bluuebunny/crossref_metadata_2025 huggingface dataset:
Spatio-temporal genetic structure of the rodent Calomys venustus in linear, fragmented habitats
Authors: Chiappero Marina B. , Sommaro Lucía V. , Priotto José W. , Wiernes María Paula , Steinmann Andrea R. , Gardenal Cristina N.
Published: December 2015

Studies about habitat fragmentation, in terms of how it affects gene flow and genetic variability, have traditionally been conducted on island-like systems in which the remaining habitats form patches embedded in a matrix. However, in agroecosystems, remaining habitats usually form linear strips along fence lines, roads, and water courses (“border” habitats). We used the rodent Calomys venustus , a species inhabiting borders in central Argentina agroecosystems, as a model to address how genetic variability is structured in linear habitats. A total of 359 rodents were captured seasonally from spring 2005 to winter 2006. Genetic variability at microsatellite loci was uniformly high, despite significant variation in population size during the sampling period. Genetic differentiation, spatial autocorrelation, and causal modeling analyses suggested that dispersion patterns in this species depend mainly on geographic distance, with unfavorable habitat like dirt roads and crop fields posing only weak (or no) resistance to dispersal. Small-scale spatial genetic structure was related to different space use patterns by females and males. Our results showed that, although greatly reduced in area, border habitats can support stable populations of species without loss of either variability or genetic connectivity.

Los efectos de la fragmentación del hábitat sobre el flujo génico y la variabilidad genética, se han estudiado tradicionalmente en sistemas tipo islas, en los cuales los hábitats remanentes forman parches embebidos en una matriz. Sin embargo, en los agroecosistemas, éstos suelen tener forma lineal a lo largo de alambrados, caminos y corrientes de agua (hábitats de “borde”). En este trabajo, utilizamos al roedor Calomys venustus , especie típica de ambientes de borde en los agroecosistemas del centro de Argentina, como modelo para estudiar cómo la variabilidad genética se estructura en hábitats lineales. Un total de 359 roedores se capturaron estacionalmente desde la primavera de 2005 hasta el invierno de 2006. La variabilidad genética encontrada en loci de microsatélites fue siempre alta, a pesar de una variación significativa del tamaño poblacional a lo largo del período de estudio. Los análisis de diferenciación genética, autocorrelación genética espacial y modelado causal sugieren que los patrones de dispersión en esta especie dependen principalmente de la distancia geográfica, y que los hábitats desfavorables como caminos de tierra y campos de cultivo representan una barrera débil (o nula) para la dispersión. La estructura genética a escala pequeña estuvo relacionada al diferente uso del espacio por parte de machos y hembras. Nuestros resultados mostraron que a pesar de tener un área reducida, los hábitat de bordes pueden mantener poblaciones estables sin pérdida de variabilidad genética o reducción del flujo génico.
Estimating the age of Risso’s dolphins ( Grampus griseus ) based on skin appearance
Authors: Hartman Karin L. , Wittich Anja , Cai Juan Juan , van der Meulen Frank H. , Azevedo José M. N.
Published: December 2015

One of Risso’s dolphin’s distinctive characteristics is the tendency to “lighten” with age due to the accumulation of unpigmented scars. These accumulated scars may provide an indication of age. Photographic skin recaptures gathered from 61 free-ranging animals over a period of 15 years were analyzed to develop a skin classification model in 6 skin stages. Classification of photographic skin captures following this model was tested by 15 experts and 13 nonexpert rankers, with a general probability of agreement of 79%. The duration of each skin stage was estimated using a statistical model based on the recorded dates in which individual animals were known to have entered and/or exited a given stage. A Bayesian approach was used to combine available photographic skin recapture data using expert knowledge as prior to predict the duration for each skin stage and thus the mean age at each stage. Results suggest that animals may live more than 45 years, which is in agreement with published information based on dental layers. The proposed skin stages can be correlated with reproduction, with the transition to stage 3 linked to the onset of maturity. Adult females are less scarified than males and were not observed in the whiter skin classes. The proposed skin stage model is noninvasive and easy to apply and could be a valuable tool in further studies of population structure and dynamics of Risso’s dolphins.
Quantification and In Vitro Bioaccessibility of Selenium from Osborne Fractions of Selenium‐Rich Cereal Grains
Authors: Dhanjal Noorpreet I. , Sharma Siddharth , Prakash N. Tejo
Published: December 2015

Cereal crops cultivated in the seleniferous belt of Punjab, India, were observed to hyperaccumulate a significantly high concentration of selenium (20–123 µg/g). Selenium concentration (µg/g) in storage proteins of wheat, maize, and rice, namely, albumin (401, 280, and 29, respectively), globulin (264, 192, and 242, respectively), glutelin (563, 359, and 178, respectively), and prolamin (629, 339, and 257, respectively) indicated variable selenium levels, with prolamin contributing significantly higher levels of selenium when compared with other proteins with reference to the total concentration of the protein fraction. The simulated gastric and gastrointestinal digestion studies indicated better accessibility of selenium during intestinal digestion, with variability across proteins and cereal types. The observations provide an insight into the bioavailability of selenium in selenium‐rich cereal grains, used in the study, and their potential use as source for selenium supplementation to deficient populations, or as “bioactive” selenium‐rich nutraceutical blends for health benefits.
Terminal Bacteroid Differentiation Is Associated With Variable Morphological Changes in Legume Species Belonging to the Inverted Repeat-Lacking Clade
Authors: Montiel Jesús , Szűcs Attila , Boboescu Iulian Z. , Gherman Vasile D. , Kondorosi Éva , Kereszt Attila
Published: December 2015

