bluuebunny/crossref_metadata_2025 huggingface dataset:
Which mothers receive a post partum home visit in Queensland, Australia? A cross-sectional retrospective study
Authors: Brodribb Wendy , Miller Yvette
Published: December 2014

Objective
Although home visiting in the early post partum period appears to have increased, there are limited data defining which women receive a visit and none that include Queensland. We aimed to investigate patterns of post partum home visiting in the public and private sectors in Queensland.

Methods
Data were collected via a retrospective cross-sectional survey of women birthing in Queensland between 1 February and 31 May 2010 at 4 months post partum (n = 6948). Logistic regression was used to assess associations between receiving a home visit and sociodemographic, clinical and hospital variables. Analyses were stratified by public and private birthing sector because of significant differences between sectors.

Results
Public sector women were more likely to receive a visit from a nurse or midwife (from the hospital or child health sector) within 10 days of hospital discharge (67.2%) than private sector women (7.2%). Length of hospital stay was associated with home visiting in both sectors. Some vulnerable subpopulations in both sectors were more likely to be visited, whereas others were not.

Conclusions
Home visiting in Queensland varies markedly between the public and private sector and is less common in some vulnerable populations. Further consideration to improving the equity of community post partum care in Queensland is needed.

What is known about the topic?
A recent paper found that most women from the public sector in Victoria and South Australia receive an early post partum home visit from a midwife or nurse. Queensland only recently implemented a program to increase post partum home visiting but who receives visits is still unknown.

What does this paper add?
No previous study has investigated which women receive early post partum home visits in Queensland, nor home visiting rates within the private sector. This paper also examines whether specific subpopulations of vulnerable post partum women are receiving home visits so that patterns of inequity or unmet needs can be identified.

What are the implications for practitioners?
Home visiting by nurses or midwives in the post partum period in Queensland was less common than in other Australian states, and varies markedly between the public and private sector. These differences highlight inequities in community post partum care that need to be addressed if women are to receive the most cost-effective and clinically appropriate care and support in the post partum period.
Three Coordination Polymers Built by Methoxyphenyl Imidazole Dicarboxylate: Solvothermal Syntheses, Crystal Structures, and Properties
Authors: Dang Ming-An , Li Zi-Feng , Liu Ying , Li Gang
Published: December 2014

Three coordination polymers [Sr(p-H2MOPhIDC)2]n (1) (p-H3MOPhIDC = 2-p-methoxyphenyl-1H-imidazole-4,5-dicarboxylic acid), {[Cd2(p-HMOPhIDC)2(4,4′-bipy)]⋅H2O}n (4,4′-bipy = 4,4′-bipyridine) (2), and [Zn(p-HMOPhIDC)(4,4′-bipy)]n (3) have been solvothermally synthesized, and structurally characterized by single-crystal X-ray diffraction. Polymer 1 indicates a three-dimensional framework, which can be simplified as a 6-connected lattice. Polymer 2 is also a three-dimensional framework, and contains mixed bridging ligands HMOPhIDC2– and 4,4′-bipy. Polymer 3 exhibits a sheet structure bearing infinite rectangles. The coordination modes of the p-H3MOPhIDC ligand, and the thermal and solid-state photoluminescence properties of the polymers have been investigated as well.
A Straightforward and Practical Approach to Chiral Inducer: (2R,3R)-1,4-Dimethoxy-1,1,4,4-tetraphenylbutane-2,3-diol
Authors: Xie Jin-Sheng , Hu Xiao-Yun , Shan Zi-Xing , Zhou Zhong-Qiang
Published: December 2014

A straightforward and practical access to chiral inducer (2R,3R)-1,4- dimethoxyl-1,1,4,4-tetraphenyl-2,3-diol has been developed. It is based on highly regioselective 2,3-cyclosulfitation of (2R,3R)-1,1,4,4-tetraphenyl-butanetetraol, in which selective protection of the secondary hydroxyls and chlorination of the tertiary hydroxyls of (2R,3R)-1,1,4,4-tetraphenyl-butanetetraol are accomplished via one step. In the preparation, methanol was used as a methylating reagent and common alkali liquor was used for cleavage of the protection group. It may be one of the most straightforward and practical syntheses of the title compound.
Synthesis of Dichotomin A: Use of a Penicillamine-Derived Pseudoproline to Furnish Native Valine Residues
Authors: Wong Michelle S. Y. , Taleski Deni , Jolliffe Katrina A.
Published: December 2014

The total synthesis of cyclic hexapeptide dichotomin A from linear peptide precursors containing penicillamine-derived pseudoproline residues is reported. The incorporation of a pseudoproline residue led to a faster reaction and higher head-to-tail cyclization yields in comparison to linear precursors containing the native valine residue. However, deprotection of the pseudoproline resulted in significant amounts of a by-product in which a threonine side chain had undergone dehydration, resulting in a low overall yield of the natural product.
Feasibility and acceptability of point-of-care testing for sexually transmissible infections among men and women in mobile van settings
Authors: Hesse Elizabeth A. , Widdice Lea E. , Patterson-Rose Sherine A. , St. Cyr Sarah , Dize Laura , Gaydos Charlotte A.
Published: December 2014

