bluuebunny/crossref_metadata_2025 huggingface dataset:
Metagenomic identification of novel enteric viruses in urban wild rats and genome characterization of a group A rotavirus
Authors: Sachsenröder Jana , Braun Anne , Machnowska Patrycja , Ng Terry Fei Fan , Deng Xutao , Guenther Sebastian , Bernstein Samuel , Ulrich Rainer G. , Delwart Eric , Johne Reimar
Published: August 2014

Rats are known as reservoirs and vectors for several zoonotic pathogens. However, information on the viruses shed by urban wild rats that could pose a zoonotic risk to human health is scare. Here, intestinal contents from 20 wild Norway rats (Rattus norvegicus) collected in the city of Berlin, Germany, were subjected to metagenomic analysis of viral nucleic acids. The determined faecal viromes of rats consisted of a variety of known and unknown viruses, and were highly variable among the individuals. Members of the families Parvoviridae and Picobirnaviridae represented the most abundant species. Novel picornaviruses, bocaviruses, sapoviruses and stool-associated circular ssDNA viruses were identified, which showed only low sequence identity to known representatives of the corresponding taxa. In addition, noroviruses and rotaviruses were detected as potential zoonotic gastroenteritis viruses. However, partial-genome sequence analyses indicated that the norovirus was closely related to the recently identified rat norovirus and the rotavirus B was closely related to the rat rotavirus strain IDIR; both viruses clustered separately from respective human virus strains in phylogenetic trees. In contrast, the rotavirus A sequences showed high identity to human and animal strains. Analysis of the nearly complete genome of this virus revealed the known genotypes G3, P[3] and N2 for three of the genome segments, whereas the remaining eight genome segments represented the novel genotypes I20–R11–C11–M10–A22–T14–E18–H13. Our results indicated a high heterogeneity of enteric viruses present in urban wild rats; their ability to be transmitted to humans remains to be assessed in the future.
Long‐term phenological trends, species accumulation rates, aphid traits and climate: five decades of change in migrating aphids
Authors: Bell James R. , Alderson Lynda , Izera Daniela , Kruger Tracey , Parker Sue , Pickup Jon , Shortall Chris R. , Taylor Mark S. , Verrier Paul , Harrington Richard
Published: August 2014

Aphids represent a significant challenge to food production. The Rothamsted Insect Survey (RIS) runs a network of 12·2‐m suction‐traps throughout the year to collect migrating aphids. In 2014, the RIS celebrated its 50th anniversary. This paper marks that achievement with an extensive spatiotemporal analysis and the provision of the first British annotated checklist of aphids since 1964.

Our main aim was to elucidate mechanisms that advance aphid phenology under climate change and explain these using life‐history traits. We then highlight emerging pests using accumulation patterns.

Linear and nonlinear mixed‐effect models estimated the average rate of change per annum and effects of climate on annual counts, first and last flights and length of flight season since 1965. Two climate drivers were used: the accumulated day degrees above 16 °C (ADD16) indicated the potential for migration during the aphid season; the North Atlantic Oscillation (NAO) signalled the severity of the winter before migration took place.

All 55 species studied had earlier first flight trends at rate of β = −0·611 ± SE 0·015 days year−1. Of these species, 49% had earlier last flights, but the average species effect appeared relatively stationary (β = −0·010 ± SE 0·022 days year−1). Most species (85%) showed increasing duration of their flight season (β = 0·336 ± SE 0·026 days year−1), even though only 54% increased their log annual count (β = 0·002 ± SE <0·001 year−1).

The ADD16 and NAO were shown to drive patterns in aphid phenology in a spatiotemporal context. Early in the year when the first aphids were migrating, the effect of the winter NAO was highly significant. Further into the year, ADD16 was a strong predictor. Latitude had a near linear effect on first flights, whereas longitude produced a generally less‐clear effect on all responses. Aphids that are anholocyclic (permanently parthenogenetic) or are monoecious (non‐host‐alternating) were advancing their phenology faster than those that were not.

Climate drives phenology and traits help explain how this takes place biologically. Phenology and trait ecology are critical to understanding the threat posed by emerging pests such as Myzus persicae nicotianae and Aphis fabae cirsiiacanthoidis, as revealed by the species accumulation analysis.
Quantifying the impact of an extreme climate event on species diversity in fragmented temperate forests: the effect of theOctober 1987 storm onBritish broadleaved woodlands
Authors: Smart Simon M. , Ellison Aaron M. , Bunce Robert G. H. , Marrs Robert H. , Kirby Keith J. , Kimberley Adam , Scott Andy W. , Foster David R.
Published: August 2014

We report the impact of an extreme weather event, theOctober 1987 severe storm, on fragmented woodlands in southernBritain. We analysed ecological changes between 1971 and 2002 in 143 200‐m2plots in 10 woodland sites exposed to the storm with an ecologically equivalent sample of 150 plots in 16 non‐exposed sites. Comparing both years, understorey plant species‐richness, species composition, soilpHand woody basal area of the tree and shrub canopy were measured.

