bluuebunny/crossref_metadata_2025 huggingface dataset:
Characterization of a second open reading frame in genome segment 10 of bluetongue virus
Authors: Stewart Meredith , Hardy Alexandra , Barry Gerald , Pinto Rute Maria , Caporale Marco , Melzi Eleonora , Hughes Joseph , Taggart Aislynn , Janowicz Anna , Varela Mariana , Ratinier Maxime , Palmarini Massimo
Published: August 2015

Viruses have often evolved overlapping reading frames in order to maximize their coding capacity. Until recently, the segmented dsRNA genome of viruses of theOrbivirusgenus was thought to be monocistronic, but the identification of the bluetongue virus (BTV) NS4 protein changed this assumption. A small ORF in segment 10, overlapping the NS3 ORF in the +1 position, is maintained in more than 300 strains of the 27 different BTV serotypes and in more than 200 strains of the phylogenetically related African horse sickness virus (AHSV). In BTV, this ORF (named S10-ORF2 in this study) encodes a putative protein 50–59 residues in length and appears to be under strong positive selection. HA- or GFP-tagged versions of S10-ORF2 expressed from transfected plasmids localized within the nucleoli of transfected cells, unless a putative nucleolar localization signal was mutated. S10-ORF2 inhibited gene expression, but not RNA translation, in transient transfection reporter assays. In both mammalian and insect cells, BTV S10-ORF2 deletion mutants (BTV8ΔS10-ORF2) displayed similar replication kinetics to wt virus.In vivo, S10-ORF2 deletion mutants were pathogenic in mouse models of disease. Although further evidence is required for S10-ORF2 expression during infection, the data presented provide an initial characterization of this ORF.
An extensive comparison of species-abundance distribution models
Authors: Baldridge Elita , Harris David J. , Xiao Xiao , White Ethan P.
Published: August 2015

A number of different models have been proposed as descriptions of the species-abundance distribution (SAD). Most evaluations of these models use only one or two models, focus only a single ecosystem or taxonomic group, or fail to use appropriate statistical methods. We use likelihood and AIC to compare the fit of four of the most widely used models to data on over 16,000 communities from a diverse array of taxonomic groups and ecosystems. Across all datasets combined the log-series, Poisson lognormal, and negative binomial all yield similar overall fits to the data. Therefore, when correcting for differences in the number of parameters the log-series generally provides the best fit to data. Within individual datasets some other distributions performed nearly as well as the log-series even after correcting for the number of parameters. The Zipf distribution is generally a poor characterization of the SAD.
Classifying Aging as a Disease in the context of ICD-11
Authors: Zhavoronkov Alex , Bhullar Bhupinder
Published: August 2015

Aging is a complex continuous multifactorial process leading to loss of function and crystalizing into the many age-related diseases. Here, we explore the arguments for classifying aging as a disease in the context of the upcoming World Health Organization’s 11th International Statistical Classification of Diseases and Related Health Problems (ICD-11), expected to be finalized in 2018. We hypothesize that classifying aging as a disease will result in new approaches and business models for addressing aging as a treatable condition, which will lead to both economic and healthcare benefits for all stakeholders. Classification of aging as a disease may lead to more efficient allocation of resources by enabling funding bodies and other stakeholders to use quality-adjusted life years (QALYs) and healthy-years equivalent (HYE) as metrics when evaluating both research and clinical programs. We propose forming a Task Force to interface the WHO in order to develop a multidisciplinary framework for classifying aging as a disease.
WMP: A novel comprehensive wheat miRNA database, including related bioinformatics software
Authors: Remita Mohamed Amine , Lord Etienne , Agharbaoui Zahra , Leclercq Mickael , Badawi Mohamed A. , Makarenkov Vladirmir , Sarhan Fathey , Diallo Abdoulaye Baniré
Published: August 2015

MicroRNAs (miRNAs) are emerging as important post tran-scriptional regulators that may regulate key plant genes responsible for agronomic traits such as grain yield and stress tolerance. Several studies identified species and clades specific miRNA families associated with plant stress regulated genes. Here, we propose a novel resource that provides data related to the expression of abiotic stress responsive miRNAs in wheat, one of the most important staple food crops. This database allows the query of small RNA libraries, includingin silicopredicted wheat miRNA sequences and the expression profiles of small RNAs identified from those libraries. Our database also provides a direct access to online miRNA prediction software tuned tode novomiRNA detection in wheat, in monocotyledon clades, as well as in other plant species. These data and software will facilitate multiple comparative analyses and reproducible studies on small RNAs and miRNA families in plants. Our web-portal is available at:http://wheat.bioinfo.uqam.ca.
A resurrection experiment finds evidence of both reduced genetic diversity and potential adaptive evolution in the agricultural weedIpomoea purpurea
Authors: Kuester Adam , Wilson Ariana , Chang Shu-mei , Baucom Regina S.
Published: August 2015

