bluuebunny/crossref_metadata_2025_split huggingface dataset:
Risk factors, Sequential Organ Failure Assessment and Model for End‐stage Liver Disease scores for predicting short term mortality in cirrhotic patients admitted to intensive care unit
Authors: CHOLONGITAS E. , SENZOLO M. , PATCH D. , KWONG K. , NIKOLOPOULOU V. , LEANDRO G. , SHAW S. , BURROUGHS A. K. 
Published: March 2006

Summary
Background  Prognostic scores in an intensive care unit (ICU) evaluate outcomes, but derive from cohorts containing few cirrhotic patients.Aims  To evaluate 6‐week mortality in cirrhotic patients admitted to an ICU, and to compare general and liver‐specific prognostic scores.Methods  A total of 312 consecutive cirrhotic patients (65% alcoholic; mean age 49.6 years). Multivariable logistic regression to evaluate admission factors associated with survival. Child–Pugh, Model for End‐stage Liver Disease (MELD), Acute Physiology and Chronic Health Evaluation (APACHE) II and Sequential Organ Failure Assessment (SOFA) scores were compared by receiver operating characteristic curves.Results  Major indication for admission was respiratory failure (35.6%). Median (range) Child–Pugh, APACHE II, MELD and SOFA scores were 11 (5–15), 18 (0–44), 24 (6–40) and 11 (0–21), respectively; 65% (n = 203) died. Survival improved over time (P = 0.005). Multivariate model factors: more organs failing (FOS) (<3 = 49.5%, ≥3 = 90%), higher FiO2, lactate, urea and bilirubin; resulting in good discrimination [area under receiver operating characteristic curve (AUC) = 0.83], similar to SOFA and MELD (AUC = 0.83 and 0.81, respectively) and superior to APACHE II and Child–Pugh (AUC = 0.78 and 0.72, respectively).Conclusions  Cirrhotics admitted to ICU with ≥3 failing organ systems have 90% mortality. The Royal Free model discriminated well and contained key variables of organ function. SOFA and MELD were better predictors than APACHE II or Child–Pugh scores.
Systematic review: the use of mesalazine in inflammatory bowel disease
Authors: BERGMAN R. , PARKES M. 
Published: March 2006

SummaryBackground Mesalazine is among the medications most commonly prescribed by gastroenterologists, having to a large extent superseded sulfasalazine (sulphasalazine). However, there are still a number of aspects regarding its use which provoke debate and controversy.Aim To provide a systematic assessment of the evidence for the use of mesalazine in ulcerative colitis and Crohn's disease.Methods References were identified using PubMed database. Additional references were identified with related article searches.Results Mesalazine has a clear role in the maintenance of remission in ulcerative colitis and management of mild to moderately active disease, although the efficacy of topical preparations or combined topical and oral is clearly superior to oral alone. Evidence that increasing the dose of oral mesalazine improves efficacy is not clear‐cut. The benefits of mesalazine in the management of acute Crohn's disease and the maintenance of remission are questionable and alternative treatments are usually more appropriate. Emerging evidence suggests that maintenance mesalazine reduces the risk of neoplastic progression in chronic ulcerative colitis. Compliance with therapy is thus important, as is an understanding of individuals most likely to default on this.Conclusion Evidence for a beneficial effect of mesalazine is largely confined to the management of ulcerative colitis.
Circulating ghrelin level is increased in coeliac disease as in functional dyspepsia and reverts to normal during gluten‐free diet
Authors: LANZINI A. , MAGNI P. , PETRONI M. L. , MOTTA M. , LANZAROTTO F. , VILLANACCI V. , AMATO M. , MORA A. , BERTOLAZZI S. , BENINI F. , RICCI C. 
Published: March 2006