We tested the hypothesis that the storm had deflected sites from the wider national trajectory of an increase in woody basal area and reduced understorey species‐richness associated with ageing canopies and declining woodland management. We also expected storm disturbance to amplify the background trend of increasing soil pH, aUK‐wide response to reduced atmospheric sulphur deposition. Path analysis was used to quantify indirect effects of storm exposure on understorey species richness via changes in woody basal area and soil pH.

By 2002, storm exposure was estimated to have increased mean species richness per 200 m2by 32%. Woody basal area changes were highly variable and did not significantly differ with storm exposure.

Increasing soil pHwas associated with a 7% increase in richness. There was no evidence that soil pHincreased more as a function of storm exposure. Changes in species richness and basal area were negatively correlated: a 3.4% decrease in richness occurred for every 0.1‐m2increase in woody basal area per plot.

Despite all sites substantially exceeding the empirical critical load for nitrogen deposition, there was no evidence that in the 15 years since the storm, disturbance had triggered a eutrophication effect associated with dominance of gaps by nitrophilous species.

Synthesis. Although the impacts of the 1987 storm were spatially variable in terms of impacts on woody basal area, the storm had a positive effect on understorey species richness. There was no evidence that disturbance had increased dominance of gaps by invasive species. This could change if recovery from acidification results in a soil pHregime associated with greater macronutrient availability.
Millennial disturbance‐driven forest stand dynamics in the Eastern Canadian taiga reconstructed from subfossil logs
Authors: Gennaretti Fabio , Arseneault Dominique , Bégin Yves
Published: August 2014

Although wildfire is the main natural disturbance factor driving changes in the North American boreal forest, understanding how the fire history of the last millennium shaped the present‐day landscape diversity is a difficult task due to the lack of palaeoecological reconstructions with high spatial (few hundreds of square metres) and temporal (annual) resolutions.

We combined a detailed inventory of the present‐day lakeshore forest of two lakes of the Eastern Canadian taiga with the dendrochronological dating of the subfossil logs that accumulated in the littoral zones facing these shores. Our objective was to compare the millennial impact of wildfires among stands of various structures and compositions. Past stem densities and fire years were reconstructed from log recruitment rates and dating of charred logs.

Multivariate analysis of the present‐day lakeshore forest revealed three and two homogeneous shore segments per site (i.e. clusters). Cluster 1 at both sites exhibited denser forest, higher dead wood values and a higher percentage of balsam fir, a fire‐sensitive species.

In total, 426 and 611 subfossil logs (mostly black spruce) were crossdated over the last ˜1400 years. Their dendrochronological analysis confirmed that each lakeshore cluster, identified from the traits of the present‐day forest, experienced a specific fire history over the last millennium (i.e. 0–5 fires of variable severity) that locally influenced forest composition, tree density and growth. Each fire triggered a specific forest structure trajectory characterized by a different stem density and rate of recovery.

Synthesis. This study provides a long‐term perspective that helps explain how the present‐day landscape diversity in the Eastern Canadian taiga reflects the site‐specific fire history over the last millennium. Fires have caused persistent and cumulative impacts resulting in a progressive opening of the forest cover along with balsam fir exclusion. Present‐day landscapes are mosaics of forest stands characterized by different times since fire and different post‐fire forest structure trajectories.
Flavor‐Enhancing Properties of Mushrooms in Meat‐Based Dishes in Which Sodium Has Been Reduced and Meat Has Been Partially Substituted with Mushrooms
Authors: Myrdal Miller A. , Mills K. , Wong T. , Drescher G. , Lee S.M. , Sirimuangmoon C. , Schaefer S. , Langstaff S. , Minor B. , Guinard J.‐X
Published: August 2014

The effects of beef substitution with crimini or white mushrooms (Agaricus bisporus) on the flavor profiles of carne asada and beef taco blends were measured with a descriptive analysis panel. Sensory mitigation of sodium reduction through the incorporation of mushrooms was also investigated in the taco blends. The substitution of beef with mushrooms in the carne asada did not alter the overall flavor strength of the dish, but the incorporation of 50% or 80% ground mushroom in the beef taco blend did enhance its overall flavor as well as mushroom, veggie, onion, garlic and earthy flavors, and umami and sweet tastes. Overall flavor intensity of the 25% reduced‐salt version of the 80% mushroom taco blend matched that of the full‐salt versions of the 100% and 50% beef formulations, thus indicating that the substitution of 80% of the meat with mushrooms did mitigate the 25% sodium reduction in terms of the overall flavor impact of the dish, even if it did not quite compensate for the reduction in salty taste. This proof‐of‐concept study for the Healthy Flavors Research Initiative indicates that because of their flavor‐enhancing umami principles, mushrooms can be used as a healthy substitute for meat and a mitigating agent for sodium reduction in meat‐based dishes without loss of overall flavor.
Kinetic and stoichiometric characterization of organoautotrophic growth of Ralstonia eutropha on formic acid in fed‐batch and continuous cultures
Authors: Grunwald Stephan , Mottet Alexis , Grousseau Estelle , Plassmeier Jens K. , Popović Milan K. , Uribelarrea Jean‐Louis , Gorret Nathalie , Guillouet Stéphane E. , Sinskey Anthony
Published: August 2014

