bluuebunny/crossref_metadata_2025_split huggingface dataset:
Non-parametric Bayesian approach to post-translational modification refinement of predictions from tandem mass spectrometry
Authors: Chung Clement , Emili Andrew , Frey Brendan J. 
Published: February 2013

AbstractMotivation: Tandem mass spectrometry (MS/MS) is a dominant approach for large-scale high-throughput post-translational modification (PTM) profiling. Although current state-of-the-art blind PTM spectral analysis algorithms can predict thousands of modified peptides (PTM predictions) in an MS/MS experiment, a significant percentage of these predictions have inaccurate modification mass estimates and false modification site assignments. This problem can be addressed by post-processing the PTM predictions with a PTM refinement algorithm. We developed a novel PTM refinement algorithm, iPTMClust, which extends a recently introduced PTM refinement algorithm PTMClust and uses a non-parametric Bayesian model to better account for uncertainties in the quantity and identity of PTMs in the input data. The use of this new modeling approach enables iPTMClust to provide a confidence score per modification site that allows fine-tuning and interpreting resulting PTM predictions.Results: The primary goal behind iPTMClust is to improve the quality of the PTM predictions. First, to demonstrate that iPTMClust produces sensible and accurate cluster assignments, we compare it with k-means clustering, mixtures of Gaussians (MOG) and PTMClust on a synthetically generated PTM dataset. Second, in two separate benchmark experiments using PTM data taken from a phosphopeptide and a yeast proteome study, we show that iPTMClust outperforms state-of-the-art PTM prediction and refinement algorithms, including PTMClust. Finally, we illustrate the general applicability of our new approach on a set of human chromatin protein complex data, where we are able to identify putative novel modified peptides and modification sites that may be involved in the formation and regulation of protein complexes. Our method facilitates accurate PTM profiling, which is an important step in understanding the mechanisms behind many biological processes and should be an integral part of any proteomic study.Availability: Our algorithm is implemented in Java and is freely available for academic use from http://genes.toronto.edu.Contact: frey@psi.utoronto.caSupplementary information: Supplementary data are available at Bioinformatics online
How much of the seabed is impacted by mobile fishing gear? Absolute estimates from Vessel Monitoring System (VMS) point data
Authors: Gerritsen Hans D. , Minto Cóilín , Lordan Colm 
Published: February 2013

Abstract
Gerritsen, H. D., Minto, C., and Lordan, C. 2013. How much of the seabed is impacted by mobile fishing gear? Absolute estimates from Vessel Monitoring System (VMS) point data. – ICES Journal of Marine Science, 70: 523–531. Demersal trawling impacts extensively on the seabed, and the extent and frequency of this impact can be assessed using Vessel Monitoring System (VMS) data (positional data of fishing vessels). Existing approaches interpolate fishing tracks from consecutive VMS locations (track interpolation) and/or aggregate VMS point data in a spatial grid (point summation). Track interpolation can be quite inaccurate with the current 2-hour time interval between VMS records, leading to biased estimates. Point summation approaches currently only produce relative estimates of impact and are highly sensitive to the grid size chosen. We propose an approach that provides absolute estimates of trawling impact from point data and is not sensitive to an arbitrary choice of grid-cell size. The method involves applying a nested grid and estimating the swept area (area covered by fishing gear) for each VMS point. We show that the ratio of the swept area to the surface area of a cell can be related to the proportion of the seabed that was impacted by the gear a given number of times. We validate the accuracy of this swept-area ratio approach using known vessel tracks and apply the method to international VMS data in the Celtic Sea.
Modelling the influence of daytime distribution on the transport of two sympatric krill species (Thysanoessa raschii and Meganyctiphanes norvegica) in the Gulf of St Lawrence, eastern Canada
Authors: Maps Frédéric , Plourde Stéphane , Lavoie Diane , McQuinn Ian , Chassé Joël 
Published: February 2013

