bluuebunny/crossref_metadata_2025 huggingface dataset:
MMinte: An application for predicting metabolic interactions among the microbial species in a community
Authors: Mendes-Soares Helena , Mundy Michael , Mendes Soares Luis , Chia Nicholas
Published: June 2016

Background.

The explosive growth of microbiome research has yielded great quantities of data. These data provide us with many answers, but raise just as many questions. 16S rDNA—the backbone of microbiome analyses—allows us to assess α-diversity, β-diversity, and microbe-microbe associations, which characterize the overall properties of an ecosystem. However, we are still unable to use 16S rDNA data to directly assess the microbe-microbe and microbe-environment interactions that determine that system's broader ecology. Thus, properties such as competition, cooperation, and nutrient conditions remain insufficiently analyzed. Here, we apply predictive community metabolic models of microbes identified with 16S rDNA data to probe the ecology of microbial communities.

Results.

We developed a methodology for the large-scale assessment of microbial metabolic interactions (MMinte)from 16S rDNA data. MMinte assesses the relative growth rates of interacting pairs of organisms within a community metabolic network and whether that interaction has a positive or negative effect. Moreover, MMinte's simulations take into account the nutritional environment, which play a strong role in determining the metabolism of individual microbes. We present two case studies that demonstrate this software's utility. In the first, we show how diet influences the nature of the microbe-microbe interactions. In the second, we use MMinte's modular feature set to better understand how the growth ofDesulfovibrio pigeris affected by, and affects the growth of, other members in a simplified gut community under metabolic conditions suggested to be determinant for their dynamics.

Conclusion.

By applying metabolic models to commonly available sequence data, MMinte grants the user insight into the metabolic relationships between microbes, highlighting important features that may relate to ecological stability, susceptibility, and cross-feeding. These relationships are at the foundation of a wide range of ecological questions that impact our ability to understand problems such as microbially-derived toxicity in colon cancer.
Heterologous protection against Asian Zika virus challenge in rhesus macaques
Authors: Aliota Matthew T. , Dudley Dawn M. , Newman Christina M. , Mohr Emma L. , Gellerup Dane D. , Breitbach Meghan E. , Buechler Connor R. , Rasheed Mustafa N. , Mohns Mariel S. , Weiler Andrea M. , Barry Gabrielle L. , Weisgrau Kim L. , Eudailey Josh A. , Rakasz Eva G. , Vosler Logan J. , Post Jennifer , Capuano Saverio , Golos Thaddeus G. , Anthony Moody M. , Permar Sallie R. , Osorio Jorge E. , Friedrich Thomas C. , O’Connor Shelby L. , O’Connor David H.
Published: June 2016

Zika virus (ZIKV) isolates are genetically diverse, but belong to two recognized lineages, termed “African” and “Asian.” Asian ZIKV infection during pregnancy causes fetal abnormalities including microcephaly. Developing an effective preventative Zika virus vaccine that protects pregnant women is essential for minimizing fetal abnormalities; at least 18 groups are developing ZIKV vaccines (Hayden, 2016). The genetic and antigenic variability of many RNA viruses limits the effectiveness of vaccines, and the degree to which immunity against one ZIKV strain could provide protection against another is unknown. Here we show that rhesus macaques infected with East African ZIKV strain MR766 are completely protected from subsequent infection with heterologous Asian ZIKV. MR766 is more genetically divergent from all known Asian ZIKV strains than Asian ZIKV strains are from one another. Therefore, ZIKV strain selection is unlikely to compromise vaccine effectiveness.

Highlights

African Zika virus (ZIKV) strain MR766 productively infects macaques (68 characters)

Immunity elicited by MR766 protects macaques against heterologous Asian ZIKV (77 characters)

In vivo restoration of a putative N-linked glycosylation site in MR766 (70 characters)

Immunogen selection is unlikely to adversely affect the breadth of vaccine protection (85 characters)

eTOC

An effective Zika virus vaccine is needed to prevent infection-associated fetal abnormalities. Macaques whose immune responses are primed by infection with East African ZIKV are completely protected from reinfection with heterologous Asian ZIKV. Any Asian ZIKV immunogen that protects against homologous challenge will likely confer protection against all other Asian ZIKV strains.
Effects of learning experience on forgetting rates of item and associative memories
Authors: Yang Jiongjiong , Zhan Lexia , Wang Yingying , Du Xiaoya , Zhou Wenxi , Ning Xueling , Sun Qing , Moscovitch Morris
Published: June 2016

Are associative memories forgotten more quickly than item memories, and does the level of original learning differentially influence forgetting rates? In this study, we addressed these questions by having participants learn single words and word pairs once (Experiment 1), three times (Experiment 2), and six times (Experiment 3) in a massed learning (ML) or a distributed learning (DL) mode. Then they were tested for item and associative recognition separately after four retention intervals: 10 min, 1 d, 1 wk, and 1 mo. The contribution of recollection and familiarity processes were assessed by participants’ remember/know judgments. The results showed that for both item and associative memories, across different degrees of learning, recollection decreased significantly and was the main source of forgetting over time, whereas familiarity remained relatively stable over time. Learning multiple times led to slower forgetting at shorter intervals, depending on recollection and familiarity processes. Compared with massed learning, distributed learning (six times) especially benefited associative memory by increasing recollection, leading to slower forgetting at longer intervals. This study highlighted the importance of process contribution and learning experiences in modulating the forgetting rates of item and associative memories. We interpret these results within the framework of a dual factor representational model of forgetting (as noted in a previous study) in which recollection is more prone to decay over time than familiarity.
Conditioning- and time-dependent increases in context fear and generalization
Authors: Poulos Andrew M. , Mehta Nehali , Lu Bryan , Amir Dorsa , Livingston Briana , Santarelli Anthony , Zhuravka Irina , Fanselow Michael S.
Published: June 2016

