bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intra-guild vs extra-guild prey: effect on predator fitness and preference of Amblyseius swirskii (Athias-Henriot) and Neoseiulus cucumeris (Oudemans) (Acari: Phytoseiidae)
Authors: Buitenhuis R. , Shipp L. , Scott-Dupree C. 
Published: May 2009

AbstractThe relationships between the predatory mites, Amblyseius swirskii (Athias-Henriot) and Neoseiulus cucumeris (Oudemans) (Acari: Phytoseiidae), and their prey, western flower thrips (Frankliniella occidentalis Pergande) (Thysanoptera: Thripidae), were investigated to determine the effects of predation on intra-guild or extra-guild prey and predator preference. Life history characteristics of both predatory mites were measured when fed eggs and larvae of the other predator species and compared to data obtained when the predators were fed thrips larvae. In addition, choice tests were conducted to determine if the predators had a preference for different prey or if they were indiscriminate predators. Amblyseius swirskii appears to be an important intra-guild predator of N. cucumeris juveniles because of a high predation rate and a preference for N. cucumeris juveniles over thrips. Neoseiulus cucumeris is also an intra-guild predator of A. swirskii juveniles; however, it has a lower predation rate than A. swirskii. Contrary to intra-guild predation theory, intra-guild prey was an equally good or better food source than thrips (extra-guild prey) for both predators, based on high oviposition rates and fast development times. The results of this study indicate a high potential for negative interactions between A. swirskii and N. cucumeris when used together in biological control of thrips.
Neural correlates of worry in generalized anxiety disorder and in normal controls: a functional MRI study
Authors: Paulesu E. , Sambugaro E. , Torti T. , Danelli L. , Ferri F. , Scialfa G. , Sberna M. , Ruggiero G. M. , Bottini G. , Sassaroli S. 
Published: May 2009

BackgroundWorry is considered a key feature of generalized anxiety disorder (GAD), whose neural correlates are poorly understood. It is not known whether the brain regions involved in pathological worry are similar to those involved in worry-like mental activity in normal subjects or whether brain areas associated with worry are the same for different triggers such as verbal stimuli or faces. This study was designed to clarify these issues.MethodEight subjects with GAD and 12 normal controls underwent functional magnetic resonance imaging (fMRI) mood induction paradigms based on spoken sentences or faces. Sentences were either neutral or designed to induce worry. Faces conveyed a sad or a neutral mood and subjects were instructed to empathize with those moods.ResultsWe found that the anterior cingulate and dorsal medial prefrontal cortex [Brodmann area (BA) 32/23 and BA 10/11] were associated with worry triggered by sentences in both subjects with GAD and normal controls. However, GAD subjects showed a persistent activation of these areas even during resting state scans that followed the worrying phase, activation that correlated with scores on the Penn State Worry Questionnaire (PSWQ). This region was activated during the empathy experiment for sad faces.ConclusionsThe results show that worry in normal subjects and in subjects with GAD is based on activation of the medial prefrontal and anterior cingulate regions, known to be involved in mentalization and introspective thinking. A dysregulation of the activity of this region and its circuitry may underpin the inability of GAD patients to stop worrying.
Dissociation of long-term verbal memory and fronto-executive impairment in first-episode psychosis
Authors: Leeson V. C. , Robbins T. W. , Franklin C. , Harrison M. , Harrison I. , Ron M. A. , Barnes T. R. E. , Joyce E. M. 
Published: May 2009

