bluuebunny/crossref_metadata_2025 huggingface dataset:
Sponges of Posidonia oceanica meadows (Sardinia, W-Mediterranean Sea)
Authors: Padiglia Andrea , Cadeddu Barbara , Demurtas Daniela , Bertolino Marco , Manconi Renata , Pronzato Roberto
Published: January 2018

Sponges are one of the main components of Mediterranean benthic ecosystems. Aim of this work was to perform a preliminary survey of conspicuous sponges in the Marine Protected Areas of Capo Caccia – Isola Piana and Asinara (North-Western Sardinia) harbouring wide Posidonia oceanica meadows. Specimens were photographed in vivo, collected along linear transects in shallow water by snorkeling and SCUBA diving, preserved (dry and/or ethanol) and identified at species level. Preliminary results show notable values of taxonomic richness when compared to previous papers confirming that P. oceanica meadows represent a suitable habitat for sponges. Some sponge species preferentially colonize rhizomes, others are found mainly in inter-mattes areas; only a few species are able to settle on leaves. Rhizomes offer a steady, permanent and shaded substratum, while leaves represent an unsteady substrate been smooth, short-lived, more exposed, and constantly moving. Sponges perform different key functional roles in the meadows: a) they host diversified invertebrate associations providing also refuge for sciaphilous invertebrates and nursery for juveniles at body surface and within canals of the aquiferous system; b) they are able to recycle particulate and dissolved organic matter acting as biofilters (active filter feeders); c) they contribute to improve circulation by pumping activity in the water column producing microcurrents particulary effective in lentic conditions. On the other side, to live in the meadows is very advantageous for sponges, gaining protection against storm surges. However data suggest the need of continuous monitoring to assess the impact of invasive algae such as those belonging to the genus Caulerpa and contribute to shed light on the problem of diversity loss by alien species.
Timing of hibernation and reproduction in the endangered New Mexico meadow jumping mouse (Zapus hudsonius luteus)
Authors: Frey Jennifer K.
Published: January 2018

Hibernation is a key life history feature that can impact many other crucial aspects of a species’ biology, such as its survival and reproduction. I examined the timing of hibernation and reproduction in the federally endangered New Mexico meadow jumping mouse (Zapus hudsonius luteus), which occurs across a broad range of latitudes and elevations in the American Southwest. Data from museum specimens and field studies supported predictions for later emergence and shorter active intervals in montane populations relative to low-elevation populations. A low-elevation population located at Bosque del Apache National Wildlife Refuge (BANWR) in the Rio Grande valley was most similar to other populations of Z. hudsonius: the first emergence date was in mid-May and there was an active interval of 162 days. In montane populations of Z. h. luteus, the date of first emergence was delayed until mid-June and the active interval was reduced to ca 130 days, similar to some populations of the western jumping mouse (Z. princeps). Last date of immergence into hibernation occurred at about the same time in all populations (mid to late October). Evidence suggests that females may have a single litter per year in montane populations. At BANWR two peaks in reproduction were expected based on similarity of active season to Z. h. preblei, but the population exhibited little detectable above-ground activity in August, which could stem from a failure of the population to produce early litters. Recommendations are made with respect to appropriate timing of surveys for Z. h. luteus.
Null Hypothesis Significance Testing: a short tutorial
Authors: Pernet Cyril R
Published: January 2018

Although thoroughly criticized, null hypothesis significance testing is the statistical method of choice in biological, biomedical and social sciences to investigate if an effect is likely. In this short tutorial, I first summarize the concepts behind the method while pointing to common interpretation errors. I then present the related concepts of confidence intervals, effect size, and Bayesian factor, and discuss what should be reported in which context. The goal is to clarify concepts, present statistical issues that researchers face using the NHST framework and highlight good practices.
Spatial micro-distribution of shoots in Posidonia oceanica (L.) Delile meadows
Authors: Bacci Tiziano , Rende Sante Francesco , Rocca Domenico , Scardi Michele
Published: January 2018

Posidonia oceanica meadows contain huge numbers of shoots and their dynamics are strictly related to spatial distribution patterns of those shoots. In order to investigate the structure of P. oceanica meadows at very small spatial scale (i.e. in the 1 cm 2 -1 m 2 range), patterns in shoot distribution were analyzed. Spatial distribution of shoots was recorded by cutting all the leaves and by digitizing shoot location from images of 10 square frames (1 m 2 ), sampled in seemingly uniformly dense meadows at two sites in Southern Italy. Spatial point patterns have been explored testing the sensitivity and robustness through different spatial indices, based on i) nearest neighbour analysis, ii) quadrat counts analysis, iii) fractal dimension. Clark & Evans nearest neighbour distance index has been proved to be the most suitable for aim of the work and it has been selected for the further analysis. Data analysis of the 10 square frames (1 m 2 ) highlighted regular spatial point patterns (R>1; p<0.0001) in most cases (8 frames), while aggregated (R<1; p<0.01) and random (R=1) spatial point patterns were rare. In addition, mean value of nearest neighbour distance of shoots in each square frame analyzed has been shown to be always close to 2 cm (min: 1.73 cm; max: 2.21 cm). The potential implications of this type of data set were highlighted. Both nearest neighbour distance of shoots and spatial point pattern typology (aggregated, random or regular) could provide useful and integrative information for the study of P. oceanica macrostructure (e.g. implementation of shoot growth models, development of new descriptors). The raw data, provided by the authors as supplementary material, are currently the first and the only information available about shoot spatial micro-distribution. In this regard, although our data set cannot represent the whole spectrum of variability in P. oceanica meadows, it certainly shed some light on the small scale patterns of P. oceanica meadows and it prompts us many questions, some of which are still unanswered.
Trace element contamination severity of coastal waters: A first bioassessment at the scale of the whole Mediterranean Sea
Authors: Richir Jonathan , Salivas-Decaux Maylis , Lafabrie Céline , Lopez y Royo Cecilia , Lejeune Pierre , Pergent Gérard , Pergent-Martini Christine , Gobert Sylvie
Published: January 2018