Formic acid, acting as both carbon and energy source, is a safe alternative to a carbon dioxide, hydrogen and dioxygen mix for studying the conversion of carbon through the Calvin–Benson–Bassham (CBB) cycle into value‐added chemical compounds by non‐photosynthetic microorganisms. In this work, organoautotrophic growth of Ralstonia eutropha on formic acid was studied using an approach combining stoichiometric modeling and controlled cultures in bioreactors. A strain deleted of its polyhydroxyalkanoate production pathway was used in order to carry out a physiological characterization. The maximal growth yield was determined at 0.16 Cmole Cmole−1 in a formate‐limited continuous culture. The measured yield corresponded to 76% to 85% of the theoretical yield (later confirmed in pH‐controlled fed‐batch cultures). The stoichiometric study highlighted the imbalance between carbon and energy provided by formic acid and explained the low growth yields measured. Fed‐batch cultures were also used to determine the maximum specific growth rate (μmax = 0.18 h−1) and to study the impact of increasing formic acid concentrations on growth yields. High formic acid sensitivity was found in R eutropha since a linear decrease in the biomass yield with increasing residual formic acid concentrations was observed between 0 and 1.5 g l−1.
The strength of badenya ties: Siblings and social security in old age—the case of urban Burkina Faso
Authors: ROTH CLAUDIA
Published: August 2014

In urban Burkina Faso, siblings play a decisive role in local social security. Badenya, the unity of children of the same mother, compensates in particular for the economic failure of an eldest son no longer in a position to fulfill his familial duties. Although the institution of badenya is strengthened as it increasingly comes into play to help a family avoid social marginalization, it is also overburdened, which makes its future uncertain. This article enhances the anthropological understanding of kinship by focusing on sibling relationships. Findings are based on interviews conducted between 2007 and 2010 with two generations in households in Bobo‐Dioulasso and on participant‐observation over the course of more than a dozen research stays since 1989.
The pros and cons of funnel plots as an aid to risk communication and patient decision making
Authors: Rakow Tim , Wright Rebecca J. , Spiegelhalter David J. , Bull Catherine
Published: August 2014

Funnel plots, which simultaneously display a sample statistic and the corresponding sample size for multiple cases, have a range of applications. In medicine, they are used to display treatment outcome rates and caseload volume by institution, which can inform strategic decisions about health care delivery. We investigated lay people's understanding of such plots and explored their suitability as an aid to individual treatment decisions. In two studies, 172 participants answered objective questions about funnel plots representing the surgical outcomes (survival or mortality rates) of institutions varying in caseload, and indicated their preferred institutions. Accuracy for extracting objective information was high, unless question phrasing was inconsistent with the plot's survival/mortality framing, or participants had low numeracy levels. Participants integrated caseload‐volume and outcome‐rate data when forming preferences, but were influenced by reference lines on the plot to make inappropriate discriminations between institutions with similar outcome rates. With careful choice of accompanying language, funnel plots can be readily understood and are therefore a useful tool for communicating risk. However, they are less effective as a decision aid for individual patient's treatment decisions, and we recommend refinements to the standard presentation of the plots if they are to be used for that purpose.
Prostate cancer mortality outcomes and patterns of primary treatment for Aboriginal men in New South Wales, Australia
Authors: Rodger Jennifer C. , Supramaniam Rajah , Gibberd Alison J. , Smith David P. , Armstrong Bruce K. , Dillon Anthony , O'Connell Dianne L.
Published: August 2014

Objective

To compare prostate cancer mortality for Aboriginal and non‐Aboriginal men and to describe prostate cancer treatments received by Aboriginal men.

Patients and methods

We analysed cancer registry records for all men diagnosed with prostate cancer in New South Wales (NSW) in 2001–2007 linked to hospital inpatient episodes and deaths. More detailed information on androgen‐deprivation therapy and radiotherapy was obtained from medical records for 87 NSW Aboriginal men diagnosed in 2000–2011. The main outcomes were primary treatment for, and death from, prostate cancer. Analysis included Cox proportional hazards regression and logistic regression.

Results

There were 259 Aboriginal men among 35 214 prostate cancer cases diagnosed in 2001–2007. Age and spread of disease at diagnosis were similar for Aboriginal and non‐Aboriginal men. Prostate cancer mortality 5 years after diagnosis was higher for Aboriginal men (17.5%, 95% confidence interval (CI) 12.4–23.3) than non‐Aboriginal men (11.4%, 95% CI 11.0–11.8). Aboriginal men were 49% more likely to die from prostate cancer (hazard ratio 1.49, 95% CI 1.07–1.99) after adjusting for differences in demographic factors, stage at diagnosis, health access and comorbidities. Aboriginal men were less likely to have a prostatectomy for localised or regional cancer than non‐Aboriginal men (adjusted odds ratio 0.60, 95% CI 0.40–0.91). Of 87 Aboriginal men with full staging and treatment information, 60% were diagnosed with localised disease. Of these, 38% had a prostatectomy (± radiotherapy), 29% had radiotherapy only and 33% had neither.