Despite the negative economic and ecological impact of weeds, relatively little is known about the evolutionary mechanisms that influence their persistence in agricultural fields. Here, we use a resurrection ecology approach and compare the genetic and phenotypic divergence of temporally sampled seed progenies ofIpomoeapurpurea, an agricultural weed that is resistant to glyphosate, the most widely used herbicide in current-day agriculture. We found striking reductions in allelic diversity between cohorts sampled nine years apart (2003 vs 2012), suggesting that populations of this species sampled from agricultural fields have experienced genetic bottleneck events that have led to lower neutral genetic diversity. Heterozygosity excess tests indicate that this bottleneck may have occurred prior to 2003. Further, a greenhouse assay of individuals sampled from the field as seed found that populations of this species, on average, exhibited modest increases in herbicide resistance over time. Our results show that populations of this noxious weed, capable of adapting to strong selection imparted by herbicide application, may lose genetic variation as a result of this or other environmental factors. We likely uncovered only modest increases in resistance between sampling cohorts due to a strong and previously identified fitness cost of resistance in this species, along with the potential that non-resistant migrants germinate from the seed bank.
Genomic and gene-expression comparisons among phage-resistant type-IV pilus mutants ofPseudomonas syringaepathovarphaseolicola
Authors: Sistrom Mark , Park Derek , O’Brien Heath E. , Wang Zheng , Guttman David S. , Townsend Jeffrey P. , Turner Paul E.
Published: August 2015

Pseudomonas syringaepv.phaseolicola(Pph) is a significant bacterial pathogen of agricultural crops, and phage ϕ6 and other members of the dsRNA virus familyCystoviridaeundergo lytic (virulent) infection of Pph, using the type IV pilus as the initial site of cellular attachment. Despite the popularity of Pph/phage ϕ6 as a model system in evolutionary biology, Pph resistance to phage ϕ6 remains poorly characterized. To investigate differences between phage ϕ6 resistant Pph strains, we examined genomic and gene expression variation among three bacterial genotypes that differ in the number of type IV pili expressed per cell: ordinary (wild-type), non-piliated, and super-piliated. Genome sequencing of non-piliated and super-piliated Pph identified few mutations that separate these genotypes from wild type Pph – and none present in genes known to be directly involved in type IV pilus expression. Expression analysis revealed that 81.1% of GO terms up-regulated in the non-piliated strain were down-regulated in the super-piliated strain. This differential expression is particularly prevalent in genes associated with respiration — specifically genes in the tricarboxylic acid cycle (TCA) cycle, aerobic respiration, and acetyl-CoA metabolism. The expression patterns of the TCA pathway appear to be generally up and down-regulated, in non-piliated and super-piliated Pph respectively. As pilus retraction is mediated by an ATP motor, loss of retraction ability might lead to a lower energy draw on the bacterial cell, leading to a different energy balance than wild type. The lower metabolic rate of the super-piliated strain is potentially a result of its loss of ability to retract.
The need for novel informatics tools for integrating and planning research in molecular and cellular cognition
Authors: Silva Alcino J. , Müller Klaus-Robert
Published: August 2015

The sheer volume and complexity of publications in the biological sciences are straining traditional approaches to research planning. Nowhere is this problem more serious than in molecular and cellular cognition, since in this neuroscience field, researchers routinely use approaches and information from a variety of areas in neuroscience and other biology fields. Additionally, the multilevel integration process characteristic of this field involves the establishment of experimental connections between molecular, electrophysiological, behavioral, and even cognitive data. This multidisciplinary integration process requires strategies and approaches that originate in several different fields, which greatly increases the complexity and demands of this process. Although causal assertions, where phenomenon A is thought to contribute or relate to B, are at the center of this integration process and key to research in biology, there are currently no tools to help scientists keep track of the increasingly more complex network of causal connections they use when making research decisions. Here, we propose the development of semiautomated graphical and interactive tools to help neuroscientists and other biologists, including those working in molecular and cellular cognition, to track, map, and weight causal evidence in research papers. There is a great need for a concerted effort by biologists, computer scientists, and funding institutions to develop maps of causal information that would aid in integration of research findings and in experiment planning.
Stress effects on the hippocampus: a critical review
Authors: Kim Eun Joo , Pellman Blake , Kim Jeansok J.
Published: August 2015

Uncontrollable stress has been recognized to influence the hippocampus at various levels of analysis. Behaviorally, human and animal studies have found that stress generally impairs various hippocampal-dependent memory tasks. Neurally, animal studies have revealed that stress alters ensuing synaptic plasticity and firing properties of hippocampal neurons. Structurally, human and animal studies have shown that stress changes neuronal morphology, suppresses neuronal proliferation, and reduces hippocampal volume. Since the inception of stress research nearly 80 years ago, much focus has been on the varying levels of hypothalamic-pituitary-adrenal (HPA) axis neuroendocrine hormones, namely glucocorticoids, as mediators of the myriad stress effects on the hippocampus and as contributing factors to stress-associated psychopathologies such as post-traumatic stress disorder (PTSD). However, reports of glucocorticoid-produced alterations in hippocampal functioning vary widely across studies. This review provides a brief history of stress research, examines how the glucocorticoid hypothesis emerged and guides contemporary stress research, and considers alternative approaches to understanding the mechanisms underlying stress effects on hippocampal functioning.
Entorhinal–hippocampal neuronal circuits bridge temporally discontiguous events
Authors: Kitamura Takashi , Macdonald Christopher J. , Tonegawa Susumu
Published: August 2015