Human activities generate large volumes of waste that supply marine coastal environments in pathogens, organic matter, nutrients and toxicants. Among the wide range of toxicants are trace elements. Since the latter are toxic for aquatic organisms from threshold levels and as they are therefore likely to cause multiple damage to the population, the community and the ecosystem levels, their environmental occurrence has to be accurately monitored in order to guarantee appropriate environmental management of coastal zones and to preserve marine coastal ecosystems and the goods and services they provide. In the framework of the STARECAPMED project, the present study aimed to monitor, for the first time, the coastal contamination of the entire Mediterranean by As, Ag, Cd, Cu, Hg, Ni and Pb, using Posidonia oceanica as bioindicator species. But sustainable coastal management also requires the development of appropriate contamination classification systems intended, among other purposes, for environmental managers and policy makers. The combined utilization of several complementary monitoring tools, i.e. water quality scale, pollution index (TEPI and TESVI) and spatial analysis (PCA, CA, correlation analysis and GIS mapping) successfully led to the development of an operational classification system of this kind. In particular, the mapping of the trace element contamination according to a new proposed 5-level water quality scale using the quantile method precisely outlined the contamination severity along Mediterranean coasts and facilitated interregional comparisons. The reliability of the use of P. oceanica as bioindicator species was further again demonstrated through several global, regional and local detailed case studies. In conclusion, holistic approaches such as developed in the present study should be privileged to accurately monitor the contamination rate of coastal waters and to transfer relevant information on this composite problem to environmental managers and policy makers.
Recent monitoring data of Posidonia oceanica meadows distributed along the Apulian coasts (Eastern-Central Mediterranean Sea) according to the 2000/60 EC Directive
Authors: Costantino Gaetano , Ungaro Nicola , Blonda Massimo , Mariani Marina , Battista Daniela , Pastorelli Anna Maria , La Mantia Rosanna , Casale Viviana , Perrino Vito , Barbone Enrico , De Gioia Michele , Assennato Giorgio
Published: January 2018

According to the Water Framework Directive (WFD), a specific monitoring of Posidonia oceanica meadows was carried out along the Apulian coasts by the Regional Agency for the Environmental Prevention and Protection (ARPA Puglia). A total of 17 sites, 11 in the Southern Adriatic Sea and 6 in the Northern Ionian Sea were investigated during two consecutive monitoring cycles (2009-2011 and 2012-2014). Sampling procedures as well as laboratory analyses (phenology and lepidochronology) were carried out according to a common methodological protocol shared at Italian national level (D.M. 260/2010) for the final ecological classification (sensu WFD) using the PREI index. In each meadow, two sampling stations were investigated by scuba divers at the fixed depth of 15 m and in correspondence of the lower bathymetric distribution limit. For each station, 9 shoots counting (40x40 cm square) and 3 covering estimates (around 5 m of radius) were carried out. In addition, 18 orthotropic shoots and a sediment sample were collected as well as some other bio-ecological data (meadow continuity, dead matte presence, bottom type, invasive algae presence, flowering, disturbance sources, lower limit type and depth). The results showed that 29% of sites were classified as “GOOD”, 59% were classified as ”MODERATE” while the remaining 12% as “POOR”, with a general slight improvement of the classification in the last monitoring cycle (2012-2014). Although the ecological quality status of the Apulian Posidonia oceanica meadows (summarized by the PREI index values) reflects the distribution of anthropic pressures on the coast (harbours, industrial and urbanized areas, river’s outlets) along a latitudinal gradient, the classification based on the rules (reference conditions and EQR boundaries for the PREI index) reported in the Italian law (D.M. 260/2010) seems to underestimate the real ecological status. Consequently, a revision of both the actual reference conditions and EQR boundaries is suggested for the BQE Posidonia oceanica in the Apulian marine waters, in order to taking account of the environmental features of two different marine basins as the south-western Adriatic Sea and the north-western Ionian Sea.
Auditory interfaces in automated driving: an international survey
Authors: Bazilinskyy Pavlo , De Winter Joost C. F.
Published: January 2018

