bluuebunny/crossref_metadata_2025_split huggingface dataset:
A large new subset of TRIM genes highly diversified by duplication and positive selection in teleost fish
Authors: van der Aa Lieke M , Levraud Jean-Pierre , Yahmi Malika , Lauret Emilie , Briolat Valérie , Herbomel Philippe , Benmansour Abdenour , Boudinot Pierre 
Published: February 2009

AbstractBackgroundIn mammals, the members of the tripartite motif (TRIM) protein family are involved in various cellular processes including innate immunity against viral infection. Viruses exert strong selective pressures on the defense system. Accordingly, antiviral TRIMs have diversified highly through gene expansion, positive selection and alternative splicing. Characterizing immune TRIMs in other vertebrates may enlighten their complex evolution.ResultsWe describe here a large new subfamily of TRIMs in teleosts, called finTRIMs, identified in rainbow trout as virus-induced transcripts. FinTRIMs are formed of nearly identical RING/B-box regions and C-termini of variable length; the long variants include a B30.2 domain. The zebrafish genome harbors a striking diversity of finTRIMs, with 84 genes distributed in clusters on different chromosomes. A phylogenetic analysis revealed different subsets suggesting lineage-specific diversification events. Accordingly, the number offintrimgenes varies greatly among fish species. Conserved syntenies were observed only for the oldestfintrims. The closest mammalian relatives aretrim16andtrim25, but they are not true orthologs. The B30.2 domain of zebrafish finTRIMs evolved under strong positive selection. The positions under positive selection are remarkably congruent in finTRIMs and in mammalian antiviral TRIM5α, concentrated within a viral recognition motif in mammals. The B30.2 domains most closely related to finTRIM are found among NOD-like receptors (NLR), indicating that the evolution of TRIMs and NLRs was intertwined by exon shuffling.ConclusionThe diversity, evolution, and features of finTRIMs suggest an important role in fish innate immunity; this would make them the first TRIMs involved in immunity identified outside mammals.
Susceptibility of rheumatoid arthritis synovial fibroblasts to FasL- and TRAIL-induced apoptosis is cell cycle-dependent
Authors: Pundt Noreen , Peters Marvin A , Wunrau Christina , Strietholt Simon , Fehrmann Carsten , Neugebauer Katja , Seyfert Christine , van Valen Frans , Pap Thomas , Meinecke Ingmar 
Published: February 2009

Abstract
Introduction
The rheumatoid arthritis (RA) synovium is characterised by the presence of an aggressive population of activated synovial fibroblasts (RASFs) that are prominently involved in the destruction of articular cartilage and bone. Accumulating evidence suggests that RASFs are relatively resistant to Fas-ligand (FasL)-induced apoptosis, but the data concerning tumour necrosis factor-related apoptosis-inducing ligand (TRAIL) have been conflicting. Here, we hypothesise that the susceptibility of RASFs to receptor-mediated apoptosis depends on the proliferation status of these cells and therefore analysed the cell cycle dependency of FasL- and TRAIL-induced programmed cell death of RASFs in vitro.

Methods
Synovial fibroblasts were isolated from patients with RA by enzymatic digestion and cultured under standard conditions. Cell cycle analysis was performed using flow cytometry and staining with propidium iodide. RASFs were synchronised or arrested in various phases of the cell cycle with 0.5 mM hydroxyurea or 2.5 μg/ml nocodazol and with foetal calf serum-free insulin-transferrin-sodium selenite supplemented medium. Apoptosis was induced by stimulation with 100 ng/ml FasL or 100 ng/ml TRAIL over 18 hours. The apoptotic response was measured using the Apo-ONE® Homogenous Caspase-3/7 Assay (Promega GmbH, Mannheim, Germany) and the Cell Death Detection (ELISAPlus) (enzyme-linked immunosorbent assay) (Roche Diagnostics GmbH, Mannheim, Germany). Staurosporin-treated cells (1 μg/ml) served as a positive control. Expression of Fas and TRAIL receptors (TRAILR1-4) was determined by fluorescence-activated cell sorting analysis.

