bluuebunny/crossref_metadata_2025 huggingface dataset:
MetaQuery: a web server for rapid annotation and quantitative analysis of specific genes in the human gut microbiome
Authors: Nayfach Stephen , Fischbach Michael A. , Pollard Katherine S.
Published: June 2015

Summary: Microbiome researchers frequently want to know how abundant a particular microbial gene or pathway is across different human hosts, including its association with disease and its co-occurrence with other genes or microbial taxa. With thousands of publicly available metagenomes, these questions should be easy to answer. However, computational barriers prevent most researchers from conducting such analyses. We address this problem with MetaQuery, a web application for rapid and quantitative analysis of specific genes in the human gut microbiome. The user inputs one or more query genes, and our software returns the estimated abundance of these genes across 1267 publicly available fecal metagenomes from American, European and Chinese individuals. In addition, our application performs downstream statistical analyses to identify features that are associated with gene variation, including other query genes (i.e. gene co-variation), taxa, clinical variables (e.g. inflammatory bowel disease and diabetes) and average genome size. The speed and accessibility of MetaQuery are a step toward democratizing metagenomics research, which should allow many researchers to query the abundance and variation of specific genes in the human gut microbiome.

Availability and implementation:  http://metaquery.docpollard.org.

Contact:  snayfach@gmail.com

Supplementary information:  Supplementary data are available at Bioinformatics online.
Lobsters: ocean icons in changing times
Authors: Briones-Fourzán Patricia , Lozano-Álvarez Enrique
Published: June 2015

The 10th International Conference and Workshop on Lobster Biology and Management was held in Cancún, Mexico, in May 2014. The papers included in this supplementary issue of the ICES Journal of Marine Science are a sample of the multidisciplinary nature of the conference and provide new knowledge of the biology, ecology, fisheries, and management and aquaculture of clawed, spiny, and slipper lobsters. The emphasis of the conference was climate change and its consequences for lobster biology, population dynamics, ecology, and fisheries. As noted in several papers, climate change is already affecting different lobster species by altering growth rates, sizes at maturity, the timing of reproductive processes, duration of larval development, and the timing and levels of settlement; by affecting key benthic habitat-forming species in settlement habitats; by increasing the risk of disease and impacting the behavioural ecology of lobsters, and by changing the spatial distribution of the stocks and, hence, affecting catches and the territorial behaviour of fishers. Other issues addressed at the conference included aquaculture and enhancement—the holy grails of lobster management—sustainable management strategies, and a fascinating review of the use of lobsters through human history. In addition to their economic importance, lobsters continue to provide valuable information to understand different marine environments in a changing climate.
Stocking is essential to meet the silver eel escapement target in a river system with currently low natural recruitment
Authors: Brämick Uwe , Fladung Erik , Simon Janek
Published: June 2015

Under the European Eel Regulation EG 1100/2007, Member States exhibiting natural habitats for the European eel (Anguilla anguilla) on their territory are obliged to prepare Eel Management Plans (EMP) containing appropriate measures to safeguard the escapement of a river system specific silver eel target biomass. Stocking is one management option to reach this target. We used various methodical approaches to study population parameters in a large lowland river under the application of a multi-annual intense stocking programme. The approaches were used to further enhance modelling of stock dynamics and silver eel escapement, in particular. Parameterizing the German Eel Model III (GEM III) with values and functions obtained for recruitment, growth, and mortality resulted in an annual escapement estimate of roughly 32 000–64 000 silver eels from 2010 to 2012. Escapement estimates based on a mark-recapture study conducted in parallel revealed somewhat lower values (11 000–25 000) for the same years. In view of the small number of natural recruits, such values are only contingent if stocking had a profound effect on silver eel production. Results from modelling annual silver eel escapement values indicate that escapement targets set in the EMP for this tributary cannot be reached without stocking. This constellation is likely to apply to other Eel Management Units with low current natural immigration values as well, and might be considered a key dilemma in eel management in such catchments due to the current confusion whether translocation of recruits yields a net benefit to the panmictic stock of the European eel.
Design and implementation of a privacy preserving electronic health record linkage tool in Chicago
Authors: Kho Abel N , Cashy John P , Jackson Kathryn L , Pah Adam R , Goel Satyender , Boehnke Jörn , Humphries John Eric , Kominers Scott Duke , Hota Bala N , Sims Shannon A , Malin Bradley A , French Dustin D , Walunas Theresa L , Meltzer David O , Kaleba Erin O , Jones Roderick C , Galanter William L
Published: June 2015

Objective To design and implement a tool that creates a secure, privacy preserving linkage of electronic health record (EHR) data across multiple sites in a large metropolitan area in the United States (Chicago, IL), for use in clinical research.

Methods The authors developed and distributed a software application that performs standardized data cleaning, preprocessing, and hashing of patient identifiers to remove all protected health information. The application creates seeded hash code combinations of patient identifiers using a Health Insurance Portability and Accountability Act compliant SHA-512 algorithm that minimizes re-identification risk. The authors subsequently linked individual records using a central honest broker with an algorithm that assigns weights to hash combinations in order to generate high specificity matches.