SummaryBackground  It is controversial whether serum ghrelin concentration is altered in coeliac disease and whether this alteration is related to nutritional impairment or to inflammatory changes of duodenal mucosa.Aim  To investigate clinical and histopathological variables affecting circulating ghrelin in coeliac patients by comparison with dyspeptic patients and with healthy controls.Methods  We measured serum ghrelin and obtained gastric and duodenal biopsies in 44 coeliac patients before and after 1‐year gluten‐free diet, in 39 dyspeptic patients and 53 healthy controls.Results  Serum ghrelin concentration was significantly higher in coeliac (531 ± 29 pg/mL, P < 0.05) and in dyspeptic patients (526 ± 14 pg/mL, P < 0.01) than in healthy controls (451 ± 8 pg/mL), and body mass index was significantly lower in coeliac (20 ± 1) and in dyspeptic patients (20 ± 1) than in healthy controls (22 ± 1, P < 0.05). In coeliac patients serum ghrelin concentration was not related to the severity of duodenal lesions. Serum ghrelin reverted to normal (399 ± 30 pg/mL) and body mass index increased significantly (0.6 ± 0.1 kg/m2 increase, P < 0.05) during gluten‐free diet despite persistent duodenal lymphocytic infiltration.Conclusions  Ghrelin concentration is increased and body mass index is decreased in coeliac and in dyspeptic patients irrespective of presence and severity of duodenal inflammation. Nutritional impairment is a key factor in elevating plasma ghrelin levels in coeliac disease.
Pharmacogenetics of thiopurine therapy in paediatric IBD patients
Authors: DE RIDDER L. , VAN DIEREN J. M. , VAN DEVENTER H. J. H. , STOKKERS P. C. F. , VAN DER WOUDE J. C. J. , VAN VUUREN A. J. , BENNINGA M. A. , ESCHER J. C. , HOMMES D. W. 
Published: March 2006

SummaryBackground  Azathioprine is widely used in the treatment of children with inflammatory bowel disease. The occurrence and type of adverse events to azathioprine may be related to thiopurine S‐methyltransferase (TPMT) enzyme activity and to inosine triphophate pyrophosphatase (ITPase) deficiency.Aim  Investigate frequencies of functional TPMT polymorphisms and ITPA polymorphisms and their association with the occurrence of adverse events during azathioprine therapy in a paediatric inflammatory bowel disease population.Methods  Seventy‐two azathioprine treated paediatric inflammatory bowel disease patients, 47% girls, mean age 12.5 years (range 6.5–17.5), were assessed for TPMT and ITPA polymorphisms and for adverse events. The relation between polymorphisms and adverse events is evaluated.Results  Of all azathioprine treated patients, 11 experienced an adverse event for which azathioprine was stopped: pancreatitis (n = 4), leucopenia (n = 2) and ‘general malaise’ (n = 5). Of the 11 patients who stopped azathioprine because of adverse events, 10 had wild‐type alleles for all investigated genotypes. Genotyping of ITPA 94C>A polymorphisms showed that two patients were homozygous, both tolerated azathioprine well.Conclusions  No association of functional ITPA and TPMT polymorphisms and the occurrence of azathioprine related adverse events could be detected. Pharmacogenetic assessment prior to thiopurine therapy does not seem warranted.
Effects of low‐dose aspirin on gastric erosions, cyclooxygenase expression and mucosal prostaglandin‐E2 do not depend on Helicobacter pylori infection
Authors: VENERITO M. , TREIBER G. , WEX T. , KUESTER D. , ROESSNER A. , DI MARIO F. , MALFERTHEINER P. 
Published: March 2006

SummaryBackground  The mechanisms by which Helicobacter pylori and low‐dose aspirin induce gastric damage are not completely elucidated.Aim  To evaluate the effects of low‐dose aspirin on gastric damage, mucosal prostaglandin‐E2 levels and cyclooxygenase‐enzyme expression in relation to the H. pylori status.Methods  Twenty healthy volunteers (H. pylori positive, n = 10; H. pylori negative, n = 10) received aspirin 100 mg/die for 1 week. At days 0, 1, 3 and 7, gastric mucosal lesions were studied by oesophagogastroduodenoscopy and histology. COX‐1 and COX‐2 were determined by immunohistochemistry and reverse‐transcriptase polymerase chain reaction, and mucosal prostaglandin‐E2 levels by enzyme‐linked immunosorbent assay. Nine H. pylori‐positive subjects repeated the protocol after H. pylori eradication.Results  All groups developed a similar number of erosions. COX‐1 and COX‐2 expression, as well as mucosal prostaglandin‐E2 levels were not influenced by H. pylori status and aspirin medication. Helicobacter pylori‐negative and H. pylori‐eradicated subjects who developed aspirin‐induced erosions had significant lower pre‐treatment antral prostaglandin‐E2 levels than those without erosions (3.6 ng/μg vs. 6.3 ng/μg protein and 3.6 ng/μg vs. 6.0 ng/μg protein, respectively, P < 0.01 Mann–Whitney U‐test).Conclusions  In healthy subjects, low‐dose aspirin for 1 week does neither affect cyclooxygenase expression nor mucosal prostaglandin‐E2 levels. Antral prostaglandin‐E2‐basal levels appear to be critical for development of aspirin‐induced gastric damage in subjects without H. pylori infection.
Nitrogen retention in the riparian zone of catchments underlain by discontinuous permafrost
Authors: O'DONNELL JONATHAN A. , JONES JEREMY B. 
Published: March 2006