A prominent feature of fear memories and anxiety disorders is that they endure across extended periods of time. Here, we examine how the severity of the initial fear experience influences incubation, generalization, and sensitization of contextual fear memories across time. Adult rats were presented with either five, two, one, or zero shocks (1.2 mA, 2 sec) during contextual fear conditioning. Following a recent (1 d) or remote (28 d) retention interval all subjects were returned to the original training context to measure fear memory and/or to a novel context to measure the specificity of fear conditioning. Our results indicate rats that received two or five shocks show an “incubation”-like enhancement of fear between recent and remote retention intervals, while single-shocked animals show stable levels of context fear memory. Moreover, when fear was tested in a novel context, 1 and 2 shocked groups failed to freeze, whereas five shocked rats showed a time-dependent generalization of context memory. Stress enhancement of fear learning to a second round of conditioning was evident in all previously shocked animals. Based on these results, we conclude that the severity or number of foot shocks determines not only the level of fear memory, but also the time-dependent incubation of fear and its generalization across distinct contexts.
Cannabinoids reverse the effects of early stress on neurocognitive performance in adulthood
Authors: Alteba Shirley , Korem Nachshon , Akirav Irit
Published: June 2016

Early life stress (ES) significantly increases predisposition to psychopathologies. Cannabinoids may cause cognitive deficits and exacerbate the effects of ES. Nevertheless, the endocannabinoid system has been suggested as a therapeutic target for the treatment of stress- and anxiety-related disorders. Here we examined whether cannabinoids administered during “late adolescence” (extensive cannabis use in humans at the ages 18–25) could reverse the long-term adverse effects of ES on neurocognitive function in adulthood. Male and female rats were exposed to ES during post-natal days (P) 7–14, injected with the cannabinoid CB1/2 receptor agonist WIN55,212-2 (WIN; 1.2 mg/kg, i.p.) for 2 wk during late adolescence (P45–60) and tested in adulthood (P90) for working memory, anxiety, and alterations in CB1 receptors (CB1r), and glucocorticoid receptors (GRs) in the stress circuit [hippocampus, prefrontal cortex (PFC), and basolateral amygdala (BLA)]. ES males and females exhibited impaired performance in short-term memory in adulthood in the spatial location and social recognition tasks; males were also impaired in the novel object recognition task. WIN administered during late adolescence prevented these stress-induced impairments and reduced anxiety levels. WIN normalized the ES-induced up-regulation in PFC-GRs and CA1–CB1r in females. In males, WIN normalized the ES-induced up-regulation in PFC-GR and down-regulation in BLA-CB1r. There is a crucial role of the endocannabinoid system in the effects of early life stress on behavior at adulthood. Differences in recognition memory and in the expression of GRs and CB1r in the fear circuit suggest sex differences in the mechanism underlying coping with stress.
Discrimination performance in aging is vulnerable to interference and dissociable from spatial memory
Authors: Johnson Sarah A. , Sacks Patricia K. , Turner Sean M. , Gaynor Leslie S. , Ormerod Brandi K. , Maurer Andrew P. , Bizon Jennifer L. , Burke Sara N.
Published: June 2016

Hippocampal-dependent episodic memory and stimulus discrimination abilities are both compromised in the elderly. The reduced capacity to discriminate between similar stimuli likely contributes to multiple aspects of age-related cognitive impairment; however, the association of these behaviors within individuals has never been examined in an animal model. In the present study, young and aged F344×BN F1 hybrid rats were cross-characterized on the Morris water maze test of spatial memory and a dentate gyrus-dependent match-to-position test of spatial discrimination ability. Aged rats showed overall impairments relative to young in spatial learning and memory on the water maze task. Although young and aged learned to apply a match-to-position response strategy in performing easy spatial discriminations within a similar number of trials, a majority of aged rats were impaired relative to young in performing difficult spatial discriminations on subsequent tests. Moreover, all aged rats were susceptible to cumulative interference during spatial discrimination tests, such that error rate increased on later trials of test sessions. These data suggest that when faced with difficult discriminations, the aged rats were less able to distinguish current goal locations from those of previous trials. Increasing acetylcholine levels with donepezil did not improve aged rats’ abilities to accurately perform difficult spatial discriminations or reduce their susceptibility to interference. Interestingly, better spatial memory abilities were not significantly associated with higher performance on difficult spatial discriminations. This observation, along with the finding that aged rats made more errors under conditions in which interference was high, suggests that match-to-position spatial discrimination performance may rely on extra-hippocampal structures such as the prefrontal cortex, in addition to the dentate gyrus.
Daily access to sucrose impairs aspects of spatial memory tasks reliant on pattern separation and neural proliferation in rats
Authors: Reichelt Amy C. , Morris Margaret J. , Westbrook Reginald Frederick
Published: June 2016

