bluuebunny/crossref_metadata_2025_split huggingface dataset:
A simple measure of the strength of convergent evolution
Authors: Arbuckle Kevin , Bennett Cheryl M. , Speed Michael P. 
Published: April 2014

Summary

Convergent evolution, the independent occurrence of phenotypic similarity, is a widespread and common phenomenon. Methods have been developed to identify instances of convergence, but there is a lack of techniques for quantifying the strength of convergence. We therefore investigated whether convergent evolution can be quantified in a meaningful way.
We have developed a simple metric (the Wheatsheaf index) that provides an index of the strength of convergent evolution incorporating both phenotypic similarity and phylogenetic relatedness. The index is comparable across any quantitative or semiquantitative traits and thus will enable the testing of various hypotheses relating to convergence.
The index performs well over a range of conditions. We apply it to an empirical example using Anolis lizard ecomorphs to demonstrate how it can be used.
The Wheatsheaf index provides an additional tool that complements methods aimed at identifying cases of convergent evolution. It will enable cases of convergence to be analysed in more detail, test hypotheses about its mechanics as an evolutionary process and, more generally, the predictability of evolution (how often do we see strong convergence and does this mean evolutionary solutions are limited?).
Continuous‐time spatially explicit capture–recapture models, with an application to a jaguar camera‐trap survey
Authors: Borchers David , Distiller Greg , Foster Rebecca , Harmsen Bart , Milazzo Lorenzo 
Published: April 2014

SummaryMany capture–recapture surveys of wildlife populations operate in continuous time, but detections are typically aggregated into occasions for analysis, even when exact detection times are available. This discards information and introduces subjectivity, in the form of decisions about occasion definition.We develop a spatiotemporal Poisson process model for spatially explicit capture–recapture (SECR) surveys that operate continuously and record exact detection times. We show that, except in some special cases (including the case in which detection probability does not change within occasion), temporally aggregated data do not provide sufficient statistics for density and related parameters, and that when detection probability is constant over time, our continuous‐time (CT) model is equivalent to an existing model based on detection frequencies. We use the model to estimate jaguar density from a camera‐trap survey and conduct a simulation study to investigate the properties of a CT estimator and discrete‐occasion estimators with various levels of temporal aggregation. This includes investigation of the effect on the estimators of spatiotemporal correlation induced by animal movement.The CT estimator is found to be unbiased and more precise than discrete‐occasion estimators based on binary capture data (rather than detection frequencies) when there is no spatiotemporal correlation. It is also found to be only slightly biased when there is correlation induced by animal movement, and to be more robust to inadequate detector spacing, while discrete‐occasion estimators with binary data can be sensitive to occasion length, particularly in the presence of inadequate detector spacing.Our model includes as a special case a discrete‐occasion estimator based on detection frequencies, and at the same time lays a foundation for the development of more sophisticated CT models and estimators. It allows modelling within‐occasion changes in detectability, readily accommodates variation in detector effort, removes subjectivity associated with user‐defined occasions and fully utilizes CT data. We identify a need for developing CT methods that incorporate spatiotemporal dependence in detections and see potential for CT models being combined with telemetry‐based animal movement models to provide a richer inference framework.
Landscape connectivity for wildlife: development and validation of multispecies linkage maps
Authors: Koen Erin L. , Bowman Jeff , Sadowski Carrie , Walpole Aaron A. 
Published: April 2014

Summary

The ability to identify regions of high functional connectivity for multiple wildlife species is of conservation interest with respect to habitat management and corridor planning. We present a method that does not require independent, field‐collected data, is insensitive to the placement of source and destination sites (nodes) for modeling connectivity, and does not require the selection of a focal species.

In the first step of our approach, we created a cost surface that represented permeability of the landscape to movement for a suite of species. We randomly selected nodes around the perimeter of the buffered study area and used circuit theory to connect pairs of nodes. When the buffer was removed, the resulting current density map represented, for each grid cell, the probability of use by moving animals.