To demonstrate the feasibility and acceptability of mobile point-of-care and near-patient testing for sexually transmissible infections, we offered services during an annual community event and surveyed event-goers. Forty-two participants were tested. When provided with options, the majority of participants chose point-of-care or near-patient testing. Trichomoniasis, chlamydia and gonorrhea were detected. All but one infected participant were notified and prescribed treatment. Participants responding to a written questionnaire reported sample self-collection and testing in a van as acceptable, although men reported self-collection in a van as less acceptable than a doctor’s office. Providing mobile point-of-care and near-patient sexually transmitted infection testing to the general population is feasible and acceptable.
Precisely cyclic sand: Self-organization of periodically sheared frictional grains
Authors: Royer John R. , Chaikin Paul M.
Published: December 2014

Significance

Granular materials are used for a wide variety of technological applications in nearly every industry and also serve as an instructive prototype for far-from-equilibrium behavior. Although they have received considerable attention, there are few general guidelines describing how they collectively organize and yield under shear, especially in physically relevant frictional grains. Using simulations, we explore the response of granular packings to slow periodic shear, systematically varying both the friction and shear. We discover a previously unidentified state in which the otherwise chaotic motion gives way to a precisely repetitive limit cycle for each individual grain. Understanding how grains self-organize into stable, periodic limit cycle configurations in this unlikely system foretells new approaches to understand yielding and memory formation in disordered materials.
Tuber physiological disorders.
Authors: Mikitzel L.
Published: December 2014

Defects in potato tubers that are brought about by unfavourable environmental factors that alter normal plant and tuber growth are called physiological disorders. The major causes of physiological disorders include improper cultural, storage or handling practices, high or low temperatures, and inadequate, excessive or uneven soil moisture or nutrient levels. Often, a disorder is caused by the combined effects of environment and cultural practices. Physiological disorders affect the external and internal appearance of tubers. Losses from many physiological disorders can be minimized by using good cultural practices that promote uniform plant and tuber growth over the course of the growing season, and by maintaining proper storage conditions. This chapter describes some tuber physiological disorders, including cracking, enlarged lenticels, greening, elephant hide, second growth, skinning and scald, pink eye, brown centre and hollow heart, bruise, blackheart, translucent end/jelly end, internal brown spot and heat necrosis, vascular discoloration, and internal anthocyanin discoloration.
Nutritional characteristics of potatoes.
Authors: Navarre D. , Goyer A. , Payyavula R. , Hellmann H.
Published: December 2014

This chapter describes the basic tuber composition and nutrient content, including minerals, vitamin C, glycoalkaloids, phenylpropanoids and carotenoids, of potato. It is shown that potatoes contain numerous health-promoting compounds in addition to complex carbohydrates. In view of their nutritional content and yields per acre, potatoes will almost certainly have a key role in "feeding the future".
Is it time to rollback dengue? - Mini Review.
Authors: Gubler D. J.
Published: December 2014

The past 40 years have seen a dramatic increase in the frequency, magnitude and geographic expansion of epidemic dengue, making it the most important vector-borne viral disease in the world. Mosquito control, the only option available for dengue control, has failed. New and innovative tools in the pipeline, however, may provide the opportunity to rollback this disease.
Coastwide Otolith Signatures of Juvenile Atlantic Menhaden, 2009–2011
Authors: Anstead Kristen A. , Schaffler Jason J. , Jones Cynthia M.
Published: December 2014

The Atlantic MenhadenBrevoortia tyrannusis a clupeid that plays a critical role in the marine food web and supports one of the largest fisheries on the U.S. East Coast. Along with a decrease in overall numbers and spawning stock biomass, recruitment levels have remained low since the 1990s. Atlantic Menhaden use numerous estuaries along the Atlantic coast for juvenile development before recruiting to the adult population, but the contribution of each of these nursery grounds is currently unknown. Chesapeake Bay is thought to contribute 70% of the total recruits, although this estimate is over 20 years old and predates current low recruitment levels. We investigated the potential of trace element (Li, Mg, Mn, Rb, Sr, Y, Ba, and Pb) and stable isotope ratio (δ13C and δ18O) signatures in otoliths to distinguish among Atlantic Menhaden collected from various nursery grounds along the U.S. Atlantic coast (Connecticut to South Carolina) during 2009–2011. Juveniles were classified to four regional nursery areas with nearly 90% accuracy. Due to significant interannual variation in the chemical signatures, our attempts to classify juveniles from adjacent year‐classes or combined year‐classes resulted in lower accuracy. However, this study provides a 3‐year library of geochemical fingerprints for assigning adults to their regions of origin. This research builds the foundation for a comprehensive estimate of Atlantic Menhaden recruitment rates from each of the major nursery areas along the U.S. Atlantic coast for 2009–2011.

