bluuebunny/crossref_metadata_2025 huggingface dataset:
A new era in palaeomicrobiology: prospects for ancient dental calculus as a long-term record of the human oral microbiome
Authors: Warinner Christina , Speller Camilla , Collins Matthew J.
Published: December 2014

The field of palaeomicrobiology is dramatically expanding thanks to recent advances in high-throughput biomolecular sequencing, which allows unprecedented access to the evolutionary history and ecology of human-associated and environmental microbes. Recently, human dental calculus has been shown to be an abundant, nearly ubiquitous, and long-term reservoir of the ancient oral microbiome, preserving not only microbial and host biomolecules but also dietary and environmental debris. Modern investigations of native human microbiota have demonstrated that the human microbiome plays a central role in health and chronic disease, raising questions about changes in microbial ecology, diversity and function through time. This paper explores the current state of ancient oral microbiome research and discusses successful applications, methodological challenges and future possibilities in elucidating the intimate evolutionary relationship between humans and their microbes.
Identification of kinship and occupant status in Mongolian noble burials of the Yuan Dynasty through a multidisciplinary approach
Authors: Cui Yinqiu , Song Li , Wei Dong , Pang Yuhong , Wang Ning , Ning Chao , Li Chunmei , Feng Binxiao , Tang Wentao , Li Hongjie , Ren Yashan , Zhang Chunchang , Huang Yanyi , Hu Yaowu , Zhou Hui
Published: December 2014

The Yuan Dynasty (AD 1271–1368) was the first dynasty in Chinese history where a minority ethnic group (Mongols) ruled. Few cemeteries containing Mongolian nobles have been found owing to their tradition of keeping burial grounds secret and their lack of historical records. Archaeological excavations at the Shuzhuanglou site in the Hebei province of China led to the discovery of 13 skeletons in six separate tombs. The style of the artefacts and burials indicate the cemetery occupants were Mongol nobles. However, the origin, relationships and status of the chief occupant (M1m) are unclear. To shed light on the identity of the principal occupant and resolve the kin relationships between individuals, a multidisciplinary approach was adopted, combining archaeological information, stable isotope data and molecular genetic data. Analysis of autosomal, mitochondrial and Y-chromosomal DNA show that some of the occupants were related. The available evidence strongly suggests that the principal occupant may have been the Mongol noble Korguz. Our study demonstrates the power of a multidisciplinary approach in elucidating information about the inhabitants of ancient historical sites.
Proxy comparison in ancient peat sediments: pollen, macrofossil and plant DNA
Authors: Parducci Laura , Väliranta Minna , Salonen J. Sakari , Ronkainen Tiina , Matetovici Irina , Fontana Sonia L. , Eskola Tiina , Sarala Pertti , Suyama Yoshihisa
Published: December 2014

We compared DNA, pollen and macrofossil data obtained from Weichselian interstadial (age more than 40 kyr) and Holocene (maximum age 8400 cal yr BP) peat sediments from northern Europe and used them to reconstruct contemporary floristic compositions at two sites. The majority of the samples provided plant DNA sequences of good quality with success amplification rates depending on age. DNA and sequencing analysis provided five plant taxa from the older site and nine taxa from the younger site, corresponding to 7% and 15% of the total number of taxa identified by the three proxies together. At both sites, pollen analysis detected the largest (54) and DNA the lowest (10) number of taxa, but five of the DNA taxa were not detected by pollen and macrofossils. The finding of a larger overlap between DNA and pollen than between DNA and macrofossils proxies seems to go against our previous suggestion based on lacustrine sediments that DNA originates principally from plant tissues and less from pollen. At both sites, we also detected
Quercus
spp. DNA, but few pollen grains were found in the record, and these are normally interpreted as long-distance dispersal. We confirm that in palaeoecological investigations, sedimentary DNA analysis is less comprehensive than classical morphological analysis, but is a complementary and important tool to obtain a more complete picture of past flora.
Twenty-five thousand years of fluctuating selection on leopard complex spotting and congenital night blindness in horses
Authors: Ludwig Arne , Reissmann Monika , Benecke Norbert , Bellone Rebecca , Sandoval-Castellanos Edson , Cieslak Michael , Fortes Gloria G. , Morales-Muñiz Arturo , Hofreiter Michael , Pruvost Melanie
Published: December 2014

Leopard complex spotting is inherited by the incompletely dominant locus,LP, which also causes congenital stationary night blindness in homozygous horses. We investigated an associated single nucleotide polymorphism in theTRPM1gene in 96 archaeological bones from 31 localities from Late Pleistocene (approx. 17 000 YBP) to medieval times. The first genetic evidence ofLPspotting in Europe dates back to the Pleistocene. We tested for temporal changes in theLPassociated allele frequency and estimated coefficients of selection by means of approximate Bayesian computation analyses. Our results show that at least some of the observed frequency changes are congruent with shifts in artificial selection pressure for the leopard complex spotting phenotype. In early domestic horses from Kirklareli–Kanligecit (Turkey) dating to 2700–2200 BC, a remarkably high number of leopard spotted horses (six of 10 individuals) was detected including one adult homozygote. However,LPseems to have largely disappeared during the late Bronze Age, suggesting selection against this phenotype in early domestic horses. During the Iron Age,LPreappeared, probably by reintroduction into the domestic gene pool from wild animals. This picture of alternating selective regimes might explain how genetic diversity was maintained in domestic animals despite selection for specific traits at different times.
DensiTree 2: Seeing Trees Through the Forest
Authors: Bouckaert Remco R. , Heled Joseph
Published: December 2014