This study investigated peoples’ opinion on auditory interfaces in contemporary cars and their willingness to be exposed to auditory feedback in automated driving. We used an Internet-based survey to collect 1,205 responses from 91 countries. The participants stated their attitudes towards two existing auditory driver assistance systems, a parking assistant (PA) and forward collision warning system (FCWS), as well as towards a futuristic augmented sound system (FS) proposed for fully automated driving. The respondents were positive towards the PA and FCWS, and rated their willingness to have these systems as 3.87 and 3.77, respectively (1 = disagree strongly, 5 = agree strongly). The respondents tolerated the FS. The results showed that a female voice is the most preferred feedback mode for the support of takeover requests in highly automated driving, regardless of whether the respondents’ country is English speaking or not. The present results could be useful for designers of automated vehicles and other stakeholders.
Mining usage patterns for the Android API
Authors: Borges Hudson S , Valente Marco Tulio
Published: January 2018

API methods are not used alone, but in groups and following patterns. However, despite being a key information for API users, most usage patterns are not described in official API documents. In this article, we report a study that evaluates the feasibility of automatically enriching API documents with information on usage patterns. For this purpose, we mine and analyze 1,952 usage patterns, from a set of 396 Android applications. As part of our findings, we report that the Android API has many undocumented and non-trivial usage patterns, which can be inferred using association rule mining algorithms. We also describe a field study where a version of the original Android documentation is instrumented with the extracted usage patterns. During 17 months, this documentation received 77,863 visits from professional Android developers.
Geometric morphometric analysis of the skull of Podocnemis spp. (Pleurodira, Podocnemididae) and its implications on the taxonomic status of Podocnemis bassleri Williams, 1956
Authors: Romano Pedro S. R. , Azevedo Sergio A. K. , Kellner Alexander W. A. , Oliveira Gustavo R.
Published: January 2018

Background. Podocnemis bassleri Williams, 1956 is the oldest definite record for Podocnemis, dating back to the Miocene of South America. However, the diagnosis of P. ba. is fragile, as assumed by Williams himself. Here we evaluated the hypothesis of P. ba. as a synonym of P. expansa by exploring the shape variation of the skull among Podocnemis spp. Methods. We collected 19 landmarks on the left side of the skull in ventral view from 33 Podocnemis spp. skulls. We included in the sample a new specimen of P. ba. from the Miocene of Acre, Brazil (MCT/RJ unnumbered) and the holotype (AMNH 1662) from the Miocene of Peru, along with: P. erythrocephala (n=3), P. ex. (n=9), P. lewyana (n=1), P. sextuberculata (n=9), P. unifilis (n=6), and P. vogli (n=3). The data was then Procrustes superimposed and a Relative Warps Analysis (RW) was performed to evaluate shape variation. Also, a multivariate regression of the Partial Warps (i.e.: the eigenvectors of the “bending energy” matrix) versus the log-transformed centroid size (the independent variable) was computed in order to evaluate the allometry in the data. All analyses were fulfilled using Rohlf’s TPS softwares. Results. The two first RWs accumulated ~52% of shape variation. The individual projection of the specimens in RW1 and RW2 showed a structure partially explained by a phylogenetic signal. P. ex. and P. se., previously considered as sister-groups, were projected in the negative scores of RW1. Also, these two species were projected, respectively, in the positive and negative scores of the RW2. The two specimens of P. ba. were nested among P. ex. specimens. Furthermore, the multivariate regression revealed an effect of the size in the shape variation: larger skulls have wider maxillae and posterior region laterally extended. Discussion. According to the literature, P. ex. and P. ba. are nearly indistinguishable (besides the larger size of the second), and Williams seems to have used the Miocene age of the second as a criterion for differentiating the two taxa. Indeed, one of the diagnostic features pointed out by Williams – slightly shorter relative distance from snout tip to posterior borders of the orbits – seems to be a taphonomic outcome. Moreover, the second diagnostic character – internal palatal processes of the maxillae abruptly dorsally projected – is extended anteroposteriorly in the MCT/RJ P. ba. specimen, as in all recent taxa. So, this character is polymorphic or also results of a taphonomic outcome. As consequence, P. ba. lacks a suitable diagnosis. Our preliminary results revealed little differences in shape of P. ex. and P. ba. and a clear allometric effect in the shape variation. In conclusion, it seems reasonable to suggest that P. ba. is a junior synonym of P. ex., although we will wait to claim it after additional analyses.
Response of the rare biosphere to environmental disturbance in a highly diverse ecosystem (Zodletone spring, OK, USA)
Authors: Coveley Suzanne , Elshahed Mostafa S , Youssef Noha H.
Published: January 2018

