bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thoracic CT findings at hypovolemic shock
Authors: Rotondo A. , Catalano O. , Grassi R. , Scialpi M. , Angelelli G. 
Published: January 2010

Purpose: To describe and discuss the thoracic CT features of hypovolemic shock. Material and Methods: From a group of 18 patients with signs of hypovolemia on contrast-enhanced abdominal CT, 11 were selected for our study as having also undergone a complete chest examination. Pulse rate, blood pressure, trauma score value, Glasgow coma scale value, surgical result, and final outcome were retrospectively evaluated. The CT features analyzed were: decreased cardiac volume, reduced caliber of the thoracic aorta, aortic branches and caval venous system, increased enhancement of the aorta, and increased enhancement of the pulmonary collapses/contusions. Results: All 11 subjects presented severe injuries and hemodynamic instability; 7 were stable enough to undergo surgery; only 1 of the 11 survived. Two patients showed none of the features of thoracic hypovolemia. All the other patients presented at least two signs: reduced caliber of the thoracic aorta in 7 cases; decreased volume of the cardiac chambers and increased aortic enhancement in 6; decreased caliber of the aortic vessels in 4; decreased caliber of the caval veins in 3; and increased enhancement of the pulmonary collapses/contusions in 3. Conclusions: In patients with hypovolemia, CT may show several thoracic findings in addition to abdominal ones. Knowledge of these features is important for distinguishing them from traumatic injuries.
Morphological Abnormalities Revealed after Successful Intra-Arterial Thrombolysis of Infra-Inguinal Native Arteries and Bypasses
Authors: Sandbæk G. , Staxrud L. E. , Rosén L. , Kolmannskog F. 
Published: January 2010

Purpose: To characterise morphological abnormalities depicted after successful intra-arterial thrombolysis; to determine whether these differed in infrainguinal native arteries and bypasses; and to evaluate whether ballon angioplasty was an appropriate treatment of stenoses in the acute phase after thrombolysis. Material and Methods: Patient records, radiology records, and angiograms from 47 patients with acute or subacute occlusions of infra-inguinal arteries (n=21) or bypasses (n=26) successfully treated with continuous intra-arterial infusion of streptokinase, urokinase or tissue plasminogen activator were retrospectively reviewed. Results: Angiographic morphological abnormalities were depicted in 18 of 21 arteries (86%) and in 23 of 26 bypasses (88%), the most common abnormality being stenoses. Haemodynamically significant stenoses were found in 15 arteries (71%) and 18 bypasses (69%). The majority of the stenoses were successfully treated with balloon angioplasty, both in native arteries (12/15; 80%) and in bypasses (14/18; 78%). Conclusion: Morphological abnormalities are most often shown after successful intra-arterial thrombolysis in arteries, autogenous and non-autogenous bypasses. In all types of conduits, stenoses are the most commonly revealed lesion, which in the majority of cases can be treated with balloon angioplasty. Shortterm outcome after catheter-directed thrombolysis and angioplasty seems fair.
Mixtures of regression models for time course gene expression data: evaluation of initialization and random effects
Authors: Scharl Theresa , Grün Bettina , Leisch Friedrich 
Published: December 2009

AbstractSummary: Finite mixture models are routinely applied to time course microarray data. Due to the complexity and size of this type of data, the choice of good starting values plays an important role. So far initialization strategies have only been investigated for data from a mixture of multivariate normal distributions. In this work several initialization procedures are evaluated for mixtures of regression models with and without random effects in an extensive simulation study on different artificial datasets. Finally, these procedures are also applied to a real dataset from Escherichia coli.Availability: The latest release versions of R packages flexmix, gcExplorer and kernlab are always available from CRAN (http://cran.r-project.org/).Contact: theresa.scharl@ci.tuwien.ac.atSupplementary information: Supplementary data are available at Bioinformatics online.
Changes in the reproductive parameters of female harp seals (Pagophilus groenlandicus) in the Northwest Atlantic
Authors: Sjare Becky , Stenson Garry B. 
Published: December 2009

