bluuebunny/crossref_metadata_2025 huggingface dataset:
Counting animal species with DNA barcodes: Canadian insects
Authors: Hebert Paul D. N. , Ratnasingham Sujeevan , Zakharov Evgeny V. , Telfer Angela C. , Levesque-Beaudin Valerie , Milton Megan A. , Pedersen Stephanie , Jannetta Paul , deWaard Jeremy R.
Published: August 2016

Recent estimates suggest that the global insect fauna includes fewer than six million species, but this projection is very uncertain because taxonomic work has been limited on some highly diverse groups. Validation of current estimates minimally requires the investigation of all lineages that are diverse enough to have a substantial impact on the final species count. This study represents a first step in this direction; it employs DNA barcoding to evaluate patterns of species richness in 27 orders of Canadian insects. The analysis of over one million specimens revealed species counts congruent with earlier results for most orders. However, Diptera and Hymenoptera were unexpectedly diverse, representing two-thirds of the 46 937 barcode index numbers (=species) detected. Correspondence checks between known species and barcoded taxa showed that sampling was incomplete, a result confirmed by extrapolations from the barcode results which suggest the occurrence of at least 94 000 species of insects in Canada, a near doubling from the prior estimate of 54 000 species. One dipteran family, the Cecidomyiidae, was extraordinarily diverse with an estimated 16 000 species, a 10-fold increase from its predicted diversity. If Canada possesses about 1% of the global fauna, as it does for known taxa, the results of this study suggest the presence of 10 million insect species with about 1.8 million of these taxa in the Cecidomyiidae. If so, the global species count for this fly family may exceed the combined total for all 142 beetle families. If extended to more geographical regions and to all hyperdiverse groups, DNA barcoding can rapidly resolve the current uncertainty surrounding a species count for the animal kingdom. A newly detailed understanding of species diversity may illuminate processes important in speciation, as suggested by the discovery that the most diverse insect lineages in Canada employ an unusual mode of reproduction, haplodiploidy.

This article is part of the themed issue ‘From DNA barcodes to biomes’.
DNA barcoding and taxonomy: dark taxa and dark texts
Authors: Page Roderic D. M.
Published: August 2016

Both classical taxonomy and DNA barcoding are engaged in the task of digitizing the living world. Much of the taxonomic literature remains undigitized. The rise of open access publishing this century and the freeing of older literature from the shackles of copyright have greatly increased the online availability of taxonomic descriptions, but much of the literature of the mid- to late-twentieth century remains offline (‘dark texts’). DNA barcoding is generating a wealth of computable data that in many ways are much easier to work with than classical taxonomic descriptions, but many of the sequences are not identified to species level. These ‘dark taxa’ hamper the classical method of integrating biodiversity data, using shared taxonomic names. Voucher specimens are a potential common currency of both the taxonomic literature and sequence databases, and could be used to help link names, literature and sequences. An obstacle to this approach is the lack of stable, resolvable specimen identifiers. The paper concludes with an appeal for a global ‘digital dashboard’ to assess the extent to which biodiversity data are available online.

This article is part of the themed issue ‘From DNA barcodes to biomes’.
Multilocus inference of species trees and DNA barcoding
Authors: Mallo Diego , Posada David
Published: August 2016

The unprecedented amount of data resulting from next-generation sequencing has opened a new era in phylogenetic estimation. Although large datasets should, in theory, increase phylogenetic resolution, massive, multilocus datasets have uncovered a great deal of phylogenetic incongruence among different genomic regions, due both to stochastic error and to the action of different evolutionary process such as incomplete lineage sorting, gene duplication and loss and horizontal gene transfer. This incongruence violates one of the fundamental assumptions of the DNA barcoding approach, which assumes that gene history and species history are identical. In this review, we explain some of the most important challenges we will have to face to reconstruct the history of species, and the advantages and disadvantages of different strategies for the phylogenetic analysis of multilocus data. In particular, we describe the evolutionary events that can generate species tree—gene tree discordance, compare the most popular methods for species tree reconstruction, highlight the challenges we need to face when using them and discuss their potential utility in barcoding. Current barcoding methods sacrifice a great amount of statistical power by only considering one locus, and a transition to multilocus barcodes would not only improve current barcoding methods, but also facilitate an eventual transition to species-tree-based barcoding strategies, which could better accommodate scenarios where the barcode gap is too small or inexistent.

