bluuebunny/crossref_metadata_2025 huggingface dataset:
Feeding patterns of red deer Cervus elaphus along an altitudinal gradient in the Bohemian Forest: effect of habitat and season
Authors: Krojerová‐Prokešová Jarmila , Barančeková Miroslava , Šustr Pavel , Heurich Marco
Published: July 2010

We studied diet composition of red deer Cervus elaphus in the Bohemian Forest by micro‐histological analysis of 207 samples of red deer faeces obtained on the Czech and the Bavarian side of the border. We carried out the research from October 2006 to February 2008, and collected samples every two months at nine monitoring plots that were situated at different altitudes (i.e. from 600 to 1,250 m a.s.l.). Our results confirmed the classification of red deer among intermediate feeders with a mixed diet of graminoids (29.4%) and concentrate food items (60.6%). Concentrate food items were dominant in their diet all year round; however, the diet composition during the winter season differed from the diet composition during the vegetation season. This change was mainly represented by the strong increase in consumption of coniferous trees (from 5.7 to 26.4%) during winter. The amount of graminoids in the diet was higher during the vegetation season, which was caused by the intensive consumption of graminoids at two top‐hill plots (up to 90% per sample). Likewise bilberry, Vaccinium myrtillus, with ripe berries was identified as an important food source only at the mountain ridge (up to 33% per sample). In agreement with our prediction, the diet composition of red deer at windthrow gaps (Blatný vrch Hill and Schachtenau) differed from the diet composition at undisturbed forest sites. At the gaps, ferns were an intensively consumed food source (up to 80% per sample). Contrary to other mountain areas, ferns made up a much larger share of the diet not only during autumn and winter but also during spring and summer. At Schachtenau, red deer also fed extensively on bramble Rubus sp., which intensively proliferates at the gaps. Diet composition of red deer in the Bohemian Forest differed between seasons, between plots at the mountain ridge and plots situated at lower altitudes as well as between windthrow gaps and undisturbed forest sites. However, further research of diet selectivity is necessary to explain in detail the observed feeding patterns.
The Ilnik wolf Canis lupus pack: use of marine mammals and offshore sea ice
Authors: Watts Dominique E. , Butler Lem G. , Dale Bruce W. , Cox R. Dave
Published: July 2010

Most wolf Canis lupus studies have been conducted in inland regions and comparatively little data are available for wolves inhabiting coastal areas. We monitored four members of a coastal wolf pack on the Alaska Peninsula during 2006‐2008. Habitat selection ratios indicated a strong association with the coastline, and we documented pack members and other wolves feeding on several species of marine mammals in these areas. In addition, pack members were observed foraging on offshore sea ice on multiple occasions. Observed spatial use and utilization of marine mammals suggest that marine‐derived subsidies may provide an important food source to coastal wolf populations. If these subsidies constitute a significant food source for coastal wolves, they likely affect wolf demographics and predator‐prey relationships in these areas.
What is the spatial unit for a wintering teal Anas crecca? Weekly day roost fidelity inferred from nasal saddles in the Camargue, southern France
Authors: Guillemain Matthieu , Devineau Olivier , Brochet Anne‐Laure , Fuster Jonathan , Fritz Hervé , Green Andy J. , Gauthier‐Clerc Michel
Published: July 2010

Dabbling ducks generally use distinct day roost and nocturnal habitats, the set of which constitute their ‘functional unit’. The rate at which these birds may switch between day roosts has never been quantified. Using resightings of nasal‐saddled birds and capture‐recapture modelling in the Camargue, southern France, we estimated the weekly probability that a teal Anas crecca switches from one day roost to another one nearby (transition probabilities). We also estimated the probability that a teal survives and remains in our study area, consisting of four neighbouring roosts (apparent survival). Birds were highly faithful to one specific water body if they remained in our study area (i.e. weekly rate of switching between roosts was only about 2‐6%), but the probability that an individual remained within one of the four roosts from one week to the next (local weekly apparent survival rate) was only 60‐70%. Intensive search efforts led to a 60% detection probability. Low local apparent survival coupled with very high site fidelity within the system suggests that two distinct strategies may coexist, i.e. frequent movement between distant winter quarters vs very high fidelity to the very same local wetland. Such strategies may be used successively by the same individuals, or may alternatively represent distinct bird categories (i.e. transients vs residents). In any case, these different strategies suggest that habitat management procedures need to be considered at both local and flyway scales simultaneously. The former may ensure that sites repeatedly used by the same individuals can provide adequate conditions to birds when they remain in a given winter quarter, while the latter will ensure transient birds find appropriate sites within the network of distant wetlands they may use as successive wintering quarters during a season.
Applications and Security of Next-Generation, User-Centric Wireless Systems
Authors: Ramstetter Jerry Rick , Yang Yaling , Yao Danfeng
Published: July 2010