Medicago and closely related legume species from the inverted repeat–lacking clade (IRLC) impose terminal differentiation onto their bacterial endosymbionts, manifested in genome endoreduplication, cell enlargement, and loss of cell-division capacity. Nodule-specific cysteine-rich (NCR) secreted host peptides are plant effectors of this process. As bacteroids in other IRLC legumes, such as Cicer arietinum and Glycyrrhiza lepidota, were reported not to display features of terminal differentiation, we investigated the fate of bacteroids in species from these genera as well as in four other species representing distinct genera of the phylogenetic tree for this clade. Bacteroids in all tested legumes proved to be larger in size and DNA content than cultured cells; however, the degree of cell elongation was rather variable in the different species. In addition, the reproductive ability of the bacteroids isolated from these legumes was remarkably reduced. In all IRLC species with available sequence data, the existence of NCR genes was found. These results indicate that IRLC legumes provoke terminal differentiation of their endosymbionts with different morphotypes, probably with the help of NCR peptides.
Arabidopsis TAF15b Localizes to RNA Processing Bodies and Contributes to snc1-Mediated Autoimmunity
Authors: Dong Oliver X. , Meteignier Louis-Valentin , Plourde Melodie B. , Ahmed Bulbul , Wang Ming , Jensen Cassandra , Jin Hailing , Moffett Peter , Li Xin , Germain Hugo
Published: December 2015

In both animals and plants, messenger (m)RNA export has been shown to contribute to immune response regulation. The Arabidopsis nuclear protein MOS11, along with the nucleoporins MOS3/Nup96/SAR3 and Nup160/SAR1 are components of the mRNA export machinery and contribute to immunity mediated by nucleotide binding leucine-rich repeat immune receptors (NLR). The human MOS11 ortholog CIP29 is part of a small protein complex with three additional members: the RNA helicase DDX39, ALY, and TAF15b. We systematically assessed the biological roles of the Arabidopsis homologs of these proteins in toll interleukin 1 receptor–type NLR (TNL)-mediated immunity using reverse genetics. Although mutations in ALY and DDX39 did not result in obvious defects, taf15b mutation partially suppressed the autoimmune phenotypes of a gain-of-function TNL mutant, snc1. An additive effect on snc1 suppression was observed in mos11-1 taf15b snc1 triple mutant plants, suggesting that MOS11 and TAF15b have independent functions. TAF15b-GFP fusion protein, which fully complemented taf15b mutant phenotypes, localized to nuclei similarly to MOS11. However, it was also targeted to cytosolic granules identified as processing bodies. In addition, we observed no change in SNC1 mRNA levels, whereas less SNC1 protein accumulated in taf15b mutant, suggesting that TAF15b contributes to SNC1 homeostasis through posttranscriptional mechanisms. In summary, this study highlights the importance of posttranscriptional RNA processing mediated by TAF15b in the regulation of TNL-mediated immunity.
Contribution of Individual Chemoreceptors to Sinorhizobium meliloti Chemotaxis Towards Amino Acids of Host and Nonhost Seed Exudates
Authors: Webb Benjamin A. , Helm Richard F. , Scharf Birgit E.
Published: December 2015

Plant seeds and roots exude a spectrum of molecules into the soil that attract bacteria to the spermosphere and rhizosphere, respectively. The alfalfa symbiont Sinorhizobium meliloti utilizes eight chemoreceptors (McpT to McpZ and IcpA) to mediate chemotaxis. Using a modified hydrogel capillary chemotaxis assay that allows data quantification and larger throughput screening, we defined the role of S. meliloti chemoreceptors in sensing its host, Medicago sativa, and a closely related nonhost, Medicago arabica. S. meliloti wild type and most single-deletion strains displayed comparable chemotaxis responses to host or nonhost seed exudate. However, while the mcpZ mutant responded like wild type to M. sativa exudate, its reaction to M. arabica exudate was reduced by 80%. Even though the amino acid (AA) amounts released by both plant species were similar, synthetic AA mixtures that matched exudate profiles contributed differentially to the S. meliloti wild-type response to M. sativa (23%) and M. arabica (37%) exudates, with McpU identified as the most important chemoreceptor for AA. Our results show that S. meliloti is equally attracted to host and nonhost legumes; however, AA play a greater role in attraction to M. arabica than to M. sativa, with McpZ being specifically important in sensing M. arabica.
Comparison of Methods of Acibenzolar-S-Methyl Application for Post-Infection Fire Blight Suppression in Pear and Apple
Authors: Johnson Kenneth B. , Temple Todd N.
Published: December 2015

