title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1769 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Grassland productivity in response to nutrient additions and herbivory is scale-dependent link: https://peerj.com/articles/2745 last-modified: 2016-12-01 description: Vegetation response to nutrient addition can vary across space, yet studies that explicitly incorporate spatial pattern into experimental approaches are rare. To explore whether there are unique spatial scales (grains) at which grass response to nutrients and herbivory is best expressed, we imposed a large (∼3.75 ha) experiment in a South African coastal grassland ecosystem. In two of six 60 × 60 m grassland plots, we imposed a scaled sampling design in which fertilizer was added in replicated sub-plots (1 × 1 m, 2 × 2 m, and 4 × 4 m). The remaining plots either received no additions or were fertilized evenly across the entire area. Three of the six plots were fenced to exclude herbivory. We calculated empirical semivariograms for all plots one year following nutrient additions to determine whether the scale of grass response (biomass and nutrient concentrations) corresponded to the scale of the sub-plot additions and compared these results to reference plots (unfertilized or unscaled) and to plots with and without herbivory. We compared empirical semivariogram parameters to parameters from semivariograms derived from a set of simulated landscapes (neutral models). Empirical semivariograms showed spatial structure in plots that received multi-scaled nutrient additions, particularly at the 2 × 2 m grain. The level of biomass response was predicted by foliar P concentration and, to a lesser extent, N, with the treatment effect of herbivory having a minimal influence. Neutral models confirmed the length scale of the biomass response and indicated few differences due to herbivory. Overall, we conclude that interpretation of nutrient limitation in grasslands is dependent on the grain used to measure grass response and that herbivory had a secondary effect. creator: Erica A.H. Smithwick creator: Douglas C. Baldwin creator: Kusum J. Naithani uri: https://doi.org/10.7717/peerj.2745 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Smithwick et al. title: PATMA: parser of archival tissue microarray link: https://peerj.com/articles/2741 last-modified: 2016-12-01 description: Tissue microarrays are commonly used in modern pathology for cancer tissue evaluation, as it is a very potent technique. Tissue microarray slides are often scanned to perform computer-aided histopathological analysis of the tissue cores. For processing the image, splitting the whole virtual slide into images of individual cores is required. The only way to distinguish cores corresponding to specimens in the tissue microarray is through their arrangement. Unfortunately, distinguishing the correct order of cores is not a trivial task as they are not labelled directly on the slide. The main aim of this study was to create a procedure capable of automatically finding and extracting cores from archival images of the tissue microarrays. This software supports the work of scientists who want to perform further image processing on single cores. The proposed method is an efficient and fast procedure, working in fully automatic or semi-automatic mode. A total of 89% of punches were correctly extracted with automatic selection. With an addition of manual correction, it is possible to fully prepare the whole slide image for extraction in 2 min per tissue microarray. The proposed technique requires minimum skill and time to parse big array of cores from tissue microarray whole slide image into individual core images. creator: Lukasz Roszkowiak creator: Carlos Lopez uri: https://doi.org/10.7717/peerj.2741 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Roszkowiak and Lopez title: Drosophila chem mutations disrupt epithelial polarity in Drosophila embryos link: https://peerj.com/articles/2731 last-modified: 2016-12-01 description: Drosophila embryogenesis has proven to be an extremely powerful system for developmental gene discovery and characterization. We isolated five new EMS-induced alleles that do not complement the l(3R)5G83 lethal line isolated in the Nüsslein-Volhard and Wieschaus screens. We have named this locus chem. Lethality of the new alleles as homozygous zygotic mutants is not completely penetrant, and they have an extended phenocritical period. Like the original allele, a fraction of mutant embryos die with cuticular defects, notably head involution and dorsal closure defects. Embryonic defects are much more extreme in germline clones, where the majority of mutant embryos die during embryogenesis and do not form cuticle, implying a strong chem maternal contribution. chem mutations genetically interact with mutations in cytoskeletal genes (arm) and with mutations in the epithelial polarity genes coracle, crumbs, and yurt. chem mutants dorsal open defects are similar to those present in yurt mutants, and, likewise, they have epithelial polarity defects. chem1 and chem3 mutations suppress yurt3, and chem3 mutants suppress crumbs1 mutations. In contrast, chem1 and coracle2 mutations enhance each other. Compared to controls, in chem mutants in embryonic lateral epithelia Crumbs expression is mislocalized and reduced, Coracle is increased and mislocalized basally at embryonic stages 13–14, then reduced at stage 16. Arm expression has a similar pattern but levels are reduced. creator: José M. Zamudio-Arroyo creator: Juan R. Riesgo-Escovar uri: https://doi.org/10.7717/peerj.2731 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Zamudio-Arroyo and Riesgo-Escovar title: Age, growth and population structure of invasive lionfish (Pterois volitans/miles) in northeast Florida using a length-based, age-structured population model link: https://peerj.com/articles/2730 last-modified: 2016-12-01 description: The effective management of invasive species requires detailed understanding of the invader’s