BackgroundVerbal memory is frequently and severely affected in schizophrenia and has been implicated as a mediator of poor clinical outcome. Whereas encoding deficits are well demonstrated, it is unclear whether retention is impaired. This distinction is important because accelerated forgetting implies impaired consolidation attributable to medial temporal lobe (MTL) dysfunction whereas impaired encoding and retrieval implicates involvement of prefrontal cortex.MethodWe assessed a group of healthy volunteers (n=97) and pre-morbid IQ- and sex-matched first-episode psychosis patients (n=97), the majority of whom developed schizophrenia. We compared performance of verbal learning and recall with measures of visuospatial working memory, planning and attentional set-shifting, and also current IQ.ResultsAll measures of performance, including verbal memory retention, a memory savings score that accounted for learning impairments, were significantly impaired in the schizophrenia group. The difference between groups for delayed recall remained even after the influence of learning and recall was accounted for. Factor analyses showed that, in patients, all variables except verbal memory retention loaded on a single factor, whereas in controls verbal memory and fronto-executive measures were separable.ConclusionsThe results suggest that IQ, executive function and verbal learning deficits in schizophrenia may reflect a common abnormality of information processing in prefrontal cortex rather than specific impairments in different cognitive domains. Verbal memory retention impairments, however, may have a different aetiology.
Can the restrictive harvest period policy conserve mopane worms in southern Africa? A bioeconomic modelling approach
Authors: AKPALU WISDOM , MUCHAPONDWA EDWIN , ZIKHALI PRECIOUS 
Published: May 2009

ABSTRACTThe mopane worm, which is the caterpillar form of the Saturnid moth Imbrasia belina Westwood, is – like other edible insects and caterpillars – a vital source of protein in southern African countries. The worms live and graze on mopane trees, which have alternative uses. With increasing commercialization of the worm, its management, which was hitherto organized as a common property resource, has been degraded to almost open access. This paper uses a bioeconomic modelling approach to show that for some optimal allocation of the mopane forest stock, the restrictive harvest period policy advocated by community leaders may not lead to sustainable harvesting of the worm.
Distribution neutral abatement policy in a model of trade and environment
Authors: DAS MONICA , DAS SANDWIP K. 
Published: May 2009

ABSTRACTThe Pollution Haven Hypothesis (PHH) states that with weak environmental policies a country can create comparative advantage in the polluting sector. This paper formulates a 3-good-3-factor model where the abatement input is a pure intermediate good. In our model, the PHH as well as the neoclassical trade theorems are valid only when environmental policies are distribution neutral. Inspired by the US Clean Air Act, we develop and estimate a dynamic panel model. We find that US environmental policies are consistent with distribution neutrality. Our results indicate that lowering abatement standards in all industries is the only way the US can become a pollution haven. In the context of our model, the PHH has damaging implications for the world environment.
‘Fair’ policies for the coffee trade – protecting people or biodiversity?
Authors: KITTI MITRI , HEIKKILÄ JAAKKO , HUHTALA ANNI 
Published: May 2009

ABSTRACTWe investigate the role that economic instruments can play in promoting economic sustainability and the preservation of biodiversity in agroforestry management in coffee production. Most of the world's coffee producers live in poverty and manage agro-ecosystems in regions that are culturally and biologically among the most diverse on the globe. Despite the relatively recent finding that bees may augment pollination and boost coffee crop yields, the short-term revenues from intense monoculture drive land-use decisions that destroy the forest strips serving as habitats for pollinating insects. Our study investigates whether farmers specialize in environmentally detrimental (sun-grown) or sustainable (shade-grown) farming, or both practices coexist. We calibrate an empirical model to characterize the equilibria and investigate the ecological and economic impacts of three alternative policy instruments: conservation fees, price premiums, and minimum wages.
Determinants of economic performance for coastal managed areas in central-southern Chile
Authors: SOBENES CATTERINA , CHÁVEZ CARLOS 
Published: May 2009

ABSTRACTWe study the economic performance of Benthic Resource Management Areas (BRMAs) in central-southern Chile. The analysis considers 26 managed areas with Agreements of Use declaring Chilean abalone (Concholepas concholepas) to be the main exploited benthic resource from 2001 to 2003. Our analysis explores the role played by several characteristics thought to be potential BRMA performance determinants. These variables were defined and grouped into four types: economic, environmental–biological, institutional–organizational, and organizational leader. Our results indicate that the price of Chilean abalone, the size of the habitable area, the target resource density, the density of other resources, and leader experience are determinant factors for the economic performance of the BRMAs under study.
Salt marsh sediment bacteria: their distribution and response to external nutrient inputs
Authors: Bowen Jennifer L , Crump Byron C , Deegan Linda A , Hobbie John E 
Published: May 2009

