bluuebunny/crossref_metadata_2025 huggingface dataset:
Endothermy in birds: underlying molecular mechanisms
Authors: Walter Isabel , Seebacher Frank
Published: July 2009

Endothermy is significant in vertebrate evolution because it changes the relations between animals and their environment. How endothermy has evolved in archosaurs (birds, crocodiles and dinosaurs) is controversial especially because birds do not possess brown adipose tissue, the specialized endothermic tissue of mammals. Internal heat production is facilitated by increased oxidative metabolic capacity, accompanied by the uncoupling of aerobic metabolism from energy (ATP) production. Here we show that the transition from an ectothermic to an endothermic metabolic state in developing chicken embryos occurs by the interaction between increased basal ATP demand(Na+/K+-ATPase activity and gene expression), increased oxidative capacity and increased uncoupling of mitochondria; this process is controlled by thyroid hormone via its effect on PGC1α and adenine nucleotide translocase (ANT) gene expression. Mitochondria become more uncoupled during development, but unlike in mammals, avian uncoupling protein(avUCP) does not uncouple electron transport from oxidative phosphorylation and therefore plays no role in heat production. Instead, ANT is the principal uncoupling protein in birds. The relationship between oxidative capacity and uncoupling indicates that there is a continuum of phenotypes that fall between the extremes of selection for increased heat production and increased aerobic activity, whereas increased cellular ATP demand is a prerequisite for increased oxidative capacity.
Thermal activation of escape swimming in post-hatching Xenopus laevis frog larvae
Authors: Sillar Keith T. , Robertson R. Meldrum
Published: July 2009

Survival requires the selection of appropriate behavioural responses in the face of danger. With respect to the threat of predation, both the decision to escape and the underlying neuronal mechanisms have been extensively studied,but processes that trigger evasion of abiotic stressors, which are potentially hazardous to survival, are less well understood. Here, we document the interplay between rhythmic locomotory and `C-start' escape swimming in Xenopus frog larvae when exposed to hyperthermic conditions. As temperature rises, swim cycle frequency increases while swim bout duration decreases, until swimming can no longer be initiated by sensory stimuli. Above a critical higher temperature, more intense sequences of spontaneous high amplitude C-start escape activity occur. Each C-start is followed by a few cycles of fast rhythmic swimming in which activity alternates between the two sides. The initial, high amplitude ventral root burst of an escape sequence propagates rostrocaudally approximately threefold faster than subsequent cycles. The high conduction velocity of this initial burst is consistent with the activation of a Mauthner neuron, one of a pair of giant reticulospinal neurons in fish and amphibians. In support of the involvement of a Mauthner neuron, unilateral lesions of the caudal hindbrain eliminated escape activity on the operated side, but activity remained on the un-operated side. Behaviourally, tadpoles responded to temperature ramps with a sequence of C-start responses in which the body arced through ∼130° in 22 ms,followed by high frequency swimming. These results suggest that high temperature activates the Mauthner neurons to trigger C-start escape behaviour.
Effects of crowding on ornithine–urea cycle enzyme mRNA expression and activity in gulf toadfish (Opsanus beta)
Authors: Laberge Tammy , Walsh Patrick J. , McDonald M. Danielle
Published: July 2009

The gulf toadfish (Opsanus beta) is a facultatively ureotelic fish that excretes primarily urea under conditions of crowding or confinement. To examine the relationship between ammonia production, urea production and the ornithine–urea cycle (O–UC) enzyme activity and mRNA expression,we subjected toadfish to two-day and seven-day crowding regimes. Plasma cortisol levels were measured and liver tissue was assayed for ammonia and urea concentrations. Liver glutamine synthetase (GS), carbamoyl phosphate synthetase III (CPS), ornithine carbamoyl transferase (OCT) and arginase (ARG)activities were also measured. Quantitative PCR was utilized to determine liver GS, CPS, OCT, ARG, argininosuccinate synthetase (ASS) and argininosuccinate lyase (ASL) mRNA expression. Hepatic ammonia concentrations decreased with increased duration of crowding whereas liver urea and circulating cortisol levels increased. An elevation in enzyme activity with increased duration of crowding was observed for all four O-UC enzymes examined. By contrast, mRNA expression was variable for the O–UC enzymes and only CPS and ASS had mRNA expression levels that were elevated in crowded fish. These results suggest that the activities of O–UC enzymes are better predictors for urea production than O–UC enzyme mRNA expression levels.
The evolution of speed, size and shape in modern athletics
Authors: Charles Jordan D. , Bejan Adrian
Published: July 2009

In the present study, we show that the fastest runners and swimmers are becoming not only faster but also heavier, taller and more slender. During the past century, the world record speeds for 100 m-freestyle and 100 m-dash have increased with body mass (M) raised to the power 1/6, in accordance with the constructal scaling of animal locomotion. The world records also show that the speeds have increased in proportion with body heights (H)raised to the power 1/2, in accordance with animal locomotion scaling. If the athlete's body is modeled with two length scales (H, body width L), the (M, H) data can be used to calculate the slenderness of the body, H/L. The world records show that the body slenderness is increasing very slowly over time.
Resolution and sensitivity of the eyes of the Asian honeybees Apis florea, Apis cerana and Apis dorsata
Authors: Somanathan Hema , Warrant Eric J. , Borges Renee M. , Wallén Rita , Kelber Almut
Published: July 2009