The entorhinal cortex (EC)–hippocampal (HPC) network plays an essential role for episodic memory, which preserves spatial and temporal information about the occurrence of past events. Although there has been significant progress toward understanding the neural circuits underlying the spatial dimension of episodic memory, the relevant circuits subserving the temporal dimension are just beginning to be understood. In this review, we examine the evidence concerning the role of the EC in associating events separated by time—or temporal associative learning—with emphasis on the function of persistent activity in the medial entorhinal cortex layer III (MECIII) and their direct inputs into the CA1 region of HPC. We also discuss the unique role of Island cells in the medial entorhinal cortex layer II (MECII), which is a newly discovered direct feedforward inhibitory circuit to CA1. Finally, we relate the function of these entorhinal cortical circuits to recent findings concerning hippocampal time cells, which may collectively activate in sequence to bridge temporal gaps between discontiguous events in an episode.
Synchrony and desynchrony in circadian clocks: impacts on learning and memory
Authors: Krishnan Harini C. , Lyons Lisa C.
Published: August 2015

Circadian clocks evolved under conditions of environmental variation, primarily alternating light dark cycles, to enable organisms to anticipate daily environmental events and coordinate metabolic, physiological, and behavioral activities. However, modern lifestyle and advances in technology have increased the percentage of individuals working in phases misaligned with natural circadian activity rhythms. Endogenous circadian oscillators modulate alertness, the acquisition of learning, memory formation, and the recall of memory with examples of circadian modulation of memory observed across phyla from invertebrates to humans. Cognitive performance and memory are significantly diminished when occurring out of phase with natural circadian rhythms. Disruptions in circadian regulation can lead to impairment in the formation of memories and manifestation of other cognitive deficits. This review explores the types of interactions through which the circadian clock modulates cognition, highlights recent progress in identifying mechanistic interactions between the circadian system and the processes involved in memory formation, and outlines methods used to remediate circadian perturbations and reinforce circadian adaptation.
Reporting human resources in annual reports
Authors: Kansal Monika , Joshi Mahesh
Published: August 2015

Purpose

– The purpose of this paper is to investigate the extent of corporate disclosure on human resources (HR) in the annual reports of top performing Indian companies.

Design/methodology/approach

– The paper explores the extent to which top 82 companies from India present information about HR in their annual reports. This study examines the annual reports of each of the top Indian firms listed on the Bombay stock exchange, using the “content analysis” method. Statistical tests have been performed to analyse the difference between the HR disclosure score across public and private sectors and disclosure variations among various industrial sectors.

Findings

– In-house training programmes has been noticed to be the favourite item of disclosure followed by safety awards/certifications and statements regarding cordial relations with the employees/unions. A majority of the Indian firms have ignored significant HR issues such as employee welfare fund, maternity/paternity leaves, holiday benefits, employee loans and adopting old age homes, etc. Overall, the study reflects low HR related disclosures. No statistically significant difference has been found between the mean HR disclosure from one industry to another and disclosure practices of the private and the public sector companies.

Practical implications

– The disclosure pattern of the Indian companies suggests that they only a few companies are concerned about employees’ welfare than the rest. This may motivate a change of the disclosure policy of the rest of the firms who may follow the reporting pattern of the most disclosing ones.

Originality/value

– This is first study on the disclosure of HR by the Indian corporate sector in the CSR domain with a disclosure analysis for a period of nine years . This research provides new directions for the literature in this area and may promote comparative studies on HR-based studies from different perspectives.
E-training adoption in the Nigerian civil service
Authors: Zainab Bello , Bhatti Muhammad Awais , Pangil Faizuniah Bt , Battour Mohamed Mohamed
Published: August 2015

Purpose

– The purpose of this paper is to highlight the factors that aid e-training adoption in the Nigerian civil service.

Design/methodology/approach

– This paper is based on a review of past literature from databases, reports, newspapers, magazines, etc. The literature recognised the role of perceived cost, computer self-efficacy, availability of resources and perceived support in e-training adoption. Using technology acceptance model (TAM), this paper explained the importance of these variables in e-training adoption in developing country context.

Findings

– The authors found that the combined role of perceived cost, computer self-efficacy, technological infrastructure, Internet facilities, power supply, organisational support, technical support and government support is critical for e-training adoption in developing countries, particularly in Nigeria. Thus, the authors proposed the combination of these variables which would encourage future research on the use of TAM in technology adoption.

Research limitations/implications

– This paper gives an elaboration of the role of computer self-efficacy, perceived cost, availability of resources and perceived support with TAM as base of the framework. This provides researchers the opportunity to test the proposed framework empirically and further suggest other variables that can aid e-training adoption in the context of developing country.

