bluuebunny/crossref_metadata_2025_split huggingface dataset:
Relationship between bacterial diversity and function under biotic control: the soil pesticide degraders as a case study
Authors: Monard Cécile , Vandenkoornhuyse Philippe , Le Bot Barbara , Binet Françoise 
Published: December 2010

Abstract
In soil, the way biotic parameters impact the relationship between bacterial diversity and function is still unknown. To understand these interactions better, we used RNA-based stable-isotope probing to study the diversity of active atrazine-degrading bacteria in relation to atrazine degradation and to explore the impact of earthworm-soil engineering with respect to this relationship. Bulk soil, burrow linings and earthworm casts were incubated with 13C-atrazine. The pollutant degradation was quantified by liquid chromatography–mass spectrometry for 8 days, whereas active atrazine degraders were identified at 2 and 8 days by sequencing the 16S ribosomal RNA in the 13C-RNA fractions from the three soil microsites. An original diversity of atrazine degraders was found. Earthworm soil engineering greatly modified the taxonomic composition of atrazine degraders with dominance of α-, β- and γ-proteobacteria in burrow linings and of Actinobacteria in casts. Earthworm soil bioturbation increased the γ-diversity of atrazine degraders over the soil microsites generated. Atrazine degradation was enhanced in burrow linings in which primary atrazine degraders, closely related to Pelomonas aquatica, were detected only 2 days after atrazine addition. Atrazine degradation efficiency was not linearly related to the species richness of degraders but likely relied on keystone species. By enhancing soil heterogeneity, earthworms sustained high phylogenetic bacterial diversity and exerted a biotic control on the bacterial diversity–function relationships. Our findings call for future investigations to assess the ecological significance of biotic controls on the relationships between diversity and function on ecosystem properties and services (for example, soil detoxification) at larger scales.
Soil Microbial Biomass And Activity In A Cork Oak Savanna
Authors: Caldeira Maria , Fangueiro David , Lecomte Xavier , Bugalho Miguel , Coutinho João , Pereira João 
Published: December 2010

AbstractCork oak savannas are composed by a sparse tree canopy (30-70 trees/ha) and a grassland understory predominantly composed of C3 annuals that survive the hot and dry Mediterranean summers as seeds in the soil. Microbial communities can be more or less efficient at converting organic substrates into microbial biomass carbon depending on the quantity and quality of organic matter inputs. The cork oak savannas have two distinct types of plant litter that can affect soil microbial biomass and activity differently: herbaceous litter and the more recalcitrant woody plant litter resulting from the trees. Spatial variability of soil microbial biomass and activity due to the tree-grassland component of cork oak savannas were evaluated in order to better understand the soil carbon dynamics of these systems.To quantify changes in soil microbial biomass and activity, measurements were performed in a Cork oak savanna in Southern Portugal. At this site 8 plots were randomly established under mature cork oak trees and paired with 8 open grassland plots. During one year soil cores (0-10 cm) were monthly collected at each site for measuring soil microbial biomass C and other eco-physiology parameters.
Results/Conclusion
Soil microbial biomass carbon (Cmic) and nitrogen (Nmic) were always higher under the tree canopy than in the open grasslands. Organic carbon (Corg) was also higher under the tree canopies. The Cmic/Corg ratio relates to the microbial activity and its potential to mineralize organic substances. The Cmic/Corg ratio was lower under the tree canopies than in the open grasslands. Less microbial biomass was supported per unit of Corg. Basal activity was always higher under the canopy than in the open grassland.Trees scattered in the savanna function as islands inducing larger soil microbial communities and higher basal activity under the canopies. Lower Cmic/Corg ratio under the tree canopies suggests a more recalcitrant nature of the litter and a decrease in relative availability of organic matter under the trees.
Automated analysis of information processing, kinetic independence and modular architecture in biochemical networks using MIDIA
Authors: Bowsher Clive G. 
Published: December 2010