Received May 28, 2014; accepted September 16, 2014
Cardiovascular fitness is associated with bias between self‐reported and objectively measured physical activity
Authors: Tomaz S. A. , Lambert E. V. , Karpul D. , Kolbe‐Alexander T. L.
Published: December 2014

The aim of this research study was to determine whether the level of agreement between self‐reported and objective measures of physical activity (PA) is influenced by cardiovascular fitness. Participants (n = 113) completed the Global Physical Activity Questionnaire (GPAQ), a health risk assessment and a sub‐maximal 12‐minute step test. Age‐predicted was used to classify participants as lower fit and higher fit (HF). ActiGraph (GT3X) accelerometers were worn for 7 consecutive days. Matthews cut points were used to calculate minutes of moderate and vigorous PA (MVPA) per week. Bland–Altman plots were used to measure limits of agreement between GPAQ and ActiGraph MVPA. The participants' mean age was 37.9 ± 12.7 years and more than 60% were categorised as HF (n = 71). Moderate PA was over‐reported in 39% of all participants. Most of the over‐reporters for moderate PA were in the HF group (64.1%). Vigorous PA was over‐reported by 72.6% of all participants. The discrepancy between self‐reported and objective measures of vigorous PA increased with increasing self‐reported time spent in vigorous PA. Fitter individuals appear to over‐report PA more than lesser fit participants, suggesting that fitness could influence the level of agreement between self‐reported and objective measures of PA.
Fast protein-depletion system utilizing tetracycline repressible promoter and N-end rule in yeast
Authors: Gnanasundram Sivakumar Vadivel , Koš Martin
Published: December 2014

A protein depletion by promoter shutoff or protein destabilization is an important tool in investigation of functions of essential genes. Various approaches using different repressible promoters, inducible degrons, or their combinations were developed. While successful, the current techniques have a drawback in that they require fusion of a large degradation tag to the target protein and/or a change in growth conditions to repress the promoter. We describe efficient protein depletion using the combination of a metabolically inert tetracycline repressible promoter with tetracycline aptamer and constitutive target protein destabilization by means of ubiquitin fusion. The target protein does not require a tag, and its elimination is several fold faster compared with standard promoter shutoff systems. A depletion time of <40 min was sufficient to achieve a robust phenotype.
Vertical mixing, critical depths, and phytoplankton growth in the Ross Sea
Authors: Smith Walker O. , Jones Randolph M.
Published: December 2014

Phytoplankton growth and biomass accumulation vary spatially and temporally in the Ross Sea, largely as a function of ice concentrations, vertical mixing depths, and iron concentrations. To assess the role of vertical mixing in bloom initiation, we used a high-resolution numerical model to estimate changes in mixed layer depths from October 1 through early December, the period where phytoplankton growth begins and biomass accumulates, and estimate critical depths for this period. Mixed layers in October ranged from the complete water column (>600 m) to ca. 200 m; over a 60-day period, the mixed layers decreased on average by 70%. Estimated critical depths were exceeded in October, but would allow growth to proceed in late October due to shoaling of mixed layer depths, consistent with the known onset of the spring bloom in the Ross Sea. We also analysed a series of stations sampled near the Ross Ice Shelf during January 2012. Mean vertical profiles for the stations indicated deep vertical mixing; mixed layer depths averaged 60 m and ranged up to 96 m. Chlorophyll concentrations within the mixed layer averaged 6.60 µg l−1, and the pigment contributions were dominated by Phaeocystis antarctica. We suggest that this mesoscale region near the ice shelf is elevated in phytoplankton biomass due to frequent mixing events that redistribute biomass to depth and replenish nutrients, which in turn are utilized by an assemblage capable of utilizing low mean irradiance levels. Thus, the deep mixed layers and high biomass concentrations represent growth over long periods under reduced mixing punctuated by short periods of deeper vertical mixing that redistribute biomass. Water column vertical mixing and phytoplankton biomass in the Ross Sea are consistent with the critical depth concept as originally proposed by Sverdrup.
Chemical and biological insecticides select distinct gene expression patterns in
Aedes aegypti
mosquito
Authors: Després Laurence , Stalinski Renaud , Faucon Frédéric , Navratil Vincent , Viari Alain , Paris Margot , Tetreau Guillaume , Poupardin Rodolphe , Riaz Muhammad Asam , Bonin Aurélie , Reynaud Stéphane , David Jean-Philippe
Published: December 2014