Motivation

Phylogenetic analysis like Bayesian MCMC or bootstrapping result in a collection of trees. Trees are discrete objects and it is generally difficult to get a mental grip on a distributions over trees. Visualisation tools like DensiTree can give good intuition on tree distributions. It works by drawing all trees in the set transparently thus highlighting areas where the tree in the set agrees. In this way, both uncertainty in clade heights and uncertainty in topology can be visualised. In our experience, a vanilla DensiTree can turn out to be misleading in that it shows too much uncertainty due to wrongly ordering taxa or due to unlucky placement of internal nodes.

Results

DensiTree is extended to allow visualisation of meta-data associated with branches such as population size and evolutionary rates. Furthermore, geographic locations of taxa can be shown on a map, making it easy to visually check there is some geographic pattern in a phylogeny. Taxa orderings have a large impact on the layout of the tree set, and advances have been made in finding better orderings resulting in significantly more informative visualisations. We also explored various methods for positioning internal nodes, which can improve the quality of the image. Together, these advances make it easier to comprehend distributions over trees.

Availability

DensiTree is freely available fromhttp://compevol.auckland.ac.nz/software/.
The Regulation of Photosynthetic Structure and Function during Nitrogen Deprivation in Chlamydomonas reinhardtii
Authors: Juergens Matthew T. , Deshpande Rahul R. , Lucker Ben F. , Park Jeong-Jin , Wang Hongxia , Gargouri Mahmoud , Holguin F. Omar , Disbrow Bradley , Schaub Tanner , Skepper Jeremy N. , Kramer David M. , Gang David R. , Hicks Leslie M. , Shachar-Hill Yair
Published: December 2014

The accumulation of carbon storage compounds by many unicellular algae after nutrient deprivation occurs despite declines in their photosynthetic apparatus. To understand the regulation and roles of photosynthesis during this potentially bioenergetically valuable process, we analyzed photosynthetic structure and function after nitrogen deprivation in the model alga Chlamydomonas reinhardtii. Transcriptomic, proteomic, metabolite, and lipid profiling and microscopic time course data were combined with multiple measures of photosynthetic function. Levels of transcripts and proteins of photosystems I and II and most antenna genes fell with differing trajectories; thylakoid membrane lipid levels decreased, while their proportions remained similar and thylakoid membrane organization appeared to be preserved. Cellular chlorophyll (Chl) content decreased more than 2-fold within 24 h, and we conclude from transcript protein and 13C labeling rates that Chl synthesis was down-regulated both pre- and posttranslationally and that Chl levels fell because of a rapid cessation in synthesis and dilution by cellular growth rather than because of degradation. Photosynthetically driven oxygen production and the efficiency of photosystem II as well as P700+ reduction and electrochromic shift kinetics all decreased over the time course, without evidence of substantial energy overflow. The results also indicate that linear electron flow fell approximately 15% more than cyclic flow over the first 24 h. Comparing Calvin-Benson cycle transcript and enzyme levels with changes in photosynthetic 13CO2 incorporation rates also pointed to a coordinated multilevel down-regulation of photosynthetic fluxes during starch synthesis before the induction of high triacylglycerol accumulation rates.
Protein Phosphatase 2A Holoenzyme Is Targeted to Peroxisomes by Piggybacking and Positively Affects Peroxisomal β-Oxidation
Authors: Kataya Amr R.A. , Heidari Behzad , Hagen Lars , Kommedal Roald , Slupphaug Geir , Lillo Cathrine
Published: December 2014

The eukaryotic, highly conserved serine (Ser)/threonine-specific protein phosphatase 2A (PP2A) functions as a heterotrimeric complex composed of a catalytic (C), scaffolding (A), and regulatory (B) subunit. In Arabidopsis (Arabidopsis thaliana), five, three, and 17 genes encode different C, A, and B subunits, respectively. We previously found that a B subunit, B′θ, localized to peroxisomes due to its C-terminal targeting signal Ser-Ser-leucine. This work shows that PP2A C2, C5, andA2 subunits interact and colocalize with B′θ in peroxisomes. C and A subunits lack peroxisomal targeting signals, and their peroxisomal import depends on B′θ and appears to occur by piggybacking transport. B′θ knockout mutants were impaired in peroxisomal β-oxidation as shown by developmental arrest of seedlings germinated without sucrose, accumulation of eicosenoic acid, and resistance to protoauxins indole-butyric acid and 2,4-dichlorophenoxybutyric acid. All of these observations strongly substantiate that a full PP2A complex is present in peroxisomes and positively affects β-oxidation of fatty acids and protoauxins.
X-ray phase-contrast computed tomography visualizes the microstructure and degradation profile of implanted biodegradable scaffolds after spinal cord injury
Authors: Takashima Kenta , Hoshino Masato , Uesugi Kentaro , Yagi Naoto , Matsuda Shojiro , Nakahira Atsushi , Osumi Noriko , Kohzuki Masahiro , Onodera Hiroshi
Published: December 2014

