bluuebunny/crossref_metadata_2025_split huggingface dataset:
T-REKS: identification of Tandem REpeats in sequences with a K-meanS based algorithm
Authors: Jorda Julien , Kajava Andrey V. 
Published: August 2009

Abstract
Motivation: Over the last years a number of evidences have been accumulated about high incidence of tandem repeats in proteins carrying fundamental biological functions and being related to a number of human diseases. At the same time, frequently, protein repeats are strongly degenerated during evolution and, therefore, cannot be easily identified. To solve this problem, several computer programs which were based on different algorithms have been developed. Nevertheless, our tests showed that there is still room for improvement of methods for accurate and rapid detection of tandem repeats in proteins.
Results: We developed a new program called T-REKS for ab initio identification of the tandem repeats. It is based on clustering of lengths between identical short strings by using a K-means algorithm. Benchmark of the existing programs and T-REKS on several sequence datasets is presented. Our program being linked to the Protein Repeat DataBase opens the way for large-scale analysis of protein tandem repeats. T-REKS can also be applied to the nucleotide sequences.
Availability: The algorithm has been implemented in JAVA, the program is available upon request at http://bioinfo.montp.cnrs.fr/?r=t-reks. Protein Repeat DataBase generated by using T-REKS is accessible at http://bioinfo.montp.cnrs.fr/?r=repeatDB.
Contact: julien.jorda@crbm.cnrs.fr; andrey.kajava@crbm.cnrs.fr
Supplementary information: Supplementary data are available at Bioinformatics online.
Determination of Atlantic bluefin tuna (Thunnus thynnus) spawning time within a transport cage in the western Mediterranean
Authors: Gordoa Ana , Olivar Maria Pilar , Arevalo Raquel , Viñas Jordi , Molí Balbina , Illas Xenia 
Published: August 2009

AbstractGordoa, A., Olivar, M. P., Arevalo, R., Viñas, J., Molí, B., and Illas, X. 2009. Determination of Atlantic bluefin tuna (Thunnus thynnus) spawning time within a transport cage in the western Mediterranean. – ICES Journal of Marine Science, 66: 2205–2210. For the first time, tuna spawning in a transport cage being towed from the western Mediterranean spawning ground to a fattening facility off the coast of northeastern Spain was examined during the 2008 fishing season. Daylight and night surface plankton samples were collected using bongo nets located in front of and behind the transport cage. The results for the different time intervals revealed clear and massive nocturnal spawning from 03:00 to 05:00, when the rear bongo was completely jammed with eggs (up to 250 000–300 000 eggs per 1000 m3). Egg size and morphology were consistent with the features of Thunnus thynnus eggs, and identification was confirmed by genetic analysis. Microscopic examination showed the eggs to be in the very early developmental stages. Spawning took place every night over the entire journey. The study showed that neither captivity nor handling/environmental changes along the route inhibited T. thynnus spawning to a very precise biological clock. The study also revealed the diel temporal concurrence of T. thynnus spawning and jellyfish larvae at the sea surface.
Remarks on “Comment on: Williams et al. (2009) Australia's deep-water reserve network: implications of false homogeneity for classifying abiotic surrogates of biodiversity, ICES Journal of Marine Science, 66: 214–224” by Peter T. Harris, Andrew D. Heap, Tara J. Anderson, and Brendan Brooke
Authors: Williams Alan , Bax Nicholas J. , Kloser Rudy J. 
Published: August 2009

Abstract
Williams, A., Bax, N. J., and Kloser, R. J. 2009. Remarks on “Comment on: Williams et al. (2009) Australia's deep-water reserve network: implications of false homogeneity for classifying abiotic surrogates of biodiversity, ICES Journal of Marine Science, 66: 214–224” by Peter T. Harris, Andrew D. Heap, Tara J. Anderson, and Brendan Brooke. – ICES Journal of Marine Science, 66: 2086–2088. Commitment by many nations at the 2002 World Summit on Sustainable Development to complete national networks of Marine Protected Areas (MPAs) by 2012 focused attention on MPA design and implementation, especially for the deep waters that make up the majority of many national EZs. Further, there is a focus on conservation in the High Seas through the Convention on Biological Biodiversity and the FAO, e.g. for seamounts and other vulnerable benthic habitats. Any manuscript that raises basic issues on one identified area for conservation is therefore a prospectively useful addition to the international debate. The Comment by Harris et al. (2009) on a paper authored by myself and colleagues (Williams et al., 2009) is a potentially useful contribution. The authors provide data, examples, and insights into aspects of the design and planning process for Australia's SE network of reserves. Here, we address the main question of how geological descriptions can be used or modified to provide the most information on marine biodiversity patterns for use in conservation planning—in the context of the major points raised by Harris et al. (2009).
Spatial segregation among fishing vessels in a multispecies fishery
Authors: Poos J. J. , Quirijns F. J. , Rijnsdorp A. D. 
Published: August 2009