Practical implications

– The result of this paper can serve as a guide to managers and policymakers to have a better understanding of the requirements for e-training adoption, especially in developing countries. This will go a long way towards designing good policies that could maximise e-training results.

Originality/value

– This paper adds to the existing literature on e-training and TAM with the suggestion of proposed variables.
Exploring the family effect on firm performance
Authors: Mani Yosra , Lakhal Lassaad
Published: August 2015

Purpose

– The purpose of this paper is to investigate how internal social capital – as a part of the familiness resources– affects family firm performance. The social capital theory states that internal social capital within family businesses is composed of three dimensions: the structural dimension, the relational dimension, and the cognitive dimension. The aim of the paper is to study the relationship between each dimension of internal social capital and family firm performance.

Design/methodology/approach

– The paper employs an empirical investigation which is based on a sample of 114 Tunisian family firms.

Findings

– Results demonstrate that the structural and relational dimensions are positively associated with financial and non-financial family firm’s performance. However, the cognitive dimension has a significant positive effect on financial performance but not on non-financial family firm performance.

Originality/value

– The proposed model aims to test the direct effect of internal social capital dimensions on financial and non-financial family firm’s performance. Besides, there is a lack of empirical evidence aiming at understanding the impact of structural, cognitive and relational social capital on the performance of family firms.
The development, content validity and inter‐rater reliability of the SMART‐Goal Evaluation Method: A standardised method for evaluating clinical goals
Authors: Bowman Julia , Mogensen Lise , Marsland Elisabeth , Lannin Natasha
Published: August 2015

Introduction

Goal setting is a complex skill. The use of formal goal writing procedures (including the use of the SMART goal model) has been advocated. However, a standardised method of writing and evaluating SMART goals is currently lacking. This study comprised of two phases. The aims of phase one was to (i) develop the SMART Goal Evaluation Method (SMART‐GEM) based on a SMART goal model; and (ii) investigate the content validity of the SMART‐GEM. The aim of phase two of the study was to test the inter‐rater reliability of the SMART‐GEM.

Methods

Development of the SMART‐ GEM involved defining and constructing evaluation criteria suitable for auditing goal statements. A content validity assessment was conducted using an expert panel of Occupational Therapists (n = 10). Inter‐rater reliability of the SMART‐GEM was examined using a purposive sample of multiple raters (n = 24).

Results

The SMART‐ GEM was rated as having good content validity (individual items CVI ranged from 0.90 to 1.00; total SMART‐ GEM CVI = 0.99, ρ = 0.05). Agreement between raters on individual items ranged from poor (κ = 0.254) to excellent (κ = 0.965) and agreement of overall grades was fair to good (κ = 0.582). Inter‐rater agreement on total scores was found to be very good (ICC = 0.895, 95% CI = 0.743 to 0.986, ρ = 0.001) with excellent internal consistency (α = 0.995).

Conclusion

The SMART‐GEM demonstrated good construct validity and very good inter‐rater reliability on total score and shows promise as a standardised method to writing and evaluating clinical goals.
Private benefits and metabolic conflicts shape the emergence of microbial interdependencies
Authors: Estrela Sylvie , Morris J. Jeffrey , Kerr Benjamin
Published: August 2015

Microbes perform many costly biological functions that benefit themselves, and may also benefit neighbouring cells. Losing the ability to perform such functions can be advantageous due to cost savings, but when they are essential for growth, organisms become dependent on ecological partners to compensate for those losses. When multiple functions may be lost, the ecological outcomes are potentially diverse, including independent organisms only; one‐way dependency, where one partner performs all functions and others none; or mutual interdependency where partners perform complementary essential functions. What drives these different outcomes? We develop a model where organisms perform ‘leaky’ functions that provide both private and public benefits to explore the consequences of privatization level, costs and essentiality on influencing these outcomes. We show that mutual interdependency is favoured at intermediate levels of privatization for a broad range of conditions. One‐way dependency, in contrast, is only favoured when privatization is low and loss‐of‐function benefits are accelerating. Our results suggest an interplay between privatization level and shape of benefits from loss in driving microbial dependencies. Given the ubiquity of microbial functions that are inevitably leaked and the ease of mutational inactivation, our findings may help to explain why microbial interdependencies are common in nature.
Cross‐talk between a regulatory small RNA, cyclic‐di‐GMP signalling and flagellar regulator FlhDC for virulence and bacterial behaviours
Authors: Yuan Xiaochen , Khokhani Devanshi , Wu Xiaogang , Yang Fenghuan , Biener Gabriel , Koestler Benjamin J. , Raicu Valerica , He Chenyang , Waters Christopher M. , Sundin George W. , Tian Fang , Yang Ching‐Hong
Published: August 2015