Results
Freshly isolated RASFs showed only low proliferation in vitro, and the rate decreased further over time, particularly when RASFs became confluent. RASFs expressed Fas, TRAIL receptor-1, and TRAIL receptor-2, and the expression levels were independent of the cell cycle. However, the proliferation rate significantly influenced the susceptibility to FasL- and TRAIL-induced apoptosis. Specifically, proliferating RASFs were less sensitive to FasL- and TRAIL-induced apoptosis than RASFs with a decreased proliferation rate. Furthermore, RASFs that were synchronised in S phase or G2/M phase were less sensitive to TRAIL-induced apoptosis than synchronised RASFs in G0/G1 phase.

Conclusions
Our data indicate that the susceptibility of RASFs to FasL- and TRAIL-induced apoptosis depends on the cell cycle. These results may explain some conflicting data on the ability of RASFs to undergo FasL- and TRAIL-mediated cell death and suggest that strategies to sensitise RASFs to apoptosis may include the targeting of cell cycle-regulating genes.
Geometrical conditions for wedging in mechanical systems with Coulomb friction
Authors: Zhechev M M , Khramova M V 
Published: February 2009

It is known that a phenomenon referred to as wedging can occur in mechanical systems with friction. This phenomenon occurs in certain system positions, and an actual mechanical system can be started from a wedged position only at the cost of irreversible deformations. Although the results of the theoretical study of wedging are of great importance in the development and operation of process automation systems, the theory of this phenomenon is still in the making. In this work, the notion of a wedgeable system is introduced and its rigorous definition is given. Within the framework of the traditional formulation, this definition reflects the properties of wedging in actual mechanical systems in the most adequate manner. Based on this notion, a number of statements on wedging conditions in mechanical systems with two and three frictional contacts are proved. Simple, convenient in use rules are given for identifying the possibility of wedging in peg-in-hole systems with two and three frictional contacts.
Automated cell disruption is a reliable and effective method of isolating RNA from fresh snap-frozen normal and malignant oral mucosa samples
Authors: Van der Vorst Sébastien , Dekairelle Anne-France , Irenge Léonid , Hamoir Marc , Robert Annie , Gala Jean-Luc 
Published: February 2009

Abstract: This study compared automated vs. manual tissue grinding in terms of RNA yield obtained from oral mucosa biopsies.: A total of 20 patients undergoing uvulectomy for sleep-related disorders and 10 patients undergoing biopsy for head and neck squamous cell carcinoma were enrolled in the study. Samples were collected, snap-frozen in liquid nitrogen, and divided into two parts of similar weight. Sample grinding was performed on one sample from each pair, either manually or using an automated cell disruptor. The performance and efficacy of each homogenization approach was compared in terms of total RNA yield (spectrophotometry, fluorometry), mRNA quantity [densitometry of specific: Although spectrophotometry and fluorometry results were comparable for both homogenization methods,: Automated tissue homogenization appears to be a versatile, quick, and reliable method of cell disruption and is especially useful in the case of small malignant samples, which show unreliable results when processed by manual homogenization.Clin Chem Lab Med 2009;47:294–301.
Adaptive Reibkraftkompensation zur modellbasierten Positionsregelung von Nanopositionier- und NanomessmaschinenModel Based Position Control of Nanopositioning- and Nanomeasuring Machines Using an Adaptive Friction Cancellation Approach
Authors: Amthor Arvid , Zschäck Stephan , Ament Christoph 
Published: February 2009

Zusammenfassung
In der vorliegenden Arbeit wird eine modellbasierte Trajektorienfolgeregelung für Positionier-aufgaben mit Nanometerauflösung vorgestellt. Hierzu wird die dominante Störgröße Reibung durch ein physikalisch motiviertes Reibmodell nachgebildet. Dieses Modell wird auf Grundlage von experimentellen Daten offline identifiziert und anschließend in einer Vorsteuerung eingesetzt. Während der Online-Phase werden die linearen Modellparameter mittels einer rekursiven Regression adaptiert, um positionsabhängige Reibkraftschwankungen zu kompensieren. Es kann in dieser Arbeit gezeigt werden, dass verglichen mit einer klassischen Regelstrategie eine modellbasierte Regelung in der Lage ist, die Dynamik des geregelten Systems signifikant zu erhöhen. Darüber hinaus kann die Regelabweichung deutlich gesenkt werden.
Schnelle Regelung von linearen Systemen mit StellgrößenbeschränkungenFast Control of Linear Systems with Input Constraints
Authors: Lens Hendrik , Adamy Jürgen 
Published: February 2009