Abstract
Motivation: Understanding the encoding and propagation of information by biochemical reaction networks and the relationship of such information processing properties to modular network structure is of fundamental importance in the study of cell signalling and regulation. However, a rigorous, automated approach for general biochemical networks has not been available, and high-throughput analysis has therefore been out of reach.
Results: Modularization Identification by Dynamic Independence Algorithms (MIDIA) is a user-friendly, extensible R package that performs automated analysis of how information is processed by biochemical networks. An important component is the algorithm's ability to identify exact network decompositions based on both the mass action kinetics and informational properties of the network. These modularizations are visualized using a tree structure from which important dynamic conditional independence properties can be directly read. Only partial stoichiometric information needs to be used as input to MIDIA, and neither simulations nor knowledge of rate parameters are required. When applied to a signalling network, for example, the method identifies the routes and species involved in the sequential propagation of information between its multiple inputs and outputs. These routes correspond to the relevant paths in the tree structure and may be further visualized using the Input–Output Path Matrix tool. MIDIA remains computationally feasible for the largest network reconstructions currently available and is straightforward to use with models written in Systems Biology Markup Language (SBML).
Availability: The package is distributed under the GNU General Public License and is available, together with a link to browsable Supplementary Material, at http://code.google.com/p/midia. Further information is at www.maths.bris.ac.uk/~macgb/Software.html.
Contact: C.Bowsher@bristol.ac.uk
Supplementary information: The Supplementary Material contains extensive description of the MIDIA package and is available at Bioinformatics online.
Using bioinformatics to predict the functional impact of SNVs
Authors: Cline Melissa S. , Karchin Rachel 
Published: December 2010

Abstract
Motivation: The past decade has seen the introduction of fast and relatively inexpensive methods to detect genetic variation across the genome and exponential growth in the number of known single nucleotide variants (SNVs). There is increasing interest in bioinformatics approaches to identify variants that are functionally important from millions of candidate variants. Here, we describe the essential components of bionformatics tools that predict functional SNVs.
Results: Bioinformatics tools have great potential to identify functional SNVs, but the black box nature of many tools can be a pitfall for researchers. Understanding the underlying methods, assumptions and biases of these tools is essential to their intelligent application.
Contact: karchin@jhu.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
An evaluation of the proposed DSM‐5 alcohol use disorder criteria using Australian national data
Authors: Mewton Louise , Slade Tim , McBride Orla , Grove Rachel , Teesson Maree 
Published: December 2010

ABSTRACTAims  To evaluate the proposed revisions to the DSM‐IV alcohol use disorder criteria using epidemiological data.Design, setting and participants  Data came from the 1997 Australian National Survey of Mental Health and Well‐Being. The sample consisted of 10 641 participants aged 18 years and over.Measurements  Alcohol use disorders were assessed using a revised version of the CIDI version 2.0. Alcohol use disorders were assessed in all respondents who indicated that they had used alcohol more than 12 times in the previous 12 months (n = 7746).Findings  The proposed introduction of a single alcohol use disorder was supported by confirmatory factor analysis (CFA). DSM‐5 criteria were all indicators of a single underlying disorder. Under DSM‐5, the prevalence of alcohol use disorders would increase by 61.7% when compared with those diagnosed under DSM‐IV. When investigating the most appropriate diagnostic threshold, the 3+ threshold maximized agreement between DSM‐IV and DSM‐5 diagnoses, and produced similar prevalence estimates to those yielded by DSM‐IV. Item response theory (IRT) analyses supported the removal of the legal criterion while provided equivocal results for the craving criterion.Conclusions  Under the proposed DSM‐IV revisions for alcohol use disorders, estimates of the prevalence in the general population would increase substantially. Whereas evidence supports some of the revisions such as a single underlying disorder, others such as the 2+ threshold for diagnosis of alcohol use disorder and the inclusion of a ‘craving’ criterion may be problematic.
The clinical impact of combining intermittent preventive treatment with home management of malaria in children aged below 5 years: cluster randomised trial
Authors: Tagbor Harry , Cairns Matthew , Nakwa Emmanuel , Browne Edmund , Sarkodie Badu , Counihan Helen , Meek Sylvia , Chandramohan Daniel 
Published: December 2010

