bluuebunny/crossref_metadata_2025_split huggingface dataset:
An alternative echo-integrating method
Authors: Aksland Magnar 
Published: January 2005

Abstract
An alternative method of estimating the number of individuals in marine populations by echo integration is presented. The method was published almost two decades ago by the same author and here it is reviewed and developed. The method is based on just two defined concepts, the Echo Abundance and the mean Echo-Value Constant, respectively. The ratio of these quantities is equal to the number of scattering individuals within a covered area. As the Echo Abundance is estimated by interpolating echo-integrator values over selected areas, the mean Echo-Value Constant can be estimated from representative resolved echoes and their detection angles from individuals in the population, as obtained by the split-beam echosounder system. Two types of estimators for the mean Echo-Value Constant are given and discussed theoretically with respect to their properties. The approach is described and discussed in relation to the conventional theory of abundance estimation by echo integration.
The consequences of different scenarios in the management of the gillnet and purse-seine fisheries targeting Pomatomus saltatrix and Cynoscion guatucupa in southern Brazil: a bio-economic approach
Authors: Lucena Flávia , O'Brien Carl M. 
Published: January 2005

Abstract
The bluefish Pomatomus saltatrix and the striped weakfish Cynoscion guatucupa are two of the most important commercially exploited species in southern Brazil. These species overlap spatially and temporally in southern Brazil and are exploited by a multi-purpose fleet. We analyse the consequences of different management options in terms of the bio-economy of the gillnet and purse-seine fisheries by considering P. saltatrix and C. guatucupa as the main targets. Development of the bio-economic model was based upon multi-fleet, single species models for P. saltatrix and C. guatucupa. The results are compared at the medium-term forecast level from stochastic simulations, and the technical interactions between the fleets that exploit the bluefish and striped weakfish are also addressed. The purse-seine fishery has a strong impact on the gillnet fishery. A management plan, which allocates moderate levels of effort for all co-existing fleets and interacting species, seems efficient, but effort should be controlled for P. saltatrix (for both fleets) and, for the gillnet fleet, relatively more trips should be allocated for C. guatucupa. For P. saltatrix, the best management relies upon the scenarios harvesting the oldest individuals.
Local influence diagnostics for the retrospective problem in sequential population analysis
Authors: Cadigan Noel G. , Farrell Patrick J. 
Published: January 2005

AbstractThe retrospective problem involves systematic differences in sequential population analysis (SPA) estimates of stock size or some other quantity in a reference year. The differences occur as successively more data are used for estimation, and they appear to be structural biases caused by a mis-specification of the SPA. In some cases the retrospective problem is so severe that the SPA is considered to be too unreliable for stock assessment purposes. There are many possible sources of retrospective patterns, and it is usually difficult in practice to determine which are more likely. We propose diagnostics to help determine the more likely causes. We use local influence diagnostics to investigate whether small changes or perturbations to SPA input components such as catches or natural mortalities can remove or reduce retrospective patterns. We show, for the fall-spawning herring stock in the southern Gulf of St. Lawrence SPA, that relatively small age- and year-specific changes to the SPA assumptions about the proportional relationship between an abundance index and stock size can result in greatly reduced retrospective patterns. We therefore conclude primafacie that these assumptions are a plausible source of the retrospective pattern. Larger changes to catches, natural mortality assumptions, or estimation weights are required to reduce the retrospective pattern. These other factors seem to be less plausible sources of the retrospective pattern, although this is best assessed by the herring stock experts who are more knowledgeable about the fishery and other scientific information for this stock.
Bone compaction enhances implant fixation in a canine gap model
Authors: Kold Søren , Rahbek Ole , Toft Marianne , Ding Ming , Overgaard Søren , Søballe Kjeld 
Published: January 2005

