bluuebunny/crossref_metadata_2025 huggingface dataset:
Analgesic efficacy and associated plasma concentration of tramadol and O-desmethyltramadol following oral administration post ovariohysterectomy in dogs
Authors: Goudie-DeAngelis Elizabeth M , Woodhouse Kerry J
Published: January 2018

Tramadol is used in both human and veterinary medicine to treat postoperative pain. The purpose of this study was to evaluate tramadol as a sole postoperative analgesic and to compare drug plasma concentration to clinical pain score. A high or low dose of tramadol was randomly assigned and administered to 14 mixed breed female dogs after ovariohysterectomy. The Short-Form of the Glasgow Composite Measure Pain Scale was used for pain evaluation post-operatively. Plasma was collected for evaluation of tramadol and O-desmethyltramadol concentrations. The effect of weight and dose on pain scores as well as how pain score correlated with plasma concentration of tramadol and O-desmethyltramadol was evaluated. A significant difference in pain score was noted between doses when weight classes were pooled. The plasma concentrations did not correlate with pain score. Based on our results, the use of tramadol as a sole analgesic agent provides inadequate postoperative pain control.
De novo clustering methods out-perform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units
Authors: Westcott Sarah L , Schloss Patrick
Published: January 2018

Background. 16S rRNA gene sequences are routinely assigned to operational taxonomic units (OTUs) that are then used to analyze complex microbial communities. A number of methods have been employed to carry out the assignment of 16S rRNA gene sequences to OTUs leading to confusion over which method is optimal. A recent study suggested that a clustering method should be selected based on its ability to generate stable OTU assignments that do not change as additional sequences are added to the dataset. In contrast, we contend that the quality of the OTU assignments, the ability of the method to properly represent the distances between the sequences, is more important.Methods. Our analysis implemented six de novo clustering algorithms including the single linkage, complete linkage, average linkage, abundance-based greedy clustering, distance-based greedy clustering, and Swarm and the open and closed-reference methods. Using two previously published datasets we used the Matthew’s Correlation Coefficient (MCC) to assess the stability and quality of OTU assignments.Results. The stability of OTU assignments did not reflect the quality of the assignments. Depending on the dataset being analyzed, the average linkage and the distance and abundance-based greedy clustering methods generated OTUs that were more likely to represent the actual distances between sequences than the open and closed-reference methods. We also demonstrated that for the greedy algorithms VSEARCH produced assignments that were comparable to those produced by USEARCH making VSEARCH a viable free and open source alternative to USEARCH. Further interrogation of the reference-based methods indicated that when USEARCH or VSEARCH were used to identify the closest reference, the OTU assignments were sensitive to the order of the reference sequences because the reference sequences can be identical over the region being considered. More troubling was the observation that while both USEARCH and VSEARCH have a high level of sensitivity to detect reference sequences, the specificity of those matches was poor relative to the true best match.Discussion. Our analysis calls into question the quality and stability of OTU assignments generated by the open and closed-reference methods as implemented in current version of QIIME. This study demonstrates that de novo methods are the optimal method of assigning sequences into OTUs and that the quality of these assignments needs to be assessed for multiple methods to identify the optimal clustering method for a particular dataset.
Bacteria associated to human saliva are major microbial components of Ecuadorian indigenous beers (chicha)
Authors: Freire Ana L. , Zapata Sonia , Mosquera Juan , Mejia Maria Lorena , Trueba Gabriel
Published: January 2018

Indigenous beers (chicha) are part of the indigenous culture in Ecuador. The fermentation process of these beers relay probably on microorganisms from: fermenting substrates, environment and human microbiota. We analyzed the microbiota of artisanal beers (including a type of beer produced after chewing boiled cassava) using bacterial culture and 16S-based tag-encoded FLX amplicon pyrosequencing (bTEFAP). Surprisingly, we found that Streptococcus salivarius and Streptococcus mutans (part of the human oral microbiota) where among the most abundant bacteria in chewed cassava and in non-chewed cassava beers. We also demonstrated that S. salivarius and S. mutans (isolated from these beers) could proliferate in cassava mush. Lactobacillus sp. was predominantly present in most types of Ecuadorian chicha.
A crime data analysis framework with geographical information support for intelligence led policing
Authors: Chamikara Mahawaga Arachchige Pathum , Galappaththi Akalanka , Yapa Roshan D , Nawarathna Ruwan D , Kodituwakku Saluka Ranasinghe , Gunatilake Jagath , Liyanage Liwan H
Published: January 2018