Results The software application successfully linked and de-duplicated 7 million records across 6 institutions, resulting in a cohort of 5 million unique records. Using a manually reconciled set of 11 292 patients as a gold standard, the software achieved a sensitivity of 96% and a specificity of 100%, with a majority of the missed matches accounted for by patients with both a missing social security number and last name change. Using 3 disease examples, it is demonstrated that the software can reduce duplication of patient records across sites by as much as 28%.

Conclusions Software that standardizes the assignment of a unique seeded hash identifier merged through an agreed upon third-party honest broker can enable large-scale secure linkage of EHR data for epidemiologic and public health research. The software algorithm can improve future epidemiologic research by providing more comprehensive data given that patients may make use of multiple healthcare systems.
National Veterans Health Administration inpatient risk stratification models for hospital-acquired acute kidney injury
Authors: Cronin Robert M , VanHouten Jacob P , Siew Edward D , Eden Svetlana K , Fihn Stephan D , Nielson Christopher D , Peterson Josh F , Baker Clifton R , Ikizler T Alp , Speroff Theodore , Matheny Michael E
Published: June 2015

Objective Hospital-acquired acute kidney injury (HA-AKI) is a potentially preventable cause of morbidity and mortality. Identifying high-risk patients prior to the onset of kidney injury is a key step towards AKI prevention.

Materials and Methods A national retrospective cohort of 1,620,898 patient hospitalizations from 116 Veterans Affairs hospitals was assembled from electronic health record (EHR) data collected from 2003 to 2012. HA-AKI was defined at stage 1+, stage 2+, and dialysis. EHR-based predictors were identified through logistic regression, least absolute shrinkage and selection operator (lasso) regression, and random forests, and pair-wise comparisons between each were made. Calibration and discrimination metrics were calculated using 50 bootstrap iterations. In the final models, we report odds ratios, 95% confidence intervals, and importance rankings for predictor variables to evaluate their significance.

Results The area under the receiver operating characteristic curve (AUC) for the different model outcomes ranged from 0.746 to 0.758 in stage 1+, 0.714 to 0.720 in stage 2+, and 0.823 to 0.825 in dialysis. Logistic regression had the best AUC in stage 1+ and dialysis. Random forests had the best AUC in stage 2+ but the least favorable calibration plots. Multiple risk factors were significant in our models, including some nonsteroidal anti-inflammatory drugs, blood pressure medications, antibiotics, and intravenous fluids given during the first 48 h of admission.

Conclusions This study demonstrated that, although all the models tested had good discrimination, performance characteristics varied between methods, and the random forests models did not calibrate as well as the lasso or logistic regression models. In addition, novel modifiable risk factors were explored and found to be significant.
Clinical implications of motor deficits related to brain tumors†
Authors: Amidei Christina , Kushner David S.
Published: June 2015

Motor deficits, including unilateral or bilateral weakness, plegia, ataxia, spasticity, and loss of complex movement execution, can occur during any brain tumor illness. Tumor location, treatment effects, and medications contribute to these deficits. Motor dysfunction has been associated with significant deterioration in health-related quality of life in patients with primary and metastatic brain tumors. Significant decrease in median overall survival has been reported in patients with motor deficits, although the reasons for this are unclear. Motor deficits, particularly gait impairment, contribute to significant symptom burden at end of life, and are the most common reasons for initiation of hospice care. Interventions must focus on prevention and amelioration of motor dysfunction throughout the disease course in order to preserve quality of life. The impact of exercise in prolonging survival and improving quality of life requires further study.
Physical conditions of the interstellar medium in star-forming galaxies at z ∼ 1.5
Authors: Hayashi Masao , Ly Chun , Shimasaku Kazuhiro , Motohara Kentaro , Malkan Matthew A. , Nagao Tohru , Kashikawa Nobunari , Goto Ryosuke , Naito Yoshiaki
Published: June 2015

We present results from Subaru Fiber Multi Object Spectrograph near-infrared spectroscopy of 118 star-forming galaxies at z ∼ 1.5 in the Subaru Deep Field. These galaxies are selected as [O ii]λ3727 emitters at z ≈ 1.47 and 1.62 from narrow-band imaging. We detect the Hα emission line in 115 galaxies, the [O iii]λ5007 emission line in 45 galaxies, and Hβ, [N ii]λ6584, and [S ii]λλ6716, 6731 in 13, 16, and 6 galaxies, respectively. Including the [O ii] emission line, we use the six strong nebular emission lines in the individual and composite rest-frame optical spectra to investigate the physical conditions of the interstellar medium in star-forming galaxies at z ∼ 1.5. We find a tight correlation between Hα and [O ii], which suggests that [O ii] can be a good star formation rate indicator for galaxies at z ∼ 1.5. The line ratios of Hα/[O ii] are consistent with those of local galaxies. We also find that [O ii] emitters have strong [O iii] emission lines. The [O iii]/[O ii] ratios are larger than normal star-forming galaxies in the local universe, suggesting a higher ionization parameter. Less massive galaxies have larger [O iii]/[O ii] ratios. With evidence that the electron density is consistent with local galaxies, the high ionization of galaxies at high redshifts may be attributed to a harder radiation field by a young stellar population and/or an increase in the number of ionizing photons from each massive star.
α‐Amylase Inhibitors from Wheat Against Development and Toxigenic Potential ofFusarium verticillioides
Authors: Mendes Gabriela R. Lemos , Alves Chiara Leal , Lopes Cavalheiro Paola , Bretanha Cristiana Costa , Pagnussatt Fernanda Arnhold , Badiale‐Furlong Eliana
Published: June 2015

