bluuebunny/crossref_metadata_2025_split huggingface dataset:
Model-driven user interfaces for bioinformatics data resources: regenerating the wheel as an alternative to reinventing it
Authors: Garwood Kevin , Garwood Christopher , Hedeler Cornelia , Griffiths Tony , Swainston Neil , Oliver Stephen G , Paton Norman W 
Published: December 2006

Abstract

Background
The proliferation of data repositories in bioinformatics has resulted in the development of numerous interfaces that allow scientists to browse, search and analyse the data that they contain. Interfaces typically support repository access by means of web pages, but other means are also used, such as desktop applications and command line tools. Interfaces often duplicate functionality amongst each other, and this implies that associated development activities are repeated in different laboratories. Interfaces developed by public laboratories are often created with limited developer resources. In such environments, reducing the time spent on creating user interfaces allows for a better deployment of resources for specialised tasks, such as data integration or analysis. Laboratories maintaining data resources are challenged to reconcile requirements for software that is reliable, functional and flexible with limitations on software development resources.

Results
This paper proposes a model-driven approach for the partial generation of user interfaces for searching and browsing bioinformatics data repositories. Inspired by the Model Driven Architecture (MDA) of the Object Management Group (OMG), we have developed a system that generates interfaces designed for use with bioinformatics resources. This approach helps laboratory domain experts decrease the amount of time they have to spend dealing with the repetitive aspects of user interface development. As a result, the amount of time they can spend on gathering requirements and helping develop specialised features increases. The resulting system is known as Pierre, and has been validated through its application to use cases in the life sciences, including the PEDRoDB proteomics database and the e-Fungi data warehouse.

Conclusion
MDAs focus on generating software from models that describe aspects of service capabilities, and can be applied to support rapid development of repository interfaces in bioinformatics. The Pierre MDA is capable of supporting common database access requirements with a variety of auto-generated interfaces and across a variety of repositories. With Pierre, four kinds of interfaces are generated: web, stand-alone application, text-menu, and command line. The kinds of repositories with which Pierre interfaces have been used are relational, XML and object databases.
Microdialysis shows metabolic effects in skin during fluid resuscitation in burn-injured patients
Authors: Samuelsson Anders , Steinvall Ingrid , Sjöberg Folke 
Published: December 2006

Abstract
Introduction
Established fluid treatment formulas for burn injuries have been challenged as studies have shown the presence of tissue hypoxia during standard resuscitation. Such findings suggest monitoring at the tissue level. This study was performed in patients with major burn injuries to evaluate the microdialysis technique for the continuous assessment of skin metabolic changes during fluid resuscitation and up to four days postburn.

Methods
We conducted an experimental study in patients with a burn injury, as represented by percentage of total body surface area burned (TBSA), of more than 25% in a university eight-bed burns intensive care unit serving about 3.5 million inhabitants. Six patients with a median TBSA percentage of 59% (range 33.5% to 90%) and nine healthy controls were examined by intracutaneous MD, in which recordings of glucose, pyruvate, lactate, glycerol, and urea were performed.

Results
Blood glucose concentration peaked on day two at 9.8 mmol/l (6.8 to 14.0) (median and range) and gradually declined on days three and four, whereas skin glucose in MD continued to increase throughout the study period with maximum values on day four, 8.7 mmol/l (4.9 to 11.0). Controls had significantly lower skin glucose values compared with burn patients, 3.1 mmol/l (1.5 to 4.6) (p < 0.001). Lactate from burn patients was significantly higher than controls in both injured and uninjured skin (MD), 4.6 mmol/l (1.3 to 8.9) and 3.8 mmol/l (1.6 to 7.5), respectively (p < 0.01). The skin lactate/pyruvate ratio (MD) was significantly increased in burn patients on all days (p < 0.001). Skin glycerol (MD) was significantly increased at days three and four in burn patients compared with controls (p < 0.01).