The manual crime recording and investigation systems in police stations all around the world are generating piles of crime documents which make storage and retrieval of reliable crime information extremely difficult as well as inefficient. Furthermore, investigators of central authorities have to manually search through these documents and communicate between the relevant police stations to obtain required information. Eventually, delays in information flow between investigators of crime incidents cannot be avoided. Sri Lanka Police too have been facing the same set of issues over many years. To get rid of pilling of large number of documents annually in police stations, Sri Lanka Police is allowed to destroy the documents related to solved crimes which are older than five years. This may destroy not only "closed files", but also very valuable information that can be used in future crime investigations.To overcome this problem, this paper proposes a web-based framework with geographical information support which contains a centralized database for crime data storage and retrieval. Geographical capabilities of the framework support not only spatial analysis but also provide an efficient solution to current manual crime map generation. Our highly secured and user friendly framework follows the state of the art layered architecture which provides an optimized data model for fast access and easy analysis of crime data. The solution consists of an affluent set of data mining tools which are essential in any crime investigation process. Security of data is ensured with data encryption for sensitive information and by limiting access to the data through a role based access method. Further the data is only accessible through a virtual private network (VPN) connecting all the police stations and other relevant departments of the Police. The proposed framework was evaluated by conducting an experimental study and the results are promising.
Exploring the psychometric properties of the English version of the Internet Addiction Test in the Pakistani population: a cross-sectional survey
Authors: Waqas Ahmed , Farooq Faisal , Bhatti Anum , Javed Saamia , Ghumman Mahrukh Elahi , Raza Mohsin , Khan Spogmai , Ahmad Waqas
Published: January 2018

Introduction: Despite growing concerns over pathological use of the Internet, studies based on validated psychometric instruments are still lacking in Pakistan. The present study aimed to examine the psychometric properties of Young’s Internet Addiction Test (IAT) in a sample of the Pakistani population. We examined the validity, internal consistency, readability and floor and ceiling effects of IAT scores.Methods: This cross-sectional study was conducted at CMH Lahore Medical College and Institute of Dentistry, Lahore, Pakistan from 1 March 2015 to 30 May 2015. A total of 522 medical and dental students completed the questionnaire, which consisted of three sections: (a) demographics and percentage grades in annual examinations, (b) a categorical question to record the estimated number of hours spent on the Internet per day, and (c) the English version of the IAT. All data were analyzed in SPSS v. 20. Principal axis factor analysis was used to validate the factor structure of the IAT in our study sample. An alpha coefficient > .7 was sought in the reliability analysis. Histograms and the values of skewness and kurtosis were analyzed for floor and ceiling effects. In addition, readability of the IAT was assessed as the Flesch Reading Ease score and Flesch-Kincaid Grade level function. Results: A total of 522 medical and dental students participated in the survey. Most respondents were female medical students enrolled in preclinical years of their degree program. Median age (min-max) of the respondents was 20 years (17-25 years). A single-factor model for IAT score explained 33.71% of the variance, with a high alpha coefficient of .893. In addition, the IAT had good face and convergent validity and no floor and ceiling effects, and was judged easy to read by participants. Conclusion: The English version of the IAT showed good psychometric properties in a sample of Pakistani university students. A single-factor model for assessing internet addiction showed good reliability and was found suitable with our study sample.
The relationship between vegetation coverage and climate elements in Yellow River Basin, China
Authors: Nie Qin , Xu Jianhua
Published: January 2018

The paper examined the vegetation coverage dynamic and its response to climate elements in Yellow River Basin from 1998 to 2008 by an integrated approach made from series methods including correlation analysis, wavelet analysis, and wavelet regression analysis. The main findings are as follows: (1) Vegetation coverage exhibited significant, positive correlation with temperature and precipitation, but negative correlation with sunshine hours and relative humidity at some sites. The correlation between NDVI and precipitation is closest, followed respectively by temperature, relative humidity, and sunshine hours. Precipitation and temperature are the two major climate elements affecting vegetation coverage dynamics. (2) The vegetation coverage dynamics reflected by NDVI time series presented nonlinear variations that depended on the time-scale. Precipitation and temperature both presented nonlinear variations that were morphologically similar with those of NDVI. These further supported the close relationship between NDVI and these two climate elements from a new perspective. (3) Although NDVI, temperature, and precipitation revealed nonlinear variations at different time scales, the vegetation coverage showed a significantly, positively linear correlation with temperature and precipitation at all the time scales under examination.
The effect of the dispersal kernel on isolation-by-distance in a continuous population
Authors: Furstenau Tara N , Cartwright Reed A
Published: January 2018