Within highly diverse ecosystems, the majority of bacterial taxa are present in low abundance as members of the rare biosphere. The rationale for the occurrence and maintenance of the rare biosphere, and the putative ecological role(s) and dynamics of its members within a specific ecosystem is currently debated. We hypothesized that in highly diverse ecosystems, a fraction of the rare biosphere acts as a backup system that readily responds to environmental disturbances. We tested this hypothesis by subjecting sediments from Zodletone spring, a sulfide- and sulfur-rich spring in southwestern OK, to incremental levels of salinity (1, 2, 3, 4, and 10% NaCl), or temperature (280, 300, 320, and 700C), and traced the trajectories of rare members of the community in response to these manipulations using 16S rRNA gene analysis. Our results indicate that multiple rare bacterial taxa are promoted from rare to abundant members of the community following such manipulations and that, in general, the magnitude of such recruitment is directly proportional to the severity of the applied manipulation. Rare members that are phylogenetically distinct from abundant taxa in the original sample (unique rare biosphere) played a more important role in the microbial community response to environmental disturbances, compared to rare members that are phylogenetically similar to abundant taxa in the original sample (non-unique rare biosphere). The results emphasize the dynamic nature of the rare biosphere, and highlight its complexity and non-monolithic nature.
A corpus-based analysis of potential linguistic indicators of corporate deception in tobacco industry documents
Authors: Brown-Johnson Cati , Rubin Donald
Published: January 2018

Introduction: To more fully understand the impact of specific language attributes on deception in corporate communication, we used a stratified random sample of tobacco industry documents to test a small number of individual potential automated linguistic indicators of corporate deception: cognitive-emotional verbs, allness and superlative terms, nonbinding verbs, and group mentality. Methods: Texts from the Tobacco Documents Corpus were categorized by audience addressed (industry internal/external) and company of origin, and compared for incidence of the deceptive language indicators. Results: Cognitive-emotional verbs were strongly associated with likely deception and most prevalent for external audiences and documents produced by the Tobacco Institute, an industry front group. Cognitive-emotional verbs include believe, think, seem, feel and realize, in opposition to action verbs (e.g. throw). Discussion: Linguistic measurements of cognitive-emotional verbs may help pinpoint deceptive and misleading corporate communication. Verb choice and the use of different classes of verbs may reflect corporate linguistic deception.
From the “ancestar” of turtles to the turtle-mouse: when Greek words are used for turtle taxon names
Authors: Vlachos Evangelos
Published: January 2018

Background. Regardless using a rank-based or a phylogenetic nomenclature code, the use of Latinized binomens to describe the extant and extinct species has been essential. Ever since the times of Linnaeus, the use of Latinized Greek names has been a common practice both for neontologists and paleontologists.

Methods. I critically analyzed the most common Greek words used as taxa names in the chelonian literature to establish their etymology and check whether the transliteration process has been done correctly. I also compared the current guidelines for the latinisation of Greek words recommended by the International Code of Zoological Nomenclature, with other alternative systems for the transformation of names formed in the Greek alphabet into Latin-based languages.

Results. The preliminary results show that some Greek words (e.g. Chelone, Emys) dominate the chelonian nomenclature, but the history of the application of many of those names is intriguing. The use of Greek words is quite common in turtle taxa names when the name describes physical properties of the animal (size, shape, colour). However, several unfortunate examples exist, as some quite successful and famous names contain misspellings or poor choice of words that resulted in meanings opposite from the ones intended by the authors.

Discussion. Naming species is an integral part of the research of both neontologists and palaeontologists, but the application of Greek words to life sciences is even far more extensive, applied to numerous terminologies as well. Forming a proper name for a taxon could aid significantly to the communication and interpretation of the scientific results. Publishing a new name requires a sense of responsibility as well, as the formation of a taxon name is a unique linguistic procedure. But in the end, to add a taxonomic side to the old shakespearean question, is not the name that is important, but the information it conveys. That which we call a turtle by any other name would be as unique.
Assessment of the environmental health status of the Marchica lagoon (Morocco, Mediterranean) using Cymodocea nodosa meadows and its associated macrofauna: preliminary results
Authors: El Kamcha Reda , Bououarour Oussama , Boutahar Loubna , El Fatouani Zineb , El Adnani Ayoub , Zourarah Bendahhou , Sghaier Yassine Ramzi , Benhoussa Abdelaziz , Bazairi Hocein
Published: January 2018

The Marchica lagoon is the single lagoon on the Mediterranean coast of Morocco. Beside its ecological and socio-economic values, the lagoon is under pressure of a complex mixture of human-mediated stressors (urbanization, pollution, overfishing, tourism, etc.). Nowadays, many institutional efforts have been undertaken to establish a sustainable management plan of the lagoon in the context of an Integrated Coastal Zone Management (ICZM) approach. Thus, understanding how these stressors impact upon ecological status and ecosystem services is a sound step for any efficient integral management. Based on sampling performed on June 2014, the present work aimed at assessing the ecological quality status (ES) of the northern part of the lagoon using Cymodocea nodosa (Ucria) Ascherson meadows and benthic macrofauna. 16 stations (11 with C. nodosa and 5 on bare sediment) were sampled using a Van Veen grab. Preliminary results showed differences between stations. Shoots biomass fluctuated between 8.02 and 61.2 g dw m-2 while the roots-rhizomes biomass oscillated between 10.8 and 235.5 g dw m-2. The root-rhizome and leaf biomass ratio revealed high values (up to 10.8) in the central sector suggesting a potential nutrient enrichment.Benthic macrofauna revealed the presence of 90 species belonging to six zoological groups and dominated by crustaceans, molluscs and polychaetes. The assessment of the ecological quality status, based on benthic macrofauna, was evaluated using Biotic Indices (AMBI, M-AMBI, Benthix, BITS). The results showed partial agreement between single index-derived ES and underlined the dependency of these biotic indices on the habitat characteristics, on the one hand, and the necessity to define specific reference conditions to the Marchica lagoon.
PAME: Plasmonic Assay Modeling Environment
Authors: Hughes Adam S , Reeves Mark E. , Liu Zhaowen
Published: January 2018