Summary1. Riparian zones function as important ecotones that reduce nitrate concentration in groundwater and inputs into streams. In the boreal forest of interior Alaska, permafrost confines subsurface flow through the riparian zone to shallow organic horizons, where plant uptake of nitrate and denitrification are typically high.2. In this study, riparian zone nitrogen retention was examined in a high permafrost catchment (approximately 53% of land area underlain by permafrost) and a low permafrost catchment (approximately 3%). To estimate the contribution of the riparian zone to catchment nitrogen retention, we analysed groundwater chemistry using an end‐member mixing model.3. Stream nitrate concentration was over twofold greater in the low permafrost catchment than the high permafrost catchment. Riparian groundwater was not significantly different between catchments, averaging 13 μm overall. Nitrogen retention, measured using the end‐member mixing model, averaged 0.75 and 0.22 mmol N m−2 day−1 in low and high permafrost catchments, respectively, over the summer. The retention rate of nitrogen in the riparian zone was 10–15% of the export in stream flow.4. Our results indicate that the riparian zone functions as an important sink for groundwater nitrate and dissolved organic carbon (DOC). However, differences in stream nitrate and DOC concentrations between catchments cannot be explained by solute inputs from riparian groundwater to the stream and differences between streams are probably attributable to deeper groundwater inputs or flows from springs that bypass the riparian zone.
The generation of diversity in systems of patches and ranked dominance
Authors: Navarro Alberto Jorge A. , Manly Bryan F. J. 
Published: March 2006

AbstractAim  Mac Nally and Lake proposed a statistic (η) for determining whether the diversity in archipelagos is better generated by several small patches (SS‐dominance) or by a few large patches (SL‐dominance). The η statistic improves the study of the generation of diversity in systems of patches, but the dependence of η on a particular species–area relationship may reduce its effectiveness. In this paper we show that η may be affected by the criterion used to distinguish between large and small patches. We propose alternative measures (ranked m‐dominance indices) for the detection of SS/SL dominance, which separate the effects of each class of patch size on the generation of diversity.Location  We use previously published species lists from three archipelagos: lizard species on 25 islands in the Gulf of California; non‐introduced species of reptiles of the Canary Islands (order Squamata); and finch species from 19 islands of the West Indies. We also use one artificial data set.Methods  Presence–absence data and the rank order of patch areas are used to define the m‐dominance indices, interpreted as measures of preferential size of patches occupied by m species. A Monte Carlo procedure is implemented for testing the significance of the observed indices. Row and column totals in the simulated presence–absence matrices are kept fixed in order to maintain differences in species richness among sites and differences in occurrence frequencies among species, but the allocation of each occurrence to a specific ranked area is randomized. The analyses are exemplified with the three published data sets taken from the literature, and a hypothetical patch system neither SS‐ nor SL‐dominated.Results  The new m‐dominance indices identified correctly the hypothetical patch system, while η was positive, suggesting an incorrect SL‐dominant result. For the lizard data set, the standardized ranked m‐dominance was significantly large for small m, confirming an SL‐dominated system. Islands of varying size in the Canary archipelago hosted restricted reptile species, but matrix sparseness seems to have caused the non‐significant results for the m‐dominance indices in this case. The overall pattern of the West Indies system shows that medium‐large islands are dominant, but most Monte Carlo analyses were not significant, also possibly as a result of matrix sparseness.Main conclusions  The m‐dominance indices have the virtue of summarizing composition–area relationships, and including Monte Carlo procedures for testing whether patch size and the type of species distribution (species restricted to m patches, m = 1,…,s) are random or not. When m is as low as 1 or 2, the m‐dominance indices may typify the role of restricted species on the generation of diversity in the system of patches. The procedure developed here can be generalized to include other ordinal properties of patches, such as isolation or habitat heterogeneity.
Use of Ecotilling as an efficient SNP discovery tool to survey genetic variation in wild populations of Populus trichocarpa
Authors: GILCHRIST ERIN J. , HAUGHN GEORGE W. , YING CHENG C. , OTTO SARAH P. , ZHUANG JUN , CHEUNG DOROTHY , HAMBERGER BJÖRN , ABOUTORABI FARIBA , KALYNYAK TATYANA , JOHNSON LEE , BOHLMANN JOERG , ELLIS BRIAN E. , DOUGLAS CARL J. , CRONK QUENTIN C. B. 
Published: March 2006

