{"_links":{"self":{"href":"https:\/\/peerj.com\/preprints\/index.json?journal=peerj"},"next":{"href":"https:\/\/peerj.com\/preprints\/index.json?journal=peerj&page=2"},"alternate":{"atom":{"type":"application\/atom+xml","href":"https:\/\/peerj.com\/preprints\/index.atom"},"rss1":{"type":"application\/rdf+xml","href":"https:\/\/peerj.com\/preprints\/index.rss1"},"rss2":{"type":"application\/rss+xml","href":"https:\/\/peerj.com\/preprints\/index.rss2"},"rss3":{"type":"text\/plain","href":"https:\/\/peerj.com\/preprints\/index.rss3"},"html":{"type":"text\/html","href":"https:\/\/peerj.com\/preprints\/index.html"}}},"_items":[{"title":"A simplified correlation between vertebrate evolution and Paleozoic geomagnetism","date":"2019-12-31","doi":"10.7287\/peerj.preprints.28002v3","language":"en","pdf_url":"https:\/\/peerj.com\/preprints\/28002v3.pdf","fulltext_html_url":"https:\/\/peerj.com\/preprints\/28002v3","technical_report_number":"e28002v3","author":"John P Staub","author_institution":"Unaffiliated researcher, Mesa, Arizona, United States","author_email":"paleopjs@yahoo.com","authors":"Staub, John P","author_institutions":"Unaffiliated researcher, Mesa, Arizona, United States","keywords":["Paleozoic","geomagnetism","vertebrates","evolution","paleontology","compendium"],"technical_report_institution":"PeerJ Preprints","publisher":"PeerJ Inc.","issn":"2167-9843","description":"Background. Despite a fifty-year failure of paleontologists to find a viable connection between geomagnetic polarity reversals and evolutionary patterns, recent paleobiology databases show that the early appearance, radiation, and diversification of Paleozoic vertebrates tends to occur during periods having frequent collapses of the Earth\u2019s geomagnetic field. The transition time during the collapse of the Earth\u2019s protective magnetic shield can last thousands of years, and the effects on biota are unknown. Solar and cosmic radiation, volcanism, climate alteration, low-frequency electromagnetic fields, depletion of ozone, the stripping of atmospheric oxygen, and increasing production of Carbon14 in the stratosphere have been proposed as possible causes, but previous studies have found no effects. Methods. Using published databases, we compiled a spreadsheet showing the first appearance of 2104 genera with each genus assigned to one of 8 major taxonomic groups. From Gradstein\u2019s Geologic Time Scale 2012, we delineated 17 Paleozoic zones with either high or low levels of polarity reversals. Results. From our compilation, 727 Paleozoic vertebrates represent the initial radiation and diversification of individual Paleozoic vertebrate clades. After compensating for sample-size and external geologic and sampling biases, the resulting Pearson\u2019s correlation coefficient between the 727 genera and geomagnetic polarity zones equals 0.8, a result that suggests a strong relationship exists between Paleozoic vertebrates and geomagnetism. Discussion. The question: is this apparent connection between geomagnetism and the evolution of Paleozoic vertebrate due to environmental or biologic factors. If biologic, why are vertebrates the only biota effected? And after an indeterminate period of time, how do vertebrates become immune to the ongoing effects of polarity reversals?","description-html":"\n
Background.<\/b> Despite a fifty-year failure of paleontologists to find a viable connection between geomagnetic polarity reversals and evolutionary patterns, recent paleobiology databases show that the early appearance, radiation, and diversification of Paleozoic vertebrates tends to occur during periods having frequent collapses of the Earth\u2019s geomagnetic field. The transition time during the collapse of the Earth\u2019s protective magnetic shield can last thousands of years, and the effects on biota are unknown. Solar and cosmic radiation, volcanism, climate alteration, low-frequency electromagnetic fields, depletion of ozone, the stripping of atmospheric oxygen, and increasing production of Carbon14 in the stratosphere have been proposed as possible causes, but previous studies have found no effects.<\/p>\n
Methods.<\/b> Using published databases, we compiled a spreadsheet showing the first appearance of 2104 genera with each genus assigned to one of 8 major taxonomic groups. From Gradstein\u2019s Geologic Time Scale 2012, we delineated 17 Paleozoic zones with either high or low levels of polarity reversals.<\/p>\n
Results. <\/b> From our compilation, 727 Paleozoic vertebrates represent the initial radiation and diversification of individual Paleozoic vertebrate clades. After compensating for sample-size and external geologic and sampling biases, the resulting Pearson\u2019s correlation coefficient between the 727 genera and geomagnetic polarity zones equals 0.8, a result that suggests a strong relationship exists between Paleozoic vertebrates and geomagnetism.<\/p>\n
Discussion.<\/b> The question: is this apparent connection between geomagnetism and the evolution of Paleozoic vertebrate due to environmental or biologic factors. If biologic, why are vertebrates the only biota effected? And after an indeterminate period of time, how do vertebrates become immune to the ongoing effects of polarity reversals?<\/p>\n ","title-html":"A simplified correlation between vertebrate evolution and Paleozoic geomagnetism","subjects":["Evolutionary Studies","Paleontology"],"identifiers":{"peerj":"28002"},"@context":"http:\/\/static.peerj.com\/context\/citation\/context.json","@type":"http:\/\/schema.org\/ScholarlyArticle","@id":"https:\/\/peerj.com\/preprints\/28002v3","_links":{"self":{"href":"https:\/\/peerj.com\/preprints\/28002.json?version=3"},"alternate":{"html":{"type":"text\/html","href":"https:\/\/peerj.com\/preprints\/28002.html?version=3"},"xml":{"type":"application\/xml","href":"https:\/\/peerj.com\/preprints\/28002.xml?version=3"},"pdf":{"type":"application\/pdf","href":"https:\/\/peerj.com\/preprints\/28002.pdf?version=3"},"rdf":{"type":"application\/rdf+xml","href":"https:\/\/peerj.com\/preprints\/28002.rdf?version=3"},"ris":{"type":"application\/x-research-info-systems","href":"https:\/\/peerj.com\/preprints\/28002.ris?version=3"},"bib":{"type":"application\/x-bibtex","href":"https:\/\/peerj.com\/preprints\/28002.bib?version=3"},"citeproc":{"type":"application\/vnd.citationstyles.csl+json","href":"https:\/\/peerj.com\/preprints\/28002.citeproc?version=3"},"bibjson":{"type":"application\/bibjson+json","href":"https:\/\/peerj.com\/preprints\/28002.bibjson?version=3"},"datacite":{"type":"application\/datacite+xml","href":"https:\/\/peerj.com\/preprints\/28002.datacite?version=3"}}}},{"title":"Development and application of a robotic zebra finch (RoboFinch) to study multimodal cues in vocal communication","date":"2019-12-30","doi":"10.7287\/peerj.preprints.28004v3","language":"en","pdf_url":"https:\/\/peerj.com\/preprints\/28004v3.pdf","fulltext_html_url":"https:\/\/peerj.com\/preprints\/28004v3","technical_report_number":"e28004v3","author":["Ralph Simon","Judith Varkevisser","Ezequiel Mendoza","Klaus Hochradel","Constance Scharff","Katharina Riebel","Wouter Halfwerk"],"author_institution":["Department of Ecological Science, VU University Amsterdam, Amsterdam, Netherlands","Institute of Biology Leiden, Leiden University, Leiden, Netherlands","Institute of Biology Leiden, Leiden University, Leiden, Netherlands","Institut f\u00fcr Biologie, Freie Universit\u00e4t Berlin, Berlin, Germany","Institute of Measurement and Sensor Technology, Private Universit\u00e4t f\u00fcr Gesundheitswissenschaften, Medizinische Informatik und Technik (UMIT), Hall, Austria","Institut f\u00fcr Biologie, Freie Universit\u00e4t Berlin, Berlin, Germany","Institute of Biology Leiden, Leiden University, Leiden, Netherlands","Department of Ecological Science, VU University Amsterdam, Amsterdam, Netherlands"],"author_email":"ralph.simon@vu.nl","authors":"Simon, Ralph; Varkevisser, Judith; Mendoza, Ezequiel; Hochradel, Klaus; Scharff, Constance; Riebel, Katharina; Halfwerk, Wouter","author_institutions":"Department of Ecological Science, VU University Amsterdam, Amsterdam, Netherlands; Institute of Biology Leiden, Leiden University, Leiden, Netherlands; Institut f\u00fcr