Abstract
Poos, J. J., Quirijns, F. J., and Rijnsdorp, A. D. 2010. Spatial segregation among fishing vessels in a multispecies fishery. – ICES Journal of Marine Science, 67: 155–164. Individual decisions of fishers on where to fish in heterogeneous environments may shape the relation between fishing effort and fishing mortality. Fishers may be viewed as individual foragers, whose decisions are aimed at optimizing short-term gain, as in ideal free distribution (IFD) theory. Although IFD assumes all foragers to be equal, they are likely to differ in competitive abilities for different prey types or target species. Here, we present an IFD-like model of a fishing fleet consisting of two components with different competitive abilities for two target species, showing that spatial segregation can result from unequal interference competition, but also in the absence of interference competition. Differences in catch efficiency between vessels for target species in combination with differences in the spatial distribution of target species can result in spatial segregation among vessel groups. The theoretical results are used to interpret the observed spatial segregation of two components within the Dutch beam trawl fleet using observations from a vessel monitoring by satellite system. However, this study cannot pinpoint which of the processes included in the theoretical model is the prime cause of the segregation within the Dutch beam trawl fleet.
Proteolysis of a Negative Regulator of Innate Immunity Is Dependent on Resistance Genes in Tomato and Nicotiana benthamiana and Induced by Multiple Bacterial Effectors
Authors: Luo Yao , Caldwell Katherine S. , Wroblewski Tadeusz , Wright Michael E. , Michelmore Richard W. 
Published: August 2009

Abstract
RPM1-interacting protein 4 (RIN4), a negative regulator of the basal defense response in plants, is targeted by multiple bacterial virulence effectors. We show that RIN4 degradation is induced by the effector AvrPto from Pseudomonas syringae and that this degradation in Solanaceous plants is dependent on the resistance protein, Pto, a protein kinase, and Prf, a nucleotide binding site–leucine-rich repeat protein. Our data demonstrate overlap between two of the best-characterized pathways for recognition of pathogen virulence effectors in plants. RIN4 interacts with multiple plant signaling components and bacterial effectors in yeast and in planta. AvrPto induces an endogenous proteolytic activity in both tomato (Solanum lycopersicum) and Nicotiana benthamiana that degrades RIN4 and requires the consensus site cleaved by the protease effector AvrRpt2. The interaction between AvrPto and Pto, but not the kinase activity of Pto, is required for proteolysis of RIN4. Analysis of many of the effectors comprising the secretome of P. syringae pv tomato DC3000 led to the identification of two additional sequence-unrelated effectors that can also induce degradation of RIN4. Therefore, multiple bacterial effectors besides AvrRpt2 elicit proteolysis of RIN4 in planta.
The Mediator Complex Subunit PFT1 Is a Key Regulator of Jasmonate-Dependent Defense inArabidopsis
Authors: Kidd Brendan N. , Edgar Cameron I. , Kumar Krish K. , Aitken Elizabeth A. , Schenk Peer M. , Manners John M. , Kazan Kemal 
Published: August 2009

AbstractJasmonate signaling plays an important role in both plant defense and development. Here, we have identified a subunit of the Mediator complex as a regulator of the jasmonate signaling pathway in Arabidopsis thaliana. The Mediator complex is a conserved multiprotein complex that acts as a universal adaptor between transcription factors and the RNA polymerase II transcriptional machinery. We report that the PHYTOCHROME AND FLOWERING TIME1 (PFT1) gene, which encodes the MEDIATOR25 subunit of Mediator, is required for jasmonate-dependent defense gene expression and resistance to leaf-infecting necrotrophic fungal pathogens. Conversely, PFT1 appears to confer susceptibility to Fusarium oxysporum, a root-infecting hemibiotrophic fungal pathogen known to hijack jasmonate responses for disease development. Consistent with this, jasmonate gene expression was suppressed in the pft1 mutant during infection with F. oxysporum. In addition, a wheat (Triticum aestivum) homolog of PFT1 complemented the defense and the developmental phenotypes of the pft1 mutant, suggesting that the jasmonate signaling functions of PFT1 may be conserved in higher plants. Overall, our results identify an important control point in the regulation of the jasmonate signaling pathway within the transcriptional machinery.
Covalent bonded Gag multimers in human immunodeficiency virus type‐1 particles
Authors: Kitagawa Yoshinori , Maeda‐Sato Masae , Tanaka Keiko , Tobiume Minoru , Sawa Hirofumi , Hasegawa Hideki , Kojima Asato , Hall William W. , Kurata Takeshi , Sata Tetsutaro , Takahashi Hidehiro 
Published: August 2009

