title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=1911 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Creating a Chinese suicide dictionary for identifying suicide risk on social media link: https://peerj.com/articles/1455 last-modified: 2015-12-15 description: Introduction. Suicide has become a serious worldwide epidemic. Early detection of individual suicide risk in population is important for reducing suicide rates. Traditional methods are ineffective in identifying suicide risk in time, suggesting a need for novel techniques. This paper proposes to detect suicide risk on social media using a Chinese suicide dictionary.Methods. To build the Chinese suicide dictionary, eight researchers were recruited to select initial words from 4,653 posts published on Sina Weibo (the largest social media service provider in China) and two Chinese sentiment dictionaries (HowNet and NTUSD). Then, another three researchers were recruited to filter out irrelevant words. Finally, remaining words were further expanded using a corpus-based method. After building the Chinese suicide dictionary, we tested its performance in identifying suicide risk on Weibo. First, we made a comparison of the performance in both detecting suicidal expression in Weibo posts and evaluating individual levels of suicide risk between the dictionary-based identifications and the expert ratings. Second, to differentiate between individuals with high and non-high scores on self-rating measure of suicide risk (Suicidal Possibility Scale, SPS), we built Support Vector Machines (SVM) models on the Chinese suicide dictionary and the Simplified Chinese Linguistic Inquiry and Word Count (SCLIWC) program, respectively. After that, we made a comparison of the classification performance between two types of SVM models.Results and Discussion. Dictionary-based identifications were significantly correlated with expert ratings in terms of both detecting suicidal expression (r = 0.507) and evaluating individual suicide risk (r = 0.455). For the differentiation between individuals with high and non-high scores on SPS, the Chinese suicide dictionary (t1: F1 = 0.48; t2: F1 = 0.56) produced a more accurate identification than SCLIWC (t1: F1 = 0.41; t2: F1 = 0.48) on different observation windows.Conclusions. This paper confirms that, using social media, it is possible to implement real-time monitoring individual suicide risk in population. Results of this study may be useful to improve Chinese suicide prevention programs and may be insightful for other countries. creator: Meizhen Lv creator: Ang Li creator: Tianli Liu creator: Tingshao Zhu uri: https://doi.org/10.7717/peerj.1455 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Lv et al. title: The first South American sandownid turtle from the Lower Cretaceous of Colombia link: https://peerj.com/articles/1431 last-modified: 2015-12-15 description: Sandownids are a group of Early Cretaceous-Paleocene turtles that for several decades have been only known by cranial and very fragmentary postcranial elements. Here I report and describe the most complete sandownid turtle known so far, including articulated skull, lower jaw and postcranial elements, from the Early Cretaceous (upper Barremian-lower Aptian, >120 Ma), Paja Formation, Villa de Leyva town, Colombia. The new Colombian sandownid is defined here as Leyvachelys cipadi new genus, new species and because of its almost identical skull morphology with a previously reported turtle from the Glen Rose Formation, Texas, USA, both are grouped in a single and officially (ICNZ rules) defined taxon. Phylogenetic analysis including L. cipadi supports once again the monophyly of Sandownidae, as belonging to the large and recently redefined Pan-Chelonioidea clade. The morphology of L. cipadi indicates that sandownids were not open marine turtles, but instead littoral to shallow marine durophagous dwellers. Leyvachelys cipadi not only constitutes the first record of sandowinds in South America, but also the earliest global record for the group. creator: Edwin Cadena uri: https://doi.org/10.7717/peerj.1431 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Cadena title: Analysis of synonymous codon usage patterns in sixty-four different bivalve species link: https://peerj.com/articles/1520 last-modified: 2015-12-14 description: Synonymous codon usage bias (CUB) is a defined as the non-random usage of codons encoding the same amino acid across different genomes. This phenomenon is common to all organisms and the real weight of the many factors involved in its shaping still remains to be fully determined. So far, relatively little attention has been put in the analysis of CUB in bivalve mollusks due to the limited genomic data available. Taking advantage of the massive sequence data generated from next generation sequencing projects, we explored codon preferences in 64 different species pertaining to the six major evolutionary lineages in Bivalvia. We detected remarkable differences across species, which are only partially dependent on phylogeny. While the intensity of CUB is mild in most organisms, a heterogeneous group of species (including Arcida and Mytilida, among the others) display higher bias and a strong preference for AT-ending codons. We show that the relative strength and direction of mutational bias, selection for