Conclusion

More research is required to explain differences in treatment and mortality for Aboriginal men with prostate cancer compared with non‐Aboriginal men. In the meantime, ongoing monitoring and efforts are needed to ensure Aboriginal men have equitable access to best care.
Candidate selection for quadrant‐based focal ablation through a combination of diffusion‐weighted magnetic resonance imaging and prostate biopsy
Authors: Matsuoka Yoh , Numao Noboru , Saito Kazutaka , Tanaka Hiroshi , Kumagai Jiro , Yoshida Soichiro , Ishioka Junichiro , Koga Fumitaka , Masuda Hitoshi , Kawakami Satoru , Fujii Yasuhisa , Kihara Kazunori
Published: August 2014

Objectives

To identify prostatic quadrants that could be preserved without intervention, using diffusion‐weighted magnetic resonance imaging (DWI) and extended core biopsy, as a step toward implementation of quadrant‐based focal ablation with potential preservation of erectile and ejaculatory functions, based on comparisons with unilateral hemi‐gland ablation.

Patients and Methods

We conducted a prebiopsy DWI study including 648 quadrants in 162 men who underwent 14‐core biopsy including anterior sampling and radical prostatectomy (RP) for localised cancer. Imaging and pathology were analysed on a quadrant basis. Each quadrant was assessed through four‐core sampling. Predictive performance of DWI and biopsy for quadrant status was analysed.

Results

On RP specimens, 170 anterior (52.5%) and 172 posterior quadrants (53.1%) harboured significant cancer. Negative predictive values of DWI, biopsy, and their combination for significant cancer were 79.7%, 70.6%, and 91.1%, respectively, in anterior quadrants, and 78.5%, 81.3%, and 91.7%, respectively, in posterior quadrants. DWI incrementally improved the negative predictive values of biopsy in anterior (P < 0.001) and posterior quadrants (P = 0.025), without untoward impacts on positive predictive values. Negative findings on both DWI and biopsy were identified in posterior quadrants of 109 sides (33.6%), but in entire hemi‐glands of 54 sides (16.7%).

Conclusions

The combination of DWI and 14‐core biopsy including anterior sampling efficiently identifies quadrants without significant cancer in men with localised prostate cancer; the remaining quadrants, therefore, could be potential candidate areas for focal ablation. Focal therapy designed based on quadrant‐based assessment could be superior to unilateral hemi‐gland ablation for preservation of posterior quadrants and retaining of sexual function in more sides.
Spatiotemporal Variability in the Reproductive Success of the Continually Flowering Shrub Dillenia suffruticosa in Borneo
Authors: Tokumoto Yuji , Sakai Shoko , Matsushita Michinari , Ohkubo Tatsuhiro , Nakagawa Michiko
Published: August 2014

Continually flowering plants bloom continuously throughout the year, as often seen in plants distributed along the roadsides or in the understory layers in Southeast Asia's tropical rain forests. Dillenia suffruticosa (Griff. ex Hook. f. & Thomson) Martelli (Dilleniaceae) is one such continually flowering shrub that flowers during periods of community‐wide mass flowering, general flowering (GF), and non‐GF. During irregularly occurring GF periods, when species of all forest layers flower synchronously for several months, some pollinators migrate to the canopy layer, where GF promotes the pollination success of participating plants. Continually flowering plants share the available pollinator community with GF plants, and the reproductive success of continually flowering plants may be affected during the GF period. To assess the effects of GF on the reproductive success of a diverse range of continually flowering plants, we examined the differences in pollinator density and reproductive success between GF and non‐GF periods in D. suffruticosa at four different research sites. Although the seed set differed among the four research sites, pollinator density and fruit set did not differ between GF and non‐GF periods or research sites. Our results suggest that the reproductive success of D. suffruticosa was maintained at an approximately constant level, regardless of the flowering phenology of the canopy layer or other vegetation components.
Species Richness, Forest Structure, and Functional Diversity During Succession in the New Guinea Lowlands
Authors: Whitfeld Timothy J. S. , Lasky Jesse R. , Damas Kipiro , Sosanika Gibson , Molem Kenneth , Montgomery Rebecca A.
Published: August 2014

Much of the world's tropical forests have been affected by anthropogenic disturbance. These forests are important biodiversity reservoirs whose diversity, structure and function must be characterized across the successional sequence. We examined changes in structure and diversity along a successional gradient in the lowlands of New Guinea. To do this, we measured and identified all stems ≥5 cm diameter in 19 0.25 ha plots ranging in age from 3 to >50 yr since disturbance. We also measured plant functional traits related to establishment, performance, and competitive ability. In addition, we examined change in forest structure, composition, species diversity, and functional diversity through succession. By using rarefaction to estimate functional diversity, we compared changes in functional diversity while controlling for associated differences in stem and species density. Basal area and species density increased with stand age while stem density was highest in intermediate secondary forests. Species composition differed strongly between mature and secondary forests. As forests increased in basal area, community‐weighted mean wood density and foliar carbon increased, whereas specific leaf area and proportion of stems with exudate decreased. Foliar nitrogen peaked in medium‐aged forests. Functional diversity was highest in mature forests, even after accounting for differences in stem and species diversity. Our study represents one of the first attempts to document successional changes in New Guinea's lowland forest. We found robust evidence that as succession proceeds, communities occupy a greater range of functional trait space even after controlling for stem and species density. High functional diversity is important for ecological resiliency in the face of global change.
National Personality Profiles and Innovation: The Role of Cultural Practices
Authors: Rossberger Robert J.
Published: August 2014