This article is part of the themed issue ‘From DNA barcodes to biomes’.
DNA barcoding in diverse educational settings: five case studies
Authors: Henter Heather J. , Imondi Ralph , James Karen , Spencer Diana , Steinke Dirk
Published: August 2016

Despite 250 years of modern taxonomy, there remains a large biodiversity knowledge gap. Most species remain unknown to science. DNA barcoding can help address this gap and has been used in a variety of educational contexts to incorporate original research into school curricula and informal education programmes. A growing body of evidence suggests that actively conducting research increases student engagement and retention in science. We describe case studies in five different educational settings in Canada and the USA: a programme for primary and secondary school students (ages 5–18), a year-long professional development programme for secondary school teachers, projects embedding this research into courses in a post-secondary 2-year institution and a degree-granting university, and a citizen science project. We argue that these projects are successful because the scientific content is authentic and compelling, DNA barcoding is conceptually and technically straightforward, the workflow is adaptable to a variety of situations, and online tools exist that allow participants to contribute high-quality data to the international research effort. Evidence of success includes the broad adoption of these programmes and assessment results demonstrating that participants are gaining both knowledge and confidence. There are exciting opportunities for coordination among educational projects in the future.

This article is part of the themed issue ‘From DNA barcodes to biomes’.
Aging increases lateral but not local inhibition of orientation processing in primary visual cortex
Authors: Wang Zhengchun , Yu Shan , Fu Yu , Zhou Yifeng , Tzvetanov Tzvetomir
Published: August 2016

Aging-related declines in vision can decrease well-being of the elder. Concerning early sensory changes as in the primary visual cortex, physiological and behavioral reports seem contradictory. Neurophysiological studies on orientation tuning properties suggested that neuronal changes might come from decreased cortical local inhibition. However, behavioral results either showed no clear deficits in orientation processing in the elder, or proposed stronger surround suppression. Through psychophysical experiments conducted on old and young human subjects combined with computational modeling, we resolved these discrepancies by demonstrating stronger lateral inhibition in the elder while neuronal orientation tuning widths, related to local inhibition, stayed globally intact across age. We confirmed this later finding by re-analyzing published neurophysiological data from rhesus monkeys, which showed no systematic tuning width changes, but instead a higher neuronal noise with aging. These results suggest a stronger lateral inhibition and mixed effects on local inhibition during aging, revealing a more complex picture of age-related effects in the central visual system than previously thought.

Significance Statement

Visual functions decline during aging, adversely affecting quality of life. Much of this dysfunction is probably mediated by disturbances in the balance between inhibition and excitation in the central visual system. It was proposed that the inhibitory function within the aging visual cortex might be modified, but huge discrepancies exist among different reports. Here we identify the specific inhibitory circuit change, which has not been clearly evaluated, by using behavioral measures, neural modeling and re-analysis of non-human primate electrophysiological data. We provide evidence that a stronger lateral inhibition and mixed effects on local inhibition during aging, revealing a more complex picture of age-related effects in the central visual system than previously thought.

Author contributions

ZCW and TT designed and analyzed behavioral experiments; ZCW performed experiments; ZCW and TT performed data analysis and neurophysiological re-analysis; YS and FY provided physiological data and discussed its re-analysis; TT performed modeling; ZCW, YFZ and TT provided project supervision and funds; ZCW and TT wrote the paper; all authors discussed and commented on the manuscript.
Central Roles for Potassium and Sucrose in Guard-Cell Osmoregulation
Authors: Talbott L. D. , Zeiger E.
Published: August 2016

Osmoregulation in guard cells of intact, attached Vicia faba leaves grown under growth chamber and greenhouse conditions was studied over a daily light cycle of stomatal movements. Under both growth conditions guard cells had two distinct osmoregulatory phases. In the first (morning) phase, opening was correlated with K+ uptake and, to a lesser extent, sucrose accumulation. In the second (afternoon) phase, in which apertures were maximal, K+ content declined and sucrose became the dominant osmoticum. Reopening of the stomata after a CO2-induced closure was accompanied by accumulation of either K+ or sucrose, depending on the time of day, indicating that a single environmental signal may use multiple osmoregulatory pathways. Malate accumulation, correlated with K+ uptake, was detected under growth chamber but not greenhouse conditions, whereas Cl- was the main K+ counterion in the greenhouse. These results indicate that guard-cell osmoregulation in the intact leaf depends on at least two different osmoregulatory pathways, K+ transport and sucrose metabolism. Furthermore, the relative importance of the K+ counterions malate and Cl- appears to be environment-dependent.
Analysis of the Expression of Anthocyanin Pathway Genes in Developing Vitis vinifera L. cv Shiraz Grape Berries and the Implications for Pathway Regulation
Authors: Boss P. K. , Davies C. , Robinson S. P.
Published: August 2016