Pervasive wireless systems have significantly improved end-users’ quality of life. As manufacturing costs decrease, communications bandwidth increases, and contextual information is made more readily available, the role of next generation wireless systems in facilitating users’ daily activities will grow. Unique security and privacy issues exist in these wireless, context-aware, often decentralized systems. For example, the pervasive nature of such systems allows adversaries to launch stealthy attacks against them. In this review paper, we survey several emergent personal wireless systems and their applications. These systems include mobile social networks, active implantable medical devices, and consumer products. We explore each system’s usage of contextual information and provide insight into its security vulnerabilities. Where possible, we describe existing solutions for defendingagainst these vulnerabilities. Finally, we point out promising future research directions for improving these systems’ robustness and security
In-Depth Analysis of Exoproteomes from Marine Bacteria by Shotgun Liquid Chromatography-Tandem Mass Spectrometry: the Ruegeria pomeroyi DSS-3 Case-Study
Authors: Christie-Oleza Joseph Alexander , Armengaud Jean
Published: July 2010

Microorganisms secrete into their extracellular environment numerous compounds that are required for their survival. Many of these compounds could be of great interest for biotechnology applications and their genes used in synthetic biology design. The secreted proteins and the components of the translocation systems themselves can be scrutinized in-depth by the most recent proteomic tools. While the secretomes of pathogens are well-documented, those of non-pathogens remain largely to be established. Here, we present the analysis of the exoproteome from the marine bacterium Ruegeria pomeroyi DSS-3 grown in standard laboratory conditions. We used a shotgun approach consisting of trypsin digestion of the exoproteome, and identification of the resulting peptides by liquid chromatography coupled to tandem mass spectrometry. Three different proteins that have domains homologous to those observed in RTX toxins were uncovered and were semi-quantified as the most abundantly secreted proteins. One of these proteins clearly stands out from the catalogue, representing over half of the total exoproteome. We also listed many soluble proteins related to ABC and TRAP transporters implied in the uptake of nutrients. The Ruegeria pomeroyi DSS-3 case-study illustrates the power of the shotgun nano-LC-MS/MS strategy to decipher the exoproteome from marine bacteria and to contribute to environmental proteomics.
Ochratoxin A in Roasted Coffee from French Supermarkets and Transfer in Coffee Beverages: Comparison of Analysis Methods
Authors: Tozlovanu Mariana , Pfohl-Leszkowicz Annie
Published: July 2010

The OTA content of 30 roasted coffees purchased in French supermarkets was evaluated by two validated different methods: one using immunoaffinity column (IAC) clean-up after alkaline extraction; the second using toluene extraction under acidic conditions. OTA recoveries (0.5 to 5 µg/kg) ranged from 16–49% with the alkaline extraction method and 55–60% with the acidic method. OTA recoveries from prepared beverages were similar with all methods (75–80%). All samples containing OTA ranged from trace (<LOQ) to 11.9 µg/kg. About 20 to 140% of OTA passed through the beverages. Recoveries of over 100% of OTA in beverages were due to three types of interferences: (i) formation of open-ring OTA (OP-OA) during alkaline extraction, (ii) isomerization of OTA during roasting, and (iii) presence of the nonchlorinated analogue OTB. The first two types of interference generate OTA derivatives that are not recognized by OTA antibodies, while OTB cross-reacts with OTA-antibodies. These analytical problems will seriously impact the amount of OTA detected, especially at the levels close to the limits from the EU legislation. Underestimation of OTA could be highly dangerous for health.
In the Line of Fire: The Challenges of Managing Tourism Operations in the Victorian Alps
Authors: Sanders Dale , Laing Jennifer
Published: July 2010

Understanding the impact of bushfires on tourism operations in Australian national parks and regional communities is of growing importance, with evidence of their increased frequency and severity linked, in part, to climate change. This is particularly critical for Australian alpine regions, given their greater emphasis on the summer season in the wake of lighter winter snowfalls. This article focuses on management issues and challenges of maintaining tourist operations within the Victorian Alps post-bushfire, including operator reactions to the bushfires and their subsequent implementation (or not) of crisis management and disaster recovery strategies. It is based on a qualitative study involving semistructured interviews with 13 tour operators based in the Mt. Buller and Alpine National Parks. Findings of this study suggest that the majority of operators will experience some impact on their business after the fires, albeit to different degrees, and point to a paucity of forward recovery planning. Operators expressed their concerns about prolonged negative media attention about the fires, but did not have strategies in place to deal with this issue proactively. There appears to be scope for assisting operators on the ground with disaster recovery, including the provision of more positive and timely media communication.
Vacations as Sweepstake Prizes: Tourism in the Service of Selling
Authors: Weaver Adam
Published: July 2010

Many sweepstakes feature vacations as prizes. Manufacturers of non-tourism products use such prizes to increase sales. This article draws upon the concept of theming and applies it to an exploratory study of sweepstakes and vacation prizes. Purposeful thematization is widespread, extending
from shopping malls to large cruise ships to Las Vegas casinos. With respect to sweepstakes, theming invites consumers to make connections between the product that is for sale and the prize. Central to marketing is the presentation of goods in such a way as to create desire for commodities,
and thus enlarge their markets. The pleasures of tourism are familiar to, and resonate with, a broad base of consumers. Through sweepstakes and vacation prizes, tourism—an activity linked to fantasy, escape, and “the extraordinary”—is used to foster the consumption
of everyday, non-tourism products. An effort is made to link tourism's symbolic meanings, often absent from the rationalized flow of daily life, to these products. Allusions to tourism have therefore expanded into the realm of routine shopping and consumption. The main contribution of this
work is to articulate a conceptual link between tourism-related sweepstake prizes and the frequently-purchased consumer goods they are used to promote.
Optical Coherence Tomography as an Adjunctive Tool for Diagnosing Papilledema in Young Patients
Authors: Martinez Michael R. , Ophir Avinoam
Published: July 2010

Purpose:

The authors examined the peripapillary (3.4-mm diameter) retinal nerve fiber layer thickness (RNFL thickness) as depicted by optical coherence tomography (OCT) in young patients with pseudopapilledema or papilledema.