Abstract
Maps, F., Plourde, S., Lavoie, D., McQuinn, I., and Chassé, J. 2014. Modelling the influence of daytime distribution on the transport of two sympatric krill species (Thysanoessa raschii and Meganyctiphanes norvegica) in the Gulf of St Lawrence, eastern Canada. – ICES Journal of Marine Science, 71: 282–292. The Gulf of St Lawrence (GSL) provides several species of North Atlantic baleen whale with an abundant supply of krill, dominated by Thysanoessa raschii and Meganyctiphanes norvegica. We aimed to quantify the differences in upstream advection resulting from the interaction between the circulation and the specific diel vertical migration of T. raschii and M. norvegica at the scale of the northwest GSL. We coupled a regional circulation model with Lagrangian models where the daytime depth followed specific functions of surface salinity. Our results help to explain the spatio-temporal variability in both T. raschii and M. norvegica distributions. We identified in particular spatio-temporal patterns in krill upstream transport. During summer and autumn, the upstream transport of krill is steady across Jacques Cartier Strait, limited across Honguedo Strait, and more sporadic across the Estuary mouth. We estimated that the upstream advection of krill particles across the Estuary mouth would be higher by 16–17% for the T. raschii than for the M. norvegica daytime behaviour. Our results also suggest that the advective processes operating on the adults during the productive season are not the only cause for the observed magnitude of the interannual and interspecific variability in krill abundance.
Evaluating ecosystem goods and services after restoration of marginal upland peatlands in South‐West England
Authors: Grand‐Clement Emilie , Anderson Karen , Smith David , Luscombe David , Gatis Naomi , Ross Martin , Brazier Richard E. 
Published: February 2013

Summary

In the UK, drainage for agricultural reclamation during the 19th and 20th centuries is responsible for an alteration of the ecological and hydrological functioning of peatlands, in turn, affecting a whole suite of ecosystem services. Today, initiatives are in place throughout the UK to reinstate this eco‐hydrological functioning by blocking drainage ditches. Effects on ecosystem services remain unclear, as does the overlapping impact of climate change on peatland recovery.

This article uses a conceptual model to present the effects of restoration on ecosystem services, that is, water provision and quality, carbon storage, biodiversity, food and fibre provision and cultural services, both immediately after ditch blocking and in the few years post‐restoration. The model is then applied in the context of Exmoor National Park, in South West England and used to perform a cost–benefit analysis of the restoration and monitoring programme, as these shallow peatlands are located in geographically marginal areas, and therefore more sensitive to climate change.

Past research indicates that some processes tend to return progressively to their predisturbance state, but whether the complete recovery of peatlands to functioning mires occurs after restoration remains unclear, partly due to the difference between the temporal and spatial scale at which processes occur (i.e. up to decadal) and are monitored (typically a few years).

Overall, on Exmoor, the long‐term benefit of peatland restoration to some ecosystem services, such as a reduction in carbon losses and improvement of water storage and quality, has the potential to balance high financial investment.

Synthesis and applications. Gaining a better understanding of the effects of peatland restoration on ecosystem services provided is essential to assess the potential value of restoration projects. Using the case of the shallow peatlands of Exmoor National Park, located in geographically marginal areas in the UK and therefore more vulnerable to the effects of climate change, we find that there is potential for both the value of carbon storage and water provision to offset the costs of restoration in the long‐term. Our results from Exmoor can provide ecological analogues of impending change further north.
The Regime of Informality in Neoliberal Times in Turkey: The Case of the Kadifekale Urban Transformation Project
Authors: Demirtas‐Milz Neslihan 
Published: February 2013

AbstractJuxtaposing the empirical findings of a qualitative research study of an urban transformation project in the Kadifekale squatter district of Izmir with the changed nature of urban politics in a neoliberal context, this article aims to trace the manifestations of the regime of informality in Turkey. Ethnographic consideration of the motives behind these projects, the way they have been carried out and their consequences for the lives of the inhabitants points to an extended space for informal politics tactically manoeuvred by state officials of various ranks. Particularly during the last two decades, neoliberal urban policies have triggered an intensification of power discrepancies in both the vertical and horizontal dimensions and a fragmentation of community structure in the localities — mainly along socioeconomic divides. This research reveals a transition from positive/passive to negative/active uses of informality in the disposition of the state towards the urban poor when the fast and efficient conduct of urban transformation projects is in question. The characteristics of the locality as a landslide zone, the already fragmented socioeconomic structure in the neighbourhood and the dense presence of Kurdish immigrants facilitate the putting into practice of informal strategies. The immigrants who cannot define a place for themselves in the simultaneously formal and informal context of the project have been seriously disadvantaged.
De novo transcriptomic analyses for non‐model organisms: an evaluation of methods across a multi‐species data set
Authors: Singhal Sonal 
Published: February 2013