High sugar diets reduce hippocampal neurogenesis, which is required for minimizing interference between memories, a process that involves “pattern separation.” We provided rats with 2 h daily access to a sucrose solution for 28 d and assessed their performance on a spatial memory task. Sucrose consuming rats discriminated between objects in novel and familiar locations when there was a large spatial separation between the objects, but not when the separation was smaller. Neuroproliferation markers in the dentate gyrus of the sucrose-consuming rats were reduced relative to controls. Thus, sucrose consumption impaired aspects of spatial memory and reduced hippocampal neuroproliferation.
Biodiversity as insurance for sapling survival in experimental tree plantations
Authors: Van de Peer Thomas , Verheyen Kris , Baeten Lander , Ponette Quentin , Muys Bart
Published: June 2016

Biodiversity can insure ecosystems against declines in their functioning by increasing the mean level of ecosystem processes and decreasing the spatial or temporal variance of these processes. On this basis, mixing tree species is expected to be an effective management strategy to reduce the risk of planting failure in young plantations.

We examined the effects of biodiversity insurance on sapling survival in three tree diversity experiments across Belgium. Based on the survival scoring of 89 254 saplings, planted in 126 plots with up to four‐species mixtures, we tested two hypotheses: (i) variability in plot‐level survival is lower for mixtures compared to monocultures due to compensation among the species (i.e. buffering effect) and (ii) mean survival is higher due to facilitation (i.e. performance‐enhancing effect).

Variation in plot‐level survival decreased strongly with diversity, indicating a buffering effect. The risk of severe planting failure was reduced in mixtures because species exhibit different survival rates; therefore, mixing ensures that not all trees in the plantation are equally susceptible to environmental stressors. In contrast, the mean plot‐level survival did not increase with diversity, and thus, an overall performance‐enhancing effect was lacking. However, species‐level analyses did show performance‐enhancing effects, where some species profited from mixing while others did not.

Synthesis and applications. We conclude that biodiversity through mixing tree species insures young experimental plantations against planting failure and is therefore highly recommended as a planting management strategy. The risk of large mortality gaps is reduced if tree plantation saplings are mixed at the scale of individual trees or small cells of trees.
Combining citizen science species distribution models and stable isotopes reveals migratory connectivity in the secretive Virginia rail
Authors: Fournier Auriel M. V. , Sullivan Alexis R. , Bump Joseph K. , Perkins Marie , Shieldcastle Mark C. , King Sammy L.
Published: June 2016

Stable hydrogen isotope (δD) methods for tracking animal movement are widely used yet often produce low resolution assignments. Incorporating prior knowledge of abundance, distribution or movement patterns can ameliorate this limitation, but data are lacking for most species. We demonstrate how observations reported by citizen scientists can be used to develop robust estimates of species distributions and to constrain δD assignments.

We developed a Bayesian framework to refine isotopic estimates of migrant animal origins conditional on species distribution models constructed from citizen scientist observations. To illustrate this approach, we analysed the migratory connectivity of the Virginia rail Rallus limicola, a secretive and declining migratory game bird in North America.

Citizen science observations enabled both estimation of sampling bias and construction of bias‐corrected species distribution models. Conditioning δD assignments on these species distribution models yielded comparably high‐resolution assignments.

Most Virginia rails wintering across five Gulf Coast sites spent the previous summer near the Great Lakes, although a considerable minority originated from the Chesapeake Bay watershed or Prairie Pothole region of North Dakota. Conversely, the majority of migrating Virginia rails from a site in the Great Lakes most likely spent the previous winter on the Gulf Coast between Texas and Louisiana.

Synthesis and applications. In this analysis, Virginia rail migratory connectivity does not fully correspond to the administrative flyways used to manage migratory birds. This example demonstrates that with the increasing availability of citizen science data to create species distribution models, our framework can produce high‐resolution estimates of migratory connectivity for many animals, including cryptic species. Empirical evidence of links between seasonal habitats will help enable effective habitat management, hunting quotas and population monitoring and also highlight critical knowledge gaps.
Genome‐centric resolution of microbial diversity, metabolism and interactions in anaerobic digestion
Authors: Vanwonterghem Inka , Jensen Paul D. , Rabaey Korneel , Tyson Gene W.
Published: June 2016

Our understanding of the complex interconnected processes performed by microbial communities is hindered by our inability to culture the vast majority of microorganisms. Metagenomics provides a way to bypass this cultivation bottleneck and recent advances in this field now allow us to recover a growing number of genomes representing previously uncultured populations from increasingly complex environments. In this study, a temporal genome‐centric metagenomic analysis was performed of lab‐scale anaerobic digesters that host complex microbial communities fulfilling a series of interlinked metabolic processes to enable the conversion of cellulose to methane. In total, 101 population genomes that were moderate to near‐complete were recovered based primarily on differential coverage binning. These populations span 19 phyla, represent mostly novel species and expand the genomic coverage of several rare phyla. Classification into functional guilds based on their metabolic potential revealed metabolic networks with a high level of functional redundancy as well as niche specialization, and allowed us to identify potential roles such as hydrolytic specialists for several rare, uncultured populations. Genome‐centric analyses of complex microbial communities across diverse environments provide the key to understanding the phylogenetic and metabolic diversity of these interactive communities.
Feeding on compatible solutes: A substrate‐induced pathway for uptake and catabolism of ectoines and its genetic control by EnuR
Authors: Schulz Annina , Stöveken Nadine , Binzen Ina M. , Hoffmann Tamara , Heider Johann , Bremer Erhard
Published: June 2016

