bluuebunny/crossref_metadata_2025_split huggingface dataset:
Studying spatial and trophic interactions between capelin and cod using individual-based modelling
Authors: Huse Geir , Johansen Geir Odd , Bogstad Bjarte , Gjøsæter Harald 
Published: August 2004

AbstractThe objective of this study was to use spatially explicit individual-based models for simulating the movement, foraging, growth, and mortality of cod and capelin in the Barents Sea in order to identify general features in their migration patterns and the consumption of capelin by cod. The individual-based models are initiated from survey data run over 1 year and validated against survey information. Directed movement is based on a combination of movement vectors and temperature boundaries, and bioenergetics models are used to calculate growth. Capelin consumption by cod is calculated from local encounters between the species. For capelin, the best movement model can be summarized as: stay southwest of the 2.5°C and 4°C temperature front at 50-m depth for juvenile and mature individuals, respectively, in winter, and migrate northwards during summer, but do not pass the −1.5°C temperature front. The best cod model was to migrate south-southwest during winter and north-northeast during summer, within the temperature range 1°C to 8°C. The annual consumption estimates found here reflected the interannual and seasonal pattern from previous studies based on stomach samples, but were generally lower. Consumption estimates varied depending on the movement models, and the best movement model also produced the consumption estimate closest to that obtained in other studies. Introducing a simple rule stating that cod should move in a randomly selected direction when the local capelin density is zero increased the consumption estimate by 30%. This suggests that more emphasis needs to be put on exploring how behavioural rules in predators and prey affect their interactions. Even though there are some discrepancies between predictions and observations, the results achieved by the model with regard to spatial distribution, growth, and consumption are promising.
Behaviour of herring (Clupea harengus L.) towards an approaching autonomous underwater vehicle
Authors: Patel Ruben , Handegard Nils Olav , Godø Olav Rune 
Published: August 2004

AbstractThe reaction of schooling wintering herring (Clupea harengus L.) in Ofotfjord in northern Norway is studied when approached by an autonomous underwater vehicle (AUV) with electrical propulsion. The reaction of herring is recorded running the AUV in the beam of the mother vessel's 38-kHz echosounder and in more detail with an onboard 120-kHz echosounder. The results indicate an insignificant reaction of herring to the approaching AUV, although some variations were observed depending on the experimental set-up. Technical uncertainty in the recordings close to the AUV transducer creates some ambiguity in the results. No reaction could be identified from the ship's sounder when the AUV passed under the vessel. Processing of the onboard echosounder data suggests a mean avoidance distance of 8.0 m in these experiments. In a realistic autonomous survey situation it is assumed that the AUV can approach as closely as 5–10 m to herring schools without affecting the acoustic observation, which makes it a potentially useful platform for hydroacoustic research and survey. More systematic studies are needed to precisely define the threshold reaction distance to the AUV, and the work should be conducted with transducers on a more silent platform than RV “Johan Hjort”, which was used in this study.
Ultrasonic tracking reveals multiple behavioural modes of snapper (Pagrus auratus) in a temperate no-take marine reserve
Authors: Egli D.P. , Babcock R.C. 
Published: August 2004

AbstractInteractions between marine reserve populations and non-reserve populations of exploited fishes have generally been modelled using simplistic assumptions about behaviour. Consequently, there is a recognized need for better information on fish movement behaviour at the appropriate spatial scales to generate more realistic interaction models. Automated ultrasonic tracking of marine fish, applied in this study, offers the potential to continuously track individuals for periods of up to several years within the study area. Snapper (Pagrus auratus) (FL: 33–68 cm) were surgically implanted with individually coded ultrasonic transmitters to monitor their movement within the Cape Rodney to Okakari Point Marine Reserve in northeast New Zealand from October 2001 to September 2002. The range of movement patterns observed includes some fish resident for the entire tracking period, while others were more mobile. Of the latter group, some fish left the array permanently while others returned after up to 83 days of continuous absence. Nearly all fish showed some level of site fidelity for varying periods of the time they were tracked. Fish activity peaked in the summer, when highest densities are known to occur. Results suggest that snapper behaviour is variable, and that patterns of habitat utilization vary between fish and also seasonally. Such a complex range of behaviours may be a key component for achieving desirable outcomes for both conservation and fisheries in marine reserves.
Role of Ca2+‐independent phospholipase A2 and n−3 polyunsaturated fatty acid docosahexaenoic acid in prostanoid production in brain: perspectives for protection in neuroinflammation
Authors: Strokin Mikhail , Sergeeva Marina , Reiser Georg 
Published: August 2004