Zusammenfassung
In diesem Artikel wird eine nichtlineare Zustandsrückführung für Regelstrecken mit linearer Dynamik und einer Stellgrößenbeschränkung vorgestellt. Die Methode ermöglicht sehr schnelle Regelvorgänge. Erreicht wird dies durch die Verknüpfung sättigender und weicher strukturvariabler Regler. Es wird ein effizientes, LMI-basiertes Entwurfsverfahren zur Bestimmung der Reglerparameter vorgestellt. Bei Nachoptimierung der Parameter mittels Suchverfahren erreicht die Regelung eine Güte, die sehr nah an die zeitoptimale Lösung heranreicht.
Über Ontologien und deren Anwendung in der AutomatisierungstechnikTowards Ontologies and Their Application in Automation Engineering
Authors: Däubler Lorenz 
Published: February 2009

Zusammenfassung
Der Beitrag beschäftigt sich mit dem Begriff der Ontologie und seiner Anwendung in der Automatisierungstechnik. Augenmerk liegt auf den formalen Ontologiedefinitionen von Gruber und Guarino. Als Anwendung wird die Überprüfung und Identifikation von strukturellen Ähnlichkeiten (Morphismen) diskutiert, die zwischen den Ontologien unterschiedlicher Gegenstandsbereiche bestehen.
Pervasive University – A Technical PerspectiveDie Pervasive University aus technischer Perspektive
Authors: Tavangarian Djamshid , Lucke Ulrike 
Published: February 2009

Abstract
The article proposes a definition for the term “Pervasive University”. It discusses the idea, history, and implications of this architecture. Furthermore, some technical prerequisites from a technical point of view are stated: Pervasive Computing itself as well as Service-Oriented Architecture, Self Organization, and Peer-to-Peer Computing. This leads to a roadmap for the implementation of a Pervasive University.
Federated Identity Management as a Basis for Integrated Information ManagementFöderiertes Identitätsmanagement als Fundament eines Integrierten Informationsmanagements
Authors: Schell Frank , Höllrigl Thorsten , Hartenstein Hannes 
Published: February 2009

Abstract
Identity management is a key component of the authorization mechanisms that govern access to the diverse IT services offered at pervasive universities. The federation paradigm proves to be a useful tool for establishing an integrated identity management system in this setting. The main principles of federations, i. e., decentralization, subsidiarity, and mutual respect among the partners, can be applied to develop a 'bi-level′ approach to identity management. For reasons that will be explained, a bi-level system is more likely to be successful at a pervasive university than the more standard 'centralized′ approach.
Kommunikationsstrukturen in einer pervasiven Lehr- und LernumgebungAspects of Communication Systems for Pervasive Learning Environments
Authors: Hegering Heinz-Gerd , Läpple Alfred , Reiser Helmut 
Published: February 2009

Zusammenfassung
Der Begriff Pervasive Universität ist bisher nicht klar definiert. Deshalb setzt sich der Beitrag zunächst mit relevanten Lerntypen auseinander, die für die Ausprägung der benötigten Kommunikationsinfrastrukturen wichtig sind. Anhand der Lerntypen werden die Anforderungen analysiert. Neu sind neben Virtualisierung und Personalisierung der Lehr- und Lernumgebungen der ubiquitäre Zugriff und als Folge eine Unterstützung aller Mobilitätsformen und kontextsensitiver Dienste. Der Beitrag macht deutlich, dass für die Betrachtung von Kommunikationsstrukturen eine integrale Betrachtung und Einbettung in universitäre Betriebs- und Organisationsprozesse unverzichtbar ist.
Pervasive Learning – A Question of ContextPervasive Learning – Eine Frage des Kontexts
Authors: Helms Niels Henrik , Larsen Lasse Juel 
Published: February 2009