Tissue engineering strategies for spinal cord repair are a primary focus of translational medicine after spinal cord injury (SCI). Many tissue engineering strategies employ three-dimensional scaffolds, which are made of biodegradable materials and have microstructure incorporated with viable cells and bioactive molecules to promote new tissue generation and functional recovery after SCI. It is therefore important to develop an imaging system that visualizes both the microstructure of three-dimensional scaffolds and their degradation process after SCI. Here, X-ray phase-contrast computed tomography imaging based on the Talbot grating interferometer is described and it is shown how it can visualize the polyglycolic acid scaffold, including its microfibres, after implantation into the injured spinal cord. Furthermore, X-ray phase-contrast computed tomography images revealed that degradation occurred from the end to the centre of the braided scaffold in the 28 days after implantation into the injured spinal cord. The present report provides the first demonstration of an imaging technique that visualizes both the microstructure and degradation of biodegradable scaffolds in SCI research. X-ray phase-contrast imaging based on the Talbot grating interferometer is a versatile technique that can be used for a broad range of preclinical applications in tissue engineering strategies.
3-Cyano-6-hydroxy-4-methyl-2-pyridone: two new pseudopolymorphs and two cocrystals with products of anin situnucleophilic aromatic substitution
Authors: Gerhardt Valeska , Bolte Michael
Published: December 2014

Four crystal structures of 3-cyano-6-hydroxy-4-methyl-2-pyridone (CMP),viz.the dimethyl sulfoxide monosolvate, C7H6N2O2·C2H6OS, (1), theN,N-dimethylacetamide monosolvate, C7H6N2O2·C4H9NO, (2), a cocrystal with 2-amino-4-dimethylamino-6-methylpyrimidine (as the salt 2-amino-4-dimethylamino-6-methylpyrimidin-1-ium 5-cyano-4-methyl-6-oxo-1,6-dihydropyridin-2-olate), C7H13N4+·C7H5N2O2−, (3), and a cocrystal withN,N-dimethylacetamide and 4,6-diamino-2-dimethylamino-1,3,5-triazine [as the solvated salt 2,6-diamino-4-dimethylamino-1,3,5-triazin-1-ium 5-cyano-4-methyl-6-oxo-1,6-dihydropyridin-2-olate–N,N-dimethylacetamide (1/1)], C5H11N6+·C7H5N2O2−·C4H9NO, (4), are reported. Solvates (1) and (2) both contain the hydroxy group in aparaposition with respect to the cyano group of CMP, acting as a hydrogen-bond donor and leading to rather similar packing motifs. In cocrystals (3) and (4), hydrolysis of the solvent molecules occurs and anin situnucleophilic aromatic substitution of a Cl atom with a dimethylamino group has taken place. Within all four structures, anR22(8) N—H...O hydrogen-bonding pattern is observed, connecting the CMP molecules, but the pattern differs depending on which O atom participates in the motif, either theorthoorparaO atom with respect to the cyano group. Solvents and coformers are attached to these arrangementsviasingle-point O—H...O interactions in (1) and (2) or by additionalR44(16) hydrogen-bonding patterns in (3) and (4). Since thein situnucleophilic aromatic substitution of the coformers occurs, the possible Watson–Crick C–G base-pair-like arrangement is inhibited, yet the cyano group of the CMP molecules participates in hydrogen bonds with their coformers, influencing the crystal packing to form chains.
Sexual signals for the colour‐blind: cryptic female mantids signal quality through brightness
Authors: Barry Katherine L. , White Thomas E. , Rathnayake Darshana N. , Fabricant Scott A. , Herberstein Marie E.
Published: December 2014

Cryptic coloration may evolve in response to selective pressure imposed by predators, yet effective intraspecific communication may require some level of detectability. This creates a tension between the benefits of sexually selected visual traits and the predatory costs imposed by greater conspicuousness, and little is known about how this tension may be ameliorated in highly cryptic species.

We explore these competing demands in the false garden mantid Pseudomantis albofimbriata, a colour‐blind and seemingly cryptic insect. We use reflectance spectrometry and receptor‐noise modelling to characterize the conspicuousness of mantid body regions in the visual systems of mates (mantids), as well as potential predators (birds) and prey (bees). We then use condition manipulation and conspecific choice tests to further explore the colour traits of interest.

Based on visual modelling, we find that male mantids are inconspicuous to conspecifics, prey and predators – that is, they are chromatically and achromatically cryptic. In contrast, female mantids are chromatically cryptic to all potential receivers, but their abdomens are achromatically conspicuous. Our food manipulation experiment shows that females in good condition (and therefore with more eggs) have brighter abdomens than females in poor condition. Choice assays show male mantids are consistently attracted to females bearing brighter abdomens.

Our results reveal brightness‐mediated sexual signalling in a colour‐blind and classically cryptic insect. By communicating in the only visual channel available to them, female mantids are conspicuously signalling their quality to mates, while potentially minimizing their conspicuousness to predators and prey. Furthermore, by signalling with only a single body region, female mantids are apparently using coincident disruptive coloration to further decrease detectability to potential eavesdroppers.