Conclusion
Despite a strategy that fulfilled conventional goals for resuscitation, there were increased lactate/pyruvate ratios, indicative of local acidosis. A corresponding finding was not recorded systemically. We conclude that MD is a promising tool for depicting local metabolic processes that are not fully appreciated when examined systemically. Because the local response in glucose, lactate, and pyruvate metabolism seems to differ from that recorded systemically, this technique may offer a new method of monitoring organs.
Immunosurveillance and Survivin-Specific T-Cell Immunity in Children With High-Risk Neuroblastoma
Authors: Coughlin Christina M. , Fleming Mark D. , Carroll Richard G. , Pawel Bruce R. , Hogarty Michael D. , Shan Xiaochuan , Vance Barbara A. , Cohen Jarish N. , Jairaj Sonya , Lord Elaina M. , Wexler Michael H. , Danet-Desnoyers Gwenn-aël H. , Pinkus Jack L. , Pinkus Geraldine S. , Maris John M. , Grupp Stephan A. , Vonderheide Robert H. 
Published: December 2006

PurposeTumor immunosurveillance influences oncogenesis and tumor growth, but it remains controversial whether clinical failure of immunosurveillance is a result of lymphocyte dysfunction or tumor escape. In this study, our goal was to characterize the physiology of tumor immunosurveillance in children with high-risk neuroblastoma (HR-NBL).Patients and MethodsImmunohistopathologic studies were carried out on 26 tumor samples from a cohort of HR-NBL patients diagnosed at Children's Hospital of Philadelphia for the 2-year period from May 2003 to May 2005. Blood from nine HLA-A2+patients in this cohort was analyzed for T cells specific for the antiapoptotic protein survivin.ResultsSurvivin protein was expressed by 26 of 26 tumors. In HLA-A2+patients, circulating cytotoxic T lymphocytes (CTLs) specific for survivin were detected by peptide/major histocompatibility complex tetramer analysis in the blood of eight of nine children with HR-NBL at the time of diagnosis. Rather than being selectively rendered anergic in vivo, circulating survivin-specific CTLs were highly functional as shown by cytotoxicity and interferon gamma enzyme-linked immunospot assays in six of nine patients. Survivin-specific CD107a mobilization by T cells was found in five of five patients. By immunohistochemistry, tumor-infiltrating T cells were few or absent in 26 of 26 tumors.ConclusionChildren with HR-NBL harbor robust cellular immune responses to the universal tumor antigen survivin at the time of diagnosis, but intratumoral T cells are strikingly rare, suggesting a failure of cellular immunosurveillance. Efforts to develop novel therapies that increase T-cell trafficking into tumor nests are warranted.
On the depth and scale of metabolic rate variation: scaling of oxygen consumption rates and enzymatic activity in the Class Cephalopoda(Mollusca)
Authors: Seibel Brad A. 
Published: December 2006

SUMMARYRecent ecological theory depends, for predictive power, on the apparent similarity of metabolic rates within broad taxonomic or functional groups of organisms (e.g. invertebrates or ectotherms). Such metabolic commonality is challenged here, as I demonstrate more than 200-fold variation in metabolic rates independent of body mass and temperature in a single class of animals,the Cephalopoda, over seven orders of magnitude size range. I further demonstrate wide variation in the slopes of metabolic scaling curves. The observed variation in metabolism reflects differential selection among species for locomotory capacity rather than mass or temperature constraints. Such selection is highest among epipelagic squids (Lolignidae and Ommastrephidae)that, as adults, have temperature-corrected metabolic rates higher than mammals of similar size.
Analyzing the effect of wind on flight: pitfalls and solutions
Authors: Shamoun-Baranes Judy , van Loon Emiel , Liechti Felix , Bouten Willem 
Published: December 2006

SUMMARY
How flying organisms alter their air speed in response to wind is important in theories of flight energetics. Numerous studies have investigated the relationship between air and wind as a function of ground speed and air speed. This study shows that this approach can lead to erroneous results, due to spurious correlations. An alternative way to analyze air speed is proposed that overcomes the problems of one-dimensional linear models. The new model is non-linear and has two explanatory variables. Using two synthetic data sets with known properties and a data set with real observations of migratory bird tracks and wind observations, we illustrate the weaknesses of the conventional analysis as well as the strengths of the newly proposed model. This leads to the conclusion that for many studies a reanalysis of the effect of wind on air speed is desirable.
Reversibly labile, sclerotization-induced elastic properties in a keratin analog from marine snails: whelk egg capsule biopolymer (WECB)
Authors: Rapoport H. Scott , Shadwick Robert E. 
Published: December 2006