Abstract
A primary focus among microbial ecologists in recent years has been to understand controls on the distribution of microorganisms in various habitats. Much less attention has been paid to the way that environmental disturbance interacts with processes that regulate bacterial community composition. We determined how human disturbance affected the distribution and community structure of salt marsh sediment bacteria by using denaturing gradient gel electrophoresis of 16S rRNA in five different habitats in each of four salt marshes located in northeastern Massachusetts, USA. Two of the four marsh creeks were experimentally enriched 15 × above background by the addition of nitrogen and phosphorus fertilizers for two or more growing seasons. Our results indicate that extrinsic factors acting at broad scales do not influence the distribution of salt marsh sediment bacteria. Intrinsic factors, controlled by local-scale environmental heterogeneity, do play a role in structuring these sediment microbial communities, although nutrient enrichment did not have a consequential effect on the microbial community in most marsh habitats. Only in one habitat, a region of the marsh creek wall that is heavily colonized by filamentous algae, did we see any effect of fertilization on the microbial community structure. When similar habitats were compared among marshes, there was considerable convergence in the microbial community composition during the growing season. Environmental factors that correlated best with microbial community composition varied with habitat, suggesting that habitat-specific intrinsic forces are primarily responsible for maintaining microbial diversity in salt marsh sediments.
Isolation and characterization of low nucleic acid (LNA)-content bacteria
Authors: Wang Yingying , Hammes Frederik , Boon Nico , Chami Mohamed , Egli Thomas 
Published: May 2009

Abstract
Most planktonic bacteria are ‘uncultivable’ with conventional methods. Flow cytometry (FCM) is one approach that has been taken to study these bacteria. In natural aquatic environments, bacteria with high nucleic acid (HNA) and low nucleic acid (LNA) content are commonly observed with FCM after staining with fluorescent dyes. Although several studies have focused on the relative abundance and in situ activities of these two groups, knowledge on the growth of particularly LNA bacteria is largely limited. In this study, typical LNA bacteria were enriched from three different freshwater sources using extinction dilution (ED) and fluorescence-activated cell sorting (FACS). We have shown for the first time that LNA bacteria can be isolated and cultivated by using sterile freshwater as a growth medium. During growth, the typical LNA characteristics (that is, low-fluorescence intensity and sideward scatter (SSC)) remained distinct from those of typical HNA bacteria. Three LNA pure cultures that are closely affiliated to the Polynucleobacter cluster according to 16S rRNA sequencing results were isolated. Owing to their small size, cells of the isolates remained intact during cryo-transmission electronic microscopy examination and showed a Gram-negative cell-wall structure. The extremely small cell volume (0.05 μm3) observed for all three isolates indicates that they are among the smallest free-living heterotrophic organisms known in culture. Their isolation and cultivation allow further detailed investigation of this group of organisms under defined laboratory conditions.
Cell cycle analysis of fetal germ cells during sex differentiation in mice
Authors: Spiller Cassy , Wilhelm Dagmar , Koopman Peter 
Published: May 2009

Background information. Primordial germ cells in developing male and female gonads are responsive to somatic cell cues that direct their sex‐specific differentiation into functional gametes. The first divergence of the male and female pathways is a change in cell cycle state observed from 12.5 dpc (days post coitum) in mice. At this time XY and XX germ cells cease mitotic division and enter G1/G0 arrest and meiosis prophase I respectively. Aberrant cell cycle regulation at this time can lead to disrupted ovarian development, germ cell apoptosis, reduced fertility and/or the formation of germ cell tumours.Results. In order to unravel the mechanisms utilized by germ cells to achieve and maintain the correct cell cycle states, we analysed the expression of a large number of cell cycle genes in purified germ cells across the crucial time of sex differentiation. Our results revealed common signalling for both XX and XY germ cell survival involving calcium signalling. A robust mechanism for apoptosis and checkpoint control was observed in XY germ cells, characterized by p53 and Atm (ataxia telangiectasia mutated) expression. Additionally, a member of the retinoblastoma family and p21 were identified, linking these factors to XY germ cell G1/G0 arrest. Lastly, in XX germ cells we observed a down‐regulation of genes involved in both G1‐ and G2‐phases of the cell cycle consistent with their entry into meiosis.Conclusion. The present study has provided a detailed analysis of cell cycle gene expression during fetal germ cell development and identified candidate factors warranting further investigation in order to understand cases of aberrant cell cycle control in these specialized cells.
Kinetic analysis of human protein arginine N-methyltransferase 2: formation of monomethyl- and asymmetric dimethyl-arginine residues on histone H4
Authors: Lakowski Ted M. , Frankel Adam 
Published: May 2009