Abstract
Modern learners have access to almost unlimited resources of information and they can obtain, share and develop knowledge through a multitude of different media. Education is a way of accessing and developing knowledge and it has gotten a new meaning. Education is now about how you handle knowledge, it is not a specific place where you can access scarce information. Pervasive or ubiquitous communication opens up for taking the organizing and design of learning landscapes a step further. Furthermore it calls for theoretical developments, which can open up for a deeper understanding of the relationship between emerging contexts, design of contexts and learning.
Effects of Transportation and Other Factors on Survival Estimates of Juvenile Salmonids in the Unimpounded Lower Columbia River
Authors: Clemens Benjamin J. , Clements Shaun P. , Karnowski Mark D. , Jepsen David B. , Gitelman Alix I. , Schreck Carl B. 
Published: February 2009

AbstractWe estimated the survival of juvenile salmonids out‐migrating through the lower Columbia River to the Pacific Ocean. We tested the null hypotheses that no association exists between survival and transportation type (including barge transportation and in‐river migration with no transportation), release date, river flow, mean body weight, and tag type. During 2002‐2004, spring‐summer (SS) and fall Chinook salmon Oncorhynchus tshawytscha and steelhead O. mykiss were implanted with uniquely coded radio or acoustic transmitter tags and released during the early, middle, and late out‐migration periods. A series of receiver lines were used to detect these fish and estimate survival. Estimated survival varied considerably with transportation type and release date for fall Chinook salmon and steelhead, but the results were dependent upon year. Estimated survival between the lowermost dam (Bonneville Dam) and the upper estuary (river kilometer 46) was relatively high for SS Chinook salmon and steelhead, whereas estimates for fall Chinook salmon were comparatively low. This order of high to low survival for SS Chinook salmon, steelhead, and fall Chinook salmon corresponds with the chronology of out‐migration timing and waning river flows. After accounting for a number of factors, estimated survival between Bonneville Dam and the upper‐estuary site did not differ significantly between steelhead that were barged and those that migrated in‐river during 2002 and 2003. Conversely, estimated survival to the upper‐estuary site was quite low for barged fall Chinook salmon in comparison with fish migrating in‐river during the middle and late release dates in 2003. Hypotheses for the low survival of barged fall Chinook salmon are presented and discussed.
Using a Passive Acoustic Survey to Identify Spotted Seatrout Spawning Sites and Associated Habitat in Tampa Bay, Florida
Authors: Walters Sarah , Lowerre‐Barbieri Susan , Bickford Joel , Mann David 
Published: February 2009

AbstractThe spatial distribution of spawning activity can affect the reproductive success of certain fishes, and locating the key areas is critical to accurately assessing and managing their populations. We determined estuarine spawning locations for spotted seatrout Cynoscion nebulosus during the 2004 summer spawning season in Tampa Bay, Florida, using a passive acoustic survey. Sound production was evaluated at each of 754 randomly selected stations for the number of individuals calling and ranged from 1‐2 individuals to large aggregations. Spawning was identified by large aggregation sounds and was detected at 8% of the selected stations. There was seasonal variability in spawning, as spawning areas were inconsistently used throughout the season. Spatially, spawning occurred in all regions of the bay except for the Hillsborough Bay region. Most spawning took place in lower Tampa Bay and the eastern portion of the middle bay. Spawning occurred most frequently near the shoreline in areas of relatively high dissolved oxygen and in association with submerged aquatic vegetation. The variability in spawning habitat, as exhibited by both the disproportionate distribution of spawning sites across Tampa Bay and the inconsistent use of spawning sites, may serve to increase the resilience of the stock. As management directives evolve to encompass habitat‐focused strategies, surveys such as this one can supply data necessary for the creation of meaningful ecosystem‐based management plans.
Temporal Variation in Trout Populations: Implications for Monitoring and Trend Detection
Authors: Dauwalter Daniel C. , Rahel Frank J. , Gerow Kenneth G. 
Published: February 2009