Greenhouse-grown, 1-year-old potted ‘Bosc’ pear and apple rootstock cultivars ‘M.9’ and ‘M.26’ were inoculated with the fire blight pathogen, Erwinia amylovora, and subjected to trunk paint, root drench, or foliar spray treatments with acibenzolar-S-methyl (ASM, 4 to 30 mg a.i./tree) to induce systemic acquired resistance. Each method of ASM treatment suppressed fire blight canker expansion by 22 to 25%. Furthermore, ASM application method and ASM treatment timing (at or ±3 weeks relative to inoculation) interacted significantly (P ≤ 0.02) in each experiment. A root drench was most effective when applied 3 weeks before inoculation (36% suppression) whereas trunk paints and foliar sprays were more effective at inoculation (43 and 34%, suppression, respectively). Sizes of fire blight cankers in potted apple rootstocks M.9 and M.26 (under scions ‘Gala’ or ‘Cameo’) inoculated directly with the pathogen were reduced by 82 and 87% after two pretreatments of ASM applied as a trunk paint or root drench, respectively. Expression of pathogenesis-related (PR) genes PR-1 and -2 in apple leaves sampled after an ASM trunk paint were elevated significantly (P ≤ 0.05) relative to control trees for at least 9 weeks after treatment. Results of this study are being used to guide field research on postinfection therapy with ASM in 1- to 10-year-old pear and apple trees where fire blight has proven difficult to manage with therapeutic pruning only.
Factors governing the behaviour of aqueous methane in narrow pores
Authors: Phan Anh , Cole David R. , Striolo Alberto
Published: December 2015

All-atom equilibrium molecular dynamics simulations were employed to investigate the behaviour of aqueous methane confined in 1-nm-wide pores obtained from different materials. Models for silica, alumina and magnesium oxide were used to construct the slit-shaped pores. The results show that methane solubility in confined water strongly depends on the confining material, with silica yielding the highest solubility in the systems considered here. The molecular structure of confined water differs within the three pores, and density fluctuations reveal that the silica pore is effectively less ‘hydrophilic’ than the other two pores considered. Comparing the water fluctuation autocorrelation function with local diffusion coefficients of methane across the hydrated pores we observed a direct proportional coupling between methane and water dynamics. These simulation results help to understand the behaviour of gas in water confined within narrow subsurface formations, with possible implications for fluid transport.
Graphene-based membranes: status and prospects
Authors: Yoon Hee Wook , Cho Young Hoon , Park Ho Bum
Published: December 2015

Recently, graphene-based membranes have been extensively studied, represented by two distinct research directions: (i) creating pores in graphene basal plane and (ii) engineering nanochannels in graphene layers. Most simulation results predict that porous graphene membranes can be much more selective and permeable than current existing membranes, also evidenced by some experimental results for gas separation and desalination. In addition, graphene oxide has been widely investigated in layered membranes with two-dimensional nanochannels, showing very intriguing separation properties. This review will cover state-of-the-art of graphene-based membranes, and also provide a material guideline on future research directions suitable for practical membrane applications.
Flux accentuation and improved rejection in graphene-based filtration membranes produced by capillary-force-assisted self-assembly
Authors: Sheath Phillip , Majumder Mainak
Published: December 2015

Separation and flux performance were compared in graphene-based membranes that differed only in the method of deposition of reduced graphene oxide platelets. Membranes with higher degree of order were produced by evaporation-induced capillary-force self-assembly, which showed higher steric rejection properties while simultaneously accentuating water permeance compared to membranes produced by the traditional vacuum filtration technique. These studies attempt to establish structure–property correlations in graphene-based membranes.
The influence of few-layer graphene on the gas permeability of the high-free-volume polymer PIM-1
Authors: Althumayri Khalid , Harrison Wayne J. , Shin Yuyoung , Gardiner John M. , Casiraghi Cinzia , Budd Peter M. , Bernardo Paola , Clarizia Gabriele , Jansen Johannes C.
Published: December 2015

Gas permeability data are presented for mixed matrix membranes (MMMs) of few-layer graphene in the polymer of intrinsic microporosity PIM-1, and the results compared with previously reported data for two other nanofillers in PIM-1: multiwalled carbon nanotubes functionalized with poly(ethylene glycol) (f-MWCNTs) and fused silica. For few-layer graphene, a significant enhancement in permeability is observed at very low graphene content (0.05 vol.%), which may be attributed to the effect of the nanofiller on the packing of the polymer chains. At higher graphene content permeability decreases, as expected for the addition of an impermeable filler. Other nanofillers, reported in the literature, also give rise to enhancements in permeability, but at substantially higher loadings, the highest measured permeabilities being at 1 vol.% for f-MWCNTs and 24 vol.% for fused silica. These results are consistent with the hypothesis that packing of the polymer chains is influenced by the curvature of the nanofiller surface at the nanoscale, with an increasingly pronounced effect on moving from a more-or-less spherical nanoparticle morphology (fused silica) to a cylindrical morphology (f-MWCNT) to a planar morphology (graphene). While the permeability of a high-free-volume polymer such as PIM-1 decreases over time through physical ageing, for the PIM-1/graphene MMMs a significant permeability enhancement was retained after eight months storage.
Interfacial layer effects on surface capacitances and electro-osmosis in electrolytes
Authors: Bonthuis Douwe Jan , Uematsu Yuki , Netz Roland R.
Published: December 2015