Fusarium verticillioidesis one of the most important pathogens in maize and is a producer of fumonisin B1(FB1). Although reports of its presence in wheat are scarce, the susceptibility of this cereal to fungus of the same genus motivates interest in investigating compounds present in the grain with inhibitory activity against this species. The aim of this study was to extract α‐amylase inhibitors from wheat and apply them in vitro to evaluate its effect on the development and expression of toxigenic potential ofF. verticillioides. The α‐amylase inhibitors, both crude (P0) and purified (P1), were applied to in vitro culture containing a pathogen mycelium disc. Mycelial growth of the pathogen, glucosamine content, α‐amylase activity, and production of FB1were investigated. All protein extracts of wheat showed the ability to inhibit pathogen growth, especially the extract P0from cultivar Quartzo, which resulted in a reduction of glucosamine content (66%) and α‐amylase activity (84%). Furthermore, the protein inhibitors showed antifumonisin effect, reducing by 33 and 47% the mycotoxin production when applied as P0and P1, respectively. These results suggest that α‐amylase inhibitor contributed to resistance against pathogen attack, acting in a diversified manner for each fungal species.
Characterization of Xanthomonas hortorum pv. pelargonii Isolated from Geranium in Serbia
Authors: Balaž Jelica , Ivanović Žarko , Davidović Andrej , Iličić Renata , Janse Jaap , Popović Tatjana
Published: June 2015

Geranium leaves and stems with symptoms of bacterial blight were collected from commercial greenhouses during the last decade in Serbia. In total, 17 isolates with colony morphology typical for the genus Xanthomonas were characterized with pathogenicity, biochemical, serological, and molecular assays. All 17 isolates reacted positive in a polymerase chain reaction (PCR) using XcpM1 and XcpM2 primers specific for Xanthomonas hortorum pv. pelargonii. In pathogenicity tests on Pelargonium zonale (leaf and stem inoculation), all isolates caused typical symptoms on leaves starting 2 days after inoculation as sunken, water-soaked, irregular lesions, and 6 to 8 days after inoculation on stems as necrotic lesions also showing yellow exudate. Symptoms resulted in general wilting of inoculated plants 20 days after inoculation. Selected phenotypic tests indicated that all isolates showed the same results as described for the bacterium X. hortorum pv. pelargonii. Repetitive sequence-based PCR typing using BOX and ERIC revealed that all isolates showed two fingerprinting profiles but (GTG)5 and REP did not reveal differences. Multilocus sequence typing of partial sequences of rpoD, dnaK, fyuA, and gyrB genes of tested isolates and sequences obtained from GenBank of Xanthomonas pathovar pathotype strains did not reveal genetic variability among the isolates, showing the same gene sequence pattern.
Similar Aggressiveness of Phenotypically and Genotypically Distinct Isolates of Sclerotinia sclerotiorum
Authors: Lehner M. S. , Lima R. C. , Carneiro J. E. S. , Paula Júnior T. J. , Vieira R. F. , Mizubuti E. S. G.
Published: June 2015

Understanding how Sclerotinia sclerotiorum aggressiveness varies among isolates may be useful for breeding programs aimed at developing common bean cultivars resistant to white mold. The aggressiveness of 20 S. sclerotiorum isolates collected in common bean fields from four Brazilian states was tested against two common bean genotypes (Pérola and A195) using two inoculation methods. The isolates were characterized using 10 microsatellite (SSR) loci, mycelial compatibility groups (MCGs), partial sequences of the oxaloacetate acetylhydrolase (OAH) gene, and morphological traits. Twenty SSR and seven OAH haplotypes, 10 MCGs, and high variability in colony morphology were found. One isolate was more aggressive when inoculated on plants of the genotype A195, but all other isolates had similar aggressiveness. Aggressiveness was not related with MCGs, SSR, OAH haplotypes, mycelial pigmentation, growth rate, or sclerotia production.
Molecular Characterization of Recombinant Strains of Potato virus Y From Saudi Arabia
Authors: Chikh-Ali Mohamad , Alruwaili Hayam , Vander Pol Dalton , Karasev Alexander V.
Published: June 2015