Plasmonic assays are an important class of optical sensors that measure biomolecular interactions in real-time without the need for labeling agents, making them especially well-suited for clinical applications. Through the incorporation of nanoparticles and fiberoptics, these sensing systems have been successfully miniaturized and show great promise for in-situ probing and implantable devices, yet it remains challenging to derive meaningful, quantitative information from plasmonic responses. This is in part due to a lack of dedicated modeling tools, and therefore we introduce PAME, an open-source Python application for modeling plasmonic systems of bulk and nanoparticle-embedded metallic films. PAME combines aspects of thin-film solvers, nanomaterials and fiber-optics into an intuitive graphical interface. Some of PAME’s features include a simulation mode, a database of hundreds of materials, and an object-oriented framework for designing complex nanomaterials, such as a gold nanoparticles encased in a protein shell. An overview of PAME’s theory and design is presented, followed by example simulations of a fiberoptic refractometer, as well as protein binding to a multiplexed sensor composed of a mixed layer of gold and silver colloids. These results provide new insights into observed responses in reflectance biosensors.
Late Cretaceous non-marine turtles of Asia: a review of taxonomic diversity and paleobiogeography
Authors: Danilov Igor , Obraztsova Ekaterina , Sukhanov Vladimir
Published: January 2018

Background. This report reviews data on taxonomic diversity and paleobiogeography of Late Cretaceous (K2) non-marine turtles of Asia accumulated since latest reviews in 2000s. K2 non-marine turtles of Asia are known from four main geographical areas: Middle Asia-Kazakhstan (MAK), Mongolia (MO), China (CH) and Japan (JA). Methods. We critically reviewed composition of non-marine turtle assemblages of the K2 for each of the mentioned geographical area to make estimates of taxonomic diversity for different ages of the K2. Based on these data we analyzed temporal distribution of taxa of non-marine turtles and change in taxonomic diversity of turtle assemblages. Results. K2 turtles of MAK are represented by eight suprageneric taxa – Adocidae (Ad), Carettochelyidae (Ca), Lindholmemydidae (Li), Macrobaenidae (Ma), Nanhsiungchelyidae (Na), Trionychidae (Tr), Eucryptodira indet. (Eu), and Testudines indet. (Te), of which Ad, Li, Ma and Tr are known from the Cenomanian(CE) – early Campanian(CA), whereas other taxa only from the CE-early Turonian(TU). Taxonomic diversity changes from 10–12 species and genera, 6–8 suprageneric taxa in the CE to 7 species and genera, 4 families in the late TU early CA. K2 turtles of MO are represented by seven suprageneric taxa – Ad, Ca, Li, Ma, Meiolaniformes (Me), Na, and Tr, of which Li, Na and Tr are known from the CE-Maastrichtian(MA), Ad, Ca, and Ma, from the CE-Santonian(SA), and Me, only from the MA. Taxonomic diversity changes from 12 species, 10 genera, 6 families in the CE – SA, 8–9 species, 7–9 genera, 3 families in the CA, and 9 species, 7–8 genera, and 4 suprageneric taxa in the MA. K2 turtles of CH are represented by three suprageneric taxa (Li, Na, and Tr), but their precise temporal distribution is poorly known. Taxonomic diversity in the K2 is 12 species, 11–12 genera, and 3 families. K2 turtles of JA are represented by six suprageneric taxa (Ad, Ca, Na, Tr, Eu, and Te), of which Na are known from the CE-SA, Tr from the Coniacian(CO)-CA, and other taxa from the CO-SA. Taxonomic diversity changes from 1 species, genus, and family in the CE-TU to 7 species and genera, and 5–6 suprageneric taxa in the CO-SA. Discussion. In MAK, most significant transformation of turtle assemblages occurred in the CE-TU, whereas transformation in the SA-CA was less significant. On the contrary, in MO, most significant transformation occurred in the SA-CA, and less significant in the CA-MA.The patterns of transformation of the K2 turtle assemblages of CH and JA are not clear. The differences in the patterns of diversity and transformations of the K2 turtle assemblages in different geographical areas of Asia may be explained by different environmental conditions in these areas at that time and influence of such factors as transgressions in coastal areas (MAK and JA) and cooling and aridizations in inland areas (MO and CH).
Morphology of cervical vertebrae of Annemys and variability of neck morphotypes in xinjiangchelyid turtles
Authors: Obraztsova Ekaterina , Danilov Igor
Published: January 2018