Biologie, Freie Universit\u00e4t Berlin, Berlin, Germany; Institute of Measurement and Sensor Technology, Private Universit\u00e4t f\u00fcr Gesundheitswissenschaften, Medizinische Informatik und Technik (UMIT), Hall, Austria","keywords":["vocal communication","animatronics","multimodal perception","zebra finch"],"technical_report_institution":"PeerJ Preprints","publisher":"PeerJ Inc.","issn":"2167-9843","description":"Understanding animal behaviour through psychophysical experimentation is often limited by insufficiently realistic stimulus representation. Important physical dimensions of signals and cues, especially those that are outside the spectrum of human perception, can be difficult to standardize and control separately with currently available recording and displaying techniques (e.g. video displays). Accurate stimulus control is in particular important when studying multimodal signals, as spatial and temporal alignment between stimuli is often crucial. Especially for audiovisual presentations, some of these limitations can be circumvented by the employment of animal robots that are superior to video presentations in all situations requiring realistic 3D presentations to animals. Here we report the development of a robotic zebra finch, called RoboFinch, and how it can be used to study vocal learning in a songbird, the zebra finch.","description-html":"\n
Understanding animal behaviour through psychophysical experimentation is often limited by insufficiently realistic stimulus representation. Important physical dimensions of signals and cues, especially those that are outside the spectrum of human perception, can be difficult to standardize and control separately with currently available recording and displaying techniques (e.g. video displays). Accurate stimulus control is in particular important when studying multimodal signals, as spatial and temporal alignment between stimuli is often crucial. Especially for audiovisual presentations, some of these limitations can be circumvented by the employment of animal robots that are superior to video presentations in all situations requiring realistic 3D presentations to animals. Here we report the development of a robotic zebra finch, called RoboFinch, and how it can be used to study vocal learning in a songbird, the zebra finch.<\/p>\n ","title-html":"Development and application of a robotic zebra finch (RoboFinch) to study multimodal cues in vocal communication","subjects":["Animal Behavior","Ecology","Zoology"],"identifiers":{"peerj":"28004"},"@context":"http:\/\/static.peerj.com\/context\/citation\/context.json","@type":"http:\/\/schema.org\/ScholarlyArticle","@id":"https:\/\/peerj.com\/preprints\/28004v3","_links":{"self":{"href":"https:\/\/peerj.com\/preprints\/28004.json?version=3"},"alternate":{"html":{"type":"text\/html","href":"https:\/\/peerj.com\/preprints\/28004.html?version=3"},"xml":{"type":"application\/xml","href":"https:\/\/peerj.com\/preprints\/28004.xml?version=3"},"pdf":{"type":"application\/pdf","href":"https:\/\/peerj.com\/preprints\/28004.pdf?version=3"},"rdf":{"type":"application\/rdf+xml","href":"https:\/\/peerj.com\/preprints\/28004.rdf?version=3"},"ris":{"type":"application\/x-research-info-systems","href":"https:\/\/peerj.com\/preprints\/28004.ris?version=3"},"bib":{"type":"application\/x-bibtex","href":"https:\/\/peerj.com\/preprints\/28004.bib?version=3"},"citeproc":{"type":"application\/vnd.citationstyles.csl+json","href":"https:\/\/peerj.com\/preprints\/28004.citeproc?version=3"},"bibjson":{"type":"application\/bibjson+json","href":"https:\/\/peerj.com\/preprints\/28004.bibjson?version=3"},"datacite":{"type":"application\/datacite+xml","href":"https:\/\/peerj.com\/preprints\/28004.datacite?version=3"}}}},{"title":"Isolation and characterization of psychrotrophic proteolytic bacteria from landfill site under temperate climatic conditions of Kashmir Himalaya","date":"2019-12-21","doi":"10.7287\/peerj.preprints.27391v2","language":"en","pdf_url":"https:\/\/peerj.com\/preprints\/27391.pdf","fulltext_html_url":"https:\/\/peerj.com\/preprints\/27391","technical_report_number":"e27391v2","author":["Basharat Hamid","Arshid Jehangir","Zahoor Ahmad Baba","Muneer Ahmad Wani","Imran Khan"],"author_institution":["Environmental Sciences, University of Kashmir, Srinagar, JAMMU & KASHMIR, India","Environmental Sciences, University of Kashmir, Srinagar, JAMMU & KASHMIR, India","Department of Soil Sciences and Agricultural Biochemistry, Sher-e-Kashmir University of Agricultural Science and Technology,Kashmir, Srinagar, JAMMU & KASHMIR, India","Environmental Sciences, University of Kashmir, Srinagar, JAMMU & KASHMIR, India","Environmental Sciences, University of Kashmir, Srinagar, JAMMU & KASHMIR, India"],"author_email":"basharat.scholar@kashmiruniversity.net","authors":"Hamid, Basharat; Jehangir, Arshid; Baba, Zahoor Ahmad; Wani, Muneer Ahmad; Khan, Imran","author_institutions":"Environmental Sciences, University of Kashmir, Srinagar, JAMMU & KASHMIR, India; Department of Soil Sciences and Agricultural Biochemistry, Sher-e-Kashmir University of Agricultural Science and Technology,Kashmir, Srinagar, JAMMU & KASHMIR, India","keywords":["Waste","Psychrotrophic","Protease","Pseudomonas florescence","16SrRNA","Landfill"],"technical_report_institution":"PeerJ Preprints","publisher":"PeerJ Inc.","issn":"2167-9843","description":"The temperate climatic regions face the problem of waste accumulation due to lower environmental temperatures. However, these regions harbor cold active microbes viz. psychrotrophic proteolytic bacteria that play an important role in the degradation of protenaceous materials of the waste stream. Hence in the present study psychrotrophic proteolytic bacteria were isolated from waste samples collected from landfill site by using random sampling method under environmental temperature of 10oC. By using serial dilution and spread plate technique a total of 8 morphologically different psychrotrophic proteolytic bacteria were isolated on skim milk agar media at pH of 7.0 and temperature of 10\u00b0C after 48hours. Under in-vitro conditions all the isolates produced significant quantities of protease over the control and diameters of hydrolysis zones ranged between 2 to 18 mm at temperature range of 5 to 20oC and after 72 hours. The corresponding quantitative protease activities of the isolates was significant that ranged between 0.5 to 2.25 U\/ml and the isolate PB2 was most efficient with highest protease activity of 2.25U\/ml at 20oC. Based on 16SrRNA analysis the isolate was identified as Pseudomonas florescence with 96% similarity. It was concluded that the isolates can grow in wide ranges of temperature and could be used for enhanced decomposition of organic wastes during lower temperature conditions in cold regions. Further the isolates could have industrial applications due to the production of cold active proteases that would help economic benefits through energy conservation.","description-html":"\n
The temperate climatic regions face the problem of waste accumulation due to lower environmental temperatures. However, these regions harbor cold active microbes viz. psychrotrophic proteolytic bacteria that play an important role in the degradation of protenaceous materials of the waste stream. Hence in the present study psychrotrophic proteolytic bacteria were isolated from waste samples collected from landfill site by using random sampling method under environmental temperature of 10o<\/sup>C. By using serial dilution and spread plate technique a total of 8 morphologically different psychrotrophic proteolytic bacteria were isolated on skim milk agar media at pH of 7.0 and temperature of 10\u00b0C after 48hours. Under in-vitro conditions all the isolates produced significant quantities of protease over the control and diameters of hydrolysis zones ranged between 2 to 18 mm at temperature range of 5 to 20o<\/sup>C and after 72 hours. The corresponding quantitative protease activities of the isolates was significant that ranged between 0.5 to 2.25 U\/ml and the isolate PB2<\/sub> was most efficient with highest protease activity of 2.25U\/ml at 20o<\/sup>C. Based on 16SrRNA analysis the isolate was identified as Pseudomonas florescence<\/i> with 96% similarity. It was concluded that the isolates can grow in wide ranges of temperature and could be used for enhanced decomposition of organic wastes during lower temperature conditions in cold regions. Further the isolates could have industrial applications due to the production of cold active proteases that would help economic benefits through energy conservation.