Methods:

In 17 consecutive patients (6 to 20 years old) with bilateral newly diagnosed papilledema or pseudopapilledema, the eye with the thicker mean global RNFL per patient was analyzed. Excluded were patients in whom cerebrospinal fluid opening pressure was between 190 and 250 mm H
2
O (“gray zone”). RNFL thickness was compared in eyes with papilledema and pseudopapilledema using the Mann–Whitney
U
test.

Results:

Papilledema was clinically diagnosed in 9 patients and pseudopapilledema in 6 patients; 2 patients were excluded. Median RNFL thickness in the eyes with papilledema was greater than that of both eyes with pseudopapilledema and controls at all 12 clock hours. In all 9 patients with papilledema, RNFL was thickened contiguously for 8 to 12 clock hours above the upper 95% confidence interval limit of normal.

Conclusion:

The peripapillary RNFL thickness as depicted by OCT was found to be a reliable adjunctive tool in the differentiation of newly diagnosed papilledema and pseudopapilledema in young patients. Larger cohorts are required to confirm these observations and conclusion.
Cranial Electrotherapy Stimulation for the Treatment of Depression
Authors: Gunther Mary , Phillips Kenneth D.
Published: July 2010

More prevalent in women than men, clinical depression affects approximately 15 million American adults in a given year. Psychopharmaceutical therapy accompanied by psychotherapy and wellness interventions (e.g., nutrition, exercise, counseling) is effective in 80% of diagnosed cases. A lesser known adjunctive therapy is that of cranial electrotherapy stimulation (CES). The major hypothesis for the use of CES in depression is that it may reset the brain to pre-stress homeostasis levels. It is conjectured that the pulsed electrical currents emitted by cranial electrical stimulators affect changes in the limbic system, the reticular activating system, and/or the hypothalamus that result in neurotransmitter secretion and downstream hormone production. While evidence is good for applied research, basic research about the mechanisms of action for CES remains in its infancy. A review of the literature provides an overview of current research findings and implications for clinical mental health practice.
El debate sobre la inmigración como discurso ontológico-político
Authors: Pinzani Alessandro
Published: July 2010

Este artículo discute algunas tesis acerca de la inmigración en general y de la inmigración clandestina en particular. Éstos son los pasos: 1) La manera mejor para discutir sobre la cuestión de la inmigración es servirse del concepto foucaltiano de dispositivo, que permite considerar el debate sobre tal cuestión como parte del mecanismo de control de la propia inmigración. 2) Hay una primera dificultad en la definición de la propia figura del inmigrante. 3) En el debate acerca de la inmigración se pueden distinguir dos discursos oficiales: el discurso del control y el discurso de la adaptación, que todavía esconden una posición de rechazo del Otro. 4) El debate establece una distinción ontológica entre los inmigrantes y los ciudadanos, en el sentido de una ontología política que busca definir la comunidad política a través de la contraposición al Otro.
La ciudadanía como ámbito de integración social ante el fenómeno de las migraciones
Authors: Santamarina Cristina
Published: July 2010

El impacto de la inmigración no puede comprenderse más que desde el conflicto del encuentro con los otros, con lo otro diferente y, por tanto, como experiencia compleja para toda cultura. No podemos tampoco esperar que esos conflictos se resuelvan en el incierto espacio de lo social ni transferir a las administraciones esta responsabilidad. La institución de la ciudadanía es la única con capacidad verdadera para acoger esta nueva realidad que golpea como un nuevo desafío a las sociedades de Europa. Porque la ciudadanía es la institución en la que aceptamos los derechos y los deberes de la pertenencia y desde la cual es posible ampliar dicha propuesta a otros, con otros bagajes, culturas y experiencias, que estén dispuestos a asumir con nosotros, esos mismos derechos y deberes.
Travesías peligrosas: los caminos hacia la ciudadanía
Authors: Cole Phillip
Published: July 2010

