bluuebunny/crossref_metadata_2025_split huggingface dataset:
The majority of endogenous microRNA targets within Alu elements avoid the microRNA machinery
Authors: Hoffman Yonit , Dahary Dvir , Bublik Debora Rosa , Oren Moshe , Pilpel Yitzhak 
Published: January 2013

Abstract
Motivation: The massive spread of repetitive elements in the human genome presents a substantial challenge to the organism, as such elements may accidentally contain seemingly functional motifs. A striking example is offered by the roughly one million copies of Alu repeats in the genome, of which ∼0.5% reside within genes’ untranslated regions (UTRs), presenting ∼30 000 novel potential targets for highly conserved microRNAs (miRNAs). Here, we examine the functionality of miRNA targets within Alu elements in 3′UTRs in the human genome.
Results: Using a comprehensive dataset of miRNA overexpression assays, we show that mRNAs with miRNA targets within Alus are significantly less responsive to the miRNA effects compared with mRNAs that have the same targets outside Alus. Using Ago2-binding mRNA profiling, we confirm that the miRNA machinery avoids miRNA targets within Alus, as opposed to the highly efficient binding of targets outside Alus. We propose three features that prevent potential miRNA sites within Alus from being recognized by the miRNA machinery: (i) Alu repeats that contain miRNA targets and genuine functional miRNA targets appear to reside in distinct mutually exclusive territories within 3′UTRs; (ii) Alus have tight secondary structure that may limit access to the miRNA machinery; and (iii) A-to-I editing of Alu-derived mRNA sequences may divert miRNA targets. The combination of these features is proposed to allow toleration of Alu insertions into mRNAs. Nonetheless, a subset of miRNA targets within Alus appears not to possess any of the aforementioned features, and thus may represent cases where Alu insertion in the genome has introduced novel functional miRNA targets.
Contact: moshe.oren@weizmann.ac.il or Pilpel@weizmann.ac.il
Supplementary information: Supplementary data are available at Bioinformatics online.
Impact of bosentan on exercise capacity in adults after the Fontan procedure: a randomized controlled trial
Authors: Schuuring Mark J. , Vis Jeroen C. , van Dijk Arie P.J. , van Melle Joost P. , Vliegen Hubert W. , Pieper Petronella G. , Sieswerda Gertjan T. , de Bruin‐Bon Rianne H.A.C.M. , Mulder Barbara J.M. , Bouma Berto J. 
Published: January 2013

AimsAn endothelin‐1 receptor blocker, shown to be effective in patients with pulmonary arterial hypertension, might decrease pulmonary vascular resistance to increase cardiac filling and consequently improve exercise capacity in Fontan patients.Methods and resultsThis was a prospective, multicentre randomized open label trial in Fontan patients. One group received bosentan for 6 months. The other group did not receive study medication for the first 3 months, followed by bosentan for 6 months. The primary endpoint was exercise capacity, and secondary endpoints were NT‐proBNP level, cardiac output, SF‐36 (Short Form‐36) quality of life (QoL), and NYHA class. Forty‐two adults (median age 29 (range 18–56) years, 52% male, 88% NYHA class I–II) from five tertiary referral centres participated in the study. Ten patients were on diuretics. Ten patients were not motivated to finish the study. Analysis of all 32 patients who finished the study at 6 months of treatment showed that mean peak V'O2 (24 vs. 25 mL/kg/min), median SQUASH score (6614 vs. 6390), median NT‐proBNP (314 vs. 274 ng/L), and mental QoL (50 vs. 51) remained unchanged as compared with baseline (P = NS, for all). After treatment, NYHA class had improved in 6 (19%), was unchanged in 24 (75%), and declined in 2 (6%) patients. Subgroup analysis on age, ventricular morphology, type of Fontan circulation, or baseline NT‐proBNP level did not reveal efficacy of bosentan. Six transient adverse effects were reported.ConclusionAn increased NT‐proBNP level was present in the majority of Fontan patients. Six months of bosentan treatment was not beneficial.Trial registrationNTR1557
Xenon and Isoflurane Reduce Left Ventricular Remodeling after Myocardial Infarction in the Rat
Authors: Roehl Anna B. , Funcke Sandra , Becker Michael M. , Goetzenich Andreas , Bleilevens Christian , Rossaint Rolf , Steendijk Paul , Hein Marc 
Published: January 2013

Abstract

Background:
Xenon and isoflurane are known to have cardioprotective properties. We tested the hypothesis that these anesthetics positively influence myocardial remodeling 28 days after experimental perioperative myocardial infarction and compared their effects.