<\/p>\n ","title-html":"Isolation and characterization of psychrotrophic proteolytic bacteria from landfill site under temperate climatic conditions of Kashmir Himalaya","subjects":["Agricultural Science","Biotechnology","Ecosystem Science","Microbiology","Environmental Contamination and Remediation"],"identifiers":{"peerj":"27391"},"@context":"http:\/\/static.peerj.com\/context\/citation\/context.json","@type":"http:\/\/schema.org\/ScholarlyArticle","@id":"https:\/\/peerj.com\/preprints\/27391","_links":{"self":{"href":"https:\/\/peerj.com\/preprints\/27391.json?version=2"},"alternate":{"html":{"type":"text\/html","href":"https:\/\/peerj.com\/preprints\/27391.html?version=2"},"xml":{"type":"application\/xml","href":"https:\/\/peerj.com\/preprints\/27391.xml?version=2"},"pdf":{"type":"application\/pdf","href":"https:\/\/peerj.com\/preprints\/27391.pdf?version=2"},"rdf":{"type":"application\/rdf+xml","href":"https:\/\/peerj.com\/preprints\/27391.rdf?version=2"},"ris":{"type":"application\/x-research-info-systems","href":"https:\/\/peerj.com\/preprints\/27391.ris?version=2"},"bib":{"type":"application\/x-bibtex","href":"https:\/\/peerj.com\/preprints\/27391.bib?version=2"},"citeproc":{"type":"application\/vnd.citationstyles.csl+json","href":"https:\/\/peerj.com\/preprints\/27391.citeproc?version=2"},"bibjson":{"type":"application\/bibjson+json","href":"https:\/\/peerj.com\/preprints\/27391.bibjson?version=2"},"datacite":{"type":"application\/datacite+xml","href":"https:\/\/peerj.com\/preprints\/27391.datacite?version=2"}}}},{"title":"Data-driven classification of the certainty of scholarly assertions","date":"2019-12-20","doi":"10.7287\/peerj.preprints.27829v2","language":"en","pdf_url":"https:\/\/peerj.com\/preprints\/27829.pdf","fulltext_html_url":"https:\/\/peerj.com\/preprints\/27829","technical_report_number":"e27829v2","author":["Mario Prieto","Helena Deus","Anita De Waard","Erik Schultes","Beatriz Garc\u00eda-Jim\u00e9nez","Mark D Wilkinson"],"author_institution":["Departamento de Biotecnolog\u00eda-Biolog\u00eda Vegetal, Escuela T\u00e9cnica Superior de Ingenier\u00eda Agron\u00f3mica, Alimentaria y de Biosistemas, Centro de Biotecnolog\u00eda y Gen\u00f3mica de Plantas, Universidad Polit\u00e9cnica de Madrid (UPM) - Instituto Nacional de Investigaci\u00f3n y Tecnolog\u00eda Agraria y Alimentaria (INIA), Madrid, Madrid, Spain","Elsevier Inc., Cambridge, MA, United States","Elsevier Research Collaborations Unit, Jericho, VT, United States","GO FAIR International Support and Coordination Office, Leiden, The Netherlands","Centro de Biotecnolog\u00eda y Gen\u00f3mica de Plantas, Universidad Polit\u00e9cnica de Madrid (UPM) - Instituto Nacional de Investigaci\u00f3n y Tecnolog\u00eda Agraria y Alimentaria (INIA);, Madrid, Madrid, Spain","Departamento de Biotecnolog\u00eda-Biolog\u00eda Vegetal, Escuela T\u00e9cnica Superior de Ingenier\u00eda Agron\u00f3mica, Alimentaria y de Biosistemas, Centro de Biotecnolog\u00eda y Gen\u00f3mica de Plantas, Universidad Polit\u00e9cnica de Madrid (UPM) - Instituto Nacional de Investigaci\u00f3n y Tecnolog\u00eda Agraria y Alimentaria (INIA);, Madrid, Madrid, Spain"],"author_email":"markw@illuminae.com","authors":"Prieto, Mario; Deus, Helena; De Waard, Anita; Schultes, Erik; Garc\u00eda-Jim\u00e9nez, Beatriz; Wilkinson, Mark D","author_institutions":"Departamento de Biotecnolog\u00eda-Biolog\u00eda Vegetal, Escuela T\u00e9cnica Superior de Ingenier\u00eda Agron\u00f3mica, Alimentaria y de Biosistemas, Centro de Biotecnolog\u00eda y Gen\u00f3mica de Plantas, Universidad Polit\u00e9cnica de Madrid (UPM) - Instituto Nacional de Investigaci\u00f3n y Tecnolog\u00eda Agraria y Alimentaria (INIA), Madrid, Madrid, Spain; Elsevier Inc., Cambridge, MA, United States; Elsevier Research Collaborations Unit, Jericho, VT, United States; GO FAIR International Support and Coordination Office, Leiden, The Netherlands; Centro de Biotecnolog\u00eda y Gen\u00f3mica de Plantas, Universidad Polit\u00e9cnica de Madrid (UPM) - Instituto Nacional de Investigaci\u00f3n y Tecnolog\u00eda Agraria y Alimentaria (INIA);, Madrid, Madrid, Spain; Departamento de Biotecnolog\u00eda-Biolog\u00eda Vegetal, Escuela T\u00e9cnica Superior de Ingenier\u00eda Agron\u00f3mica, Alimentaria y de Biosistemas, Centro de Biotecnolog\u00eda y Gen\u00f3mica de Plantas, Universidad Polit\u00e9cnica de Madrid (UPM) - Instituto Nacional de Investigaci\u00f3n y Tecnolog\u00eda Agraria y Alimentaria (INIA);, Madrid, Madrid, Spain","keywords":["text mining","scholarly communication","certainty","FAIR Data","machine learning"],"technical_report_institution":"PeerJ Preprints","publisher":"PeerJ Inc.","issn":"2167-9843","description":"The grammatical structures scholars use to express their assertions are intended to convey various degrees of certainty or speculation. Prior studies have suggested a variety of categorization systems for scholarly certainty; however, these have not been objectively tested for their validity, particularly with respect to representing the interpretation by the reader, rather than the intention of the author. In this study, we use a series of questionnaires to determine how researchers classify various scholarly assertions, using three distinct certainty classification systems. We find that there are three distinct categories of certainty along a spectrum from high to low. We show that these categories can be detected in an automated manner, using a machine learning model, with a cross-validation accuracy of 89.2% relative to an author-annotated corpus, and 82.2% accuracy against a publicly-annotated corpus. This finding provides an opportunity for contextual metadata related to certainty to be captured as a part of text-mining pipelines, which currently miss these subtle linguistic cues. We provide an exemplar machine-accessible representation - a Nanopublication - where certainty category is embedded as metadata in a formal, ontology-based manner within text-mined scholarly assertions.","description-html":"\n The grammatical structures scholars use to express their assertions are intended to convey various degrees of certainty or speculation. Prior studies have suggested a variety of categorization systems for scholarly certainty; however, these have not been objectively tested for their validity, particularly with respect to representing the interpretation by the reader, rather than the intention of the author. In this study, we use a series of questionnaires to determine how researchers classify various scholarly assertions, using three distinct certainty classification systems. We find that there are three distinct categories of certainty along a spectrum from high to low. We show that these categories can be detected in an automated manner, using a machine learning model, with a cross-validation accuracy of 89.2% relative to an author-annotated corpus, and 82.2% accuracy against a publicly-annotated corpus. This finding provides an opportunity for contextual metadata related to certainty to be captured as a part of text-mining pipelines, which currently miss these subtle linguistic cues. We provide an exemplar machine-accessible representation - a Nanopublication - where certainty category is embedded as metadata in a formal, ontology-based manner within text-mined scholarly assertions.