200 research outputs found
Erythrocyte biomarker-based validation of a diet history method used in a dietary intervention trial
Sequence Dependent Melting and Refolding Dynamics of RNA UNCG Tetraloops Using Temperature-Jump/Drop Infrared Spectroscopy
Time-resolved temperature-jump/drop infrared (IR) spectroscopy
has been used to measure the impact of stem base sequence on the melting
and refolding dynamics of ribonucleic acid (RNA) tetraloops. A series
of three 12-nucleotide RNA hairpin sequences were studied, each featuring
a UACG tetraloop motif and a double-stranded stem containing four
base pairs. In each case, the stem comprised three GC pairs plus a
single AU base pair inserted at the closing point of the loop (RNAloop), in the middle of the stem (RNAmid), or at
the stem terminus (RNAend). Results from analogous DNA
tetraloop (TACG) sequences were also obtained. Inclusion of AU or
AT base pairs in the stem leads to faster melting of the stem-loop
structure compared to a stem sequence featuring four GC base pairs
while refolding times were found to be slower, consistent with a general
reduction in stem-loop stability caused by the AU/AT pair. Independent
measurement of the dynamic timescales for melting and refolding of
ring vibrational modes of guanine (GR) and adenine (AR) provided position-specific insight into hairpin dynamics.
The GR-derived data showed that DNA sequences melted more
quickly (0.5 ± 0.1 to 0.7 ± 0.1 μs at 70 °C)
than analogous RNA sequences (4.3 ± 0.4 to 4.4 ± 0.3 μs
at 70 °C). Position-sensitive data from the AR modes
suggests that DNA hairpins begin melting from the terminal end of
the stem toward the loop while RNA sequences begin melting from the
loop. Refolding timescales for both RNA and DNA hairpins were found
to be similar (250 ± 50 μs at 70 °C) except for RNAend and DNAloop which refolded much more slowly
(746 ± 36 and 430 ± 31 μs, respectively), showing
that the refolding pathway is significantly impaired by the placement
of AU/AT pairs at different points in the stem. We conclude that conformational
changes of analogous pairs of RNA and DNA tetraloops proceed by different
mechanisms
Safety and Efficacy of Elbasvir/Grazoprevir in Patients With Hepatitis C Virus Infection and Compensated Cirrhosis: An Integrated Analysis
Background & Aims
Persons with hepatitis C virus (HCV) infection are at risk of progressive liver disease, cirrhosis, and decompensation. We analyzed the effects of the direct-acting antiviral agents elbasvir and grazoprevir in patients with HCV infection and compensated cirrhosis, combining data from 6 clinical trials.
Methods
We performed an integrated analysis of 402 patients with HCV genotype 1, 4, or 6 infection and Child-Pugh A compensated cirrhosis enrolled in 6 clinical trials. All patients received elbasvir/grazoprevir 50 mg/100 mg once daily, with or without ribavirin, for 12−18 weeks. The primary end point was sustained virologic response 12 weeks after completion of therapy (SVR12), defined as a level of HCV RNA <15 IU/mL.