Methods:
A total of 60 male Sprague–Dawley rats were subjected to 60min of coronary artery occlusion and 120min of reperfusion. Prior to ischemia, the animals were randomized for the different narcotic regimes (0.6 vol% isoflurane, 70 vol% xenon, or intraperitoneal injection of s-ketamine). Acute injury was quantified by echocardiography and troponin I. After 4 weeks, left ventricular function was assessed by conductance catheter to quantify hemodynamic compromise. Cardiac remodeling was characterized by quantification of dilatation, hypertrophy, fibrosis, capillary density, apoptosis, and expression of fetal genes (α/β myosin heavy chains, α-skeletal actin, periostin, and sarco/endoplasmic reticulum Ca

2+

-ATPase).

Results:
Whereas xenon and isoflurane impeded the acute effects of ischemia-reperfusion on hemodynamics and myocardial injury at a comparable level, differences were found after 4 weeks. Xenon in contrast to isoflurane or ketamine anesthetized animals demonstrated a lower remodeling index (0.7±0.1 vs. 0.9±0.3 and 1.0±0.3g/ml), better ejection fraction (62±9 vs. 49±7 and 35±6%), and reduced expression of β-myosin heavy chain and periostin. The effects on hypertrophy, fibrosis, capillary density, and apoptosis were comparable.

Conclusions:
Compared to isoflurane and s-ketamine, xenon limited progressive adverse cardiac remodeling and contractile dysfunction 28 days after perioperative myocardial infarction.
Estimating transmission of avian influenza in wild birds from incomplete epizootic data: implications for surveillance and disease spread
Authors: Hénaux Viviane , Parmley Jane , Soos Catherine , Samuel Michael D. 
Published: January 2013

Summary

Estimating disease transmission in wildlife populations is critical to understand host–pathogen dynamics, predict disease risks and prioritize surveillance activities. However, obtaining reliable estimates for free‐ranging populations is extremely challenging. In particular, disease surveillance programs may routinely miss the onset or end of epizootics and peak prevalence, limiting the ability to evaluate infectious processes.

We used profile likelihood to estimate the force of infection (FOI) in a low pathogenic avian influenza virus (LPAIv) epizootic model from censored time series of LPAIv prevalence in hatch‐year waterfowl (order Anseriformes) at postbreeding and migration sites in North America.

We found a mean LPAIv FOI of 0·12 day−1 [95% CI, 0·00–0·39], corresponding to an incidence rate of 0·11 day−1, with geographic heterogeneity (min–max: 0·02–0·23 day−1) among study sites. These high infection rates indicate that most hatch‐year waterfowl are likely infected with LPAIv early in the fall migration.

Comparison of model‐predicted and observed immunity confirmed our assumption of naïve hatch‐year waterfowl and suggested long‐term immunity (>6 months) for adults.

Using the mean LPAIv incidence rate, we predict a shorter and lower epizootic curve for highly pathogenic avian influenza virus (HPAIv; 5 weeks with peak prevalence of 28% and 30% mortality) than LPAIv (8 weeks with peak prevalence of 50%). These findings indicate it is harder to detect HPAIv than LPAIv with swabs from live birds, which are commonly used during disease surveillance.