SUMMARY
Egg capsules from two caenogastropod whelks, Busycon canaliculatumand Kelletia kelletii, were studied to investigate the genesis of mechanical properties of nascent capsules and to formulate a biomechanical model of this material. Scanning electron microscopy revealed that the capsules possess fibrous hierarchical arrangements at all stages during processing while the mechanical integrity is developing. This suggests that an as yet uncharacterized sclerotization mechanism occurring in the ventral pedal gland primarily binds these fibrous components together. Decomposing the mechanical behavior of WECB through various physical and chemical treatments led us to develop a model for the structure and mechanical properties of this material that supports its designation as a keratin analog. Keratin mechanical models were applied to WECB in its representation as an intermediate state between matrix-free intermediate filament (IF)-type proteins and the more complex composite materials incorporating IFs such as keratin.
Phenotypic flexibility in the basal metabolic rate of laughing doves:responses to short-term thermal acclimation
Authors: McKechnie Andrew E. , Chetty Kinesh , Lovegrove Barry G. 
Published: December 2006

SUMMARYMany birds exhibit considerable phenotypic flexibility in maintenance energy requirements, and up- or downregulate basal metabolic rate (BMR) over time scales of days to weeks during thermal acclimation. However, the extent to which individual birds can reverse the direction of BMR adjustments over short time scales remains unknown. In this study, we examined metabolic responses to short-term thermal acclimation in laughing doves Streptopelia senegalensis. In 30 wild-caught doves (mean body mass=92.6 g) divided into three experimental groups of 10 birds each, initial BMR averaged 0.760±0.036 W. Thereafter, each group was acclimated to one of three acclimation air temperatures (Tacc=10, 22 or 35°C) for 21 days, during which time the doves were housed in individual cages. Following the first acclimation period (acclimation I), BMR (W) was significantly lower and was negatively and linearly related to Tacc [BMR=0.714-0.005Tacc]. Acclimation I BMR varied from 0.546±0.039 W in doves acclimated to Tacc=35°C to 0.665±0.058 W at Tacc=10°C. A second acclimation period of a further 21 days (acclimation II) revealed that the direction of BMR adjustments could be reversed within individuals, with acclimation II BMR again negatively and linearly related to Tacc. The slope of the relationship between BMR and Tacc following acclimation II was not significantly different to that following acclimation I. BMR exhibited consistent inter-individual variation, with a low but significant repeatability of 0.113. The within-individual BMR variation of up to 26% that we observed in laughing doves reveals that BMR is a highly flexible trait in this species, and reiterates the need to take phenotypic plasticity into account in comparative analyses of avian energetic parameters.
Chemicalversusmechanical bioerosion of coral reefs by boring sponges - lessons fromPione cf. vastifica
Authors: Zundelevich A. , Lazar B. , Ilan M. 
Published: December 2006

SUMMARYBioerosion by boring sponges is an important mechanism shaping the structure of coral reefs all around the world. To determine the excavation rate by boring sponges, we developed a system in which chemical and mechanical boring rates [calcium carbonate (CaCO3) dissolution and chip production, respectively] were measured simultaneously in experimental tanks containing reefal rock inhabited by a boring sponge. Pione cf. vastifica (Hancock 1849) was chosen as a model species to study the erosion rate of boring sponges. It is an abundant species in the coral reefs of the Nature Reserve Reef, Elat, Gulf of Aqaba, northern Red Sea, reaching maximum abundance at 25-30 m. The rate of chemical bioerosion was determined from the increase in tank-seawater alkalinity over time, and the mechanical bioerosion rate was estimated from the total amount of CaCO3 chips produced over the same time interval. The measured bioerosion rate of P. cf. vastifica was 2.3 g m-2 sponge day-1, showing seasonal but not diurnal variations, suggesting that the zooxanthellae harboring the sponge have no effect on its boring rate. The experiments indicated clearly that per each mass of chips that P. cf. vastificaproduces during its boring activity, it dissolves three masses of reef CaCO3 framework. Assuming that some additional boring sponges can use a similar strategy of bioerosion, these findings suggest that chips, the most obvious erosion products of boring sponges, represent only a small fraction of boring sponge bioerosion capacity.
Feeding, fins and braking maneuvers: locomotion during prey capture in centrarchid fishes
Authors: Higham Timothy E. 
Published: December 2006