Potato virus Y (PVY) exists as a complex of strains, many of which are recombinants. The practical importance of PVY recombinant strains has increased due to their ability to induce potato tuber necrotic ring spot disease (PTNRD) that seriously affects tuber quality. In Saudi Arabia, potato production has increased fivefold during the last three decades, reaching 460,000 tons per year. Although PVY has been reported as one of the main viruses affecting potatoes, no information is available on PVY strains circulating in the country. In August 2014, a survey was conducted in a seed potato field at Al-Jouf, Saudi Arabia. PVY-positive samples selected based on visual symptoms and serological reactivity were subjected to strain typing using multiplex RT-PCR assays and were determined to represent recombinant PVY strains. Whole genome sequences were determined for two representative isolates, S2 and S9, through direct sequencing of a series of overlapping RT-PCR fragments for each isolate, and found to represent strains PVY-NE11 and PVYZ (SYR-III), respectively. One of the recombinant types, SYR-III, was previously found in nearby Syria and Jordan, but the second recombinant, PVY-NE11, was found before only in the United States. Both recombinants, PVY-NE11 and SYR-III, were previously found associated with PTNRD and thought to be rare. The current identification of PVY-NE11 and SYR-III in seed potato in a new geographic region suggests that these recombinants may not be as rare as previously believed. This is the first report on the occurrence of recombinant strains of PVY in potato in Saudi Arabia, and the first report on the PVY-NE11 strain of PVY found in potato outside of the United States.
Influence of Temperature and Humidity on the Viability of Ophiognomonia clavigignenti-juglandacearum Conidia
Authors: Moore M. J. , Ostry M. E.
Published: June 2015

Butternut canker, caused by the fungus Ophiognomonia clavigignenti-juglandacearum, primarily kills butternut (Juglans cinerea). Rain splash and local air currents are the primary means of conidia dispersal but that does not explain its long-distance spread and infection of isolated trees. Dispersal by insect or animal vectors or plant material likely necessitates the ability for conidia to tolerate drying for a period of time over variable temperature and humidity conditions. The objective of this study was to determine the influence of temperature and humidity on conidial germination and survival of air-dried conidia. Conidia collected from 1-month-old cultures germinated on water agar over a wide range of temperatures (4 to 32°C) and were viable after brief periods at 36°C when returned to a lower temperature. Viability of air-dried conidia held on nylon membranes at various temperatures and humidities varied from less than a day at 28°C and 90% relative humidity (RH) to a mean of 15 days at 20°C and 80% RH. RH had the least effect on viability at 12°C, with conidia remaining viable for 7 days at most humidity levels tested. Conidia held at 100% RH began germinating on the membranes after 21 days. Conidia in a water suspension remained viable for 168 days at all temperatures tested. These results suggest that O. clavigignenti-juglandacearum conidia may remain viable on the surface of a vector or plant material and seed for over 2 weeks, given the proper conditions, or for much longer if in water or in an environment of saturated humidity. This potential may, in part, explain the frequent presence of the disease on isolated trees.
Sexual signalling by females: do unmated females increase their signalling effort?
Authors: Simmons Leigh W.
Published: June 2015

Theory predicts that females should invest least in mate searching when young, but increase their effort with age if they remain unmated. Few studies have examined variation in female sexual signalling. Female Dawson's burrowing bees (
Amegilla dawsoni
) search for males by signalling their receptivity on emergence, but many leave the emergence site unmated and must attract males at feeding sites. Female bees prevented from mating on emergence had more extreme versions of cuticular hydrocarbon profiles that make them attractive to males, lending empirical evidence of adaptive shifts in female mating effort.
Douglas Samuel Jones MBE. 10 January 1922 — 26 November 2013
Authors: Sleeman B. D. , Abrahams I. D.
Published: June 2015

Douglas Jones was an extremely creative and influential mathematician. His contributions to the theory of electromagnetic and acoustic waves and his development of original and exceptionally powerful mathematical techniques with which to study them has led to the solution of problems of both practical and social importance. His work is fundamental to the design and performance of radar antennae wherein it is necessary to optimize their transmitting and receiving characteristics. Jones also investigated the manner in which electromagnetic waves interact with objects having sharp edges. These studies are basic to the construction of ‘stealth’ aircraft, in which the geometrical shape is designed to minimize the aircraft’s signature. When supersonic airliner capability was realized in the development of Concorde there was considerable public concern regarding the excessive noise created during take-off and landing and the impact of ‘sonic boom’ on built-up areas. This prompted investigations into the noise levels experienced on the ground due to a moving acoustic source. This inspired Douglas to develop a mathematical theory of noise shielding. To address these difficult problems he developed powerful techniques of analysis: these included the asymptotic expansion of multidimensional integrals and the generalization of the method of stationary phase; the solution of integral equations arising in diffraction and obstacle scattering theory; the development of multidimensional generalized functions; uniform asymptotics and Stokes’ phenomenon; the Wiener–Hopf technique; and powerful numerical techniques to solve integral equations arising in electromagnetic wave theory.
David Rees. 29 May 1918 — 16 August 2013
Authors: Sharp R. Y.
Published: June 2015