Dickeya dadantii is a globally dispersed phytopathogen which causes diseases on a wide range of host plants. This pathogen utilizes the type III secretion system (T3SS) to suppress host defense responses, and secretes pectate lyase (Pel) to degrade the plant cell wall. Although the regulatory small RNA (sRNA) RsmB, cyclic diguanylate monophosphate (c‐di‐GMP) and flagellar regulator have been reported to affect the regulation of these two virulence factors or multiple cell behaviours such as motility and biofilm formation, the linkage between these regulatory components that coordinate the cell behaviours remain unclear. Here, we revealed a sophisticated regulatory network that connects the sRNA, c‐di‐GMP signalling and flagellar master regulator FlhDC. We propose multi‐tiered regulatory mechanisms that link the FlhDC to the T3SS through three distinct pathways including the FlhDC‐FliA‐YcgR3937 pathway; the FlhDC‐EcpC‐RpoN‐HrpL pathway; and the FlhDC‐rsmB‐RsmA‐HrpL pathway. Among these, EcpC is the most dominant factor for FlhDC to positively regulate T3SS expression.
The Sovereign Yield Curve and the Macroeconomy in China
Authors: Yan Yifeng , Guo Ju'e
Published: August 2015

A dynamic Nelson–Siegel model is adopted to estimate three time‐varying factors of yield curves, the level, the slope and the curvature, and a vector autoregressive model is built to study interactions between macro variables and the yield curve. Results show that, first, money supply growth is a more effective instrument to curb inflation than the monetary policy interest rate; however, the central bank also adjusts the interest rate to stabilize money supply. Second, investment is an important measure to stimulate the Chinese economy, but it also pushes up money supply growth, which results in higher inflation. Third, the yield curve reacts significantly to innovations to investment growth and money supply growth. The segmentation of China's bond market hinders the efficient implementation of monetary policy, and the monetary policy transmission mechanism is still weak in China. Finally, interactions between the yield curve and the macroeconomy in China are nearly unidirectional. Macroeconomic variables reshape the yield curve, but direct adjustments of the yield curve do not significantly change macroeconomic variables. Due to the incomplete liberalization of financial markets, there exists a wide disjunction between the real economy and financial markets in China.
Internationalization of the RMB, Capital Market Openness and Financial Reforms in China
Authors: Aizenman Joshua
Published: August 2015

This paper provides an overview of Chinese financial and trade integration in recent decades, and the challenges facing China in the coming years. China had been a prime example of export‐led growth, benefiting from learning by doing, and by adopting foreign know‐how, supported by a complex industrial policy. While the resultant growth has been spectacular, it comes with hidden but growing costs and distortions. The Chinese export‐led growth path has been challenged by its own success, and the global financial crisis forced China toward rebalancing, which is a work in progress. Reflecting on the internationalization of the CNY, rapid acceleration of the commercial internationalization of the CNY is expected. In contrast, there are no clear‐cut reasons to rush with the full CNY financial internationalization: the gains from CNY financial internationalization are overrated.
Resource conservation strategies for rice‐wheat cropping systems on partially reclaimed sodic soils of the Indo‐Gangetic region, and their effects on soil carbon
Authors: Mishra V.K. , Srivastava S. , Bhardwaj A.K. , Sharma D.K. , Singh Y.P. , Nayak A.K.
Published: August 2015

The Indo‐Gangetic plain is characterized by intensive agriculture, largely by resource‐poor small and marginal farmers. Vast swathes of salt‐affected areas in the region provide both challenges and opportunities to bolster food security and sequester carbon after reclamation. Sustainable management of reclaimed soils via resource conservation strategies, such as residue retention, is key to the prosperity of the farmer, as well as increases the efficiency of expensive initiatives to further reclaim sodic land areas, which currently lay barren. After five years of experimentation on resource conservation strategies for rice‐wheat systems on partially reclaimed sodic soils of the Indo‐Gangetic region, we evaluated changes in different soil carbon pools and crop yield. Out of all resource conservation techniques which were tested, rice‐wheat crop residue addition (30% of total production) was most effective in increasing soil organic carbon (SOC). In rice, without crop residue addition (WCR), soils under zero‐tillage with transplanting, summer ploughing with transplanting and direct seeding with brown manuring showed a significant increase in SOC over the control (puddling in rice, conventional tillage in wheat). In these treatments relatively higher levels of carbon were attained in all aggregate fractions compared to the control. Soil aggregate sizes in meso (0.25‐2.0 mm) and macro (2‐8 mm) ranges increased, whereas micro (< 0.25 mm) fractions decreased in soils under zero‐till practices, both with and without crop residue addition. Direct seeding with brown manuring and zero tillage with transplanting also showed an increase of 135% and 95%, respectively, over the control in microbial biomass carbon, without crop residue incorporation. In zero tillage with transplanting treatment, both with and without crop residue showed significant increase in soil carbon sequestration potential. Though the changes in accrued soil carbon did not bring about significant differences in terms of grain yield, overall synthesis in terms of balance between yield and carbon sequestration indicated that summer ploughing with transplanting and zero tillage with transplanting sequestered significantly higher rates of carbon, yet yielded on par with conventional practices. These could be appropriate alternatives to immediately replace conventional tillage and planting practices for rice‐wheat cropping systems in the sodic soils of the Indo‐Gangetic region.
Recent Trends in the Use of Natural Antioxidants for Meat and Meat Products
Authors: Kumar Yogesh , Yadav Deep Narayan , Ahmad Tanbir , Narsaiah Kairam
Published: August 2015