Synthesis and applications. Our study highlights the potential of integrating incomplete surveillance data with epizootic models to quantify disease transmission and immunity. This modelling approach provides an important tool to understand spatial and temporal epizootic dynamics and inform disease surveillance. Our findings suggest focusing highly pathogenic avian influenza virus (HPAIv) surveillance on postbreeding areas where mortality of immunologically naïve hatch‐year birds is most likely to occur, and collecting serology to enhance HPAIv detection. Our modelling approach can integrate various types of disease data facilitating its use with data from other surveillance programs (as illustrated by the estimation of infection rate during an HPAIv outbreak in mute swans Cygnus olor in Europe).
Effects of predator specialization, host plant and climate on biological control of aphids by natural enemies: a meta‐analysis
Authors: Diehl Eva , Sereda Elvira , Wolters Volkmar , Birkhofer Klaus 
Published: January 2013

Summary

Aphids are among the most severe invertebrate pests of crops and cause high economic losses. The control of aphids by natural enemies is an essential ecosystem service with high relevance to management strategies applied in agricultural plant production and horticulture. However, the current knowledge on the effectiveness of specialist and generalist predators in aphid control with respect to host plants and climatic conditions has not yet been summarized in a meta‐analytical approach.

We collected 60 studies providing 168 independent cases of predator exclusion experiments to analyse how predator and host plant group and climatic conditions affect aphid control by natural enemies.

Effects of natural enemies on aphid populations were strongest in assemblages that included specialist predators, either alone or with generalist predators. Generalists alone also reduced aphid numbers significantly, but not to the same extent as specialists.

Effects of natural enemies were weaker on aphid populations feeding on legumes compared with aphids on grasses or herbs. The percentage reduction of aphids feeding on grasses, herbs or legumes was higher in treatments with assemblages or specialists alone compared with generalists with the largest difference on grasses.

According to all field studies from the temperate zone, effects of natural enemies on aphid populations were strongest in areas with high precipitation seasonality. A relationship between predator effects and temperature seasonality was only found for the USA.

Synthesis and applications. Specialist predators alone or assemblages of specialists and generalists had the strongest effect on aphid populations, especially when either feeding on grasses and herbs or when exposed to extreme weather events. The control of aphids by natural enemies is most promising in grass and herb crops, whereas it is less suited for controlling aphids in legume crops. Facing climate change, the effect of extreme weather events on aphid control by natural enemies will have further implications for developing management strategies for aphid control in the future.
Isolation of two new Dehalococcoides mccartyi strains with dissimilar dechlorination functions and their characterization by comparative genomics via microarray analysis
Authors: Lee Patrick K. H. , Cheng Dan , West Kimberlee A. , Alvarez‐Cohen Lisa , He Jianzhong 
Published: January 2013

SummaryMicrobial reductive dechlorination of trichloroethene (TCE) in groundwater often results in the accumulation of dichloroethenes (DCEs). Dehalococcoides mccartyi (Dhc) are the only known bacteria capable of dechlorination beyond DCE to non‐toxic ethene. In this study, two newly isolated Dhc strains (11a and 11a5) with dissimilar functional abilities are described. Strain 11a reductively dechlorinates TCE, 1,1‐DCE, cis‐DCE, trans‐DCE, and vinyl chloride (VC) to ethene, while strain 11a5 dechlorinates TCE and all three DCE isomers only to VC. Each of these dechlorination reactions are coupled to growth by these strains. The VC dechlorination rate of strain 11a occurs at a rate of 258 nmol per min per mg of protein, about two times faster than previously reported stains. Strain 11a possesses the vcrA gene while strain 11a5 contains the tceA gene. Strains 11a and 11a5 share 100% 16S rRNA gene sequence identity with previously sequenced Dhc strains BAV1 and CBDB1, placing it within the Pinellas subgroup, and 85.4% and 89.5% of all genes present in the CBDB1 and BAV1 genomes were detected in strains 11a and 11a5, respectively, using a custom‐designed microarray targeting four sequenced Dhc strains. Genes that were not detected in strains 11a and 11a5 are mostly within the high plasticity regions or integrated elements of the sequenced strains. This study reports the functional description and comparative genomics of two additional Dhc isolates and provides evidence that the observed functional incongruence between the activity and core genome phylogenies of Dhc strains is likely driven by the horizontal transfer of key reductive dehalogenase‐encoding genes.
Deliberative and Participatory Democracy in the UK
Authors: Davidson Stewart , Elstub Stephen 
Published: January 2013