Ectoine and 5‐hydroxyectoine are widely synthesized microbial osmostress protectants. They are also versatile nutrients but their catabolism and the genetic regulation of the corresponding genes are incompletely understood. Using the marine bacterium Ruegeria pomeroyi DSS‐3, we investigated the utilization of ectoines and propose a seven steps comprising catabolic route that entails an initial conversion of 5‐hydroxyectoine to ectoine, the opening of the ectoine ring, and the subsequent degradation of this intermediate to l‐aspartate. The catabolic genes are co‐transcribed with three genes encoding a 5‐hydroxyectoine/ectoine‐specific TRAP transporter. A chromosomal deletion of this entire gene cluster abolishes the utilization of ectoines as carbon and nitrogen sources. The presence of ectoines in the growth medium triggers enhanced expression of the importer and catabolic operon, a process dependent on a substrate‐inducible promoter that precedes this gene cluster. EnuR, a member of the MocR/GabR‐type transcriptional regulators, controls the activity of this promoter and functions as a repressor. EnuR contains a covalently bound pyridoxal‐5’‐phosphate, and we suggest that this co‐factor is critical for the substrate‐mediated induction of the 5‐hydroxyectoine/ectoine import and catabolic genes. Bioinformatics showed that ectoine consumers are restricted to the Proteobacteria and that EnuR is likely a central regulator for most ectoine/5‐hydroxyectoine catabolic genes.
Fetal sex and maternal risk of pre‐eclampsia/eclampsia: a systematic review and meta‐analysis
Authors: Jaskolka D , Retnakaran R , Zinman B , Kramer CK
Published: June 2016

Background

A preponderance of male fetuses in pregnancies complicated by pre‐eclampsia was described over 40 years ago. Since then, however, there has been conflicting evidence in the literature, with some studies supporting a male preponderance, some demonstrating no relationship with fetal sex, and others reporting increased risk in pregnancies bearing females.

Objectives

In this context, we sought to conduct a systematic review and meta‐analysis to objectively evaluate the relationship between fetal sex and maternal risk of pre‐eclampsia/eclampsia.

Search strategy

Studies from January 1950 to April 2015 were identified from PUBMED and EMBASE.

Selection criteria

This systematic review and meta‐analysis evaluated 22 articles reporting data on fetal sex and prevalence of pre‐eclampsia/eclampsia.

Data collection and analysis

Data were extracted by two independent reviewers. Pooled estimates of the relative risk (RR) were calculated by random‐effects model.

Main results

Male fetus was considered the exposure and prevalence of maternal pre‐eclampsia/eclampsia was the outcome of interest. We identified 534 studies through electronic searches and three studies through manual searches. Twenty‐two studies fulfilled the inclusion criteria, yielding data on 3 163 735 women. Pooled analyses of these studies showed no association between male fetal sex and maternal risk of pre‐eclampsia/eclampsia (RR 1.01; 95% confidence interval, 95% CI 0.97–1.05); however, a subgroup analysis including only studies that evaluated the non‐Asian population (n = 2 931 771 women) demonstrated that male fetal sex was associated with increased maternal risk of pre‐eclampsia/eclampsia (RR 1.05; 95% CI 1.03–1.06; I2 = 10%; P = 0.33).

Conclusion

Male fetal sex is associated with maternal risk of pre‐eclampsia/eclampsia in the non‐Asian population.

Tweetable abstract

Fetal sex is associated with maternal risk of pre‐eclampsia/eclampsia in the non‐Asian population.
Relationship between biodiversity and landscape structure in the Gyungan stream basin, central Korea
Authors: Lim Chi Hong , Kim Gyung Soon , An Ji Hong , You Byung Ho , Bae Yang Seop , Byun Hwa Geun , Lee Chang Seok
Published: June 2016

The relationship between landscape structure and biodiversity was investigated in the Gyungan stream basin, central Korea, in order to prepare a biodiversity conservation plan. The study area was divided into upstream, midstream, downstream and Gonjiam stream sub‐watersheds based on the land use pattern of each sub‐watershed. The quality of the terrestrial landscape was assessed by connectivity and percentages of deciduous broad‐leaved forest and urbanized area. The quality of the terrestrial landscape was the highest in the downstream sub‐watershed followed by Gonjiam stream, midstream and upstream sub‐watersheds. The quality of the riparian landscape assessed by percentages of the number and the area that the wetland vegetation elements occupy in the whole area showed a similar trend to that of terrestrial landscape. The diversity of all taxa including fish, reptiles and amphibians, birds, mammals and wetland vegetation except benthic macroinvertebrates was the highest downstream. The diversity of benthic macroinvertebrates was the highest in the Gonjiam stream sub‐watershed. Thus, biodiversity was shown to be the highest in the downstream sub‐watershed, followed, in order, by Gonjiam stream, midstream and upstream sub‐watersheds in proportion to landscape quality. On the other hand, the quality of the aquatic environment based on the ecological score of benthic macroinvertebrate (ESB) index was the highest downstream, followed, in order, by upstream, Gonjiam stream and midstream areas. This trend is different from that of biodiversity. In order to improve landscape quality degraded by excessive land use and to increase biodiversity, we recommended a restoration plan that addresses both ecosystem and landscape.
The Effect of Joint Auditor Pair Composition on Audit Quality: Evidence from Impairment Tests
Authors: Lobo Gerald J. , Paugam Luc , Zhang Dana , Casta Jean François
Published: June 2016