David Rees completed his Cambridge undergraduate studies in mathematics in summer 1939; in his first three months of postgraduate work in autumn 1939 he produced a characterization of completely 0-simple semigroups. War then intervened: he worked until the end of the war at Bletchley Park, the British codebreaking centre in Buckinghamshire, where he was part of a team that broke the Enigma code regularly for some critical months during 1940. After the war he first worked at Manchester University, but moved to Cambridge University in 1948. In the immediate postwar period, he continued with research into semigroups and non-commutative algebra. His first paper was very influential, and he is considered by semigroup theorists to be one of the founding fathers of their subject.
An analytical approach to bistable biological circuit discrimination using real algebraic geometry
Authors: Siegal-Gaskins Dan , Franco Elisa , Zhou Tiffany , Murray Richard M.
Published: June 2015

Biomolecular circuits with two distinct and stable steady states have been identified as essential components in a wide range of biological networks, with a variety of mechanisms and topologies giving rise to their important bistable property. Understanding the differences between circuit implementations is an important question, particularly for the synthetic biologist faced with determining which bistable circuit design out of many is best for their specific application. In this work we explore the applicability of Sturm's theorem—a tool from nineteenth-century real algebraic geometry—to comparing ‘functionally equivalent’ bistable circuits without the need for numerical simulation. We first consider two genetic toggle variants and two different positive feedback circuits, and show how specific topological properties present in each type of circuit can serve to increase the size of the regions of parameter space in which they function as switches. We then demonstrate that a single competitive monomeric activator added to a purely monomeric (and otherwise monostable) mutual repressor circuit is sufficient for bistability. Finally, we compare our approach with the Routh–Hurwitz method and derive consistent, yet more powerful, parametric conditions. The predictive power and ease of use of Sturm's theorem demonstrated in this work suggest that algebraic geometric techniques may be underused in biomolecular circuit analysis.
Module-based construction of plasmids for chromosomal integration of the fission yeast
Schizosaccharomyces pombe
Authors: Kakui Yasutaka , Sunaga Tomonari , Arai Kunio , Dodgson James , Ji Liang , Csikász-Nagy Attila , Carazo-Salas Rafael , Sato Masamitsu
Published: June 2015

Integration of an external gene into a fission yeast chromosome is useful to investigate the effect of the gene product. An easy way to knock-in a gene construct is use of an integration plasmid, which can be targeted and inserted to a chromosome through homologous recombination. Despite the advantage of integration, construction of integration plasmids is energy- and time-consuming, because there is no systematic library of integration plasmids with various promoters, fluorescent protein tags, terminators and selection markers; therefore, researchers are often forced to make appropriate ones through multiple rounds of cloning procedures. Here, we establish materials and methods to easily construct integration plasmids. We introduce a convenient cloning system based on Golden Gate DNA shuffling, which enables the connection of multiple DNA fragments at once: any kind of promoters and terminators, the gene of interest, in combination with any fluorescent protein tag genes and any selection markers. Each of those DNA fragments, called a ‘module’, can be tandemly ligated in the order we desire in a single reaction, which yields a circular plasmid in a one-step manner. The resulting plasmids can be integrated through standard methods for transformation. Thus, these materials and methods help easy construction of knock-in strains, and this will further increase the value of fission yeast as a model organism.
The development of a segment-based musculoskeletal model of the lower limb: introducing F
ree
B
ody
Authors: Cleather Daniel J. , Bull Anthony M. J.
Published: June 2015

Traditional approaches to the biomechanical analysis of movement are joint-based; that is the mechanics of the body are described in terms of the forces and moments acting at the joints, and that muscular forces are considered to create moments about the joints. We have recently shown that segment-based approaches, where the mechanics of the body are described by considering the effect of the muscle, ligament and joint contact forces on the segments themselves, can also prove insightful. We have also previously described a simultaneous, optimization-based, musculoskeletal model of the lower limb. However, this prior model incorporates both joint- and segment-based assumptions. The purpose of this study was therefore to develop an entirely segment-based model of the lower limb and to compare its performance to our previous work. The segment-based model was used to estimate the muscle forces found during vertical jumping, which were in turn compared with the muscular activations that have been found in vertical jumping, by using a Geers' metric to quantify the magnitude and phase errors. The segment-based model was shown to have a similar ability to estimate muscle forces as a model based upon our previous work. In the future, we will evaluate the ability of the segment-based model to be used to provide results with clinical relevance, and compare its performance to joint-based approaches. The segment-based model described in this article is publicly available as a GUI-based M
atlab
® application and in the original source code (at
www.msksoftware.org.uk
).
Experimental evidence for convergent evolution of maternal care heuristics in industrialized and small-scale populations
Authors: Kushnick Geoff , Hanowell Ben , Kim Jun-Hong , Langstieh Banrida , Magnano Vittorio , Oláh Katalin
Published: June 2015