Research Highlights and Abstract This article: Provides an overview of the development of deliberative and participatory democracy in the UK. Critically analyses the success of consecutive UK national governments in fostering deliberative and participatory processes. Surveys the development of deliberative and participatory processes in the UK at sub-national and local level. Provides a starting point for comparative politics on deliberative and participatory democracy between the UK and other polities. This article responds to Michael Saward's call for a more context-specific approach to the study of democracy by exploring developments in, obstacles to, and prospects for, a more deliberative and participatory model of democracy in the UK. A review is undertaken first of the New Labour and coalition governments' attempts at constitutional reform, in order to assess the implications these efforts have had, and continue to have, for the institutionalisation of such a model of democracy. Despite proclamations of lofty ambition successive UK governments have wrapped themselves in the straightjacketing logic of the Westminster model of parliamentary government. As a consequence their actual proposals lack ambition and are often incoherent. The story told in this respect is therefore one of largely unrealised rhetoric. The ‘largely’ qualifier is included, however, in recognition of the space created by Labour's constitutional reforms for participation at the peripheries of governance. The second section of the article focuses on these spaces by, first, commenting briefly on whether the participatory aspirations of the architects of Scottish devolution have been realised before, second, examining the use of specific deliberative mechanisms—such as citizens'juries, deliberative polls and participatory budgeting—at varying locations within the political system and in public agencies and services. Evidence of democratic innovation is presented; however, any optimism on this front must be tempered, as the power-sharing potential of such mechanisms, and their capacity to move us towards a more comprehensive and joined-up deliberative system in the UK, is hampered by the lack of a facilitating institutional landscape. Finally, an overview is provided of the three remaining articles that make up this special section on deliberative and participatory democracy in the UK.
From Road Town to Shanghai: Situating the Caribbean in Global Capital Flows to China
Authors: Vlcek William 
Published: January 2013

Research Highlights and Abstract This article: Assesses the role of Caribbean offshore financial centres (OFCs) in FDI flows to China. Argues the OFC provides financial intermediation services beyond simply tax minimisation. Demonstrates a similar use of the OFC in other developing economies. Suggests the position of the OFC in global finance continues to evolve. This article examines the prominent location of offshore financial centres (OFCs) among the leading origin and destination points for foreign direct investment (FDI) to China. The OFC (characterised as a tax haven) frequently has been ignored or assumed out of analyses on Chinese FDI as simply servicing tax minimisation practices. This article challenges that assumption and emphasises the financial intermediation role performed by the Caribbean OFC beyond practices of tax arbitrage. Through the use of an international business company (IBC) registered in an OFC these jurisdictions perform several functions for investors, to include providing access to foreign capital markets, reducing tax obligations across multiple jurisdictions and concealing potential politically-sensitive beneficial ownership of the investment. This assessment for the role of the OFC in circuits of global capital involving FDI to China demonstrates that China's relationship with the OFC is different from that experienced by Europe and North America.
Ethnic Cleansing, Ethical Smearing and Irish Historians
Authors: Fitzpatrick David 
Published: January 2013

AbstractDo most academic historians of twentieth‐century Ireland conform to a ‘constitutional narrative’, driven by a moral imperative to subvert republican interpretations? Has their shared political agenda led to widespread distortion, suppression, ‘elision’ and falsification of the evidential record? Is it high time to root out ‘the insidious influence of Irish public histories presented as objective historical evidence'? In the view of John M. Regan, the answer in all cases is an emphatic ‘yes’. This riposte to his recent article in History examines the credibility of Regan's critique, with particular attention to his claim that the late Peter Hart was guilty of ‘academic fraud’ in his controversial analysis of republican sectarianism and ‘ethnic cleansing’ in the Irish revolution. When closely examined, Regan's analysis seems perverse and untenable, implicitly relying on a reductionist conspiracy theory which ignores the rich variety and sound scholarship displayed by several generations of historians of modern Ireland.
Between fruit variability of the bioactive compounds, β‐carotene and mangiferin, in mango (Mangifera indica)
Authors: Hewavitharana Amitha K. , Tan Zhi W. , Shimada Ryo , Shaw Paul N. , Flanagan Bernadine M. 
Published: January 2013