Under models of isolation-by-distance, population structure is determined by the probability of identity-by-descent between pairs of genes according to the geographic distance between them. Well established analytical results indicate that the relationship between geographical and genetic distance depends mostly on the neighborhood size of the population, \(N_b = 4\pi\sigma^2 D_e\), which represents a standardized measure of gene flow. To test this prediction, we model local dispersal of haploid individuals on a two-dimensional torus using seven dispersal kernels: Rayleigh, Exponential, Half-normal, Triangular, Gamma, Lomax and Pareto. When neighborhood size is held constant, the distributions produce similar patterns of isolation-by-distance, confirming predictions. Considering this, we propose that the triangular distribution is the appropriate null distribution for isolation-by-distance studies. Under the triangular distribution, dispersal is uniform within an area of \(4\pi\sigma^2\) (i.e. the neighborhood area), which suggests that the common description of neighborhood size as a measure of a local panmictic population is valid for popular families of dispersal distributions. We further show how to draw from the triangular distribution efficiently and argue that it should be utilized in other studies in which computational efficiency is important.
Spectroscopic studies on Permian plant fossils in the Pedra de Fogo Formation from the Parnaíba Basin, Brazil
Authors: Conceição Domingas , da Silva João , Cisneros Juan , Iannuzzi Roberto , Viana Bartolomeu C , Saraiva Gilberto , Sousa Joel , Freire Paulo T
Published: January 2018

The “Pedra de Fogo” Formation dated from the Permian period (approximately 280 million years ago), belongs to the sedimentary Parnaiba Basin, located in the northeastern region of Brazil. It is recognized by their well preserved fossil contents and it is notable for having several fossilized trunks in the growing position. Specimens from different localities were selected in order to perform spectroscopic studies and X-ray diffraction analysis, as well, for the purpose of identifying and characterizing compounds related to the fossilized materials. These different techniques allowed to obtain information from the molecular spectra in organic and inorganic substances, which are present in these above stated fossils and in the atomic elements, as well as the crystalline phases. These aforementioned studies have revealed promising paleoenvironmental interpretations about their depositional strata. Regarding the techniques, these have enabled inferences with respect to the fossil diagenetic events and allowed a better understanding of the fossilized process and the mineralogical characteristics of the living environment, where the plants were buried. This study presents physical and/or chemical properties of the fossilized plants through vibrational spectroscopies, SEM/EDS spectroscopy and X-ray diffraction techniques. Based on the results duly obtained, we were able to identify the presence of silica and confirm that the dominant process of the fossilized specimens investigated has occurred through quartz silicification with the contribution of persistence from amorphous carbon.
Realities of rarity: climatically and ecologically restricted, critically endangered Kandian Torrent Toads (Adenomus kandianus) breed en masse
Authors: Meegaskumbura Madhava , Wijayathilaka Nayana , Abayalath Nirodha , Senevirathne Gayani
Published: January 2018

Endemic to Sri Lanka, genus Adenomus contains two torrent-associated toad species whose ecology and natural history in the wild is virtually unknown. Adenomus kelaartii is relatively common, with a wide geographic distribution. Its sister species, A. kandianus, however, is restricted to two isolated populations in fast-disappearing montane and sub-montane forests. Formally declared extinct after not being recorded for over a century, a few A. kandianus were rediscovered in 2012 and redescribed as "the world's rarest toad". Here we report the results of a two-year study of the occurrence, habits and habitat associations of adult and larval A. kandianus using both general surveys and quadrat sampling. We show this to be a secretive species with a patchy distribution. Non-breeding female toads dwell in primary-forest habitats, but after heavy and sudden downpours they form large mating congregations in large streams. Amplexed pairs swim synchronously, enabling them to traverse fast currents. Egg-laying sites remain unknown, but the ability to dive and vocalize underwater, and characteristics of the eggs, suggest that they lay eggs in dark recesses of the stream. Tadpoles show microhabitat partitioning within the stream, with the greatest diversity of stages in slow-flowing rocky areas. The more robust stages possessing sucker discs exploit rocky-rapids, while metamorphic stages inhabit stream margins. We use DNA-barcoding to show the existence of two disparate toad populations. Distribution modeling with forest-cover layers added, predict a very small remaining area of suitable habitats. Conservation of this climatically and ecologically restricted species hinge largely on the preservation of high-elevation primary and riparian forests and unpolluted torrents.
A robust hierarchical model of daily stream temperature using air-water temperature synchronization, autocorrelation, and time lags
Authors: Letcher Benjamin H , Hocking Daniel J , O'Neill Kyle , Whiteley Andrew R , Nislow Keith H , O'Donnell Matthew J
Published: January 2018