En este artículo sostengo que la política de ciudadanía e inmigración en el Reino Unido, y en otras potencias europeas, está fundada en una ansiedad postcolonial, heredera de su historia colonial. Por lo que respecta al Reino Unido, el viajero de Europa occidental es civilizado y, por tanto, bienvenido, sin ninguna restricción de acceso al territorio y con la ciudadanía de la UE compartida. En cambio, no es tan bienvenido el viajero procedente de Europa del este. Los viajeros de más allá de la “frontera” europea se enfrentan incluso a un mayor número de restricciones si viajan al Reino Unido buscando la ciudadanía nacional. Su viaje se ha hecho más peligroso durante los últimos años tanto físicamente como en términos políticos y legales. Mientras que la teoría política liberal ha “olvidado” su pasado colonial y escribe sobre un mundo en el que el colonialismo y la esclavitud nunca sucedieron, las regulaciones sobre inmigración y ciudadanía en el Reino Unido parecen incapaces de olvidar el pasado y la narrativa colonial que determinaron cómo dicho pasado fue comprendido en su momento. En este artículo examino los desarrollos más recientes en la legislación de ciudadanía e inmigración del Reino Unido y su probable desarrollo futuro en contraposición a estos antecedentes.
Fronteras de cristal de la inmigración. Visión de los inmigrantes del Este Europeo en España
Authors: Marcu Silvia
Published: July 2010

Símbolos de barrera y de aprendizaje de la existencia, emblemas de nuestro naufragio civilizatorio, las fronteras siguen constituyendo, aún en el siglo XXI, una referencia importante, pese a que nos encontremos en plena era de la globalización. El artículo se propone presentar y analizar la problemática de la adaptación del inmigrante en el espacio de la inmigración. Toma como ejemplo, el inmigrante de la Europa del Este en España, y se guía a partir del discurso inmigrante. La primera parte aborda el espacio fronterizo como simbología y el laberinto imaginario de las fronteras; a continuación se realiza, mediante estudio cualitativo, un análisis de los factores que conducen al mantenimiento de la inadecuación inicial del extranjero y el modo en el cual se autopercibe éste en España. Finalmente, se presentan, simbólicamente, las fronteras de cristal de la inmigración, desde la voz del inmigrante.
Fc Receptor-Like A Associates with Intracellular IgG and IgM but Is Dispensable for Antigen-Specific Immune Responses
Authors: Wilson Timothy J. , Gilfillan Susan , Colonna Marco
Published: July 2010

FcR-like (FcRL) proteins comprise a family of lymphocyte receptors with homology to FcγRI. Among these receptors, FcRLA is uniquely interesting due to its intracellular localization, unusual structural features, and high expression within human germinal center and marginal zone B cells. Our analysis of human cell lines has confirmed that this receptor is not secreted but is maintained as an intracellular protein in B cells where it interacts with Igs, consistent with a possible role in Ab assembly. By generating FcRLA-specific antisera as well as knockout mice, we were able to unequivocally demonstrate that FcRLA protein is expressed exclusively in all mouse B cells. We also found that FcRLA is not required for the generation of Ag-specific humoral immune responses to T-dependent or T-independent Ags. However, given its highly conserved structure and universal expression within B cells, it is probable that FcRLA functions similarly in humans and mice. Cumulatively, our data suggest that FcRLA plays a role in Ig assembly that can be compensated for by other proteins.
Reverse Modeling for Domain-Driven Engineering of Publishing Technology
Authors: Brüggemann-Klein Anne , Demirel Tamer , Pagano Dennis , Tai Andreas
Published: July 2010

We report in this paper on a technique that we call reverse modeling. Reverse modeling starts with a conceptual model that is formulated in one or more generic modeling technologies such as UML or XML Schema. It abstracts from that model a custom, domain-specific meta-model and re-formulates the original model as an instance of the new meta-model. We demonstrate the value of reverse modeling with two case studies: One domain-specific meta-model facilitates design and user interface of a so-called instance generator for broadcasting productions metadata. Another one structures the translation of XML-encoded printer data for invoices into semantic XML. In a further section of this paper, we take a more general view and survey patterns that have evolved in the conceptual modeling of documents and data and that implicitly suggest sound meta-modeling constructs.

Taken together, the two case studies and the survey of patterns in conceptual models bring us one step closer to our superior goal of developing a meta-meta-modeling facility whose instances are custom meta-models for conceptual document and data models. The research that is presented in this paper brings forward a core set of elementary constructors that a meta-meta-modeling facility should provide.
XQuery Design Patterns
Authors: Candillon William , Brantner Matthias , Knochenwefel Dennis
Published: July 2010

Design patterns are widely used inside the object-oriented community. They are proven mature and reusable solutions that facilitate the development of modules with minimal coupling. Moreover, design patterns are also high-level constructs that contribute to improve the communication between developers.

Nowadays, XQuery and its family of specifications are used beyond just querying XML collections and documents. XQuery is more and more used as a multi-paradigm, fully-fledged programming language. The aim of this paper is (1) to motivate the need for XQuery design patterns using a real-world example application and (2) to explore the existence of general design solutions to solve recurring problems in large-scale XQuery applications.
The EXPath Packaging System
Authors: Georges Florent
Published: July 2010

This paper introduces the EXPath Packaging System. It describes the problems addressed by application and library packaging, and the current lack of existing solutions for XML technologies, before describing the Packaging System itself, its structure, its usages and its implementations. It introduces briefly other systems built (or that could be built) on top of this system, like a packaging for web applications written using only XML technologies, an online repository of libraries and applications, or standard structures for XML projects.
Schema Component Paths for Schema Analysis
Authors: Holstege Mary
Published: July 2010

Schema component paths define an XPath-like syntax for describing and navigating W3C XML Schema component models. Canonical schema component paths provide a unique, string-comparable designator for each component in schema. MHSCD is a driver than can generate canonical schema component paths or non-canonical schema component paths to a certain depth, or locate a component or set of components in a schema given a schema component path.