translational efficiency and for translational accuracy contribute to the establishment of synonymous codon usage in bivalves. Although many aspects underlying bivalve CUB still remain obscure, we provide for the first time an overview of this phenomenon in this large, commercially and environmentally important, class of marine invertebrates. creator: Marco Gerdol creator: Gianluca De Moro creator: Paola Venier creator: Alberto Pallavicini uri: https://doi.org/10.7717/peerj.1520 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Gerdol et al. title: Evaluating pharmacological models of high and low anxiety in sheep link: https://peerj.com/articles/1510 last-modified: 2015-12-14 description: New tests of animal affect and welfare require validation in subjects experiencing putatively different states. Pharmacological manipulations of affective state are advantageous because they can be administered in a standardised fashion, and the duration of their action can be established and tailored to suit the length of a particular test. To this end, the current study aimed to evaluate a pharmacological model of high and low anxiety in an important agricultural and laboratory species, the sheep. Thirty-five 8-month-old female sheep received either an intramuscular injection of the putatively anxiogenic drug 1-(m-chlorophenyl)piperazine (mCPP; 1 mg/kg; n = 12), an intravenous injection of the putatively anxiolytic drug diazepam (0.1 mg/kg; n = 12), or acted as a control (saline intramuscular injection n = 11). Thirty minutes after the treatments, sheep were individually exposed to a variety of tests assessing their general movement, performance in a ‘runway task’ (moving down a raceway for a food reward), response to startle, and behaviour in isolation. A test to assess feeding motivation was performed 2 days later following administration of the drugs to the same animals in the same manner. The mCPP sheep had poorer performance in the two runway tasks (6.8 and 7.7 × slower respectively than control group; p < 0.001), a greater startle response (1.4 vs. 0.6; p = 0.02), a higher level of movement during isolation (9.1 steps vs. 5.4; p < 0.001), and a lower feeding motivation (1.8 × slower; p < 0.001) than the control group, all of which act as indicators of anxiety. These results show that mCPP is an effective pharmacological model of high anxiety in sheep. Comparatively, the sheep treated with diazepam did not display any differences compared to the control sheep. Thus we suggest that mCPP is an effective treatment to validate future tests aimed at assessing anxiety in sheep, and that future studies should include other subtle indicators of positive affective states, as well as dosage studies, so conclusions on the efficacy of diazepam as a model of low anxiety can be drawn. creator: Rebecca E. Doyle creator: Caroline Lee creator: David M. McGill creator: Michael Mendl uri: https://doi.org/10.7717/peerj.1510 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Doyle et al. title: Modeling the ecologic niche of plague in sylvan and domestic animal hosts to delineate sources of human exposure in the western United States link: https://peerj.com/articles/1493 last-modified: 2015-12-14 description: Plague has been established in the western United States (US) since 1900 following the West Coast introduction of commensal rodents infected with Yersinia pestis via early industrial shipping. Over the last century, plague ecology has transitioned through cycles of widespread human transmission, urban domestic transmission among commensal rodents, and ultimately settled into the predominantly sylvan foci that remain today where it is maintained alternatively by enzootic and epizootic transmission. While zoonotic transmission to humans is much less common in modern times, significant plague risk remains in parts of the western US. Moreover, risk to some threatened species that are part of the epizootic cycle can be quite substantive. This investigation attempted to predict the risk of plague across the western US by modeling the ecologic niche of plague in sylvan and domestic animals identified between 2000 and 2015. A Maxent machine learning algorithm was used to predict this niche based on climate, altitude, land cover, and the presence of an important enzootic species, Peromyscus maniculatus. This model demonstrated good predictive ability (AUC = 86%) and identified areas of high risk in central Colorado, north-central New Mexico, and southwestern and northeastern California. The presence of P. maniculatus, altitude, precipitation during the driest and wettest quarters, and distance to artificial surfaces, all contributed substantively to maximizing the gain function. These findings add to the known landscape epidemiology and infection ecology of plague in the western US and may suggest locations of particular risk to be targeted for wild and domestic animal intervention. creator: Michael Walsh creator: MA Haseeb uri: https://doi.org/10.7717/peerj.1493 license: http://creativecommons.org/licenses/by/4.0/ rights: ©2015 Walsh and Haseeb title: Emerging semantics to link phenotype and environment link: https://peerj.com/articles/1470 last-modified: 2015-12-14 description: Understanding the interplay between environmental conditions and phenotypes is a fundamental goal of biology. Unfortunately, data