AbstractA new bone preparation technique, compaction, has increased fixation of implants inserted with exact‐fit or press‐fit to bone. Furthermore, a demonstrated spring‐back effect of compacted bone might be of potential value in reducing the initial gaps that often exist between clinical inserted implants and bone. However, it is unknown whether the compression and breakage of trabeculae during the compaction procedure results in impaired gap‐healing of compacted bone. Therefore, we compared compaction with conventional drilling in a canine gap model. Grit‐blasted titanium implants (diameter 6 mm) were bilaterally inserted into cavities initially expanded to 8 mm diameters in the proximal humeri. Each dog served as its own control; thus, one humerus had the implant cavity prepared with compaction, the other with drilling. Eight dogs were euthanized after 2 weeks, and 7 dogs after 4 weeks. Humeri from additional 7 dogs represented time 0. At time 0 a spring‐back effect of compacted bone was demonstrated as cavities, initially expanded to 8 mm by compaction, were reduced to a median cavity diameter of 6.6 mm. In contrast, cavities initially expanded to 8 mm by drilling, had a median cavity diameter of 8.0 mm at time 0. Compaction significantly increased all pushout parameters at 2 weeks. Compaction significantly increased peri‐implant bone density at 0 and 2 weeks, and bone implant contact at 2 and 4 weeks. The faster mechanical and histological fixation with compaction indicates that the beneficial effect of reduced gap size, as compacted bone springs back, is not eliminated by an impaired gap‐healing of compacted bone. © 2004 Orthopaedic Research Society. Published by Elsevier Ltd. All rights reserved.
The influence of bone allograft processing on osteoblast attachment and function
Authors: Hofmann A. , Konrad L. , Hessmann M. H. , Küuchle R. , Korner J. , Rompe J. D. , Rommens P. M. 
Published: January 2005

AbstractIn order to assess the influence of eight different sterilisation and disinfection methods for bone allografts on adhesion, proliferation, and differentiation of human bone marrow stromal cells (BMSC), cells were grown in culture and then plated onto pieces of human bone allografts. Following processing methods were tested: autoclavation (AUT), low‐temperature‐plasma sterilisation of demineralised allografts (D‐LTP), ethylene oxide sterilisation (EtO), fresh frozen bone (FFB), 80°C‐thermodisinfection (80°C), γ‐irradiation (Gamma), chemical solvent disinfection (CSD), and Barrycidal®‐disinfection (BAR). The seeding efficiency was determined after one hour to detect the number of attached cells before mitosis started. The cell viability was determined after 3, 7, and 21 days. Tests to confirm the osteoblastic differentiation included histochemical alkaline phosphatase staining and RT‐PCR for osteocalcin.Human BMSC showed greatest attachment affinities for D‐LTP‐, 80°C‐, and CSD‐allografts, whereas less cells were found attached to AUT‐, EtO‐, FFB‐, Gamma‐, and BAR‐probes. Cell viability assays at day 3 revealed highest proliferation rates within the FFB‐ and 80°C‐groups, whereas after 21 days most viable cells were found in D‐LTP‐, 80°C‐, CSD‐, and Gamma‐groups. BAR‐treatment showed a considerably toxic effect and therefore was excluded from all further experiments. Highest AP‐activity and gene expression of osteocalcin were detected in the D‐LTP‐group in comparison with all other groups.In summary, our results demonstrate that cell adhesion, final population, and function of BMSC are influenced by different disinfection and sterilisation methods. Therefore, processing‐related alterations of BMSC‐function may be important for the success of bone grafting. The experimental setup used in the present work may be useful for further optimisation of bone allograft processing. © 2004 Orthopaedic Research Society. Published by Elsevier Ltd. All rights reserved.
An Auxin Transport Independent Pathway Is Involved in Phosphate Stress-Induced Root Architectural Alterations in Arabidopsis. Identification of BIG as a Mediator of Auxin in Pericycle Cell Activation
Authors: López-Bucio José , Hernández-Abreu Esmeralda , Sánchez-Calderón Lenin , Pérez-Torres Anahí , Rampey Rebekah A. , Bartel Bonnie , Herrera-Estrella Luis 
Published: January 2005