Anthocyanin synthesis in Vitis vinifera L. cv Shiraz grape berries began 10 weeks postflowering and continued throughout berry ripening. Expression of seven genes of the anthocyanin biosynthetic pathway (phenylalanine ammonia lyase [PAL], chalcone synthase [CHS], chalcone isomerase [CHI], flavanone-3-hydroxylase [F3H], dihydroflavonol 4-reductase [DFR], leucoanthocyanidin dioxygen-ase [LDOX], and UDP glucose-flavonoid 3-o-glucosyl transferase [UFGT]) was determined. In flowers and grape berry skins, expression of all of the genes, except UFGT, was detected up to 4 weeks postflowering, followed by a reduction in this expression 6 to 8 weeks postflowering. Expression of CHS, CHI, F3H, DFR, LDOX, and UFGT then increased 10 weeks postflowering, coinciding with the onset of anthocyanin synthesis. In grape berry flesh, no PAL or UFGT expression was detected at any stage of development, but CHS, CHI, F3H, DFR, and LDOX were expressed up to 4 weeks postflowering. These results indicate that the onset of anthocyanin synthesis in ripening grape berry skins coincides with a coordinated increase in expression of a number of genes in the anthocyanin biosynthetic pathway, suggesting the involvement of regulatory genes. UFGT is regulated independently of the other genes, suggesting that in grapes the major control point in this pathway is later than that observed in maize, petunia, and snapdragon.
Evidence for an Elongation/Reduction/C1-Elimination Pathway in the Biosynthesis of n-Heptane in Xylem of Jeffrey Pine
Authors: Savage T. J. , Hristova M. K. , Croteau R.
Published: August 2016

The biosynthetic pathway to n-heptane was investigated by examining the effect of the β-keto acyl-acyl carrier protein synthase inhibitor (2R,3S)-2,3-epoxy-4-oxo-7E,10E-dodecadienamide (cerulenin), a thiol reagent (β-mercaptoethanol), and an aldehydetrapping reagent (hydroxylamine) on the biosynthesis of n-[14C]heptane and putative intermediates in xylem sections of Jeffrey pine (Pinus jeffreyi Grev. & Balf.) incubated with [14C]acetate. Cerulenin inhibited C18 fatty acid biosynthesis but had relatively little effect on radiolabel incorporation into C8 fatty acyl groups and n-heptane. β-Mercaptoethanol inhibited n-heptane biosynthesis, with a corresponding accumulation of radiolabel into both octanal and 1-octanol, whereas hydroxylamine inhibited both n-heptane and 1-octanol biosynthesis, with radiolabel accumulation in octyl oximes. [14C]Octanal was converted to both n-heptane and 1-octanol when incubated with xylem sections, whereas [14C]1-octanol was converted to octanal and n-heptane in a hydroxylamine-sensitive reaction. These results suggest a pathway for the biosynthesis of n-heptane whereby acetate is polymerized via a typical fatty acid synthase reaction sequence to yield a C8 thioester, which subsequently undergoes a two-electron reduction to generate a free thiol and octanal, the latter of which alternately undergoes an additional, reversible reduction to form 1-octanol or loss of C1 to generate n-heptane.
Molecular and Structural Changes in Chlamydomonas under Limiting CO2 (A Possible Mitochondrial Role in Adaptation)
Authors: Geraghty A. M. , Spalding M. H.
Published: August 2016

When Chlamydomonas reinhardtii cells are transferred to limiting CO2, one response is the induction of a CO2-concentrating mechanism (CCM) with components that remain to be identified. Characterization of membrane-associated proteins induced by this transfer revealed that synthesis of the 21-kD protein (LIP-21) was regulated at the level of translatable message abundance and correlated well with the induction of CCM activity. Phase partitioning of LIP-21 and the previously characterized LIP-36 showed that both appeared to be peripherally associated with membranes, which limits their potential to function as transporters of inorganic carbon. Ultrastructural changes that occur when cells are transferred to limiting CO2 were also examined to help form a model for the CCM or other aspects of adaptation to limiting CO2. Changes were observed in vacuolization, starch distribution, and mitochondrial location. The mitochondria relocated from within the cup of the chloroplast to between the chloroplast envelope and the plasma membrane. In addition, immunogold labeling demonstrated that LIP-21 was localized specifically to the peripheral mitochondria. These data suggest that mitochondria, although not previously incorporated into models for the CCM, may play an important role in the cell's adaptation to limiting CO2.
Understanding users’ continuance intention to use online library resources based on an extended expectation-confirmation model
Authors: Joo Soohyung , Choi Namjoo
Published: August 2016

Purpose

This study aims to investigate the factors affecting students’ continuance intention to use online library resources (OLRs) in the context of academic libraries. Based on an extended expectation confirmation theory (ECT), the effects of usefulness, confirmation and resource quality on continuance intention to use OLRs were examined.

Design/methodology/approach

To empirically test the model, a survey study was conducted. Data were collected from 606 student library users at a large state university in the USA. The collected data were analysed quantitatively to answer seven hypotheses using partial least squares method.

Findings

The findings revealed that both usefulness and confirmation had a positive direct and indirect influence on continuance intention. Also, the effect of resource quality on continuance intention was found to be significant. Satisfaction had a mediating effect on the relationship between usefulness, confirmation and resource quality, and continuance intention.