Component paths can be applied to various schema analysis tasks. The set of canonical schema component paths provides a simple signature for a schema that is robust to differences in the physical organization of the schema document. Comparing two such signatures gives a quick "what's changed between these two schema versions?" summary. This signature can also be used for the calculation of basic schema complexity metrics, including basic counts of components of various types.
gXML, a New Approach to Cultivating XML Trees in Java
Authors: Lewis Amelia A. , Johnson Eric E.
Published: July 2010

A number of issues facing the use of XML tree models in Java are enumerated: multiplicity, interoperability, variability, and weight. The gXML API, following the Handle/Body design pattern and conforming to the XQuery Data Model specification XDM, is proposed as a solution to these problems, and as a platform for advancing the state of the art for XML in Java. gXML is not a new tree model, but a unified API and model following a rigorous, external specification, which can be used with any tree model for which a "bridge" has been developed. Applications and processors targeting the gXML API may then use any supported tree model, as appropriate for the task.
DITA or Not?
Authors: Price Lynne A.
Published: July 2010

Use of DITA has become so pervasive that some users assume that anyone who inquires about moving to an XML environment must use DITA. Often, the selection of DITA is independent of DITA's strengths such as ease of reuse, specialization, support of distributed authoring, and availability of the Open Toolkit. While numerous DITA case studies have been published, such reports tend to focus on what was accomplished rather than how the approach was chosen, and typically reflect successful implementations in large organizations. This study focusses on why end users, consultants, and tools have chosen to use or to avoid DITA. While this should not be considered an unbiased or scientifically balanced survey, anecdotal evidence such as this can be valuable to organizations faced with similar decisions.
There are No Documents
Authors: Renear Allen H. , Wickett Karen M.
Published: July 2010

Last year at Balisage (2009) we considered the claim that documents cannot be modified. Our analysis took the form of identifying and evaluating possible responses to this inconsistent triad: 1) Documents are strings; 2) Strings cannot be modified; 3) Documents can be modified. Late this spring we were surprised to realize that our survey of possible responses to the document modifiability puzzle had overlooked one response: There are no documents. We turn to that neglected response now.
Java Integration of XQuery - an Information-Unit Oriented Approach
Authors: Rennau Hans-Jürgen
Published: July 2010

An infrastructure for integrating XQuery into Java systems is described. The infrastructure comprises a new API (XQJPLUS, built on the standard API XQJ) and a tool for Java code generation. The basic idea of the approach is to deliver query results not in terms of query result items, but in terms of “information units”, ready-to-use entities assembled from the result items. The assembly process is guided by control information embedded into the query result, so that the query controls exactly what will be delivered, and in which form. Information units can represent information in a great variety of forms, including many map types and custom objects. The information units produced by a query are collected into a special container ("info tray") which offers name-based, intuitive access to the units. The query-specific structure of an info tray may be formally defined by a tray schema from which an "info shape" can be generated, a Java class representing a specific kind of info tray and offering compiler checked data access. Info trays also support data integration, as their possibly very heterogeneous contents can be addressed in a uniform way, using path-like expressions.
XML Pipeline Processing in the Browser
Authors: Toman Vojtěch
Published: July 2010

With the growing interest in end-to-end XML web application development models, many web applications are becoming predominantly XML-based, requiring XML processing capabilities not only on the-server-side, but often also on the client-side. This paper discusses the potential benefits of using XProc for XML pipeline processing in the web browser and describes the developments of a JavaScript-based XProc implementation.
The high cost of risk aversion
Authors: Usdin B. Tommie
Published: July 2010

Avoiding risk is not always the way to minimize risk.
Stand-alone Encoding of Document History
Authors: Vion-Dury Jean-Yves
Published: July 2010

This paper describes an approach to encapsulate together an XML document and its history (i.e. the various significant states it adopted along its life cycle) into a single standalone XML document. Our proposal introduces an XML data model suited to capture versioning information combined with an operational model to handle such encapsulated data. We describe basic operators involved along the transformation process of the document/history pair, mainly designed around the principle of maintaining coherence properties.
Platform Independence 2010 - Helping Documents Fly Well in Emerging Architectures
Authors: Wrightson Ann
Published: July 2010

Parallel processing and memory bottlenecks dominate current platform architecture conversations. After many years on the sidelines, parallel architectures are rapidly becoming mainstream, with more parallelism the obvious way to gain yet more performance. Feeding data to and from all these parallel cycles is also becoming more challenging.