Abstract
Arabidopsis (Arabidopsis thaliana) plants display a number of root developmental responses to low phosphate availability, including primary root growth inhibition, greater formation of lateral roots, and increased root hair elongation. To gain insight into the regulatory mechanisms by which phosphorus (P) availability alters postembryonic root development, we performed a mutant screen to identify genetic determinants involved in the response to P deprivation. Three low phosphate-resistant root lines (lpr1-1 to lpr1-3) were isolated because of their reduced lateral root formation in low P conditions. Genetic and molecular analyses revealed that all lpr1 mutants were allelic to BIG, which is required for normal auxin transport in Arabidopsis. Detailed characterization of lateral root primordia (LRP) development in wild-type and lpr1 mutants revealed that BIG is required for pericycle cell activation to form LRP in both high (1 mm) and low (1 μ m) P conditions, but not for the low P-induced alterations in primary root growth, lateral root emergence, and root hair elongation. Exogenously supplied auxin restored normal lateral root formation in lpr1 mutants in the two P treatments. Treatment of wild-type Arabidopsis seedlings with brefeldin A, a fungal metabolite that blocks auxin transport, phenocopies the root developmental alterations observed in lpr1 mutants in both high and low P conditions, suggesting that BIG participates in vesicular targeting of auxin transporters. Taken together, our results show that auxin transport and BIG function have fundamental roles in pericycle cell activation to form LRP and promote root hair elongation. The mechanism that activates root system architectural alterations in response to P deprivation, however, seems to be independent of auxin transport and BIG.
Cyanidioschyzon merolae Genome. A Tool for Facilitating Comparable Studies on Organelle Biogenesis in Photosynthetic Eukaryotes
Authors: Misumi Osami , Matsuzaki Motomichi , Nozaki Hisayoshi , Miyagishima Shin-ya , Mori Toshiyuki , Nishida Keiji , Yagisawa Fumi , Yoshida Yamato , Kuroiwa Haruko , Kuroiwa Tsuneyoshi 
Published: January 2005

Abstract
The ultrasmall unicellular red alga Cyanidioschyzon merolae lives in the extreme environment of acidic hot springs and is thought to retain primitive features of cellular and genome organization. We determined the 16.5-Mb nuclear genome sequence of C. merolae 10D as the first complete algal genome. BLASTs and annotation results showed that C. merolae has a mixed gene repertoire of plants and animals, also implying a relationship with prokaryotes, although its photosynthetic components were comparable to other phototrophs. The unicellular green alga Chlamydomonas reinhardtii has been used as a model system for molecular biology research on, for example, photosynthesis, motility, and sexual reproduction. Though both algae are unicellular, the genome size, number of organelles, and surface structures are remarkably different. Here, we report the characteristics of double membrane- and single membrane-bound organelles and their related genes in C. merolae and conduct comparative analyses of predicted protein sequences encoded by the genomes of C. merolae and C. reinhardtii. We examine the predicted proteins of both algae by reciprocal BLASTP analysis, KOG assignment, and gene annotation. The results suggest that most core biological functions are carried out by orthologous proteins that occur in comparable numbers. Although the fundamental gene organizations resembled each other, the genes for organization of chromatin, cytoskeletal components, and flagellar movement remarkably increased in C. reinhardtii. Molecular phylogenetic analyses suggested that the tubulin is close to plant tubulin rather than that of animals and fungi. These results reflect the increase in genome size, the acquisition of complicated cellular structures, and kinematic devices in C. reinhardtii.
Nitric Oxide Mediates Gravitropic Bending in Soybean Roots
Authors: Hu Xiangyang , Neill Steven J. , Tang Zhangcheng , Cai Weiming 
Published: January 2005

Abstract
Plant roots are gravitropic, detecting and responding to changes in orientation via differential growth that results in bending and reestablishment of downward growth. Recent data support the basics of the Cholodny-Went hypothesis, indicating that differential growth is due to redistribution of auxin to the lower sides of gravistimulated roots, but little is known regarding the molecular details of such effects. Here, we investigate auxin and gravity signal transduction by demonstrating that the endogenous signaling molecules nitric oxide (NO) and cGMP mediate responses to gravistimulation in primary roots of soybean (Glycine max). Horizontal orientation of soybean roots caused the accumulation of both NO and cGMP in the primary root tip. Fluorescence confocal microcopy revealed that the accumulation of NO was asymmetric, with NO concentrating in the lower side of the root. Removal of NO with an NO scavenger or inhibition of NO synthesis via NO synthase inhibitors or an inhibitor of nitrate reductase reduced both NO accumulation and gravitropic bending, indicating that NO synthesis was required for the gravitropic responses and that both NO synthase and nitrate reductase may contribute to the synthesis of the NO required. Auxin induced NO accumulation in root protoplasts and asymmetric NO accumulation in root tips. Gravistimulation, NO, and auxin also induced the accumulation of cGMP, a response inhibited by removal of NO or by inhibitors of guanylyl cyclase, compounds that also reduced gravitropic bending. Asymmetric NO accumulation and gravitropic bending were both inhibited by an auxin transport inhibitor, and the inhibition of bending was overcome by treatment with NO or 8-bromo-cGMP, a cell-permeable analog of cGMP. These data indicate that auxin-induced NO and cGMP mediate gravitropic curvature in soybean roots.
Phylogenetic Analyses Identify 10 Classes of the Protein Disulfide Isomerase Family in Plants, Including Single-Domain Protein Disulfide Isomerase-Related Proteins
Authors: Houston Norma L. , Fan Chuanzhu , Xiang (Jenny) Qiu-Yun , Schulze Jan-Michael , Jung Rudolf , Boston Rebecca S. 
Published: January 2005

