. However, the methodology is general and even more applicable to oil drift trajectories, drifting ships and hazardous material that exhibit non-linear state changes such as evaporation, chemical weathering, capsizing or swamping. The backtracking method is tested against the drift trajectory of a life raft and is shown to predict closely the initial release position of the raft and its subsequent trajectory.Comment: 28 pages, 8 figures, 2 table

Patient-Derived Organoids from Multiple Colorectal Cancer Liver Metastases Reveal Moderate Intra-patient Pharmacotranscriptomic Heterogeneity

Peer reviewe

What can go wrong will go wrong: Birthday effects and early tracking in the German school system

At the age of ten German pupils are given a secondary school track recommendation which largely determines the actual track choice. Track choice has major effects on the life course, mainly through labor market outcomes. Using data from the German PISA extension study, we analyze the effect of month of birth and thus relative age on such recommendations. We find that younger pupils are less often recommended to and actually attend Gymnasium, the most attractive track in terms of later life outcomes. Flexible enrolment and grade retention partly offset these inequalities and the relative age effect dissipates as students age

The Norwegian Stroke in the Young Study (NOR-SYS): Rationale and design

Peer reviewe

Analysis of the Aspergillus fumigatus Proteome Reveals Metabolic Changes and the Activation of the Pseurotin A Biosynthesis Gene Cluster in Response to Hypoxia

The mold Aspergillus fumigatus is the most important airborne fungal pathogen. Adaptation to hypoxia represents an important virulence attribute for A. fumigatus. Therefore, we aimed at obtaining a comprehensive overview about this process on the proteome level. To ensure highly reproducible growth conditions, an oxygen-controlled, glucose-limited chemostat cultivation was established. Two-dimensional gel electrophoresis analysis of mycelial and mitochondrial proteins as well as two-dimensional Blue Native/SDS-gel separation of mitochondrial membrane proteins led to the identification of 117 proteins with an altered abundance under hypoxic in comparison to normoxic conditions. Hypoxia induced an increased activity of glycolysis, the TCA-cycle, respiration, and amino acid metabolism. Consistently, the cellular contents in heme, iron, copper, and zinc increased. Furthermore, hypoxia induced biosynthesis of the secondary metabolite pseurotin A as demonstrated at proteomic, transcriptional, and metabolite levels. The observed and so far not reported stimulation of the biosynthesis of a secondary metabolite by oxygen depletion may also affect the survival of A. fumigatus in hypoxic niches of the human host. Among the proteins so far not implicated in hypoxia adaptation, an NO-detoxifying flavohemoprotein was one of the most highly up-regulated proteins which indicates a link between hypoxia and the generation of nitrosative stress in A. fumigatus