<\/p>\n ","title-html":"Data-driven classification of the certainty of scholarly assertions","subjects":["Bioinformatics","Computational Science","Data Mining and Machine Learning"],"identifiers":{"peerj":"27829"},"@context":"http:\/\/static.peerj.com\/context\/citation\/context.json","@type":"http:\/\/schema.org\/ScholarlyArticle","@id":"https:\/\/peerj.com\/preprints\/27829","_links":{"self":{"href":"https:\/\/peerj.com\/preprints\/27829.json?version=2"},"alternate":{"html":{"type":"text\/html","href":"https:\/\/peerj.com\/preprints\/27829.html?version=2"},"xml":{"type":"application\/xml","href":"https:\/\/peerj.com\/preprints\/27829.xml?version=2"},"pdf":{"type":"application\/pdf","href":"https:\/\/peerj.com\/preprints\/27829.pdf?version=2"},"rdf":{"type":"application\/rdf+xml","href":"https:\/\/peerj.com\/preprints\/27829.rdf?version=2"},"ris":{"type":"application\/x-research-info-systems","href":"https:\/\/peerj.com\/preprints\/27829.ris?version=2"},"bib":{"type":"application\/x-bibtex","href":"https:\/\/peerj.com\/preprints\/27829.bib?version=2"},"citeproc":{"type":"application\/vnd.citationstyles.csl+json","href":"https:\/\/peerj.com\/preprints\/27829.citeproc?version=2"},"bibjson":{"type":"application\/bibjson+json","href":"https:\/\/peerj.com\/preprints\/27829.bibjson?version=2"},"datacite":{"type":"application\/datacite+xml","href":"https:\/\/peerj.com\/preprints\/27829.datacite?version=2"}}}},{"title":"A roadmap for gene functional characterisation in wheat","date":"2019-12-18","doi":"10.7287\/peerj.preprints.26877v2","language":"en","pdf_url":"https:\/\/peerj.com\/preprints\/26877.pdf","fulltext_html_url":"https:\/\/peerj.com\/preprints\/26877","technical_report_number":"e26877v2","author":["Nikolai M Adamski","Philippa Borrill","Jemima Brinton","Sophie Harrington","Clemence Marchal","Alison R Bentley","Wiliam D Bovill","Luigi Cattivelli","James Cockram","Bruno Contreras-Moreira","Brett Ford","Sreya Ghosh","Wendy Harwood","Keywan Hassani-Pak","Sadiye Hayta","Lee T Hickey","Kostya Kanyuka","Julie King","Marco Maccaferri","Guy Naamati","Curtis J Pozniak","Ricardo H Ramirez-Gonzalez","Carolina Sansaloni","Ben Trevaskis","Luzie U Wingen","Brande BH Wulff","Cristobal Uauy"],"author_institution":["Crop Genetics, John Innes Centre, Norwich, United Kingdom","School of Biosciences, University of Birmingham, Birmingham, United Kingdom","Crop Genetics, John Innes Centre, Norwich, United Kingdom","Crop Genetics, John Innes Centre, Norwich, United Kingdom","Crop Genetics, John Innes Centre, Norwich, United Kingdom","John Bingham Laboratory, National Institute of Agricultural Botany (NIAB), Cambridge, United Kingdom","Commonwealth Scientific and Industrial Research Organisation Agriculture and Food (CSIRO), Canberra, Australia","Research Centre for Genomics and Bioinformatics, Council for Agricultural Research and Economics, Fiorenzuola d'Arda, Italy","John Bingham Laboratory, National Institute of Agricultural Botany (NIAB), Cambridge, United Kingdom","The European Bioinformatics Institute, Hinxton, United Kingdom","Commonwealth Scientific and Industrial Research Organisation Agriculture and Food (CSIRO), Canberra, Australia","Crop Genetics, John Innes Centre, Norwich, United Kingdom","Crop Genetics, John Innes Centre, Norwich, United Kingdom","Rothamsted Research, Harpenden, United Kingdom","Crop Genetics, John Innes Centre, Norwich, United Kingdom","Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Australia","Rothamsted Research, Harpenden, United Kingdom","Division of Plant and Cop Sciences, The University of Nottingham, Loughborough, United Kingdom","Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy","The European Bioinformatics Institute, Hinxton, United Kingdom","Crop Development Centre, University of Saskatchewan, Saskatoon, Canada","Crop Genetics, John Innes Centre, Norwich, United Kingdom","International Maize and Wheat Improvement Center (CIMMYT), El Batan, Mexico","Commonwealth Scientific and Industrial Research Organisation Agriculture and Food (CSIRO), Canberra, Australia","Crop Genetics, John Innes Centre, Norwich, United Kingdom","Crop Genetics, John Innes Centre, Norwich, United Kingdom","Crop Genetics, John Innes Centre, Norwich, United Kingdom"],"author_email":"cristobal.uauy@jic.ac.uk","authors":"Adamski, Nikolai M; Borrill, Philippa; Brinton, Jemima; Harrington, Sophie; Marchal, Clemence; Bentley, Alison R; Bovill, Wiliam D; Cattivelli, Luigi; Cockram, James; Contreras-Moreira, Bruno; Ford, Brett; Ghosh, Sreya; Harwood, Wendy; Hassani-Pak, Keywan; Hayta, Sadiye; Hickey, Lee T; Kanyuka, Kostya; King, Julie; Maccaferri, Marco; Naamati, Guy; Pozniak, Curtis J; Ramirez-Gonzalez, Ricardo H; Sansaloni, Carolina; Trevaskis, Ben; Wingen, Luzie U; Wulff, Brande BH; Uauy, Cristobal","author_institutions":"Crop Genetics, John Innes Centre, Norwich, United Kingdom; School of Biosciences, University of Birmingham, Birmingham, United Kingdom; John Bingham Laboratory, National Institute of Agricultural Botany (NIAB), Cambridge, United Kingdom; Commonwealth Scientific and Industrial Research Organisation Agriculture and Food (CSIRO), Canberra, Australia; Research Centre for Genomics and Bioinformatics, Council for Agricultural Research and Economics, Fiorenzuola d'Arda, Italy; The European Bioinformatics Institute, Hinxton, United Kingdom; Rothamsted Research, Harpenden, United Kingdom; Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Australia; Division of Plant and Cop Sciences, The University of Nottingham, Loughborough, United Kingdom; Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy; Crop Development Centre, University of Saskatchewan, Saskatoon, Canada; International Maize and Wheat Improvement Center (CIMMYT), El Batan, Mexico","keywords":["wheat","polyploid","genomics","expression","transgenics","TILLING","training","breeding"],"technical_report_institution":"PeerJ Preprints","publisher":"PeerJ Inc.","issn":"2167-9843","description":"To adapt to the challenges of climate change and the growing world population, it is vital to increase global crop production. Understanding the function of genes within staple crops will accelerate crop improvement by allowing targeted breeding approaches. Despite the importance of wheat, which provides 20 % of the calories consumed by humankind, a lack of genomic information and resources has hindered the functional characterisation of genes in this species. The recent release of a high-quality reference sequence for wheat underpins a suite of genetic and genomic resources that support basic research and breeding. These include accurate gene model annotations, gene expression atlases and gene networks that provide background information about putative gene function. In parallel, sequenced mutation populations, improved transformation protocols and structured natural populations provide rapid methods to study gene function directly. We highlight a case study exemplifying how to integrate these resources to study gene function in wheat and thereby accelerate improvement in this important crop. We hope that this review provides a helpful guide for plant scientists, especially those expanding into wheat research for the first time, to capitalise on the discoveries made in Arabidopsis and other plants. This will accelerate the improvement of wheat, a complex polyploid crop, of vital importance for food and nutrition security.","description-html":"\n To adapt to the challenges of climate change and the growing world population, it is vital to increase global crop production. Understanding the function of genes within staple crops will accelerate crop improvement by allowing targeted breeding approaches. Despite the importance of wheat, which provides 20 % of the calories consumed by humankind, a lack of genomic information and resources has hindered the functional characterisation of genes in this species. The recent release of a high-quality reference sequence for wheat underpins a suite of genetic and genomic resources that support basic research and breeding. These include accurate gene model annotations, gene expression atlases and gene networks that provide background information about putative gene function. In parallel, sequenced mutation populations, improved transformation protocols and structured natural populations provide rapid methods to study gene function directly. We highlight a case study exemplifying how to integrate these resources to study gene function in wheat and thereby accelerate improvement in this important crop. We hope that this review provides a helpful guide for plant scientists, especially those expanding into wheat research for the first time, to capitalise on the discoveries made in Arabidopsis<\/i> and other plants. This will accelerate the improvement of wheat, a complex polyploid crop, of vital importance for food and nutrition security.