AbstractEcotilling was used as a simple nucleotide polymorphism (SNP) discovery tool to examine DNA variation in natural populations of the western black cottonwood, Populus trichocarpa, and was found to be more efficient than sequencing for large‐scale studies of genetic variation in this tree. A publicly available, live reference collection of P. trichocarpa from the University of British Columbia Botanical Garden was used in this study to survey variation in nine different genes among individuals from 41 different populations. A large amount of genetic variation was detected, but the level of variation appears to be less than in the related species, Populus tremula, based on reported statistics for that tree. Genes examined varied considerably in their level of variation, from PoptrTB1 which had a single SNP, to PoptrLFY which had more than 23 in the 1000‐bp region examined. Overall nucleotide diversity, measured as Total, was relatively low at 0.00184. Linkage disequilibrium, on the other hand, was higher than reported for some woody plant species, with mean r2 equal to 0.34. This study reveals the potential of Ecotilling as a rapid genotype discovery method to explore and utilize the large pool of genetic variation in tree species.
FAST‐TRACK: Waves of parthenogenesis in the desert: evidence for the parallel loss of sex in a grasshopper and a gecko from Australia
Authors: KEARNEY MICHAEL , BLACKET MARK J. , STRASBURG JARED L. , MORITZ CRAIG 
Published: March 2006

AbstractThe rarity of parthenogenesis, reproduction without sex, is a major evolutionary puzzle. To understand why sexual genetic systems are so successful in nature, we must understand why parthenogenesis sometimes evolves and persists. Here we use DNA sequence data to test for similarities in the tempo and mode of the evolution of parthenogenesis in a grasshopper and a lizard from the Australian desert. We find spectacular congruence between genetic and geographic patterns of parthenogenesis in these distantly related organisms. In each species, parthenogenesis evolved twice and appears to have expanded in parallel waves across the desert, suggesting a highly general selective force against sex.
Molecular detection of predation by soil micro‐arthropods on nematodes
Authors: READ D. S. , SHEPPARD S. K. , BRUFORD M. W. , GLEN D. M. , SYMONDSON W. O. C. 
Published: March 2006

AbstractThe relative importance of the factors driving change in the population dynamics of nematodes in the soil is almost completely unknown. Top‐down control by micro‐arthropod predators may have a significant impact on nematode population dynamics. We report experiments showing that mites and Collembola were capable of reducing nematode numbers in the laboratory and were feeding on a targeted nematode species in the field. A PCR‐based approach was developed for the detection of predation on three species of slug‐ and insect‐pathogenic nematodes:Phasmarhabditis hermaphrodita,Heterorhabditis megidisandSteinernema feltiae. The collembolanFolsomia candidaand the mesostigmatid miteStratiolaelaps mileswere employed as model predators to calibrate post‐ingestion prey DNA detection times. Fragments of cytochrome oxidase I (COI) mtDNA were sequenced and species‐specific primers were designed, amplifying 154‐, 154‐ and 203‐bp fragments for each of the nematode species. Detection times for nematode DNA within the guts of Collembola were longer than in mites, with half‐lives (50% of samples testing positive) of 08.75 h and 05.03 h, respectively.F. candidasignificantly reduced numbers of the nematodeH. megidis, with rates of predation of ∼0.4 nematode infective juveniles per collembolan per hour over 10 h. Four taxa of field‐caught micro‐arthropod that had been exposed to the nematodeP. hermaphroditafor a period of 12 h were analysed and significant numbers of three taxa tested positive. This is the first application of PCR techniques for the study of nematophagy and the first time these techniques have been used to measure predation on nematodes in the field.
Insights into the mating habits of the tiger salamander (Ambystoma tigrinum tigrinum) as revealed by genetic parentage analyses
Authors: GOPURENKO DAVID , WILLIAMS ROD N. , McCORMICK CORY R. , DeWOODY J. ANDREW 
Published: March 2006