AbstractWe summarized the temporal variation in populations of inland trout Salmo, Salvelinus, and Oncorhynchus spp. from streams in North America and determined the statistical power to detect trends over time. The coefficients of variation in abundance averaged 49% (SD = 27%; range = 15‐108%) over time for all ages of trout. Temporal variation was lower when more age‐classes were monitored, but whether abundance or biomass was more variable differed among populations. Detecting population trends was difficult when using the traditional α = 0.05 criterion. For example, detecting a 5% annual decline with good power (1 ‐ β ≥ 0.80) would require about 20 years if only one site were monitored. Even when α was relaxed to 0.20, 15 years were required to detect a 5% annual decline when the variation was average. Using a network of sites improved the ability to detect changes: A 5% annual decline at α = 0.05 could be detected in 10 years when 30 sites were monitored. For high‐value populations, it may require relaxing α to ensure that declines are detected, even if this increases the risk of claiming change when none has occurred and thus undertaking unnecessary management action. For example, a 5% annual decline could be detected with good power (≥0.80) in 8 years when a network of 30 sites is monitored at α = 0.20. Thus, biologists should monitor the least‐variable component of a population, monitor a network of sites, and increase α for species of concern to ensure that real population trends are detected. Estimates of trend parameters (and their uncertainty) should be considered in addition to whether or not a statistical test for trend is significant. A pilot study or existing data can help estimate the variation that is typical of the population(s) to be monitored, determine whether trends can be reliably detected, and identify how much risk needs to be incurred to detect trends.
Effects of Gastric and Surgical Insertions of Dummy Ultrasonic Transmitters on Juvenile Chinook Salmon in Seawater
Authors: Hall J. E. , Chamberlin J. , Kagley A. N. , Greene C. , Fresh K. L. 
Published: February 2009

AbstractThe objective of this study was to develop guidance for tagging methods for juvenile Chinook salmon Oncorhynchus tshawytscha in their first ocean year by evaluating the effects of tagging during this critical life stage. We compared survival over 42 d among juvenile hatchery Chinook salmon receiving surgically implanted dummy ultrasonic transmitters (equivalent to VEMCO V7‐1 L tags) ranging from 2.6% to 8.8% of body mass with that of fish receiving gastrically implanted tags. Survival was significantly lower in fish receiving gastrically implanted transmitters (21%) than for the gastric‐sham (66%), surgery (61%), surgery‐sham (58%), and control treatments (90%). Survival was also significantly higher in the control treatment than in all other treatments. The results of this study indicate that surgical insertion into the peritoneal cavity is the preferred method of transmitter implantation in juvenile Chinook salmon in their first ocean year and that the transmitters should be less than 5.8% of the fish's body mass to reduce transmitter‐related mortality.
Effects of Fish Size, Habitat, Flow, and Density on Capture Probabilities of Age‐0 Rainbow Trout Estimated from Electrofishing at Discrete Sites in a Large River
Authors: Korman Josh , Yard Mike , Walters Carl , Coggins Lewis G. 
Published: February 2009

AbstractWe estimated size‐specific capture probabilities of age‐0 rainbow troutOncorhynchus mykissin the Lee's Ferry Reach of the Colorado River, Arizona, by backpack and boat electrofishing at discrete shoreline sites using both depletion and mark‐recapture experiments. Our objectives were to evaluate the feasibility of estimating capture probability for juvenile fish in larger rivers; to determine how it is influenced by fish size, habitat, flow, density, and recovery period; and to test population closure assumptions. There was no mortality among the 351 rainbow trout that were captured by electrofishing, marked, and held for 24 h. Of a total of 2,966 fish that were marked and released, only 0.61% were captured outside of mark‐recapture sites, and total emigration from mark‐recapture sites was 2.2‐2.6%. These data strongly suggest that populations within discrete sites can be treated as effectively closed for the 24‐h period between marking and recapture. Eighty percent of capture probability estimates from 66 depletion experiments and 42 mark‐recapture experiments ranged from 0.28 to 0.75 and from 0.17 to 0.45, respectively, and the average coefficient of variation of estimates was 0.26. There was strong support for a fish size‐capture probability relationship that accounted for the differences in vulnerability across habitat types. Smaller fish were less vulnerable in high‐angle shorelines that were sampled by boat electrofishing. There was little support for capture probability models that accounted for within‐day and across‐month variation in flow. The effects of fish density on capture probability were challenging to discern, variable among habitat types and estimation methodologies, and confounded with the effect of fish size. As capture probability estimates were generally precise and the closure assumption was met, our results demonstrate that electrofishing‐based mark‐recapture experiments at discrete sites can be used to estimate the abundance of juvenile fish in large rivers.