title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&month=2013-05 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Benthic communities at two remote Pacific coral reefs: effects of reef habitat, depth, and wave energy gradients on spatial patterns link: https://peerj.com/articles/81 last-modified: 2013-05-28 description: Kingman Reef and Palmyra Atoll in the central Pacific are among the most remote coral reefs on the planet. Here we describe spatial patterns in their benthic communities across reef habitats and depths, and consider these in the context of oceanographic gradients. Benthic communities at both locations were dominated by calcifying organisms (54–86% cover), namely hard corals (20–74%) and crustose coralline algae (CCA) (10–36%). While turf algae were relatively common at both locations (8–22%), larger fleshy macroalgae were virtually absent at Kingman (<1%) and rare at Palmyra (0.7–9.3%). Hard coral cover was higher, but with low diversity, in more sheltered habitats such as Palmyra’s backreef and Kingman’s patch reefs. Almost exclusive dominance by slow-growing Porites on Kingman’s patch reefs provides indirect evidence of competitive exclusion, probably late in a successional sequence. In contrast, the more exposed forereef habitats at both Kingman and Palmyra had higher coral diversity and were characterized by fast-growing corals (e.g., Acropora and Pocillopora), indicative of more dynamic environments. In general at both locations, soft coral cover increased with depth, likely reflecting increasingly efficient heterotrophic abilities. CCA and fleshy macroalgae cover decreased with depth, likely due to reduced light. Cover of other calcified macroalgae, predominantly Halimeda, increased with depth. This likely reflects the ability of many calcifying macroalgae to efficiently harvest light at deeper depths, in combination with an increased nutrient supply from upwelling promoting growth. At Palmyra, patterns of hard coral cover with depth were inconsistent, but cover peaked at mid-depths at Kingman. On Kingman’s forereef, benthic community composition was strongly related to wave energy, with hard coral cover decreasing and becoming more spatially clustered with increased wave energy, likely as a result of physical damage leading to patches of coral in localized shelter. In contrast, the cover of turf algae at Kingman was positively related to wave energy, reflecting their ability to rapidly colonize newly available space. No significant patterns with wave energy were observed on Palmyra’s forereef, suggesting that a more detailed model is required to study biophysical coupling there. Kingman, Palmyra, and other remote oceanic reefs provide interesting case studies to explore biophysical influences on benthic ecology and dynamics. creator: Gareth J. Williams creator: Jennifer E. Smith creator: Eric J. Conklin creator: Jamison M. Gove creator: Enric Sala creator: Stuart A. Sandin uri: https://doi.org/10.7717/peerj.81 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Williams et al. title: Determinants of neonatal mortality in rural India, 2007–2008 link: https://peerj.com/articles/75 last-modified: 2013-05-28 description: Background. Despite the growing share of neonatal mortality in under-5 mortality in the recent decades in India, most studies have focused on infant and child mortality putting neonatal mortality on the back seat. The development of focused and evidence-based health interventions to reduce neonatal mortality warrants an examination of factors affecting it. Therefore, this study attempt to examine individual, household, and community level factors affecting neonatal mortality in rural India.Data and methods. We analysed information on 171,529 singleton live births using the data from the most recent round of the District Level Household Survey conducted in 2007–08. Principal component analysis was used to create an asset index. Two-level logistic regression was performed to analyse the factors associated with neonatal deaths in rural India.Results. The odds of neonatal death were lower for neonates born to mothers with secondary level education (OR = 0.60, p = 0.01) compared to those born to illiterate mothers. A progressive reduction in the odds occurred as the level of fathers’ education increased. The odds of neonatal death were lower for infants born to unemployed mothers (OR = 0.89, p = 0.00) compared to those who worked as agricultural worker/farmer/laborer. The odds decreased if neonates belonged to Scheduled Tribes (OR = 0.72, p = 0.00) or ‘Others’ caste group (OR = 0.87, p = 0.04) and to the households with access to improved sanitation (OR = 0.87, p = 0.02), pucca house (OR = 0.87, p = 0.03) and electricity (OR = 0.84, p = 0.00). The odds were higher for male infants (OR = 1.21, p = 0.00) and whose mother experienced delivery complications (OR = 1.20, p = 0.00). Infants whose mothers received two tetanus toxoid injections (OR = 0.65, p = 0.00) were less likely to die in the neonatal period. Children of higher