SummaryObjective  To investigate the impact of seasonal intermittent preventive treatment (IPTc) on malaria‐related morbidity in children <5 years of age who already had access to home‐based management of malaria (HMM) for presumptive treatment of fevers.Method  Thirty community‐based drug distributors (CDDs) from all 13 communities of a rural subdistrict in Ghana were trained to provide prompt treatment for presumptive malaria using artesunate‐amodiaquine (AS+AQ) to all children under 5 years of age. Six communities were randomised to also receive bimonthly courses of seasonal IPTc with AS+AQ in May, July and September of 2007. The primary outcome was the incidence rate of febrile episodes diagnosed presumptively as malaria by the CDDs in the communities in each intervention group. Cross‐sectional surveys were conducted to determine the prevalence of parasitaemia and anaemia among the study children.Results  During the 6 months in which IPTc was delivered, incidence of fevers in communities given HMM+IPTc was lower than in communities given HMM alone, but this difference was not statistically significant (protective efficacy: 37.0%(95% CI: −9.7 to 63.8; P = 0.14). However, incidence of presumptive malaria was significantly lower in IPTc communities when only children who received all three courses of IPTc were included in the analysis: protective efficacy 61.5% (95% CI:31.2–78.5; P = 0.018). Protection with IPTc was not followed by rebound morbidity in the following year. At the end of the intervention period, prevalence of asymptomatic parasitaemia was lower in communities that had received IPTc, but there were no differences in anaemia or haemoglobin concentration.Conclusion  In this study area, incidence of fevers was lower in communities given three courses of IPTc during the time of peak transmission than in communities that received only HMM. However, high levels of coverage for IPTc will be necessary for maximum impact.
Disturbed energy metabolism after lung and heart transplantation
Authors: Forli Liv , Bollerslev Jens , Simonsen Svein , Isaksen Gunhild A. , Godang Kristin , Pripp Are H. , Bjortuft Oystein 
Published: December 2010

Forli L, Bollerslev J, Simonsen S, Isaksen GA, Godang K, Pripp AH, Bjortuft O. Disturbed energy metabolism after lung and heart transplantation.  Clin Transplant 2011: 25: E136–E143. © 2010 John Wiley & Sons A/S.Abstract:  Overweight, in combination with other cardiovascular risk factors, reduces survival after transplantation. The aim of this prospective study was to observe leptin, adiponectin, and energy intake as predictors of body mass index (BMI) and body composition and as risk factors associated with metabolic syndrome after lung and heart transplantation. After pre‐operative baseline investigations, 35 lung and 59 heart recipients were followed and re‐investigated two, six, and 12 months after transplantation. Linear regressions were performed to predict BMI and body composition. The lung recipients had a substantial weight gain after transplantation. Leptin increased, especially in the lung recipients and positively predicted BMI. Energy intake predicted BMI before and at two months after transplantation, but not after 12 months. Percentage trunk fat increased and lean mass decreased. Before transplantation, the dominant determinant of lean mass was adiponectin (positively associated), while after it was leptin (negatively associated), controlled for possible confounding variables (including prednisolone). Metabolic syndrome 12 months after transplantation was associated with higher leptin, greater weight gain without increased energy intake. After transplantation, a disturbed energy metabolism is indicated, where adiponectin and especially leptin are involved and a disadvantageous body composition is favored with increased body fat and decreased lean mass.
Host plant effects on morphometric characteristics of Liriomyza huidobrensis, L. sativae and L. trifolii (Diptera: Agromyzidae)
Authors: Musundire R. , Chabi‐Olaye A. , Krüger K. 
Published: December 2010