<\/p>\n ","title-html":"A roadmap for gene functional characterisation in wheat","subjects":["Genomics","Plant Science"],"identifiers":{"peerj":"26877"},"@context":"http:\/\/static.peerj.com\/context\/citation\/context.json","@type":"http:\/\/schema.org\/ScholarlyArticle","@id":"https:\/\/peerj.com\/preprints\/26877","_links":{"self":{"href":"https:\/\/peerj.com\/preprints\/26877.json?version=2"},"alternate":{"html":{"type":"text\/html","href":"https:\/\/peerj.com\/preprints\/26877.html?version=2"},"xml":{"type":"application\/xml","href":"https:\/\/peerj.com\/preprints\/26877.xml?version=2"},"pdf":{"type":"application\/pdf","href":"https:\/\/peerj.com\/preprints\/26877.pdf?version=2"},"rdf":{"type":"application\/rdf+xml","href":"https:\/\/peerj.com\/preprints\/26877.rdf?version=2"},"ris":{"type":"application\/x-research-info-systems","href":"https:\/\/peerj.com\/preprints\/26877.ris?version=2"},"bib":{"type":"application\/x-bibtex","href":"https:\/\/peerj.com\/preprints\/26877.bib?version=2"},"citeproc":{"type":"application\/vnd.citationstyles.csl+json","href":"https:\/\/peerj.com\/preprints\/26877.citeproc?version=2"},"bibjson":{"type":"application\/bibjson+json","href":"https:\/\/peerj.com\/preprints\/26877.bibjson?version=2"},"datacite":{"type":"application\/datacite+xml","href":"https:\/\/peerj.com\/preprints\/26877.datacite?version=2"}}}},{"title":"An introduction to phylosymbiosis","date":"2019-12-11","doi":"10.7287\/peerj.preprints.27879v2","language":"en","pdf_url":"https:\/\/peerj.com\/preprints\/27879.pdf","fulltext_html_url":"https:\/\/peerj.com\/preprints\/27879","technical_report_number":"e27879v2","author":["Shen Jean Lim","Seth R Bordenstein"],"author_institution":["Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States","Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States","Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, United States","Vanderbilt Microbiome Initiative, Vanderbilt University, Nashville, Tennessee, United States","Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, United States"],"author_email":"s.bordenstein@vanderbilt.edu","authors":"Lim, Shen Jean; Bordenstein, Seth R","author_institutions":"Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, United States; Vanderbilt Microbiome Initiative, Vanderbilt University, Nashville, Tennessee, United States; Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, Tennessee, United States","keywords":["symbiosis","phylosymbiosis","microbiome","host-microbe interactions","natural selection","microbial ecology","speciation"],"technical_report_institution":"PeerJ Preprints","publisher":"PeerJ Inc.","issn":"2167-9843","description":"Phylosymbiosis was recently formulated to support a hypothesis-driven framework for the characterization of a new, cross-system trend in host-associated microbiomes. Defining phylosymbiosis as \u201cmicrobial community relationships that recapitulate the phylogeny of their host\u201d, we review the relevant literature and data in the last decade, emphasizing frequently used methods and regular patterns observed in analyses. Quantitative support for phylosymbiosis is provided by statistical methods evaluating higher microbiome variation between host species than within host species, topological similarities between the host phylogeny and microbiome dendrogram, and a positive association between host genetic relationships and microbiome beta diversity. Significant degrees of phylosymbiosis are prevalent, but not universal, in microbiomes of plants and animals from terrestrial and aquatic habitats. Consistent with natural selection shaping phylosymbiosis, microbiome transplant experiments demonstrate reduced host performance and\/or fitness upon host-microbiome mismatches. Hybridization can also disrupt phylosymbiotic microbiomes and cause hybrid pathologies. The pervasiveness of phylosymbiosis carries several important implications for advancing knowledge of eco-evolutionary processes that impact host-microbiome interactions and future applications of precision microbiology. Important future steps will be to examine phylosymbiosis beyond bacterial communities, apply evolutionary modeling for an increasingly sophisticated understanding of phylosymbiosis, and unravel the host and microbial mechanisms that contribute to the pattern. This review serves as a gateway to experimental, conceptual, and quantitative themes of phylosymbiosis and outlines opportunities ripe for investigations from a diversity of disciplines.","description-html":"\n Phylosymbiosis was recently formulated to support a hypothesis-driven framework for the characterization of a new, cross-system trend in host-associated microbiomes. Defining phylosymbiosis as \u201cmicrobial community relationships that recapitulate the phylogeny of their host\u201d, we review the relevant literature and data in the last decade, emphasizing frequently used methods and regular patterns observed in analyses. Quantitative support for phylosymbiosis is provided by statistical methods evaluating higher microbiome variation between host species than within host species, topological similarities between the host phylogeny and microbiome dendrogram, and a positive association between host genetic relationships and microbiome beta diversity. Significant degrees of phylosymbiosis are prevalent, but not universal, in microbiomes of plants and animals from terrestrial and aquatic habitats. Consistent with natural selection shaping phylosymbiosis, microbiome transplant experiments demonstrate reduced host performance and\/or fitness upon host-microbiome mismatches. Hybridization can also disrupt phylosymbiotic microbiomes and cause hybrid pathologies. The pervasiveness of phylosymbiosis carries several important implications for advancing knowledge of eco-evolutionary processes that impact host-microbiome interactions and future applications of precision microbiology. Important future steps will be to examine phylosymbiosis beyond bacterial communities, apply evolutionary modeling for an increasingly sophisticated understanding of phylosymbiosis, and unravel the host and microbial mechanisms that contribute to the pattern. This review serves as a gateway to experimental, conceptual, and quantitative themes of phylosymbiosis and outlines opportunities ripe for investigations from a diversity of disciplines.<\/p>\n ","title-html":"An introduction to phylosymbiosis","subjects":["Biodiversity","Bioinformatics","Evolutionary Studies","Microbiology"],"identifiers":{"peerj":"27879"},"@context":"http:\/\/static.peerj.com\/context\/citation\/context.json","@type":"http:\/\/schema.org\/ScholarlyArticle","@id":"https:\/\/peerj.com\/preprints\/27879","_links":{"self":{"href":"https:\/\/peerj.com\/preprints\/27879.json?version=2"},"alternate":{"html":{"type":"text\/html","href":"https:\/\/peerj.com\/preprints\/27879.html?version=2"},"xml":{"type":"application\/xml","href":"https:\/\/peerj.com\/preprints\/27879.xml?version=2"},"pdf":{"type":"application\/pdf","href":"https:\/\/peerj.com\/preprints\/27879.pdf?version=2"},"rdf":{"type":"application\/rdf+xml","href":"https:\/\/peerj.com\/preprints\/27879.rdf?version=2"},"ris":{"type":"application\/x-research-info-systems","href":"https:\/\/peerj.com\/preprints\/27879.ris?version=2"},"bib":{"type":"application\/x-bibtex","href":"https:\/\/peerj.com\/preprints\/27879.bib?version=2"},"citeproc":{"type":"application\/vnd.citationstyles.csl+json","href":"https:\/\/peerj.com\/preprints\/27879.citeproc?version=2"},"bibjson":{"type":"application\/bibjson+json","href":"https:\/\/peerj.com\/preprints\/27879.bibjson?version=2"},"datacite":{"type":"application\/datacite+xml","href":"https:\/\/peerj.com\/preprints\/27879.datacite?version=2"}}}},{"title":"Seven myths on crowding and peripheral vision","date":"2019-12-06","doi":"10.7287\/peerj.preprints.27353v4","language":"en","pdf_url":"https:\/\/peerj.com\/preprints\/27353.pdf","fulltext_html_url":"https:\/\/peerj.com\/preprints\/27353","technical_report_number":"e27353v4","author":"Hans Strasburger","author_institution":["Institute of Medical Psychology, Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen, M\u00fcnchen, Germany","Dept. of