Abstract
Protein disulfide isomerases (PDIs) are molecular chaperones that contain thioredoxin (TRX) domains and aid in the formation of proper disulfide bonds during protein folding. To identify plant PDI-like (PDIL) proteins, a genome-wide search of Arabidopsis (Arabidopsis thaliana) was carried out to produce a comprehensive list of 104 genes encoding proteins with TRX domains. Phylogenetic analysis was conducted for these sequences using Bayesian and maximum-likelihood methods. The resulting phylogenetic tree showed that evolutionary relationships of TRX domains alone were correlated with conserved enzymatic activities. From this tree, we identified a set of 22 PDIL proteins that constitute a well-supported clade containing orthologs of known PDIs. Using the Arabidopsis PDIL sequences in iterative BLAST searches of public and proprietary sequence databases, we further identified orthologous sets of 19 PDIL sequences in rice (Oryza sativa) and 22 PDIL sequences in maize (Zea mays), and resolved the PDIL phylogeny into 10 groups. Five groups (I–V) had two TRX domains and showed structural similarities to the PDIL proteins in other higher eukaryotes. The remaining five groups had a single TRX domain. Two of these (quiescin-sulfhydryl oxidase-like and adenosine 5′-phosphosulfate reductase-like) had putative nonisomerase enzymatic activities encoded by an additional domain. Two others (VI and VIII) resembled small single-domain PDIs from Giardia lamblia, a basal eukaryote, and from yeast. Mining of maize expressed sequence tag and RNA-profiling databases indicated that members of all of the single-domain PDIL groups were expressed throughout the plant. The group VI maize PDIL ZmPDIL5-1 accumulated during endoplasmic reticulum stress but was not found within the intracellular membrane fractions and may represent a new member of the molecular chaperone complement in the cell.
Functional and Developmental Impact of Cytosolic Protein N-Terminal Methionine Excision in Arabidopsis
Authors: Ross Simon , Giglione Carmela , Pierre Michèle , Espagne Christelle , Meinnel Thierry 
Published: January 2005

Abstract
Protein N-terminal methionine (Met) excision (NME) is carried out by two types of Met aminopeptidases (MAPs), MAP1 and MAP2, in eukaryotes. Three enzymes, MAP1A, MAP2A, and MAP2B, have been identified in the cytoplasm of Arabidopsis (Arabidopsis thaliana). MAP transcript quantification revealed a predominance of MAP2B and developmental and organ-specific regulation of both MAP1A and MAP2s. By combining reverse genetics and reverse chemogenomics in transgenic plant lines, we have devised specific and reversible switches for the investigation of the role of cytoplasmic NME in Arabidopsis and of the respective contributions of the two types of cytoplasmic MAPs throughout development. dsRNA interference and knockout (KO) plant lines targeting either MAP1A alone or both MAP2s simultaneously were constructed and shown to display wild-type phenotypes. In the MAP1A KO context, modulating MAP2 activity by treatment with various concentrations of the specific drug fumagillin impaired plant development, with particularly strong effects on the root system. Reciprocally, complete MAP2 inhibition in various MAP1A knocked-down genetic backgrounds also generated a gradient of developmentally abnormal plants, but the effects on the root system were milder than in the KO context. In the absence of MAP2 activity, the severity of the phenotype in the MAP1A knocked-down lines was correlated to the extent of MAP1A mRNA accumulation. Complete cytoplasmic NME inactivation blocked development after plant germination. Thus, in plants, (1) cytoplasmic NME is essential; (2) MAP1A and MAP2s are functionally interchangeable, which is not the case in fungi and animals, as a complete block of either MAP-type activity does not cause any visible molecular or phenotypic effect; and (3) a minimal level of cytoplasmic MAP is required for normal development.
A distinct subset of chemokines dominates the mucosal chemokine response in inflammatory bowel disease
Authors: Puleston J. , Cooper M. , Murch S. , Bid K. , Makh S. , Ashwood P. , Bingham A. H. , Green H. , Moss P. , Dhillon A. , Morris R. , Strobel S. , Gelinas R. , Pounder R. E. , Platt A. 
Published: January 2005