Using a sample of firms from France, where the law requires the use of two auditors, we study the effect of auditor pair composition on audit quality by examining a specific account, goodwill impairment. We document that firms audited by a Big 4–non‐Big 4 auditor pair (BS) are more likely to book an impairment and book a larger impairment than firms audited by a Big 4–Big 4 auditor pair (BB) when low‐performance indicators suggest a greater likelihood of impairment. Moreover, firms audited by a BB pair reduce impairment disclosures when they book impairments, while firms audited by a BS pair do not, suggesting lower transparency for firms audited by a BB pair. Our results inform investors and firms in mandatory joint audit regimes, as well as regulators who are considering requiring joint audits.
Detecting evolutionarily significant units above the species level using the generalised mixed Yule coalescent method
Authors: Humphreys Aelys M. , Rydin Catarina , Jønsson Knud A. , Alsop David , Callender‐Crowe Leah M. , Barraclough Timothy G.
Published: June 2016

There is renewed interest in inferring evolutionary history by modelling diversification rates using phylogenies. Understanding the performance of the methods used under different scenarios is essential for assessing empirical results. Recently, we introduced a new approach for analysing broadscale diversity patterns, using the generalised mixed Yule coalescent (GMYC) method to test for the existence of evolutionarily significant units above the species (higher ESUs). This approach focuses on identifying clades as well as estimating rates, and we refer to it as clade‐dependent. However, the ability of the GMYC to detect the phylogenetic signature of higher ESUs has not been fully explored, nor has it been placed in the context of other, clade‐independent approaches.

We simulated >32 000 trees under two clade‐independent models: constant‐rate birth‐death (CRBD) and variable‐rate birth‐death (VRBD), using parameter estimates from nine empirical trees and more general parameter values. The simulated trees were used to evaluate scenarios under which GMYC might incorrectly detect the presence of higher ESUs.

The GMYC null model was rejected at a high rate on CRBD‐simulated trees. This would lead to spurious inference of higher ESUs. However, the support for the GMYC model was significantly greater in most of the empirical clades than expected under a CRBD process. Simulations with empirically derived parameter values could therefore be used to exclude CRBD as an explanation for diversification patterns. In contrast, a VRBD process could not be ruled out as an alternative explanation for the apparent signature of hESUs in the empirical clades, based on the GMYC method alone. Other metrics of tree shape, however, differed notably between the empirical and VRBD‐simulated trees. These metrics could be used in future to distinguish clade‐dependent and clade‐independent models.

In conclusion, detection of higher ESUs using the GMYC is robust against some clade‐independent models, as long as simulations are used to evaluate these alternatives, but not against others. The differences between clade‐dependent and clade‐independent processes are biologically interesting, but most current models focus on the latter. We advocate more research into clade‐dependent models for broad diversity patterns.
Evaluation of statistical methods and sampling designs for the assessment of microhabitat selection based on point data
Authors: Gorosito Irene L. , Marziali Bermúdez Mariano , Douglass Richard J. , Busch María
Published: June 2016

Information on resource selection by a species is essential for understanding the species’ ecology, distribution and requirements for survival. Research on habitat selection frequently relies on animal detection at point locations to determine which resource units are used. A variety of approaches and statistical tools can be employed for assessing selection based on habitat variables measured in those units. The aim of this work was to evaluate the reliability of common sampling designs and statistical methods in detecting habitat selection at fine scales based on point data

We reviewed literature on microhabitat selection to determine characteristics of typical studies and analysed simulated small‐mammal live‐trapping data as a case study. We considered various scenarios differing in the number of sampled units and sampling duration. For each scenario, a set of simulated surveys was analysed through two univariate tests (Welch's t‐ and Mann–Whitney U‐test), generalized linear models (GLMs), mixed‐effect models (GLMMs) and occupancy models (OMs).

Analysis of simulated data revealed that overall performance of all statistical methods improved with increased trapping effort. Univariate tests were especially sensitive to the number of sampling units, while modelling methods took also advantage of longer trapping sessions. Univariate tests and GLMs provided partially correct information in most cases, whereas GLMMs and OMs offered higher probabilities of fully describing simulated habitat preferences.

With typical sampling efforts, appropriate statistical analysis of point data is able to provide a moderately accurate description of habitat selection at small scales, in spite of the violation of closure and independence assumptions of applied models. Modelling approaches are proliferating; we encourage using models that can deal with multiple sources of variability, such as GLMMs and OMs, when data are hierarchically structured. There is no a priori best survey design; it should be chosen according to the scope and goals of the study, environment heterogeneity, species characteristics and practical constraints. Researchers should realize that sampling design and statistical methods likely affect conclusions regarding habitat selection.
Triplet MaxCut: a new toolkit for rooted supertree
Authors: Sevillya Gur , Frenkel Zeev , Snir Sagi
Published: June 2016

The rapid increase of molecular, as well as other types, of available classification data has created the need to combine this data into a unified hypothesis.