Bees of the genus Apis are important foragers of nectar and pollen resources. Although the European honeybee, Apis mellifera, has been well studied with respect to its sensory abilities, learning behaviour and role as pollinators, much less is known about the other Apis species. We studied the anatomical spatial resolution and absolute sensitivity of the eyes of three sympatric species of Asian honeybees, Apis cerana, Apis florea and Apis dorsata and compared them with the eyes of A. mellifera. Of these four species, the giant honeybee A. dorsata (which forages during moonlit nights) has the lowest spatial resolution and the most sensitive eyes, followed by A. mellifera, A. cerana and the dwarf honeybee, A. florea (which has the smallest acceptance angles and the least sensitive eyes). Moreover, unlike the strictly diurnal A. cerana and A. florea, A. dorsata possess large ocelli, a feature that it shares with all dim-light bees. However, the eyes of the facultatively nocturnal A. dorsata are much less sensitive than those of known obligately nocturnal bees such as Megalopta genalis in Panama and Xylocopa tranquebarica in India. The differences in sensitivity between the eyes of A. dorsataand other strictly diurnal Apis species cannot alone explain why the former is able to fly, orient and forage at half-moon light levels. We assume that additional neuronal adaptations, as has been proposed for A. mellifera, M. genalis and X. tranquebarica, might exist in A. dorsata.
Ntc90 is required for recruiting first step factor Yju2 but not for spliceosome activation
Authors: Chang Kae-Jiun , Chen Hsin-Chou , Cheng Soo-Chen
Published: July 2009

The Prp19-associated complex (NineTeen Complex [NTC]) is required for spliceosome activation by specifying interactions of U5 and U6 with pre-mRNA on the spliceosome after the release of U4. The NTC consists of at least eight protein components, including two tetratricopeptide repeat (TPR)-containing proteins, Ntc90 and Ntc77. Ntc90 has nine copies of the TPR with seven clustered in the carboxy-terminal half of the protein, and interacts with all identified NTC components except for Prp19 and Ntc25. It forms a stable complex with Ntc31, Ntc30, and Ntc20 in the absence of Ntc25, when other interactions between NTC components are disrupted. In this study, we used both biochemical and genetic methods to analyze the structure of Ntc90, and its function in maintaining the integrity of the NTC and in NTC-mediated spliceosome activation. Our results show that Ntc90 interacts with Ntc31, Ntc30, and other NTC components through different regions of the protein, and that its function may be regulated by Ntc31 and Ntc30. Ntc90 is not required for the association of Prp19, Ntc85, Ntc77, Ntc25, and Ntc20, or for their binding to the spliceosome. It is also not required for NTC-mediated spliceosome activation, but is required for the recruitment of Yju2, which is involved in the first catalytic reaction after the function of Prp2. Our results demonstrate a novel role of the NTC in recruiting splicing factors to the spliceosome after its activation.
RNA Extraction from Archival Formalin-Fixed Paraffin-Embedded Tissue: A Comparison of Manual, Semiautomated, and Fully Automated Purification Methods
Authors: Bohmann Kerstin , Hennig Guido , Rogel Uwe , Poremba Christopher , Mueller Berit Maria , Fritz Peter , Stoerkel Stephan , Schaefer Karl-L
Published: July 2009

Background: Formalin-fixed paraffin-embedded (FFPE) tumor material represents a valuable resource for the analysis of RNA-based biomarkers, both in research laboratories and in routine clinical testing. A robust and automated RNA-extraction method with a high sample throughput is required.

Methods: We evaluated extraction performance for 4 silica-based RNA-extraction protocols: (a) a fully automated, bead-based RNA-isolation procedure; (b) its manual counterpart; (c) a semiautomated bead-based extraction system; and (d) a manual column-based extraction kit. RNA from 360 sections (90 sections per extraction method) of 30 FFPE tumor blocks up to 20 years of age was purified and analyzed by quantitative reverse-transcription PCR for ESR1 (estrogen receptor 1), PGR (progesterone receptor), ERBB2 [v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)], and RPL37A (ribosomal protein L37a).

Results: The semiautomated protocol gave the best yield. The 3 bead-based methods showed good across-method correlations in both yield and relative mRNA amounts (r = 0.86–0.95 and 0.98, respectively). In contrast, correlations between any of the bead-based methods and the manual column-based method were worse (r = 0.77–0.95 and 0.96, respectively). The fully automated method showed the lowest variation from section to section (root mean square error, 0.32–0.35 Cq, where Cq is the quantification cycle) and required the least hands-on time (1 h).