Worldwide evolution of mosquito resistance to chemical insecticides represents a major challenge for public health, and the future of vector control largely relies on the development of biological insecticides that can be used in combination with chemicals (integrated management), with the expectation that populations already resistant to chemicals will not become readily resistant to biological insecticides. However, little is known about the metabolic pathways affected by selection with chemical or biological insecticides. Here we show that
Aedes aegypti
, a laboratory mosquito strain selected with a biological insecticide (
Bacillus thuringiensis israelensis
, Bti) evolved increased transcription of many genes coding for endopeptidases while most genes coding for detoxification enzymes were under-expressed. By contrast, in strains selected with chemicals, genes encoding detoxification enzymes were mostly over-expressed. In all the resistant strains, genes involved in immune response were under-transcribed, suggesting that basal immunity might be a general adjustment variable to compensate metabolic costs caused by insecticide selection. Bioassays generally showed no evidence for an increased susceptibility of selected strains towards the other insecticide type, and all chemical-resistant strains were as susceptible to Bti as the unselected parent strain, which is a good premise for sustainable integrated management of mosquito populations resistant to chemicals.
Population properties affect inbreeding avoidance in moose
Authors: Herfindal Ivar , Haanes Hallvard , Røed Knut H. , Solberg Erling J. , Markussen Stine S. , Heim Morten , Sæther Bernt-Erik
Published: December 2014

Mechanisms reducing inbreeding are thought to have evolved owing to fitness costs of breeding with close relatives. In small and isolated populations, or populations with skewed age- or sex distributions, mate choice becomes limited, and inbreeding avoidance mechanisms ineffective. We used a unique individual-based dataset on moose from a small island in Norway to assess whether inbreeding avoidance was related to population structure and size, expecting inbreeding avoidance to be greater in years with larger populations and even adult sex ratios. The probability that a potential mating event was realized was negatively related to the inbreeding coefficient of the potential offspring, with a stronger relationship in years with a higher proportion or number of males in the population. Thus, adult sex ratio and population size affect the degree of inbreeding avoidance. Consequently, conservation managers should aim for sex ratios that facilitate inbreeding avoidance, especially in small and isolated populations.
Network morphospace
Authors: Avena-Koenigsberger Andrea , Goñi Joaquín , Solé Ricard , Sporns Olaf
Published: December 2014

The structure of complex networks has attracted much attention in recent years. It has been noted that many real-world examples of networked systems share a set of common architectural features. This raises important questions about their origin, for example whether such network attributes reflect common design principles or constraints imposed by selectional forces that have shaped the evolution of network topology. Is it possible to place the many patterns and forms of complex networks into a common space that reveals their relations, and what are the main rules and driving forces that determine which positions in such a space are occupied by systems that have actually evolved? We suggest that these questions can be addressed by combining concepts from two currently relatively unconnected fields. One is theoretical morphology, which has conceptualized the relations between morphological traits defined by mathematical models of biological form. The second is network science, which provides numerous quantitative tools to measure and classify different patterns of local and global network architecture across disparate types of systems. Here, we explore a new theoretical concept that lies at the intersection between both fields, the ‘network morphospace’. Defined by axes that represent specific network traits, each point within such a space represents a location occupied by networks that share a set of common ‘morphological’ characteristics related to aspects of their connectivity. Mapping a network morphospace reveals the extent to which the space is filled by existing networks, thus allowing a distinction between actual and impossible designs and highlighting the generative potential of rules and constraints that pervade the evolution of complex systems.
Ocean acidification alters the material properties of
Mytilus edulis
shells
Authors: Fitzer Susan C. , Zhu Wenzhong , Tanner K. Elizabeth , Phoenix Vernon R. , Kamenos Nicholas A. , Cusack Maggie
Published: December 2014

Ocean acidification (OA) and the resultant changing carbonate saturation states is threatening the formation of calcium carbonate shells and exoskeletons of marine organisms. The production of biominerals in such organisms relies on the availability of carbonate and the ability of the organism to biomineralize in changing environments. To understand how biomineralizers will respond to OA the common blue mussel,
Mytilus edulis
, was cultured at projected levels of
p
CO
2
(380, 550, 750, 1000 µatm) and increased temperatures (ambient, ambient plus 2°C). Nanoindentation (a single mussel shell) and microhardness testing were used to assess the material properties of the shells. Young's modulus (
E
), hardness (
H
) and toughness (
K
IC
) were measured in mussel shells grown in multiple stressor conditions. OA caused mussels to produce shell calcite that is stiffer (higher modulus of elasticity) and harder than shells grown in control conditions. The outer shell (calcite) is more brittle in OA conditions while the inner shell (aragonite) is softer and less stiff in shells grown under OA conditions. Combining increasing ocean
p
CO
2
and temperatures as projected for future global ocean appears to reduce the impact of increasing
p
CO
2
on the material properties of the mussel shell. OA may cause changes in shell material properties that could prove problematic under predation scenarios for the mussels; however, this may be partially mitigated by increasing temperature.
The collecting activities of James Cuninghame FRS on the voyage of
Tuscan
to China (Amoy) between 1697 and 1699
Authors: Jarvis Charles E. , Oswald Philip H.
Published: December 2014