Many properties of the interfacial layer of water at surfaces differ significantly from those of bulk water. The consequences are most significant for the double-layer capacitance and the electrokinetic properties. We model the interfacial hydration layer by a modified dielectric constant and a modified local viscosity over a single interfacial width. Analytic expressions in the low-charge Debye–Hückel approximation are derived and shown to describe experimental surface capacitance and electro-osmotic data in a unified framework.
Observation and analysis of the Coulter effect through carbon nanotube and graphene nanopores
Authors: Agrawal Kumar Varoon , Drahushuk Lee W. , Strano Michael S.
Published: December 2015

Carbon nanotubes (CNTs) and graphene are the rolled and flat analogues of graphitic carbon, respectively, with hexagonal crystalline lattices, and show exceptional molecular transport properties. The empirical study of a single isolated nanopore requires, as evidence, the observation of stochastic, telegraphic noise from a blocking molecule commensurate in size with the pore. This standard is used ubiquitously in patch clamp studies of single, isolated biological ion channels and a wide range of inorganic, synthetic nanopores. In this work, we show that observation and study of stochastic fluctuations for carbon nanopores, both CNTs and graphene-based, enable precision characterization of pore properties that is otherwise unattainable. In the case of voltage clamp measurements of long (0.5–1 mm) CNTs between 0.9 and 2.2 nm in diameter, Coulter blocking of cationic species reveals the complex structuring of the fluid phase for confined water in this diameter range. In the case of graphene, we have pioneered the study and the analysis of stochastic fluctuations in gas transport from a pressurized, graphene-covered micro-well compartment that reveal switching between different values of the membrane permeance attributed to chemical rearrangements of individual graphene pores. This analysis remains the only way to study such single isolated graphene nanopores under these realistic transport conditions of pore rearrangements, in keeping with the thesis of this work. In summary, observation and analysis of Coulter blocking or stochastic fluctuations of permeating flux is an invaluable tool to understand graphene and graphitic nanopores including CNTs.
Genomic DNA preparation enabling multiple replicate reads for accurate nanopore sequencing
Authors: Tsavachidou Dimitra
Published: December 2015

Sequencing at single-nucleotide resolution using nanopore devices is performed with reported error rates 10.5–20.7% (Ip et al., 2015). Since errors occur randomly during sequencing, repeating the sequencing procedure for the same DNA strands several times can generate sequencing results based on consensus derived from replicate readings, thus reducing overall error rates.

The method presented in this manuscript constructs copies of a nucleic acid molecule that are consecutively connected to the nucleic acid molecule. Such copies are useful because they can be sequenced by a nanopore device, enabling replicate reads, thus improving overall sequencing accuracy.
MPRAnator: a web-based tool for the design of Massively Parallel Reporter Assay experiments
Authors: Georgakopoulos-Soares Ilias , Jain Naman , Gray Jesse , Hemberg Martin
Published: December 2015

DNA regulatory elements contain short motifs where transcription factors (TFs) can bind to modulate gene expression. Although the broad principles of TF regulation are well understood, the rules that dictate how combinatorial TF binding translates into transcriptional activity remain largely unknown. With the rapid advances in DNA synthesis and sequencing technologies and the continuing decline in the associated costs, high-throughput experiments can be performed to investigate the regulatory role of thousands of oligonucleotide sequences simultaneously. Nevertheless, designing high-throughput reporter assay experiments such as Massively Parallel Reporter Assays (MPRAs) and similar methods remains challenging. We introduce MPRAnator, a set of tools that facilitate rapid design of MPRA experiments. With MPRA Motif design, a set of variables provides fine control of how motifs are placed into sequences therefore allowing the user to investigate the rules that govern TF occupancy. MPRA SNP design can be used to investigate the functional effects of single or combinations of SNPs at regulatory sequences. Finally, the Transmutation tool allows for the design of negative controls by permitting scrambling, reversing, complementing or introducing multiple random mutations in the input sequences or motifs.
An approximation of the error back-propagation algorithm in a predictive coding network with local Hebbian synaptic plasticity
Authors: Whittington James C.R. , Bogacz Rafal
Published: December 2015

To efficiently learn from feedback, cortical networks need to update synaptic weights on multiple levels of cortical hierarchy. An effective and well-known algorithm for computing such changes in synaptic weights is the error back-propagation algorithm. However, in the back-propagation algorithm, the change in synaptic weights is a complex function of weights and activities of neurons not directly connected with the synapse being modified, whereas the changes in biological synapses are determined only by the activity of pre-synaptic and post-synaptic neurons. Several models have been proposed that approximate the back-propagation algorithm with local synaptic plasticity, but these models require complex external control over the network or relatively complex plasticity rules. Here we show that a network developed in the predictive coding framework can efficiently perform supervised learning fully autonomously, employing only simple local Hebbian plasticity. Furthermore, for certain parameters, the weight change in the predictive coding model converges to that of the back-propagation algorithm. This suggests that it is possible for cortical networks with simple Hebbian synaptic plasticity to implement efficient learning algorithms in which synapses in areas on multiple levels of hierarchy are modified to minimize the error on the output.
The impact of amplification on differential expression analyses by RNA-seq
Authors: Parekh Swati , Ziegenhain Christoph , Vieth Beate , Enard Wolfgang , Hellmann Ines
Published: December 2015

Currently quantitative RNA-Seq methods are pushed to work with increasingly small starting amounts of RNA that require amplification. However, it is unclear how much noise or bias amplification introduces and how this effects precision and accuracy of RNA quantification. To assess the effects of amplification, reads that originated from the same RNA molecule (PCR-duplicates) need to be identified. Computationally, read duplicates are defined via their mapping position, which does not distinguish PCR- from natural duplicates and hence it is unclear how to treat duplicate reads.