Abstract
Sjare, B., and Stenson, G. B. 2010. Changes in the reproductive parameters of female harp seals (Pagophilus groenlandicus) in the Northwest Atlantic. – ICES Journal of Marine Science, 67: 304–315. Changes in female harp seal (Pagophilus groenlandicus) reproductive parameters from 1980 to 2004, and long-term trends since the early 1950s, are evaluated. Estimates of the total number of seals in the Northwest Atlantic declined from ∼3.0 million in the 1950s to 1.8 million in the early 1970s, then increased steadily to 5.5 million in 1996, at which relatively stable level it has remained since. Pregnancy rates increased from ∼86% in the 1950s to a high of 98% in the mid-1960s, then declined to ∼65–70% by the early 1990s; the rate then varied between 45 and 70% from 2000 to 2004. Concurrently, the mean age at sexual maturity decreased from 5.8 (s.e = 0.02) years in the mid-1950s to 4.1 (s.e. = 0.02) in the late 1970s, increased to 5.5 (s.e. = 0.03) years by the early 1990s, and peaked at 5.7 (s.e. = 0.01) in 1995. From 2000 to 2004, mean age varied from 4.9 (s.e. = 0.01) to 6.0 (s.e. = 0.01) years. Although the direction of change in each of the parameters was consistent with a density-dependent response, changes in population size explained relatively little of the variability observed, suggesting that other ecological or environmental factors were influential.
Estimating EAF indicators from scientific trawl surveys: theoretical and practical concerns
Authors: Jouffre Didier , Borges Maria de Fatima , Bundy Alida , Coll Marta , Diallo Ibrahima , Fulton Elizabeth A. , Guitton Jérôme , Labrosse Pierre , Abdellahi Khairdine ould Mohamed , Masumbuko Bora , Thiao Djiga 
Published: December 2009

Abstract
Jouffre, D., Borges, M. F., Bundy, A., Coll, M., Diallo, I., Fulton, E. A., Guitton, J., Labrosse, P., Mohamed Abdellahi, K. o., Masumbuko, B., and Thiao, D. 2010. Estimating EAF indicators from scientific trawl surveys: theoretical and practical concerns. – ICES Journal of Marine Science, 67: 796–806. Under the context of an ecosystem approach to fisheries (EAF), there is keen interest in providing insights into the evolution of exploited ecosystems using simple ecosystem indicators. Many nations have long-term scientific research surveys, originally driven by conventional approaches in fisheries assessment and management. The aim of this study is to address the practical concerns linked to current objectives of monitoring simple EAF indicators, using data from surveys that were not historically designed for the purpose. Based on the results of an expert survey designed to collect expert knowledge on research surveys from scientists working on different ecosystems worldwide, a list of challenges faced during indicator estimation is highlighted, along with associated concerns and constraints. The work provides additional information useful in the interpretation of the results obtained on the state and trends of ecosystems using EAF indicators by the IndiSeas WG. Further, the related discussion provides potential pathways that could be useful for future research and development aiming to improve the ecosystem indicator approach in the operational context of EAF. The question of the utility for EAF of using historical dataseries of scientific trawl series is also discussed. Such long-term series are concluded to be useful, that they are even inescapable (since the past cannot be resamplied), and that EAF therefore brings a supplementary reason for continuing such monitoring and to incorporate new insights in how research surveys may be conducted.
Fixed negative charge and the Donnan effect: a description of the driving forces associated with brain tissue swelling and oedema
Authors: Elkin Benjamin S. , Shaik Mohammed A. , Morrison Barclay 
Published: January 2010

Cerebral oedema or brain tissue swelling is a significant complication following traumatic brain injury or stroke that can increase the intracranial pressure (ICP) and impair blood flow. Here, we have identified a potential driver of oedema: the negatively charged molecules fixed within cells. This fixed charge density (FCD), once exposed, could increase ICP through the Donnan effect. We have shown that metabolic processes and membrane integrity are required for concealing this FCD as slices of rat cortex swelled immediately (within 30 min) following dissection if treated with 2 deoxyglucose + cyanide (2DG+CN) or Triton X-100. Slices given ample oxygen and glucose, however, did not swell significantly. We also found that dead brain tissue swells and shrinks in response to changes in ionic strength of the bathing medium, which suggests that the Donnan effect is capable of pressurizing and swelling brain tissue. As predicted, a non-ionic osmolyte, 1,2 propanediol, elicited no volume change at 2000×10
−3
osmoles l
−1
(Osm). Swelling data were well described by triphasic mixture theory with the calculated reference state FCD similar to that measured with a 1,9 dimethylmethylene blue assay. Taken together, these data suggest that intracellular fixed charges may contribute to the driving forces responsible for brain swelling.
Mounting, Embedding, and Sectioning of Early Rabbit Embryos
Authors: Püschel Bernd , Bitzer Eva , Blum Martin , Viebahn Christoph 
Published: January 2010