Results
Among treatment-naïve and treatment-experienced patients receiving elbasvir/grazoprevir for 12 weeks, 97.8% (135 of 138) and 88.9% (48 of 54) achieved SVR12, respectively. Among patients receiving elbasvir/grazoprevir for 12 weeks, addition of ribavirin did not increase the proportion of treatment-naïve patients (90.3%, 28 of 31) or treatment-experienced patients who achieved an SVR12 (91.4%, 74 of 81). All (49 of 49) treatment-experienced patients receiving elbasvir/grazoprevir with ribavirin for 16 or 18 weeks, and 93.9% (46 of 49) of patients receiving elbasvir/grazoprevir without ribavirin for 16 or 18 weeks achieved SVR12. Virologic failure was higher among patients with HCV genotype 1a infections compared with patients with genotype 1b or 4 infections, particularly in patients who had not responded to previous interferon therapy. Baseline tests for resistance-associated substitutions (RASs) led to an individualized approach for selecting treatment duration and established a need for ribavirin for patients with HCV genotype 1a infection and RASs, regardless of treatment history. Among patients with HCV genotype 1a infection with and without baseline RASs in HCV nonstructural protein 5A who received elbasvir/grazoprevir for 12 weeks, 73% (8 of 11) and 98% (96 of 98) achieved SVR12, respectively. Both patients with HCV genotype 1a infection with baseline RASs who received 16 or 18 weeks of elbasvir/grazoprevir and ribavirin achieved SVR12. Grade 3 or 4 increases in levels of alanine aminotransferase and aspartate aminotransferase, which did not cause symptoms, were reported in 2.3% (6 of 264) of patients receiving elbasvir/grazoprevir. Serious adverse events were reported in 3% (8 of 264) patients and no patient had a decompensation-related event.
Conclusions
In an analysis of data from 6 clinical trials, rates of SVR12 ranged from 89% to 100% in patients with HCV genotype 1, 4, or 6 infections and compensated cirrhosis treated with elbasvir/grazoprevir, with or without ribavirin. Addition of ribavirin to a 12-week regimen of elbasvir/grazoprevir had little effect on the proportion of treatment-naïve or treatment-experienced patients who achieved an SVR12. However, virologic failure did not occur in any treatment-experienced patients when the duration of elbasvir/grazoprevir and ribavirin therapy was extended to 16 or 18 weeks. Baseline analysis of RASs (or in the absence of this test, a history of nonresponse to interferon) can be used to determine treatment duration and the need for ribavirin in patients with HCV genotype 1a infection
Trust and Reputation Modelling for Tourism Recommendations Supported by Crowdsourcing
Tourism crowdsourcing platforms have a profound influence
on the tourist behaviour particularly in terms of travel planning. Not
only they hold the opinions shared by other tourists concerning tourism
resources, but, with the help of recommendation engines, are the pillar
of personalised resource recommendation. However, since prospective
tourists are unaware of the trustworthiness or reputation of crowd publishers,
they are in fact taking a leap of faith when then rely on the
crowd wisdom. In this paper, we argue that modelling publisher Trust &
Reputation improves the quality of the tourism recommendations supported
by crowdsourced information. Therefore, we present a tourism
recommendation system which integrates: (i) user profiling using the
multi-criteria ratings; (ii) k-Nearest Neighbours (k-NN) prediction of the
user ratings; (iii) Trust & Reputation modelling; and (iv) incremental
model update, i.e., providing near real-time recommendations. In terms
of contributions, this paper provides two different Trust & Reputation
approaches: (i) general reputation employing the pairwise trust values
using all users; and (ii) neighbour-based reputation employing the pairwise
trust values of the common neighbours. The proposed method was
experimented using crowdsourced datasets from Expedia and TripAdvisor
platforms.info:eu-repo/semantics/publishedVersio
Livestock trade networks for guiding animal health surveillance
BACKGROUND: Trade in live animals can contribute to the introduction of exotic diseases, the maintenance and spread endemic diseases. Annually millions of animals are moved across Europe for the purposes of breeding, fattening and slaughter. Data on the number of animals moved were obtained from the Directorate General Sanco (DG Sanco) for 2011. These were converted to livestock units to enable direct comparison across species and their movements were mapped, used to calculate the indegrees and outdegrees of 27 European countries and the density and transitivity of movements within Europe. This provided the opportunity to discuss surveillance of European livestock movement taking into account stopping points en-route. RESULTS: High density and transitivity of movement for registered equines, breeding and fattening cattle, breeding poultry and pigs for breeding, fattening and slaughter indicates that hazards have the potential to spread quickly within these populations. This is of concern to highly connected countries particularly those where imported animals constitute a large proportion of their national livestock populations, and have a high indegree. The transport of poultry (older than 72 hours) and unweaned animals would require more rest breaks than the movement of weaned animals, which may provide more opportunities for disease transmission. Transitivity is greatest for animals transported for breeding purposes with cattle, pigs and poultry having values of over 50%. CONCLUSIONS: This paper demonstrated that some species (pigs and poultry) are traded much more frequently and at a larger scale than species such as goats. Some countries are more vulnerable than others due to importing animals from many countries, having imported animals requiring rest-breaks and importing large proportions of their national herd or flock. Such knowledge about the vulnerability of different livestock systems related to trade movements can be used to inform the design of animal health surveillance systems to facilitate the trade in animals between European member states. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12917-015-0354-4) contains supplementary material, which is available to authorized users
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Individual common variants exert weak effects on the risk for autism spectrum disorders.