Introduction to Decision Analysis

The three papers of the proposed session, "Aspects of Sustainability in Digital Humanities", examine the increasingly important topic of sustainability from the point of view of three different fi elds of research: library and information science, cultural heritage management, and linguistics. Practically all disciplines in science and the humanities are nowadays confronted with the task of providing data collections that have a very high degree of sustainability. This task is not only concerned with the long-term archiving of digital resources and data collections, but also with aspects such as, for example, interoperability of resources and applications, data access, legal issues, fi eld-specifi c theoretical approaches, and even political interests. The proposed session has two primary goals. Each of the three papers will present the most crucial problems that are relevant for the task of providing sustainability within the given fi eld or discipline. In addition, each paper will talk about the types of digital resources and data collections that are in use within the respective fi eld (for example, annotated corpora and syntactic treebanks in the fi eld of linguistics). The main focus, however, lies in working on the distinction between fi eld-specifi c and universal aspects of sustainability so that the three fi elds that will be examined -library and information science, cultural heritage management, linguistics -can be considered case studies in order to come up with a more universal and all-encompassing angle on sustainability. Especially for introductory texts and fi eld -independent best-practice guidelines on sustainability it is extremely important to have a solid distinction between universal and fi eld-specifi c aspects. The same holds true for the integration of sustainability-related informational units into fi eld-independent markup languages that have a very broad scope of potential applications, such as the TEI guidelines published by the Text Encoding Initiative. Following are short descriptions of the three papers: The paper "Sustainability in Cultural Heritage Management" by Øyvind Eide, Christian-Emil Ore, and Jon Holmen discusses technical and organisational aspects of sustainability with regard to cultural heritage information curated by institutions such as, for example, museums. Achieving organisational sustainability is a task that not only applies to the staff of a museum but also to education and research institutions, as well as to national and international bodies responsible for our common heritage. Digital Humanities 2008 _____________________________________________________________________________ _____________________________________________________________________________ 22 Vital to the sustainability of collections is information about the collections themselves, as well as individual items in those collections. "Sustaining Collection Value: Managing Collection/ Item Metadata Relationships", by Allen H. Renear, Richard Urban, Karen Wickett, Carole L. Palmer, and David Dubin, examines the diffi cult problem of managing collection level metadata in order to ensure that the context of the items in a collection is accessible for research and scholarship. They report on ongoing research and also have preliminary suggestions for practitioners. The fi nal paper "Sustainability of Annotated Resources in Linguistics", by Georg Rehm, Andreas Witt, Erhard Hinrichs, and Marga Reis, provides an overview of important aspects of sustainability with regard to linguistic resources. The authors demonstrate which of these several aspects can be considered specifi c for the fi eld of linguistics and which are more general. Paper 1: Sustainability in Cultural Heritage Management Øyvind Eide, Christian-Emil Ore, Jon Holmen University of Oslo, Norway Introduction During the last decades, a large amount of information in cultural heritage institutions have been digitised, creating the basis for many different usage scenarios. We have been working in this area for the last 15 years, through projects such as the Museum Project in Norway (Holmen et al., 2004). We have developed routines, standardised methods and software for digitisation, collection management, research and education. In this paper, we will discuss long term sustainability of digital cultural heritage information. We will discuss the creation of sustainable digital collections, as well as some problems we have experienced in this process. We have divided the description of sustainability in three parts. First we will describe briefl y the technical part of sustainability work (section 2). After all, this is a well known research area on its own, and solutions to many of the problems at hand are known, although they may be hard to implement. We will then use the main part of the paper to discuss what we call organisational sustainability (section 3), which may be even more important than the technical part in the future -in our opinion, it may also be more diffi cult to solve. Finally, we briefl y address the scholarly part of sustainability (section 4). Technical Sustainability Technical sustainability is divided in two parts: preservation of the digital bit patterns and the ability to interpret the bit pattern according to the original intention. This is an area where important work is being done by international bodies such as UNESCO Organisational Sustainability Although there is no sustainability without the technical part, described above, taken care of, the technical part alone is not enough. The organisation of the institution responsible for the information also has to be taken into consideration. In an information system for memory institutions it is important to store the history of the information. Digital versions of analogue sources should be stored as accurate replica, with new information linked to this set of historical data so that one always has access to up-to-date versions of the information, as well as to historical stages in the development of the information (Holmenetal.,2004, p.223). To actually store the fi les, the most important necessity is large, stable organisations taking responsibility. If the responsible institution is closed without a correct transfer of custody for the digital material, it can be lost easily. An example of this is the Newham Archive (Dunning, 2001) incident. When the Newham Museum Archaeological Service was closed down, only a quick and responsible reaction of the sacked staff saved the result of ten years of work in the form of a data dump on fl oppies. Even when the data fi les are kept, lack of necessary metadata may render them hard to interpret. In the Newham case the data were physically saved but a lot of work was needed to read the old data formats, and some of the information was not recoverable. Similar situations may even occur in large, stable organisations. The Bryggen Museum in Bergen, Norway, is a part of the University Museum in Bergen and documents the large excavation of the medieval town at the harbour in Bergen which took place from the 1950s to the 1970s. The museum stored the information in a large