AbstractAmong urodeles, ambystomatid salamanders are particularly amenable to genetic parentage analyses because they are explosive aggregate breeders that typically have large progeny arrays. Such analyses can lead to direct inferences about otherwise cryptic aspects of salamander natural history, including the rate of multiple mating, individual reproductive success, and the spatial distribution of clutches. In 2002, we collected eastern tiger salamander (Ambystoma tigrinum tigrinum) egg masses (> 1000 embryos) from a ~80 m linear transect in Indiana, USA. Embryos were genotyped at four variable microsatellite loci and the resulting progeny array data were used to reconstruct multilocus genotypes of the parental dams and sires for each egg mass. UPGMA analysis of genetic distances among embryos resolved four instances of egg mass admixture, where two or more females had oviposited at exactly the same site resulting in the mixing of independent cohorts. In total, 41 discrete egg masses were available for parentage analyses. Twenty‐three egg masses (56%) consisted exclusively of full‐siblings (i.e. were singly sired) and 18 (44%) were multiply sired (mean 2.6 males/clutch). Parentage could be genetically assigned to one of 17 distinct parent pairs involving at least 15 females and 14 different males. Reproductive skew was evident among males who sired multiply sired clutches. Additional evidence of the effects of sexual selection on male reproductive success was apparent via significant positive correlations between male mating and reproductive success. Females frequently partitioned their clutches into multiple discrete egg masses that were separated from one another by as many as 43 m. Collectively, these data provide the first direct evidence for polygynandry in a wild population of tiger salamanders.
Control of the endonuclease activity of type I restriction‐modification systems is required to maintain chromosome integrity following homologous recombination
Authors: Blakely Garry W. , Murray Noreen E. 
Published: March 2006

SummaryA type I restriction‐modification enzyme will bind to an unmethylated target sequence in DNA and, while still bound to the target, translocate DNA through the protein complex in both directions. DNA breakage occurs when two translocating complexes collide. However, if type I restriction‐modification systems bind to unmodified target sequences within the resident bacterial chromosome, as opposed to incoming ‘foreign’ DNA, their activity is curtailed; a process known as restriction alleviation (RA). We have identified two genes in Escherichia coli, rnhA and recG, mutations in which lead to the alleviation of restriction. Induction of RA in response to these mutations is consistent with the production of unmodified target sequences following DNA synthesis associated with both homologous recombination and R‐loop formation. This implies that a normal function of RA is to protect the bacterial chromosome when recombination generates unmodified products. For EcoKI, our experiments demonstrate the contribution of two pathways that serve to protect unmodified DNA in the bacterial chromosome: the primary pathway in which ClpXP degrades the restriction endonucleas and a mechanism dependent on the lar gene within Rac, a resident, defective prophage of E. coli K‐12. Previously, the potential of the second pathway has only been demonstrated when expression of lar has been elevated. Our data identify the effect of lar from the repressed prophage.
Dynamics of stomatal water relations following leaf excision
Authors: POWLES JULIA E. , BUCKLEY THOMAS N. , NICOTRA ADRIENNE B. , FARQUHAR GRAHAM D. 
Published: March 2006

ABSTRACTWe examined the stomatal response to leaf excision in an evergreen woody shrub,Photinia × fraseri, using a novel combination of gas exchange, traditional water relations and modelling. Plants were kept outdoors in mild winter conditions (average daily temperature range: −1 to 12 °C) before being transferred to a glasshouse (temperature range: 20–30 °C) and allowed to acclimate for different periods before experiments. ‘Glasshouse plants’ were acclimated for at least 9 d, and ‘outdoor plants’ were acclimated for fewer than 3 d before laboratory gas exchange experiments. The transient stomatal opening response to leaf excision was roughly twice as long in outdoor plants as in glasshouse plants. To elucidate the reason for this difference, we inferred variables of stomatal water relations (epidermal and guard cell turgor pressures and guard cell osmotic pressure:Pe,Pgandπg, respectively) from stomatal conductance (gs) and bulk leaf water potential (ψl), using a hydromechanical model ofgs.ψlwas calculated from cumulative post‐excision transpirational water loss using empirical relationships betweenψland relative water content obtained on similar leaves. InferredPgandPeboth declined immediately after leaf excision. Inferredπgalso declined after a lag period. The kinetics ofπgadjustment after the lag were similar in outdoors and glasshouse plants, but the lag period was much longer in outdoor plants. This suggests that the longer transient opening response in outdoor plants resulted from slower induction, not slower execution, of guard cell osmoregulation. We discuss the implications of our results for the mechanism of short‐term stomatal responses to hydraulic perturbations, for dynamic modelling ofgsand for leaf water status regulation.