AbstractVarious diseases of the central nervous system are characterized by induction of inflammatory events, which involve formation of prostaglandins. Production of prostaglandins is regulated by activity of phospholipases A2 and cyclooxygenases. These enzymes release the prostaglandin precursor, the n−6 polyunsaturated fatty acid, arachidonic acid and oxidize it into prostaglandin H2. Docosahexaenoic acid, which belongs to the n−3 class of polyunsaturated fatty acids, was shown to reduce production of prostaglandins after in vivo and in vitro administration. Nevertheless, the fact that in brain tissue cellular phospholipids naturally have a uniquely high content of docosahexaenoic acid was ignored so far in studies of prostaglandin formation in brain tissue. We consider the following possibilities: docosahexaenoic acid might attenuate production of prostaglandins by direct inhibition of cyclooxygenases. Such inhibition was found with the isolated enzyme. Another possibility, which has been already shown is reduction of expression of inducible cyclooxygenase‐2. Additionally, we propose that docosahexaenoic acid could influence intracellular Ca2+ signaling, which results in changes of activity of Ca2+‐dependent phospholipase A2, hence reducing the amount of arachidonic acid available for prostaglandin production. Astrocytes, the main type of glial cells in the brain control the release of arachidonic acid, docosahexaenoic acid and the formation of prostaglandins. Our recently obtained data revealed that the release of arachidonic and docosahexaenoic acids in astrocytes is controlled by different isoforms of phospholipase A2, i.e. Ca2+‐dependent phospholipase A2 and Ca2+‐independent phospholipase A2, respectively. Moreover, the release of arachidonic and docosahexaenoic acids is differently regulated through Ca2+‐ and cAMP‐dependent signal transduction pathways. Based on analysis of the current literature and our own data we put forward the hypothesis that Ca2+‐independent phospholipase A2 and docosahexaenoic acid are promising targets for treatment of inflammatory related disorders in brain. We suggest that Ca2+‐independent phospholipase A2 and docosahexaenoic acid might be crucially involved in brain‐specific regulation of prostaglandins.
Selective changes in expression of different nicotinic receptor subtypes in brain and adrenal glands of mice carrying human mutated gene for APP or over‐expressing human acetylcholinestrase
Authors: Mousavi Malahat , Bednar Ivan , Nordberg Agneta 
Published: August 2004

AbstractIn this study, we investigated regulatory mechanisms and plasticity of the nicotinic acetylcholine receptors (nAChRs) in the brain and adrenal glands of two transgenic mice models over‐expressing human β‐amyloid precursor protein (APPSWETg) and human AChE enzyme (hAChE‐Tg), respectively. All animals were studied at 3 months of age. Binding studies showed higher 125I‐α‐bungarotoxin (α7 nAChRs) and 3H‐epibatidine (α3 and α4 nAChRs) binding in the brain cortex and adrenal glands of hAChE‐Tg mice compared to control mice. The APPSWETg mice showed a significantly lower relative level for the α4 mRNA in the brain cortex as well as a lower level of α3 mRNA, and higher level of α7 mRNA in the adrenal glands compared to control mice. A higher relative mRNA level of α3 and α4 nAChRs was observed in the brain as well as of α3 and α7 nAChRs in the adrenal glands of hAChE‐Tg mice compared to control mice.Different nicotinic receptor plasticity is revealed in the brain cortex and adrenal glands in two transgenic mice models with different underlying pathophysiological mechanisms. Deposition of β‐amyloid (Aβ) may impair neurotransmitter activity in brain as well as in the adrenal gland.
Turning the heterogeneous into homogeneous: studies on selectively isolated GABAergic interneuron subsets
Authors: Berghuis Paul , Dobszay Marton B. , Ibanez Raquel Martin , Ernfors Patrik , Harkany Tibor 
Published: August 2004