that include observations on phenotype and environment are highly heterogeneous and thus difficult to find and integrate. One approach that is likely to improve the status quo involves the use of ontologies to standardize and link data about phenotypes and environments. Specifying and linking data through ontologies will allow researchers to increase the scope and flexibility of large-scale analyses aided by modern computing methods. Investments in this area would advance diverse fields such as ecology, phylogenetics, and conservation biology. While several biological ontologies are well-developed, using them to link phenotypes and environments is rare because of gaps in ontological coverage and limits to interoperability among ontologies and disciplines. In this manuscript, we present (1) use cases from diverse disciplines to illustrate questions that could be answered more efficiently using a robust linkage between phenotypes and environments, (2) two proof-of-concept analyses that show the value of linking phenotypes to environments in fishes and amphibians, and (3) two proposed example data models for linking phenotypes and environments using the extensible observation ontology (OBOE) and the Biological Collections Ontology (BCO); these provide a starting point for the development of a data model linking phenotypes and environments. creator: Anne E. Thessen creator: Daniel E. Bunker creator: Pier Luigi Buttigieg creator: Laurel D. Cooper creator: Wasila M. Dahdul creator: Sami Domisch creator: Nico M. Franz creator: Pankaj Jaiswal creator: Carolyn J. Lawrence-Dill creator: Peter E. Midford creator: Christopher J. Mungall creator: Martín J. Ramírez creator: Chelsea D. Specht creator: Lars Vogt creator: Rutger Aldo Vos creator: Ramona L. Walls creator: Jeffrey W. White creator: Guanyang Zhang creator: Andrew R. Deans creator: Eva Huala creator: Suzanna E. Lewis creator: Paula M. Mabee uri: https://doi.org/10.7717/peerj.1470 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Thessen et al. title: Best practices for assessing ocean health in multiple contexts using tailorable frameworks link: https://peerj.com/articles/1503 last-modified: 2015-12-10 description: Marine policy is increasingly calling for maintaining or restoring healthy oceans while human activities continue to intensify. Thus, successful prioritization and management of competing objectives requires a comprehensive assessment of the current state of the ocean. Unfortunately, assessment frameworks to define and quantify current ocean state are often site-specific, limited to a few ocean components, and difficult to reproduce in different geographies or even through time, limiting spatial or temporal comparisons as well as the potential for shared learning. Ideally, frameworks should be tailorable to accommodate use in disparate locations and contexts, removing the need to develop frameworks de novo and allowing efforts to focus on the assessments themselves to advise action. Here, we present some of our experiences using the Ocean Health Index (OHI) framework, a tailorable and repeatable approach that measures health of coupled human-ocean ecosystems in different contexts by accommodating differences in local environmental characteristics, cultural priorities, and information availability and quality. Since its development in 2012, eleven assessments using the OHI framework have been completed at global, national, and regional scales, four of which have been led by independent academic or government groups. We have found the following to be best practices for conducting assessments: Incorporate key characteristics and priorities into the assessment framework design before gathering information; Strategically define spatial boundaries to balance information availability and decision-making scales; Maintain the key characteristics and priorities of the assessment framework regardless of information limitations; and Document and share the assessment process, methods, and tools. These best practices are relevant to most ecosystem assessment processes, but also provide tangible guidance for assessments using the OHI framework. These recommendations also promote transparency around which decisions were made and why, reproducibility through access to detailed methods and computational code, repeatability via the ability to modify methods and computational code, and ease of communication to wide audiences, all of which are critical for any robust assessment process. creator: Julia S. Stewart Lowndes creator: Erich J. Pacheco creator: Benjamin D. Best creator: Courtney Scarborough creator: Catherine Longo creator: Steven K. Katona creator: Benjamin S. Halpern uri: https://doi.org/10.7717/peerj.1503 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Lowndes et al. title: On the embryonic cell division beyond the contractile ring mechanism: experimental and computational investigation of effects of vitelline confinement, temperature and egg size link: https://peerj.com/articles/1490 last-modified: 2015-12-10 description: Embryonic cell division is a mechanical process which is predominantly driven by contraction of the cleavage furrow and response of the remaining cellular matter. While most previous studies focused on contractile ring mechanisms of cytokinesis, effects of environmental factors such