Our data reveal a novel example of the way in which the trade‐off between sexual selection for conspicuousness and natural selection for crypsis may be mediated in a visual signalling system. Such signals may be common in apparently cryptic species, and this study once again demonstrates the importance of analysing visual signals beyond the capacity of human vision.
Phylogenetic niche conservatism – common pitfalls and ways forward
Authors: Münkemüller Tamara , Boucher Florian C. , Thuiller Wilfried , Lavergne Sébastien
Published: December 2014

The prevalence of phylogenetic niche conservatism (PNC) in nature is still a conflicting issue. Disagreement arises from confusion over its precise definition and the variety of approaches to measure its prevalence. Recent work highlighted that common measures ofPNCstrongly depend on the assumptions of the underlying model of niche evolution. However, this warning has not been well recognized in the applied literature and questionable approaches are still frequently applied.

The aim of this study is to draw attention to the assumptions underlying commonly applied simple measures ofPNC. We used a series of simulations to illustrate how misleading results can be if assumptions of niche evolution are violated, that the violation of assumptions is a common phenomenon and that testing assumptions requires in‐depth pretest.

We conclude that the seemingly simple measures ofPNC, such as phylogenetic signal (PS) and evolutionary rate, are not so easy to apply if one accounts for the necessity to test model assumptions. In addition, these measures can be difficult to interpret. The common assumption that strong PS indicatesPNCwill be often invalid. In addition, the interpretation of some measures, for example the conclusion that evolutionary rate is slow enough to indicatePNC, requires a comparison with another clade, another trait or well‐developed null model assumptions and thus additional data.

We suggest that studies investigatingPNCshould always compare alternative evolutionary models and that model comparisons should in particular include flexible niche evolution models such as multiple‐optimaOUmodels, although these are computational intensive. These models are directly inherited from the concept of macroevolutionary adaptive landscape and can indicatePNCeither by relative few peak shifts or by narrow peaks in the adaptive landscape. A test ofPNCthus requires comparing these parameters of the macroevolutionary landscape between clades or time periods.

The general prevalence ofPNCin nature should be evaluated only based on studies keeping up to the high standards of communicating the used definition ofPNC, testing the assumptions made in the modelling approaches and including newly developed models in a model comparison approach.
Cruising the rain forest floor: butterfly wing shape evolution and gliding in ground effect
Authors: Cespedes Ann , Penz Carla M. , DeVries Philip J.
Published: December 2014

Flight is a key innovation in the evolutionary success of insects and essential to dispersal, territoriality, courtship and oviposition. Wing shape influences flight performance and selection likely acts to maximize performance for conducting essential behaviours that in turn results in the evolution of wing shape. As wing shape also contributes to fitness, optimal shapes for particular flight behaviours can be assessed with aerodynamic predictions and placed in an ecomorphological context.

Butterflies in the tribe Haeterini (Nymphalidae) are conspicuous members of understorey faunas in lowland Neotropical forests. Field observations indicate that the five genera in this clade differ in flight height and behaviour: four use gliding flight at the forest floor level, and one utilizes flapping flight above the forest floor. Nonetheless, the association of ground level gliding flight behaviour and wing shape has never been investigated in this or any other butterfly group.

We used landmark‐based geometric morphometrics to test whether wing shapes in Haeterini and their close relatives reflected observed flight behaviours. Four genera of Haeterini and some distantly related Satyrinae showed significant correspondence between wing shape and theoretical expectations in performance trade‐offs that we attribute to selection for gliding in ground effect. Forewing shape differed between sexes for all taxa, and male wing shapes were aerodynamically more efficient for gliding flight than corresponding females. This suggests selection acts differentially on male and female wing shapes, reinforcing the idea that sex‐specific flight behaviours contribute to the evolution of sexual dimorphism.

Our study indicates that wing shapes in Haeterini butterflies evolved in response to habitat‐specific flight behaviours, namely gliding in ground effect along the forest floor, resulting in ecomorphological partitions of taxa in morphospace. The convergent flight behaviour and wing morphology between tribes of Satyrinae suggest that the flight environment may offset phylogenetic constraints. Overall, this study provides a basis for exploring similar patterns of wing shape evolution in other taxa that glide in ground effect.
Erosion of beta diversity under interacting global change impacts in a semi‐arid grassland
Authors: Eskelinen Anu , Harrison Susan
Published: December 2014

Human impacts are often thought of as homogenizing natural communities, but it is unclear how these impacts interact to alter the beta diversity (spatial variability) of plant communities.

In a grassland with high beta diversity along a soil fertility gradient, we asked which combinations of nutrient enrichment, precipitation enhancement and disturbance would homogenize communities along the gradient by allowing dominant species from one part of the gradient to increase their abundances in other parts of the gradient. In particular, joint addition of nutrients and water might especially benefit resource‐acquisitive and/or exotic species, which have been observed to compete well in resource‐rich conditions; this would tend to reduce variation in species composition across the gradient. To alleviate dispersal limitation as a constraint on treatment responses, we added seeds of 15 species abundant in different parts of the soil fertility gradient to our 132 plots.

Fertilization and water addition allowed species from fertile soils to increase their abundance in infertile soils, an effect that strengthened with time. Disturbance permitted species from infertile soils to increase in abundance in infertile soils, but only transiently. Plant height, specific leaf area and exotic status best predicted the abilities of species to attain greater cover in harsh habitats under ameliorated conditions. Among‐habitat beta diversity of seeded species was reduced by the interactive effect of fertilization and watering, although not by watering alone.