Maternal care decision rules should evolve responsiveness to factors impinging on the fitness pay-offs of care. Because the caretaking environments common in industrialized and small-scale societies vary in predictable ways, we hypothesize that heuristics guiding maternal behaviour will also differ between these two types of populations. We used a factorial vignette experiment to elicit third-party judgements about likely caretaking decisions of a hypothetical mother and her child when various fitness-relevant factors (maternal age and access to resources, and offspring age, sex and quality) were varied systematically in seven populations—three industrialized and four small-scale. Despite considerable variation in responses, we found that three of five main effects, and the two severity effects, exhibited statistically significant industrialized/ small-scale population differences. All differences could be explained as adaptive solutions to industrialized versus small-scale caretaking environments. Further, we found gradients in the relationship between the population-specific estimates and national-level socio-economic indicators, further implicating important aspects of the variation in industrialized and small-scale caretaking environments in shaping heuristics. Although there is mounting evidence for a genetic component to human maternal behaviour, there is no current evidence for interpopulation variation in candidate genes. We nonetheless suggest that heuristics guiding maternal behaviour in diverse societies emerge via convergent evolution in response to similar selective pressures.
Tangle machines
Authors: Moskovich Daniel , Carmi Avishy Y.
Published: June 2015

Tangle machines are topologically inspired diagrammatic models. Their novel feature is their natural notion of equivalence. Equivalent tangle machines may differ locally, but globally they share the same information content. The goal of tangle machine equivalence is to provide a context-independent method to select, from among many ways to perform a task, the ‘best’ way to perform the task. The concept of equivalent tangle machines is illustrated through examples in which tangle machines represent networks for distributed information processing, networks of adiabatic quantum computations, and iterative computations.
Extending Lévy search theory from one to higher dimensions: Lévy walking favours the blind
Authors: Reynolds A. M.
Published: June 2015

A diverse range of organisms, including T cells,
E. coli
, honeybees, sharks, turtles, bony fish, jellyfish, wandering albatrosses and even human hunter–gatherers have movement patterns that can be approximated by Lévy walks (LW; sometimes called Lévy flights in the biological and ecological literature). These observations lend support to the ‘Lévy flight foraging hypothesis’ which asserts that natural selection should have led to adaptations for Lévy flight foraging, because Lévy flights can optimize search efficiencies. The hypothesis stems from a rigorous theory of one-dimensional searching and from simulation data for two-dimensional searching. The potential effectiveness of three-dimensional Lévy searches has not been examined but is central to a proper understanding of marine predators and T cells which have provided the most compelling empirical evidence for LW. Here I extend Lévy search theory from one to three dimensions. The new theory predicts that three-dimensional Lévy searching can be advantageous but only when targets are large compared with the perceptual range of the searchers, i.e. only when foragers are effectively blind and need to come into contact with a target to establish its presence. This may explain why effective blindness is a common factor among three-dimensional Lévy walkers.
Electro-osmotic flow in a rotating rectangular microchannel
Authors: Ng Chiu-On , Qi Cheng
Published: June 2015

An analytical model is presented for low-Rossby-number electro-osmotic flow in a rectangular channel rotating about an axis perpendicular to its own. The flow is driven under the combined action of Coriolis, pressure, viscous and electric forces. Analytical solutions in the form of eigenfunction expansions are developed for the problem, which is controlled by the rotation parameter (or the inverse Ekman number), the Debye parameter, the aspect ratio of the channel and the distribution of zeta potentials on the channel walls. Under the conditions of fast rotation and a thin electric double layer (EDL), an Ekman–EDL develops on the horizontal walls. This is essentially an Ekman layer subjected to electrokinetic effects. The flow structure of this boundary layer as a function of the Ekman layer thickness normalized by the Debye length is investigated in detail in this study. It is also shown that the channel rotation may have qualitatively different effects on the flow rate, depending on the channel width and the zeta potential distributions. Axial and secondary flows are examined in detail to reveal how the development of a geostrophic core may lead to a rise or fall of the mean flow.
Requirements for plant coexistence through pollination niche partitioning
Authors: Benadi Gita
Published: June 2015

Plant–pollinator interactions are often thought to have been a decisive factor in the diversification of flowering plants, but to be of little or no importance for the maintenance of existing plant diversity. In a recent opinion paper, Pauw (2013
Trends Ecol. Evol
. 28, 30–37. (
doi:10.1016/j.tree.2012.07.019
)) challenged this view by proposing a mechanism of diversity maintenance based on pollination niche partitioning. In this article, I investigate under which conditions the mechanism suggested by Pauw can promote plant coexistence, using a mathematical model of plant and pollinator population dynamics. Numerical simulations show that this mechanism is most effective when the costs of searching for flowers are low, pollinator populations are strongly limited by resources other than pollen and nectar, and plant–pollinator interactions are sufficiently specialized. I review the empirical literature on these three requirements, discuss additional factors that may be important for diversity maintenance through pollination niche partitioning, and provide recommendations on how to detect this coexistence mechanism in natural plant communities.
Ocean acidification impairs crab foraging behaviour
Authors: Dodd Luke F. , Grabowski Jonathan H. , Piehler Michael F. , Westfield Isaac , Ries Justin B.
Published: June 2015