While it is apparent that rare variation can play an important role in the genetic architecture of autism spectrum disorders (ASDs), the contribution of common variation to the risk of developing ASD is less clear. To produce a more comprehensive picture, we report Stage 2 of the Autism Genome Project genome-wide association study, adding 1301 ASD families and bringing the total to 2705 families analysed (Stages 1 and 2). In addition to evaluating the association of individual single nucleotide polymorphisms (SNPs), we also sought evidence that common variants, en masse, might affect the risk. Despite genotyping over a million SNPs covering the genome, no single SNP shows significant association with ASD or selected phenotypes at a genome-wide level. The SNP that achieves the smallest P-value from secondary analyses is rs1718101. It falls in CNTNAP2, a gene previously implicated in susceptibility for ASD. This SNP also shows modest association with age of word/phrase acquisition in ASD subjects, of interest because features of language development are also associated with other variation in CNTNAP2. In contrast, allele scores derived from the transmission of common alleles to Stage 1 cases significantly predict case status in the independent Stage 2 sample. Despite being significant, the variance explained by these allele scores was small (Vm< 1%). Based on results from individual SNPs and their en masse effect on risk, as inferred from the allele score results, it is reasonable to conclude that common variants affect the risk for ASD but their individual effects are modest
A Mass Spectrometry-Based Profiling of Interactomes of Viral DDB1- and Cullin Ubiquitin Ligase-Binding Proteins Reveals NF-κB Inhibitory Activity of the HIV-2-Encoded Vpx
Viruses and hosts are situated in a molecular arms race. To avoid morbidity and mortality, hosts evolved antiviral restriction factors. These restriction factors exert selection pressure on the viruses and drive viral evolution toward increasingly efficient immune antagonists. Numerous viruses exploit cellular DNA damage-binding protein 1 (DDB1)-containing Cullin RocA ubiquitin ligases (CRLs) to induce the ubiquitination and subsequent proteasomal degradation of antiviral factors expressed by their hosts. To establish a comprehensive understanding of the underlying protein interaction networks, we performed immuno-affinity precipitations for a panel of DDB1-interacting proteins derived from viruses such as mouse cytomegalovirus (MCMV, Murid herpesvirus [MuHV] 1), rat cytomegalovirus Maastricht MuHV2, rat cytomegalovirus English MuHV8, human cytomegalovirus (HCMV), hepatitis B virus (HBV), and human immunodeficiency virus (HIV). Cellular interaction partners were identified and quantified by mass spectrometry (MS) and validated by classical biochemistry. The comparative approach enabled us to separate unspecific interactions from specific binding partners and revealed remarkable differences in the strength of interaction with DDB1. Our analysis confirmed several previously described interactions like the interaction of the MCMV-encoded interferon antagonist pM27 with STAT2. We extended known interactions to paralogous proteins like the interaction of the HBV-encoded HBx with different Spindlin proteins and documented interactions for the first time, which explain functional data like the interaction of the HIV-2-encoded Vpr with Bax. Additionally, several novel interactions were identified, such as the association of the HIV-2-encoded Vpx with the transcription factor RelA (also called p65). For the latter interaction, we documented a functional relevance in antagonizing NF-κB-driven gene expression. The mutation of the DDB1 binding interface of Vpx significantly impaired NF-κB inhibition, indicating that Vpx counteracts NF-κB signaling by a DDB1- and CRL-dependent mechanism. In summary, our findings improve the understanding of how viral pathogens hijack cellular DDB1 and CRLs to ensure efficient replication despite the expression of host restriction factors