James Cuninghame's visit to China (1697–99) yielded a great deal of valuable information on both natural and artificial objects as well as items of contemporaneous trade interest (for example china clay and a scarlet dye). However, the circumstances surrounding the voyage have long been unclear. Although it has previously been assumed that Cuninghame must have travelled on an East India Company vessel, it now seems that he was aboard
Tuscan
, one of two private trading ships (interlopers) bound for Amoy under the command of Henry Gough. After an incident in La Palma (Canary Islands), only
Tuscan
proceeded to China after her release by the Spanish authorities. Study of surviving correspondence between Cuninghame and a Canarian cleric, Juan Bautista Poggio, has contributed to a better understanding of the events in the early part of the voyage. Cuninghame made extensive natural history collections during the six months that
Tuscan
remained in Amoy, before returning to England in 1699, where his specimens delighted his London supporters, James Petiver and Hans Sloane.
Nickel hydroxides and related materials: a review of their structures, synthesis and properties
Authors: Hall David S. , Lockwood David J. , Bock Christina , MacDougall Barry R.
Published: December 2014

This review article summarizes the last few decades of research on nickel hydroxide, an important material in physics and chemistry, that has many applications in engineering including, significantly, batteries. First, the structures of the two known polymorphs, denoted asα-Ni(OH)2andβ-Ni(OH)2, are described. The various types of disorder, which are frequently present in nickel hydroxide materials, are discussed including hydration, stacking fault disorder, mechanical stresses and the incorporation of ionic impurities. Several related materials are discussed, including intercalatedα-derivatives and basic nickel salts. Next, a number of methods to prepare, or synthesize, nickel hydroxides are summarized, including chemical precipitation, electrochemical precipitation, sol–gel synthesis, chemical ageing, hydrothermal and solvothermal synthesis, electrochemical oxidation, microwave-assisted synthesis, and sonochemical methods. Finally, the known physical properties of the nickel hydroxides are reviewed, including their magnetic, vibrational, optical, electrical and mechanical properties. The last section in this paper is intended to serve as a summary of both the potentially useful properties of these materials and the methods for the identification and characterization of ‘unknown’ nickel hydroxide-based samples.
Cardiac function in an endothermic fish: cellular mechanisms for overcoming acute thermal challenges during diving
Authors: Shiels H. A. , Galli G. L. J. , Block B. A.
Published: December 2014

Understanding the physiology of vertebrate thermal tolerance is critical for predicting how animals respond to climate change. Pacific bluefin tuna experience a wide range of ambient sea temperatures and occupy the largest geographical niche of all tunas. Their capacity to endure thermal challenge is due in part to enhanced expression and activity of key proteins involved in cardiac excitation–contraction coupling, which improve cardiomyocyte function and whole animal performance during temperature change. To define the cellular mechanisms that enable bluefin tuna hearts to function during acute temperature change, we investigated the performance of freshly isolated ventricular myocytes using confocal microscopy and electrophysiology. We demonstrate that acute cooling and warming (between 8 and 28°C) modulates the excitability of the cardiomyocyte by altering the action potential (AP) duration and the amplitude and kinetics of the cellular Ca2+transient. We then explored the interactions between temperature, adrenergic stimulation and contraction frequency, and show that when these stressors are combined in a physiologically relevant way, they alter AP characteristics to stabilize excitation–contraction coupling across an acute 20°C temperature range. This allows the tuna heart to maintain consistent contraction and relaxation cycles during acute thermal challenges. We hypothesize that this cardiac capacity plays a key role in the bluefin tunas' niche expansion across a broad thermal and geographical range.
Experimental defaunation of terrestrial mammalian herbivores alters tropical rainforest understorey diversity
Authors: Camargo-Sanabria Angela A. , Mendoza Eduardo , Guevara Roger , Martínez-Ramos Miguel , Dirzo Rodolfo
Published: December 2014

It has been suggested that tropical defaunation may unleash community-wide cascading effects, leading to reductions in plant diversity. However, experimental evidence establishing cause–effect relationships thereof is poor. Through a 5 year exclosure experiment, we tested the hypothesis that mammalian defaunation affects tree seedling/sapling community dynamics leading to reductions in understorey plant diversity. We established plot triplets (
n
= 25) representing three defaunation contexts: terrestrial-mammal exclosure (TE), medium/large mammal exclosure (PE) and open access controls (C). Seedlings/saplings 30–100 cm tall were marked and identified within each of these plots and re-censused three times to record survival and recruitment. In the periods 2010–2011 and 2011–2013, survival was greater in PE than in C plots and recruitment was higher in TE plots than in C plots. Overall, seedling density increased by 61% in TE plots and 23% in PE plots, whereas it decreased by 5% in C plots. Common species highly consumed by mammals (e.g.
Brosimum alicastrum
and
Ampelocera hottlei
) increased in their abundance in TE plots. Rarefaction curves showed that species diversity decreased in TE plots from 2008 to 2013, whereas it remained similar for C plots. Given the prevalence of tropical defaunation, we posit this is an anthropogenic effect threatening the maintenance of tropical forest diversity.
Mutualism between co-introduced species facilitates invasion and alters plant community structure
Authors: Prior Kirsten M. , Robinson Jennifer M. , Meadley Dunphy Shannon A. , Frederickson Megan E.
Published: December 2014