Background. Xinjiangchelyidae are a group of basal cryptodires from the Middle Jurassic – Early Cretaceous of Asia and Early Cretaceous of Europe. Recent studies show that xinjiangchelyids are rather uniform and conservative in their shell morphology and comparatively more variable in skull shape. Morphology and variability of cervical vertebra(e) (CV) of xinjiangchelyids remain poorly known. More or less complete series of CV were described for Xinjiangchelys qiguensis and X. tianshanensis, whereas for other xinjiangchelyids they are alternately unknown or often incomplete, deformed and need additional preparation. Methods. We examined several hundred isolated CV of a xinjiangchelyid Annemys sp. from the Middle Jurassic (Bathonian) Itat Formation of Berezovsk Quarry, Krasnoyarsk Territory, West Siberia, Russia. Some of these CV are well preserved and three-dimensional and allow reconstruction of the complete series of CV of Annemys. Results. The formula of CV is (2(3()4()5()6()7()8), although C8 is rarely amphicoelous. Previously, xinjiangchelyids were thought to have only amphicoelous CV. All CV are relatively short (similar to other forms of Annemys, shorter than in X. tianshanensis and much shorter than in X. qiguensis). The anterior and posterior central articulations are approximately on one level. The anterior central articulations form a wide triangle (C2), equilateral triangle (C3, C4), or wide oval (C5–C8); the posterior central articulations form a narrow oval (C2–C5, C8), roundish (C6) or wide oval (C7). The ventral keel is low on the anterior CV and high on C7 and C8, a condition similar to some sinemydids/macrobaenids and more advanced cryptodires. The parapophyses are located at the posteroventral edge of the centrum in C2–C5, and at the anteroventral edge of the centrum in C6–C8. The articular surfaces of the prezygapophyses face dorsolateral in C2 or dorsomedial in more posterior CV, forming an angle of about 20° from the horizontal in C3 and C4 and about 30–35° in C5–C8. The postzygapophyses are widely separated, unlike X. qiguensis and similar to other forms of Annemys and X. tianshanensis. Isolated cervical ribs are present in the material, but their associations with CV are unclear. Discussion. Our study shows that xinjiangchelyids were more variable in the morphology of their CV than thought previously. They demonstrate three neck morphotypes: the short-necked (Annemys), medium-necked (X. tianshanensis) and long-necked (X. qiguensis). In addition to length of CV, these morphotypes differ in cervical formula, shapes of central articulations, and patterns of cervical rib attachment. Morphology of the CV of Annemys suggests the possibility of both vertical and lateral movements of the neck that agrees with recent studies on neck mobility of primitive turtles.
Virtual hepatic surgery scenarios using manipulated real liver models
Authors: Zygomalas Apollon , Megalooikonomou Vasileios , Koutsouris Dimitrios , Karavias Dimitrios , Karagiannidis Ioannis , Amanatidis Theofilos , Maroulis Ioannis , Giokas Konstantinos , Karavias Dionissios
Published: January 2018

Background. High quality patient specific 3D liver models can be nowadays exported using computer liver segmentation algorithms. Specific 3D image editing tools can be used to manipulate the liver models and create virtual surgical cases. Objective. The aim of our study was to create virtual hepatic surgery scenarios using a novel liver segmentation and preoperative planning application and evaluating it as an educational tool. Method. A liver segmentation and preoperative planning application was developed on MATLAB® 2013a. Special image editing tools were designed to allow manipulation of the exported 3D liver models. Three pathological and two liver imaging datasets from healthy patients were used for the validation. The 3D liver models which have been created after liver segmentation were then manipulated by; 1) changing tumors’ volumes, 2) adding tumors and 3) designing liver injuries. Addition fictitious clinical information were implemented. Residents were asked to study the virtual cases and propose resection plans. Their scenarios were evaluated and discussed with specialized liver surgeons. The Kirkpatrick’s four levels model of learning evaluation was used. Results. Up to 30 different virtual liver surgical cases were created. The number of virtual scenarios that could be designed is theoretically unlimited. The residents quickly and effectively learned to evaluate critical anatomical and pathological structures and propose liver resection plans considering liver surgery principles. Conclusions. Virtual hepatic surgery scenarios allowed for a rapid education without the need to wait for similar real cases. The proposed liver segmentation and hepatectomy simulation application can be used for educational purposes.
Genetic structure of Oryza glumaepatula wild rice populations and evidence of introgression from O. sativa in Costa Rica
Authors: Fuchs Eric J , Meneses Martínez Allan , Calvo Amanda , Muñoz Melania , Arrieta-Espinoza Griselda
Published: January 2018