INTRODUCTIONThis protocol describes various methods for visualizing cellular labeling in early rabbit embryos at high resolution using stereomicroscopy, compound light microscopy, or electron microscopy. Embedding media are chosen according to the level of resolution needed: For low-magnification stereomicroscopy, optimal spreading of large, flat, thin embryonic discs is achieved by mounting embryos in Mowiol on regular microscope slides. Gelatin/BSA embedding is useful for quickly cutting a complete series of thick (e.g., 30-μm) sections in defined planes from large (e.g., somite stage) paraformaldehyde-fixed embryos prelabeled by immunofluorescence or in situ hybridization. Higher cellular and subcellular resolution of such specimens usually requires embedding in Technovit, a hydrophilic methacrylate-based resin suited for light microscopic analysis of 5-μm serial sections. Araldite is a translucent, hydrophobic epoxy-based resin used for serial semi-thin (1-μm) and ultrathin (80-nm) sections amenable to consecutive (and correlative) light and electron microscopic analysis. Specimens to be embedded in Araldite must be much harder than those embedded in hydrophilic resins, requiring at least 1% glutaraldehyde in the primary fixative. Unfortunately, strong cross-linking by glutaraldehyde prevents the use of antibodies/nucleotide probes post-fixation; glutaraldehyde autofluorescence also thwarts the use fluorescent stains. Finally, semi-thin cryosections can be cut from unfixed or paraformaldehyde-fixed specimens embedded in “tissue freezing medium,” offering the opportunity for highly sensitive light microscopic analysis of antigen distribution. Here, subcellular structures can be identified up to the level of individual mitochondria; greater resolution can be obtained by correlating such samples with similar specimens analyzed using other techniques.
Embryo Transfer in Rabbits: Figure 1.
Authors: Daniel Nathalie , Renard Jean-Paul 
Published: January 2010

INTRODUCTIONBecause there is a particularly narrow time window for implantation in rabbits, embryo transfer in this species requires a high degree of synchrony between the physiological status of the recipient doe and the developmental stage of the embryo at the time of transfer. In some cases, however, especially after in vitro culture of reconstructed embryos or after an extended culture period (e.g. overnight), the pregnancy rate obtained after embryo transfer into asynchronous recipients can be increased relative to synchronous transfers. In addition to the surgical methods required, this protocol describes two scenarios for the preparation of recipient does: an asynchronous scenario for embryos produced by intracytoplasmic sperm injection (ICSI) and a synchronous scenario for the transfer of thawed morulae.
Mass Culture of Paramecium tetraurelia: Figure 1.
Authors: Beisson Janine , Bétermier Mireille , Bré Marie-Hélène , Cohen Jean , Duharcourt Sandra , Duret Laurent , Kung Ching , Malinsky Sophie , Meyer Eric , Preer John R. , Sperling Linda 
Published: January 2010

INTRODUCTIONClonal cell lines of Paramecium tetraurelia can be established easily by single cell isolation. Given a constant supply of food, P. tetraurelia cells will remain in the vegetative phase of their life cycle and, at 27°C, will divide by binary fission every 6 h. P. tetraurelia is suitable for a range of biochemical and molecular studies such as mitochondrial genetics, post-translational tubulin modifications, variant genetic codes, programmed genome rearrangements (and their epigenetic regulation by noncoding RNAs), and RNA interference. This protocol describes the methods required to grow high-density mass cultures of P. tetraurelia in quantities sufficient to provide the material required for biochemical and molecular biological studies.
Silencing Specific Paramecium tetraurelia Genes by Feeding Double-Stranded RNA
Authors: Beisson Janine , Bétermier Mireille , Bré Marie-Hélène , Cohen Jean , Duharcourt Sandra , Duret Laurent , Kung Ching , Malinsky Sophie , Meyer Eric , Preer John R. , Sperling Linda 
Published: January 2010