Originality/value

This study is one of the first attempts that adopted the ECT to understand students’ continuance intention to use OLRs. In addition, the effect of the multiple dimensions of resource quality – accessibility, credibility, coverage, and format – on users’ continuance intention to use OLRs was investigated.
The moderating role of consumer characteristics in the relationship between website quality and perceived usefulness
Authors: Wang Edward Shih-Tse
Published: August 2016

Purpose

– Online group buying (OGB) websites have rapidly increased in number in recent years and have become an interesting model for online transactions. Previous studies have shown that consumers’ individual characteristics are critical in group buying participation and the perceived usefulness (PU) of an information system, whereas the role of consumer characteristics on the OGB website-quality-PU relationship remains unclear. The purpose of this paper is to investigate whether consumer characteristics (i.e. gender and utilitarian orientation) moderate the OGB website-quality-PU relationship.

Design/methodology/approach

– A total of 658 OGB website consumers participated in this study. Data were analysed by employing hierarchical moderated regression method.

Findings

– The primary findings are as follows. First, the effect of system quality on consumer PU of the OGB website was stronger for male consumers than for female consumers. Second, the effect of information quality on PU was stronger for high-utility-orientated consumers than for low-utility-orientated consumers.

Originality/value

– Because of the increasing importance of e-commerce and the growing number of shoppers purchasing from OGB websites, the finding provides enhanced understanding of OGB consumers for segmentation strategies.
Bank accounting disclosure, information content in stock prices, and stock crash risk
Authors: Du Chan , Song Liang , Wu Jia
Published: August 2016

Purpose

This paper aims to examine how banks’ accounting disclosure policies affect information content in stock prices and stock crash risk.

Design/methodology/approach

This paper uses 1996-2013 as the sample period. The final sample includes 10,045 observations in 37 countries. This paper uses stock return synchronicity to measure information content in stock prices. This study uses the frequency difference between extremely negative and positive stock returns to measure stock crash risk. To measure the level of bank accounting disclosure, this research follows Nier and Baumann (2006) to construct an aggregate disclosure index based on inclusions and omissions of a series of items in a bank’s annual accounting reports.

Findings

This paper finds that banks’ stocks have lower stock return synchronicity and fewer extremely negative returns if banks have higher levels of financial statement disclosure. These results suggest that banks’ stocks have higher information content and lower crash risk if banks’ information environment is more transparent.

Originality/value

Overall, this paper provides new insight about how to increase banks’ transparency and the safety of the banking industry, which is beneficial to economic growth. To increase banks’ transparency and reduce the possibility of extremely negative stock returns, one way to regulate banks is to increase their accounting disclosure. In addition, the extant literature (Chen et al., 2006, Durnev et al., 2003, 2004; Wurgler, 2000) demonstrates that firms with lower stock return synchronicity have more transparent information environments and higher investment efficiency. Thus, this paper finds that higher levels of bank accounting disclosure are associated with lower stock return synchronicity, which further reduces banks’ opacity and increases banks’ investment efficiency. Finally, compared to business firms, stock crash risk has much direr consequences because one bank’s stock crash will affect overall financial stability. Thus, it is important for authorities to know the effects of accounting disclosure on bank stock crash risk.
Audit failure of New Zealand finance companies – an exploratory investigation
Authors: Kabir Humayun , Su Li , Rahman Asheq
Published: August 2016

Purpose

The setting of private finance companies that failed in New Zealand during 2006-2012 was characterized by weaker corporate governance and enforcement of securities law. This paper aims to explore audit failure in this setting and examine whether auditors erred in their audits of the failed finance companies and whether the audit failure rate of Big N auditors was different from that of non-Big N auditors.

Design/methodology/approach

This paper adopts the archival research method and uses three sets of evidence to assess audit failure – the frequency of going concern opinion (GCO) prior to failure, misstatements in the last audited financial statements, and the violation of the Code of Ethics.

Findings

The study finds that only 41 per cent of the sample companies received the GCO in their last audit prior to failure and provides evidence of material misstatements in the financial statements of a number of failed finance companies that received clean audit opinions prior to failure and breaches of the Code of Ethics by a number of auditors. These results strongly indicate audit failure for a number of failed finance companies. The audit failure rate, however, appears less for Big N auditors than for non-Big N auditors.

Practical implications

The study draws attention of the stock market regulator and the accounting profession to an area, the audit of private finance companies, that needs better quality audits.

Originality/value

This paper provides systematic evidence of audit failure in failed finance companies in New Zealand. It also furnishes preliminary evidence of Big N auditors compensating for weaker corporate governance.
Sustainability assurance: an emerging market for the accounting profession
Authors: Wong Joshua , Wong Norman , Li Willow Yangliu , Chen Li
Published: August 2016

Purpose

The purpose of this study is to examine firm-specific characteristics that influence firms’ choice of assurance provider in sustainability assurance. The market for sustainability assurance consists of three types: accounting firms (particularly the Big 4 firms), non-accounting specialist consulting firms (that specialise only in sustainability issues) and non-accounting general consulting firms (that provide general advisory/consulting services).