Integrating adverse effect analysis into environmental risk assessment for exotic generalist arthropod biological control agents: a three-tiered framework
Environmental risk assessments (ERAs) are required before utilizing exotic arthropods for biological control (BC). Present ERAs focus on exposure analysis (host/prey range) and have resulted in approval of many specialist exotic biological control agents (BCA). In comparison to specialists, generalist arthropod BCAs (GABCAs) have been considered inherently risky and less used in classical biological control. To safely consider exotic GABCAs, an ERA must include methods for the analysis of potential effects. A panel of 47 experts from 14 countries discussed, in six online forums over 12 months, scientific criteria for an ERA for exotic GABCAs. Using four case studies, a three-tiered ERA comprising Scoping, Screening and Definitive Assessments was developed. The ERA is primarily based on expert consultation, with decision processes in each tier that lead to the approval of the petition or the subsequent tier. In the Scoping Assessment, likelihood of establishment (for augmentative BC), and potential effect(s) are qualitatively assessed. If risks are identified, the Screening Assessment is conducted, in which 19 categories of effects (adverse and beneficial) are quantified. If a risk exceeds the proposed risk threshold in any of these categories, the analysis moves to the Definitive Assessment to identify potential non-target species in the respective category(ies). When at least one potential non-target species is at significant risk, long-term and indirect ecosystem risks must be quantified with actual data or the petition for release can be dismissed or withdrawn. The proposed ERA should contribute to the development of safe pathways for the use of low risk GABCAs
Impact of foods enriched with n-3 long-chain polyunsaturated fatty acids on erythrocyte n-3 levels and cardiovascular risk factors
Consumption of fish or fish oils rich in the n-3 long chain PUFA EPA and DHA may improve multiple risk factors for CVD. The objective of this study was to determine whether regular consumption of foods enriched with n-3 long-chain PUFA can improve n-3 long-chain PUFA status (erythrocytes) and cardiovascular health. Overweight volunteers with high levels of triacylglycerols (TG; >1.6 mmol/l) were enrolled in a 6-month dietary intervention trial conducted in Adelaide (n 47) and Perth (n 39), and randomised to consume control foods or n-3-enriched foods to achieve an EPA + DHA intake of 1 g/d. Test foods were substituted for equivalent foods in their regular diet. Erythrocyte fatty acids, plasma TG and other CVD risk factors were monitored at 0, 3 and 6 months. There were no significant differences between groups for blood pressure, arterial compliance, glucose, insulin, lipids, C-reactive protein (CRP) or urinary 11-dehydro-thromboxane B2 (TXB2) over 6 months, even though regular consumption of n-3-enriched foods increased EPA + DHA intake from 0.2 to 1.0 g/d. However, the n-3 long-chain PUFA content of erythrocytes increased by 35 and 53 % at 3 and 6 months, respectively, in subjects consuming the n-3-enriched foods. These increases were positively associated with measures of arterial compliance and negatively associated with serum CRP and urinary 11-dehydro-TXB2 excretion. Sustainable increases in dietary intakes and erythrocyte levels of n-3 long-chain PUFA can be achieved through regular consumption of suitably enriched processed foods. Such increases may be associated with reduced CV risk.Karen J. Murphy, Barbara J. Meyer, Trevor A. Mori, Valerie Burke, Jackie Mansour, Craig S. Patch, Linda C. Tapsell, Manny Noakes, Peter A. Clifton, Anne Barden, Ian B. Puddey, Lawrence J. Beilin and Peter R. C. How
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