SUMMARYLocomotion is an integral aspect of the prey capture strategy of almost every predatory animal. For fishes that employ suction to draw prey into their mouths, locomotor movements are vital for the correct positioning of the mouth relative to the prey item. Despite this, little is known regarding the relationships between locomotor movements and prey capture. To gain insights into how fishes move during prey capture and the mechanisms underlying deceleration during prey capture, I measured the fin and body movements of largemouth bass, Micropterus salmoides, and bluegill sunfish, Lepomis macrochirus. Using a high-speed video camera (500 frames s-1), I captured locomotor and feeding movements in lateral and ventral (via a mirror) view. Largemouth bass swam considerably faster than bluegill during the approach to the prey item, and both species decelerated substantially following prey capture. The mean magnitude of deceleration was significantly higher in largemouth bass (-1089 cm s-2) than bluegill (-235 cm s-2), and the timing of maximum deceleration was much later for largemouth bass (30.3 ms after maximum gape) than bluegill (6.7 ms after maximum gape). Both species employed their pectoral, anal and caudal fins in order to decelerate during prey capture. However, largemouth bass protracted their pectoral fins more and faster,likely contributing to the greater magnitude of deceleration in the species. The primary mechanism for increased deceleration was an increase in approach speed. The drag forces experienced by the fins and body are proportional to the velocity of the flow squared. Thus, the braking forces exerted by fins,without any change in kinematics, will increase exponentially with small increases in swimming speed, perhaps allowing these fishes to achieve higher braking forces at higher swimming speeds without altering body or fin kinematics. This result can likely be extended to other maneuvers such as turning.
Preparation of Ag Core–Cu Shell Nanoparticles by Microwave-assisted Alcohol Reduction Process
Authors: Nakamura Takashi , Tsukahara Yasunori , Yamauchi Tomohisa , Sakata Takao , Mori Hirotaro , Wada Yuji 
Published: December 2006

Abstract
We have succeeded in rapidly preparing Ag core–Cu shell nanoparticles (denoted as Cu/Ag nanoparticles) having 10–40 nm in size by a microwave (MW)-assisted alcohol reduction process. The core–shell nanoparticles were prepared by step-by-step successive reduction of a silver precursor and then of a copper precursor added after the formation of silver nanoparticles in 1-heptanol.
Photoluminescence Property of Titanate Layered Oxide Intercalated with Tb3+ Ions by Electrostatic Self-assembly Deposition Method
Authors: Ida Shintaro , Ogata Chikako , Inoue Taishi , Izawa Kazuyoshi , Unal Ugur , Altuntasoglu Ozge , Matsumoto Yasumichi 
Published: December 2006

Abstract
Titanate layered oxide intercalated with Tb3+ ions was prepared by electrostatic self-assembly deposition method using the exfoliated H2Ti4O9 (Ti4O9 nanosheet). The naked Tb3+ green emission through energy transfer from Ti4O9 nanosheet was observed. The efficiency of the energy transfer decreased with decrease in the layer distance.
Adolf Harnacks Vorlesung über ‚Encyklopädie der Theologie‘ (1884)
Authors: Steck Friedemann 
Published: December 2006

Abstract
In the course of his active teaching career of over fifty years, Adolf von Harnack only once lectured on the „Encyclopaedia of Theology“. This occured in the summer of 1884 when he was a young university professor in Gießen, lecturing twice a week from 9 to 10 in the morning. The handwritten script of the dictation booklet (36 pp.) has so far gone unnoticed in the literature. It is documented here for the first time and in a full reproduction. These lecture notes present a condensed, overall impression of Harnack's concept of theology, probably unlike any other his texts. Of particular interest is the detailed outline of a concept of religion that Harnack developed through an intense examination of drafts on this topic by Friedrich Schleiermacher and Albrecht Ritschl as well as Ritschl's prominent students, Julius Kaftan and Wilhelm Herrmann. Within the history of Harnack's opus, the lecture for the Encyclopaedia was done in close working relationship with the great literary project of the Lehrbuch der Dogmengeschichte (1885–89).
Theologiestudium in Tübingen vor 100 Jahren – im Spiegel der Briefe des Studienanfängers Paul Althaus an seine Eltern
Authors: Jasper Gotthard 
Published: December 2006