AbstractThe amazing morphological and electrophysiological diversity of cortical GABAergic interneurons subserves the broad diversity of processes these cells modulate in neuronal networks. Until recently, interneuron development and functions have been extensively studied in heterogeneous in vitro and in vivo systems containing both excitatory and inhibitory components. However, mechanisms of interneuron specification during development, key signaling mechanisms controlling the establishment of particular inhibitory neuron subsets, and the spatial and temporal regulation of their integration in neuronal microcircuits remain poorly understood. Selective isolation of particular interneuron subsets may significantly extend our knowledge on the scenario of neurochemical and electrophysiological specification of developing interneurons, identification of signaling cues directing their axon growth, and principles of their anterograde and retrograde synaptic communication with other cell types. Here, we show that selective isolation of perisomatic inhibitory cells containing either parvalbumin or cholecystokinin reveals major differences in the temporal dynamics of their functional differentiation, and their dependence on target‐derived signals like brain‐derived neurotrophic factor and endocannabinoids. In addition, we discuss therapeutic prospects of modulating increased excitatory output in the hippocampus and subthalamic nucleus by re‐adjusting the inhibitory control of principal cells.
Neuronal trauma model: in search of Thanatos
Authors: Cole Kasie , Perez‐Polo J. Regino 
Published: August 2004

AbstractTrauma to the nervous system triggers responses that include oxidative stress due to the generation of reactive oxygen species (ROS). DNA is a major macromolecular target of ROS, and ROS‐induced DNA strand breaks activate poly(ADP‐ribose)polymerase‐1 (PARP‐1). Upon activation PARP‐1 uses NAD+ as a substrate to catalyze the transfer of ADP‐ribose subunits to a host of nuclear proteins. In the face of extensive DNA strand breaks, PARP‐1 activation can lead to depletion of intracellular NAD(P)(H) pools, large decreases in ATP, that threaten cell survival. Accordingly, inhibition of PARP‐1 activity after acute oxidative injury has been shown to increase cell survival. When NGF‐differentiated PC12 cells, an in vitro neuronal model, are exposed to H2O2 there is increased synthesis of poly ADP‐ribose and decreases in intracellular NAD(P)(H) and ATP. Addition of the chemical PARP inhibitor 3‐aminobenzamide (AB) prior to H2O2 exposure blocks the synthesis of poly ADP‐ribose and maintains intracellular NAD(P)(H) and ATP levels. H2O2 injury is characterized by an immediate, necrotic cell death 2 h after injury and a delayed apoptotic‐like death 12–24 h after injury. This apoptotic‐like death is characterized by apoptotic membrane changes and apoptotic DNA fragmentation but is not associated with measurable caspase‐3 activity. AB delays cell death beyond 24 h and increases cell survival by ∼25%. This protective effect is accompanied by significantly decreased necrosis and the apoptotic‐like death associated with H2O2 exposure. AB also restores caspase‐3 which can be attributed to the activation of the upstream activator of caspase‐3, caspase‐9. Thus, the maintenance of intracellular ATP levels associated with PARP‐1 inhibition shifts cell death from necrosis to apoptosis and from apoptosis to cell survival. Furthermore, the shift from necrosis to apoptosis may be explained, in part, by an energy‐dependent activation of caspase‐9.
HapBlock: haplotype block partitioning and tag SNP selection software using a set of dynamic programming algorithms
Authors: Zhang Kui , Qin Zhaohui , Chen Ting , Liu Jun S. , Waterman Michael S. , Sun Fengzhu 
Published: August 2004

Abstract
Summary: Recent studies have revealed that linkage disequilibrium (LD) patterns vary across the human genome with some regions of high LD interspersed with regions of low LD. Such LD patterns make it possible to select a set of single nucleotide polymorphism (SNPs; tag SNPs) for genome-wide association studies. We have developed a suite of computer programs to analyze the block-like LD patterns and to select the corresponding tag SNPs. Compared to other programs for haplotype block partitioning and tag SNP selection, our program has several notable features. First, the dynamic programming algorithms implemented are guaranteed to find the block partition with minimum number of tag SNPs for the given criteria of blocks and tag SNPs. Second, both haplotype data and genotype data from unrelated individuals and/or from general pedigrees can be analyzed. Third, several existing measures/criteria for haplotype block partitioning and tag SNP selection have been implemented in the program. Finally, the programs provide flexibility to include specific SNPs (e.g. non-synonymous SNPs) as tag SNPs.
Availability: The HapBlock program and its supplemental documents can be downloaded from the website http://www.cmb.usc.edu/~msms/HapBlock
Contact: fsun@usc.edu
OntologyTraverser: an R package for GO analysis
Authors: Young A. , Whitehouse N. , Cho J. , Shaw C. 
Published: August 2004