Conclusions: The fully automated RNA-purification method showed the best reproducibility in gene expression analyses of neighboring sections of tissue blocks between 3 and 20 years of age and required the least overall and hands-on times. This method appears well suited for high-throughput RNA analyses in both routine clinical testing and translational research studies with archived FFPE material.
Analysis of High Temperature Fluctuations on Asphalt Pavement of Cement Concrete Bridge
Authors: Shaopeng Wu , Wang Hong , Chen Mingyu
Published: July 2009

In this study a 2-D finite element model of a multilayered pavement structure of a cement concrete bridge was developed to calculate the temperature fluctuations in summer due to thermal environmental conditions for 1 week. The different specific heat capacity and absorptivity factors of the asphalt layers were considered. The results indicate that the surface temperature’s fluctuation of the pavement is similar to the outside atmosphere temperature; the maximum temperature and temperature gradient of asphalt pavement decreased gradually from the top down; the larger the specific heat capacity is, the less the maximum surface temperature becomes; the larger the absorptivity factor of asphalt pavement is, the higher the maximum surface temperature becomes. It is concluded that 2-D finite element analysis proved to be an interesting tool to simulate the transient behavior of asphalt concrete pavements. The suggested simulation model can predict the pavement temperature at different levels of bituminous layers with good accuracy, which can provide engineers some guidance on the rutting resistance.
Design and Implementation of a Gel Treatment to Shut Off Water in a High-Temperature, High-Pressure Fractured Reservoir
Authors: Cheung S. K. , Quilter R. M.
Published: July 2009

This paper reports a process to design a water shutoff job for a high-temperature, high-pressure fractured reservoir. We also report the results from a field case history.

For effective water shutoff in fractured systems, the selected gel needs to have long-term stability at the downhole temperature, adequate gel strength, and needs to adhere strongly enough to the surface of the formation fracture; otherwise, the water shutoff may not be effective because the produced water might push the gel out or bypass it.

We report an actual field treatment for a well offshore California. The well has a downhole temperature of 250°F with a potential differential pressure of 1000 psi. We pumped 480 Bbls of gel, or about 44 Bbls of gel per effective perforated foot. The treatment was economic, with a payoff period of two weeks. It shut off 50% of the water production and increased the oil production by 300%. However, the shutoff lasted only three months. This might be due to inadequate gel volume, or other factors. We suggested Best Practice Ideas and Lesson Learned.
Characterization of Contaminant Sites Using Sparse Well Data
Authors: Nikravesh Masoud , Cox Lea , Faybishenko Boris , Aminzadeh Fred
Published: July 2009

In order to plan the remediation of contaminant sites, it is of great importance to estimate the mass and a three-dimensional extent of contaminants in soils and rocks. Estimation of the volume and mass of contaminants is usually based on sparse well data. However, data from containinant sites are often difficult to analyze due to their uncertainty. In addition, methods of obtaining data are laborious and expensive. Therefore, minimizing sampling plans to reduce the number of wells to be drilled and samples to be taken are of great economic benefit. In this paper, we present a robust model that is based on a neural network technique. The model has the ability to infer general rules and extract typical patterns from the data available, and recognize input-output mapping parameters from complex multi-dimensional field data. This approach gives our model the ability to interpolate between typical patterns of data, and then extrapolate to a region beyond the training domains. The model requires minimum input information to estimate the total mass and/or volume, shape, and distribution of a contaminant in 2-D and 3-D spaces. For all cases we studied (Alameda County sites, Yucca Mountain tuff core, and computer generated examples), predicted mass converged to the actual total mass. In addition, the technique developed was used to optimize the location and the orientation of each new well to be drilled based on data gathered from previous wells.
Errors in Water Retention Curves Determined with Pressure Plates
Authors: Bittelli Marco , Flury Markus
Published: July 2009

Pressure plates are commonly used to measure the soil water retention curve. Low plate and soil conductance, lack of plate–soil contact, and soil dispersion, however, make this method often unreliable at low water potentials. We investigated how errors in the determination of the water retention curve affect the soil hydraulic properties and the computation of plant‐available water. We first determined soil water retention data for a silt loam soil using pressure plates only and a combination of pressure plates and a dew point meter. The two sets of soil water retention data were then analyzed using different models for describing the hydraulic properties. The soil water retention curves determined with the two methods deviated at potentials less than about −20 m H2O, with the pressure plate apparatus data yielding larger water contents than the dew point meter at the same water potentials. These results indicate that soil water retention curves determined from pressure plates may be in error at potentials less than −20 m H2O, which may lead to substantial errors in water flow calculations. These errors can be eliminated by using a combination of pressure plates and dew point measurements to determine the water retention curve.
Nitrogen Management for Irrigated Potato Production under Conventional and Reduced Tillage
Authors: Alva A. K. , Collins H. P. , Boydston R. A.
Published: July 2009

Potato (Solanum tuberosumL.) field studies were conducted under center pivot irrigation for 4 yr using large plots and standard industry cultural practices to evaluate tillage effects (reduced vs. conventional) and different N management practices (preplant plus in‐season N rates of 56 + 280, 112 + 224, 112 + 336, and 112 + 112 kg N ha−1). Despite growing conditions that produced tuber yields up to 80 Mg ha−1, potato size distribution and tuber specific gravity were similar across different tillage and N management practices with minor exceptions in one out of 4 yr. Reduced tillage avoided four equipment passes compared with conventional tillage. Tuber yield and quality were similar across all N rates. Increasing the frequency of in‐season N application from five to 10 at a given N rate did not produce increased tuber yield or improved quality. This study demonstrated no negative effects of reduced tillage for irrigated potato production. The optimal N fertilization program appears to be 112 kg N ha−1preplant application and a similar in‐season N rate in five applications on a 2‐wk interval beginning 4 wk after seedling emergence. Therefore, reduced tillage offers an option for saving energy and labor costs without compromising tuber yield or quality, and thus provides an economic incentive in addition to the benefits of reducing soil erosion and enhancing soil biology and soil quality.
Diversity and Dynamics of Methanotrophs within an Experimental Landfill Cover Soil
Authors: Jugnia Louis-B. , Aït-Benichou Samah , Fortin Nathalie , Cabral Alexandre R. , Greer Charles W.
Published: July 2009