Wild crop relatives are an important source of genetic diversity for crop improvement. However, gene flow from cultivated species into wild species may prove detrimental. Introgression may lead to changes in wild species by incorporating alleles from domesticated species, which may increase the likelihood of extinction. The objective of the present study is to analyze how genetic diversity is distributed within and among populations of the wild rice species Oryza glumaepatula in Costa Rica. We also evaluated if there is evidence of introgression between wild rice and commercial varieties of O. sativa since it is cultivated commonly in close proximity to wild rice populations. Individuals from all known O. glumaepatula populations in Costa Rica were collected. With the aid of 455 AFLP markers, we characterized the genetic diversity and structure among seven populations in northern Costa Rica. Given the dominant nature of our markers, Bayesian estimates of genetic structure were used. We also compared genetic diversity estimates between O. glumaepatula individuals and O. sativa commercial rice. Our results show that O. glumaepatula populations in Costa Rica have moderately high levels of genetic diversity, comparable to those found in South American populations. This is likely a result of large population size. Despite the restricted distributions of this wild species, in Costa Rica most populations are composed of several thousand individuals, thus reducing the effects of drift on genetic diversity. Our results also found low but significant structure (\theta=0.03±0.001) among populations that are separated by ~10 Km within a single river. The position of the population along the river did not influence genetic diversity estimates or differences among populations. This river does not have a strong current and meadows or seeds may easily move upstream, thus homogenizing genetic diversity across populations regardless of river position. Ample gene flow through pollen, seeds or detached culms within the same river reduces genetic structure. A Bayesian structure analysis showed that individuals from two populations share a significant proportion of their genomes with O. sativa genome. These results suggest that the low levels of genetic structure found in these populations are likely the result of introgression from cultivated O. sativa populations. These results expose an important biohazard as recurrent hybridization may reduce genetic diversity of this wild rice species. Introgression may transfer commercial traits into the only populations of O. glumaepatula in Costa Rica, which in turn could alter genetic diversity and increase the likelihood of local extinction. These results have important implications for in situ conservation strategies of the only wild populations of O. glumaepatula in Costa Rica.
Microview: a medical application focusing on the diagnosis of diseases
Authors: Michopoulos Alexandros , Ntakakis George , Zamanis Stamoulis , Petinaki Efthimia
Published: January 2018

MicroView was made to make the connection between medicine and mobile technology reality, in order to achieve that we transform the widely used mobile devices (smartphones, tablets) into diagnostic tools. MicroView is a medical application that focuses on the diagnosis of diseases whose causes or results can be detected in biological fluids such as CSF, urine and blood. The diagnosis is achieved by innovative image processing algorithms that detect the presence and the number of the white blood cells in the biological sample. The app has been tested in 37 urine and 23 CSF samples. The accuracy of the app was 92%. In conclusion the app offers a quicker, easier and friendlier diagnosis to young scientists but also experienced professionals can be benefit from it, since all images are in electronic form and can provide a way of result confirmation.
An ontology to support evidence-based Functional Behavioral Assessments
Authors: Taibi Davide , Chiazzese Giuseppe , Merlo Gianluca , Seta Luciano
Published: January 2018

The term Functional Behavioral Assessment (FBA) refers to a set of multiple assessment strategies aimed to identify specific antecedents and consequences that maintain a target behaviour (Du Paul, 1996). In the context of FBA, standards and protocols to support the data exchange between researchers, health professionals and therapist are under-represented. Moreover, there is a need for sharing common actions and assessment practices in order to improve the application of the FBA. To meet these goals, we propose the definition of an FBA ontology as a tool to describe three specific aspects related to individual, behavioural and assessment data in different contexts of everyday life such as school, family and social environments. The individual data include: diagnoses, medications, school information, discipline referrals and other events, thus providing a comprehensive overview of the individuals and the network of support people with specific roles that collaborates on the individual’s care. The behavioural data include the description of an individual´s target behaviour, and information about places and settings in which the behaviour occurs. The assessment gathers structural behavioural data collections, according to systematic direct observation, and in compliance to the ABC model (antecedents, behavior, and consequences) commonly used in the Cognitive Behavioral Therapy (CBT) for identifying behavioural functions, and designing intervention plans. This data is relevant in supporting statistical analysis in order to evaluate the efficacy of the behavioural treatments. Moreover, the FBA ontology provides a complete model that enables integration and interlinking with other Linked Open Data datasets and repositories thus supporting the sharing of appropriate resources such as behavioural patterns, effective intervention strategies, and behavioural treatments. Finally, the ontology provides the basis for the designing of software applications to support the functional assessment processes. This ontology has been applied in the framework of the WHAAM (Web Health Application for ADHD Monitoring) project, aimed to promote the FBA approach to the behavioural treatment of ADHD children. References: DuPaul, G. J., & Ervin, R. A. (1996). Functional assessment of behaviors related to attention-deficit/hyperactivity disorder: Linking assessment to intervention design. Behavior Therapy, 27(4).
Human performance at old age
Authors: Rittweger Jörn
Published: January 2018

Force plates are a straightforward tool to assess human acceleration as an indicator of human performance. Understanding of the physical principle, and also of the test instruction is required to arrive at meaingful results and interpretations. Notably, performance and physiology levels can differ. A series of studies in healthy people has yielded that peak jumping power is a robust, ecological measure of performance and physiology. It shows a very pronounced decline with age. Morover, these studies reveal that sports is beneficial for muscles and bones. Some benefits by sports diminish with age (bone, muscle), but fracture reduction by sports extends into 10th decade of life.
On the accurate description of social and genetic mating systems
Authors: MacManes Matthew D
Published: January 2018