Synthesis. Our findings are a novel demonstration of how interacting global change factors reduce beta diversity by eroding the biotic and abiotic resistances that control community structure along soil fertility gradients.
The development and validation of a method for quantifying olanzapine in human plasma by liquid chromatography tandem mass spectrometry and its application in a pharmacokinetic study
Authors: Cavalcanti Bedor Noely Camila Tavares , Galindo Bedor Danilo César , Miranda de Sousa Carlos Eduardo , Nunes Bonifácio Felipe , da Mota Castelo Branco Daniel , Bastos Leal Leila , Pereira de Santana Davi
Published: December 2014

A rapid method using liquid chromatography tandem mass spectrometry for the quantification of olanzapine (OLZ) in human plasma was developed and validated. Venlafaxine was used as the internal standard (IS), and the samples were extracted from 400‐μL human plasma with methyl tert‐butyl ether for liquid–liquid extraction.

Chromatography was performed using an ACE C18, 125 × 4.6‐mm i.d., 5‐μm column. The mobile phase consisted of water with 0.1% formic acid for solvent A and acetonitrile with 0.1% formic acid for solvent B (50 : 50 v/v) in isocratic mode. The flow rate was 1.2 mL/min. The retention times for OLZ and the IS were 0.78 and 1.04 min, respectively. Tandem mass spectrometry operating in positive electrospray ionization mode with multiple reaction monitoring was used to detect OLZ and the IS (m/z: 313.1 > 256.1 and 278.1 > 260.2, respectively).

No significant matrix effects were observed on OLZ and the IS retention times, and the mean recovery of OLZ was 90.08%. The assay was linear in the concentration range of 1–20 ng/mL (R2 = 0.9976). The intra‐ and inter‐day precision were < 11.60% and the accuracy was < 1.66%.

This validated method was successfully applied to a pharmacokinetic study in which 10‐mg OLZ tablets were administered to healthy volunteers and their plasma OLZ levels were monitored over time. The tests showed that the OLZ test and reference drug (Zyprexa®) were bioequivalent, as 90% of the confidence intervals were within the 80–125% interval proposed by regulatory agencies.
Political Theory: The Nordic Scene
Authors: Malnes Raino
Published: December 2014

This article helps those who are not already familiar with normative political theory to find their way around theNordic scene. It surveys works that have come out of theNordic countries from 1990 onwards. They are filed under five headings: (1) studies of political decision making; (2) distributive and retributive justice; (3) priorities and standards of policy in assorted areas; (4) boundaries between jurisdictions; and (5) meta‐normative matters. Before the survey begins, and in a sequel to the last part of it, the nature of normative political theory will be explicated.
Drivers of Inpatient Hospital Experience Using the HCAHPS Survey in a Canadian Setting
Authors: Kemp Kyle A. , Chan Nancy , McCormack Brandi , Douglas‐England Kathleen
Published: December 2014

Objective

To identify factors associated with patients’ overall rating of inpatient hospital care.

Data Sources

Two years of patient interview data (April 1, 2011 to March 31, 2013), linked to inpatient administrative records.

Study Design

Patients rated their overall health on a scale of 0 (worst care) to 10 (best care) using the HCAHPS instrument administered via telephone, up to 42 days postdischarge. Logistic regression was used to generate odds ratios for each independent predictor.

Data Extraction

HCAHPS data were linked to inpatient records based on health care numbers and dates of service. The outcome (overall health experience) was collapsed into two groups (10 vs. 0–9).

Principal Findings

Overall hospital experience of 0–9 was associated with younger age, male gender, higher level of education, being born in Canada, urgent admission, not having a family practitioner as the most responsible provider service, and not being discharged home. A length of stay of less than 3 days was protective. The c‐statistic for the multivariate model was 0.635.

Conclusions

Our results are novel in the Canadian population. Several questions for future research have been generated, in addition to opportunities for quality improvement within our own organization.
Assessing the Implications of a Structured Decision‐Making Tool for Recidivism in a Statewide Analysis
Authors: Baglivio Michael T. , Greenwald Mark A. , Russell Mark
Published: December 2014

Research Summary

The Florida Department of Juvenile Justice has implemented a disposition matrix to guide recommendations made by juvenile probation officers to the court. This study examines whether recidivism rates for dispositions/placements made within the suggested range of this matrix differ from those outside of the suggested range. Using a sample of 38,117 juvenile offenders, we found that the dispositions/placements within the suggested range had an average recidivism rate of 19.4%, whereas those whose dispositions were outside the range had an average recidivism rate twice as high (38.7%). Furthermore, dispositions/placements that were the least restrictive option within the suggested range performed best. Dispositions above the suggested range (more restrictive) performed poorly, although those below the suggested range (less restrictive than suggested) performed the worst. These results held for males and females, across race/ethnicity, and across risk to reoffend levels.