birth order were less likely to die compared to first birth order.Conclusion. Ensuring the consumption of an adequate quantity of Tetanus Toxoid (TT) injections by pregnant mothers, targeting vulnerable groups like young, first time and Scheduled Caste mothers, and improving overall household environment by increasing access to improved toilets, electricity, and pucca houses could also contribute to further reductions in neonatal mortality in rural India. Any public health interventions aimed at reducing neonatal death in rural India should consider these factors. creator: Aditya Singh creator: Abhishek Kumar creator: Amit Kumar uri: https://doi.org/10.7717/peerj.75 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Singh et al. title: Some poleward movement of British native vascular plants is occurring, but the fingerprint of climate change is not evident link: https://peerj.com/articles/77 last-modified: 2013-05-28 description: Recent upperward migration of plants and animals along altitudinal gradients and poleward movement of animal range boundaries have been confirmed by many studies. This phenomenon is considered to be part of the fingerprint of recent climate change on the biosphere. Here I examine whether poleward movement is occurring in the vascular plants of Great Britain. The ranges of plants were determined from detection/non-detection data in two periods, 1978 to 1994 and 1995 to 2011. From these, the centre of mass of the population was calculated and the magnitude and direction of range shifts were determined from movements of the centre of mass. A small, but significant, northward movement could be detected in plants with expanding ranges, but not among declining species. Species from warmer ranges were not more likely to be moving northward, nor was dispersal syndrome a predictor of migration success. It is concluded that simply looking at northward movement of species is not an effective way to identify the effect of climate change on plant migration and that other anthropogenic changes obscure the effect of climate. creator: Quentin J. Groom uri: https://doi.org/10.7717/peerj.77 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Groom title: PeptideBuilder: A simple Python library to generate model peptides link: https://peerj.com/articles/80 last-modified: 2013-05-21 description: We present a simple Python library to construct models of polypeptides from scratch. The intended use case is the generation of peptide models with pre-specified backbone angles. For example, using our library, one can generate a model of a set of amino acids in a specific conformation using just a few lines of python code. We do not provide any tools for energy minimization or rotamer packing, since powerful tools are available for these purposes. Instead, we provide a simple Python interface that enables one to add residues to a peptide chain in any desired conformation. Bond angles and bond lengths can be manipulated if so desired, and reasonable values are used by default. creator: Matthew Z. Tien creator: Dariya K. Sydykova creator: Austin G. Meyer creator: Claus O. Wilke uri: https://doi.org/10.7717/peerj.80 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Tien et al. title: Alu elements in primates are preferentially lost from areas of high GC content link: https://peerj.com/articles/78 last-modified: 2013-05-21 description: The currently-accepted dogma when analysing human Alu transposable elements is that ‘young’ Alu elements are found in low GC regions and ‘old’ Alus in high GC regions. The correlation between high GC regions and high gene frequency regions make this observation particularly difficult to explain. Although a number of studies have tackled the problem, no analysis has definitively explained the reason for this trend. These observations have been made by relying on the subfamily as a proxy for age of an element. In this study, we suggest that this is a misleading assumption and instead analyse the relationship between the taxonomic distribution of an individual element and its surrounding GC environment. An analysis of 103906 Alu elements across 6 human chromosomes was carried out, using the presence of orthologous Alu elements in other primate species as a proxy for age. We show that the previously-reported effect of GC content correlating with subfamily age is not reflected by the ages of the individual elements. Instead, elements are preferentially lost from areas of high GC content over time. The correlation between GC content and subfamily may be due to a change in insertion bias in the young subfamilies. The link between Alu subfamily age and GC region was made due to an over-simplification of the data and is incorrect. We suggest that use of subfamilies as a proxy for age is inappropriate and that the analysis of ortholog presence in other primate species provides a deeper insight into the data. creator: Elizabeth HB Hellen creator: John FY Brookfield uri: https://doi.org/10.7717/peerj.78 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Hellen & Brookfield title: National estimates of emergency department visits for pediatric severe sepsis in the United States link: https://peerj.com/articles/79 last-modified: 2013-05-21 description: Objective. We sought to determine the characteristics of children presenting to United States (US) Emergency Departments (ED) with severe sepsis.Study design. Cross-sectional analysis using data from the National Hospital Ambulatory Medical Care Survey (NHAMCS). Using triage vital signs and ED diagnoses (defined by the International Classification of Diseases, Ninth Revision codes), we identified children <18 years old presenting with both infection (triage fever or ICD-9 infection) and organ dysfunction (triage hypotension or ICD-9 organ dysfunction).Results. Of 28.2 million pediatric patients presenting to US EDs each year, severe sepsis was present in 95,055 (0.34%; 95% CI: 0.29–0.39%). Fever and respiratory infection were the most common indicators of an infection. Hypotension and respiratory failure were the most common indicators of organ dysfunction. Most severe sepsis occurred in children ages 31 days–1 year old (32.1%). Most visits for pediatric severe sepsis occurred during winter months (37.4%), and only 11.1% of patients arrived at the ED by ambulance. Over half of severe sepsis cases were self-pay or insured by Medicaid. A large portion (44.1%) of pediatric severe sepsis ED visits occurred in the South census region. ED length of stay was over 3 h, and 16.5% were admitted to the hospital.Conclusion. Nearly 100,000 children annually present to US EDs with severe sepsis. The findings of this study highlight the unique characteristics of children treated in the ED for severe sepsis. creator: Sara Singhal creator: Mathias W. Allen creator: John-Ryan McAnnally creator: Kenneth S. Smith creator: John P. Donnelly creator: Henry E. Wang uri: https://doi.org/10.7717/peerj.79 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Singhal et al. title: Palm-based diacylglycerol fat dry fractionation: effect of crystallisation temperature, cooling rate and agitation speed on physical and chemical properties of fractions link: https://peerj.com/articles/72 last-modified: 2013-05-14 description: Fractionation which separates the olein (liquid) and stearin (solid) fractions of oil is used to modify the physicochemical properties of fats in order to extend its applications. Studies showed that the properties of fractionated end products can be affected by fractionation processing conditions. In the present study, dry fractionation of palm-based diacylglycerol (PDAG) was performed at different: cooling rates (0.05, 0.5, 1.0, 1.5, 2.0, 2.5 and 3.0°C/min), end-crystallisation temperatures (30, 35, 40, 45 and 50°C) and agitation speeds (30, 50, 70, 90 and 110 rpm) to determine the effect of these parameters on the properties and yield of the solid and liquid portions. To determine the physicochemical properties of olein and stearin fraction: Iodine value (IV), fatty acid composition (FAC), acylglycerol composition, slip melting point (SMP), solid fat content (SFC), thermal behaviour tests were carried out. Fractionation of PDAG fat changes the chemical composition of liquid and solid fractions. In terms of FAC, the major fatty acid in olein and stearin fractions were oleic (C18:1) and palmitic (C16:0) respectively. Acylglycerol composition showed that olein and stearin fractions is concentrated with TAG and DAG respectively. Crystallization temperature, cooling rate and agitation speed does not affect the IV, SFC, melting and cooling properties of the stearin fraction. The stearin fraction was only affected by cooling rate which changes its SMP. On the other hand, olein fraction was affected by crystallization temperature and cooling rate but not agitation speed which caused changes in IV, SMP, SFC, melting and crystallization behavior. Increase in both the crystallization temperature and cooling rate caused a reduction of IV, increment of the SFC, SMP, melting and crystallization behaviour of olein fraction and vice versa. The fractionated stearin part melted above 65°C while the olein melted at 40°C. SMP in olein fraction also reduced to a range of 26 to 44°C while SMP of stearin fractions increased to (60–62°C) compared to PDAG. creator: Razam Ab Latip creator: Yee-Ying Lee creator: Teck-Kim Tang creator: Eng-Tong Phuah creator: Choon-Min Lee creator: Chin-Ping Tan creator: Oi-Ming Lai uri: https://doi.org/10.7717/peerj.72 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Ab Latip et al. title: Eye blink correction: a test on the preservation of common ERP components using a regression based technique link: https://peerj.com/articles/76 last-modified: 2013-05-14 description: Eye blinks are a pervasive problem in electroencephalography research as they contaminate the brain signal. This paper tests the merits of a software tool employing the regression-based Gratton method that claims to remove the detrimental effects of the eye blink and leaves the activity