We found that using nodes that were randomly located around the perimeter of the buffered study area was less biased by node placement than randomly selecting nodes within the study area. We also found that a buffer of ≥ 20% of the study area width was sufficient to remove the effects of node placement on current density. We tested our method by creating a map of connectivity in the Algonquin to Adirondack region in eastern North America, and we validated the map with independently collected data. We found that amphibians and reptiles were more likely to cross roads in areas of high current density, and fishers (Pekania [Martes] pennanti) used areas with high current density within their home ranges.

Our approach provides an efficient and cost effective method of predicting areas with relatively high landscape connectivity for multiple species..
Allergens on desktop surfaces in preschools and elementary schools of urban children with asthma
Authors: Kanchongkittiphon W. , Sheehan W. J. , Friedlander J. , Chapman M. D. , King E.‐M. , Martirosyan K. , Baxi S. N. , Permaul P. , Gaffin J. M. , Kopel L. , Bailey A. , Fu C. , Petty C. R. , Gold D. R. , Phipatanakul W. 
Published: April 2014

AbstractDesktop dust has been studied as a source of food allergen, but not as a source of potential aeroallergen exposure. Thirty‐six wiped samples from desktop surfaces were collected from preschools and schools. Samples were analyzed for detectable levels of common aeroallergens including Alternaria, cockroach, dog, dust mite, cat, mouse, and rat allergens by immunoassay. Mouse allergen was the most prevalent, detectable in 97.2% of samples. Cat allergen was detectable in 80.6% of samples, and dog allergen was detectable in 77.8% of samples. Other allergens were not as prevalent. Mouse was the only allergen that was highly correlated with settled floor dust collected from the same rooms (r = 0.721, P < 0.001). This is the first study to detect aeroallergens on desktop surfaces by using moist wipes. Allergens for mouse, cat, and dog were highly detectable in wipes with mouse desktop surface levels correlating with levels in vacuumed floor dust.
Transforming growth factor‐beta 1 pathways in inflammatory airway diseases
Authors: Yang Y. , Zhang N. , Lan F. , Van Crombruggen K. , Fang L. , Hu G. , Hong S. , Bachert C. 
Published: April 2014

AbstractTransforming growth factor‐beta 1 (TGF‐β1) has been reported being involved in the remodeling and immunosuppression processes of inflammatory airway diseases; understanding the regulation of TGF‐β1 is therefore a key to unravel the pathomechanisms of these diseases. This review briefly summarizes the current knowledge on the influencing factors for driving TGF‐β1 and its regulatory pathways in inflammatory airway diseases and discusses possible therapeutic approaches to TGF‐β1 control. The factors include smoking and oxidative stress, prostaglandins (PGs), leukotrienes (LTs), bradykinin (BK), and microRNAs (miRs). Based on the summary, new innovative treatment strategies may be developed for inflammatory airway diseases with an impaired expression of TGF‐β1.
Postoperative morphine concentration in infants with or without biliary atresia and its association with hepatic blood flow
Authors: Wang X. , Qiao Z. W. , Zhou Z. J. , Zhuang P. J. , Zheng S. 
Published: April 2014

SummaryWe measured pre‐operative hepatic blood flow and postoperative morphine concentration in infants with or without biliary atresia. Thirty‐four infants (0–3 months) with biliary atresia undergoing portoenterostomy (Kasai operation) were included and hepatic blood flow was assessed by magnetic resonance imaging before surgery in 12 of them. Sixteen subjects (0–3 months) without liver disease undergoing abdominal or pelvic surgery acted as controls and six of them had hepatic blood flow assessed. Intravenous morphine (8 μg.kg−1.h−1) was administered to all patients postoperatively. The median (IQR [range]) relative hepatic blood flow was 3.51 (2.72–3.88 [1.68–4.43]) with and 3.15 (2.66–4.42 [2.30–5.01]) without biliary atresia (p = 0.851). The median (IQR [range]) morphine concentration after 24 h infusion was 5.9 (4.5–16.4 [2.9–42.2]) ng.ml−1and 6.4 (3.2–12.0 [1.9–48.6]) ng.ml−1, respectively (p = 0.460). An inverse regression relation was found between the morphine concentration and the hepatic perfusion index (R2 = 0.519, p = 0.001). Compensatory increases in hepatic arterial blood flow maintain the total hepatic blood flow in infants with biliary atresia.
Psychometric evaluation of a direct observation of procedural skills assessment tool for ultrasound‐guided regional anaesthesia
Authors: Watson M. J. , Wong D. M. , Kluger R. , Chuan A. , Herrick M. D. , Ng I. , Castanelli D. J. , Lin L. , Lansdown A. K. , Barrington M. J. 
Published: April 2014