Policy Implications

Implementation of structured decision‐making tools leads to questions from stakeholders and front‐line staff charged with using those tools regarding their effectiveness. Research and theory‐based justifications do not hold the weight actual data from the implementation population provide. These tools help control costs, facilitate planning, and can improve outcomes. Monthly monitoring of adherence rates, development of override and management oversight protocols, and regular feedback to front‐line staff are critical components of success.
Selection of Autochthonous Strains as Starter Cultures for Fermented Fish Products
Authors: Speranza Barbara , Racioppo Angela , Bevilacqua Antonio , Beneduce Luciano , Sinigaglia Milena , Corbo Maria Rosaria
Published: December 2014

This paper was the 1st research focusing on the design of a halophilic lactic starter for the production of fermented fish products using a quantitative approach, based on the evaluation of the growth index and acidification score, as well as on the use of a multivariate approach to select the most promising strains. Fifty‐nine strains were randomly selected from salted fish and phenotypically characterized through Gram staining, catalase activity, glucose metabolism, H2S and indole production, nitrate reduction, citrate utilization, and hydrolysis of arginine, esculin, casein, gelatin, starch, Tween 80, and urea. Then the Gram positive isolates (44 out of 59) were studied for their growth at different temperatures (10, 25, 40, and 55 °C), salt (0%, 20%, and 30%), pHs (4.5 and 9.5), and acidification score in lab medium. Data were modelled through growth index and used as input to run a preliminary cluster analysis and a principal component analysis. Three promising strains were selected, identified as members of the genus Pediococcus and used for the validation at laboratory level through the assessment of their performances in the production of a fermented fish sauce. The results were really promising as their use not only reduced the fermentation time (2 d) but also improved the microbiological quality of the final product. This paper represents a 1st report on the use of a simple step‐by‐step methodology to select promising halophilic strains for the optimization of a starter for fish‐fermented products.
Power analysis for generalized linear mixed models in ecology and evolution
Authors: Johnson Paul C. D. , Barry Sarah J. E. , Ferguson Heather M. , Müller Pie
Published: December 2014

‘Will my study answer my research question?’ is the most fundamental question a researcher can ask when designing a study, yet when phrased in statistical terms – ‘What is the power of my study?’ or ‘How precise will my parameter estimate be?’ – few researchers in ecology and evolution (EE) try to answer it, despite the detrimental consequences of performing under‐ or over‐powered research. We suggest that this reluctance is due in large part to the unsuitability of simple methods of power analysis (broadly defined as any attempt to quantify prospectively the ‘informativeness’ of a study) for the complex models commonly used in EE research. With the aim of encouraging the use of power analysis, we present simulation from generalized linear mixed models (GLMMs) as a flexible and accessible approach to power analysis that can account for random effects, overdispersion and diverse response distributions.

We illustrate the benefits of simulation‐based power analysis in two research scenarios: estimating the precision of a survey to estimate tick burdens on grouse chicks and estimating the power of a trial to compare the efficacy of insecticide‐treated nets in malaria mosquito control. We provide a freely available R function, sim.glmm, for simulating from GLMMs.

Analysis of simulated data revealed that the effects of accounting for realistic levels of random effects and overdispersion on power and precision estimates were substantial, with correspondingly severe implications for study design in the form of up to fivefold increases in sampling effort. We also show the utility of simulations for identifying scenarios where GLMM‐fitting methods can perform poorly.

These results illustrate the inadequacy of standard analytical power analysis methods and the flexibility of simulation‐based power analysis for GLMMs. The wider use of these methods should contribute to improving the quality of study design in EE.
Exposure to point‐of‐sale displays and changes in susceptibility to smoking: findings from a cohort study of school students
Authors: Bogdanovica Ilze , Szatkowski Lisa , McNeill Ann , Spanopoulos Dionysis , Britton John
Published: December 2014

Aims

To investigate the association between frequency of visiting shops and noticing of tobacco point‐of‐sale (PoS) displays and the development of susceptibility to smoking, or smoking uptake, in secondary school students.

Design

Two surveys of a school based cohort study carried out in 2011 and 2012.

Settings

Nottinghamshire, UK.

Participants

A total of 2270 children aged 11–16 years from eight schools in Nottinghamshire.

Measurements

We investigated changes in susceptibility to smoking and smoking status in relation to frequency of visiting shops and noticing PoS displays and number of tobacco brands recognized, controlling for a range of potential confounders. Susceptibility to smoking was defined using a set of three questions covering intentions to try smoking, to smoke within the next year and likelihood of smoking if a best friend offered a cigarette. For the analysis we used multinomial logistic regression.

Findings

Among non‐susceptible never smokers, noticing PoS displays more frequently was associated independently with an increased risk of becoming susceptible to smoking [adjusted relative risk ratio (RRR) = 1.74; 99% confidence interval (CI) = 1.13–2.69], but was not associated with smoking uptake. Recognizing a higher number of brands among non‐susceptible never smokers doubled the risk of becoming susceptible to smoking and of becoming a smoker, but this did not have a significant effect on transition to smoking among susceptible never smokers. Frequency of noticing tobacco PoS displays was not associated significantly with smoking uptake among those who were susceptible never smokers at baseline.

Conclusions

Noticing tobacco point‐of‐sale displays more often and recognizing a higher number of tobacco brands is associated with an increased risk of becoming susceptible to smoking among adolescents in the United Kingdom, and recognizing a higher number of brands is associated positively with an increased risk of smoking uptake.
Assessment of sexual health and sexual needs in residential aged care
Authors: McAuliffe Linda , Bauer Michael , Fetherstonhaugh Deirdre , Chenco Carol
Published: December 2014

Aim

To investigate if, when and how assessments regarding residents' sexual health and needs occur within Australian residential aged care facilities.