Here, we generate and analyse RNA-seq datasets prepared using three different protocols (Smart-Seq, TruSeq and UMI-seq). We find that a large fraction of computationally identified read duplicates can be explained by sampling and fragmentation bias. Consequently, the computational removal of duplicates does not improve accuracy, power or FDR, but can actually worsen them. Even when duplicates are experimentally identified by unique molecular identifiers (UMIs), power and FDR are only mildly improved. However, the pooling of samples as made possible by the early barcoding of the UMI-protocol leads to an appreciable increase in the power to detect differentially expressed genes.
Hilbert-Schmidt and Sobol sensitivity indices for static and time series Wnt signaling measurements in colorectal cancer - Part A
Authors: sinha shriprakash
Published: December 2015

Ever since the accidental discovery of Wingless [Sharma R.P., Drosophila information service, 1973, 50, p 134], research in the field of Wnt signaling pathway has taken significant strides in wet lab experiments and various cancer clinical trials, augmented by recent developments in advanced computational modeling of the pathway. Information rich gene expression profiles reveal various aspects of the signaling pathway and help in studying different issues simultaneously. Hitherto, not many computational studies exist which incorporate the simultaneous study of these issues. This manuscript • explores the strength of contributing factors in the signaling pathway, • analyzes the existing causal relations among the inter/extracellular factors effecting the pathway based on prior biological knowledge and • investigates the deviations in fold changes in the recently found prevalence of psychophysical laws working in the pathway. To achieve this goal, local and global sensitivity analysis is conducted on the (non)linear responses between the factors obtained from static and time series expression profiles using the density (Hilbert-Schmidt Information Criterion) and variance (Sobol) based sensitivity indices. The results show the advantage of using density based indices over variance based indices mainly due to the former’s employment of distance measures & the kernel trick via Reproducing kernel Hilbert space (RKHS) that capture nonlinear relations among various intra/extracellular factors of the pathway in a higher dimensional space. In time series data, using these indices it is now possible to observe where in time, which factors get influenced & contribute to the pathway, as changes in concentration of the other factors are made. This synergy of prior biological knowledge, sensitivity analysis & representations in higher dimensional spaces can facilitate in time based administration of target therapeutic drugs & reveal hidden biological information within colorectal cancer samples. Code has been made available at Google drive onhttps://drive.google.com/folderview?id=0B7Kkv8wlhPU-Q2NBZGt1ZERrSVE&usp=sharing
metilene: fast and sensitive calling of differentially methylated regions from bisulfite sequencing data
Authors: Jühling Frank , Kretzmer Helene , Bernhart Stephan H. , Otto Christian , Stadler Peter F. , Hoffmann Steve
Published: December 2015

The detection of differentially methylated regions (DMRs) is a necessary prerequisite for characterizing different epigenetic states. We present a novel program, metilene, to identify DMRs within whole-genome and targeted data with unrivaled specificity and sensitivity. A binary segmentation algorithm combined with a two-dimensional statistical test allows the detection of DMRs in large methylation experiments with multiple groups of samples in minutes rather than days using off-the-shelf hardware. metilene outperforms other state-of-the-art tools for low coverage data and can estimate missing data. Hence, metilene is a versatile tool to study the effect of epigenetic modifications in differentiation/development, tumorigenesis, and systems biology on a global, genome-wide level. Whether in the framework of international consortia with dozens of samples per group, or even without biological replicates, it produces highly significant and reliable results.
Experimental evidence for within‐ and cross‐seasonal effects of fear on survival and reproduction
Authors: Elliott Kyle H. , Betini Gustavo S. , Dworkin Ian , Norris D. Ryan
Published: December 2015

Fear of predation can have non‐lethal effects on individuals within a season but whether, and to what extent, these effects carry over into subsequent seasons is not known.

Using a replicated seasonal population of the common fruit fly, Drosophila melanogaster, we examined both within‐ and cross‐seasonal effects of fear on survival and reproductive output.

Compared to controls, flies exposed to the scent of mantid (Tenodera sinensis) predators in the non‐breeding season had 64% higher mortality, and lost 60% more mass by the end of the non‐breeding season and, in the subsequent breeding season, produced 20% fewer offspring that weighed 9% less at maturity. Flies exposed to the scent of mantids in the breeding season did not produce fewer offspring, but their offspring developed faster and weighed less as adults compared to the controls.