Protein arginine N-methyltransferases (PRMTs) methylate arginine residues within proteins using S-adenosyl-L-methionine (AdoMet) to form S-adenosyl-L-homocysteine and methylarginine residues. All PRMTs produce ω-NG-monomethylarginine (MMA) residues and either asymmetric ω-NG,NG-dimethylarginine (aDMA) or symmetric ω-NG,N′G-dimethylarginine (sDMA) residues, referred to as Type I or Type II activity respectively. Here we report methylation activity from PRMT2 and compare it with PRMT1 activity using UPLC-MS/MS (ultra-performance liquid chromatography–tandem MS), gel electrophoresis, and thin-layer chromatography. We show that PRMT2 is a Type I enzyme and that the ratio of aDMA to MMA produced by PRMTs 1 and 2 is dependent on the substrate, regardless of rate or Km, suggesting that the reactions for both enzymes are distributive rather than processive. Using UPLC-MS/MS we find that, for PRMT2, the dissociation constant (KAs) and Km of AdoMet and the Km of histone H4 are similar to values for PRMT1, whereas the PRMT2 kcat is 800-fold less than the PRMT1 kcat. Although PRMT2 activity is substantially lower than PRMT1 in vitro, the fact that both enzymes selectively methylate histone H4 suggest that PRMT2, like PRMT1, may act as a transcription co-activator through this modification.
Dynamic aspects of ascorbic acid metabolism in the circulation: analysis by ascorbate oxidase with a prolonged in vivo half-life
Authors: Kasahara Emiko , Kashiba Misato , Jikumaru Mika , Kuratsune Daisuke , Orita Kumi , Yamate Yurika , Hara Kenjiro , Sekiyama Atsuo , Sato Eisuke F. , Inoue Masayasu 
Published: May 2009

Because AA (L-ascorbic acid) scavenges various types of free radicals to form MDAA (monodehydroascorbic acid) and DAA (dehydroascorbic acid), its regeneration from the oxidized metabolites is critically important for humans and other animals that lack the ability to synthesize this antioxidant. To study the dynamic aspects of AA metabolism in the circulation, a long acting AOase (ascorbate oxidase) derivative was synthesized by covalently linking PEG [poly(ethylene glycol)] to the enzyme. Fairly low concentrations of the modified enzyme (PEG–AOase) rapidly decreased AA levels in isolated fresh plasma and blood samples with a concomitant increase in their levels of MDAA and DAA. In contrast, relatively high doses of PEG–AOase were required to decrease the circulating plasma AA levels of both normal rats and ODS (osteogenic disorder Shionogi) rats that lack the ability to synthesize AA. Administration of 50 units of PEG–AOase/kg of body weight rapidly decreased AA levels in plasma and the kidney without affecting the levels in other tissues, such as the liver, brain, lung, adrenal grand and skeletal muscles. PEG–AOase slightly, but significantly, decreased glutathione (GSH) levels in the liver without affecting those in other tissues. Suppression of hepatic synthesis of GSH by administration of BSO [L-buthionin-(S,R)-sulfoximine] enhanced the PEG–AOase-induced decrease in plasma AA levels. These and other results suggest that the circulating AA is reductively regenerated from MDAA extremely rapidly and that hepatic GSH plays important roles in the regeneration of this antioxidant.
Ku-0063794 is a specific inhibitor of the mammalian target of rapamycin (mTOR)
Authors: García-Martínez Juan M. , Moran Jennifer , Clarke Rosemary G. , Gray Alex , Cosulich Sabina C. , Chresta Christine M. , Alessi Dario R. 
Published: May 2009