Supertree methods are essential when amalgamating phylogenetic information from various, possibly conflicting, sources into a single tree. The goal of a supertree algorithm is to satisfy maximally each such source of information in the output tree.

Triplets, rooted trees over three leaves, are the minimal piece of such information when dealing with rooted trees. Due to its fundamental role in phylogenetics, extensive effort has been dedicated to several aspects regarding triplets’ research.

We have devised a new tool, Triplet MaxCut (TMC), performing various operations in rooted supertree, principally amalgamating rooted trees based on amalgamating rooted triplets. The utility and efficiency of the algorithm is demonstrated by both simulation study and four real data supertree inputs.
Selection biases in observational studies affect associations between ‘moderate’ alcohol consumption and mortality
Authors: Naimi Timothy S. , Stockwell Timothy , Zhao Jinhui , Xuan Ziming , Dangardt Frida , Saitz Rich , Liang Wenbin , Chikritzhs Tanya
Published: June 2016

Selection biases may lead to systematic overestimate of protective effects from ‘moderate’ alcohol consumption. Overall, most sources of selection bias favor low‐volume drinkers in relation to non‐drinkers. Studies that attempt to address these types of bias generally find attenuated or non‐significant relationships between low‐volume alcohol consumption and cardiovascular disease, which is the major source of possible protective effects on mortality from low‐volume consumption. Furthermore, observed mortality effects among established low‐volume consumers are of limited relevance to health‐related decisions about whether to initiate consumption or to continue drinking purposefully into old age. Short of randomized trials with mortality end‐points, there are a number of approaches that can minimize selection bias involving low‐volume alcohol consumption.
Oocyte competence in in vitro fertilization and intracytoplasmic sperm injection patients suffering from endometriosis and its possible association with subsequent treatment outcome: a matched case–control study
Authors: Shebl Omar , Sifferlinger Ida , Habelsberger Alwin , Oppelt Peter , Mayer Richard B. , Petek Erwin , Ebner Thomas
Published: June 2016

Introduction

Endometriosis affects up to 15% of women of reproductive age. There is an obvious lack of studies dealing with morphological parameters of oocyte morphology in endometriosis patients in assisted reproduction. One aim of the study is to describe oocyte morphology in patients undergoing intracytoplasmic sperm injection suffering from endometriosis. In addition, the impact of endometriosis on in vitro fertilization results is analyzed. Both in vitro fertilization and intracytoplasmic sperm injection patients are then matched with an endometriosis‐free control group for highlighting the possible association of endometriosis with pregnancy outcome.

Material and methods

Oocyte morphology of endometriosis patients was assessed in two groups. Both study group and control group consisted of 129 in vitro fertilization/intracytoplasmic sperm injection cycles each. Patients were matched according to anti‐Müllerian hormone, female age, previous treatment cycles, and method of fertilization. Endometriosis was graded according to the revised American Society for Reproductive Medicine guidelines of 1997.

Results

Patients with endometriosis had a significantly lower rate of mature oocytes (p < 0.03) and morphologically normal oocytes (p < 0.001). In particular, brownish oocytes (p < 0.009; stage I–IV) and the presence of refractile bodies (p < 0.001; stage IV) were found to be increased. Endometriosis stage IV was associated with significantly worse‐quality oocytes than stages I–III (p < 0.01). Fertilization was significantly reduced in conventional in vitro fertilization but not in intracytoplasmic sperm injection (p < 0.03). This was due to lower fertilization rates in stage III–IV endometriosis compared with stage I–II (p < 0.04). No difference was observed with respect to rates of implantation, clinical pregnancy, miscarriage, live birth, and malformation.

Conclusions

Endometriosis patients, in particular those with severe endometriosis, present lower‐quality oocytes. Once fertilized, no impairment of further preimplantation embryo development and pregnancy outcome right up to healthy live birth rate has to be expected.
Reproducibility of the water‐drinking test in patients with exfoliation syndrome and exfoliative glaucoma
Authors: Özyol Erhan , Özyol Pelin , Karalezli Aylin
Published: June 2016

Purpose

To evaluate the reproducibility of intraocular pressure (IOP) peaks and fluctuations detected during the water‐drinking test (WDT) in patients with exfoliation syndrome (XFS) and exfoliative glaucoma (XFG).

Methods

This prospective study included 34 XFS and 30 XFG patients. Each patient was evaluated twice, with the two WDTs performed on a 30‐day interval. We recorded IOP peak (highest IOP during the WDT) and IOP fluctuation (IOP peak minus IOP before the test). Bland–Altman analysis was applied to assess the agreement of IOP peaks and fluctuations between the two consecutive visits. We defined reproducible as within 4 mmHg for IOP peak and within 2 mmHg for IOP fluctuation.

Results

There were no significant differences in IOP values, IOP peaks and IOP fluctuations between the two visits for both XFS and XFG patients (p > 0.05, for all). The coefficient of repeatability for IOP peak was 2.5 mmHg and 3.5 mmHg in XFS and XFG patients respectively and for IOP fluctuation, it was 2.1 mmHg and 2.2 mmHg. None of the XFS or XFG patients had an IOP peak difference higher than 4 mmHg. Intraocular pressure (IOP) fluctuation differences above 2.0 mmHg were found in 8.8% of XFS patients and 16.6% of XFG patients.