life history. This information is essential for modeling population growth and predicting rates of expansion, quantifying ecological impacts and assessing the efficacy of removal and control strategies. Indo-Pacific lionfish (Pterois volitans/miles) have rapidly invaded the western Atlantic, Gulf of Mexico and Caribbean Sea with documented negative impacts on native ecosystems. To better understand the life history of this species, we developed and validated a length-based, age-structured model to investigate age, growth and population structure in northeast Florida. The main findings of this study were: (1) lionfish exhibited rapid growth with seasonal variation in growth rates; (2) distinct cohorts were clearly identifiable in the length-frequency data, suggesting that lionfish are recruiting during a relatively short period in summer; and (3) the majority of lionfish were less than two years old with no lionfish older than three years of age, which may be the result of culling efforts as well as ontogenetic habitat shifts to deeper water. creator: Eric G. Johnson creator: Mary Katherine Swenarton uri: https://doi.org/10.7717/peerj.2730 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Johnson and Swenarton title: A methodology for the design of experiments in computational intelligence with multiple regression models link: https://peerj.com/articles/2721 last-modified: 2016-12-01 description: The design of experiments and the validation of the results achieved with them are vital in any research study. This paper focuses on the use of different Machine Learning approaches for regression tasks in the field of Computational Intelligence and especially on a correct comparison between the different results provided for different methods, as those techniques are complex systems that require further study to be fully understood. A methodology commonly accepted in Computational intelligence is implemented in an R package called RRegrs. This package includes ten simple and complex regression models to carry out predictive modeling using Machine Learning and well-known regression algorithms. The framework for experimental design presented herein is evaluated and validated against RRegrs. Our results are different for three out of five state-of-the-art simple datasets and it can be stated that the selection of the best model according to our proposal is statistically significant and relevant. It is of relevance to use a statistical approach to indicate whether the differences are statistically significant using this kind of algorithms. Furthermore, our results with three real complex datasets report different best models than with the previously published methodology. Our final goal is to provide a complete methodology for the use of different steps in order to compare the results obtained in Computational Intelligence problems, as well as from other fields, such as for bioinformatics, cheminformatics, etc., given that our proposal is open and modifiable. creator: Carlos Fernandez-Lozano creator: Marcos Gestal creator: Cristian R. Munteanu creator: Julian Dorado creator: Alejandro Pazos uri: https://doi.org/10.7717/peerj.2721 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Fernandez-Lozano et al. title: Risk factors for in-hospital mortality after coronary artery bypass grafting in patients 80 years old or older: a retrospective case-series study link: https://peerj.com/articles/2667 last-modified: 2016-12-01 description: BackgroundAge remains a significant and unmodifiable risk factor for cardiovascular diseases, and an increasing number of patients older than 80 years of age undergo Coronary Artery Bypass Grafting (CABG). Old age is also an independent risk factor for postoperative complications. The aim of this study is to describe the population of patients 80 years of age or older who underwent CABG procedure and to assess the mortality rate and risk factors for in-hospital mortality.MethodsA retrospective case-series study analyzing 388 consecutive patients aged 80 years of age or older who underwent isolated CABG procedure between 2010 and 2014 in the Department of Cardiovascular Surgery and Transplantology, John Paul II Hospital, Krakow.ResultsIn-hospital mortality stood at 7%, compared to 3.4% for all isolated CABG procedures at our Institution. In an univariate logistic regression analysis, risk factors for in-hospital mortality were as follows: NYHA class (p = 0.005, OR 1.95, 95% CI [1.23–3.1]), prolonged mechanical ventilation (p < 0.001, OR 7.08, 95% CI [2.47–20.3]), rethoracotomy (p = 0.04, OR 3.31, 95% CI [1.04–10.6]), duration of the procedure and ECC (for every 10 min p = 0.01, OR 1.01, 95% CI [1.0–1.01]; p = 0.03, OR 1.01, 95% CI [1.0–1.02], respectively), PRBC, FFP, and PLT transfusion (for every unit transfused p = 0.004, OR 1.42, 95% CI [1.12–1.8]; p = 0.002, OR 1.55, 95% CI [1.18–2.04]; p = 0.009, OR 1.93, 95% CI [1.18–3.14], respectively). Higher LVEF (p = 0.02, OR 0.97, 95% CI [0.94–0.99]) and LIMA graft implantation (p = 0.04, OR 0.36, 95% CI [0.13–0.98) decreased the in-hospital mortality. Death before discharge was more often observed in patients with multiple risk factors for cardiovascular diseases (0–2 –5.7%; 3–7.4%, 4–26.6%; p = 0.03).ConclusionsOlder age is associated with higher in-hospital mortality after isolated CABG at our Institution. Risk stratification scores and individualized risk evaluation, centered on comorbidities, NYHA class and left ventricular function, should be assessed in all cases. Whenever suitable, LIMA grafts should be used. Prolonged procedure and ECC time worsen the short-term outcome. Elderly individuals should be closely monitored postoperatively and the care should be focused on excessive blood loss and respiratory failure. creator: Jacek Piątek creator: Anna Kędziora creator: Janusz Konstanty-Kalandyk creator: Grzegorz Kiełbasa creator: Marta Olszewska creator: Bryan HyoChan Song creator: Karol Wierzbicki creator: Irena Milaniak creator: Tomasz Darocha creator: Dorota