Water temperature is a primary driver of stream ecosystems and commonly forms the basis of stream classifications. Robust models of stream temperature are critical as the climate changes, but estimating daily stream temperature poses several important challenges. We developed a statistical model that accounts for many challenges that can make stream temperature estimation difficult. Our model identifies the yearly period when air and water temperature are synchronized, accommodates hysteresis, incorporates time lags, deals with missing data and autocorrelation and can include external drivers. In a small stream network, the model performed well (RMSE = 0.59 °C), identified a clear warming trend (0.063 °C · y-1) and a widening of the synchronized period (2.9 d · y-1). We also carefully evaluated how missing data influenced predictions. Missing data within a year had a small effect on performance (~ 0.05% average drop in RMSE with 10% fewer days with data). Missing all data for a year decreased performance (~ 0.6 °C jump in RMSE), but this decrease was moderated when data were available from other streams in the network. Straightforward incorporation of external drivers (e.g. land cover, basin size) should allow this modeling framework to be readily applied across multiple sites and at multiple spatial scales.
Hawksbill x loggerhead sea turtle hybrids at Bahia, Brazil: where do their offspring go?
Authors: Proietti Maira C , Reisser Julia , Marins Luis F. , Marcovaldi Maria A. , Soares Luciano S , Monteiro Danielle , Wijeratne Sarath E.M. , Pattiaratchi Charitha , Secchi Eduardo R.
Published: January 2018

Hybridization between hawksbill (Eretmochelys imbricata) and loggerhead (Caretta caretta) breeding groups is unusually common in Bahia state, Brazil. Such hybridization is possible because hawksbill and loggerhead nesting activities overlap temporally and spatially along the coast of this state. Nevertheless, the destinations of their offspring are not yet known. This study is the first to identify immature hawksbill x loggerhead hybrids (n = 4) from this rookery by analyzing the mitochondrial DNA (mtDNA) of 157 immature turtles morphologically identified as hawksbills. We also compare for the first time modeled dispersal patterns of hawksbill, loggerhead, and hybrid offspring considering hatching season and oceanic phase duration of turtles. Particle movements varied according to season, with a higher proportion of particles dispersing southwards throughout loggerhead and hybrid hatching seasons, and northwards during hawksbill season. Hybrids from Bahia were not present in important hawksbill feeding grounds of Brazil, being detected only at areas more common for loggerheads. The genetic and oceanographic findings of this work indicate that these immature hybrids, which are morphologically similar to hawksbills, could be adopting behavioral traits typical of loggerheads, such as feeding in temperate waters of the western South Atlantic. Understanding the distribution, ecology, and migrations of these hybrids is essential for the development of adequate conservation and management plans.
Comparing the fluctuations of the intrinsically disordered C-terminal domain of human SELK free in water and in lipid membrane
Authors: Polo Andrea , Guariniello Stefano , Colonna Giovanni , Ciliberto Gennaro , Costantini Susan
Published: January 2018

SELK is a single-pass trans-membrane protein that resides in the endoplasmic reticulum membrane (ER) with a C-terminal domain exposed to the cytoplasm that is known to interact with different components of the endoplasmic reticulum associated to the protein degradation (ERAD) pathway. This protein is resulted to be up-expressed in hepatocellular carcinoma and in other cancers, therefore there is a need to analyze its structure-function relationships. In this work we performed a detailed analysis of the C-terminal domain sequence of SELK, modeled its three-dimensional structure and analyzed its conformational changes by Molecular Dynamics simulations. Our analysis showed that the C-terminal domain of SELK is a weak polyelectrolyte and specifically, a polycation, which has the characteristic molecular signature of natively disordered segments. Since the search by BLAST has not evidenced possible templates with an acceptable sequence identity percentage with the C-terminal sequence of SELK, its three-dimensional structure was modeled by ab initio modeling. The best model is characterized by one short helix and the most part of residues with no regular secondary structure elements. This model was subjected to MD simulation at neutral pH in water to assess the stability of the modelled structural organization free in solution. To deepen the structural analysis of the C terminal domain, we have also studied the organization of the whole protein inserted into the membrane by a procedure of comparative modeling between fold recognition and folding ab initio. Then, the complete structure of SELK was subjected to MD simulations in the lipid bilayer and a water box. Analyzing the MD trajectories, we found that the C-terminal domain of SELK is still highly mobile during the simulation in water-lipid bilayer by showing a decrease of the structural compactness, a lesser number of H-bonds, as well as a higher value of the total void volume and of the total solvent accessible area compared to the simulation in only water system. However, in both the simulations this region is stabilized mainly by a marked number of H-bonds, and pi-cation and IAC interactions, which suggest a globule organization very different from the classic globular one. Furthermore, water-protein interaction data suggest, as for other IDPs, that the hydration water tends to cluster around the protein facilitating its organization to globule.
The (mis)measurement of the Dark Triad Dirty Dozen: Exploitation at the core of the scale
Authors: Kajonius Petri J , Persson Björn N , Rosenberg Patricia , Garcia Danilo
Published: January 2018