What does this have to do with XML? Surely all this is under the hood, something for compiler designers, software architects and other non-content people to worry about? The answer is that these issues can't be totally hidden under the hood. Balisageurs as content-folks and interoperability-folks need to pay attention now to the high level information design heuristics that will prevent our data structures being the ones that happen to run like treacle (or molasses) on the coming generations of faster, larger and neater systems.
Report from the Field: PubMed Central, an XML-based Archive of Life Sciences Journal Articles
Authors: Beck Jeff
Published: July 2010

PubMed Central (PMC) is an XML-based archive of life sciences journal literature at the U.S. National Institutes of Heath that allows public access to full-text journal articles. The archive was created in 2000 and has grown steadily to over 2 million records. The project has been successful in part because of the strict XML control and the flexibility that PMC givesre its submitters.

This paper gives an overview of the PMC data evaluation process; the XML processing model; the PMC philosophy toward XML use, including use of the NLM DTD, XML Taggging Style, usability or reusablilty of the XML, public XML tools, and our people; and some challenges we continue to face maintaining the archive.
A formal approach to XML semantics: implications for archive standards
Authors: Dombrowski Andrew , Dombrowski Quinn
Published: July 2010

Previous literature characterizing XML semantics (Sperberg-McQueen et al. 2000, Renear et al. 2002, Piez 2002) takes reasonably syntactically and semantically plausible markup and/or schemas as a starting point. In contrast, for this paper we aim to work towards such a schema as an idealized end goal, by characterizing the necessary— if not sufficient— semantic constraints that differentiate a schema intended for archival use from nonsense and implausible schemas, as well as schemas that fail to sufficiently take semantics into account. In addition to the goal of providing a novel approach to the perenially thorny problem of XML semantics, we are particularly concerned with the interaction between the goals of archival purposes and XML semantics.
Metadata for Long Term Preservation of Product Data
Authors: Lubell Joshua
Published: July 2010

Product data can be usefully defined as structured information about objects that are produced by industrial and business processes. In terms of information types, data formats, usage, and lifespan, product data is both complex and diverse, encompassing 3D image modeling information, dimensions, tolerances, and other model annotations, supplementary material such as test analysis, videos, datasets, and human-readable documentation. Although the metadata issues in this problem space present some unique challenges, there are valuable lessons to be learned from the library metadata and packaging standards and how they relate to product metadata. Extending the library standards to represent subsets of information from emerging product lifecycle management standards could help tame the complexity of long-term archival of product data.
Portico: A Case Study in the Use of XML for the Long-Term Preservation of Digital Artifacts
Authors: Morrissey Sheila , Meyer John , Bhattarai Sushil , Kurdikar Sachin , Ling Jie , Stoeffler Matthew , Thanneeru Umadevi
Published: July 2010

In the problem space of long-term preservation of digital objects, the disciplined use of XML affords a reasonable solution to many of the issues associated with ensuring the interpretability and renderability of at least some digital artifacts. This paper describes the experience of Portico, a digital preservation service that preserves scholarly literature in electronic form. It describes some of the challenges and practices entailed in processing and producing XML for the archive, including issues of syntax, semantics, linking, versioning, and prospective issues of scale, variety of formats, and the larger infrastructure of tools and practices required for the use of XML for the long haul.
Beyond Eighteen Wheels
Authors: Quin Liam R. E.
Published: July 2010

When documents are stored for any significant length of time, or when they are used, whether continuously or occasionally, over an extended period, the original people and culture and context associated with their creation become unavailable. If the documents are to remain useful, it is necessary to retain sufficient knowledge about how they can be used that the future people involved can still gain value from them.

This document is a position paper for discussion.
A brief history of markup of social science data: from punched cards to "the life cycle" approach
Authors: Ruus Laine
Published: July 2010

Traditional quantitative social science data analysis requires three ingredients: the raw data, metadata (what we used to call a codebook), and software. Software changes all the time, within some limits. Raw data without metadata is useless: it might as well be generated by a random number generator. And metadata without data is like the index to a periodical the last remaining copy of which was sent for recycling last month. Over time, metadata have been expected to support many different functions, and microsolutions have never quite satisfied many, much less all, of those functions. Until recently, that is: a roughly 25-year process of historical evolution has led to DDI, the Data Documentation Initiative, which unites several levels of metadata in one emerging standard.
Sustainability of Linguistic Resources Revisited
Authors: Rehm Georg , Schonefeld Oliver , Trippel Thorsten , Witt Andreas
Published: July 2010

Data providers, users, and funders alike want and need sustainability of language resources (e.g. language corpora, grammars, etc.); sustainability requires making the resources available according to defined processes, platforms, or archives in a reproducible and reliable way. A three-year project on sustainability of linguistic resources conducted at Tübingen, Hamburg, and Potsdam illuminates some of the difficulties: the prevalence of stand-off markup (requiring a layer of specialized tools atop the XML stack), machine-generated XML of low clarity, ad hoc non-standard tag sets, discoverability, and selection criteria for long-term archiving. XML and other standards are necessary but not sufficient ingredients in the mix.
Production of dissolved organic carbon by sloppy feeding in the copepods Acartia tonsa, Centropages typicus, and Temora longicornis
Authors: Møller Eva Friis
Published: July 2010