as pericellular vitelline membrane and temperature on the mechanics of dividing cells were rarely studied. Here, we apply a model-based analysis to the time-lapse imaging data of two species (Saccoglossus kowalevskii and Xenopus laevis) with relatively large eggs, with the goal of revealing the effects of temperature and vitelline envelope on the mechanics of the first embryonic cell division. We constructed a numerical model of cytokinesis to estimate the effects of vitelline confinement on cellular deformation and to predict deformation of cellular contours. We used the deviations of our computational predictions from experimentally observed cell elongation to adjust variable parameters of the contractile ring model and to quantify the contribution of other factors (constitutive cell properties, spindle polarization) that may influence the mechanics and shape of dividing cells. We find that temperature affects the size and rate of dilatation of the vitelline membrane surrounding fertilized eggs and show that in native (not artificially devitellinized) egg cells the effects of temperature and vitelline envelope on mechanics of cell division are tightly interlinked. In particular, our results support the view that vitelline membrane fulfills an important role of micromechanical environment around the early embryo the absence or improper function of which under moderately elevated temperature impairs normal development. Furthermore, our findings suggest the existence of scale-dependent mechanisms that contribute to cytokinesis in species with different egg size, and challenge the view of mechanics of embryonic cell division as a scale-independent phenomenon. creator: Evgeny Gladilin creator: Roland Eils creator: Leonid Peshkin uri: https://doi.org/10.7717/peerj.1490 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Gladilin et al. title: Efficiently detecting outlying behavior in video-game players link: https://peerj.com/articles/1502 last-modified: 2015-12-10 description: In this paper, we propose a method for automatically detecting the times during which game players exhibit specific behavior, such as when players commonly show excitement, concentration, immersion, and surprise. The proposed method detects such outlying behavior based on the game players’ characteristics. These characteristics are captured non-invasively in a general game environment. In this paper, cameras were used to analyze observed data such as facial expressions and player movements. Moreover, multimodal data from the game players (i.e., data regarding adjustments to the volume and the use of the keyboard and mouse) was used to analyze high-dimensional game-player data. A support vector machine was used to efficiently detect outlying behaviors. We verified the effectiveness of the proposed method using games from several genres. The recall rate of the outlying behavior pre-identified by industry experts was approximately 70%. The proposed method can also be used for feedback analysis of various interactive content provided in PC environments. creator: Young Bin Kim creator: Shin Jin Kang creator: Sang Hyeok Lee creator: Jang Young Jung creator: Hyeong Ryeol Kam creator: Jung Lee creator: Young Sun Kim creator: Joonsoo Lee creator: Chang Hun Kim uri: https://doi.org/10.7717/peerj.1502 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Kim et al. title: Volatile anesthetics suppress glucose-stimulated insulin secretion in MIN6 cells by inhibiting glucose-induced activation of hypoxia-inducible factor 1 link: https://peerj.com/articles/1498 last-modified: 2015-12-10 description: Proper glycemic control is one of the most important goals in perioperative patient management. Insulin secretion from pancreatic β-cells in response to an increased blood glucose concentration plays the most critical role in glycemic control. Several animal and human studies have indicated that volatile anesthetics impair glucose-stimulated insulin secretion (GSIS). A convincing GSIS model has been established, in which the activity of ATP-dependent potassium channels (KATP) under the control of intracellular ATP plays a critical role. We previously reported that pimonidazole adduct formation and stabilization of hypoxia-inducible factor-1α (HIF-1α) were detected in response to glucose stimulation and that MIN6 cells overexpressing HIF-1α were resistant to glucose-induced hypoxia. Genetic ablation of HIF-1α or HIF-1β significantly inhibited GSIS in mice. Moreover, we previously reported that volatile anesthetics suppressed hypoxia-induced HIF activation in vitro and in vivo.To examine the direct effect of volatile anesthetics on GSIS, we used the MIN6 cell line, derived from mouse pancreatic β-cells. We performed a series of experiments to examine the effects of volatile anesthetics (sevoflurane and isoflurane) on GSIS and demonstrated that these compounds inhibited the glucose-induced ATP increase, which is dependent on intracellular hypoxia-induced HIF-1 activity, and suppressed GSIS at a clinically relevant dose in these cells. creator: Kengo Suzuki creator: Yoshifumi Sato creator: Shinichi Kai creator: Kenichiro Nishi creator: Takehiko Adachi creator: Yoshiyuki Matsuo creator: Kiichi Hirota uri: https://doi.org/10.7717/peerj.1498 license: http://creativecommons.org/licenses/by/4.0/ rights: © 2015 Suzuki et al.