Conclusions

Intraocular pressure (IOP) peak and IOP fluctuation have a reproducibility, both in XFS and in XFG.
Cardiovascular effects of cyclooxygenase‐2 inhibitors: a mechanistic and clinical perspective
Authors: Patrono Carlo
Published: June 2016

Linked Articles

This article is part of a joint Themed section with the British Journal of Pharmacology on Targeting Inflammation to Reduce Cardiovascular Disease Risk: a Realistic Clinical Prospect? The rest of the Themed section will appear in a future issue of BJP and will be available at http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1476‐5381

Prostaglandin (PG) H synthase 2 [also referred to colloquially as cyclooxygenase (COX) 2] represents a key enzyme in arachidonic acid metabolism in health and disease. It is both constitutively expressed in several human tissues (e.g. kidney and brain) and induced in various cell types (including monocytes/macrophages, vascular endothelial cells and colorectal cancer cells) in response to inflammatory cytokines, laminar shear stress and growth factors. Products of COX‐2 activity (e.g. PGE2 and prostacyclin) are involved in diverse physiological and pathophysiological processes, including renal haemodynamics and the control of blood pressure, endothelial thromboresistance, pain and inflammation, and colorectal tumorigenesis. Therefore, it is not surprising that COX‐2 inhibitors display multifaceted clinical effects, ranging from reduced pain and inflammation to increased blood pressure, an increased risk of atherothrombotic events and a decreased risk of colorectal cancer. The aim of the present article was to review the cardiovascular effects of COX‐2 inhibitors [traditional nonsteroidal anti‐inflammatory drugs (tNSAIDs) and coxibs alike], with a focus on the mechanisms contributing to the clinical readouts of COX‐2 inhibition.
Unhealthy behaviour modification, psychological distress, and 1‐year survival in cardiac rehabilitation
Authors: Gostoli Sara , Roncuzzi Renzo , Urbinati Stefano , Morisky Donald E. , Rafanelli Chiara
Published: June 2016

Objective

Cardiac rehabilitation (CR) is considered the recommended secondary prevention treatment for cardiovascular diseases (CVD), in terms of health behaviours and, secondarily, better cardiac outcomes promotion. However, the role of psychiatric and psychosomatic distress on the efficacy of CR is unclear. This research aimed to evaluate the impact of CR on unhealthy behaviour modification and cardiac course, considering the moderating role of depression, anxiety, and psychosomatic syndromes.

Design

A longitudinal design between and within groups was employed. The assessment was repeated four times: at admission to CR (T1), at discharge (T2), 6 (T3) and 12 months following CR completion (T4).

Method

One hundred and eight patients undergoing CR versus 85 patients with CVD not referred to CR, underwent psychiatric, psychosomatic, and health behaviour assessment. The assessment included the Structured Clinical Interview for DSM‐IV (depression and anxiety), the interview based on Diagnostic Criteria for Psychosomatic Research, GOSPEL Study questionnaire (health behaviours), Pittsburgh Sleep Quality Index, and 8‐item Morisky Medication Adherence Scale.

Results

Cardiac rehabilitation was associated with maintenance of physical activity, improvement of behavioural aspects related to food consumption, stress management, and sleep quality. On the contrary, CR was not associated with weight loss, healthy diet, and medication adherence. Depression and psychosomatic syndromes seem to moderate the modification of specific health‐related behaviours (physical activity, behavioural aspects of food consumption, stress management, and pharmacological adherence).

Conclusion

In CR settings, an integrated assessment including both psychiatric and psychosomatic syndromes is needed to address psychological factors associated with unhealthy behaviour modification.

Statement of contribution

What is already known on this subject?

Cardiac rehabilitation (CR) is considered a class 1A treatment recommendation and the most cost‐effective model of secondary prevention to reduce cardiovascular events.

There is evidence about the association between psychological distress and both unhealthy behaviour and cardiac course.

Depression and psychosomatic distress, such as type A behaviour and demoralization, are frequently associated with CVD course. However, the role of psychiatric and psychosomatic distress in CR is not well known.

What does this study add?

CR exerted a protective effect on physical activity and a positive effect on eating behaviour, stress management, and quality of sleep.

CR did not show any particular effect on smoking, overweight/obesity, dietary habits, medication adherence, and patients’ 1‐year survival.

Findings from this study suggest the importance to consider specific psychological and psychosomatic aspects in affecting lifestyle.
Minority acculturation and peer rejection: Costs of acculturation misfit with peer‐group norms
Authors: Celeste Laura , Meeussen Loes , Verschueren Karine , Phalet Karen
Published: June 2016