Anthropogenic elevation of atmospheric CO
2
is driving global-scale ocean acidification, which consequently influences calcification rates of many marine invertebrates and potentially alters their susceptibility to predation. Ocean acidification may also impair an organism's ability to process environmental and biological cues. These counteracting impacts make it challenging to predict how acidification will alter species interactions and community structure. To examine effects of acidification on consumptive and behavioural interactions between mud crabs (
Panopeus herbstii
) and oysters (
Crassostrea virginica
), oysters were reared with and without caged crabs for 71 days at three
p
CO
2
levels. During subsequent predation trials, acidification reduced prey consumption, handling time and duration of unsuccessful predation attempt. These negative effects of ocean acidification on crab foraging behaviour more than offset any benefit to crabs resulting from a reduction in the net rate of oyster calcification. These findings reveal that efforts to evaluate how acidification will alter marine food webs should include quantifying impacts on both calcification rates and animal behaviour.
Quantitative genetic analysis of brain size variation in sticklebacks: support for the mosaic model of brain evolution
Authors: Noreikiene Kristina , Herczeg Gábor , Gonda Abigél , Balázs Gergely , Husby Arild , Merilä Juha
Published: June 2015

The mosaic model of brain evolution postulates that different brain regions are relatively free to evolve independently from each other. Such independent evolution is possible only if genetic correlations among the different brain regions are less than unity. We estimated heritabilities, evolvabilities and genetic correlations of relative size of the brain, and its different regions in the three-spined stickleback (
Gasterosteus aculeatus
). We found that heritabilities were low (average
h
2
= 0.24), suggesting a large plastic component to brain architecture. However, evolvabilities of different brain parts were moderate, suggesting the presence of additive genetic variance to sustain a response to selection in the long term. Genetic correlations among different brain regions were low (average
r
G
= 0.40) and significantly less than unity. These results, along with those from analyses of phenotypic and genetic integration, indicate a high degree of independence between different brain regions, suggesting that responses to selection are unlikely to be severely constrained by genetic and phenotypic correlations. Hence, the results give strong support for the mosaic model of brain evolution. However, the genetic correlation between brain and body size was high (
r
G
= 0.89), suggesting a constraint for independent evolution of brain and body size in sticklebacks.
Effects of MDMA on socioemotional feelings, authenticity, and autobiographical disclosure in healthy volunteers in a controlled setting
Authors: Baggott Matthew J. , Coyle Jeremy R. , Siegrist Jennifer D. , Garrison Kathleen , Galloway Gantt , Mendelson John E.
Published: June 2015

The drug 3,4-methylenedioxymethamphetamine (MDMA, “ecstasy”, “molly”) is a widely used illicit drug and experimental adjunct to psychotherapy. MDMA has unusual, poorly understood socioemotional effects, including feelings of interpersonal closeness and sociability. To better understand these effects, we conducted a within-subjects double-blind placebo controlled study of the effects of 1.5 mg/kg oral MDMA on social emotions and autobiographical disclosure in a controlled setting. MDMA displayed both sedative- and stimulant-like effects, including increased self-report anxiety. At the same time, MDMA positively altered evaluation of the self (i.e., increasing feelings of authenticity) while decreasing concerns about negative evaluation by others (i.e., decreasing social anxiety). Consistent with these feelings, MDMA increased how comfortable participants felt describing emotional memories. Overall, MDMA produced a prosocial syndrome that seemed to facilitate emotional disclosure and that appears consistent with the suggestion that it represents a novel pharmacological class.
Stochastic evolutionary games in dynamic populations
Authors: Huang Weini , Hauert Christoph , Traulsen Arne
Published: June 2015

Frequency dependent selection and demographic fluctuations play important roles in evolutionary and ecological processes. Under frequency dependent selection, the average fitness of the population may increase or decrease based on interactions between individuals within the population. This should be reflected in fluctuations of the population size even in constant environ ments. Here, we propose a stochastic model, which naturally combines these two evolutionary ingredients by assuming frequency dependent competition between different types in an individual-based model. In contrast to previous game theoretic models, the carrying capacity of the population and thus the population size is determined by pairwise competition of individuals mediated by evolutionary games and demographic stochasticity. In the limit of infinite population size, the averaged stochastic dynamics is captured by the deterministic competitive LotkaVolterra equations. In small populations, demographic stochasticity may instead lead to the extinction of the entire population. As the population size is driven by the fitness in evolutionary games, a population of cooperators is less prone to go extinct than a population of defectors, whereas in the usual systems of fixed size, the population would thrive regardless of its average payoff.
A phase-space beam position monitor for synchrotron radiation
Authors: Samadi Nazanin , Bassey Bassey , Martinson Mercedes , Belev George , Dallin Les , de Jong Mark , Chapman Dean
Published: June 2015