Three experimental biocovers were installed during the summer of 2006 at the St‐Nicéphore landfill in Québec (Canada). The main objectives of the experimental program were to assess the efficiency of these biocovers in reducing CH4emissions and to monitor the evolution in space and time of the dynamics and diversity of methanotrophic bacteria that may be responsible for CH4abatement. Dynamics of methanotroph populations derived from most probable number (MPN) counts exhibited different steps (lag, growth, and collapse phases), with mean abundances decreasing somewhat with depth. Methanotroph diversity, as assessed by denaturing gradient gel electrophoresis showed changes over time in the community structure. These changes were dependent on the sampling depth and only Type I methanotrophs belonging essentially to the genusMethylobacterwere retrieved from our samples. Given the youthful character of the system under study, together with the reported behavior of this functional group of methanotrophs, it was concluded that Type I methanotrophs forming the community structure might reflect pioneer species with a potentially high growth rate (r‐strategists) that become numerically dominant reducing the evenness of species distribution. These results contribute to the generally limited body of knowledge on methanotroph diversity in landfill cover soils.
Tracing Sediment Movement on a Semiarid Watershed using Rare Earth Elements
Authors: Polyakov V. O. , Kimoto A. , Nearing M. A. , Nichols M. H.
Published: July 2009

A multi‐tracer method employing rare earth elements (REE) was used to determine sediment yield and to track sediment movement in a small semiarid watershed. A 0.33‐ha watershed near Tombstone, AZ was divided into five morphological units, each tagged with one of five REE oxides. Relative contribution of each unit to the total sediment yield was determined by collecting runoff and sediment, and the spatial redistribution of sediment was determined from sampling the soil surface. Average sediment yield was 1.0 Mg ha−1 yr−1 from the entire watershed, but varied between 0.1 Mg ha−1 yr−1 from the upper slope to 5.0 Mg ha−1 yr−1 from the lower channel. Little re‐deposition occurred in the channels indicating an effective transport system. The erosion pattern and rates were in agreement with the current morphology of the watershed, which has a well‐developed channel network.
Microbial Indicators of Eutrophication in Everglades Wetlands
Authors: Wright Alan L. , Ramesh Reddy K. , Newman Susan
Published: July 2009

Nutrient loading has been implicated as a major cause of ecological changes in Everglades wetlands. The main objective of this study was to assess changes in microbial indicators in response to nutrient loading across the Everglades landscape. Soil chemical, physical, and microbial properties were measured for nutrient‐impacted and oligotrophic sites within Water Conservation Area (WCA)‐1, WCA‐2a, WCA‐3a, and Taylor Slough of Everglades National Park. Impacts of nutrient loading were most evident by the development of gradients in floc and soil total P from peripheral to interior areas of all wetlands following the paths of surface water flow. Floc was more responsive to nutrient loading than the underlying soil. The sensitive indicators of eutrophication were floc and soil total P, microbial biomass P, and mineralized P. Total P averaged 185 and 140% greater for nutrient‐impacted than oligotrophic areas for floc and soil (0–3 cm), respectively. Microbial biomass P averaged 97 and 52% higher at nutrient‐impacted than oligotrophic areas for floc and soil, respectively. Mineralized P was the most sensitive indicator of eutrophication, being 689 and 135% higher at nutrient‐impacted than oligotrophic areas for floc and soil, respectively. Microbial indicators in WCA‐3a and Taylor Slough were more responsive to nutrient loading than in WCA‐1 and WCA‐2a, which received higher P loads. Delineation of nutrient‐impacted and oligotrophic areas in Everglades wetlands may serve as a baseline to assess future impacts of eutrophication. The consistent pattern in the response of microbial processes to nutrient loading across the range of conditions in different Everglades wetlands demonstrates their suitability as sensitive indicators of eutrophication.
Après Bush, Le Déluge?
Authors: Auerbach Alan J. , Gale William G.
Published: July 2009

Although this year's record deficit has attracted a lot of attention, the real concern is the unsustainability of the federal budget over the next 10 years and longer. The budget situation presents policy makers with a very delicate balancing act between encouraging economic recovery and establishing fiscal sustainability, according to Alan Auerbach of U.C. Berkeley and William Gale of Brookings.
Unlearned Lessons from the Housing Bubble
Authors: Shiller Robert J.
Published: July 2009

Land isn't that scarce and people just don't seem to understand how little housing should and will appreciate long term. These irrational expectations are likely to bite us again and again with more housing bubbles, according to Robert Shiller.
On Inferring Demand for Health Care in the Presence of Anchoring and Selection Biases
Authors: Bhattacharya Jay , Isen Adam
Published: July 2009