AbstractHigh‐throughput sequencing (HTS) is revolutionizing biological research by enabling scientists to quickly and cheaply query variation at a genomic scale. Despite the increasing ease of obtaining such data, using these data effectively still poses notable challenges, especially for those working with organisms without a high‐quality reference genome. For every stage of analysis – from assembly to annotation to variant discovery – researchers have to distinguish technical artefacts from the biological realities of their data before they can make inference. In this work, I explore these challenges by generating a large de novo comparative transcriptomic data set data for a clade of lizards and constructing a pipeline to analyse these data. Then, using a combination of novel metrics and an externally validated variant data set, I test the efficacy of my approach, identify areas of improvement, and propose ways to minimize these errors. I find that with careful data curation, HTS can be a powerful tool for generating genomic data for non‐model organisms.
Minimum effective volume of ropivacaine 7.5 mg/ml for an ultrasound‐guided infraclavicular brachial plexus block
Authors: FLOHR‐MADSEN S. , YTREBØ L. M. , KREGNES S. , WILSGAARD T. , KLAASTAD Ø. 
Published: February 2013

BackgroundUltrasound guidance has been shown to reduce the minimum effective volume (MEV) of local anaesthetics for several peripheral nerve blocks. Although the lateral sagittal infraclavicular block (LSIB) is a well‐established anaesthesia method, MEV for this technique has not been established. Our aim with this study was to determine the MEV using ropivacaine 7.5 mg/ml for the LSIB method.MethodsTwenty‐five adult American Society of Anesthesiologists physical status I‐II patients scheduled for hand surgery received an ultrasound‐guided LSIB with ropivacaine 7.5 mg/ml. A successful block was defined as anaesthesia or analgesia for all five sensory nerves distal to the elbow, 30 min after local anaesthetic injection. The MEV for a successful block in 50% of the patients was determined by using the staircase up‐and‐down method introduced by Dixon and Massey. Logistic regression and probit transformation were applied to estimate the MEV for a successful block in 95% of the patients.ResultsThe patients received ropivacaine 7.5 mg/ml volumes in the range of 12.5–30 ml. The MEVs in 50% and 95% of the patients were 19 ml [95% confidence interval (CI), 14–27] and 31 ml (95% CI, 18–45), respectively.ConclusionsFor surgery distal to the elbow, the MEV in 95% of patients for an ultrasound‐guided LSIB with ropivacaine 7.5 mg/ml was estimated to be 31 ml (95% CI, 18–45 ml). Further studies should determine the factors that influence the volume of local anaesthetic required for a successful infraclavicular block.
The impact of acute tryptophan depletion on attentional performance in adult patients with ADHD
Authors: Mette C. , Zimmermann M. , Grabemann M. , Abdel‐Hamid M. , Uekermann J. , Biskup C. S. , Wiltfang J. , Zepf F. D. , Kis B. 
Published: February 2013

ObjectiveTo date, the impact of the neurotransmitter serotonin (5‐HT) on different neuropsychological functions in adults with attention deficit hyperactivity disorder (ADHD) is underinvestigated. We aimed to examine the effects of acute tryptophan depletion (ATD) and the resulting reduction in central nervous 5‐HT synthesis on target/non‐target discrimination ability and sustained attention in adults with ADHD using an AX‐Continuous Performance Test (AX‐CPT).MethodTwenty male patients with ADHD (age: M = 30.25 SD = 9.37) and twenty male healthy controls (age: M = 27.90 SD = 6.01) received ATD on one day and a tryptophan‐balanced control condition (BAL) on another day in a double‐blind within‐subject crossover design. A continuous performance test (AX‐CPT) with three conditions (AX, AY, and BX) was administered on both days under depleted and sham‐depleted conditions.ResultsIn patients omissions increased after ATD when compared with BAL. Patient's reaction time decreased after ATD when compared with BAL, which was contrasted by opposite effects in controls. Patients showed fewer correct responses (AX condition) and showed a higher rate of errors (condition AXE) independent of ATD or BAL intake.ConclusionThe present preliminary results are indicative of the contribution of serotonergic neurotransmission to attentional processes in adults with ADHD.
Toll‐like receptors in Neonatal Sepsis
Authors: O’Hare Fiona M , William Watson R , Molloy Eleanor J 
Published: February 2013