This study investigates the relationship between personality factors, cultural practices, and innovativeness on the national level. Hitherto no study has been done which considers these factors simultaneously. We argue that the relationship between national aggregated personality factors and the level of national innovation is mediated by national cultural practices. Our model is based on three arguments: First, Five Factor theory and cultural theory state that the national personality profile of a country influences its cultural practices. Second, person‐environment‐fit theory argues that personality factors can best manifest themselves in an appropriate environment. Third, in contrast to the individual level, we argue that on the national level cultural practices may not act as a moderator but as a mediator. Based on the triangulation of three datasets, we subsequently test our model on a sample ofN = 33 countries. Our results demonstrate that innovation‐relevant national personality profiles are closely linked with innovation‐relevant national cultural practices. Further, we show that national cultural practices mediate the relationship between national personality profiles and national innovativeness. Additionally, we reveal that the recently proposed relationship between nationally aggregated personality profiles and national innovativeness virtually disappears as soon as national cultural practices are integrated into the model.
Sub‐crestal positioning of implants results in higher bony crest resorption: an experimental study in dogs
Authors: Cesaretti Gianfranco , Lang Niklaus P. , Salata Luiz A. , Schweikert Michael T. , Gutierrez Hernandez Maria Elena , Botticelli Daniele
Published: August 2014

Objective

To compare peri‐implant soft‐ and hard‐tissue integration at implants installed juxta‐ or sub‐crestally. Furthermore, differences in the hard and soft peri‐implant tissue dimensions at sites prepared with drills or sonic instruments were to be evaluated.

Material and methods

Three months after tooth extraction in six dogs, recipient sites were prepared in both sides of the mandible using conventional drills or a sonic device (Sonosurgery®). Two implants with a 1.7‐mm high‐polished neck were installed, one with the rough/smooth surface interface placed at the level of the buccal bony crest (control) and the second placed 1.3 mm deeper (test). After 8 weeks of non‐submerged healing, biopsies were harvested and ground sections prepared for histological evaluation.

Results

The buccal distances between the abutment/fixture junction (AF) and the most coronal level of osseointegration (B) were 1.6 ± 0.6 and 2.4 ± 0.4 mm; between AF and the top of the bony crest (C), they were 1.4 ± 0.4 and 2.2 ± 0.2 mm at the test and control sites, respectively. The top of the peri‐implant mucosa (PM) was located more coronally at the test (1.2 ± 0.6 mm) compared to the control sites (0.6 ± 0.5 mm). However, when the original position of the bony crest was taken into account, a higher bone loss and a more apical position of the peri‐implant mucosa resulted at the test sites.

Conclusions

The placement of implants into a sub‐crestal location resulted in a higher vertical buccal bone resorption and a more apical position of the peri‐implant mucosa in relation to the level of the bony crest at implant installation. Moreover, peri‐implant hard‐tissue dimensions were similar at sites prepared with either drills or Sonosurgery®.
Organ donation video messaging: differential appeal, emotional valence, and behavioral intention
Authors: Rodrigue J. R. , Fleishman A. , Vishnevsky T. , Fitzpatrick S. , Boger M.
Published: August 2014

Video narratives increasingly are used to draw the public's attention to the need for more registered organ donors. We assessed the differential impact of donation messaging videos on appeal, emotional valence, and organ donation intentions in 781 non‐registered adults. Participants watched six videos (four personal narratives, one informational video without personal narrative, and one unrelated to donation) with or without sound (subtitled), randomly sequenced to minimize order effects. We assessed appeal, emotional valence, readiness to register as organ donors, and donation information‐seeking behavior. Compared to other video types, one featuring a pediatric transplant recipient (with or without sound) showed more favorable appeal (p < 0.001), generated more positive emotional valence (p < 0.01), and had the most favorable impact on organ donor willingness (p < 0.001). Ninety‐five (12%) participants clicked through to a donation website after viewing all six videos. Minority race (OR = 1.94, 95% CI = 1.20, 3.13, p = 0.006), positive change in organ donor readiness (OR = 0.26, 95% CI = 0.14, 0.48, p < 0.001), and total positive emotion (OR = 1.05, 95% CI = 1.03, 1.07, p < 0.001) were significant multivariable predictors of clicking through to the donation website. Brief, one‐min videos can have a very dramatic and positive impact on willingness to consider donation and behavioral intentions to register as an organ donor.
Baby steps: investigating the development of perceptual–motor couplings in infancy
Authors: de Klerk Carina C.J.M. , Johnson Mark H. , Heyes Cecilia M. , Southgate Victoria
Published: August 2014