AbstractAimAs the use of nutraceuticals has become increasingly popular, there is now a general interest regarding the amount of fruit one must consume in order to fulfil the recommended intake of a particular bioactive. Consequently, the variation in the amount of bioactive between apparently equivalent (variety, maturity) fruits has become an important factor to consider. The present study is conducted to principally address the variation of bioactives between fruits, which has received scant attention in the literature.MethodsKensington Pride mangoes were chosen as the fruit of interest and two signature bioactive compounds, β‐carotene and mangiferin representing two extreme polarities, were chosen to study inter‐ and intra‐fruit variability. Visible spectrometry and HPLC‐tandem mass spectrometry were used to measure the compounds.ResultsThe intra‐ and inter‐fruit variability of mangiferin content was found to be 12.7% and 139%, respectively (n = 10). The intra‐fruit variability of β‐carotene was 2.57%, while the inter‐fruit variability was 38.5% (n = 10).
Evaluation of an electronic record prototype incorporating the Nutrition Care Process and International Dietetics and Nutrition Terminology
Authors: O'Sullivan Therese A. 
Published: January 2013

AbstractAimThis research aimed to evaluate an online electronic record prototype incorporating the Nutrition Care Process and International Dietetics and Nutrition Terminology.MethodsConcept design and programming were conducted to create a prototype from an existing online records program. Twelve dietitians from Perth and surrounds trialled the prototype. Online anonymous questionnaires assessed attitudes and confidence around using the Nutrition Care Process and standardised terminology, current practices and opinions on the prototype. A focus group further investigated topics in more detail.ResultsPart implementation of the Nutrition Care Process (e.g. nutrition diagnosis only) was reported by 42% of dietitians; the remainder planned to implement in the future. Developing new record systems was identified as the most costly area of implementation, followed by dietitian training. After trialling the prototype, dietitians reported an increase of confidence of 17% in using the terminology if they had access to an electronic system. Focus group discussions indicated dietitians felt the prototype was easy to use, acted as a guide to documenting using the care process and terminology, and would be useful in national e‐health records. They expressed interest in using an electronic system for research purposes including quality control, investigating intervention effectiveness and justifying the role of dietitians on a productivity basis.ConclusionsResults of this pilot study support the concept that an electronic system using standardised terminology is likely to be well accepted by dietitians, and suggests further development of the prototype into a fully functioning system with scope for national electronic health record interoperability.
Treatment response in the neck: p16+ versus p16− oropharyngeal cancer
Authors: Mak Daisy , Hicks Rodney J , Rischin Danny , Solomon Ben , Peters Lester , Bressel Mathias , Young Richard J , Corry June 
Published: January 2013

AbstractIntroductionTo compare nodal response rates following chemoradiotherapy in patients with p16+ and p16− oropharyngeal squamous cell carcinoma (OPSCC).MethodsPatients with node‐positive OPSCC treated at Peter MacCallum Cancer Centre on the published phase I–III tirapazamine trials were identified. All patients had conventional assessment (clinical examination (CA), CT and/or MRI) and positron emission tomography (PET) at both baseline and 2–4 months post‐treatment.ResultsThere were 30 p16+ and 18 p16− patients, the former group having significantly higher stage nodal disease (P = 0.016). The mean overall reduction in nodal size at post‐treatment assessment was similar in p16+ and p16− patients (78% vs. 75%), and no statistically significant difference in nodal complete response (CR) rates was detected by either CA (50% vs. 39%, P = 0.35) or PET/PET‐CT (93% vs. 83%, P = 0.19). PET was significantly more accurate in determining the true nodal CR rate in both groups, with a negative predictive value of 96%.ConclusionNodal response rates following chemoradiotherapy appear to be similar in p16+ and p16− patients when assessed by either CA or PET/PET‐CT. However, higher nodal CR was seen in PET/PET‐CT compared with CA in both groups. Metabolic imaging is more accurate than CA in assessing nodal response post‐treatment.