Antioxidants are added to fresh and processed meat and meat products to prevent lipid oxidation, retard development of off‐flavors, and improve color stability. In the food industry, they can be divided into natural and synthetic antioxidants. Synthetic antioxidants have been confirmed for their toxicological and carcinogenic effects. Thus, the food industry now chooses natural products over synthetic ones. This review provides an overview of the current trends in the use of antioxidants from natural sources, for potential applications in meat and meat products. These natural antioxidants contain some active compounds, which exert antioxidative potential in meat and meat products by different mechanisms of action. The efficient extraction of these antioxidants from their natural sources, along with establishing their in vitro and in producto antioxidant activity, has been a great challenge for researchers engaged in this field. Therefore, this review is focused on all these aspects, along with current studies related to this area, to provide in‐depth information to readers.
The Potential of High‐throughput Metagenomic Sequencing of Aquatic Bacterial Communities to Estimate the Postmortem Submersion Interval
Authors: Benbow Mark Eric , Pechal Jennifer L. , Lang Jennifer M. , Erb Racheal , Wallace John R.
Published: August 2015

Human remains can be discovered in freshwater or marine ecosystems, circumstances where insects and other invertebrates have infrequently been used for understanding the time of postmortem submersion. In this study, the identification and succession of epinecrotic bacterial communities on vertebrate remains were described during decomposition in a temperate headwater stream during two seasons (summer and winter). Bacterial communities were characterized with 454 pyrosequencing and analyzed at phyletic and generic taxonomic resolutions. There was a significant increase in genera richness over decomposition during both seasons. Additionally, multivariate statistical modeling revealed significant differences in bacterial communities between seasons at both taxonomic resolutions and siginificant genera differences among sampling days within each season, suggesting a succession of these communities. These data are the first to describe aquatic bacterial succession using high‐throughput metagenomic sequencing on vertebrate remains submerged in a freshwater habitat, and provide initial evidence for their potential use in forensic investigations.
An Improved Equation forTBSandADD: Establishing a Reliable Postmortem Interval Framework for Casework and Experimental Studies
Authors: Moffatt Colin , Simmons Tal , Lynch‐Aird Jeanne
Published: August 2015

Megyesi et al.'s (J Forensic Sci, 2005, 50, 618) paper was important to forensic anthropology as it introduced a quantitative framework for estimating time since death in human cadavers, based upon physical appearance by way of scoring on a novel scale. However, errors concerning rounding, temperature scale, and incorrect use of a statistical regression model render their predictive formula unusable. Based upon only their more reliable data, a more appropriate regression model to predict accumulated degree days (ADD) from total body score (TBS) is presented. The new model is also a superior fit (r2 = 0.91) and produces markedly narrower confidence intervals than the original, which also allowed impossible, negativeADDvalues. Explanations of the shortcomings in the original analysis and calculations are presented, which it is hoped will help forensic scientists avoid making similar mistakes.
The rpb2 gene represents a viable alternative molecular marker for the analysis of environmental fungal communities
Authors: Větrovský Tomáš , Kolařík Miroslav , Žifčáková Lucia , Zelenka Tomáš , Baldrian Petr
Published: August 2015

Although the commonly used internal transcribed spacer region of rDNA (ITS) is well suited for taxonomic identification of fungi, the information on the relative abundance of taxa and diversity is negatively affected by the multicopy nature of rDNA and the existence of ITS paralogues. Moreover, due to high variability, ITS sequences cannot be used for phylogenetic analyses of unrelated taxa. The part of single‐copy gene encoding the second largest subunit of RNA polymerase II (rpb2) was thus compared with first spacer of ITS as an alternative marker for the analysis of fungal communities in spruce forest topsoil, and their applicability was tested on a comprehensive mock community. In soil, rpb2 exhibited broad taxonomic coverage of the entire fungal tree of life including basal fungal lineages. The gene exhibited sufficient variation for the use in phylogenetic analyses and taxonomic assignments, although it amplifies also paralogues. The fungal taxon spectra obtained with rbp2 region and ITS1 corresponded, but sequence abundance differed widely, especially in the basal lineages. The proportions of OTU counts and read counts of major fungal groups were close to the reality when rpb2 was used as a molecular marker while they were strongly biased towards the Basidiomycota when using the ITS primers ITS1/ITS4. Although the taxonomic placement of rbp2 sequences is currently more difficult than that of the ITS sequences, its discriminative power, quantitative representation of community composition and suitability for phylogenetic analyses represent significant advantages.
Road density and wetland context alter population structure of a freshwater turtle
Authors: Hamer Andrew J. , Harrison Lee J. , Stokeld Danielle
Published: August 2015