Background: The dark side of human character has been conceptualized in the Dark Triad Model: Machiavellianism, psychopathy, and narcissism. These three dark traits are often measured using single long instruments for each one of the traits. Nevertheless, there is a necessity of short and valid personality measures in psychological research. As an independent research group, we replicated the factor structure, convergent validity and item response for one of the most recent and widely used short measures to operationalize these malevolent traits, namely, Jonason’s Dark Triad Dirty Dozen. We aimed to expand the understanding of what the Dirty Dozen really captures because the mixed results on construct validity in previous research. Method: We used the largest sample to date to respond to the Dirty Dozen (N = 3,698). We firstly investigated the Dirty Dozen’s factor structure using Confirmatory Factor Analysis. Secondly, using sub-sample (n = 500) and correlation analyses, we investigated the Dirty Dozen dark traits convergent validity to Machiavellianism measured by the Mach-IV, psychopathy measured by Eysenck’s Personality Questionnaire Revised, narcissisms using the Narcissism Personality Inventory, and both neuroticism and extraversion from the Eysenck’s questionnaire. Finally, besides these Classic Test Theory analyses, we analyzed the responses for each Dirty Dozen item using Item Response Theory (IRT). Results: The results confirmed previous findings of a bi-factor model fit: one latent core dark trait, plus the three dark traits. An additional exploratory distribution analysis showed that all three Dirty Dozen traits had a striking bi-modal distribution, which might indicate unconcealed social undesirability with the items. The three Dirty Dozen traits did converge to, although not strongly, with the contiguous single Dark Triad scales (r between .41-.49). The probabilities of filling out steps on the Dirty Dozen narcissism-items were much higher than on the Dirty Dozen items for Machiavellianism and psychopathy. Overall, the Dirty Dozen instrument delivered the most predictive value with persons with average and high Dark Triad traits (Theta > -0.5). Moreover, the Dirty Dozen scale was better conceptualized as measured of a combined Machiavellianism-psychopathy factor, not narcissism, that can be replaced with item 4: ‘I tend to exploit others towards my own end’. Conclusion: The Dirty Dozen showed a consistent factor structure, a relatively convergent validity similar to that found in earlier studies. Narcissism measured using the Dirty Dozen, however, did not contribute with information to the core constitution of the Dirty Dozen construct. More importantly, the results imply a Single Item Dirty Dark Triad (SIDDT) measure of a manipulative and anti-social core as the content of the Dirty Dozen scale.
Microbiological activity and carbon mineralization in pampean soils with different agricultural use intensity
Authors: Castro-Huerta Ricardo A , Momo Fernando R , Falco Liliana B , Di Ciocco César A , Coviella Carlos E
Published: January 2018

The processes involved in the flows of matter and energy of terrestrial ecosystems depends heavily on soil biological activity, the current conventional agricultural managements could alter the biological mechanisms involved in decomposition and nutrient cycling in agroecosystems. The aim of this study was to compare the activity levels and soil microbial biomass between different agricultural pampean soil uses and its relationship to carbon mineralization. 25 years of agricultural use were compared with 25 years of ecological reserve naturalized where each agroecosystem soil were collected at 61 - 125 - 183 - 236 - 302 - 368 - 431 - 488 days for measuring their moisture, organic matter, enzymatic activity, microbial biomass carbon, soil respiration, metabolic quotient, microbial quotient and carbon mineralization rate. The distance between agroecosystems is less than 800 m, thus assuming the same soil and climatic conditions. The data were evaluated by Friedman test finding significant differences in moisture, organic matter, enzymatic activity, soil respiration y microbial quotient (p< 0.01). Difference was also found in the microbial mineralization rate of carbon (p< 0.1).
Diagnosing the dangerous demography of manta rays using life history theory
Authors: Dulvy Nicholas K , Pardo Sebastián A. , Simpfendorfer Colin A. , Carlson John K.
Published: January 2018