Medical Psychology, Georg-August Universit\u00e4t G\u00f6ttingen, G\u00f6ttingen, Germany"],"author_email":"strasburger@uni-muenchen.de","authors":"Strasburger, Hans","author_institutions":"Institute of Medical Psychology, Ludwig-Maximilians-Universit\u00e4t M\u00fcnchen, M\u00fcnchen, Germany; Dept. of Medical Psychology, Georg-August Universit\u00e4t G\u00f6ttingen, G\u00f6ttingen, Germany","keywords":["Crowding","Psychophysics","Perception","Reading","Visual acuity","Peripheral vision","Fovea","Sensory systems","Vision science","Visual field"],"technical_report_institution":"PeerJ Preprints","publisher":"PeerJ Inc.","issn":"2167-9843","description":"Crowding has become a hot topic in vision research and some fundamentals are now widely agreed upon. For the classical crowding task, one would likely agree with the following statements. (1) Bouma\u2019s law can, succinctly and unequivocally, be stated as saying that critical distance for crowding is about half the target\u2019s eccentricity. (2) Crowding is predominantly a peripheral phenomenon. (3) Peripheral vision extends to at most 90\u00b0 eccentricity. (4) Resolution threshold (the minimal angle of resolution, MAR) increases strongly and linearly with eccentricity. Crowding increases at an even steeper rate. (5) Crowding is asymmetric as Bouma has shown. For that inner-outer asymmetry, the peripheral flanker has more effect. (6) Critical crowding distance corresponds to a constant cortical distance in primary visual areas like V1. (7) Except for Bouma\u2019s seminal paper in 1970, crowding research mostly became prominent starting in the 2000s. I propose the answer is \u2018not really\u2019 or \u2018not quite\u2019 to these assertions. So should we care? I think we should, before we write the textbook chapters for the next generation.","description-html":"\n Crowding has become a hot topic in vision research and some fundamentals are now widely agreed upon. For the classical crowding task, one would likely agree with the following statements. (1) Bouma\u2019s law can, succinctly and unequivocally, be stated as saying that critical distance for crowding is about half the target\u2019s eccentricity. (2) Crowding is predominantly a peripheral phenomenon. (3) Peripheral vision extends to at most 90\u00b0 eccentricity. (4) Resolution threshold (the minimal angle of resolution, MAR) increases strongly and linearly with eccentricity. Crowding increases at an even steeper rate. (5) Crowding is asymmetric as Bouma has shown. For that inner-outer asymmetry, the peripheral flanker has more effect. (6) Critical crowding distance corresponds to a constant cortical distance in primary visual areas like V1. (7) Except for Bouma\u2019s seminal paper in 1970, crowding research mostly became prominent starting in the 2000s. I propose the answer is \u2018not really\u2019 or \u2018not quite\u2019 to these assertions. So should we care? I think we should, before we write the textbook chapters for the next generation.<\/p>\n ","title-html":"Seven myths on crowding and peripheral vision","subjects":["Computational Biology","Neuroscience","Anatomy and Physiology","Ophthalmology","Psychiatry and Psychology"],"identifiers":{"peerj":"27353"},"@context":"http:\/\/static.peerj.com\/context\/citation\/context.json","@type":"http:\/\/schema.org\/ScholarlyArticle","@id":"https:\/\/peerj.com\/preprints\/27353","_links":{"self":{"href":"https:\/\/peerj.com\/preprints\/27353.json?version=4"},"alternate":{"html":{"type":"text\/html","href":"https:\/\/peerj.com\/preprints\/27353.html?version=4"},"xml":{"type":"application\/xml","href":"https:\/\/peerj.com\/preprints\/27353.xml?version=4"},"pdf":{"type":"application\/pdf","href":"https:\/\/peerj.com\/preprints\/27353.pdf?version=4"},"rdf":{"type":"application\/rdf+xml","href":"https:\/\/peerj.com\/preprints\/27353.rdf?version=4"},"ris":{"type":"application\/x-research-info-systems","href":"https:\/\/peerj.com\/preprints\/27353.ris?version=4"},"bib":{"type":"application\/x-bibtex","href":"https:\/\/peerj.com\/preprints\/27353.bib?version=4"},"citeproc":{"type":"application\/vnd.citationstyles.csl+json","href":"https:\/\/peerj.com\/preprints\/27353.citeproc?version=4"},"bibjson":{"type":"application\/bibjson+json","href":"https:\/\/peerj.com\/preprints\/27353.bibjson?version=4"},"datacite":{"type":"application\/datacite+xml","href":"https:\/\/peerj.com\/preprints\/27353.datacite?version=4"}}}},{"title":"A simple method for the selective quantification of polyethylene, polypropylene, and polystyrene plastic debris in soil by pyrolysis-gas chromatography\/mass spectrometry","date":"2019-12-05","doi":"10.7287\/peerj.preprints.27989v2","language":"en","pdf_url":"https:\/\/peerj.com\/preprints\/27989.pdf","fulltext_html_url":"https:\/\/peerj.com\/preprints\/27989","technical_report_number":"e27989v2","author":["Zacharias Steinmetz","Aaron Kintzi","Katherine Mu\u00f1oz","Gabriele E. Schaumann"],"author_institution":["iES Landau, Institute for Environmental Sciences, Group of Environmental and Soil Chemistry, University of Koblenz\u2013Landau, Landau, Germany","iES Landau, Institute for Environmental Sciences, Group of Environmental and Soil Chemistry, University of Koblenz\u2013Landau, Landau, Germany","Interdisciplinary Research Group on Environmental Issues, Universit\u00e4t Koblenz\u2013Landau, Landau, Germany","iES Landau, Institute for Environmental Sciences, Group of Environmental and Soil Chemistry, University of Koblenz\u2013Landau, Landau, Germany"],"author_email":["steinmetz-z@uni-landau.de","schaumann@uni-landau.de"],"authors":"Steinmetz, Zacharias; Kintzi, Aaron; Mu\u00f1oz, Katherine; Schaumann, Gabriele E.","author_institutions":"iES Landau, Institute for Environmental Sciences, Group of Environmental and Soil Chemistry, University of Koblenz\u2013Landau, Landau, Germany; Interdisciplinary Research Group on Environmental Issues, Universit\u00e4t Koblenz\u2013Landau, Landau, Germany","keywords":["Py-GC\/MS","Microplastics","Nanoplastics","Plastic mulching","Agriculture","Soil organic matter"],"technical_report_institution":"PeerJ Preprints","publisher":"PeerJ Inc.","issn":"2167-9843","description":"The lack of adequate analytical methods for the quantification of plastic debris in soil challenges a better understanding of their occurrence and fate in the terrestrial environment. With this proof-of-principle study, we developed a simple and fast method for the selective quantification of the three most environmentally relevant polymers polyethylene (PE), polypropylene (PP), and polystyrene (PS) in soil using pyrolysis-gas chromatography\/mass spectrometry (Py-GC\/MS). In order to facilitate the preparation of calibration series and to better account for the heterogeneity of soil matrix, polymers were dissolved in 1,2,4-trichlorobenzene (TCB) at 120 \u00b0C. Thereby, liquid sample aliquots from up to 4 g of solid sample became amenable to pyrolysis without further preparation. To evaluate the performance of this approach, three reference soils with 1.73\u20135.16 % organic carbon (Corg) were spiked at 50 and 250 \u03bcg g\u22121 of each polymer and extracted with TCB. A prior cleanup step with methanol, flocculation with KAl(SO4)2, and Fenton digestion were tested for their suitability to reduce potentially interfering Corg. Calibration curves responded linearly (adj. R2 > 0.996) with instrumental detection limits of 1\u201386 ng corresponding to method detection limits of 1\u201386 \u03bcg g\u22121. The measurement repeatability was 3.2\u20137.2 % relative standard deviation. Recoveries of 70\u2013128 % were achieved for plastic contents of 250 \u03bcg g\u22121 extracted with TCB without prior cleanup from soils with less than 2.5 % Corg. A higher Corg particularly interfered with the quantification of PE. The addition of non-target polymers (polyethylene terephthalate, polyvinyl chloride, poly(methyl methacrylate), and tire wear particles) did not interfere with the quantification of the analytes highlighting the selectivity of the method. Further research is needed to determine low plastic contents in soils exceeding 2.5 % Corg. With 1\u20133 h processing time per sample, our method has the potential for routine analyses