In the contingent valuation literature, anchoring bias poses problems when using an iterative bidding game to infer willingness to pay. This bias occurs when the willingness to pay estimate is sensitive to the initially presented starting value. More generally, whenever a survey format is used and not all of those contacted participate, selection bias raises concerns about the representativeness of the sample. In this paper, we estimate students' willingness to pay for student health care at Stanford University while accounting for both of these biases. As there is no cost sharing for students, we assess willingness to pay by having a random sample of students play an on line iterative bidding game. Our main results are that (1) demand for student health care is elastic by conventional standards; (2) ignoring anchoring bias would lead to a substantially biased measure of the demand elasticity; and (3) standard selection correction methods indicate no bias from selective non-response and newer bounding methods support this conclusion of elastic demand.
“Losers” and the Sub‐Prime Mortgage Crisis
Authors: Cline Andrew R
Published: July 2009

Until early 2009, “loser” was a sympathetic term identifying victims of the 2008‐2009 recession. That use shifted to a derogatory label for people who benefit from government largesse — sub‐prime mortgage borrowers — at the expense of “honest” and “hardworking” Americans. Labels “transform and magnify” behavior into a character failing. Gans (1995) sees a “war of words” in American culture that uses pejorative labels “that stereotype, stigmatize, and harass the poor by questioning their morality and their values.” This essay examines the case of CNBC reporter Rick Santelli's use of “loser” as a pejorative label and the influence of that use on media punditry about the mortgage crisis of 2008‐2009.
Comparison of the modified fluorescent method and conventional Ziehl–Neelsen method in the detection of acidfast bacilli in lymphnode aspirates
Authors: Annam Vamseedhar , Kulkarni Mohan H , Puranik Rekha B
Published: July 2009

Objectives:

The objectives were to correlate the modified fluorescent method with the conventional Ziehl–Neelsen (ZN) method for the detection of acid-fast bacilli (AFB) and, also to study the efficacy and advantages of using the auramine–rhodamine stain on lymph node aspirates under fluorescent microscopy.

Methods:

In 108 consecutive patients with a clinical suspicion of tuberculosis (TB) presenting with lymphadenopathy, fine needle aspirations were performed. Smears from the aspirates were processed for routine cytology, the conventional ZN method, and the modified fluorescent method. The significance of the modified fluorescent method over the conventional ZN method was analyzed using the chi-square test.

Results:

Out of 108 aspirates, 102 were studied and remaining 6 were excluded from the study due to diagnosis of malignancy in 4.04% (4/6) and inadequate aspiration in 2.02% (2/6). Among the 102 aspirates, 44.11% (45/102) were positive for AFB on the conventional ZN method, 58.9% (60/102) were indicative of TB on cytology, while the smear positive increased to 81.37% (83/102) on the modified fluorescent method.

Conclusions:

Fluorescent microscopy has the advantage of speed and ease of screening, and reduces observer fatigue. The modified fluorescent method was found to be more advantageous than routine cytology and conventional ZN method, particularly in paucibacillary cases. The bacillary positivity rates were higher in the modified fluorescent method than in the ZN method. Hence, the modified fluorescent method can be an adjuvant when used with routine cytology for the identification of AFB.
Dirty laundry: Committee disasters, what happened, what we learned
Authors: Bosak Jon , Cournane Mavis , Durusau Patrick , Mason James David , Orchard David , Wood Lauren
Published: July 2009

Markup standards and projects are created, managed, and sometimes destroyed through group process. While this process is often a bit bumpy, there are some occasions when it goes spectacularly badly. Tales of these committee disasters can be not only entertaining, but also (and more importantly) informative. Panelists will spend a maximum of 10 minutes each, describing a committee/working group disaster of some sort, including: what went wrong, how it could have been prevented, how it could have been (or how it was) resolved. Participants may anonymize their tales of woe, provided they assure us that the events they describe actually occurred and that that they were actually involved.
REST Oriented Architectures (ROA): Taking a resourceful approach to web data
Authors: Cagle Kurt
Published: July 2009

Resource Oriented Architectures use the fundamental characteristics of the web itself in order to provide and update content on the web. While much of the philosophy concerning REST has been around since the early 1990s, the tools for turning these philosophies into working systems are only now becoming feasible. The fundamental tenets of ROA — that the web itself is primarily a giant database, that resources are abstractions that can be manifest in different representations, that a query-oriented resource architecture is more robust than a verb-oriented services architecture, and that a common publishing and syndication protocol is necessary to make such an architectural system work — are being adopted increasingly by people who realize that services oriented architecture are not effective at getting data from users or providing it to them in an easy to use way, but that ROA can do precisely that.

Such a shift in perception is necessary but will nonetheless take a while to happen. It's necessary because the amount of information on the web is piling up faster than it can be indexed, and because under the current architectures the cost of developing "editors" for that data is prohibitive compared to the value of that information. It's necessary because the data within organizations is getting more complex than can be readily handled with a name/value approach to application development, and is increasingly contained within non-traditional data sources — Excel spreadsheets or Microsoft Word documents, for instance, or external data streams.