INTRODUCTIONThis protocol describes an easy and efficient method to knock down gene expression in a homology-dependent manner by feeding Paramecium with bacteria-producing double-stranded (ds) RNA corresponding to a portion of the target gene. The target sequence is cloned in a plasmid between two convergent T7 promoters (the L4440 plasmid) and used to transform an E. coli strain devoid of RNase III activity and expressing the T7 polymerase gene under the control of an inducible Plac promoter (strain HT115-DE3). Inserts corresponding to ~400 bp of the coding sequence to be silenced are recommended; very short inserts (<100 bp) have variable silencing efficiencies. As a rule, pairs of paralogs resulting from the most recent whole-genome duplication are so similar in sequence that dsRNA from one paralog will cosilence both. Although the level of sequence identity required has not been explored fully, more divergent paralogs can occasionally be co-silenced too. When Paramecium tetraurelia cells feed on these bacteria, dsRNA reaches the cytoplasm through unknown mechanisms and triggers a potent RNA interference (RNAi) response, resulting in the degradation of the targeted mRNA. The protocol generally gives a visible phenotype in 24-48 h, depending on the targeted gene, a delay which might correspond to the time necessary for the pre-existing protein stock to be diluted by cell growth. Silencing induced in this manner is only post-transcriptional; when cells are transferred back to normal medium bacterized with Klebsiella pneumoniae, the phenotype usually reverts to wild type within a few cell divisions.
DNA Microinjection into the Macronucleus of Paramecium
Authors: Beisson Janine , Bétermier Mireille , Bré Marie-Hélène , Cohen Jean , Duharcourt Sandra , Duret Laurent , Kung Ching , Malinsky Sophie , Meyer Eric , Preer John R. , Sperling Linda 
Published: January 2010

INTRODUCTIONThis protocol describes a highly efficient procedure for transforming the vegetative macronucleus of Paramecium tetraurelia by DNA microinjection. Any microinjected DNA will be replicated without the need for specific origins and can be stably maintained at a wide range of copy numbers throughout vegetative growth as minichromosomes that are formed in vivo by the addition of telomeric sequences to the ends of linear monomers and multimers. A variable fraction of the injected DNA also integrates into endogenous macronuclear chromosomes by nonhomologous recombination. Endogenous transcription signals are recognized, allowing appropriate regulation of gene expression. This technique is used for complementation cloning of genes altered in mutants and for expression of modified genes, e.g., green fluorescent protein (GFP) fusions. Microinjection of nonexpressible constructs at high copy numbers can also be used to specifically silence homologous endogenous genes by transgene-induced RNA interference. Note that transformed clones are somatic transformants, and therefore can be maintained only during the vegetative phase of the life cycle (<200 cell divisions), i.e., only as long as they do not enter sexual reproduction or senescence. Cells must be kept in continuous exponential growth by providing a constant supply of food; starving cells with a clonal age ≥20 divisions, since the last sexual event will inevitably trigger meiosis, resulting in the loss of the transformed macronucleus and its replacement by a new macronucleus that develops from the germline micronuclei.
Auxin Response inArabidopsisunder Cold Stress: Underlying Molecular Mechanisms
Authors: Shibasaki Kyohei , Uemura Matsuo , Tsurumi Seiji , Rahman Abidur 
Published: December 2009

AbstractTo understand the mechanistic basis of cold temperature stress and the role of the auxin response, we characterized root growth and gravity response of Arabidopsis thaliana after cold stress, finding that 8 to 12 h at 4°C inhibited root growth and gravity response by ∼50%. The auxin-signaling mutants axr1 and tir1, which show a reduced gravity response, responded to cold treatment like the wild type, suggesting that cold stress affects auxin transport rather than auxin signaling. Consistently, expression analyses of an auxin-responsive marker, IAA2-GUS, and a direct transport assay confirmed that cold inhibits root basipetal (shootward) auxin transport. Microscopy of living cells revealed that trafficking of the auxin efflux carrier PIN2, which acts in basipetal auxin transport, was dramatically reduced by cold. The lateral relocalization of PIN3, which has been suggested to mediate the early phase of root gravity response, was also inhibited by cold stress. Additionally, cold differentially affected various protein trafficking pathways. Furthermore, the inhibition of protein trafficking by cold is independent of cellular actin organization and membrane fluidity. Taken together, these results suggest that the effect of cold stress on auxin is linked to the inhibition of intracellular trafficking of auxin efflux carriers.
PLAZA: A Comparative Genomics Resource to Study Gene and Genome Evolution in Plants
Authors: Proost Sebastian , Van Bel Michiel , Sterck Lieven , Billiau Kenny , Van Parys Thomas , Van de Peer Yves , Vandepoele Klaas 
Published: December 2009