The directed harvest and global trade in the gill plates of mantas, and other mobulid rays, has led to increased fishing pressure and steep population declines in some locations. The slow life history, particularly of the manta rays, is cited as a key reason why such species have little capacity to withstand directed fisheries. Here, we place their life history and demography in the context of other sharks and rays. Despite the limited availability of data, we use life history theory and comparative analysis to develop plausible ranges of somatic growth rate, annual pup production and age at maturity to estimate risk of extinction (maximum intrinsic rate of population increase rmax) using a variant of the classic Euler-Lotka model. Manta ray rmax is most sensitive to the length of the reproductive cycle, and the median rmax of 0.11 year-1(CI: 0.089-0.137) is one of the lowest known of the 106 sharks and rays for which we have comparable demographic information. In common with other unprotected, unmanaged, high-value large-bodied species with low or very low productivity, manta rays are unlikely to sustain unmonitored, unregulated exploitation and may face increasing local and regional extinction risk.
DNA barcode data accurately identify higher taxa
Authors: Coddington Jonathan A , Agnarsson Ingi , Cheng Ren-Chung , Čandek Klemen , Driskell Amy , Frick Holger , Gregorič Matjaž , Kostanjšek Rok , Kropf Christian , Kweskin Matthew , Lokovšek Tjaša , Pipan Miha , Vidergar Nina , Kuntner Matjaž
Published: January 2018

The use of unique DNA sequences as a method for taxonomic identification is no longer fundamentally controversial, even though debate continues on the best markers, methods, and technology to use. Although both existing databanks such as GenBank and BOLD, as well as reference taxonomies, are imperfect, in best case scenarios “barcodes” (whether single or multiple, organelle or nuclear, loci) clearly are an increasingly fast and inexpensive method of identification, especially as compared to manual identification of unknowns by increasingly rare expert taxonomists. Because most species on Earth are undescribed, a complete reference database at the species level is impractical in the near term. The question therefore arises whether unidentified species can, using DNA barcodes, be accurately assigned to more inclusive groups such as genera and families—taxonomic ranks of putatively monophyletic groups for which the global inventory is more complete and stable. We used a carefully chosen test library of CO1 sequences from 49 families, 313 genera, and 816 species of spiders to assess the accuracy of genus and family-level identifications. We used BLAST queries of each sequence against the entire library and got the top ten hits resulting in 8160 hits. The percent sequence identity was reported from these hits (PIdent, range 75-100%). Accurate identification (PIdent above which errors totaled less than 5%) occurred for genera at PIdent values > 95 and families at PIdent values ≥ 91, suggesting these as heuristic thresholds for generic and familial identifications in spiders. Accuracy of identification increases with numbers of species/genus and genera/family in the library; above five genera per family and fifteen species per genus all identifications were correct. We propose that using percent sequence identity between conventional barcode sequences may be a feasible and reasonably accurate method to identify animals to family/genus. However, the quality of the underlying database impacts accuracy of results; many outliers in our dataset could be attributed to taxonomic and/or sequencing errors in BOLD and GenBank. It seems that an accurate and complete reference library of families and genera of life could provide accurate higher level taxonomic identifications cheaply and accessibly, within years rather than decades.
Unraveling zucchini transcriptome response to aphids
Authors: Vitiello Alessia , Scarano Daria , D'Agostino Nunzio , Digilio Maria Cristina , Pennacchio Francesco , Corrado Giandomenico , Rao Rosa
Published: January 2018

Cucurbita pepo belongs to the Cucurbitaceae, the second-most large horticultural family of economic importance after Solanaceae. One major issue related to zucchini cultivation is the damage caused by aphids such as Aphis gossypii (Homoptera: Aphididae). The aim of this study is the identification of candidate genes involved in zucchini plant response to A. gossypii. In order to monitor the effect of zucchini-aphid interaction at transcriptomic level, zucchini plants (cv “San Pasquale”) were grown in controlled conditions in presence or absence of A. gossypii. Leaf material was collected at 24, 48 and 96 hours after aphid infestation. RNA extracted was sequenced using the Illumina HiSeq 2500 platform. The sequencing generated ~34 million of paired-end reads of 100 nucleotides in length per sample. High quality reads were de novo assembled into 71,648 transcripts. About 94% of the assembled transcripts contain coding sequences that could be translated into proteins. Over 60% of the transcripts were functionally annotated and assigned to one or more InterPro domains and Gene Ontology terms. A subset of 42,517 sequences of the C. pepo transcriptome was used for read mapping and differentially expressed genes (DEG) identification. Largest number of DEG were observed after 48 hours from aphid infestation. The transcriptome represents a high-quality reference for read alignment and DEG call. The understanding of the molecular response of infested plants will be essential to develop new tools for A. gossypii control.
Relationships between taxonomic and functional diversity: insights into assembly processes
Authors: Stagnol Doriane , Bacouillard Lise , Davoult Dominique
Published: January 2018