Adoption will take time, however, because such an approach reduces the competitive barrier impedence that corporations can utilize to sell services, because it will take time to educate people in the underlying technologies and because there is a long-standing belief that ROA and SOA systems are incompatible. The rapidity at which companies lined up behind AtomPub, on the other hand, points to the fact that many IT organizations recognize the value to themselves that an AtomPub-type architecture opens up, while the educational curve is frankly true of most technologies — it will happen, slower than its proponents may hope but faster than its critics anticipate.
Linking Page Images to Transcriptions with SVG
Authors: Cayless Hugh A.
Published: July 2009

This paper will present the results of ongoing experimentation with the linking of manuscript images to TEI transcriptions. The method being tested involves the automated conversion of images containing text to SVG, using Open Source tools. Once the text has been converted to SVG paths, these can be grouped in the document to mark the words therein and these groups can then be linked using standard methods to tokenized versions of the transcriptions. The goal of these experiments is to achieve a much more fine-grained linking and annotation mechanism than is so far possible with available tools, e.g. the Image Markup Tool and TEI P5 facsimile markup, both of which annotate only rectangular sections of an image. The method envisioned here would produce a legible tracing of the word, expressed in XML, to which transcripts and annotations might be attached and which can be superimposed upon the original image.
Translation between RDF and Topic Maps: Divide and Translate
Authors: Dichev Christo , Dicheva Darina , Ditcheva Boriana , Moran Mike
Published: July 2009

This paper addresses the issue of sharing and integrating data across RDF and Topic Map representations. The novel aspect of tackling the RDF - Topic Maps interoperability problem is the attempt to identify the right balance between the following key aspects: (i) semantics-preserving data translation; (ii) completeness of the translation; (iii) pragmatics and usability of the translation. The proposed strategy towards achieving this goal is based on exploiting the ontological correspondence between RDF and Topic Maps. The design focus is placed on a translation respecting the meaning and the readability of the RDF - Topic Maps translation. The paper analyzes the feasibility of the interoperability task, presents some requirements derived from this analysis, and proposes a method for RDF - Topic Maps translation. The proposed method is implemented as a plug-in of the TM4L topic maps editor.
Office Suite Markup: Is it worthwhile?
Authors: Durusau Patrick
Published: July 2009

There is a lot of smoke but is there any fire? Microsoft, Sun, IBM, Oracle, Google, Redhat and others are contending over two XML vocabularies for office documents (word processor, spread sheet, presentation tool, etc.) at the moment. Fans of OOXML or ODF are hard to find among people who have spent the last twenty years researching and developing markup and markup systems. In fact, many in the markup community dismiss these efforts as unimportant and/or uninteresting. Patrick Durusau, the editor of ODF and who has called for the co-evolution of OOXML and ODF in an ISO context thinks they are important, possibly very important. Come find out what has captured the interest of at least one topic map and overlapping markup theorist.
Using Atom Categorization to Build Dynamic Applications
Authors: Miłowski R. Alexander
Published: July 2009

Atom feeds provide the ability to categorize both the feed and its entries. This categorization provides a simple and easy way for feed authors to associated terms and semantics to their feed contents. By using this categorization, authors can keep their information organized while re-purposing them to build dynamic web applications.
The Apache Qpid XML Exchange
Authors: Robie Jonathan
Published: July 2009

XML is widely used for messaging applications. Message-oriented Middleware (MOM) is a natural fit for XML messaging, but it has been plagued by a lack of standards. Each vendor's system uses its own proprietary protocols, so clients from one system generally can not communicate with servers from another system. Developers who are drawn to XML because it is simple, open, interoperable, language independent, and platform independent often use REST for messaging because it shares the same virtues. When XML developers need high-performance, guaranteed delivery, transactions, security, management, asynchronous notification, or direct support for common messaging paradigms like point-to-point, broadcast, request/response, and publish/subscribe, they have been forced to sacrifice some of the virtues that drew them to XML in the first place. Java JMS is an API, defined only for Java, and it does not define a wire protocol that would allow applications running on different platforms or written in different languages to interoperate. SOAP and Web Services offer interoperability if the same underlying protocols are used and if the same WSI-protocol is used by all parties, but at the cost of more complexity than a MOM system. And as the basic components of enterprise messaging have been added piece by piece to the original specifications, Web Services have become complex, defined in a large number of overlapping specifications, without a coherent and simple architecture.

The new Advanced Message Queueing Protocol (AMQP) is an open, language independent, platform independent standard for enterprise messaging. It provides precisely the coherent and simple architecture that has been missing for sophisticated messaging applications. Red Hat Enterprise MRG includes a multi-language, multi-platform, open source implementation of AMQP. We develop the messaging component as part of the upstream Apache Qpid project. In order to meet the needs of XML messaging systems, we contributed the Apache Qpid XML Exchange, which provides XQuery-based routing for XML content and message properties. Together, AMQP, Apache Qpid, and the Qpid XML Exchange provide a solid foundation for mission critical XML messaging applications.
Parser Possibilities: Why Write A Markup Parser
Authors: Smith Norman Earl
Published: July 2009

In the early days of XML, there seemed to be a new XML parser just about every week. This was in stark contrast to SGML where there might be half a dozen working parsers ever written. As XML matured and SAX became the first defacto XML parser API, the new parser stream pretty much slowed to a trickle. Once robust XML parsers, such as Expat, became widely available, there seemed little reason left to write you own parser. Expat is robust, fast, and still provides the XML under pinnings for many programming languages.