With 14C‐labeled phytoplankton as tracer, dissolved organic carbon (DOC) produced by sloppy feeding was measured for three species of marine copepods (Acartia tonsa, Centropages typicus, and Temora longicornis) grazing on the differently sized phytoplankton (Rhodomonas salina, Heterocapsa rotundata, and Ditylum brightwelli). DOC production per prey cleared was not dependent on prey concentration, whereas the relative size of the prey was important. When the prey was more than 39 times smaller than the copepod (measured as equivalent spherical diameter) no DOC production by sloppy feeding was measured. When the prey was larger, the fraction of carbon cleared that was lost as DOC by sloppy feeding was a function of the copepod‐prey size ratio. The DOC production by the three species could be predicted from a common regression.
Temporal dynamics and regulation of lake metabolism
Authors: Staehr Peter A. , Sand-Jensen Kaj
Published: July 2010

We studied temporal dynamics and regulation of oxygen metabolism in the upper mixed layer of a nutrientrich shallow Danish lake by continuous measurements of oxygen, irradiance, wind, and temperature and frequent measurements of algal chlorophyll, organic pools, and inorganic nutrients. Chlorophyll, algal growth rate, and mean irradiance (Emean) in the mixed surface layer were calculated daily from continuous measurements of irradiance and temperature with depth. There were three to four distinct maxima in gross primary production (GPP) and community respiration (R) during the summer season and minima from fall to spring after broad‐scale changes in irradiance, temperature, mixing depth, and biomass and growth rate of the algal community and concentrations of inorganic nutrients. Lake metabolism was annually balanced (mean GPP :R 1.04 in 2003 and 1.01 in 2004), with net autotrophy occurring mainly from mid‐May to mid‐September (mean GPP:R 1.14 in 2003 and 1.10 in 2004), and net heterotrophy outside this period (mean GPP:R 0.60 in 2003 and 0.81 in 2004). However, GPP :R varied two‐ to threefold from day to day because lower surface irradiance, higher mixing depth, and thus lower Emean significantly reduced GPP. Normalizing GPP to chlorophyll provided an index of algal growth potential (GPPB), which followed a hyperbolic relationship to Emean, and both parameters were related to blooms and collapses of algal biomass. Metabolic rates were much more variable from day to day than algal biomass, which integrates growth and loss processes over longer periods. The continuous approach to lake metabolism provides better data and can provide a more accurate picture than averages of a few discrete measurements. Weekly averages reflected the characteristic seasonal peaks and troughs also observed for algal biomass, whereas monthly averages did not. Daily measurements of lake metabolism, therefore, can provide the optimal background for evaluating temporal changes and regulation of algal biomass and organic pools in nutrient‐rich shallow lakes.
Optical properties of the “clearest” natural waters
Authors: Morel André , Gentili Bernard , Claustre Hervé , Babin Marcel , Bricaud Annick , Ras Joséphine , Tièche Fanny
Published: July 2010

Optical measurements within both the visible and near ultraviolet (UV) parts of the spectrum (305–750 nm) were recently made in hyperoligotrophic waters in the South Pacific gyre (near Easter Island). The diffuse attenuation coefficients for downward irradiance, Kd(λ), and the irradiance reflectances, R(λ), as derived from hyperspectral (downward and upward) irradiance measurements, exhibit very uncommon values that reflect the exceptional clarity of this huge water body. The Kd(λ) values observed in the UV domain are even below the absorption coefficients found in current literature for pure water. The R(λ) values (beneath the surface) exhibit a maximum as high as 13% around 390 nm. From these apparent optical properties, the absorption and backscattering coefficients can be inferred by inversion and compared to those of (optically) pure seawater. The total absorption coefficient (atot) exhibits a flat minimum (~ 0.007 m−1) around 410‐420 nm, about twice that of pure water. At 310 nm, atot may be as low as 0.045 m−1, i.e., half the value generally accepted for pure water. The particulate absorption is low compared to those of yellow substance and water and represents only ~15% of atot in the 305‐420‐nm domain. The backscattering coefficient is totally dominated by that of water molecules in the UV domain. Because direct laboratory determinations of pure water absorption in the UV domain are still scarce and contradictory, we determine a tentative upper bound limit for this elusive coefficient as it results from in situ measurements.
A time series of environmental tracer data from deep meromictic Lake Lugano, Switzerland
Authors: Aeschbach-Hertig W. , Holzner C. P. , Hofer M. , Simona M. , Barbieri A. , Kipfer R.
Published: July 2010