AbstractBody size of herbivorous insects may be directly related to host plant characteristics (e.g. nutrition, chemical composition) and positively linked to performance of the herbivore and its parasitoids. Differences in adult body size of Liriomyza huidobrensis, L. sativae and L. trifolii reared on Pisum sativum, Phaseolus vulgaris, Vicia faba and Solanum lycopersicum were assessed to determine the effect of host plants on adult size. Furthermore, morphometric wing and hind tibia measurements were used to determine suitability as proxy measures for adult size. Based on canonical and linear discriminant analyses, two distinct Liriomyza morphospecies groups were recognized across all plant species. The first cluster represented L. huidobrensis and the second L. sativae and L. trifolii. The overall degree of correct classification of the three species across all plants tested (correct observation) with cross validation was estimated at 85%. Liriomyza huidobrensis, the largest species, showed no differences in the variables measured when reared on the four plant species. However, different plant species seem to influence wing and hind tibia measurements in L. trifolii to a greater extent than in L. huidobrensis and L. sativae. The first two canonical variates could not separate the populations of L. huidobrensis and L. sativae reared on different plant species, but showed separation of L. trifolii populations into two clusters: firstly, insects reared on V. faba and secondly, insects reared on P. vulgaris and S. lycopersicum. Hind tibia length strongly correlated with wing length. Both can be used to determine adult size of the three Liriomyza species. This study provides some new evidence for the existence of differential preferences by Liriomyza species for the four host plant species. This, therefore, warrants larger scale field studies to test for positive preference‐performance of Liriomyza species on these plant species and to determine possible consequences at the third tritrophic level.
Species distribution models for the alien invasive Asian Harlequin ladybird (Harmonia axyridis)
Authors: Bidinger K. , Lötters S. , Rödder D. , Veith M. 
Published: December 2010

AbstractThe Asian Harlequin ladybird (Harmonia axyridis) is a globally invasive alien species. We developed species distribution models (SDMs) aiming at an explanation of the observed native and invasive distributions and the prediction of the species’ potential distribution. SDMs were built based on bioclim parameters with Maxent (i) on known native occurrence only (SDMnat), (ii) on known European invasive occurrence only (SDMinv) and (iii) by combining both previous approaches (SDMall). Results indicate that SDMinvmatch the observed European invasive range better than SDMnator SDMall. The origin of Asian founders in Europe remains unknown. SDMinvhighlighted a restricted area in China which may represent the region of origin of the European Harlequin ladybird, leaving the possibility of within‐species climate niche variation. As a result, when targeting the worldwide potential of invasiveness ofH. axyridis, SDMallmay reveal maximum results uncovering the species’ potential distribution. These results have to be seen in the framework of conceptual problems and pitfalls when generating SDMs including niche definition, niche shift, sampling bias, biological importance of predictors and model transferability uncertainties.
Genetic architecture of plant height in winter rye introgression libraries
Authors: Miedaner T. , Müller B. U. , Piepho H.‐P. , Falke K. C. 
Published: December 2010

With 4 figures and 1 table AbstractPlant height is an important trait for breeding and as fitness criterion in natural populations of rye (Secale cereale L.). Our objectives were to investigate the inheritance of plant height in rye introgression libraries and estimate the covariation between per se and testcross performance. Two introgression libraries containing each of 40 BC2S3 candidate introgression lines (pre‐ILs) were tested at five locations in two years for per se and testcross performance. Donor population was the Iranian primitive rye accession Altevogt 14160. Plant height of the donor population was 145 ± 3.6 cm as population and 152 ± 2.9 and 132 ± 2.8 cm when crossed to the two testers, respectively. Pre‐ILs were much closer to the recurrent parent, but still most of them exceeded the recurrent parent in per se performance. Estimates of the genotypic variance were significant (P = 0.01) for both per se and testcross performance. Entry‐mean heritabilities were high in both libraries (0.97 and 0.94, respectively). Donor chromosome segments (DCS) of 59 of 72 pre‐ILs had a significant (P = 0.05) effect on plant height compared to the recurrent parent. For the testcrosses, 10 pre‐ILs still contributed DCS with significantly (P = 0.05) taller effects. Genotypic correlations between pre‐ILs per se and as testcrosses were moderate for the two testers. In conclusion, plant height per se has a complex inheritance with many loci spread across the entire genome. Hybrid breeding, however, facilitates the use of genetic resources because the tallness is less pronounced in the testcrosses.
Development and characterization of genomic microsatellite markers in safflower (Carthamus tinctorius L.)
Authors: Hamdan Y. A. S. , García‐Moreno M. J. , Redondo‐Nevado J. , Velasco L. , Pérez‐Vich B. 
Published: December 2010