Abstract
In view of the subsequent career of the leading Lutheran theologian Paul Althaus (1888–1966), the student letters reproduced here obtain considerable biographical weight: 1913 doctorate in Göttingen, 1914 habilitated and a privatdozent, during the war an volunteer orderly, then a hospital and provincial pastor in Lodz, 1919–1924 Professor in Rostock, 1924–1966 Professor of systematic theology and New Testament exegesis in Erlangen. Althaus' letters shed light on the family and confessional traditions in which he originated, just as they do on his connections with a fervent church as well as a national and patriotic life. In addition, they illustrate the outstanding powers of observation and formulation as well as the intelligence and wide interests of the young student, all qualities of importance for his later career. In addition, the student letters of the 18–19 year old Paul Althaus describe the conditions of studying in Tübingen a hundred years ago. The professors then instructing there, among them, especially Adolf Schlatter, are also vividly described in their various roles, just as the letters richly narrate aspects of the general conduct of studies, life in fraternities – Althaus was active in the Nicaren, a non-duelling Christian association – as well as the many student rambles through the woods.
Dynamische Drehmomentmessung. Drehmomentaufnehmer in Leistungsprüfständen (Dynamic Torque Measurement. Torque Transducers in Power Test Stands)
Authors: Andrae Jürgen , Wegener Georg 
Published: December 2006

In diesem Beitrag soll näher darauf eingegangen werden, wie dynamische Drehmomente in Leistungsprüfständen entstehen und welche Auswirkungen sie auf den Drehmomentaufnehmer und auf das Messsignal haben.
Als dynamische Drehmomentquellen fungieren Verbrennungsmotoren sowie elektrische Antriebe, aber auch parasitäre Einflüsse können dynamische Drehmomentanteile erzeugen. Aufgrund des mechanischen Übertragungsverhaltens des Wellenstrangs, in den der Drehmomentaufnehmer integriert ist, können die erzeugten dynamischen Belastungen als Anregung für Torsions-, Axial- und Biegeschwingungen fungieren. Die Kenntnis oder Abschätzung dieser Belastungen sind für die Auswahl eines geeigneten Drehmomentaufnehmers entscheidend.
Mechanisms of pathogenesis in Chagas disease
Authors: Kierszenbaum Felipe 
Published: December 2006

AbstractChagas disease, caused by the obligate unicellular parasite Trypanosoma cruzi, presents itself in a diverse collection of clinical manifestations, ranging from severe, fatal heart and digestive tract pathologies to unapparent or minor alterations that do not compromise survival. Over the years, a number of mechanisms have been proposed to explain the pathogenesis of chagasic tissue lesions, all of which have faced some criticism or been received with skepticism. This article excludes the autoimmunity hypothesis for Chagas disease because it has been extensively reviewed elsewhere, and summarizes the various alternative hypotheses that have been advanced over the years. For each of these hypotheses, an outline of its main tenets and key findings that support them is presented. This is followed by the results and comments that have challenged them and the caveats that stand on their way to wider acceptance. It is hoped that this writing will draw attention to our shortcomings in understanding the pathogenesis of Chagas disease, which, unfortunately, continues to figure among the most serious health problems of the American continent.
Selective retrieval and induced forgetting in eyewitness memory
Authors: Migueles Malen , García‐Bajos Elvira 
Published: December 2006

AbstractThis study analyses retrieval‐induced forgetting (RIF) in eyewitness memory. Selective retrieval of specific information about an event could cause eyewitnesses to forget related contents. Based on a video of a man being robbed while withdrawing money from a cash machine, we examined the effects of partial retrieval on the most relevant aspects of the event: actions (Experiment 1) and offender characteristics (Experiment 2), in both immediate and long‐term recall (24 hours). In both experiments long‐term recall was a replica of immediate recall for correct information as well as errors. The effects of partial retrieval practice were also repeated in long‐term recall. Conventional RIF was found for offender characteristics but selective retrieval of the actions of the event produced no comparable effect. It is assumed that the organisation and integration of the actions of the event protected them from RIF. Copyright © 2006 John Wiley & Sons, Ltd.