Design/methodology/approach

Using a sample selected from the top 100 publicly listed companies in the UK and USA that published a sustainability report in 2010 and 2011, respectively, for which assurance was obtained, a multinomial logistic regression model is applied by regressing the three types of assurance providers on firm size, leverage, profit, liquidity, percentage of strategic shareholding and two control variables – country and year.

Findings

The results indicate that the choice of sustainability assurance provider is related to firm size, profitability, liquidity and country.

Research limitations/implications

There may be relevant variables omitted from the empirical analysis; results of this study may not be able to be generalized beyond the sample selected; and the sample size is relatively small.

Practical implications

Sustainability assurance is a viable assurance service that the accounting profession can provide.

Originality/value

This study helps in identifying the types of firms that are likely to demand assurance services provided by accounting firms.
A fresh approach reveals how dispersal shapes metacommunity structure in a human‐altered landscape
Authors: Downes Barbara J. , Lancaster Jill , Glaister Alena , Bovill William D.
Published: August 2016

To understand species losses from disturbed landscapes, it is important to distinguish the effects of degraded environmental conditions from those caused by barriers to dispersal between habitat patches. To assess the relative importance of these effects, we developed a new approach using permutation and association tests applied to rank abundance data, using the invertebrate fauna of two rivers in two seasons.

Our study streams were Hughes Creek and Seven Creeks, in south‐eastern Australia, which have both been degraded by agriculture in downstream sections. We collected benthic invertebrates and also dispersing individuals (drift, terrestrial adults) during two seasons in 2007–2008. Study sites spanned strong environmental gradients as well as the main dispersal route (up‐ and down‐channel). Environmental data were analysed to set up permutation tests on rank abundances. Survey and disperser data were contrasted using contingency table analyses.

The results suggest dispersal plays a strong role in community structure. Environmental effects were evident and strongest upstream, but evidence of environmental effects was weak over much of the gradient. Many species had different distributions in different data sets or dispersers that were abundant at locations distant from centres of benthic distribution.

Our results differ from many studies, but few have been able to evaluate dispersal effects directly. Our method provides a practical approach for evaluating the role dispersal plays in driving species abundance patterns across landscapes, thus bridging a gap between theory and practice.

Synthesis and applications. Managers typically use indices of ecosystem health that assume environmental conditions largely determine species diversity and abundance. Dispersal between habitat patches is known to be important, but there are no reliable methods to assess the role dispersal may play. We provide an approach that allows both dispersal and environmental effects on species distributions to be evaluated from survey data. This may open the way for dispersal information to be incorporated into management actions. Additionally, the approach should allow improved siting of restoration projects that depend greatly on successful dispersal of individuals for successful outcomes.
Modelling flight heights of lesser black‐backed gulls and great skuas from GPS: a Bayesian approach
Authors: Ross‐Smith Viola H. , Thaxter Chris B. , Masden Elizabeth A. , Shamoun‐Baranes Judy , Burton Niall H. K. , Wright Lucy J. , Rehfisch Mark M. , Johnston Alison
Published: August 2016

Wind energy generation is increasing globally, and associated environmental impacts must be considered. The risk of seabirds colliding with offshore wind turbines is influenced by flight height, and flight height data usually come from observers on boats, making estimates in daylight in fine weather. GPS tracking provides an alternative and generates flight height information in a range of conditions, but the raw data have associated error.

Here, we present a novel analytical solution for accommodating GPS error. We use Bayesian state‐space models to describe the flight height distributions and the error in altitude measured by GPS for lesser black‐backed gulls and great skuas, tracked throughout the breeding season. We also examine how location and light levels influence flight height.

Lesser black‐backed gulls flew lower by night than by day, indicating that this species would be less likely to encounter turbine blades at night, when birds’ ability to detect and avoid them might be reduced. Gulls flew highest over land and lowest near the coast. For great skuas, no significant relationships were found between flight height, time of day and location.

We consider four ‘collision risk windows’, corresponding to the airspace swept by rotor blades for different offshore wind turbine designs. We found the highest proportion of birds at risk for a 22–250 m turbine (up to 9% for great skuas and 34% for lesser black‐backed gulls) and the lowest for a 30–258 m turbine. Our results suggest lesser black‐backed gulls are at greater risk of collision than great skuas, especially by day.

Synthesis and applications. Our novel modelling approach is an effective way of resolving the error associated with GPS tracking data. We demonstrate its use on GPS measurements of altitude, generating important information on how breeding seabirds use their environment. This approach and the associated data also provide information to improve avian collision risk assessments for offshore wind farms. Our modelling approach could be applied to other GPS data sets to help manage the ecological needs of seabirds and other species at a time when the pressures on the marine environment are growing.
Evidence of small‐scale spatial structuring of phytoplankton alpha‐ and beta‐diversity in the open ocean
Authors: Mousing Erik Askov , Richardson Katherine , Bendtsen Jørgen , Cetinić Ivona , Perry Mary Jane
Published: August 2016

Phytoplankton assemblages in the open ocean are usually assumed to be mixed on local scales unless large semi‐permanent density discontinuities separating water masses are present. Recent modelling studies have, however, suggested that ephemeral submesoscale oceanographic features leading to only subtle density discontinuities may be important for controlling phytoplankton alpha‐ and beta‐diversity patterns. Until now, no empirical evidence has been presented to support this hypothesis.