The stability of the photon beam position on synchrotron beamlines is critical for most if not all synchrotron radiation experiments. The position of the beam at the experiment or optical element location is set by the position and angle of the electron beam source as it traverses the magnetic field of the bend-magnet or insertion device. Thus an ideal photon beam monitor would be able to simultaneously measure the photon beam's position and angle, and thus infer the electron beam's position in phase space. X-ray diffraction is commonly used to prepare monochromatic beams on X-ray beamlines usually in the form of a double-crystal monochromator. Diffraction couples the photon wavelength or energy to the incident angle on the lattice planes within the crystal. The beam from such a monochromator will contain a spread of energies due to the vertical divergence of the photon beam from the source. This range of energies can easily cover the absorption edge of a filter element such as iodine at 33.17 keV. A vertical profile measurement of the photon beam footprint with and without the filter can be used to determine the vertical centroid position and angle of the photon beam. In the measurements described here an imaging detector is used to measure these vertical profiles with an iodine filter that horizontally covers part of the monochromatic beam. The goal was to investigate the use of a combined monochromator, filter and detector as a phase-space beam position monitor. The system was tested for sensitivity to position and angle under a number of synchrotron operating conditions, such as normal operations and special operating modes where the photon beam is intentionally altered in position and angle at the source point. The results are comparable with other methods of beam position measurement and indicate that such a system is feasible in situations where part of the synchrotron beam can be used for the phase-space measurement.
Disseminated infection caused by Emmonsia pasteuriana in a renal transplant recipient
Authors: Feng Peiying , Yin Songchao , Zhu Guoxing , Li Meirong , Wu Benquan , Xie Yang , Ma Han , Zhang Jun , Cheng Cailian , de Hoog Gerrit Sijbrand , Lu Chun , Lai Wei
Published: June 2015

Emmonsia pasteuriana is a thermally dimorphic fungus identified in very few human cases. Here, we report a case of a 43‐year‐old male renal transplant patient from China presenting with multiple painful skin eruptions on his head, nose and left thigh, later accompanied by respiratory failure. Histopathology of the biopsy collected from the left thigh upper ulcer and occipital nodule both demonstrated chronic inflammation with granuloma formation and yeast‐like elements. Emmonsia pasteuriana was cultured from two biopsy specimens and their identity was confirmed by sequencing of the rDNA internal transcribed spacer. The patient in intensive care showed marked clinical improvement with antifungal treatment.
Does presentation of smooth pureed meals improve patients consumption in an acute care setting: A pilot study
Authors: Farrer Olivia , Olsen Carla , Mousley Kate , Teo Emily
Published: June 2015

Aim

Malnutrition is a concern across all Australian hospitals and is associated with negative clinical outcomes in up to 60% inpatients, with a further 10% exacerbated by the presence of dysphagia. Providing adequate nutrition for patients requiring a texture‐modified diet often results in meals that look and taste less appealing and which are nutritionally diluted. This article aims is to review change in oral intake using food moulding techniques within an acute care institution for patients on Texture C—smooth pureed meals.

Methods

This was a 2 week pilot study. Patients were provided smooth pureed lunch either as non‐moulded or a moulded meal. Main meal wastage was weighed and reasons for waste were documented. If patients met the inclusion criteria, a short satisfaction survey was also administered.

Results

Analysis using a chi‐squared test comparison saw significance in the proportion of patients increasing oral intake from <1/4 meal eaten to >3/4 meal, when in the moulded form (P = 0.03). Median plate waste was reduced by over 100 g in the treatment group but there was no significant change overall. Limited data for patient satisfaction concluded no significance in meal preference.

Conclusions

The pilot study suggests that using a moulded smooth puree diet can increase mean oral intake and reduce main meal wastage, but a larger sample size is required to demonstrate statistical significance. However, the pilot study effect size (0.55) is large enough to warrant further research interest in this area and results do suggest relevancy in clinical practice for replication.
Identification of polyamine‐responsive bacterioplankton taxa in South Atlantic Bight
Authors: Lu Xinxin , Sun Shulei , Hollibaugh James T. , Mou Xiaozhen
Published: June 2015

Putrescine and spermidine are short‐chained aliphatic polyamines (PAs) that are ubiquitously distributed in seawater. These compounds may be important sources of dissolved organic carbon and nitrogen for marine bacterioplankton. Here, we used pyrotag sequencing to quantify the response of bacterioplankton to putrescine and spermidine amendments in microcosms established using surface waters collected at various stations in the South Atlantic Bight in October 2011. Our analysis showed that PA‐responsive bacterioplankton consisted of bacterial taxa that are typically dominant in marine systems. Rhodobacteraceae (Alphaproteobacteria) was the taxon most responsive to PA additions at the nearshore site. Gammaproteobacteria of the families Piscirickettsiaceae; Vibrionaceae; and Vibrionaceae and Pseudoalteromonadaceae, were the dominant PA‐responsive taxa in samples from the river‐influenced coastal station, offshore station and open ocean station, respectively. The spatial variability of PA‐responsive taxa may be attributed to differences in composition of the initial bacterial community and variations of in situ physiochemical conditions among sites. Our results also provided the first empirical evidence that Gammaproteobacteria might play an important role in PA transformation in marine systems.