SummaryAssessment tools must be investigated for reliability, validity and feasibility before being implemented. In 2013, the Australian and New Zealand College of Anaesthetists introduced workplace‐based assessments, including a direct observation of a procedural skills assessment tool. The objective of this study was to evaluate the psychometric properties of this assessment tool for ultrasound‐guided regional anaesthesia. Six experts assessed 30 video‐recorded trainee performances of ultrasound‐guided regional anaesthesia. Inter‐rater reliability, assessed using absolute agreement intraclass correlation coefficients, varied from 0.10 to 0.49 for the nine individual nine‐point scale items, and was 0.25 for a ‘total score’ of all items. Internal consistency was measured by correlation between ‘total score’ and ‘overall performance’ scale item (r = 0.68, p < 0.001). Construct validity was demonstrated by the ‘total score’ correlating with trainee experience (r = 0.51, p = 0.004). The mean time taken to complete assessments was 6 min 35 s.
The use of a nasogastric tube to facilitate nasotracheal intubation: a randomised controlled trial
Authors: Lim C.‐W. , Min S.‐W. , Kim C.‐S. , Chang J.‐E. , Park J.‐E. , Hwang J.‐Y. 
Published: April 2014

SummaryDuring nasotracheal intubation, the tracheal tube passes through either the upper or lower pathway in the nasal cavity, and it has been reported to be safer that the tracheal tube passes though the lower pathway, just below the inferior turbinate. We evaluated the use of a nasogastric tube as a guide to facilitate tracheal tube passage through the lower pathway, compared with the ‘conventional’ technique (blind insertion of the tracheal tube into the nasal cavity). A total of 60 adult patients undergoing oral and maxillofacial surgery were included in the study. In 20 out of 30 patients (66.7%) with the nasogastric tube‐guided technique, the tracheal tube passed through the lower pathway, compared with 8 out of 30 patients (26.7%) with the ‘conventional’ technique (p = 0.004). Use of the nasogastric tube‐guided technique reduced the incidence and severity of epistaxis (p = 0.027), improved navigability (p = 0.034) and required fewer manipulations (p = 0.001) than the ‘conventional’ technique.
Bacterial contamination of surgical scrub suits worn outside the operating theatre: a randomised crossover study
Authors: Hee H. I. , Lee S. , Chia S. N. , Lu Q. S. , Liew A. P. Q. , Ng A. 
Published: April 2014

SummaryIn this study, we aimed to evaluate the bacterial contamination of surgical scrub suits worn outside the operating theatre. We randomised 16 anaesthetists on separate occasions into one of 3 groups: restricted to the operating theatre only; theatre and surgical wards; and theatre and departmental office. For each group, sample fabric pieces attached to the chest, waist and hip areas of each suit were removed at 150 min intervals between 08:30 and 16:00 on the day of study, and sent for microbiological assessment. Mean bacterial counts increased significantly over the course of the working day (p = 0.036), and were lower in the chest compared to the hip (p = 0.007) and waist areas (p = 0.016). The mean (SD) bacterial counts, expressed as colony‐forming units per cm2 at 16:00 on the day of study, were 25.2 (43.5) for those restricted to theatre and 18.5 (25.9) and 17.9 (31.0) for those allowed out to visit the ward and office, respectively (p = 0.370). We conclude that visits to ward and office did not significantly increase bacterial contamination of scrub suits.
Epigallocatechin Gallate Promotes the Development of Mouse 2‐Cell Embryos In Vitro by Regulating Mitochondrial Activity and Expression of Genes Related to p53 Signalling Pathway
Authors: Zhang Weiyu , Lv Junjie , Zhang Yanqin , Jiang Yufei , Chu Chenfeng , Wang Shie 
Published: April 2014