There are cells in our motor cortex that fire both when we perform and when we observe similar actions. It has been suggested that these perceptual‐motor couplings in the brain develop through associative learning during correlated sensorimotor experience. Although studies with adult participants have provided support for this hypothesis, there is no direct evidence that associative learning also underlies the initial formation of perceptual–motor couplings in the developing brain. With the present study we addressed this question by manipulating infants’ opportunities to associate the visual and motor representation of a novel action, and by investigating how this influenced their sensorimotor cortex activation when they observed this action performed by others. Pre‐walking 7–9‐month‐old infants performed stepping movements on an infant treadmill while they either observed their own real‐time leg movements (Contingent group) or the previously recorded leg movements of another infant (Non‐contingent control group). Infants in a second control group did not perform any steps and only received visual experience with the stepping actions. Before and after the training period we measured infants’ sensorimotor alpha suppression, as an index of sensorimotor cortex activation, while they watched videos of other infants’ stepping actions. While we did not find greater sensorimotor alpha suppression following training in the Contingent group as a whole, we nevertheless found that the strength of the visuomotor contingency experienced during training predicted the amount of sensorimotor alpha suppression at post‐test in this group. We did not find any effects of motor experience alone. These results suggest that the development of perceptual–motor couplings in the infant brain is likely to be supported by associative learning during correlated visuomotor experience.
The genetic control of aposematic black pigmentation in hemimetabolous insects: insights from Oncopeltus fasciatus
Authors: Liu Jin , Lemonds Thomas R. , Popadić Aleksandar
Published: August 2014

Variations in body pigmentation, encompassing both the range of specific colors as well as the spatial arrangement of those colors, are among the most noticeable and lineage‐specific insect features. However, the genetic mechanisms responsible for generating this diversity are still limited to several model species that are primarily holometabolous insects. To address this lack of knowledge, we utilize Oncopeltus fasciatus, an aposematic hemimetabolous insect, as a new model to study insect pigmentation. First, to determine the genetic regulation of black pigment production in Oncopeltus, we perform an RNAi analysis on three core genes involved in the melanin pathway, tyrosine hydroxylase (TH), dopa decarboxylase (DDC), and laccase 2 (lac2). The black pigmentation is affected in all instances, showing that the black pigments in this species are derived from the melanin pathway. The results of the DDC RNAi are particularly informative because they reveal that it is Dopamine melanin, not DOPA melanin, which is the predominant component of black pigments in Oncopeltus. Second, we test whether pigmentation follows a two‐step model where the spatial pre‐mapping of enzymatic activity is followed by vein‐dependent transportation of melanin substances. We confirm the existence of the first step by observing that premature wings develop black pigmentation when exposed to melanin precursors. In addition, we provide evidence for the second step by showing that wing melanin patterning is disrupted when vein transportation is halted. These findings bring novel insights from a hemimetabolous species and establish a framework for subsequent studies on the mechanisms of pigment production and patterning responsible for variations in insect coloration.
Weight and fat distribution in patients taking valproate: A valproate‐discordant gender‐matched twin and sibling pair study
Authors: Petty Sandra J. , Kantor Susan , Lawrence Kate M. , Berkovic Samuel F. , Collins Marnie , Hill Keith D. , Makovey Joanna , Sambrook Philip N. , O'Brien Terence J. , Wark John D.
Published: August 2014

Objectives

Chronic treatment with valproate (VPA) is commonly associated with weight gain, which potentially has important health implications, in particular increased central fat distribution. We utilized a VPA‐discordant same‐sex, twin and matched sibling pair study design to primarily examine for differences in fat distribution between patients with epilepsy treated with VPA compared to their matched twin or sibling control. Weight, blood pressure, and leptin levels were assessed.

Methods

Height, weight, waist and hip measurements, exercise, blood pressure (BP), and serum leptin levels were measured. Body composition was measured using dual‐energy x‐ray absorptiometry (DXA). Abdominal fat was expressed as a percentage of the abdominal region (AFat%); and of whole body fat (WBF); (AFat%WBF). Mean within‐pair differences were assessed (VPA‐user and nonuser). Restricted maximum likelihood (REML) linear mixed model analysis was fitted to examine associations of anthropometrics, zygosity, gender, menopausal status, VPA dose and duration, with weight and AFat%.

Results

We studied 19 pairs of VPA‐discordant, gender‐matched (five male, 14 female) twins and siblings. Mean (standard deviation, SD) duration of therapy for VPA users was 11.0 (7.4) years. There were no statistically significant within‐pair differences in age, height, weight, body mass index (BMI), BP, leptin level, WBF, AFat%, or AFat%WBF. For pairs in which VPA‐user was treated for >11 years there were statistically significant mean within‐pair differences in AFat%, (+7.1%, p = 0.03, n = 10 pairs), mean BP (+11.0 mm Hg, p = 0.006, n = 8 pairs); but not in AFat%WBF. VPA duration was positively associated with weight (estimate +0.98 kg/per year of VPA, p = 0.03); VPA treatment duration and dose were not significantly associated with AFat%.