ABSTRACTThe oligomerization of HIV‐1 Gag and Gag‐Pol proteins, which are assembled at the plasma membrane, leads to viral budding. The budding generally places the viral components under non‐reducing conditions. Here the effects of non‐reducing conditions on Gag structures and viral RNA protection were examined. Using different reducing conditions and SDS‐PAGE, it was shown that oligomerized Gag possesses intermolecular covalent bonds under non‐reducing conditions. In addition, it was demonstrated that the mature viral core contains a large amount of covalent bonded Gag multimers, as does the immature core. Viral genomic RNA becomes sensitive to ribonuclease in reducing conditions. These results suggest that, under non‐reducing conditions, covalent bonded Gag multimers are formed within the viral particles and play a role in protection of the viral genome.
Characterization of integrons and antimicrobial resistance genes in clinical isolates of Gram‐negative bacteria from Palestinian hospitals
Authors: Hussein Amjad I. A. , Ahmed Ashraf M. , Sato Maiko , Shimamoto Tadashi 
Published: August 2009

ABSTRACTSixty Gram‐negative bacterial isolates were collected from Palestinian hospitals in 2006. Thirty‐two (53.3%) isolates showed multidrug resistance phenotypes. PCR and DNA sequencing were used to characterize integrons and antimicrobial resistance genes. PCR screening showed that 19 (31.7%) and five (8.3%) isolates were positive for class 1 and class 2 integrons, respectively. DNA‐sequencing results for the captured antimicrobial resistance gene cassettes within class 1 integrons identified the following genes: dihydrofolate reductases, dfrA1, dfrA5, dfrA7, dfrA12, dfrA17 and dfrA25; aminoglycoside adenyltransferases, aadA1, aadA2, aadA5, aadA12 and aadB; aminoglycoside acetyltransferase, aac(6′)‐Ib; and chloramphenicol resistance gene, cmlA1. ESBL were identified in 25 (41.7%) isolates. The identified ESBL were blaCTX‐M‐15, blaCTX‐M‐56, blaOXA‐1, blaSHV‐1, blaSHV‐12, blaSHV‐32 and blaTEM‐1 genes. Moreover, we characterized the plasmid‐mediated quinolone resistance genes, aac(6′)‐Ib‐cr and qnrB2, which were detected in seven (11.7%) and two (3.3%) isolates, respectively. In this study various types of antibiotic resistance genes have been identified in Gram‐negative bacteria from Palestinian hospitals, many of which are reported in the Middle East area for the first time.
Review article: the modern management of portal vein thrombosis
Authors: CHAWLA Y. , DUSEJA A. , DHIMAN R. K. 
Published: August 2009

SummaryBackground  Portal vein thrombosis (PVT) is an important cause of portal hypertension. It may occur as such with or without associated cirrhosis and hepatocellular carcinoma. Information on its management is scanty.Aim  To provide an update on the modern management of portal vein thrombosis. Information on portal vein thrombosis in patients with and without cirrhosis and hepatocellular carcinoma is also updated.Methods  A pubmed search was performed to identify the literature using search items portal vein thrombosis‐aetiology and treatment and portal vein thrombosis in cirrhosis and hepatocellular carcinoma.Results  Portal vein thrombosis occurs because of local inflammatory conditions in the abdomen and prothrombotic factors. Acute portal vein thrombosis is usually symptomatic when associated with cirrhosis and/or superior mesenteric vein thrombosis. Anticoagulation should be given for 3–6 months if detected early. If prothrombotic factors are identified, anticoagulation should be given lifelong. Chronic portal vein thrombosis usually presents with well tolerated upper gastrointestinal bleed. It is diagnosed by imaging, which demonstrates a portal cavernoma in place of a portal vein. Anticoagulation does not have a definite role, but bleeds can be treated with endotherapy or shunt surgery. Rarely liver transplantation may be considered.Conclusion  Role of anticoagulation in chronic portal vein thrombosis needs to be further studied.
Clinical trial: ulcerative colitis maintenance treatment with 5‐ASA: a 1‐year, randomized multicentre study comparing MMX® with Asacol®
Authors: PRANTERA C. , KOHN A. , CAMPIERI M. , CAPRILLI R. , COTTONE M. , PALLONE F. , SAVARINO V. , STURNIOLO G. C. , VECCHI M. , ARDIA A. , BELLINVIA S. 
Published: August 2009