I believe there remain many valid reasons for writing your own markup language parser. This paper identifies reasons you might want to write a custom parser and examines the choices I made writing mlParser.
Markup Discontinued
Authors: Sperberg-McQueen C. M. , Huitfeldt Claus
Published: July 2009

That the textual phenomena of interest for markup are not always hierarchically arranged is well known and widely discussed. Less frequently discussed is the fact that they are also not always contiguous, so that the units of our analysis cannot always correspond to single elements in the document. Various notations for discontinuous elements exist, but the mapping from those notations to data structures has not been well analysed or understood. And as far as we know, there are no standard mechanisms for validating discontinuous elements. We propose a data structure (a modification of the Goddag structure) to better handle discontinuous elements: we relax the rule that every pair of elements where one contains the other be related by a path of parent/child links. Parent/child links are then not an automatic result of containment. We conclude with a brief sketch of the issues involved in extending current validation mechanisms to handle discontinuity.
A non-backwards-compatible update: a difficult decision
Authors: Lapeyre Deborah Aleyne
Published: July 2009

The U.S. National Library of Medicine (NLM) Journal/Book Tag Sets have been widely adopted by libraries, archives, and commercial publishers. The users are widely distributed, generally unknown to each other, and in many cases unknown to the Tag Set advisory group, owners, and secretariat. The first five revisions to the Tag Sets were backwards compatible, but the most recent is not. The decision to make a non-backwards-compatible revision was not taken lightly. It was made based on several factors, including a decision to favor the needs of future users over the convenience of current users.
Versioning fundamentals
Authors: Orchard David
Published: July 2009

Active XML vocabularies change over time, undergoing the inevitable evolution called versioning. Versioning means adding, deleting, or changing the elements, element content, number of occurrences, attributes, or attribute values described by an XML schema. Approaches to versioning fall into several classes, including compatible, backwards-compatible, forwards-compatible, and strategy-what-strategy. Specific rules enable the successful use of these strategies, such as the "must ignore unknowns" rule, the "must understand models" rule, and prescriptions for the use of version identifiers. Basic versioning concepts and vocabulary will be illustrated using a set-based model for determining compatibility.
Managing multiple vocabularies across a global enterprise
Authors: Shifrin Laurel
Published: July 2009

Organizations share vocabularies across disparate user groups and data to maximize the value of their investment in XML, and, without question, those XML vocabularies need to change as the businesses evolve and expand. Managing change to DTDs and schemas is difficult enough with a small group of co-located users working on the same content types. What happens when you have hundreds of XML consumers spread across the globe and they have completely different requirements, systems, and content? Get a view of the challenges of implementing change management and vocabulary versioning on a very large scale.
A Substrate‐Selective Nanoreactor Made of Molecularly Imprinted Polymer Containing Catalytic Silver Nanoparticles
Authors: Li Song jun , Gong Shaoqin
Published: July 2009

An original, substrate‐selective nanoreactor is designed and characterized. The nanoreactor made of a 4‐nitrophonel (NP)‐imprinted polymer and Ag nanoparticles, can specifically recognize NP compared with its analogues 4‐nitrophenyl acetate (NPA) and 2,6‐dimethyl‐4‐nitrophenol (DNP). Under comparable conditions, this nanoreactor significantly accelerated the reduction of NP; however, much less acceleration is shown for its analogues. Unlike traditional Ag nanoreactors, which lack molecular recognition abilities, this unique nanoreactor is composed of molecularly imprinted networks, making substrate‐selective catalysis feasible.
Validation of self‐reported occupational exposures in meatpacking workers
Authors: Lander Lina , Sorock Gary , Stentz Terry L. , Eisen Ellen A. , Mittleman Murray , Hauser Russ , Perry Melissa J.
Published: July 2009

Objective

The ability of workers to accurately recall exposures that occur on the day of their injury is considered a potential limitation of case‐crossover studies. This study assessed validity of occupational exposures reported by uninjured workers at a Midwestern meatpacking plant.

Methods

One hundred thirty‐six workers were observed for 60 min while working and then interviewed within 8 days (median 3 days) about exposures during the observation period. The level of agreement between self‐reports and direct observations was assessed using kappas and intraclass correlation coefficients.

Results

Excellent agreement was found between observed and reported work location (κ = 0.97, 95% CI: 0.92–1.0), task (κ = 0.83, 95% CI: 0.76–0.91) and tools used (κ = 0.88, 95% CI: 0.81–0.95). Personal protective equipment varied by work type and location, and agreement between observed and reported usage varied from excellent to poor for various items. Excellent agreement was found for tool sharpening (κ = 0.89, 95% CI: 0.82–0.97); good agreement for occurrence of break during the observation period (κ = 0.60, 95% CI: 0.45–0.74); and poor agreement for equipment malfunction, line stoppages, being tired, unusual task, unusual work method, being distracted, rushing, slipping, or falling.