Significance

This study demonstrated a relationship between long‐term VPA use and abdominal adiposity (AFat%), which could have significant health implications. We recommend ongoing monitoring of weight, BMI, and blood pressure for patients taking VPA.
The interrelationship between anti‐Müllerian hormone, ovarian follicular populations and age in mares
Authors: Claes A. , Ball B. A. , Scoggin K. E. , Esteller‐Vico A. , Kalmar J. J. , Conley A. J. , Squires E. L. , Troedsson M. H. T.
Published: August 2014

Reasons for performing study

Anti‐Müllerian hormone (AMH) is a granulosa‐cell‐derived glycoprotein, which plays an important inhibitory role during folliculogenesis. Concentrations of AMH are highly correlated with antral follicle counts (AFCs) in other species, which in turn are related to follicular reserve. Relatively little is known about AMH and AFC in the mare.

Objectives

To determine plasma AMH concentrations and AFCs in mares of different ages, to measure the repeatability of AMH concentrations and AFCs within and across oestrous cycles and to assess the relationship between plasma AMH concentrations and AFCs with regard to mare age and follicle size.

Study design

An observational study examining the relationship between AMH, AFC and age in 45 mares.

Methods

Young (3–8 years), middle‐aged (9–18 years) and old mares (19–27 years) were examined by transrectal ultrasonography over 2 or 3 oestrous cycles. Plasma AMH concentrations and AFCs were determined, and antral follicles were classified by size into different groups.

Results

Plasma AMH concentrations varied widely between mares within similar age groups. Antral follicle counts were significantly lower in old mares than in young and middle‐aged mares, and AMH concentrations were significantly lower in old than in middle‐aged mares. A positive relationship was detected between AFC and AMH, and this relationship varied by mare age with a strong correlation in older mares (ρ = 0.86; P<0.0001), a moderate correlation in middle‐aged mares (ρ = 0.60; P = 0.01) and no correlation in young mares (ρ = 0.40, P<0.4). The AMH concentrations were significantly related to the number of antral follicles between 6 and 20 mm in diameter, and the repeatability of AFCs and AMH concentrations was high within and between oestrous cycles.

Conclusions

Our findings indicate that the relationship between AMH and AFC varies across age groups, and concentrations of AMH might be a better reflection of reproductive age than calendar age.
Towards elucidating the stability, dynamics and architecture of the nucleosome remodeling and deacetylase complex by using quantitative interaction proteomics
Authors: Kloet Susan L. , Baymaz H. Irem , Makowski Matthew , Groenewold Vincent , Jansen Pascal W. T. C. , Berendsen Madeleine , Niazi Hassin , Kops Geert J. , Vermeulen Michiel
Published: August 2014

The nucleosome remodeling and deacetylase (NuRD) complex is an evolutionarily conserved chromatin‐associated protein complex. Although the subunit composition of the mammalian complex is fairly well characterized, less is known about the stability and dynamics of these interactions. Furthermore, detailed information regarding protein–protein interaction surfaces within the complex is still largely lacking. Here, we show that the NuRD complex interacts with a number of substoichiometric zinc finger‐containing proteins. Some of these interactions are salt‐sensitive (ZNF512B and SALL4), whereas others (ZMYND8) are not. The stoichiometry of the core subunits is not affected by high salt concentrations, indicating that the core complex is stabilized by hydrophobic interactions. Interestingly, the RBBP4 and RBBP7 proteins are sensitive to high nonionic detergent concentrations during affinity purification. In a subunit exchange assay with stable isotope labeling by amino acids in cell culture (SILAC)‐treated nuclear extracts, RBBP4 and RBBP7 were identified as dynamic core subunits of the NuRD complex, consistent with their proposed role as histone chaperones. Finally, using cross‐linking MS, we have uncovered novel features of NuRD molecular architecture that complement our affinity purification‐MS/MS data. Altogether, these findings extend our understanding of MBD3–NuRD structure and stability.

Structured digital abstract

MBD3 physically interacts with ZNF512B,  HDAC1,  ZMYND8,  GATAD2B,  SALL4,  GATAD2A,  ZNF592,  MTA3,  ZNF687,  CDK2AP1,  CHD3,  ZNF532,  HDAC2,  MTA2,  CHD4, MTA1,  KPNA2,  CHD5,  RBBP4 and RBBP7 by pull down (View interaction)

CDK2AP1 physically interacts with MBD3,  MTA3,  HDAC2,  GATAD2A,  CHD4,  CDK2AP1,  MTA2,  HDAC1,  MTA1,  CHD3,  GATAD2B,  MBD2,  RBBP4 and RBBP7 by pull down (View interaction)

MBD3 physically interacts with MTA2,  MTA3,  RBBP4,  RBBP7,  HDAC2,  HDAC1,  CHD4,  CHD3 and MTA1 by cross-linking study (View interaction)
Transcriptional and epigenetic regulation of T‐helper lineage specification
Authors: Tripathi Subhash K. , Lahesmaa Riitta
Published: August 2014

Combined with TCR stimuli, extracellular cytokine signals initiate the differentiation of naive CD4+ T cells into specialized effector T‐helper (Th) and regulatory T (Treg) cell subsets. The lineage specification and commitment process occurs through the combinatorial action of multiple transcription factors (TFs) and epigenetic mechanisms that drive lineage‐specific gene expression programs. In this article, we review recent studies on the transcriptional and epigenetic regulation of distinct Th cell lineages. Moreover, we review current study linking immune disease‐associated single‐nucleotide polymorphisms with distal regulatory elements and their potential role in the disease etiology.
The interface between transcriptional and epigenetic control of effector and memory CD8+ T‐cell differentiation
Authors: Gray Simon M. , Kaech Susan M. , Staron Matthew M.
Published: August 2014