AbstractPreliminary studies have found that the epigallocatechin gallate (EGCG) at proper concentration could promote development of pre‐implantation mouse embryos in vitro. However, the underlying mechanisms have not been well understood. In this study, we collected 1‐cell embryos from Kunming (KM) mice, cultured them in M16 medium or M16 medium supplemented with 10 μg/mL EGCG and investigated the effects of EGCG on mitochondrial activity and reactive oxygen species (ROS) level of 2‐cell embryos. Furthermore, we explored expression differences of genes related to p53 signalling pathway in 2‐cell embryos using a PCR array. The results showed that ROS level and mitochondrial membrane potential were significantly lower in embryos cultured in the EGCG group than in the M16 group (p < 0.05), while the adenosine triphosphate content was slightly lower than in the M16 group (p > 0.05). PCR array test results showed that 18 genes were differentially expressed, among which eight genes involving cell growth, cell cycle regulation and mRNA transcription were up‐regulated and 10 genes involving apoptosis, cell cycle arrest and DNA repair were down‐regulated in the EGCG groups. It is concluded that EGCG could promote the development of 1‐cell embryos in vitro possibly due to its ability to scavenge ROS and regulate mitochondrial activity. In addition, EGCG could influence expression of genes related to p53 signalling pathway in 2‐cell embryos and promote cell cycle progression.
Pre‐clinical and Clinical Safety Studies of CMX‐2043: A Cytoprotective Lipoic Acid Analogue for Ischaemia–Reperfusion Injury
Authors: Kates Steven A. , Lader Alan S. , Casale Ralph , Beeuwkes Reinier 
Published: April 2014

AbstractCMX‐2043 is an α‐lipoic acid analogue targeted to reduction of cellular injury and organ damage due to ischaemia–reperfusion injury (IRI). It has been shown to be effective in a rat model of cardiac IRI. The studies here reported evaluate its safety and pharmacokinetic profile in preparation for human clinical studies in procedures associated with IRI. Safety and tolerability were tested in standard pre‐clinical in vitro and animal models and in a Phase 1 human clinical trial. CMX‐2043 did not bind to a wide range of receptors and specific targets at approximately 4 μg/mL (10 μM). It was not mutagenic by Ames assay, did not produce chromosome aberrations in Chinese hamster ovary (CHO) cells, and was negative for clastogenic potential. Toxicological studies in rats including both single and 14‐day repeat intravenous doses and in dogs (single intravenous dose) with a 2‐week recovery period were conducted. The NOAEL in rats and dogs was 30 and >10 mg/kg, respectively. No serious adverse events were reported in a placebo‐controlled, sequential dose escalation Phase 1 clinical trial. The low toxicity in the pre‐clinical studies and the absence of adverse events in the Phase 1 trial have supported investigation of CMX‐2043 in a human efficacy trial.
Reperfusion Therapy with Low‐Dose Insulin or Insulin‐Like Growth Factor 2; Myocardial Function and Infarct Size in a Porcine Model of Ischaemia and Reperfusion
Authors: Salminen Pirjo‐Riitta , Dahle Geir Olav , Moen Christian Arvei , Wergeland Anita , Jonassen Anne Kristin , Haaverstad Rune , Matre Knut , Grong Ketil 
Published: April 2014

AbstractIn an open‐chest porcine model, we examined whether myocardial pharmacological conditioning at the time of reperfusion with low‐dose insulin or insulin‐like growth factor 2 (IGF2), not affecting serum glucose levels, could reduce infarct size and improve functional recovery. Two groups of anaesthetized pigs with either 60 or 40 min. of left anterior descending artery occlusion (total n = 42) were randomized to receive either 0.9% saline, insulin or IGF2 infusion for 15 min., starting 5 min. before a 180‐min. reperfusion period. Repeated fluorescent microsphere injections were used to confirm ischaemia and reperfusion. Area at risk and infarct size was determined with Evans blue and triphenyltetrazolium chloride staining. Local myocardial function was evaluated with multi‐layer radial tissue Doppler strain and speckle‐tracking strain from epicardial echocardiography. Western blotting and TUNEL staining were performed to explore apoptosis. Infarct size did not differ between treatment groups and was 56.7 ± 6.8%, 49.7 ± 9.6%, 56.2 ± 8.0% of area at risk for control, insulin and IGF2 group, respectively, in the 60‐min. occlusion series. Corresponding values were 45.6 ± 6.0%, 48.4 ± 7.2% and 34.1 ± 5.8% after 40‐min. occlusion. Global and local cardiac function did not differ between treatment groups. No differences related to treatment could be found in myocardial tissue cleaved caspase‐3 content or the degree of TUNEL staining. Reperfusion therapy with low‐dose insulin or with IGF2 neither reduced infarct size nor improved function in reperfused myocardium in this in vivo porcine model.
Bayesian estimation of the phylogeography of African gorillas with genome‐differentiated population trees
Authors: Kim Joungyoun , Larget Bret 
Published: April 2014