database. Eventually the system became obsolete and the database fi les were stored at the University. But there were no explicit routines for the packing and future unpacking of such digital information. Later, when the fi les were imported into a new system, parts of the original information were not recovered. Fortunately all the excavation documentation was originally done on paper so in principle no information was lost. Digital Humanities 2008 _____________________________________________________________________________ _____________________________________________________________________________ 23 Such incidents are not uncommon in the museum world. A general problem, present in both examples above, is the lack of metadata. The scope of each database table and column is well known when a system is developed, but if it is not documented, such meta-information is lost. In all sectors there is a movement away from paper to born digital information. When born digital data based on archaeological excavations is messed up or lost -and we are afraid this will happen -then parts of our cultural heritage are lost forever. An archaeological excavation destroys its own sources and an excavation cannot be repeated. For many current excavation projects a loss of data like the Bryggen Museum incident would have been a real catastrophe. The Newham example demonstrates weak planning for negative external effects on information sustainability, whereas the Bergen example shows how a lack of proper organisational responsibility for digital information may result in severe information loss. It is our impression that in many memory institutions there is too little competence on how to introduce information technologies in an organisation to secure both interchange of information between different parts of the organisation and long-term sustainability of the digital information. A general lack of strategies for long term preservation is documented in a recent Norwegian report (Gausdal, 2006, p.23). When plans are made in order to introduce new technology and information systems into an organisation one has to adapt the system to the organisation or the organisation to the system. This is often neglected and the information systems are not integrated in the everyday work of the staff. Thus, the best way to success is to do this in collaboration and understanding with the employees. This was pointed out by Professor Kristen Nygaard. In a paper published in 1992 describing the uptake of Simula I from 1965 onwards, Nygaard states: "It was evident that the Simula-based analyses were going to have a strong infl uence on the working conditions of the employees: job content, work intensity and rhythm, social cooperation patterns were typical examples" (Nygaard, 1992, p. 53). Nygaard focused on the situation in the ship building industry, which may be somewhat distant from the memory institutions. Mutate mutandis, the human mechanisms are the same. There is always a risk of persons in the organisation sabotaging or neglecting new systems. Scholarly Sustainability When a research project is fi nished, many researchers see the report or articles produced as the only output, and are confi dent that the library will take care of their preservation. But research in the humanities and beyond are often based on material collected by the researcher, such as ethnographic objects, sound recordings, images, and notes. The scholarly conclusions are then based on such sources. To sustain links from sources to testable conclusions, they have to be stored so that they are accessible to future researchers. Introduction Collections of texts, images, artefacts, and other cultural objects are usually designed to support particular research and scholarly activities. Toward that end collections themselves, as well as the items in the collections, are carefully developed and described. These descriptions indicate such things as the purpose of the collection, its subject, the method of selection, size, nature of contents, coverage, completeness, representativeness, and a wide range of summary characteristics, such as statistical features. This information enables collections to function not just as aggregates of individual data items but as independent entities that are in some sense more than the sum of their parts, as intended by their creators and curators Unfortunately, collection-level metadata is often unavailable or ignored by retrieval and browsing systems, with a corresponding loss in the ability of users to fi nd, understand, and use items in collections The now familiar example of this challenge is the "'on a horse' problem", where a collection with the collection-level subject "Theodore Roosevelt" has a photograph with the item-level annotation "on a horse" [Wendler, 2004] Item-level access across multiple collections (as is provided not only by popular Internet search engines, but also specialized federating systems, such as OAI portals) will not allow the user to effectively use a query with keywords "Roosevelt" and "horse" to fi nd this item, or, if the item is retrieved using item-level metadata alone, to use collection-level information to identify the person on the horse as Roosevelt. The problem is more complicated and consequential than the example suggests and the lack of a systematic understanding of the nature of the logical relationships between collectionlevel metadata and item-level metadata is an obstacle to the development of remedies. This understanding is what is required not only to guide the development of contextaware search and exploitation, but to support management and curation policies as well. The problem is also timely: even as recent research continues to confi rm the key role that collection context plays in the scholarly use of information resources In what follows we describe our plans to develop a framework for classifying and formalizing collection-level/item-level metadata relationships. This undertaking is part of a larger project, recently funded by US Institute for Museum and Library Services (IMLS), to develop tools for improved retrieval and exploitation across multiple collections. 1 Varieties of Collection/Item Metadata Relationships In some cases the relationship between collection-level metadata and item-level metadata attributes appears similar to non-defeasible inheritance. For instance, consider the Dublin Core Collections Application Profi le element marcrel: OWN, adapted from the MARC cataloging record standard. It is plausible that within many legal and institutional contexts whoever owns a collection owns each of the items in the collection, and so if a collection has a value for the marcrel: OWN attribute then each member of the collection will have the same value for marcrel:OWN. (For the purpose of our example it doesn't matter whether or not this is actually true of marcrel:OWN, only that some attributes are sometimes used by metadata librarians with an understanding of this sort, while others, such as dc:identifi er, are not). In other cases the collection-level/item-level metadata relationship is almost but not quite this simple. Consider the collection-level attribute myCollection:itemType, intended to characterize the type of objects in a collection, with values such as "image," "text," "software," etc. (we assume heterogeneous collections). 