With 2 tables AbstractSpecific and robust marker resources available for safflower breeding are scarce. The present research was aimed at developing a collection of genomic microsatellite (SSR) markers and to assess their informativeness. A genomic library enriched for AC‐ and AG‐ repeats was constructed from safflower DNA. Around 35% of the 768 clones that were isolated and sequenced contained SSR sequences. From these, 108 unique primer pairs were designed. The majority of the SSRs contained simple di‐nucleotide motifs (77 of 108), most of them being perfect repeats (63 of 77). Reference allele length ranged from 95 to 414 bp, averaging 241.2 bp. The 108 SSRs were amplified in a set of ten safflower lines. From 88 SSR markers that amplified successfully, 64 of them detected polymorphism among the ten safflower lines genotyped. The number of alleles per locus ranged from 2 to 8 (mean value of 3.2), whereas heterozygosity ranged from 0.18 to 0.86 (mean value of 0.52). These genomic SSR markers will contribute to advance in safflower molecular breeding.
Role of preoperative platelet level in clinical and pathological outcomes after surgery for renal cortical malignancies
Authors: Wosnitzer Matthew , Polland Allison , Hai Qiong , Hruby Gregory , McKiernan James 
Published: December 2010

Study Type – Therapy (case series)  Level of Evidence 4 What's known on the subject? and What does the study add? Preoperative platelet count (PLT), which reflects the systemic inflammatory response, has been previously identified in several small studies as useful prognostic factor in a number of cancers including renal cell carcinoma. This study is the largest study to our knowledge to investigate the relationship between platelets and surgical outcomes in patients with renal cell carcinoma. Thrombocytosis (PLT > 400) was associated with and was an independent predictor of decreased overall and disease‐specific survival in patients undergoing extirpative renal surgery, and was associated with larger tumour size, and higher TNM stage at surgery.OBJECTIVE • To investigate preoperative platelet level (PLT) as a prognostic factor for pathologic and clinical outcomes following surgery for renal cortical malignancy.PATIENTS AND METHODS • 1422 patients underwent radical or partial nephrectomy at our institution from 1988–2009 for renal cortical lesions.• The cohort with available PLT values was divided into group 1 (PLT ≤ 400 × 109) and (PLT > 400 × 109) based on institutional laboratory upper threshold (400 × 109 cells/liter).RESULTS • 961 patients were divided into groups 1 (n = 870) and 2 (n = 91), with mean age at surgery of 61 and 60 years, 70.6% and 50.6% males (P ≤ 0.0001), 56% undergoing radical nephrectomy in each group, 39.1% vs. 22% undergoing partial nephrectomy (P = 0.001) respectively.• Groups differed significantly inmedian tumour size (5.06 vs. 7.28 cm) (P ≤ 0.001), pathologic T stage (P = 0.002), and metastases (P ≤ 0.0001). No significant difference existed regarding histologic findings at surgery.• With median follow‐up of 24 months, PLT > 400 × 109 cells/liter was associated with decreased overall (OS) and disease‐specific survival (DSS) using log rank test (P ≤ 0.0001).• On multivariate analysis, controlling for TNM stage, histology, and tumour diameter, PLT > 400 × 109cells/liter independently predicted decreased OS (HR 1.67, P = 0.007) and DSS (HR 2.39, P = 0.001). As a continuous variable, PLT predicted OS (HR 1.002, P = 0.005) and DSS (HR 1.003, P = 0.004).• With metastatic patients excluded, PLT was significantly associated with OS and DSS, but was not an independent predictor.CONCLUSION • PLT is a clinically significant independent predictor of OS and DSS in continuous and categorical analyses in patients undergoing renal cortical malignancy surgery. PLT may be clinically useful for risk stratifying patients undergoing surgery for renal cancer, especially for prognosis assessment of patients with renal cortical malignancy and micrometastatic disease at surgery.