Method

A census of all Australian residential aged care facilities was conducted. A survey developed specifically for the project was posted to all 2766 residential aged care services in Australia. Eight weeks were allowed for the return of surveys.

Results

A total of 1094 completed surveys were returned, representing a 39.7% response rate. The type of information most often collected concerned disruptive sexual behaviour, and assessments most frequently occurred following disruptive behaviour. One‐quarter of facilities reported having a sexual health/needs assessment form, although only 10 facilities provided evidence of this.

Conclusion

Survey responses indicated that sexual health and needs are not routinely assessed in residential aged care, and facilities do not commonly have a dedicated sexual health/needs assessment form to guide them through an assessment process.
Th17‐ and Treg‐related cytokine and mRNA expression are associated with acute and resolving Kawasaki disease
Authors: Guo M. M.‐H. , Tseng W.‐N. , Ko C.‐H. , Pan H.‐M. , Hsieh K.‐S. , Kuo H.‐C.
Published: December 2014

Background

Kawasaki disease is a vasculitis most commonly afflicting children <5 years of age. Many autoimmune diseases are associated with up‐regulation of T helper (Th) 17 cells, and down‐regulation Treg cells. Few studies have examined the Th17/Treg expression in Kawasaki disease.

Methods

Blood samples were obtained from 186 children with Kawasaki disease at 24 h before IVIG therapy, followed by 3 days and 21 days after IVIG therapy. Thirty children with an acute febrile infectious disease and 30 healthy children were obtained as control. Plasma levels of Th17‐ and Treg‐related cytokines including IL‐6, IL‐17A, IL‐10, TGF‐β, and mRNA expression levels of RORγt and Foxp3 were tested.

Results

Patients with Kawasaki disease had higher levels of plasma IL‐17A (25.35 ± 3.21 vs 7.78 ± 1.78 pg/ml, P < 0.001) and IL‐6 (152.29 ± 21.94 vs 38.63 ± 12.40 pg/ml, P < 0.001) when compared to the febrile control group. IVIG resulted in a reduction in IL‐6 and IL‐17A at both 3 and 21 days after IVIG therapy. FoxP3 levels increased significantly 3 days after IVIG therapy (2.28 ± 0.34 vs 0.88 ± 0.14, P < 0.001). IVIG resistance was associated with higher levels of IL‐10 and IL‐17A.

Conclusion

Kawasaki disease was associated with higher IL‐17A and IL‐6, a cytokine profile similar to other autoimmune diseases. IVIG therapy resulted in increased expression of Treg‐related FoxP3. IVIG resistance was associated with higher levels of IL‐10 and IL‐17A. Our findings provide further evidence that Kawasaki disease is an autoimmune‐like disease.
Retinal fluorescence lifetime imaging ophthalmoscopy measures depend on the severity of Alzheimer's disease
Authors: Jentsch Susanne , Schweitzer Dietrich , Schmidtke Kai‐Uwe , Peters Sven , Dawczynski Jens , Bär Karl‐Jürgen , Hammer Martin
Published: December 2014

Purpose

To determine alterations in the retina of patients with Alzheimer's disease (AD) by the newly developed technique of fluorescence lifetime imaging ophthalmoscopy (FLIO) in a pilot study.

Methods

FLIO set‐up uses a scanning laser ophthalmoscope (HRA2, Heidelberg Engineering, Germany), which was modified by the use of an excitation pulse laser BLD440 (Becker&Hickl, Berlin, Germany) and detection of fluorescence lifetime by time‐correlated single photon counting (TCSPC; Becker&Hickl) in two spectral channels (channel 1: 490–560 nm, channel 2: 560–700 nm). Least square fit of three exponential functions was used for fluorescence decay analysis. That resulted in three fluorescent components with lifetimes τi, amplitudes αi and relative contributions Qi. 16 patients with AD (mean age 77.2 ± 7.0 years) were investigated. After regular ophthalmic investigation, FLIO examination and OCT examination were performed. Alzheimer‐specific clinical data were collected (MMSE, cerebrospinal fluid (CSF) concentration of amyloid‐β (1‐42), total‐tau and phosphorylated tau181 (p‐tau181) protein).

Results

The FLIO parameters of the second fluorescent component α2 and Q2 (channel 2) correlated significantly with MMSE score (Q2, R = −0.757, p = 0.007; α2, R = −0.618, p = 0.043) as well as p‐tau181‐protein concentration in CSF (Q2, R = 0.919, p = 0.009; α2, R = 0.881, p = 0.020) in patients with AD. OCT measurements of retinal nerve fibre layer thickness, optic disc excavation and macular thickness neither correlated with Alzheimer‐specific CSF data nor MMSE score.