Generalized mutualisms are often predicted to be resilient to changes in partner identity. Variation in mutualism-related traits between native and invasive species however, can exacerbate the spread of invasive species (‘invasional meltdown’) if invasive partners strongly interact. Here we show how invasion by a seed-dispersing ant (
Myrmica rubra
) promotes recruitment of a co-introduced invasive over native ant-dispersed (myrmecochorous) plants. We created experimental communities of invasive (
M. rubra
) or native ants (
Aphaenogaster rudis
) and invasive and native plants and measured seed dispersal and plant recruitment. In our mesocosms, and in laboratory and field trials,
M. rubra
acted as a superior seed disperser relative to the native ant. By contrast, previous studies have found that invasive ants are often poor seed dispersers compared with native ants. Despite belonging to the same behavioural guild, seed-dispersing ants were not functionally redundant. Instead, native and invasive ants had strongly divergent effects on plant communities: the invasive plant dominated in the presence of the invasive ant and the native plants dominated in the presence of the native ant. Community changes were not due to preferences for coevolved partners: variation in functional traits of linked partners drove differences. Here, we show that strongly interacting introduced mutualists can be major drivers of ecological change.
FORGE: A tool to discover cell specific enrichments of GWAS associated SNPs in regulatory regions
Authors: Dunham Ian , Kulesha Eugene , Iotchkova Valentina , Morganella Sandro , Birney Ewan
Published: December 2014

Genome wide association studies provide an unbiased discovery mechanism for numerous human diseases. However, a frustration in the analysis of GWAS is that the majority of variants discovered do not directly alter protein-coding genes. We have developed a simple analysis approach that detects the tissue-specific regulatory component of a set of GWAS SNPs by identifying enrichment of overlap with DNase I hotspots from diverse tissue samples. Functional element Overlap analysis of the Results of GWAS Experiments (FORGE) is available as a web tool and as standalone software and provides tabular and graphical summaries of the enrichments. Conducting FORGE analysis on SNP sets for 260 phenotypes available from the GWAS catalogue reveals numerous overlap enrichments with tissue–specific components reflecting the known aetiology of the phenotypes as well as revealing other unforeseen tissue involvements that may lead to mechanistic insights for disease.
The accurate assessment of small-angle X-ray scattering data
Authors: Grant Thomas D. , Luft Joseph R. , Carter Lester G. , Matsui Tsutomu , Weiss Thomas M. , Martel Anne , Snell Edward H.
Published: December 2014

Small-angle X-ray scattering (SAXS) has grown in popularity in recent times with the advent of bright synchrotron X-ray sources, powerful computational resources and algorithms enabling the calculation of increasingly complex models. However, the lack of standardized data-quality metrics presents difficulties for the growing user community in accurately assessing the quality of experimental SAXS data. Here, a series of metrics to quantitatively describe SAXS data in an objective manner using statistical evaluations are defined. These metrics are applied to identify the effects of radiation damage, concentration dependence and interparticle interactions on SAXS data from a set of 27 previously described targets for which high-resolution structures have been determinedviaX-ray crystallography or nuclear magnetic resonance (NMR) spectroscopy. The studies show that these metrics are sufficient to characterize SAXS data quality on a small sample set with statistical rigor and sensitivity similar to or better than manual analysis. The development of data-quality analysis strategies such as these initial efforts is needed to enable the accurate and unbiased assessment of SAXS data quality.
Uniqueness of models from small-angle scattering data: the impact of a hydration shell and complementary NMR restraints
Authors: Kim Henry S. , Gabel Frank
Published: December 2014

Small-angle scattering (SAS) has witnessed a breathtaking renaissance and expansion over the past 15 years regarding the determination of biomacromolecular structures in solution. While important issues such as sample quality, good experimental practice and guidelines for data analysis, interpretation, presentation, publication and deposition are increasingly being recognized, crucial topics such as the uniqueness, precision and accuracy of the structural models obtained by SAS are still only poorly understood and addressed. The present article provides an overview of recent developments in these fields with a focus on the influence of complementary NMR restraints and of a hydration shell on the uniqueness of biomacromolecular models. As a first topic, the impact of incorporating NMR orientational restraints in addition to SAS distance restraints is discussed using a quantitative visual representation that illustrates how the possible conformational space of a two-body system is reduced as a function of the available data. As a second topic, the impact of a hydration shell on modelling parameters of a two-body system is illustrated, in particular on its inter-body distance. Finally, practical recommendations are provided to take both effects into account and promising future perspectives of SAS approaches are discussed.
Memprot: a program to model the detergent corona around a membrane protein based on SEC–SAXS data
Authors: Pérez Javier , Koutsioubas Alexandros
Published: December 2014