Using hydrographic and taxonomic composition data collected near Iceland during the period of the 2008 spring bloom, we show that the distribution of phytoplankton alpha‐ and beta‐diversity was related to submesoscale heterogeneity in oceanographic conditions. Distinct phytoplankton communities as well as differences in richness were identified on either side of a front delimiting surface waters of slightly different (˜0.03) salinities.

Alpha‐diversity was significantly higher on the high salinity side of the front compared to the low salinity side. This difference was primarily driven by the presence of several large diatom species in the high salinity region, especially of the genusChaetoceroswhich dominated the biomass here. By investigating beta‐diversity in relation to environmental and spatiotemporal variables, we show that the regional distribution of phytoplankton taxa was influenced by both different environmental conditions on either side of the front and dispersal limitation across the front. Changes in beta‐diversity were primarily driven by turnover rather than nestedness and were apparently controlled by different processes in each region.

Synthesis. This study shows that small‐scale and ephemeral density discontinuities created by submesoscale frontal dynamics can play a major role in structuring patterns of phytoplankton diversity. Evidence is presented that they can generate changes in environmental conditions (leading to environmental filtering) and act as physical (dispersal) barriers for phytoplankton transport. The study suggests that dispersal barriers are potentially of much greater importance for phytoplankton diversity at local scales than currently recognized and indicates that drivers of marine phytoplankton diversity are similar to those structuring diversity of land plants.
VIOLENT OFFENDING AND VICTIMIZATION IN ADOLESCENCE: SOCIAL NETWORK MECHANISMS AND HOMOPHILY*
Authors: TURANOVIC JILLIAN J. , YOUNG JACOB T.N.
Published: August 2016

Although violent offending and victimization share many features, they can affect adolescent social relationships in distinct ways. To understand these differences, we take a network approach to examine the mechanisms responsible for similarities (i.e., homophily) in violent offending and violent victimization among friends. Our goal is to determine whether the social network mechanisms that produce homophily for violent offending are similar to or different from those that produce homophily for violent victimization. By using stochastic actor‐oriented modeling and two waves of friendship network data for 1,948 respondents from the National Longitudinal Study of Adolescent to Adult Health, we examine homophily mechanisms of preference for similarity, avoidance, and influence with respect to youth violence and victimization. The results demonstrate that homophily observed for violent offending primarily reflects selection of similar others, whereas homophily observed for victimization reflects the tendency among alters to avoid victimized youth. These findings have important implications for future research and suggest that, among adolescents, violent offending and victimization homophily are the result of unique social processes.
Multi‐tissue stable‐isotope analyses can identify dietary specialization
Authors: Bond Alexander L. , Jardine Timothy D. , Hobson Keith A.
Published: August 2016

Individual specialization along one or more niche axes is now recognized as an integral and ubiquitous aspect of populations. A major challenge, however, is quantifying the level of specialization using robust metrics that are applicable across species and ecosystems. Measuring stable‐isotope values in multiple tissues with different isotopic turnover rates could be one mechanism for quantifying specialization.

We used simulation studies of stable‐isotope values to investigate how the recently proposed relative index of specialization varies in relation to variance in prey isotope values, diet–tissue discrimination factors, specialist group size and tissue half‐life, and applied specialization metrics to two systems – Australian freshwater fish and marine birds in the Canadian Arctic.

In all simulations, populations comprised entirely of generalists were easily separated from those with even small amounts (5%) of individual specialization. In some cases, however, specialization measured using isotope values with bimodal distributions may appear similar to those with univariate distributions, but this can be detected by examining the original data. All fish and bird species examined showed varying degrees of individual specialization.

Analysing stable isotopes in multiple tissues can provide a useful index of the degree of specialization within a population that can be compared to the same metric measured in other groups or species.
Do Emergency Medicine Residency Graduates Feel Prepared to Manage Closed Fractures After Training?
Authors: Pittman Mark A. , Yarris Lalena M. , Lall Michelle D. , Smith Jessica L. , Wills Charlotte P. , Ufberg Jacob W. , Hegarty Cullen B. , Love Jeffrey N.
Published: August 2016

Objectives

Fractures comprise 3% of all emergency department (ED) visits. Although emergency physicians are often responsible for managing most of the initial care of these patients, many report a lack of proficiency and comfort with these skills. The primary objective was to assess how prepared recent emergency medicine (EM) residency graduates felt managing closed fractures upon completion of residency. Secondary objectives included whether residency training or independent practice contributed most to the current level of comfort with these procedures and which fractures were most commonly reduced without orthopedic consultation.