Conclusions

Agreement between observed and reported occupational exposures varied widely. Self‐reported exposures are utilized in many occupational studies, and future exposure validity assessment studies should continue to improve retrospective study methods. Valid exposures will allow researchers to better understand injury etiology and ultimately prevent injuries from occurring. Am. J. Ind. Med. Am. J. Ind. Med. 52:707–715, 2009. © 2009 Wiley‐Liss, Inc.
Familial congenital unilateral cerebral ventriculomegaly: Delineation of a distinct genetic disorder
Authors: Zaki Maha S. , Afifi Hanan H. , Barkovich AJ. , Gleeson Joseph G.
Published: July 2009

We identified two female siblings, derived from healthy first cousin parents, with congenital unilateral cerebral ventriculomegaly detected prenatally. Patient 1 underwent ventriculoperitoneal shunt operation at 1 week old, while Patient 2 was followed without surgical intervention. Both patients presented with mild developmental delay and hemiparesis contralateral to the involved hemisphere. Focal seizures were observed in Patient 1, whose neuroimaging revealed posterior insular polymicrogyria in the normal sized ventricle hemisphere and retrocerebellar cyst. Both siblings displayed near absence of white matter with marked thinning of the overlying cortex in the affected hemisphere and very thin corpus callosum. Investigations revealed no other system involvement and karyotyping was normal. Normal TORCH screening in subsequent pregnancies, normal parental coagulation profile and undetectable maternal autoantibodies suggested against the possible role of extrinsic factors as an etiological factor for unilateral ventriculomegaly. Parents had normal brain imaging findings. We suggest delineation of a distinct developmental brain defect, most likely of autosomal recessive inheritance. © 2009 Wiley‐Liss, Inc.
Suggestive evidence for linkage of ADHD features in bipolar disorder to chromosome 10p14
Authors: Joo Eun‐Jeong , Greenwood Tiffany A. , Schork Nicholas , McKinney Rebecca A. , Sadovnick A. Dessa , Remick Ronald A. , Keck Paul E. , McElroy Susan L. , Kelsoe John R.
Published: July 2009

Higher rates of bipolar disorder amongst the first‐degree relatives of probands with ADHD, and increased rates of ADHD in the relatives of bipolar probands have been reported in many studies. This suggests some commonality in the genetic basis for bipolar disorder and ADHD. We hypothesized that ADHD symptoms in bipolar disorder may access a quantitative subphenotype that is genetically less complex and therefore advantageous for mapping studies. The Wender Utah Rating Scale (WURS) was used to quantify ADHD features in 57 bipolar families collected for linkage studies. The factor structure of the WURS was first examined, and heritability was estimated. Linkage analysis was then conducted using the WURS total score and factor scores as quantitative traits. Three factors were identified: impulsivity and defiant behavior, mood instability and anxiety, and inattention. The total WURS and factor scores were each significantly heritable ($0.34 < {\rm h}_{\rm r}^2 < 0.49$) in bipolar families. The inattention factor obtained maximum evidence of linkage on chromosome 10p14 (LOD = 3.35, 25 cM). A LOD score of 2.06 for the total WURS score was found on chromosome 12q24 region. Childhood ADHD features in patients with bipolar disorder are heritable and may represent a genetically distinct dimension of illness. 10p14, in particular may contain a locus for inattention in bipolar disorder. Quantitative dimensional phenotypes such as this may be useful for both mapping of genes and understanding the role of genes in bipolar disorder. © 2009 Wiley‐Liss, Inc.
Chimpanzee seed dispersal quantity in a tropical montane forest of Rwanda
Authors: Gross‐Camp Nicole D. , Masozera Michel , Kaplin Beth A.
Published: July 2009

We describe chimpanzee seed dispersal in the tropical montane forest of Nyungwe National Park (NNP), Rwanda, for a total of three years from January 1998 through May 2000 and May 2006 through March 2007. Relatively few studies have examined chimpanzee seed dispersal in montane communities where there are generally fewer fruiting tree species than in lowland forests. Such studies may reveal new insights into chimpanzee seed dispersal behaviors and the role that they play in forest regeneration processes. Chimpanzees are large‐bodied, highly frugivorous, and tend to deposit the seeds of both large‐ and small‐seeded fruits they consume in a viable state. We found that chimpanzees dispersed a total of 37 fruiting species (20 families) in their feces, 35% of which were large‐seeded trees (≥0.5 cm). A single large‐seeded tree, Syzygium guineense, was the only species to be dispersed in both wadges and feces. Based on phenological patterns of the top five large‐seeded tree species found in chimpanzee feces, our results indicate that chimpanzees do not choose fruits based on their availability. There was, however, a positive relationship between the presence of Ekebergia capensis seeds in chimpanzee feces and S. guineense seeds in chimpanzee wadges and their respective fruit availabilities. Our data reveal that proportionately fewer chimpanzee fecal samples at NNP contained seeds than that reported in two other communities in the Albertine Rift including one at mid‐elevation and one in montane forest. As in other chimpanzee communities, seeds of Ficus spp. were the most common genus in NNP chimpanzee feces. Our data do not support previous studies that describe Ficus spp. as a fallback food for chimpanzees and highlights an intriguing relationship between chimpanzees and the large‐seeded tree species, S. guineense. Am. J. Primatol. 71:901–911, 2009. © 2009 Wiley‐Liss, Inc.