Immunity to many intracellular pathogens requires the proliferation, differentiation, and function of CD8+ cytotoxic T lymphocytes (CTLs). While the majority of effector CTLs die upon clearance of the pathogen, a small proportion of them survive to become long‐lived memory CTLs. Memory CTLs can provide protective immunity against re‐exposure to the same pathogen and are the principle motivation behind T‐cell‐ based vaccine design. While a large body of cellular immunologic research has proven invaluable to define effector and memory CTLs by their different phenotypes and functions, an emerging focus in the field has been to understand how environmental cues regulate CTL differentiation on a genomic level. Genome‐wide studies to profile transcriptional and epigenetic changes during infection have revealed that dynamic changes in DNA methylation patterns and histone modifications accompany transcriptional signatures that define and regulate CTL differentiation states. In this review, we emphasize the importance of epigenetic regulation of CD8+ T‐cell differentiation and the likely role that transcription factors play in this process.
The regulatory network of B‐cell differentiation: a focused view of early B‐cell factor 1 function
Authors: Boller Sören , Grosschedl Rudolf
Published: August 2014

During the last decades, many studies have investigated the transcriptional and epigenetic regulation of lineage decision in the hematopoietic system. These efforts led to a model in which extrinsic signals and intrinsic cues establish a permissive chromatin context upon which a regulatory network of transcription factors and epigenetic modifiers act to guide the differentiation of hematopoietic lineages. These networks include lineage‐specific factors that further modify the epigenetic landscape and promote the generation of specific cell types. The process of B lymphopoiesis requires a set of transcription factors, including Ikaros, PU.1, E2A, and FoxO1 to ‘prime’ cis‐regulatory regions for subsequent activation by the B‐lineage‐specific transcription factors EBF1 and Pax‐5. The expression of EBF1 is initiated by the combined action of E2A and FoxO1, and it is further enhanced and maintained by several positive feedback loops that include Pax‐5 and IL‐7 signaling. EBF1 acts in concert with Ikaros, PU.1, Runx1, E2A, FoxO1, and Pax‐5 to establish the B cell‐specific transcription profile. EBF1 and Pax‐5 also collaborate to repress alternative cell fates and lock cells into the B‐lineage fate. In addition to the functions of EBF1 in establishing and maintaining B‐cell identity, EBF1 is required to coordinate differentiation with cell proliferation and survival.
Transcriptional and epigenetic networks of helper T and innate lymphoid cells
Authors: Shih Han‐Yu , Sciumè Giuseppe , Poholek Amanda C. , Vahedi Golnaz , Hirahara Kiyoshi , Villarino Alejandro V. , Bonelli Michael , Bosselut Remy , Kanno Yuka , Muljo Stefan A. , O'Shea John J.
Published: August 2014

The discovery of the specification of CD4+ helper T cells to discrete effector ‘lineages’ represented a watershed event in conceptualizing mechanisms of host defense and immunoregulation. However, our appreciation for the actual complexity of helper T‐cell subsets continues unabated. Just as the Sami language of Scandinavia has 1000 different words for reindeer, immunologists recognize the range of fates available for a CD4+ T cell is numerous and may be underestimated. Added to the crowded scene for helper T‐cell subsets is the continuously growing family of innate lymphoid cells (ILCs), endowed with common effector responses and the previously defined ‘master regulators’ for CD4+ helper T‐cell subsets are also shared by ILC subsets. Within the context of this extraordinary complexity are concomitant advances in the understanding of transcriptomes and epigenomes. So what do terms like ‘lineage commitment’ and helper T‐cell ‘specification’ mean in the early 21st century? How do we put all of this together in a coherent conceptual framework? It would be arrogant to assume that we have a sophisticated enough understanding to seriously answer these questions. Instead, we review the current status of the flexibility of helper T‐cell responses in relation to their genetic regulatory networks and epigenetic landscapes. Recent data have provided major surprises as to what master regulators can or cannot do, how they interact with other transcription factors and impact global genome‐wide changes, and how all these factors come together to influence helper cell function.
Vitamin E and wound healing: an evidence‐based review
Authors: Hobson Rachel
Published: August 2014

Vitamin E has been demonstrated to modulate cellular signalling, gene expression and affect wounds infected with methicillin‐resistant Staphylococcus aureus (MRSA), thus influencing wound healing. This evidence‐based review aimed to identify and evaluate current research assessing the properties of vitamin E in relation to wound healing, through its role as an antioxidant and its influence on connective tissue growth factor (CTGF), MRSA and gene transcription. Literature dated from 1996 to 2012, published in English, involving either animals or adult humans with an acute or chronic wound were included. The databases that contained relevant articles were narrowed down to four, and a total of 33 identified studies were included. The literature review revealed that there is a significant dearth of robust studies establishing the effects of vitamin E on wound healing, and further research is clearly warranted.