Methods

An anonymous online survey was sent to graduates from seven EM residency programs over a 3‐month period to evaluate closed fracture reduction training, practice, and comfort level. Each site primary investigator invited graduates from 2010 to 2014 to participate and followed a set schedule of reminders.

Results

The response rate was 287/384 (74.7%) and included 3‐year (198/287, 69%) and 4‐year (89/287, 31%) programs. Practice in community, academic, and hybrid ED settings was reported by 150/287 (52.3%), 64/287 (22.3%), and 73/287 (25.4%), respectively. It was indicated by 137/287 (47.7%) that they reduce closed fractures without a bedside orthopedic consultation greater than 75% of the time. The majority of graduates felt not at all prepared (35/287, 12.2%) or somewhat prepared (126/287, 43.9%) upon residency graduation. Postresidency independent practice contributed most to the current level of comfort for 156/287 (54.4%). The most common fractures requiring reduction were wrist/distal radius and/or ulna, next finger/hand, and finally, ankle/distal tibia and/or fibula.

Conclusions

Although most recent graduates feel at least “somewhat” prepared to manage closed fractures in the ED, most felt that independent practice was a greater contributor to their current level of comfort than residency training. Recent graduates indicate that fracture reduction without orthopedic consultation is common in today's clinical practice. This survey identifies common fractures requiring reduction which EM residencies may wish to consider prioritizing in their emergency orthopedic curricula to better prepare their residents for independent clinical practice.
A genome‐wide association study of heat stress‐associated SNPs in catfish
Authors: Jin Y. , Zhou T. , Geng X. , Liu S. , Chen A. , Yao J. , Jiang C. , Tan S. , Su B. , Liu Z.
Published: August 2016

Heat tolerance is a complex and economically important trait for catfish genetic breeding programs. With global climate change, it is becoming an increasingly important trait. To better understand the molecular basis of heat stress, a genome‐wide association study (GWAS) was carried out using the 250 K catfish SNP array with interspecific backcross progenies, which derived from crossing female channel catfish with male F1 hybrid catfish (female channel catfish × male blue catfish). Three significant associated SNPs were detected by performing an EMMAX approach for GWAS. The SNP located on linkage group 14 explained 12.1% of phenotypical variation. The other two SNPs, located on linkage group 16, explained 11.3 and 11.5% of phenotypical variation respectively. A total of 14 genes with heat stress related functions were detected within the significant associated regions. Among them, five genes—TRAF2, FBXW5, ANAPC2, UBR1 and KLHL29— have known functions in the protein degradation process through the ubiquitination pathway. Other genes related to heat stress include genes involved in protein biosynthesis (PRPF4 and SYNCRIP), protein folding (DNAJC25), molecule and iron transport (SLC25A46 and CLIC5), cytoskeletal reorganization (COL12A1) and energy metabolism (COX7A2, PLCB1 and PLCB4) processes. The results provide fundamental information about genes and pathways that is useful for further investigation into the molecular mechanisms of heat stress. The associated SNPs could be promising candidates for selecting heat‐tolerant catfish lines after validating their effects on larger and various catfish populations.
The relationships between symptoms and quality of life over the course of cognitive‐behavioral therapy for panic disorder in Japan
Authors: Ogawa Sei , Kondo Masaki , Okazaki Jynya , Imai Risa , Ino Keiko , Furukawa Toshi A , Akechi Tatsuo
Published: August 2016

Introduction

This study examined the relationships between changes in symptoms and changes in quality of life (QOL) during cognitive‐behavioral therapy (CBT) for panic disorder (PD).

Methods

We treated 198 PD patients with group CBT in Japan. Using multiple regression analysis, we examined the associations between changes in QOL and changes in PD symptoms or comorbid psychological symptoms during CBT.

Results

Changes in anticipatory anxiety, agoraphobic fear/avoidance, and somatization were significant predictors of changes in some aspects of QOL.

Discussion

It might be useful to decrease somatization, anticipatory anxiety, and agoraphobic fear to improve QOL in CBT for PD.
In vitro safety assessments and antimicrobial activities of Lactobacillus rhamnosus strains isolated from a fermented mare's milk
Authors: Aryantini Ni Putu Desy , Yamasaki Eiki , Kurazono Hisao , Sujaya I Nengah , Urashima Tadasu , Fukuda Kenji
Published: August 2016