Roads are detrimental to wildlife populations that require contiguous networks of terrestrial and aquatic habitats. Many species of freshwater turtles are sensitive to habitat fragmentation caused by roads, and are susceptible to road mortality during overland migrations. The common long‐necked turtle (Chelodina longicollis) is anAustralian freshwater turtle that frequently moves between wetlands, and so populations may incur negative impacts from road effects. Here, we assessed the relationship betweenC. longicollisand road density and landscape variables within populations inhabiting 20 wetlands distributed throughout greaterMelbourne,Australia. The size frequency distribution ofC. longicollisat sites surrounded by high road densities was skewed towards larger individuals, but there was no difference in the frequency of juveniles between high and low road density sites. Regression modelling revealed a clear positive relationship between road density and carapace length (CL) ofC. longicollis; the meanCLat a site with the highest road density was predicted to be 23% greater than meanCLat a site surrounded by no roads. FemaleCLwas also positively related to road density. There was a clear positive relationship between wetland age andCL, although this relationship was not as strong. While there was no relationship evident between road density and the proportion of femaleC. longicollisat a site, more females were captured at smaller ephemeral sites surrounded by a high proportion of green open space and located near drainage lines. We did not find evidence of sex‐related differences in road effects. These results suggest that roads may be affectingC. longicollisin the study area, but the direct cause of any effects is difficult to identify.
2015 RANZCOG Arthur Wilson Memorial Oration ‘From little things, big things grow: The importance of periconception medicine’
Authors: Norman Robert J.
Published: August 2015

The time of our conception is when we are most vulnerable to survival and growing as a healthy human being. Genetic and environmental effects on gametes and the developing embryo can be literally life‐and‐death events with regard to the successful outcome of pregnancy. In the past decade, we have also understood that environmental factors under which the gametes grow and the embryo develops have lifelong implications with regard to developmental origins of health and disease. We now know that parenting begins before conception in that a compromised egg or sperm from either parent can alter the trajectory of development even if the embryo and intrauterine environment is optimal. There are now a large number of factors known to impact on the gametes to adversely affect them, including obesity, nutrition, cigarette smoking and environmental pollutants. The increasing use of in vitro fertilisation across the world exposes developing embryos to less than optimal environmental conditions through altered culture media, gases and potential pollutants from plastics, air and water. Many of these environmental exposures have not undergone experimental investigation and yet widely implemented in thousands of laboratories across the world. There have been many attempts to set up periconception planning either through the health service, the print and electronic media or through government action. We as a profession, as well as our Colleges, could do much better job in this area of preventative medicine by developing better guidelines and education for professional colleagues, the health service and the community.
Perinatal mental health: Fathers – the (mostly) forgotten parent
Authors: Wong Olivia , Nguyen Tram , Thomas Naomi , Thomson‐Salo Frances , Handrinos Dennis , Judd Fiona
Published: August 2015

Introduction

The importance of parental mental health as a determinant of infant and child outcomes is increasingly acknowledged. Yet, there is limited information regarding paternal mental health during the perinatal period. The aim of this review is to summarize existing clinical research regarding paternal mental health in the perinatal period in various contexts, and its possible impact on infant development.

Method

An electronic literature search was conducted using MEDLINE and PubMed databases. Key texts were used to cross‐check for any further articles of interest.

Results

Men are at increased risk of mental health problems during the transition to fatherhood, as well as during the perinatal period. Paternal mental health during the perinatal period has been shown to impact on their child's emotional and behavioral development. However, research addressing the needs of fathers with mental illness and the impact of their illness on their infant and family has been limited.

Conclusions

A paradigm shift is required, from a focus on women following childbirth and women with pre‐existing psychiatric disorders, to a broader family perspective with the focus firmly on parent–infant relationships. This paradigm shift needs to involve greater research into the fathering role and paternal mental illness during the perinatal period, including further studies into risk factors, impact on the family system, and the most appropriate form of intervention and service provision.
Underdiagnosis of depression in an economically deprived population in Macao, China
Authors: Lao Cheng‐Kin , Chan Yok‐Man , Tong Henry Hoi‐Yee , Chan Alexandre
Published: August 2015

Introduction

Previous literature revealed an association between low income and depression. Despite the availability of effective treatments, depression is often underdiagnosed and undertreated. This study was designed to evaluate the prevalence of depressive symptoms and their impact on health‐related quality of life (HRQoL) in a low‐income population in Macao.

Methods

This cross‐sectional study targeted the adult beneficiaries of local food bank program. The program was established to provide food assistance to the residents who had low income but were ineligible for government financial assistance. All data were collected through interview and questionnaires. The Patient Health Questionnaire (PHQ‐9) was used for assessing depressive symptoms. Information about depression diagnosis was obtained by the self‐report method. HRQoL levels were measured by the 12‐item Short‐Form Health Survey, Version 2.0.