AbstractSummary: Gene Ontology (GO) annotations have become a major tool for analysis of genome-scale experiments. We have created OntologyTraverser—an R package for GO analysis of gene lists. Our system is a major advance over previous work because (1) the system can be installed as an R package, (2) the system uses Java to instantiate the GO structure and the SJava system to integrate R and Java and (3) the system is also deployed as a publicly available web tool.Availability: Our software is academically available through http://franklin.imgen.bcm.tmc.edu/OntologyTraverser/. Both the R package and the web tool are accessible.Contact: cashaw@bcm.tmc.edu
A new algorithm for detecting low-complexity regions in protein sequences
Authors: Shin Sung W. , Kim Sam M. 
Published: August 2004

Abstract
Motivation: Pair-wise alignment of protein sequences and local similarity searches produce many false positives because of compositionally biased regions, also called low-complexity regions (LCRs), of amino acid residues. Masking and filtering such regions significantly improves the reliability of homology searches and, consequently, functional predictions. Most of the available algorithms are based on a statistical approach. We wished to investigate the structural properties of LCRs in biological sequences and develop an algorithm for filtering them.
Results: We present an algorithm for detecting and masking LCRs in protein sequences to improve the quality of database searches. We developed the algorithm based on the complexity analysis of subsequences delimited by a pair of identical, repeating subsequences. Given a protein sequence, the algorithm first computes the suffix tree of the sequence. It then collects repeating subsequences from the tree. Finally, the algorithm iteratively tests whether each subsequence delimited by a pair of repeating subsequences meets a given criteria. Test results with 1000 proteins from 20 families in Pfam show that the repeating subsequences are a good indicator for the low-complexity regions, and the algorithm based on such structural information strongly compete with others.
Availability: http://bioinfo.knu.ac.kr/research/CARD/
Contact: swshin@bioinfo.knu.ac.kr
Recombination Analysis Tool (RAT): a program for the high-throughput detection of recombination
Authors: Etherington Graham J. , Dicks Jo , Roberts Ian N. 
Published: August 2004

Abstract
Motivation: Recombination can be a prevailing drive in shaping genome evolution. RAT (Recombination Analysis Tool) is a Java-based tool for investigating recombination events in any number of aligned sequences (protein or DNA) of any length (short viral sequences to full genomes). It is an uncomplicated and intuitive application and allows the user to view only the regions of sequence alignments they are interested in.
Results: RAT was applied to viral sequences. Its utility was demonstrated through the detection of a known recombinant of HIV and a detailed analysis of Noroviruses, the most common cause of viral gastroenteritis in humans.
Availability: RAT, along with a user's guide, is freely available from http://jic-bioinfo.bbsrc.ac.uk/bioinformatics-research/staff/graham_etherington/RAT.htm
Contact: Graham.Etherington@bbsrc.ac.uk
Dual-genome primer design for construction of DNA microarrays
Authors: Andersson Anders , Bernander Rolf , Nilsson Peter 
Published: August 2004

Abstract
Motivation: Microarray experiments using probes covering a whole transcriptome are expensive to initiate, and a major part of the costs derives from synthesizing gene-specific PCR primers or hybridization probes. The high costs may force researchers to limit their studies to a single organism, although comparing gene expression in different species would yield valuable information.
Results: We have developed a method, implemented in the software DualPrime, that reduces the number of primers required to amplify the genes of two different genomes. The software identifies regions of high sequence similarity, and from these regions selects PCR primers shared between the genomes, such that either one or, preferentially, both primers in a given PCR can be used for amplification from both genomes. To assure high microarray probe specificity, the software selects primer pairs that generate products of low sequence similarity to other genes within the same genome. We used the software to design PCR primers for 2182 and 1960 genes from the hyperthermophilic archaea Sulfolobus solfataricus and Sulfolobus acidocaldarius, respectively. Primer pairs were shared among 705 pairs of genes, and single primers were shared among 1184 pairs of genes, resulting in a saving of 31% compared to using only unique primers. We also present an alternative primer design method, in which each gene shares primers with two different genes of the other genome, enabling further savings.
3. Availability: The software is freely available at http://www.biotech.kth.se/molbio/microarray/
Contact: anders.andersson@biotech.kth.se
Histology of Injected Autologous Fascia in the Paralyzed Canine Vocal Fold
Authors: Reijonen Petri , Leivo Ilmo , Nevalainen Timo , Rihkanen Heikki 
Published: September 2004