Safety and probiotic characteristics such as antimicrobial activities of three Lactobacillus rhamnosus strains, FSMM15, FSMM22 and FSMM26, previously isolated as potential probiotics from fermented mare's milk were investigated. The three FSMM strains were susceptible to ampicillin, gentamycin, kanamycin, streptomycin, tetracycline and chloramphenicol, whereas they were resistant to erythromycin (minimal inhibitory concentration (MIC) = 4−8 µg/mL) and clindamycin (MIC = 4 µg/mL); bioconversion of bile salts, hemolytic activity and mucin degradation activity were negative; enzymatic activities of α‐chymotrypsin and β‐glucosidase were detected, but those of α‐galactosidase, β‐glucuronidase and N‐acetyl‐β‐glucosaminidase, were undetectable. Among the strains, strain FSMM15 was chosen as a safer probiotic candidate due mainly to the lack of plasminogen binding ability. Despite lower acid production of strain FSMM15 than others, its cell‐free culture supernatant inhibited growths of Salmonella Typhimurium LT‐2, Shigella sonnei, Listeria monocytogenes, and Escherichia coli O157 with comparable levels of ampicillin, suggesting a favorable aspect of strain FSMM15 as a probiotic strain.
Detecting Rare and Common Haplotype–Environment Interaction under Uncertainty of Gene–Environment Independence Assumption
Authors: Zhang Yuan , Lin Shili , Biswas Swati
Published: August 2016

Finding rare variants and gene–environment interactions (GXE) is critical in dissecting complex diseases. We consider the problem of detecting GXE where G is a rare haplotype and E is a nongenetic factor. Such methods typically assume G-E independence, which may not hold in many applications. A pertinent example is lung cancer—there is evidence that variants on Chromosome 15q25.1 interact with smoking to affect the risk. However, these variants are associated with smoking behavior rendering the assumption of G-E independence inappropriate. With the motivation of detecting GXE under G-E dependence, we extend an existing approach, logistic Bayesian LASSO, which assumes G-E independence (LBL-GXE-I) by modeling G-E dependence through a multinomial logistic regression (referred to as LBL-GXE-D). Unlike LBL-GXE-I, LBL-GXE-D controls type I error rates in all situations; however, it has reduced power when G-E independence holds. To control type I error without sacrificing power, we further propose a unified approach, LBL-GXE, to incorporate uncertainty in the G-E independence assumption by employing a reversible jump Markov chain Monte Carlo method. Our simulations show that LBL-GXE has power similar to that of LBL-GXE-I when G-E independence holds, yet has well-controlled type I errors in all situations. To illustrate the utility of LBL-GXE, we analyzed a lung cancer dataset and found several significant interactions in the 15q25.1 region, including one between a specific rare haplotype and smoking.
A Framework for Bayesian Nonparametric Inference for Causal Effects of Mediation
Authors: Kim Chanmin , Daniels Michael J. , Marcus Bess H. , Roy Jason A.
Published: August 2016

We propose a Bayesian non-parametric (BNP) framework for estimating causal effects of mediation, the natural direct, and indirect, effects. The strategy is to do this in two parts. Part 1 is a flexible model (using BNP) for the observed data distribution. Part 2 is a set of uncheckable assumptions with sensitivity parameters that in conjunction with Part 1 allows identification and estimation of the causal parameters and allows for uncertainty about these assumptions via priors on the sensitivity parameters. For Part 1, we specify a Dirichlet process mixture of multivariate normals as a prior on the joint distribution of the outcome, mediator, and covariates. This approach allows us to obtain a (simple) closed form of each marginal distribution. For Part 2, we consider two sets of assumptions: (a) the standard sequential ignorability (Imai et al., 2010) and (b) weakened set of the conditional independence type assumptions introduced in Daniels et al. (2012) and propose sensitivity analyses for both. We use this approach to assess mediation in a physical activity promotion trial.
Advances in drug delivery to high grade gliomas
Authors: Frosina Guido
Published: August 2016

If cancer is hard to be treated, brain cancer is even more, caused by the inability of many effective drugs given systemically to cross the blood brain and blood tumor barriers and reach adequate concentrations at the tumor sites. Effective delivery of drugs to brain cancer tissues is thus a necessary, albeit not sufficient, condition to effectively target the disease. In order to analyze the current status of research on drug delivery to high grade gliomas (HGG‐WHO grades III and IV), the most frequent and aggressive brain cancers, a literature search was conducted in PubMed using the terms: “drug delivery and brain tumor” over the publication year 2015. Currently explored drug delivery techniques for HGG include the convection and permeabilization‐enhanced deliveries, drug‐releasing depots and Ommaya reservoirs. The efficacy/safety ratio widely varies among these techniques and the success of current efforts to increase this ratio widely varies as well.
Redox‐based therapeutics in neurodegenerative disease
Authors: McBean G J , López M G , Wallner F K
Published: August 2016

This review describes recent developments in the search for effective therapeutic agents that target redox homeostasis in neurodegenerative disease. The disruption to thiol redox homeostasis in Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis and multiple sclerosis is discussed, together with the experimental strategies that are aimed at preventing, or at least minimizing, oxidative damage in these diseases. Particular attention is given to the potential of increasing antioxidant capacity by targeting the Nrf2 pathway, the development of inhibitors of NADPH oxidases that are likely candidates for clinical use, together with strategies to reduce nitrosative stress and mitochondrial dysfunction. We describe the shortcomings of compounds that hinder their progression to the clinic and evaluate likely avenues for future research.

Linked Articles

This article is part of a themed section on Redox Biology and Oxidative Stress in Health and Disease. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v174.12/issuetoc