The application of small-angle X-ray scattering (SAXS) to structural investigations of transmembrane proteins in detergent solution has been hampered by two main inherent hurdles. On the one hand, the formation of a detergent corona around the hydrophobic region of the protein strongly modifies the scattering curve of the protein. On the other hand, free micelles of detergent without a precisely known concentration coexist with the protein–detergent complex in solution, therefore adding an uncontrolled signal. To gain robust structural information on such systems from SAXS data, in previous work, advantage was taken of the online combination of size-exclusion chromatography (SEC) and SAXS, and the detergent corona around aquaporin-0, a membrane protein of known structure, could be modelled. A precise geometrical model of the corona, shaped as an elliptical torus, was determined. Here, in order to better understand the correlations between the corona model parameters and to discuss the uniqueness of the model, this work was revisited by analyzing systematic SAXS simulations over a wide range of parameters of the torus.
ISPyB for BioSAXS, the gateway to user autonomy in solution scattering experiments
Authors: De Maria Antolinos Alejandro , Pernot Petra , Brennich Martha E. , Kieffer Jérôme , Bowler Matthew W. , Delageniere Solange , Ohlsson Staffan , Malbet Monaco Stephanie , Ashton Alun , Franke Daniel , Svergun Dmitri , McSweeney Sean , Gordon Elspeth , Round Adam
Published: December 2014

Logging experiments with the laboratory-information management system ISPyB (Information System for Protein crystallography Beamlines) enhances the automation of small-angle X-ray scattering of biological macromolecules in solution (BioSAXS) experiments. The ISPyB interface provides immediate user-oriented online feedback and enables data cross-checking and downstream analysis. To optimize data quality and completeness, ISPyBB (ISPyB for BioSAXS) makes it simple for users to compare the results from new measurements with previous acquisitions from the same day or earlier experiments in order to maximize the ability to collect all data required in a single synchrotron visit. The graphical user interface (GUI) of ISPyBB has been designed to guide users in the preparation of an experiment. The input of sample information and the ability to outline the experimental aims in advance provides feedback on the number of measurements required, calculation of expected sample volumes and time needed to collect the data: all of this information aids the users to better prepare for their trip to the synchrotron. A prototype version of the ISPyBB database is now available at the European Synchrotron Radiation Facility (ESRF) beamline BM29 and is already greatly appreciated by academic users and industrial clients. It will soon be available at the PETRA III beamline P12 and the Diamond Light Source beamlines I22 and B21.
In pursuit of an accurate spatial and temporal model of biomolecules at the atomistic level: a perspective on computer simulation
Authors: Gray Alan , Harlen Oliver G. , Harris Sarah A. , Khalid Syma , Leung Yuk Ming , Lonsdale Richard , Mulholland Adrian J. , Pearson Arwen R. , Read Daniel J. , Richardson Robin A.
Published: December 2014

Despite huge advances in the computational techniques available for simulating biomolecules at the quantum-mechanical, atomistic and coarse-grained levels, there is still a widespread perception amongst the experimental community that these calculations are highly specialist and are not generally applicable by researchers outside the theoretical community. In this article, the successes and limitations of biomolecular simulation and the further developments that are likely in the near future are discussed. A brief overview is also provided of the experimental biophysical methods that are commonly used to probe biomolecular structure and dynamics, and the accuracy of the information that can be obtained from each is compared with that from modelling. It is concluded that progress towards an accurate spatial and temporal model of biomacromolecules requires a combination of all of these biophysical techniques, both experimental and computational.
Piketty's challenge for sociology
Authors: Savage Mike
Published: December 2014

This paper argues that Piketty's book should not simply be seen as that of an economist, but that it contains significant resources for sociologists to draw upon. These are firstly, this approach to social science and his use of visualizations which chime closely with recent claims about the power of description. Secondly I consider his conceptualization of time and history – which in rebutting epochal arguments about the speed of contemporary change allows for a much better appreciation of the ‘long durée’; and finally his conceptualization of social classes and privilege through his elaboration of a sociology of accumulation and inheritance. In all these ways, Piketty's work assists in developing an account of elites and wealth which should be highly productive for future sociology.
Capital in the twenty‐first century: a critique
Authors: Soskice David
Published: December 2014

I set out and explain Piketty's model of the dynamics of capitalism based on two equations and the r > g inequality (his central contradiction of capitalism). I then take issue with Piketty's analysis of the rebuilding of inequality from the 1970s to the present on three grounds: First, his model is based on the (neo‐classical) assumption that companies are essentially passive actors who invest the amount savers choose to accumulate at equilibrium output – leading to the counterintuitive result that companies respond to the secular fall in growth (and hence their product markets) from the 1970s on by increasing their investment relative to output; this does indeed imply increased inequality on Piketty's β measure, the ratio of capital to output. I suggest a more realistic model in which businesses determine investment growth based on their expectations of output growth, with monetary policy bringing savings into line with business‐determined investment; the implication of this model is that β does not change at all. And in fact as other recent empirical work which I reference has noted, β has not changed significantly over these recent decades. Hence Piketty's central analysis of the growth of contemporary inequality requires rethinking. Second, despite many references to the need for political economic analysis, Piketty's analysis of the growth of inequality in the period from the 1970s to the present is almost devoid of it, his explanatory framework being purely mathematical. I sketch what a political economic framework might look like during a period when politics was central to inequality. Third, inequality in fact rose on a variety of dimensions apart from β (including poverty which Piketty virtually makes no reference to in this period), but it is unclear what might explain why inequality rose in these other dimensions.
Gendering inequality: a note on Piketty's Capital in the Twenty‐First Century
Authors: Perrons Diane
Published: December 2014