AbstractToll‐like receptors are vital transmembrane receptors that initiate the innate immune response to many micro‐organisms. The discovery of these receptors has improved our understanding of host–pathogen interactions, and these receptors play an important role in the pathogenesis of multiple neonatal conditions such as sepsis and brain injury. Toll‐like receptors, especially TLRs 2 and 4, are associated with necrotizing enterocolitis, periventricular leukomalacia and sepsis.ConclusionToll‐like receptor modulation may potentially be used as immunomodulators in the management of neonatal sepsis.
Mark‐Specific Hazard Ratio Model with Multivariate Continuous Marks: An Application to Vaccine Efficacy
Authors: Juraska M. , Gilbert P. B. 
Published: February 2013

AbstractSummaryIn randomized placebo‐controlled preventive HIV vaccine efficacy trials, an objective is to evaluate the relationship between vaccine efficacy to prevent infection and genetic distances of the exposing HIV strains to the multiple HIV sequences included in the vaccine construct, where the set of genetic distances is considered as the continuous multivariate “mark” observed in infected subjects only. This research develops a multivariate mark‐specific hazard ratio model in the competing risks failure time analysis framework for the assessment of mark‐specific vaccine efficacy. It allows improved efficiency of estimation by employing the semiparametric method of maximum profile likelihood estimation in the vaccine‐to‐placebo mark density ratio model. The model also enables the use of a more efficient estimation method for the overall log hazard ratio in the Cox model. In addition, we propose testing procedures to evaluate two relevant hypotheses concerning mark‐specific vaccine efficacy. The asymptotic properties and finite‐sample performance of the inferential procedures are investigated. Finally, we apply the proposed methods to data collected in the Thai RV144 HIV vaccine efficacy trial.
The Changing Landscape of the Canadian Food Market: Ethnicity and the Market for Ethnic Food
Authors: Cranfield John 
Published: February 2013

This paper explores the interplay between immigration, ethnic diversity, and food demand in Canada. Attention focuses on the consequences of an increasingly diverse population on demand for food. The notion of dietary acculturation is discussed in the context of a fragmenting market for foods in Canada. A research agenda is presented with the intent to stimulate research that addresses the role of ethnicity in shaping demand for food in Canada. As Canada becomes more ethnically diverse, the landscape of the Canadian food environment will evolve. Understanding the impact of such change on demand for foods in Canada will become increasingly important. Such understanding can help inform the supply side of the market in terms of retail and food service location decisions, as well as decisions related to the marketing mix.Dans le présent article nous analysons l’interaction entre l’immigration, la diversité ethnique et la demande alimentaire au Canada et examinons tout particulièrement les répercussions de l’accroissement de la diversité ethnique sur la demande alimentaire. Nous abordons la notion d’acculturation alimentaire dans un contexte de segmentation du marché alimentaire au Canada. Nous présentons un programme de recherche qui vise à stimuler la recherche sur le rôle de l’ethnicité dans la détermination de la demande alimentaire au Canada. Plus la population canadienne se diversifiera sur le plan ethnique, plus l’environnement alimentaire évoluera, d’où l’importance de bien déterminer les répercussions de cette diversification sur la demande alimentaire au Canada. La détermination de ces répercussions aidera les acteurs du côté de l’offre à prendre des décisions quant à l’emplacement des magasins d’alimentation et des établissements de restauration et à la logistique commerciale (marketing mix).
A comparison of supermatrix and supertree methods for multilocus phylogenetics using organismal datasets
Authors: Janies Daniel A. , Studer Jonathon , Handelman Samuel K. , Linchangco Gregorio 
Published: February 2013