Our results demonstrate how effects of fear can be manifested both within and across seasons and emphasize the importance of understanding how events throughout the annual cycle influence individual success of animals living in seasonal environments.
Public Sector Collaboration: Are We Doing It Well and Could We Do It Better?
Authors: Wilkins Peter , Phillimore John , Gilchrist David
Published: December 2015

Improving collaboration by public sector agencies is an important element of many public sector reforms. Common approaches include introducing responsibilities under legislation and policy decisions, the provision of information and guidance, and strengthening third‐party oversight. To identify how collaboration is being practised, this paper reviews evidence from over one hundred reports by Auditors‐General and Ombudsmen in Australia and New Zealand to identify key attributes of collaboration, and assesses these further by examining three reports in detail. It concludes that problems that have been known for many years continue to constrain public sector effectiveness. Although continuing existing approaches may assist in improving collaboration, the paper argues that there is a need to adopt more systematic approaches to organisational capacity for collaboration. It further identifies that changes in the external environment such as technology‐based innovation may demand rapid progress and change in relation to collaboration.
The maverick dialogics of religious rivalry in Sri Lanka: inspiration and contestation in a new messianic Buddhist movement
Authors: Mahadev Neena
Published: December 2015

A strand of Sri Lankan Buddhist revivalism that emerged in 2008 offers an unconventional rejoinder to evangelical efforts to intensify conversions. Pentecostals assert that Christ offers instantaneous salvation whereas Theravāda Buddhism demands slow passage through many lifetimes of suffering. In contrast to concomitant political efforts to curb conversions, one maverick Buddhist monk implicitly responded to such competitive theological provocations by enlisting devotees to engage in ritual and moral cultivation to foreshorten the far‐future arrival of the messianicBodhisatvaMaitreya. Neither derivative, nor ‘syncretic’, the maverick's efforts to fortify Buddhism are nevertheless dialogically responsive to multiple sources of religious competition. Following the traffic of aspiration, contestation, and charismatic affinity between Buddhism and rival religiosities, on one side, andwithinBuddhism, on the other, the ethnography discloses a multi‐religious milieu. Within it, several competing religiosities stir the anxieties of Sinhala Buddhist nationalists. Old and new rivalries pose constraints, even as they provide fodder for religious innovation.
‘Follow me, and I will make you fishers of men’: the moral and political scales of migration in the central Mediterranean
Authors: Ben‐Yehoyada Naor
Published: December 2015

This article offers recent dynamics of unauthorized migration and interception in the central Mediterranean as an example of historical anthropology of transnational region formation. It exemplifies how we can rescale classical themes in Mediterraneanist anthropology – hospitality, in this case – to illuminate transnational processes. I argue that anthropologists actually share with human rights advocates and European officials these ways of thinking about the scales of the moral and the political dimensions of migration, and I offer an alternative understanding of the scales of action, responsibility, and sovereignty as well as a clue about how regions come to life.
Obesity‐related endometrial cancer: an update on survivorship approaches to reducing cardiovascular death
Authors: Laskey RA , McCarroll ML , von Gruenigen VE
Published: December 2015

As the rate of obesity increases worldwide, so will the number of women diagnosed with obesity‐related malignancy. The strongest correlation between obesity and cancer is endometrial cancer (EC). Obesity is the most significant modifiable risk factor for development of EC and also contributes to the most common cause of death in EC survivors—cardiovascular disease (CVD). Most cancer survivors after diagnosis do not implement lifestyle changes aimed at weight‐loss and CVD risk reduction. This selective review highlights recent novel and unique approaches for managing CVD co‐morbidities in EC survivorship.

Tweetable abstract

This selective review highlights recent novel and unique approaches to CVD co‐morbidities in EC survivorship.
Maternal abdominal subcutaneous fat thickness as a predictor for adverse pregnancy outcome: a longitudinal cohort study
Authors: Kennedy NJ , Peek MJ , Quinton AE , Lanzarone V , Martin A , Benzie R , Nanan R
Published: December 2015

Objective

To assess maternal abdominal subcutaneous fat thickness (SFT) measured by ultrasound as an independent predictor of adverse pregnancy outcomes.

Design

A prospective longitudinal cohort study performed on pregnancies delivered between 2012 and 2014.

Setting

Sydney, Australia.

Population

About 1510 pregnant women attending routine obstetric ultrasounds.

Methods

Maternal SFT was measured on routine ultrasounds at 11–14 weeks’ gestation (SFT1) and 18–22 weeks’ gestation (SFT2). SFT measurements were assessed for estimating risks for obesity‐related pregnancy outcomes using logistic regression modelling adjusted for maternal age, parity, smoking status and body mass index (BMI).

Main outcome measures

Hypertensive disease, gestational diabetes, caesarean section, low birthweight, preterm delivery, neonatal respiratory distress, Apgar scores, and admission to a neonatal intensive care unit.

Results

SFT1 and SFT2 were measured on 1461 and 1363 women, respectively. Mean thickness (range) were 21.2 mm (6.9–73.9) for SFT1 and 20.3 mm (7.5–68.0) for SFT2. Complete outcome data were available for 1385 pregnancies. In all, 54% of the women were overweight/obese. The SFT measures decreased from early to mid‐pregnancy in overweight/obese women. There was moderate correlation between BMI and SFT1 (R2 = 0.56) and BMI and SFT2 (R2 = 0.55). In a multivariate model, SFT1 and SFT2 were better predictors for adverse pregnancy outcomes than BMI.

Conclusion

Maternal SFT is a significant independent predictor of adverse pregnancy outcomes. Incorporation of SFT into future models for adverse pregnancy outcome may prove valuable.