Thomas Piketty's Capital in the Twenty‐First Century is remarkable for moving inequality from the margins to mainstream debate through detailed analysis of longitudinal statistics and, for an economist, by advocating an interdisciplinary perspective and writing in a witty and accessible style. With reference to the post 1970 period, when wage increases are largely responsible for the increase in inequality, Piketty shows how patrimonial capitalists (elite managers) in the top decile and centile of the distribution appropriate a growing share of social wealth as a consequence of their ‘power to set their own remuneration’ in the context of tolerant social norms rather than through their productive contributions. Piketty raises but defers the question of where these social norms come from to other disciplines. A Feminist Economics perspective indicates that these questions are central to a more inclusive form of economic analysis and such an approach would enrich Piketty's analysis in two main ways. First, by paying greater attention to the processes and social norms through which inequalities are produced and justified and second by highlighting the ways in which inequality is experienced differently depending not only on class, but also on other aspects of identity including gender. This approach also suggests that it is necessary to supplement the ex‐post redistributive policies recommended by Piketty: a global wealth tax and more steeply progressive income tax, with ex‐ante measures to stop the rise in wage inequality in the first place, especially by bridging the huge gulf that exists between those who care for people and those who manage money.
Detection and decay rates of prey and prey symbionts in the gut of a predator through metagenomics
Authors: Paula Débora P. , Linard Benjamin , Andow David A. , Sujii Edison R. , Pires Carmen S. S. , Vogler Alfried P.
Published: December 2014

DNA methods are useful to identify ingested prey items from the gut of predators, but reliable detection is hampered by low amounts of degraded DNA. PCR‐based methods can retrieve minute amounts of starting material but suffer from amplification biases and cross‐reactions with the predator and related species genomes. Here, we use PCR‐free direct shotgun sequencing of total DNA isolated from the gut of the harlequin ladybird Harmonia axyridis at five time points after feeding on a single pea aphid Acyrthosiphon pisum. Sequence reads were matched to three reference databases: Insecta mitogenomes of 587 species, including H. axyridis sequenced here; A. pisum nuclear genome scaffolds; and scaffolds and complete genomes of 13 potential bacterial symbionts. Immediately after feeding, multicopy mtDNA of A. pisum was detected in tens of reads, while hundreds of matches to nuclear scaffolds were detected. Aphid nuclear DNA and mtDNA decayed at similar rates (0.281 and 0.11 h−1 respectively), and the detectability periods were 32.7 and 23.1 h. Metagenomic sequencing also revealed thousands of reads of the obligate Buchnera aphidicola and facultative Regiella insecticola aphid symbionts, which showed exponential decay rates significantly faster than aphid DNA (0.694 and 0.80 h−1, respectively). However, the facultative aphid symbionts Hamiltonella defensa, Arsenophonus spp. and Serratia symbiotica showed an unexpected temporary increase in population size by 1–2 orders of magnitude in the predator guts before declining. Metagenomics is a powerful tool that can reveal complex relationships and the dynamics of interactions among predators, prey and their symbionts.
Who uses methadone services in China? Monitoring the world's largest methadone programme
Authors: Sullivan Sheena G. , Wu Zunyou , Rou Keming , Pang Lin , Luo Wei , Wang Changhe , Cao Xiaobin , Yin Wenyuan , Liu Enwu , Mi Guodong ,   National Methadone Maintenance Treatment Working Group
Published: December 2014

Aims

To describe the data collected by the Chinese methadone maintenance treatment (MMT) system and the characteristics of clients entering the programme.

Design

Descriptive study using routinely collected data from the MMT data management system for the period March 2004 and March 2010.

Setting

All MMT clinics in China.

Participants

Clients who enrolled for services between March 2004 and March 2010.

Measurements

Routinely collected data included: demographic information; drug use, sexual and criminal behaviours; status of infection with human immunodeficiency virus (HIV), hepatitis C virus (HCV) and syphilis; random urine‐opiate test results; and the daily methadone dose received. Differences among clients by year were examined.

Findings

During the period examined, there were 251 974 clients attending 684 clinics in 27 provinces. Overall, the mean age was 34.4 years, 83.8% were male, 70.2% were unemployed, 75% had ever injected drugs, 17% had shared needles and 7.4% were HIV‐positive. The profile of clients changed over time, with fewer HIV‐positive individuals, fewer injecting drug users, fewer needle‐sharers, fewer females and fewer unemployed. Half the clients dropped out within 6 months. The average final dose received was 49.4 mg. The estimated probability of interrupting treatment before 6 months was 52.5%.

Conclusions

The profile of clients enrolling in methadone maintenance treatment in China is continually changing and appears to be associated with reduced risk of HIV. High dropout in the programme may limit its effectiveness. The availability of a centralized, real‐time data system was extremely useful for monitoring the progress of the Chinese methadone maintenance treatment programme.