Mating systems are critical determinants of the intensity of sexual selection and sexual conflict, but understanding how variation in reproductive behavior influences these phenomena requires consistent, accurate descriptions of the array of mating arrangements observed in nature. As understanding of animal mating systems has evolved, behavioral ecologists have shifted from using behavioral information to an increasing reliance on genetic data to characterize patterns of reproductive behavior and success. Although genetic data are critical for an accurate accounting of parentage and reproductive success, they exclude critical information regarding the nature of behavioral relationships among reproductive partners, thereby potentially confounding fundamentally different types of mating systems. I contend that the ability to identify common evolutionary trends and their underlying selective pressures is significantly enhanced by using a terminological framework that differentiates explicitly between social and genetic mating systems. Furthermore, inclusion of both types of information can reveal new and intriguing relationships between behavior and fitness that further our understanding of how selection shapes mating systems. Here, I offer behavioral ecologists a new terminological framework for the study of mating systems that allows us to more appropriately merge genetic with behavioral data in an attempt to improve our understanding of this critical aspect of animal behavior. Lastly, I suggest a potential way in which we can begin to fully embrace the complexity of animal mating systems, in part via the adoption of a more quantitative framework for behavioral and genetic data.
Ghost-tree: creating hybrid-gene phylogenetic trees for diversity analyses
Authors: Fouquier Jennifer , Rideout Jai R , Bolyen Evan , Chase John H , Shiffer Arron , McDonald Daniel , Knight Rob , Caporaso J Gregory , Kelley Scott T.
Published: January 2018

Ghost-tree is a bioinformatics tool that integrates sequence data from two genetic markers into a single phylogenetic tree that can be used for diversity analyses. Our approach uses one genetic marker whose sequences can be aligned across organisms spanning divergent taxonomic groups (e.g., fungal families) as a “foundation” phylogeny. A second, more rapidly evolving genetic marker is then used to build “extension” phylogenies for more closely related organisms (e.g., fungal species or strains) that are then grafted on to the foundation tree by mapping taxonomic names. We apply ghost-tree to graft fungal extension phylogenies derived from ITS sequences onto a foundation phylogeny derived from fungal 18S sequences. The result is a phylogenetic tree, compatible with the commonly used UNITE fungal database, that supports phylogenetic diversity analysis (e.g., UniFrac) of fungal communities profiled using ITS markers. Availability: ghost-tree is pip-installable. All source code, documentation, and test code are available under the BSD license at https://github.com/JTFouquier/ghost-tree.
Assessment of catfish farming in Osogbo (Nigeria) and its environs
Authors: Adelakun Kehinde Moruff , Amali Rosemary Patrick , Ogundiwin Damilare Ibukun , Bakare Kayo
Published: January 2018

As Fish farming (Aquaculture) is the most efficient husbandry method for animal protein production, an assessment of catfish farming in Osogbo and Osun state was undertaken. An assessment was carried out among 53 catfish farmers between January and April, 2013 using questionnaires conducted via face-to-face interviews. The results revealed that there are large numbers of fish farms in and around the Osogbo area. Twenty (37.74%) of the fish farms are commercial farms while thirty-three (62.36%) are homestead. Results also showed that there were more males are than females working in these fish farms. The two prominent religious faiths, Islam and Christianity are both represented by the employees, indicating that it there are no religious restrictions. The semi-intensive system of fish farming with concrete and earthen ponds was being adopted by the farmers and there has been steady development over the last five years. Insufficient funds for expansion, unpredictable weather, fishseed mortality, irregular price of feed ingredients and pricing of products, among other factors, are the major challenges faced. Useful suggestions and recommendations are offered to address these challenges and sustain business growth.
An unusual archosauriform tooth increases known tetrapod diversity in the lower portion of the Chinle Formation (Late Triassic) of southeastern Utah, USA
Authors: Lopez Andres , St. Aude Isabella , Alderete David , Alvarez David , Aultman Hannah , Busch Dominique , Bustamante Rogelio , Cirks Leah , Lopez Martin , Moncada Adriana , Ortega Elizabeth , Verdugo Carlos , Gay Robert J
Published: January 2018

An unusual tetrapod tooth was discovered in the Upper Triassic Chinle Formation of southeastern Utah. The tooth was originally hypothesized to pertain to Revueltosaurus, but further investigations have rejected that hypothesis. In this paper, we compare MNA V10668 to other known fossil tooth crowns from the Chinle Formation and assign the tooth to the least inclusive clade currently available, Archosauriformes, based on the presence of mesial and distal serrations, a distal keel, and a conical mesiodistal profile. Using data found in other publications and pictures of other teeth, we compare this specimen to other Triassic dental taxa. MNA V10668 shares some similarities with Crosbysaurus, Tecovasaurus, and several other named taxa, including a teardrop-shaped labiolingual profile, but possesses a unique combination of characteristics not found in other archosauromorph teeth. This increases the known diversity of archosauromorphs from the Chinle Formation and represents the first tooth of this morphotype to be found from Utah in the Late Triassic.