Sobczyk creator: Bogusław Kapelak uri: https://doi.org/10.7717/peerj.2667 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Piątek et al. title: On the intrinsic sterility of 3D printing link: https://peerj.com/articles/2661 last-modified: 2016-12-01 description: 3D printers that build objects using extruded thermoplastic are quickly becoming commonplace tools in laboratories. We demonstrate that, with appropriate handling, these devices are capable of producing sterile components from a non-sterile feedstock of thermoplastic without any treatment after fabrication. The fabrication process itself results in sterilization of the material. The resulting 3D printed components are suitable for a wide variety of applications, including experiments with bacteria and cell culture. creator: Russell Y. Neches creator: Kaitlin J. Flynn creator: Luis Zaman creator: Emily Tung creator: Nicholas Pudlo uri: https://doi.org/10.7717/peerj.2661 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Neches et al. title: Development of olfactory epithelium and associated structures in the green iguana, Iguana iguana—light and scanning electron microscopic study link: https://peerj.com/articles/2561 last-modified: 2016-12-01 description: The ontogenesis of the nasal cavity has been described in many mammalian species. The situation is different with reptiles, despite the fact that they have become relatively common as pets. In this study we focused on the ontogenesis of the olfactory epithelium, as well as other types of epithelia in the nasal cavity of pre-hatched green iguanas (Iguana iguana). Collection of samples began from day 67 of incubation and continued every four days until hatching. Microscopic examination revealed that significant morphological changes in the nasal cavity began approximately at day 91 of ontogenesis. Approximately at this same stage, the nasal cavity epithelium began to differentiate. The cavity was divided into two compartments by a cartilaginous disc. The ventral compartment bulged rostrally and eventually opened up into the external environment. Three clearly demarcated areas of epithelium in the nasal cavity were visible at day 107. creator: Olga Sapoznikov creator: Petr Cizek creator: Frantisek Tichy uri: https://doi.org/10.7717/peerj.2561 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Sapoznikov et al. title: Development and evaluation of a novel vaccine against prevalent invasive multi-drug resistant strains of Streptococcus pneumoniae link: https://peerj.com/articles/2737 last-modified: 2016-11-30 description: Streptococcus pneumoniae is a pathogen that causes serious invasive infections, such as septicemia, meningitis and pneumonia in addition to mild upper respiratory tract infections. Protection from pneumococcal diseases is thought to be mediated mainly by serotype-specific antibodies to capsular antigens. Pneumococcal conjugate vaccine consists of sugars (polysaccharides) from the capsule of the bacterium S. pneumoniae that are conjugated to a carrier protein. Three pneumococcal conjugated vaccines, each directed against a group of serotypes, are registered in Egypt; however, local vaccine production is required to cover the most prevalent serotypes. In this work, capsular polysaccharide from the most current and prevalent serotypes in Egypt were extracted, purified and conjugated to bovine serum albumin (BSA). The polysaccharide protein conjugate was purified through ultrafiltration technique and molecular size distribution was compared to an available vaccine. The immunogenicity of the prepared vaccine was examined via two methods: First, by measuring the levels of the elicited antibodies in the sera of the vaccinated mice; second, by challenging the vaccinated groups of mice with approximately 107 CFU of each specific serotype and determining the degree of protection the developled vaccine offers. Our results show that the developed conjugated capsular polysaccharide vaccine is highly immunogenic and protective in mice. This finding illustrates the importance of tracking the most recent and predominant peneumococcal serotypes to generate effective vaccines, instead of using expensive imported vaccines with large number of serotypes which might not be even present in the community. creator: Rehab H. Bahy creator: Hayam M. Hamouda creator: Amal S. Shahat creator: Aymen S. Yassin creator: Magdy A. Amin uri: https://doi.org/10.7717/peerj.2737 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Bahy et al. title: A 4D CT digital phantom of an individual human brain for perfusion analysis link: https://peerj.com/articles/2683 last-modified: 2016-11-30 description: Brain perfusion is of key importance to assess brain function. Modern CT scanners can acquire perfusion maps of the cerebral parenchyma in vivo at submillimeter resolution. These perfusion maps give insights into the hemodynamics of the cerebral parenchyma and are critical for example for treatment decisions in acute stroke. However, the relations between acquisition parameters, tissue attenuation curves, and perfusion values are still poorly understood and cannot be unraveled by studies involving humans because of ethical concerns. We present a 4D CT digital phantom specific for an individual human brain to analyze these relations in a bottom-up fashion. Validation of the signal and noise components was based on 1,000 phantom simulations of 20 patient imaging data. This framework was applied to quantitatively assess the relation between radiation dose and perfusion values, and to quantify the signal-to-noise ratios of penumbra regions with decreasing sizes in white and gray matter. This is the first 4D CT digital phantom that enables to address clinical questions without having to expose the patient to additional radiation dose. creator: Rashindra Manniesing creator: Christoph Brune creator: Bram van Ginneken creator: Mathias Prokop uri: https://doi.org/10.7717/peerj.2683 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2016 Manniesing et al.