Tweetable abstract

Maternal abdominal ultrasound fat thickness measurement predicts adverse pregnancy outcomes.
Antenatal dietary and lifestyle advice for women who are overweight or obese and the effect on fetal growth and adiposity: the LIMIT randomised trial
Authors: Grivell RM , Yelland LN , Deussen A , Crowther CA , Dodd JM
Published: December 2015

Objective

To report the influence of maternal overweight and obesity on fetal growth and adiposity and effects of an antenatal dietary and lifestyle intervention among these women on measures of fetal growth and adiposity as secondary outcomes of the LIMIT Trial.

Design

Randomised controlled trial.

Setting

Public maternity hospitals in metropolitan Adelaide, South Australia.

Population

Pregnant women with a body mass index ≥ 25 kg/m2, and singleton gestation between 10+0 and 20+0 weeks.

Methods

Women were randomised to Lifestyle Advice or continued Standard Care and offered two research ultrasound scans at 28 and 36 weeks of gestation.

Main outcome measures

Ultrasound measures of fetal growth and adiposity.

Results

For each fetal body composition parameter, mean Z‐scores were substantially higher when compared with population standards. Fetuses of women receiving Lifestyle Advice demonstrated significantly greater mean mid‐thigh fat mass, when compared with fetuses of women receiving Standard Care (adjusted difference in means 0.17; 95% CI 0.02–0.32; P = 0.0245). While subscapular fat mass increased between 28 and 36 weeks of gestation in fetuses in both treatment groups, the rate of adipose tissue deposition slowed among fetuses of women receiving Lifestyle Advice, when compared with fetuses of women receiving Standard Care (P = 0.0160). No other significant differences were observed.

Conclusions

These findings provide the first evidence of changes to fetal growth following an antenatal dietary and lifestyle intervention among women who are overweight or obese.

Tweetable abstract

Lifestyle advice for overweight and obese pregnant women modifies fetal body composition.
BJOG Editor's Choice
Authors: Chien Patrick
Published: December 2015

Deputy Editor‐in‐Chief, Dr Patrick Chien, discusses his top articles from this issue in an audio podcast available at https://soundcloud.com/bjog/january-editors-choice-2016
How reliable is the Ki‐67 cytological index in grading pancreatic neuroendocrine tumors? A meta‐analysis
Authors: Li Jun , Lin Jin Ping , Shi Liu Hong , Wang Wei Jia , Li Ai Qing , Si Jian Min , Chen Shu Jie
Published: December 2015

Objective

To investigate the accuracy of the cytological Ki‐67 index in distinguishing intermediate and high‐grade (G2 + G3) from low‐grade (G1) pancreatic neuroendocrine tumors (PNETs).

Methods

Two investigators independently searched databases to identify eligible studies using the following term: (‘Ki‐67’) AND (‘pancreatic endocrine tumor’ OR ‘pancreatic neuroendocrine tumor’ OR ‘pancreatic endocrine tumour’ OR ‘pancreatic neuroendocrine tumour’ OR ‘pancreatic endocrine tumors’ OR ‘pancreatic neuroendocrine tumors’ OR ‘pancreatic endocrine tumours’ OR ‘pancreatic neuroendocrine tumours’), and meta‐analysis was performed to calculate the pooled sensitivity, specificity, positive (PLR) and negative likelihood ratio (NLR), and diagnostic odds ratio (DOR).

Results

A total of 263 lesions from 13 studies were included in the study. The pooled sensitivity and specificity of Ki‐67 (cut‐off value: 2%) in the differential diagnosis of G2 + G3 from G1 PNETs were 64% and 87%, respectively. The pooled PLR, NLR and DOR were 3.96, 0.42 and 11.21, respectively. The area under the summary receiver operating characteristic curve (AUROC) was 0.8397. While the cut‐off value of Ki‐67 index was set as 5%, the sensitivity and specificity were increased up to 69% and 93%, respectively, and the AUROC was increased to 0.955.

Conclusion

The cytological Ki‐67 index is very useful in distinguishing intermediate and high‐grade from low‐grade PNETs, and a cut‐off value of 5% had a better predictive value compared with that of 2%.
Intraclonal genome diversity of the major Pseudomonas aeruginosa clones C and PA14
Authors: Fischer Sebastian , Klockgether Jens , Morán Losada Patricia , Chouvarine Philippe , Cramer Nina , Davenport Colin F. , Dethlefsen Sarah , Dorda Marie , Goesmann Alexander , Hilker Rolf , Mielke Samira , Schönfelder Torben , Suerbaum Sebastian , Türk Oliver , Woltemate Sabrina , Wiehlmann Lutz , Tümmler Burkhard
Published: December 2015

Bacterial populations differentiate at the subspecies level into clonal complexes. Intraclonal genome diversity was studied in 100 isolates of the two dominant Pseudomonas aeruginosa clones C and PA14 collected from the inanimate environment, acute and chronic infections. The core genome was highly conserved among clone members with a median pairwise within‐clone single nucleotide sequence diversity of 8 × 10−6 for clone C and 2 × 10−5 for clone PA14. The composition of the accessory genome was, on the other hand, as variable within the clone as between unrelated clones. Each strain carried a large cargo of unique genes. The two dominant worldwide distributed P. aeruginosa clones combine an almost invariant core with the flexible gain and loss of genetic elements that spread by horizontal transfer.
A model‐derived short‐term estimation method of effective size for small populations with overlapping generations
Authors: Grimm Annegret , Gruber Bernd , Hoehn Marion , Enders Katrin , Henle Klaus
Published: December 2015

If not actively managed, small and isolated populations lose their genetic variability and the inbreeding rate increases. Combined, these factors limit the ability of populations to adapt to environmental changes, increasing their risk of extinction. The effective population size (Ne) is proportional to the loss of genetic diversity and therefore of considerable conservation relevance. However, estimators of Ne that account for demographic parameters in species with overlapping generations require sampling of populations across generations, which is often not feasible in long‐lived species.