Conclusions

Unlike conventional techniques, such as OCT, the new technique of FLIO revealed changes in the retina of patients with AD in relation to Alzheimer‐specific markers in this pilot study.
Influence of race and crossbreeding on casein micelles size
Authors: Freitas Denise R. , Fonseca Leorges M. , Souza Fernando N. , Ladeira Cristiane V. G. , Diniz Soraia A. , Haddad João Paulo A. , Ferreira Diêgo S. , Santoro Marcelo M. , Cerqueira Mônica M. O. P.
Published: December 2014

Casein (CN) micelles are colloidal aggregates of protein dispersed in milk, the importance of which in the dairy industry is related to functionality and yield in dairy products. The objective of this work was to investigate the correlation of milk CN micelles diameter from Holstein and Zebu crossbreds with milk composition (protein, fat, lactose, total and nonfat solids and milk urea nitrogen), somatic cell count (SCC), age, lactation stage and production. Average casein micelles diameters of milk samples obtained from 200 cows were measured using photon correlation spectroscopy and multiple regression analysis was used to find relationship between variables. CN micelle diameter, SCC and nonfat solids were different between animals with different Holstein crossbreed ratios, which suggests influence of genetic factors, mammary gland health and milk composition. Overall, results indicate the potential use of CN micelle diameter as a tool to select animals to produce milk more suitable to cheese production.
In vitro development of OPU‐derived bovine embryos cultured either individually or in groups with the silk protein sericin and the viability of frozen‐thawed embryos after transfer
Authors: Isobe Tomohiro , Ikebata Yoshihisa , Do Lanh Thi Kim , Tanihara Fuminori , Taniguchi Masayasu , Otoi Takeshige
Published: December 2014

The optimization of single‐embryo culture conditions is very important, particularly in the in vitro production of bovine embryos using the ovum pick‐up (OPU) procedure. The purpose of this study was to examine the development of embryos derived from oocytes obtained by OPU that were cultured either individually or in groups in medium supplemented with or without sericin and to investigate the viability of the frozen‐thawed embryos after a direct transfer. When two‐cell‐stage embryos were cultured either individually or in groups for 7 days in CR1aa medium supplemented with or without 0.5% sericin, the rates of development to blastocysts and freezable blastocysts were significantly lower for the embryos cultured individually without sericin than for the embryos cultured in groups with or without sericin. Moreover, the rate of development to freezable blastocysts of the embryos cultured individually with sericin was significantly higher than that of the embryos cultured without sericin. When the frozen‐thawed embryos were transferred directly to recipients, the rates of pregnancy, abortion, stillbirth and normal calving in the recipients were similar among the groups, irrespective of the culture conditions and sericin supplementation. Our findings indicate that supplementation with sericin during embryo culture improves the quality of the embryos cultured individually but not the viability of the frozen‐thawed embryos after transfer to recipients.
Effect of fat content on sensory characteristics of marbled beef from Japanese Black steers
Authors: Iida Fumiko , Saitou Kaoru , Kawamura Tadashi , Yamaguchi Shizuko , Nishimura Toshihide
Published: December 2014

To analyze the sensory characteristics of meat samples with a crude fat content between 23.8% and 48.6% taken from 34 Japanese Black steers, we grilled the meat and subjected it to analytical sensory evaluation. We also measured the amounts of moisture, protein, nucleic acid and glutamic acid. An increase in crude fat content increased the tenderness, juiciness, and fattiness in the meat quality evaluation. An increase in crude fat content reduced the crude protein and moisture contents; it also slightly reduced the nucleic acid and glutamic acid contents, although when the reductions in these umami components were assessed relative to the moisture content they changed little. Increasing the fat content up to a certain point greatly enhanced the umami intensity and beef flavor intensity in the meat quality evaluation and raised the overall evaluation score; the peak of the appropriate crude fat content for these purposes was about 36%.
Both farming practices and landscape characteristics determine the diversity of characteristic and rare arable weeds in organically managed fields
Authors: Rotchés‐Ribalta Roser , Blanco‐Moreno José Manuel , Armengot Laura , Chamorro Lourdes , Sans Francesc Xavier
Published: December 2014

Questions

Do both current and past (short‐term) farming practices and landscape characteristics have an effect on the diversity of characteristic and rare arable plant communities in organic fields? What is the role of farm management strategies, apart from farm spatial configuration, in determining the diversity components of these species sets?

Location

Thirty‐two farms scattered across NE Spain (Catalonia).

Methods

Specialist species of arable fields, belonging to the Secalietalia cerealis Br‐Bl. 1936, were surveyed at the edges of organically managed fields. We assessed the effects of farm management and landscape characteristics at the field and farm scales on α‐, β‐ and γ‐diversity values of these characteristic arable species. Analyses were also conducted on a subset of Secalietalia species that are considered to be rare. Statistical analyses were performed using multimodel inference determined on the basis of all possible models from an a priori set.

Results

Field variables, such as years since conversion to organic management, proportion of cereal crops in the rotation and autumn sowing, had a positive effect, whereas growing non‐cereal crops and fertilization had a negative effect on the richness of characteristic species. The field area had a positive effect on the species richness of characteristic and rare arable plants. At the farm level, the proportion of cereal crop fields to the total amount of fields affected both β and γ characteristic diversity. The landscape variables at the farm level only influenced the β‐diversity of rare species.

Conclusions

The effects of management and landscape on arable weed diversity depended on whether the field or the farm is the focus of the analysis. Characteristic and rare arable species were more affected by factors operating at local scales. Characteristic species richness responded positively to sowing cereal crops, autumn sowing and periodic soil disturbances but was negatively affected by slurry fertilization. Thus, policies promoting some of the former practices should favour characteristic arable species and mitigate the decline of the rare arable species.