and screening studies of agricultural systems to be complemented with microspectroscopic techniques for additional information on particle shapes and sizes.","description-html":"\n The lack of adequate analytical methods for the quantification of plastic debris in soil challenges a better understanding of their occurrence and fate in the terrestrial environment. With this proof-of-principle study, we developed a simple and fast method for the selective quantification of the three most environmentally relevant polymers polyethylene (PE), polypropylene (PP), and polystyrene (PS) in soil using pyrolysis-gas chromatography\/mass spectrometry (Py-GC\/MS). In order to facilitate the preparation of calibration series and to better account for the heterogeneity of soil matrix, polymers were dissolved in 1,2,4-trichlorobenzene (TCB) at 120 \u00b0C. Thereby, liquid sample aliquots from up to 4 g of solid sample became amenable to pyrolysis without further preparation. To evaluate the performance of this approach, three reference soils with 1.73\u20135.16 % organic carbon (Corg<\/sub>) were spiked at 50 and 250 \u03bcg g\u22121<\/sup> of each polymer and extracted with TCB. A prior cleanup step with methanol, flocculation with KAl(SO4<\/sub>)2<\/sub>, and Fenton digestion were tested for their suitability to reduce potentially interfering Corg<\/sub>. Calibration curves responded linearly (adj. R2<\/sup> > 0.996) with instrumental detection limits of 1\u201386 ng corresponding to method detection limits of 1\u201386 \u03bcg g\u22121<\/sup>. The measurement repeatability was 3.2\u20137.2 % relative standard deviation. Recoveries of 70\u2013128 % were achieved for plastic contents of 250 \u03bcg g\u22121<\/sup> extracted with TCB without prior cleanup from soils with less than 2.5 % Corg<\/sub>. A higher Corg<\/sub> particularly interfered with the quantification of PE. The addition of non-target polymers (polyethylene terephthalate, polyvinyl chloride, poly(methyl methacrylate), and tire wear particles) did not interfere with the quantification of the analytes highlighting the selectivity of the method. Further research is needed to determine low plastic contents in soils exceeding 2.5 % Corg<\/sub>. With 1\u20133 h processing time per sample, our method has the potential for routine analyses and screening studies of agricultural systems to be complemented with microspectroscopic techniques for additional information on particle shapes and sizes.<\/p>\n ","title-html":"A simple method for the selective quantification of polyethylene, polypropylene, and polystyrene plastic debris in soil by pyrolysis-gas chromatography\/mass spectrometry","subjects":["Soil Science","Environmental Contamination and Remediation"],"identifiers":{"peerj":"27989"},"@context":"http:\/\/static.peerj.com\/context\/citation\/context.json","@type":"http:\/\/schema.org\/ScholarlyArticle","@id":"https:\/\/peerj.com\/preprints\/27989","_links":{"self":{"href":"https:\/\/peerj.com\/preprints\/27989.json?version=2"},"alternate":{"html":{"type":"text\/html","href":"https:\/\/peerj.com\/preprints\/27989.html?version=2"},"xml":{"type":"application\/xml","href":"https:\/\/peerj.com\/preprints\/27989.xml?version=2"},"pdf":{"type":"application\/pdf","href":"https:\/\/peerj.com\/preprints\/27989.pdf?version=2"},"rdf":{"type":"application\/rdf+xml","href":"https:\/\/peerj.com\/preprints\/27989.rdf?version=2"},"ris":{"type":"application\/x-research-info-systems","href":"https:\/\/peerj.com\/preprints\/27989.ris?version=2"},"bib":{"type":"application\/x-bibtex","href":"https:\/\/peerj.com\/preprints\/27989.bib?version=2"},"citeproc":{"type":"application\/vnd.citationstyles.csl+json","href":"https:\/\/peerj.com\/preprints\/27989.citeproc?version=2"},"bibjson":{"type":"application\/bibjson+json","href":"https:\/\/peerj.com\/preprints\/27989.bibjson?version=2"},"datacite":{"type":"application\/datacite+xml","href":"https:\/\/peerj.com\/preprints\/27989.datacite?version=2"}}}},{"title":"Preferences and constraints: The value of economic games for studying human behavior","date":"2019-12-04","doi":"10.7287\/peerj.preprints.27355v2","language":"en","pdf_url":"https:\/\/peerj.com\/preprints\/27355.pdf","fulltext_html_url":"https:\/\/peerj.com\/preprints\/27355","technical_report_number":"e27355v2","author":["Anne C Pisor","Matthew M Gervais","Benjamin G Purzycki","Cody T Ross"],"author_institution":["Department of Anthropology, Washington State University, Pullman, WA, United States","Department of Human Behavior, Ecology, and Culture, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany","Department of Psychology, University of British Columbia, Vancouver, Canada","Department of Psychology, Simon Fraser University, Burnaby, Canada","Department of Human Behavior, Ecology, and Culture, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany","Department of the Study of Religion, Aarhus University, Aarhus, Denmark","Department of Human Behavior, Ecology, and Culture, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany"],"author_email":"anne.pisor@wsu.edu","authors":"Pisor, Anne C; Gervais, Matthew M; Purzycki, Benjamin G; Ross, Cody T","author_institutions":"Department of Anthropology, Washington State University, Pullman, WA, United States; Department of Human Behavior, Ecology, and Culture, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany; Department of Psychology, University of British Columbia, Vancouver, Canada; Department of Psychology, Simon Fraser University, Burnaby, Canada; Department of the Study of Religion, Aarhus University, Aarhus, Denmark","keywords":["social science","lab in the field","cross-cultural comparisons","methods","experiments","replication"],"technical_report_institution":"PeerJ Preprints","publisher":"PeerJ Inc.","issn":"2167-9843","description":"As economic games have spread from experimental economics to other social sciences, so too have critiques of their usefulness for drawing inferences about the \u201creal world.\u201d What these criticisms often miss is that games can be used to reveal individuals\u2019 private preferences in ways that observational and interview data cannot; further, economic games can be designed such that they do provide insights into real-world behavior. Here, we draw on our collective experience using economic games in field contexts to illustrate how researchers can strategically alter the framing or design of economic games to draw inferences about private-world or real-world preferences. A detailed case study from coastal Colombia provides an example of the subtleties of game design and how games can be combined fruitfully with self-report data. We close with a list of concrete recommendations for how to modify economic games to better match particular research questions and research contexts.","description-html":"\n As economic games have spread from experimental economics to other social sciences, so too have critiques of their usefulness for drawing inferences about the \u201creal world.\u201d What these criticisms often miss is that games can be used to reveal individuals\u2019 private preferences in ways that observational and interview data cannot; further, economic games can be designed such that they do<\/i> provide insights into real-world behavior. Here, we draw on our collective experience using economic games in field contexts to illustrate how researchers can strategically alter the framing or design of economic games to draw inferences about private-world or real-world preferences. A detailed case study from coastal Colombia provides an example of the subtleties of game design and how games can be combined fruitfully with self-report data. We close with a list of concrete recommendations for how to modify economic games to better match particular research questions and research contexts.