We created an individual‐based model that allows calculation of Ne based on demographic parameters that can be obtained in a time period much shorter than a generation. It can be adapted to every life‐history parameter combination. The model is freely available as an r‐package NEff.

The model was first used in a simulation experiment observing changes in Ne in response to different degrees of generational overlap. Results showed that increased generational overlap slowed annual rates of heterozygosity loss, resulting in higher annual effective sizes (Ny) but decreased Ne per generation. Adding the effect of different recruitment rates only affected Ne for populations with low generational overlap.

The model was further tested using real population data of the Australian arboreal gecko Gehyra variegata. Simulation results were compared to genetic analyses and matched estimates of the real population very well.

Unlike other estimation methods of Ne, NEff neither requires long time series of population monitoring nor genetic analyses of changes in gene frequencies. Thus, it seems to be the first method for calculating Ne within short time periods and comparably low costs facilitating the use of Ne in applied conservation and management.
Intracavernous delivery of clonal mesenchymal stem cells rescues erectile function in the streptozotocin‐induced diabetic mouse
Authors: Ryu J.‐K. , Kim D.‐H. , Song K.‐M. , Ryu D.‐S. , Kim S.‐N. , Shin D.‐H. , Yi T. , Suh J.‐K. , Song S. U.
Published: December 2015

The major hurdle for the clinical application of stem cell therapy is the heterogeneous nature of the isolated cells, which may cause different treatment outcomes. The aim of this study was to examine the effectiveness of mouse clonal bone marrow‐derived stem cells (BMSCs) obtained from a single colony by using subfractionation culturing method for erectile function in diabetic animals. Twelve‐week‐old C57BL/6J mice were divided into four groups: controls, diabetic mice, and diabetic mice treated with a single intracavernous injection of PBS (20 μL) or clonal BMSCs (3 × 105 cells/20 μL). Clonal BMSCs were isolated from 5‐week‐old C3H mice. Two weeks after treatment, erectile function was measured by electrical stimulation of the cavernous nerve. The penis was stained with antibodies to PECAM‐1, smooth muscle α‐actin, neuronal nitric oxide synthase (nNOS), neurofilament, and phosphorylated endothelial NOS (phospho‐eNOS). We also performed Western blot for phospho‐eNOS, and eNOS in the corpus cavernosum tissue. Local delivery of clonal BMSCs significantly restored cavernous endothelial and smooth muscle cell contents, and penile nNOS and neurofilament contents, and induced eNOS phosphorylation (Ser1177) in diabetic mice. Intracavernous injection of clonal BMSCs induced significant recovery of erectile function, which reached 80–90% of the control values. Clonal BMSCs successfully restored erectile function through dual angiogenic and neurotrophic effects in diabetic mice. The homogenous nature of clonal mesenchymal stem cells may allow their clinical applications and open a new avenue through which to treat diabetic erectile dysfunction.
No increased risk of coronary heart disease for patients receiving androgen deprivation therapy for prostate cancer in Chinese/Taiwanese men
Authors: Wang L. H. , Liu C. K. , Chen C. H. , Kao L. T. , Lin H. C. , Huang C. Y.
Published: December 2015

The relationship between androgen deprivation therapy (ADT) and coronary heart disease (CHD) remains controversial. Furthermore, the majority of such studies focused on Caucasian populations, and there is still a paucity of studies among Asian populations. This population‐based study aimed to investigate the relationship between ADT and CHD in an ethnic Chinese (i.e., Taiwanese) population. We used data sourced from the Taiwan ‘Longitudinal Health Insurance Database'. This study included 1278 patients with prostate cancer in the study group and 1278 subjects without prostate cancer in the comparison group. Each patient was individually tracked for a 3‐year period to identify those who had subsequently received a diagnosis of CHD. The results showed that the incidence rate of CHD during the 3‐year follow‐up period was 4.69 (95% CI: 2.99–5.48) per 100 person‐years and 2.67 (95% CI: 2.15–3.27) per 100 person‐years for the study and comparison cohort, respectively. The Cox proportional hazard regression showed that the hazard ratio for CHD during the 3‐year follow‐up period for prostate cancer patients was 1.65 (95% confidence interval (CI) = 1.25–2.16) compared with comparison subjects after adjusting for patients' geographic location, monthly income, urbanization level, hypertension, diabetes, hyperlipidemia, and stroke. However, we failed to find a significant difference in the adjusted hazard of CHD during the 3‐year follow‐up period between prostate cancer patients who did and those who did not receive ADT (hazard ratio = 1.12, 95% CI = 0.79–1.59). We concluded that prostate cancer but not ADT was significantly associated with CHD. In addition, a common cause of prostate cancer and coronary heart disease could exist.