Results

A total of 272 study participants were included for analysis. Based on the PHQ‐9 scores, 27.6% of the participants suffered from moderate to severe depressive symptoms. Among them, 76% were not diagnosed with depression. Those with moderate to severe depressive symptoms had significantly lower levels of HRQoL (P < 0.001). Anxiety disorders (OR = 9.71, 95% CI = 2.36–40.06), migraine (OR = 3.88, 95% CI = 1.55–9.73), and poor to fair self‐rated health (OR = 6.30, 95% CI = 1.95–20.40) were the independent factors associated with moderate to severe depressive symptoms.

Discussion

Underdiagnosis of depression was prevalent in this low‐income population. There is a need to raise their awareness of mental disorders and improve their access to mental health services.
Effects of adding an arbuscular mycorrhizal fungi inoculum and of distance to donor sites on plant species recolonization following topsoil removal
Authors: Torrez Vania , Ceulemans Tobias , Mergeay Joachim , de Meester Luc , Honnay Olivier
Published: August 2015

Questions

Does addition of an arbuscular mycorrhizal fungi (AMF) inoculum increase the short‐term restoration success of nutrient‐poor grassland (NPG) after topsoil removal? Does distance to intact remnant grassland (IRG) patches affect restoration success, and does the effect of inoculum addition depend on distance to IRGs?

Location

Meerdaal forest, Oud‐Heverlee, Belgium.

Methods

In a topsoil‐removed site of 8.5 ha, where 24 IRG patches (ca. 10% of the area) were kept, 48 plots (1 m2) were established at three distances (5, 10 and 20 m) from the edge of IRG patches. Half of the plots at each distance class were inoculated with a custom‐made AMF inoculum, whereas the remaining plots were used as controls. We recorded plant species abundance in the plots, just before addition of the AMF inoculum and 1 yr after. We used repeated measures ANOVA to test for effects of inoculum addition, distance to IRG patches and their interaction on plant species richness, diversity and plant community similarity between IRG patches and plots. We also evaluated the response of AMF‐dependent plant species, specialist species of NPG and species with specific seed dispersal adaptations.

Results

Adding the inoculum positively affected species richness and/or diversity of all plant species, AMF‐dependent species and specialist species. It increased plant community similarity to the IRG patches. Increasing distance from IRG patches had a negative effect on richness and/or diversity of all plant species and specialist species. The positive effect of inoculum addition on richness and/or diversity of all species, AMF‐dependent species and specialist species decreased with increasing distance from IRG patches to the plots, likely indicating priority effects.

Conclusions

The application of a custom‐made AMF inoculum increased the short‐term restoration success of NPG after topsoil removal. Dispersal limitation of specialist plant species of NPG, however, likely negatively affected the effect of inoculum addition. Apart from the AMF effect, the reported strongly positive short‐time effect of inoculation was likely due to the high density of IRG patches at the site, and the presence of organic matter and other micro‐organisms in the inoculum.
The Cross-Cut Statistic and its Sensitivity to Bias in Observational Studies with Ordered Doses of Treatment
Authors: Rosenbaum Paul R.
Published: August 2015

A common practice with ordered doses of treatment and ordered responses, perhaps recorded in a contingency table with ordered rows and columns, is to cut or remove a cross from the table, leaving the outer corners—that is, the high-versus-low dose, high-versus-low response corners—and from these corners to compute a risk or odds ratio. This little remarked but common practice seems to be motivated by the oldest and most familiar method of sensitivity analysis in observational studies, proposed by Cornfield et al. (1959), which says that to explain a population risk ratio purely as bias from an unobserved binary covariate, the prevalence ratio of the covariate must exceed the risk ratio. Quite often, the largest risk ratio, hence the one least sensitive to bias by this standard, is derived from the corners of the ordered table with the central cross removed. Obviously, the corners use only a portion of the data, so a focus on the corners has consequences for the standard error as well as for bias, but sampling variability was not a consideration in this early and familiar form of sensitivity analysis, where point estimates replaced population parameters. Here, this cross-cut analysis is examined with the aid of design sensitivity and the power of a sensitivity analysis.
Subsampling Versus Bootstrapping in Resampling-Based Model Selection for Multivariable Regression
Authors: De Bin Riccardo , Janitza Silke , Sauerbrei Willi , Boulesteix Anne-Laure
Published: August 2015

In recent years, increasing attention has been devoted to the problem of the stability of multivariable regression models, understood as the resistance of the model to small changes in the data on which it has been fitted. Resampling techniques, mainly based on the bootstrap, have been developed to address this issue. In particular, the approaches based on the idea of “inclusion frequency” consider the repeated implementation of a variable selection procedure, for example backward elimination, on several bootstrap samples. The analysis of the variables selected in each iteration provides useful information on the model stability and on the variables’ importance. Recent findings, nevertheless, show possible pitfalls in the use of the bootstrap, and alternatives such as subsampling have begun to be taken into consideration in the literature. Using model selection frequencies and variable inclusion frequencies, we empirically compare these two different resampling techniques, investigating the effect of their use in selected classical model selection procedures for multivariable regression. We conduct our investigations by analyzing two real data examples and by performing a simulation study. Our results reveal some advantages in using a subsampling technique rather than the bootstrap in this context.