AbstractIt has been proposed that supertree approaches should be applied to large multilocus datasets to achieve computational tractability. Large datasets such as those derived from phylogenomics studies can be broken into many locus‐specific tree searches and the resulting trees can be stitched together via a supertree method. Using simulated data, workers have reported that they can rapidly construct a supertree that is comparable to the results of heuristic tree search on the entire dataset. To test this assertion with organismal data, we compare tree length under the parsimony criterion and computational time for 20 multilocus datasets using supertree (SuperFine and SuperTriplets) and supermatrix (heuristic search in TNT) approaches. Tree length and computational times were compared among methods using the Wilcoxon matched‐pairs signed rank test. Supermatrix searches produced significantly shorter trees than either supertree approach (SuperFine or SuperTriplets; P < 0.0002 in both cases). Moreover, the processing time of supermatrix search was significantly lower than SuperFine+locus‐specific search (P < 0.01) but roughly equivalent to that of SuperTriplets+locus‐specific search (P > 0.4, not significant). In conclusion, we show by using real rather than simulated data that there is no basis, either in time tractability or in tree length, for use of supertrees over heuristic tree search using a supermatrix for phylogenomics.
Dose‐dependent effect of radiation on titanium implants: a quantitative study in rabbits
Authors: Li Jun Yuan , Pow Edmond Ho Nang , Zheng Li Wu , Ma Li , Kwong Dora Lai Wan , Cheung Lim Kwong 
Published: February 2013

AbstractObjectivesThe aim of the study was to investigate the dose‐dependent effect of radiation on dental implant stability and osseointegration using a series of quantitative analyses.Material and methodsSix rabbits were randomly assigned to 15 and 30 Gy radiation groups. Each rabbit received radiation at the tibial and femoral metaphyseal region of left hind leg. The right leg was used as control. Implant surgery was performed on tibial and femoral metaphyses after 1 week. Totally 24 implants were inserted. The animals were killed at postoperative week four. Implant stability was measured using resonance frequency analysis. Ratio of bone volume to total volume (BV/TV), rate of bone growth, and bone‐to‐implant contact (BIC) were assessed using micro‐computed tomography (micro‐CT), fluorochrome labeling analysis, and histomorphometric analysis, respectively.ResultsAfter 4 weeks of healing, all implants were integrated (n = 6). Implant stability was significantly compromised by 15 Gy (P = 0.010) and 30 Gy (P = 0.025) of radiation. Radiation decreased BV/TV, and the significant effect was detected at the dose of 15 Gy (P = 0.008) and 30 Gy (P < 0.001). Bone growth in osseointegration was impaired by radiation. In 15 Gy group, the radiation side showed significant lower rate of bone growth than the control side at week 3 (P = 0.001), while the undistinguishable signals on 30 Gy radiation side suggested the low rate of new bone formation at each time point. Histomorphological BIC had no significant difference between 15 Gy control side and 15 Gy radiation side. 30 Gy radiation side showed a significantly lower BIC than 30 Gy control side (P < 0.001) as well as 15 Gy radiation side (P < 0.001).ConclusionsImplant stability and osseointegration were compromised by radiation. Radiation compromised osseointegration in a dose‐dependent manner.
On the dimensionality of ecological stability
Authors: Donohue Ian , Petchey Owen L. , Montoya José M. , Jackson Andrew L. , McNally Luke , Viana Mafalda , Healy Kevin , Lurgi Miguel , O'Connor Nessa E. , Emmerson Mark C. 
Published: February 2013

AbstractEcological stability is touted as a complex and multifaceted concept, including components such as variability, resistance, resilience, persistence and robustness. Even though a complete appreciation of the effects of perturbations on ecosystems requires the simultaneous measurement of these multiple components of stability, most ecological research has focused on one or a few of those components analysed in isolation. Here, we present a new view of ecological stability that recognises explicitly the non‐independence of components of stability. This provides an approach for simplifying the concept of stability. We illustrate the concept and approach using results from a field experiment, and show that the effective dimensionality of ecological stability is considerably lower than if the various components of stability were unrelated. However, strong perturbations can modify, and even decouple, relationships among individual components of stability. Thus, perturbations not only increase the dimensionality of stability but they can also alter the relationships among components of stability in different ways. Studies that focus on single forms of stability in isolation therefore risk underestimating significantly the potential of perturbations to destabilise ecosystems. In contrast, application of the multidimensional stability framework that we propose gives a far richer understanding of how communities respond to perturbations.