SummaryBackground : Inflammatory bowel disease (IBD) is characterised by intense mucosal recruitment of activated leukocytes. Chemokines determine inflammatory leukocyte recruitment and retention.Aim : To compare expression of the entire chemokine family within colonic mucosa from IBD patients and uninflamed controls.Methods : A microarray of cDNAs, representing every member of this superfamily and their cognate receptors, was hybridised with probes derived from colonoscopic biopsies.Results : A distinct subset of chemokines, consisting of CXCLs 1–3 and 8 and CCL20, was upregulated in active colonic IBD, compared with uninflamed areas or tissue from controls. Increased expression of their cognate receptors, CXCR1, CXCR2 and CCR6, was confirmed by quantitative PCR and immunohistochemistry. An identical chemokine response was induced in Caco‐2 cells by stimulation with interleukin (IL)‐1β, but not tumour necrosis factor‐alpha (TNF‐α). By contrast, IL‐1β and TNF‐α were synergistic in an HT29 cell line and primary keratinocytes.Conclusions : IL‐1β and TNF‐α appear to be the pivotal mediators of a previously unidentified coordinated epithelial chemokine response that dominates the mucosal chemokine environment in inflamed IBD tissue.
Rebound acid hypersecretion after long‐term inhibition of gastric acid secretion
Authors: Fossmark R. , Johnsen G. , Johanessen E. , Waldum H. L. 
Published: January 2005

SummaryBackground : Rebound acid hypersecretion develops after the use of acid inhibitors.Aim : To estimate the duration of hypersecretion and to elucidate the role of the enterochromaffin‐like (ECL) cell in rebound acid hypersecretion.Methods : Patients waiting for anti‐reflux surgery who had used a proton pump inhibitor daily > 1 year were included. All patients discontinued taking acid inhibiting drugs after the operation. Basal and pentagastrin stimulated acid output was measured at 4, 8, 16 and 26 weeks postoperatively. Oxyntic mucosal biopsies were collected before and 26 weeks after the operation for counting of histidine decarboxylase (HDC) immunoreactive cells. Serum chromogranin A (CgA) and gastrin were measured before and at 4, 8, 16 and 26 weeks after the operation.Results : Pentagastrin stimulated acid secretion was higher at 4 and 8 weeks than at 26 weeks after the operation. Gastrin and CgA were significantly reduced at 4 and 8 weeks, respectively. The number of HDC immunoreactive cells was reduced by 60% at 26 weeks postoperative.Discussion : Rebound acid hypersecretion lasts more than 8 weeks, but less than 26 weeks after long‐term proton pump inhibition.Conclusion : The findings indicate that not only the parietal cell mass, but also ECL cell mass and activity are involved in the mechanism of acid hypersecretion.
A double‐blind dose‐escalating trial comparing novel mesalazine pellets with mesalazine tablets in active ulcerative colitis
Authors: Marakhouski Y. , Fixa B. , Holomán J. , Hulek P. , Lukas M. , Bátovský M. , Rumyantsev V. G. , Grigoryeva G. , Stolte M. , Vieth M. , Greinwald R. ,   The International Salofalk Study Group
Published: January 2005

SummaryBackground : Mesalazine as the treatment standard for ulcerative colitis can be applied in different galenical preparations.Aim : A novel formulation of mesalazine pellets with delayed and prolonged release characteristics was compared with conventional Eudragit L‐coated tablets. Furthermore, the effect of mesalazine dose escalation on nonresponders was evaluated in both treatment groups.Methods : A total of 233 patients with mild to moderately active ulcerative colitis were randomized to receive either mesalazine (1.5 g/day in three doses) as pellets (n = 115) or tablets (n = 118) for 8 weeks. At insufficient response, the dose was increased to 3.0 g.Results : The clinical remission rate (clinical activity index ≤ 4) for pellets was 67% vs. 68% for tablets which statistically proved to be not inferior (significance level α = 2.5%). In patients without dose increase, the remission rate was 47% (pellets) vs. 42% (tablets). Endoscopic improvement was observed in 80% (pellets) vs. 83% (tablets), and histological improvement in 48% (pellets) vs. 52% (tablets) of patients.Conclusions : Mesalazine pellets are as effective as tablets in the treatment of mild to moderately active ulcerative colitis. Dose escalation to 3.0 g/day is a valid option for nonresponders to a starting dose of 1.5 g/day.