SummaryBackground  5‐ASA‐MMX® (1.2 g/tablet) is a 5‐aminosalicylic acid formulation, designed for once‐daily dosing in the treatment of ulcerative colitis.Aim  To evaluate the efficacy and safety of 5‐ASA‐MMX (2.4 g/day, once daily), compared with Asacol® (2.4 g/day, twice daily) in the maintenance of left‐sided UC, through a double‐blind, double‐dummy, parallel‐group, randomized, comparator study.Methods  In all, 331 patients with UC were randomized to receive either 5‐ASA‐MMX 2.4 g/day, once daily, or Asacol 2.4 g/day, twice daily, for 12 months. All patients were in remission for ≥1 month prior to the trial, with ≥1 documented relapse in the previous year. The co‐primary endpoints of this study were the proportion of patients in clinical, and clinical and endoscopic remission following 12 months’ treatment.Results  In the intent‐to‐treat population, excluding those with major protocol deviations, 68.0 and 65.9% patients in the 5‐ASA‐MMX and Asacol groups, respectively, were in clinical remission (P = 0.69), and 60.9 and 61.7% of patients, respectively, were in clinical and endoscopic remission (P = 0.89). Diary card data revealed statistically significant treatment differences favouring 5‐ASA‐MMX. Both treatments were similarly tolerated.Conclusions  Once‐daily 5‐ASA‐MMX is similarly effective with a comparable safety profile to Asacol administered twice daily, for the maintenance treatment of ulcerative colitis.
Effects of bisacodyl on ascending colon emptying and overall colonic transit in healthy volunteers
Authors: MANABE N. , CREMONINI F. , CAMILLERI M. , SANDBORN W. J. , BURTON D. D. 
Published: August 2009

SummaryBackground The mechanism of action of bisacodyl in the unprepared human colon remains unclear.Aim To evaluate the effect of oral bisacodyl on the overall and regional colonic transit in humans.Methods In a double‐blind, randomized, placebo‐controlled study of 25 healthy participants, effects of oral bisacodyl (5 mg p.o. per day) and placebo on colonic transit were compared. A validated scintigraphy method was used to measure colonic transit. The primary transit endpoints, ascending colon emptyingt1/2and geometric centre of colon isotope at 24 h (overall transit), were compared (Wilcoxon rank sum test).Results There were significant treatment effects on ascending colont1/2, with the bisacodyl group demonstrating accelerated emptying [median 6.5 h, interquartile range 5.0–8.0 h] relative to the placebo group [11.0 h (7.0–17.1);P = 0.03]. Numerical differences in colonic geometric centre 24 h [bisacodyl median 3.0 (2.2–3.8), placebo 4.0 (3.1–4.6)] were not significant (P = 0.19). There were no significant differences observed in geometric centre 4 h.Conclusion Oral 5 mg bisacodyl accelerates ascending colon in the unprepared colon in healthy adults; this action may contribute to the drug’s efficacy in constipation.
Effect of Heliothis subflexa herbivory on fruit abscission by Physalis species: the roles of mechanical damage and chemical factors
Authors: PETZOLD JENNIFER , BROWNIE CAVELL , GOULD FRED 
Published: August 2009

Abstract.1. Insect oral secretions are important for the induction of a number of plant responses, but the relative role of mechanical damage in the induction of these responses is often not well understood. Damage from the frugivore Heliothis subflexa, a specialist on Physalis species, causes herbivore‐induced fruit abscission. In this field study, we examined the separate and combined effects of mechanical damage and H. subflexa oral secretions on Physalis fruit abscission.2. To determine the relative role of mechanical and chemical factors, the following treatments were administered to fruit: (1) three levels of mechanical damage, (2) natural herbivore damage by control larvae and by larvae surgically treated to inhibit saliva secretion, and (3) injection of H.subflexa oral secretions and a water control. Abscission of mechanically damaged fruit with and without the addition of oral secretions was also compared.3. Mechanical damage was sufficient to cause fruit abscission, and the addition of oral secretions to mechanically damaged fruit did not cause an increase in fruit abscission. Normal caterpillars and those treated to inhibit saliva secretion caused similar abscission rates.4. Though most studies examining the effects of insect oral secretions on induced plant responses find these chemical stimuli to be important or essential, the results of the present study showed that oral secretions are not necessary for fruit abscission. Future work is needed to determine the relative importance of mechanical damage in herbivore‐induced plant responses in other systems.
Adapted DAX‐8 fractionation method for dissolved organic matter (DOM) from soils: development, calibration with test components and application to contrasting soil solutions
Authors: Amery F. , Vanmoorleghem C. , Smolders E. 
Published: August 2009