<\/p>\n ","title-html":"Preferences and constraints: The value of economic games for studying human behavior","subjects":["Anthropology","Evolutionary Studies","Psychiatry and Psychology"],"identifiers":{"peerj":"27355"},"@context":"http:\/\/static.peerj.com\/context\/citation\/context.json","@type":"http:\/\/schema.org\/ScholarlyArticle","@id":"https:\/\/peerj.com\/preprints\/27355","_links":{"self":{"href":"https:\/\/peerj.com\/preprints\/27355.json?version=2"},"alternate":{"html":{"type":"text\/html","href":"https:\/\/peerj.com\/preprints\/27355.html?version=2"},"xml":{"type":"application\/xml","href":"https:\/\/peerj.com\/preprints\/27355.xml?version=2"},"pdf":{"type":"application\/pdf","href":"https:\/\/peerj.com\/preprints\/27355.pdf?version=2"},"rdf":{"type":"application\/rdf+xml","href":"https:\/\/peerj.com\/preprints\/27355.rdf?version=2"},"ris":{"type":"application\/x-research-info-systems","href":"https:\/\/peerj.com\/preprints\/27355.ris?version=2"},"bib":{"type":"application\/x-bibtex","href":"https:\/\/peerj.com\/preprints\/27355.bib?version=2"},"citeproc":{"type":"application\/vnd.citationstyles.csl+json","href":"https:\/\/peerj.com\/preprints\/27355.citeproc?version=2"},"bibjson":{"type":"application\/bibjson+json","href":"https:\/\/peerj.com\/preprints\/27355.bibjson?version=2"},"datacite":{"type":"application\/datacite+xml","href":"https:\/\/peerj.com\/preprints\/27355.datacite?version=2"}}}},{"title":"Knockdown of AMP-activated protein kinase \u03b12 impairs epithelial-mesenchymal transition in rat renal tubular epithelial cells by downregulating v-ets erythroblastosis virus E26 oncogene homolog-1 and ribosomal protein S6 kinase A1","date":"2019-12-02","doi":"10.7287\/peerj.preprints.27992v2","language":"en","pdf_url":"https:\/\/peerj.com\/preprints\/27992.pdf","fulltext_html_url":"https:\/\/peerj.com\/preprints\/27992","technical_report_number":"e27992v2","author":["Xiaoming Yin","Fujiang Ma","Xu Fan","Qi Zhao","Xin Liu","Yi Yang"],"author_institution":["Department of Pediatric Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China","Tianjin children\u2019s hospital, Tianjin, Hebei, China","Department of Pediatric Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China","Department of Pediatric Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China","Department of Pediatric Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China","Department of Pediatric Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China"],"author_email":"yangy2@sj-hospital.org","authors":"Yin, Xiaoming; Ma, Fujiang; Fan, Xu; Zhao, Qi; Liu, Xin; Yang, Yi","author_institutions":"Department of Pediatric Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China; Tianjin children\u2019s hospital, Tianjin, Hebei, China","keywords":["AMPK\u03b12","Epithelial mesenchymal transition","ETS1","Ingenuity Pathway Analysis","RPS6KA1","Ureteropelvic junction obstruction","Gene Microarray","renal fibrosis","ERK\/MAPK pathway","TGF-\u03b21 "],"technical_report_institution":"PeerJ Preprints","publisher":"PeerJ Inc.","issn":"2167-9843","description":"Background. Epithelial mesenchymal transition (EMT) plays an important regulatory role in obstructive nephropathy and renal fibrosis. As an intracellular energy sensor, AMP-activated protein kinase (AMPK) is essential in the process of EMT. The aim of this study was to reveal changes in the expression of AMPK\u03b12 and to elucidate which AMPK\u03b12 genes play a role during EMT. Methods. In this study, TGF-\u03b21 was used to induce EMT in normal rat renal tubular epithelial (NRK-52E) cells. The shAMPK\u03b12 lentivirus was used to interfere with AMPK\u03b12 expression in EMT-derived NRK-52E cells, where AMPK\u03b12 expression and EMT were detected. Differential gene expression after the AMPK\u03b12 knockdown in EMT-derived NRK-52E cells was examined using a gene microarray. Possible regulatory pathways were analyzed using ingenuity pathway analysis (IPA) and differentially expressed genes were partially verified by quantitative real-time polymerase chain reaction (qRT-PCR) and western blotting. Results. It was found that AMPK\u03b12 was upregulated in TGF-\u03b21-induced EMT-derived NRK-52E cells. EMT progression was significantly inhibited after the expression of AMPK\u03b12 was downregulated by the shAMPK\u03b12 lentivirus. A total of 1,588 differentially expressed genes were detected after the AMPK\u03b12 knockdown in NRK-52E cells in which EMT occurred. The ERK\/MAPK pathway was significantly impaired after the AMPK\u03b12 knockdown, as indicated by the IPA analysis. Furthermore, qRT-PCR and western blot results revealed that the expression of AMPK\u03b12, v-ets erythroblastosis virus E26 oncogene homolog-1 (ETS1), and ribosomal protein S6 kinase A1 (RPS6KA1) was upregulated after EMT in NRK-52E cells, while expression of ETS1 and RPS6KA1 was downregulated after the AMPK\u03b12 knockdown. Conclusions. AMPK\u03b12 plays an important role in the regulation of rat renal tubular EMT, which may be achieved by modulating ETS1 and RPS6KA1 in the ERK\/MAPK pathway.","description-html":"\n <\/b> Background. <\/b>Epithelial mesenchymal transition (EMT) plays an important regulatory role in obstructive nephropathy and renal fibrosis. As an intracellular energy sensor, AMP-activated protein kinase (AMPK) is essential in the process of EMT. The aim of this study was to reveal changes in the expression of AMPK\u03b12 and to elucidate which AMPK\u03b12 genes play a role during EMT. Methods. <\/b>In this study, TGF-\u03b21 was used to induce EMT in normal rat renal tubular epithelial (NRK-52E) cells. The shAMPK\u03b12 lentivirus was used to interfere with AMPK\u03b12 expression in EMT-derived NRK-52E cells, where AMPK\u03b12 expression and EMT were detected. Differential gene expression after the AMPK\u03b12 knockdown in EMT-derived NRK-52E cells was examined using a gene microarray. Possible regulatory pathways were analyzed using ingenuity pathway analysis (IPA) and differentially expressed genes were partially verified by quantitative real-time polymerase chain reaction (qRT-PCR) and western blotting. Results. <\/b>It was found that AMPK\u03b12 was upregulated in TGF-\u03b21-induced EMT-derived NRK-52E cells. EMT progression was significantly inhibited after the expression of AMPK\u03b12 was downregulated by the shAMPK\u03b12 lentivirus. A total of 1,588 differentially expressed genes were detected after the AMPK\u03b12 knockdown in NRK-52E cells in which EMT occurred. The ERK\/MAPK pathway was significantly impaired after the AMPK\u03b12 knockdown, as indicated by the IPA analysis. Furthermore, qRT-PCR and western blot results revealed that the expression of AMPK\u03b12, v-ets erythroblastosis virus E26 oncogene homolog-1 (ETS1), and ribosomal protein S6 kinase A1 (RPS6KA1) was upregulated after EMT in NRK-52E cells, while expression of ETS1 and RPS6KA1 was downregulated after the AMPK\u03b12 knockdown. Conclusions. <\/b>AMPK\u03b12 plays an important role in the regulation of rat renal tubular EMT, which may be achieved by modulating ETS1 and RPS6KA1 in the ERK\/MAPK pathway.<\/p>\n ","title-html":"Knockdown of AMP-activated protein kinase \u03b12 impairs epithelial-mesenchymal transition in rat renal tubular epithelial cells by downregulating v-ets erythroblastosis virus E26 oncogene homolog-1 and ribosomal protein S6 kinase A1","subjects":["Cell Biology","Urology"],"identifiers":{"peerj":"27992"},"@context":"http:\/\/static.peerj.com\/context\/citation\/context.json","@type":"http:\/\/schema.org\/ScholarlyArticle","@id":"https:\/\/peerj.com\/preprints\/27992","_links":{"self":{"href":"https:\/\/peerj.com\/preprints\/27992.json?version=2"},"alternate":{"html":{"type":"text\/html","href":"https:\/\/peerj.com\/preprints\/27992.html?version=2"},"xml":{"type":"application\/xml","href":"https:\/\/peerj.com\/preprints\/27992.xml?version=2"},"pdf":{"type":"application\/pdf","href":"https:\/\/peerj.com\/preprints\/27992.pdf?version=2"},"rdf":{"type":"application\/rdf+xml","href":"https:\/\/peerj.com\/preprints\/27992.rdf?version=2"},"ris":{"type":"application\/x-research-info-systems","href":"https:\/\/peerj.com\/preprints\/27992.ris?version=2"},"bib":{"type":"application\/x-bibtex","href":"https:\/\/peerj.com\/preprints\/27992.bib?version=2"},"citeproc":{"type":"application\/vnd.citationstyles.csl+json","href":"https:\/\/peerj.com\/preprints\/27992.citeproc?version=2"},"bibjson":{"type":"application\/bibjson+json","href":"https:\/\/peerj.com\/preprints\/27992.bibjson?version=2"},"datacite":{"type":"application\/datacite+xml","href":"https:\/\/peerj.com\/preprints\/27992.datacite?version=2"}}}}]}