mTOR (mammalian target of rapamycin) stimulates cell growth by phosphorylating and promoting activation of AGC (protein kinase A/protein kinase G/protein kinase C) family kinases such as Akt (protein kinase B), S6K (p70 ribosomal S6 kinase) and SGK (serum and glucocorticoid protein kinase). mTORC1 (mTOR complex-1) phosphorylates the hydrophobic motif of S6K, whereas mTORC2 phosphorylates the hydrophobic motif of Akt and SGK. In the present paper we describe the small molecule Ku-0063794, which inhibits both mTORC1 and mTORC2 with an IC50 of ∼10 nM, but does not suppress the activity of 76 other protein kinases or seven lipid kinases, including Class 1 PI3Ks (phosphoinositide 3-kinases) at 1000-fold higher concentrations. Ku-0063794 is cell permeant, suppresses activation and hydrophobic motif phosphorylation of Akt, S6K and SGK, but not RSK (ribosomal S6 kinase), an AGC kinase not regulated by mTOR. Ku-0063794 also inhibited phosphorylation of the T-loop Thr308 residue of Akt phosphorylated by PDK1 (3-phosphoinositide-dependent protein kinase-1). We interpret this as implying phosphorylation of Ser473 promotes phosphorylation of Thr308 and/or induces a conformational change that protects Thr308 from dephosphorylation. In contrast, Ku-0063794 does not affect Thr308 phosphorylation in fibroblasts lacking essential mTORC2 subunits, suggesting that signalling processes have adapted to enable Thr308 phosphorylation to occur in the absence of Ser473 phosphorylation. We found that Ku-0063794 induced a much greater dephosphorylation of the mTORC1 substrate 4E-BP1 (eukaryotic initiation factor 4E-binding protein 1) than rapamycin, even in mTORC2-deficient cells, suggesting a form of mTOR distinct from mTORC1, or mTORC2 phosphorylates 4E-BP1. Ku-0063794 also suppressed cell growth and induced a G1-cell-cycle arrest. Our results indicate that Ku-0063794 will be useful in delineating the physiological roles of mTOR and may have utility in treatment of cancers in which this pathway is inappropriately activated.
CycSim—an online tool for exploring and experimenting with genome-scale metabolic models
Authors: Le Fèvre F. , Smidtas S. , Combe C. , Durot M. , d'Alché-Buc Florence , Schachter V. 
Published: May 2009

Abstract
Summary: CycSim is a web application dedicated to in silico experiments with genome-scale metabolic models coupled to the exploration of knowledge from BioCyc and KEGG. Specifically, CycSim supports the design of knockout experiments: simulation of growth phenotypes of single or multiple gene deletions mutants on specified media, comparison of these predictions with experimental phenotypes and direct visualization of both on metabolic maps. The web interface is designed for simplicity, putting constraint-based modelling techniques within easier reach of biologists. CycSim also functions as an online repository of genome-scale metabolic models.
Availability: http://www.genoscope.cns.fr/cycsim
Contact: cycsim@genoscope.cns.fr
Approximate Bayesian feature selection on a large meta-dataset offers novel insights on factors that effect siRNA potency
Authors: Klingelhoefer Jochen W. , Moutsianas Loukas , Holmes Chris 
Published: May 2009

Abstract
Motivation: Short interfering RNA (siRNA)-induced RNA interference is an endogenous pathway in sequence-specific gene silencing. The potency of different siRNAs to inhibit a common target varies greatly and features affecting inhibition are of high current interest. The limited success in predicting siRNA potency being reported so far could originate in the small number and the heterogeneity of available datasets in addition to the knowledge-driven, empirical basis on which features thought to be affecting siRNA potency are often chosen. We attempt to overcome these problems by first constructing a meta-dataset of 6483 publicly available siRNAs (targeting mammalian mRNA), the largest to date, and then applying a Bayesian analysis which accommodates feature set uncertainty. A stochastic logistic regression-based algorithm is designed to explore a vast model space of 497 compositional, structural and thermodynamic features, identifying associations with siRNA potency.
Results: Our algorithm reveals a number of features associated with siRNA potency that are, to the best of our knowledge, either under reported in literature, such as anti-sense 5′ −3′ motif ‘UCU’, or not reported at all, such as the anti-sense 5′ -3′ motif ‘ACGA’. These findings should aid in improving future siRNA potency predictions and might offer further insights into the working of the RNA-induced silencing complex (RISC).
Contact: cholmes@stats.ox.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.