2 Unlike the preceding case we cannot conclude that if a collection has the value "image" for myCollection: itemType then the items in that collection also have the value "image" for that same attribute. This is because an item which is an image is not itself a collection of images and therefore cannot have a non-null value for myCollection:itemType. However, while the rule for propagating the information represented by myCollection:itemType from collections to items is not simple propagation of attribute and value, it is nevertheless simple enough: if a collection has a value, say "image," for myCollection:itemType, then the items in the collection have the same value, "image" for a corresponding attribute, say, myItem:type, which indicates the type of item (cf. the Dublin Core metadata element dc:type). The attribute myItem:type has the same domain of values as myCollection: itemType, but a different semantics. Digital Humanities 2008 _____________________________________________________________________________ _____________________________________________________________________________ 25 When two metadata attributes are related as myCollection: itemType and myItem:type we might say the fi rst can be vconverted to the other. Roughly: a collection-level attribute A v-converts to an item-level attribute B if and only if whenever a collection has the value z for A, every item in the collection has the value z for B. This is the simplest sort of convertibility -the attribute changes, but the value remains the same. Other sorts of conversion will be more complex. We note that the sort of propagation exemplifi ed by marcrel:OWN is a special case of v-convertibility: marcrel:OWN v-converts to itself. This analysis suggests a number of broader issues for collection curators. Obviously the conversion of collection-level metadata to item-level metadata, when possible, can improve discovery and exploitation, especially in item-focused searching across multiple collections. But can we even in the simplest case be confi dent of conversion without loss of information? For example, it may be that in some cases an "image" value for myCollection:itemType conveys more information than the simple fact that each item in the collection has "image" value for myItem:type. Moreover there are important collection-level attributes that both (i) resist any conversion and (ii) clearly result in loss of important information if discarded. Intriguingly these attributes turn out to be carrying information that is very tightly tied to the distinctive role the collection is intended to play in the support of research and scholarship. Obvious examples are metadata indicating that a collection was developed according to some particular method, designed for some particular purpose, used in some way by some person or persons in the past, representative (in some respect) of a domain, had certain summary statistical features, and so on. This is precisely the kind of information that makes a collection valuable to researchers, and if it is lost or inaccessible, the collection cannot be useful, as a collection, in the way originally intended by its creators. . The registry currently contains records for 202 collections. An item-level metadata repository was also developed, which so far has harvested 76 collections using the OAI-PMH protocol 6 . Our research initially focused on overcoming the technical challenges of aggregating large heterogeneous collections of item-level records and gathering collections descriptions from contributors. We conducted studies on how content contributors conceived of the roles of collection descriptions in digital environments The DCC/CIMR Project In 2007 we received a new three year IMLS grant to continue the development of the registry and to explore how a formal description of collection-level/item-level metadata relationships could help registry users locate and use digital items. This latter activity, CIMR, (Collection/Item Metadata Relationships), consists of three overlapping phases. The fi rst phase is developing a logic-based framework of collection-level/ itemlevel metadata relationships that classifi es metadata into varieties of convertibility with associated rules for propagating information between collection and item levels and supporting further inferencing. Next we will conduct empirical studies to see if our conjectured taxonomy matches the understanding and behavior of metadata librarians, metadata specifi cation designers, and registry users. Finally we will design and implement pilot applications using the relationship rules to support searching, browsing, and navigation of the DCC Registry. These applications will include non-convertible and convertible collection-level/item-level metadata relationships. One outcome of this project will be a proposed specifi cation for a metadata classifi cation code that will allow metadata specifi cation designers to indicate the collectionlevel/itemlevel metadata relationships intended by their specifi cation. Such a specifi cation will in turn guide metadata librarians in assigning metadata and metadata systems designers in designing systems that can mobilize collection level metadata to provide improved searching, browsing, understanding, and use by end users. We will also draft and make electronically available RDF/OWL bindings for the relationship categories and inference rules. Preliminary Guidance for Practitioners A large part of the problem of sustainability is ensuring that information will be valuable, and as valuable as possible, to multiple audiences, for multiple purposes, via multiple tools, and over time. Although we have only just begun this project, already some preliminary general recommendations can be made to the different stakeholders in collection management. Note that tasks such as propagation must be repeated not only as new objects are added or removed but, as new information about objects and collections becomes available. Digital Humanities 2008 _____________________________________________________________________________ _____________________________________________________________________________ 26 For metadata standards developers: 1. Metadata standards should explicitly document the relationships between collectionlevel metadata and itemlevel metadata. Currently we have neither the understanding nor the formal mechanisms for such documentation but they should be available soon. For systems designers: 2. Information in convertible collection-level metadata should be propagated to items in order to make contextual information fully available to users, especially users working across multiple collections. (This is not a recommendation for how to manage information internally, but for how to represent it to the user; relational tables may remain in normal forms.) 3. Information in item-level metadata should, where appropriate, be propagated to collection level metadata. 4. Information in non-convertible collection-level meta