How do minority adolescents’ personal acculturation preferences and peer norms of acculturation affect their social inclusion in school? Turkish and Moroccan minority adolescents (N = 681) reported their preferences for heritage culture maintenance, mainstream culture adoption, and their experiences of peer rejection as a key indicator of adjustment problems. Additionally, we aggregated peer acculturation norms of maintenance and adoption within ethnically diverse classrooms (N = 230 in 50 Belgian schools), distinguishing between co‐ethnic (Turkish or Moroccan classmates only,N = 681) and cross‐ethnic norms (also includingN = 1,930 other classmates). Cross‐ethnic peer‐group norms (of adoption and maintenance) and co‐ethnic norms (of maintenance, marginally) predicted minority experiences of peer rejection (controlling for ethnic composition). Moreover, misfit of minorities’ own acculturation preferences with both cross‐ethnic and co‐ethnic peer‐group norms was harmful. When cross‐ethnic norms stressed adoption, ‘integrationist’ minority youth – who combined culture adoption with maintenance – experienced most peer rejection. Yet, when co‐ethnic peers stressed maintenance, ‘assimilationist’ minority youth experienced most rejection. In conclusion, acculturation misfit with peer‐group norms is a risk factor for minority inclusion in ethnically diverse environments.
Peptide‐based tumor inhibitor encoding mitochondrial p14ARF is highly efficacious to diverse tumors
Authors: Saito Ken , Iioka Hidekazu , Kojima Chie , Ogawa Mikako , Kondo Eisaku
Published: June 2016

p14ARF is one of the major tumor suppressors conventionally identified both as the mdm2‐binding molecule restoring p53 function in the nucleus, and as a nucleophosmin‐binding partner inside the nucleolous to stabilize ribosomal RNA. However, its recently reported mitochondrial localization has pointed to novel properties as a tumor suppressor. At the same time, functional peptides are gaining much attention in nanomedicine for their in vivo utility as non‐invasive biologics. We previously reported the p14ARF‐specific peptide that restored the sensitivity to gefitinib on the gefitinib‐resistant lung cancer cells. Based on the information of this prototype peptide, here we generated the more powerful anti‐tumor peptide “r9‐CatB‐p14 MIS,” which comprises the minimal inhibitory sequence of the mitochondrial targeting p14ARF protein in combination with the proteolytic cleavage site for cathepsin B, which is activated in various tumor cells, fused with the nine‐polyarginine‐domain for cell penetration, and demonstrated its novel action of regulating mitochondrial function in accordance with localization of endogenous p14ARF. The p14 MIS peptide showed a potent tumor inhibiton in vitro and in vivo against not only lung cancer cells but also tumor cells of diverse lineages, via modulating mitochondrial membrane potential, with minimal cytotoxicity to non‐neoplastic cells and tissues. Hence, this mitochondrially targeted p14 peptide agent provides a novel basis for non‐invasive peptide‐based antitumor therapeutics.
Nek2 siRNA therapy using a portal venous port–catheter system for liver metastasis in pancreatic cancer
Authors: Kokuryo Toshio , Hibino Shigeru , Suzuki Kazushi , Watanabe Katsutaka , Yokoyama Yukihiro , Nagino Masato , Senga Takeshi , Hamaguchi Michinari
Published: June 2016

Nek2 (NIMA‐related kinase 2) is a serine‐threonine kinase and human homolog of the mitotic regulator NIMA of Aspergillus nidulan. We reported the efficiency of Nek2 siRNA in several cancer xenograft models using cholangiocarcinoma, breast cancer and colorectal cancer. Pancreatic cancer is difficult to treat due to its rapid progression and resistance to chemotherapy. Novel treatments are urgently required to improve survival in pancreatic cancer, and siRNA are a promising therapeutic option. However, finding an in vivo drug delivery system of siRNA remains a major problem for clinical application. In this study, the overexpression of Nek2 was identified in pancreatic cancer cell lines. Nek2 siRNA inhibited tumor growth in a subcutaneous xenograft mouse model of pancreatic cancer, prolonged the survival time in an intraperitoneal xenograft mouse model and efficiently prevented the progression of liver metastasis using a portal venous port–catheter system. Taken together, Nek2 is an effective therapeutic target in pancreatic cancer. An adequate delivery system is considered important in treating advanced pancreatic cancer, such as peritoneal dissemination and liver metastasis. Further investigations are required on the safety and side effects of the portal venous port–catheter system. We hope that Nek2 siRNA will be a novel therapeutic strategy for pancreatic cancer with liver metastasis and peritoneal dissemination.
Multitargeted bioactive ligands for PPARs discovered in the last decade
Authors: Zhang Jun , Liu Xin , Xie Xian‐Bin , Cheng Xian‐Chao , Wang Run‐Ling
Published: June 2016

Type 2 diabetes took insulin resistance as the main clinical manifestation. PPARs have been reported to be the therapeutic targets of metabolic disorders, such as obesity, hypertension, diabetes, and cardiovascular disease. Previously, PPARγ agonist rosiglitazone was restricted in clinic due to cardiomyocytes infarction, weight gain, and other serious side‐effects, which were mainly due to the single and selective PPARγ agonism. In recent years, multitarget‐directed PPAR agonists with synergistic reaction as well as fewer side‐effect have been the hot topic in designing promising agents. In this review, we updated and generalized the development of PPARγ partial agonists, PPARγ antagonists, PPARα/γ dual agonists, PPARδ partial agonists, PPARδ antagonists, PPARα/δ dual agonists, PPARγ/δ dual agonists, and PPARα/γ/δ pan‐agonists published in recent decade. Most of these molecules were modified from known structures or came from high‐throughput screening. Among these molecules, some were expected to be promising drugs against metabolic disorders, while others seemed to provide new insight for designing novel PPAR agents.