An 11‐yr (1990–2001) time series of tritium‐helium‐3 (3H‐3He) apparent water ages as well as one sulfur hexafluoride (SF6) profile were used to study the development of the vertical mixing dynamics of the deep, meromictic northern basin of Lake Lugano. The density stratification of the water column was dominated by an increase in dissolved ions with depth, which remained approximately constant during the 1990s. The deep‐water temperature increased steadily during this period, passing a threshold above which cooling of the surface water could force convection. However, increasingly mild winter temperatures prevented the occurrence of a turnover until 2005. The maximum apparent 3H‐3He water age increased from about 16 yr in 1990 to 23 yr in 2001. The maximum apparent SF6 age in 2001 was 12.8 yr. The large difference between the apparent 3H‐3He and SF6 ages is at least partly due to nonlinear effects of mixing, causing SF6 ages to underestimate the true mean deep‐water residence time, whereas 3H‐3He ages overestimate it. The decreasing concentrations of 3H and 3He are more reliable indicators of the continuous deep‐water exchange in the lake than are the apparent ages. Budget calculations using the tracer concentrations reveal an annual renewal of the deep water below 100 m in depth by about 8% and enable the calculation of long‐term mean profiles of the effective vertical turbulent diffusivity Kz. No trend in the mixing intensity during the 1990s could be determined. The radiogenic He flux into the lake is comparable to estimates of the whole crustal degassing flux.
Effects of nonlocal turbulence on the mass transfer of dissolved species to reef corals
Authors: Falter James L. , Atkinson Marlin J. , Lowe Ryan J. , Monismith Stephen G. , Koseff Jeffrey R.
Published: July 2010

We examined the importance of nonlocal turbulence to the mass transfer of dissolved species from both cylinders and models of reef coral. Solid gypsum cylinders and gypsum‐coated model coral were dissolved in an outdoor flume at mean flow speeds of 4.5 and 10 cm s−1. Three model corals were used: two branched forms of the genera Acropora and Pocillopora, and one lobate form of the genus Platygyra. Turbulence intensities (Tu) were measured as the ratio of the standard deviation of the time‐variant flow to the mean. Tu of between 5% and 55% were created independently of the mean flow by pumping water through two vertical arrays of jets. Mass transfer coefficients increased by 10‐70% with turbulence intensity for all forms at both mean flow speeds considered (p < 0.05); however, mass transfer coefficients for the branched coral were not as sensitive to changes in turbulence intensity as for the lobate coral. Results for the cylinders were consistent with the engineering literature and indicate that the effects of turbulence intensity on mass transfer become weaker when branch size or flow speed (or both) become very small. Turbulence intensities measured around experimental coral communities and above naturally occurring reef communities typically vary between 15% and 35%. Assuming an average turbulence intensity of around 25%, then ignoring the effects of nonlocal turbulence altogether would result in uncertainties in mass transfer coefficients of at most ±10% for the lobate coral form and ±5% for the branched coral forms. Measuring external turbulence in bulk flows is not necessary for most evaluations of biogeochemical rates in benthic reef systems.
Turbulent mixing and phytoplankton spring bloom development in a deep lake
Authors: Peeters Frank , Straile Dietmar , Lorke Andreas , Ollinger Dieter
Published: July 2010

A one‐dimensional (1‐D) mechanistic phytoplankton model combined with a 1‐D hydrodynamic model was applied to simulate phytoplankton growth during winter and spring in deep monomictic Upper Lake Constance. Modeled chlorophyll a concentrations agree well with data from the 8‐y time period considered. In particular, the interannual variation in the timing of phytoplankton growth is adequately simulated by the model. The onset of phytoplankton blooms in Upper Lake Constance is not sensitive to variations in the photosynthetically active radiation, the sinking velocity of the algae, or the effect of water temperature on biological process rates, but is primarily determined by turbulent diffusion (i.e., by the transition from strong mixing in winter and early spring to weak mixing). The transition in mixing conditions and thus also the beginning of phytoplankton population growth correlates with the build up of the first slight temperature stratification. Simulations performed without consideration of phytoplankton loss due to grazing overestimate algal biomass soon after the onset of algal growth. Including grazing by zooplankton substantially improves the agreement between model and data and suggests that ciliate grazing in particular leads to a significant reduction of phytoplankton abundance in spring after the start of the algal bloom.
Sensitivity of herbivorous zooplankton to phosphorus‐deficient diets: Testing stoichiometric theory and the growth rate hypothesis
Authors: Ferrão-Filho Aloysio da S. , Tessier Alan J. , DeMott William R.
Published: July 2010

Stoichiometry and growth rate variation are related aspects of the ecology and evolution of consumer‐resource interactions. In zooplankton, these concepts have been explored primarily in a few species of Daphnia. We used growth bioassays and changes in animal P content to quantify the sensitivity of four herbivorous cladoceran species to algal resources representing a gradient in C: P ratios ranging from 140 to 1,000, offered at both low and high food levels. Supplements of phosphate, Synechococcus, or P‐sufficient algae were used to test for P, energy, and fatty acid limitation. Phosphorus assimilation was estimated by isotope techniques (32P) to test the hypothesis of digestion resistance in P‐limited algae. The cladoceran species differed in sensitivity to P deficiency at both low and high food levels, although sensitivity was less at low food. The P content of the two Daphnia species changed substantially along the C: P ratio gradient, contradicting the notion of strict homeostasis, whereas the two other cladoceran species showed tight P homeostasis. Consistent with stoichiometric theory, the two species with the highest P content were also more sensitive to P deficiency. Growth rate was related to P content across the four species at the high food level and at low C: P ratios, supporting the growth rate hypothesis. The addition of supplements to P deficient algae improved animal's growth rates, showing both P and energy limitation, but no evidence for fatty acid limitation. Lower assimilation efficiency for P‐deficient algae suggests that digestion resistance can be a factor in the food quality of P‐deficient resources.