Among the potential indicators of biodiversity, those based on the functional traits of species are interesting because they measure the aspects of diversity that potentially affect community assembly and function. However, trait-based approaches are still rarely considered and little is known about the degree to which taxonomic diversity (TD) and functional diversity (FD) are correlated. Yet, this relationship is thought to depend on the extent of ecological redundancy within the assemblage, i.e. the number of taxonomically distinct species that exhibit similar ecological functions. In this study, we characterized taxonomic and functional diversity within and between two marine habitats (rocky shore vs mudflats) under human-induced disturbances. Models were also used to test whether the relationship between TD and FD differed according to the indices used to characterize them. We found little effect of human disturbance on the shape of the TD-FD relationship, whereas communities of the mudflat appeared to be less redundant than those of rocky shore. This could be explained by the assembly rules of ecosystems: biotic filtering (competition and resource partitioning) reduces redundancy by selecting for functionally dissimilar species, whereas abiotic filtering increases redundancy by selecting for similar species sharing adaptations to a particular environment. The rocky shore environment is characterized by heterogeneity that allows the formation of distinct ecological niches that can be colonized by similar species: the abiotic filtering does not limit the redundancy permitted by habitat. Conversely, in the more homogeneous environment of mudflat, the biotic filter mitigates redundancy. Trait-mediated abiotic filtering appears to play an important role in community assembly in complex habitats, whereas the relative importance of competitive exclusion appears to be greater in homogeneous habitats.
Association between neurological soft signs, temperament and character in patients with schizophrenia and non-psychotic relatives
Authors: Galindo Liliana , Pastoriza Francisco , Bergé Daniel , Mané Anna , Picado Marisol , Bulbena Antonio , Robledo Patricia , Pérez Victor , Vilarroya Oscar , Cloninger Claude Robert
Published: January 2018

The heritability of schizophrenia and most personality traits has been well established, but the role of personality in susceptibility to schizophrenia remains uncertain. The aim of this study was to test for an association between personality traits and Neurological Soft Signs (NSS), a well-known biological marker of schizophrenia, in non-psychotic relatives of patients with schizophrenia. For this purpose, we evaluated the NSS scale and personality measured by the Temperament and Character inventory (TCI-R) in three groups of subjects: 29 patients with schizophrenia, 24 unaffected relatives and 37 controls. The results showed that patients with schizophrenia were more asocial (higher harm avoidance and lower reward dependence), more perseverative (higher persistence), and more schizotypal (lower self-directedness and cooperativeness, higher self-transcendence). The unaffected relatives showed higher harm avoidance, lower self-directedness and cooperativeness than the healthy controls. Higher NSS scores and sub-scores were found in patients and non-psychotic relatives compared with the controls. Among all the patients, total NSS scores were positively correlated with harm avoidance but negatively correlated with novelty seeking and persistence. Total NSS were also correlated with low scores on self-directedness and cooperativeness, which are indicators of personality disorder. Our results show that susceptibility to NSS and to schizophrenia are both related to individual differences in the temperament and character features in non-psychotic relatives of patients with schizophrenia. High harm avoidance, low persistence, low self-directedness and low cooperativeness contribute to both the risk of NSS and schizophrenia. These findings highlight the value of using both assessments to study high risk populations.
DNA barcoding and taxonomy: dark taxa and dark texts
Authors: Page Roderic D M
Published: January 2018