AbstractObjective To evaluate the histology of minced and injected autologous fascia graft in the augmentation of unilateral vocal fold paralysis.Study Design Prospective study using a canine model.Methods Nine dogs were operated. At first, a piece of fascia was harvested from fascia lata and minced into tiny chips with a scalpel. Cutting off a section of the recurrent nerve paralyzed the right vocal fold. The minced fascia‐paste (0.1 mL) was injected using a pressure syringe into the paralyzed thyroarytenoid muscle under direct laryngoscopy. Two animals were killed at 3 days, one at 10 days, three at 6 months, and three at 12 months postinjection. Each dog underwent laryngectomy and serial coronal sections of paraffin blocks from the posterior part of the vocal folds were made.Results The dogs experienced no complications perioperatively or during follow‐up. Under microscopy, muscle of the paralyzed vocal fold was atrophied in comparison to the contralateral control. There was an acute inflammatory reaction induced by the graft. This did not exist in the specimens taken at 6 and 12 months. No extensive edema, areas of necrosis, or formation of granulomas was seen at any time. Maturation of the graft was characterized by active collagen remodeling up to 12 months. At that time the graft consisted of firm, condensed fibrous tissue. Scar formation around the graft was moderate, and the subepithelial layer of the vocal fold remained undisturbed. Each graft consisted of singular foreign bodies from the polyamide mincing plate. We cannot exclude that their presence would have had an impact on the final architecture of the graft.Conclusion In a canine vocal fold, the free fascia graft is well tolerated and after 12 months a well‐organized, collagen rich tissue is seen on histological sections. The findings are in accordance with clinical studies applying free fascia grafts.
Human Papilloma Virus and p53 Expression in Carcinomas Associated With Sinonasal Papillomas: A Danish Epidemiological Study 1980–1998
Authors: Buchwald Christian , Lindeberg Henning , Pedersen Bodil Laub , Franzmann Maria‐Benedicte 
Published: September 2004

AbstractObjectives To determine a putative role and relation between human papilloma virus (HPV) and p53 in the etiology of sinonasal carcinomas associated with papillomas.Study Design The study group consists of all patients with sinonasal carcinomas associated with papillomas diagnosed in Denmark from 1980 to 1998. After reviewing our national pathological files, tumor tissues from 36 patients were collected, comprising 15% of the total cases of sinonasal carcinomas. In 35 cases a squamous cell carcinoma was demonstrated and in one case an adenocarcinoma was evident. Inverted papilloma was associated with carcinoma in 31 cases and exophytic papillomas in 5 cases. The material was investigated for HPV using polymerase chain reaction analyses with two sets of consensus primers (GP5+/GP6+ and MY09/MY11). The HPV‐positive cases were submitted to dot‐blot hybridization to establish the HPV type. Using immunohistochemistry, the p53 expression was determined. A p53 overexpression is defined as positive staining in 10% or more of the tumor cells.Results Among 30 examined cases of carcinomas associated with inverted papillomas, 4 cases were HPV‐positive (13%). P53 overexpression was not shown among the HPV‐positive cases, whereas p53 overexpression was seen in 21 of the 24 (88%) examined HPV‐negative cases. Among the 5 carcinomas associated with exophytic papillomas, HPV was demonstrated together with p53 overexpression in 3 cases (60%). In addition, one case more was with p53 overexpression.Conclusion An inverse relation between HPV and p53 overexpression in sinonasal carcinomas associated with inverted papillomas appears to have been demonstrated. HPV and p53 might also have an etiological role among the carcinomas associated with exophytic papillomas.