SummaryPhylogeography investigates the historical process that is responsible for the contemporary geographic distributions of populations in a species. The inference is made on the basis of molecular sequence data sampled from modern‐day populations. The estimates, however, may fluctuate depending on the relevant genomic regions, because the evolution mechanism of each genome is unique, even within the same individual. In this article, we propose a genome‐differentiated population tree model that allows the existence of separate population trees for each homologous genome. In each population tree, the unique evolutionary characteristics account for each genome, along with their homologous relationship; therefore, the approach can distinguish the evolutionary history of one genome from that of another. In addition to the separate divergence times, the new model can estimate separate effective population sizes, gene‐genealogies and other mutation parameters. For Bayesian inference, we developed a Markov chain Monte Carlo (MCMC) methodology with a novel MCMC algorithm which can mix over a complicated state space. The stability of the new estimator is demonstrated through comparison with the Monte Carlo samples and other methods, as well as MCMC convergence diagnostics. The analysis of African gorilla data from two homologous loci reveals discordant divergence times between loci, and this discrepancy is explained by male‐mediated gene flows until the end of the last ice age.
Combined estimating equation approaches for semiparametric transformation models with length‐biased survival data
Authors: Cheng Yu‐Jen , Huang Chiung‐Yu 
Published: April 2014

SummarySurvival data are subject to length‐biased sampling when the survival times are left‐truncated and the underlying truncation time random variable is uniformly distributed. Substantial efficiency gains can be achieved by incorporating the information about the truncation time distribution in the estimation procedure [Wang (1989)Journal of the American Statistical Association84, 742–748; Wang (1996)Biometrika83, 343–354]. Under the semiparametric transformation models, the maximum likelihood method is expected to be fully efficient, yet it is difficult to implement because the full likelihood depends on the nonparametric component in a complicated way. Moreover, its asymptotic properties have not been established. In this article, we extend the martingale estimating equation approach [Chen et al. (2002)Biometrika89, 659–668; Kim et al. (2013)Journal of the American Statistical Association108, 217–227] and the pseudo‐partial likelihood approach [Severini and Wong (1992)The Annals of Statistics4, 1768–1802; Zucker (2005)Journal of the American Statistical Association100, 1264–1277] for semiparametric transformation models with right‐censored data to handle left‐truncated and right‐censored data. In the same spirit of the composite likelihood method [Huang and Qin (2012)Journal of the American Statistical Association107, 946–957], we further construct another set of unbiased estimating equations by exploiting the special probability structure of length‐biased sampling. Thus the number of estimating equations exceeds the number of parameters, and efficiency gains can be achieved by solving a simple combination of these estimating equations. The proposed methods are easy to implement as they do not require additional programming efforts. Moreover, they are shown to be consistent and asymptotically normally distributed. A data analysis of a dementia study illustrates the methods.
TEL@work: Toward integration of theory and practice
Authors: Tynjälä Päivi , Häkkinen Päivi , Hämäläinen Raija 
Published: April 2014

AbstractThis paper examines technology‐enhanced learning at work in the context of the integrative pedagogy model. The basic idea behind this model is to create learning environments whereby the four basic elements of professional expertise (ie, theoretical, practical, self‐regulative and sociocultural knowledge) can be integrated. The paper illustrates two basic ways of applying the model in technology‐enhanced learning at work. First, examples of how to make use of existing technologies, especially social media, to empower learning at work is presented, and second, an instance of the way the model is used in the design of specific technologies for enhancing collaborative learning in the work context is described. The paper concludes that the integrative pedagogy model has the potential to serve both as a principle for designing technologies and for applying existing technologies for workplace learning.