SummaryMost methods to fractionate natural dissolved organic matter (DOM) rely on sorption of acidified DOM samples onto XAD‐8 or DAX‐8 resin. Procedural differences among methods are large and their interpretation is limited because there is a lack of calibration with DOM model molecules. An automated column‐based DOM fractionation method was set up for 10‐ml DOM samples, dividing DOM into hydrophilic (HPI), hydrophobic acid (HPOA) and hydrophobic neutral (HPON) fractions. Fifteen DOM model components were tested in isolation and in combination. Three reference DOM samples of the International Humic Substances Society were included to facilitate comparison with other methods. Aliphatic low‐molecular‐weight acids (LMWAs) and carbohydrates were classified as HPI DOM, but some LMWAs showed also a partial HPO character. Aromatic LMWAs and polyphenols partitioned in the HPOA fraction, menadione (quinone) and geraniol (terpenoid) in HPON DOM. Molecules with log Kow > 0.5 had negligible HPI fractions. The HPO molecules except geraniol had specific UV absorbance (SUVA, measure for aromaticity) >3 litres g−1 cm−1 while HPI molecules had SUVA values <3 litres g−1 cm−1. Distributions of DOM from eight soils ranged from 31 to 72% HPI, 25 to 46% HPOA and 2 to 28% HPON of total dissolved organic carbon. The SUVA of the HPI DOM was consistently smaller compared with the HPOA DOM. The SUVA of the natural DOM samples was not explained statistically by fractionation and the variation coefficient of SUVA among samples was not reduced by fractionation. Hence, fractionation did not reduce the variability in this DOM property, which casts some doubts on the practical role of DOM fractionation in predicting DOM properties.
Diversity of total, nitrogen‐fixing and denitrifying bacteria in an acid forest soil
Authors: Rösch C. , Bothe H. 
Published: August 2009

SummaryTo assess the diversity of total, denitrifying and N2‐fixing bacteria in a nitrogen (N)‐limited, acid forest soil, isolated DNA was analysed for the genes 16S rRNA, nosZ and nifH. Sequence information for these genes was obtained from clone libraries and from our TReFID computer program, which employs terminal restriction patterns for bacteria using multiple restriction enzymes. Both approaches indicated that Proteobacteria (α‐ and γ‐groups) and Acidobacteria dominated. A comprehensive list of bacteria retrieved from this soil is provided and compared with literature data on the bacterial community compositions from other sites. The study indicated that the current PCR conditions with the primers employed allowed retrieval of only a portion of the bacteria occurring in soils. Massive treatment of a soil plot with NH4NO3 caused an increase in the N content, which was rapidly followed by an enhancement of carbon (C) content. Thus the C/N ratio stayed below 16.0 and the soil remained N‐limited. This may explain why the bacterial diversity did not undergo drastic shifts as was tentatively inferred from the available data sets.
Anticipatory anxiety in children visiting the dentist: lack of effect of preparatory information
Authors: OLUMIDE FUNMI , NEWTON J TIM , DUNNE STEPHEN , GILBERT DAVID B. 
Published: August 2009

Aim.  This study sought to explore whether viewing a leaflet explaining the benefits of dental treatment would have a significant impact on children's anticipatory anxiety.Method.  Fifty children aged 8–12, attending the paediatric dental clinic of King's College Hospital, London, took part in this triple‐masked, randomized control study. The participants were randomly allocated to one of two groups and either shown an intervention leaflet containing child‐friendly dental information (the experimental group) or a leaflet with child‐friendly information on the benefits of healthy eating (the control group). Using the Facial Image Scale, anxiety was measured when the children arrived for their dental appointment, once before reading the leaflet and again after reading the leaflet.Results.  There was no statistically significant effect of the experimental leaflet on self‐reported anxiety levels in this study, although anxiety levels did drop slightly in both groups after reading a leaflet.Conclusions.  Providing paediatric patients with preparatory information about what to expect from a visit to the dentist had no effect on anticipatory anxiety in comparison to reading a leaflet about healthy eating. We speculate that reading, or cognitive processing, may have some beneficial effect. Future work should investigate this possibility.