of the brain. The efficacy of the correction tool was tested on five common stimulus-locked Event Related Potential (ERP) components used in a standard Go/Nogo task. Results suggested that the ‘corrected’ data could be predicted from data containing no eye blinks, suggesting the tool does not distort the data to great extent. This effect was found significant for all components, except for the P3. The conclusion is that this tool distorts the data at acceptable levels, yet caution should be taken when interpreting later components, like the P3. creator: Steven Woltering creator: Narges Bazargani creator: Zhong-Xu Liu uri: https://doi.org/10.7717/peerj.76 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Woltering et al. title: A holistic evolutionary and structural study of flaviviridae provides insights into the function and inhibition of HCV helicase link: https://peerj.com/articles/74 last-modified: 2013-05-07 description: Viral RNA helicases are involved in duplex unwinding during the RNA replication of the virus. It is suggested that these helicases represent very promising antiviral targets. Viruses of the flaviviridae family are the causative agents of many common and devastating diseases, including hepatitis, yellow fever and dengue fever. As there is currently no available anti-Flaviviridae therapy, there is urgent need for the development of efficient anti-viral pharmaceutical strategies. Herein, we report the complete phylogenetic analysis across flaviviridae alongside a more in-depth evolutionary study that revealed a series of conserved and invariant amino acids that are predicted to be key to the function of the helicase. Structural molecular modelling analysis revealed the strategic significance of these residues based on their relative positioning on the 3D structures of the helicase enzymes, which may be used as pharmacological targets. We previously reported a novel series of highly potent HCV helicase inhibitors, and we now re-assess their antiviral potential using the 3D structural model of the invariant helicase residues. It was found that the most active compound of the series, compound C4, exhibited an IC50 in the submicromolar range, whereas its stereoisomer (compound C12) was completely inactive. Useful insights were obtained from molecular modelling and conformational search studies via molecular dynamics simulations. C12 tends to bend and lock in an almost “U” shape conformation, failing to establish vital interactions with the active site of HCV. On the contrary, C4 spends most of its conformational time in a straight, more rigid formation that allows it to successfully block the passage of the oligonucleotide in the ssRNA channel of the HCV helicase. This study paves the way and provides the necessary framework for the in-depth analysis required to enable the future design of new and potent anti-viral agents. creator: Dimitrios Vlachakis creator: Vassiliki Lila Koumandou creator: Sophia Kossida uri: https://doi.org/10.7717/peerj.74 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Vlachakis et al. title: Ammonium hydroxide treatment of Aβ produces an aggregate free solution suitable for biophysical and cell culture characterization link: https://peerj.com/articles/73 last-modified: 2013-05-07 description: Alzheimer’s disease is the leading cause of dementia in the elderly. Pathologically it is characterized by the presence of amyloid plaques and neuronal loss within the brain tissue of affected individuals. It is now widely hypothesised that fibrillar structures represent an inert structure. Biophysical and toxicity assays attempting to characterize the formation of both the fibrillar and the intermediate oligomeric structures of Aβ typically involves preparing samples which are largely monomeric; the most common method by which this is achieved is to use the fluorinated organic solvent 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP). Recent evidence has suggested that this method is not 100% effective in producing an aggregate free solution. We show, using dynamic light scattering, size exclusion chromatography and small angle X-ray scattering that this is indeed the case, with HFIP pretreated Aβ peptide solutions displaying an increased proportion of oligomeric and aggregated material and an increased propensity to aggregate. Furthermore we show that an alternative technique, involving treatment with strong alkali results in a much more homogenous solution that is largely monomeric. These techniques for solubilising and controlling the oligomeric state of Aβ are valuable starting points for future biophysical and toxicity assays. creator: Timothy M. Ryan creator: Joanne Caine creator: Haydyn D.T. Mertens creator: Nigel Kirby creator: Julie Nigro creator: Kerry Breheney creator: Lynne J. Waddington creator: Victor A. Streltsov creator: Cyril Curtain creator: Colin L. Masters creator: Blaine R. Roberts uri: https://doi.org/10.7717/peerj.73 license: http://creativecommons.org/licenses/by/3.0/ rights: © 2013 Ryan et al.