AbstractThe number of sequenced genomes of representatives within the green lineage is rapidly increasing. Consequently, comparative sequence analysis has significantly altered our view on the complexity of genome organization, gene function, and regulatory pathways. To explore all this genome information, a centralized infrastructure is required where all data generated by different sequencing initiatives is integrated and combined with advanced methods for data mining. Here, we describe PLAZA, an online platform for plant comparative genomics (http://bioinformatics.psb.ugent.be/plaza/). This resource integrates structural and functional annotation of published plant genomes together with a large set of interactive tools to study gene function and gene and genome evolution. Precomputed data sets cover homologous gene families, multiple sequence alignments, phylogenetic trees, intraspecies whole-genome dot plots, and genomic colinearity between species. Through the integration of high confidence Gene Ontology annotations and tree-based orthology between related species, thousands of genes lacking any functional description are functionally annotated. Advanced query systems, as well as multiple interactive visualization tools, are available through a user-friendly and intuitive Web interface. In addition, detailed documentation and tutorials introduce the different tools, while the workbench provides an efficient means to analyze user-defined gene sets through PLAZA's interface. In conclusion, PLAZA provides a comprehensible and up-to-date research environment to aid researchers in the exploration of genome information within the green plant lineage.
DGAT1andPDAT1Acyltransferases Have Overlapping Functions inArabidopsisTriacylglycerol Biosynthesis and Are Essential for Normal Pollen and Seed Development
Authors: Zhang Meng , Fan Jilian , Taylor David C. , Ohlrogge John B. 
Published: December 2009

AbstractTriacylglycerol (TAG) biosynthesis is a principal metabolic pathway in most organisms, and TAG is the major form of carbon storage in many plant seeds. Acyl-CoA:diacylglycerol acyltransferase 1 (DGAT1) is the only acyltransferase enzyme that has been confirmed to contribute to TAG biosynthesis in Arabidopsis thaliana seeds. However, dgat1 null mutants display only a 20 to 40% decrease in seed oil content. To determine whether other enzymes contribute to TAG synthesis, candidate genes were expressed in TAG-deficient yeast, candidate mutants were crossed with the dgat1-1 mutant, and target genes were suppressed by RNA interference (RNAi). An in vivo role for phospholipid:diacylglycerol acyltransferase 1 (PDAT1; At5g13640) in TAG synthesis was revealed in this study. After failing to obtain double homozygous plants from crossing dgat1-1 and pdat1-2, further investigation showed that the dgat1-1 pdat1-2 double mutation resulted in sterile pollen that lacked visible oil bodies. RNAi silencing of PDAT1 in a dgat1-1 background or DGAT1 in pdat1-1 background resulted in 70 to 80% decreases in oil content per seed and in disruptions of embryo development. These results establish in vivo involvement of PDAT1 in TAG biosynthesis, rule out major contributions by other candidate enzymes, and indicate that PDAT1 and DGAT1 have overlapping functions that are essential for normal pollen and seed development of Arabidopsis.
Diet composition ofXenopus borealisin Taita Hills: effects of habitat and predator size
Authors: Bwong Beryl A. , John Measey G. 
Published: January 2010

AbstractFrogs in the genusXenopusare ubiquitous in sub‐Saharan Africa, yet very little is recorded on their ecology. They are commonly found in anthropogenically disturbed habitats, but how do these compare to conspecifics from natural habitats? The diet ofXenopus borealisfrom three different sites in Taita Hills, Kenya was established based on a sample of 77 (54 females and 23 males) specimens from two disturbed and one pristine sites.Xenopus borealisfrom all the sites was found to be a dietary generalist, feeding predominantly on invertebrates. A total of twelve invertebrate orders both terrestrial and aquatic were recorded in addition to amphibian eggs, tadpoles and fish. Frogs from the pristine forest were smaller and had ingested more terrestrial prey items than frogs in the disturbed open habitat ponds. The stomach content (both by mass and quantity) was independent of body size. The results suggest thatX. borealisis an opportunistic generalist predator which may be constrained by food availability in its natural habitat. However, disturbed habitats provide abundant food items which are enough to significantly increase the mean size of the population.