Both classical taxonomy and DNA barcoding are engaged in the task of digitising the living world. Much of the taxonomic literature remains undigitised. The rise of open access publishing this century, and the freeing of older literature from the shackles of copyright has greatly increased the online availability of taxonomic descriptions, but much of the literature of the mid- to late twentieth century remains oﬄine ("dark texts"). DNA barcoding is generating a wealth of computable data that in many ways is much easier to work with than classical taxonomic descriptions, but many of the sequences are not identiﬁed to species level. These "dark taxa" hamper the classical method of integrating biodiversity data using shared taxonomic names. Voucher specimens are a potential common currency of both the taxonomic literature and sequence databases, and could be used to help link names, literature, and sequences. An obstacle to this approach is the lack of stable, resolvable specimen identiﬁers. The paper concludes with an appeal for a global "digital dashboard" to assess the extent to which biodiversity data is available online.
Preliminary characterization of little brown bats (Myotis lucifugus) immune MHC II DRB alleles using next-generation sequencing
Authors: Palmer Jonathan M. , Berkman Leah K. , Marquardt Paula E , Donner Deahn M. , Jusino Michelle A. , Lindner Daniel L.
Published: January 2018

Genes of the major histocompatibility complex (MHC) are of great interest to molecular ecologists due to their role in the immune response and the complex evolutionary mechanisms affecting their abundance and distribution. Next generation sequencing (NGS) offers the best potential for characterizing such genes by overcoming the low throughput constraints associated with traditional cloning and Sanger sequencing. However, available bioinformatics methods to effectively filter MHC data acquired through NGS are complex and have not been widely applied. Here we present a method to sequence MHC II DRB of the little brown bat (Myotis lucifugus) using semi-conductor sequencing on the Ion Torrent Personal Genome Machine (PGM) and subsequently analyze the data using a modified UPARSE clustering algorithm. As proof of concept, preliminary characterization of the MHC II DRB alleles of 15 little brown bats was accomplished through PGM sequencing. Analysis identified 24 MHC II DRB alleles overall and a high number of alleles per individual (average 6.8 ± 3.5, range 1 – 12), indicating little brown bats may have among the highest number of MHC DRB loci documented in mammals. Our method provides a framework for studying MHC II DRB diversity in little brown bats, which are experiencing significant population declines in North America due to the recent emergence of white-nose syndrome (WNS).
Apparent source levels and active communication space of whistles of free-ranging Indo-Pacific humpback dolphins (Sousa chinensis) in the Pearl River Estuary and Beibu Gulf, China
Authors: Wang Zhi-Tao , Au Whitlow , Rendell Luke , Wang Ke-Xiong , Wu Hai-Ping , Wu Yu-Ping , Liu Jian-Chang , Duan Guo-Qin , Cao Han-Jiang , Wang Ding
Published: January 2018

Background. Knowledge of species-specific vocalization characteristics and their associated active communication space, the effective range over which a communication signal can be detected by a conspecific, is critical for understanding the impacts of underwater acoustic pollution, as well as other threats. Methods. We used a two-dimensional cross-shaped hydrophone array system to record the whistles of free-ranging Indo-Pacific humpback dolphins (Sousa chinensis) in shallow-water environments of the Pearl River Estuary (PRE) and Beibu Gulf (BG), China. Using hyperbolic position fixing, which exploits time differences of arrival of a signal between pairs of hydrophone receivers, we obtained source location estimates for whistles with good signal-to-noise ratio (SNR≥10 dB) and not polluted by other sounds and back-calculated their apparent source levels. Combining with the masking levels (including simultaneous noise levels, masking tonal threshold, and the Sousa auditory threshold) and the custom made site-specific sound propagation models, we further estimated their active communication space (ACS). Results. Humpback dolphins produced whistles with average root-mean-square apparent source levels (ASL) of 138.5 ± 6.8 (mean ± standard deviation) and 137.2 ± 7.0 dB re 1μPa in PRE (N=33) and BG (N=209), respectively. We found statistically significant differences in ASLs among different whistle contour types. The mean and maximum ACS of whistles were estimated to be 14.7 ± 2.6 (median ± quartiledeviation) and 17.1± 3.5 m in PRE, and 34.2 ± 9.5 and 43.5 ± 12.2 m in BG. Using just the auditory threshold as the masking level produced the mean and maximum ACSat of 24.3 ± 4.8 and 35.7± 4.6 m for PRE, and 60.7 ± 18.1 and 74.3 ± 25.3 m for BG. The small ACSs were due to the high ambient noise level. Significant differences in ACSs were also observed among different whistle contour types. Discussion. Besides shedding some light for evaluating appropriate noise exposure levels and information for the regulation of underwater acoustic pollution, these baseline data can also be used for aiding the passive acoustic monitoring of dolphin populations, defining the boundaries of separate groups in a more biologically meaningful way during field surveys, and guiding the appropriate approach distance for local dolphin-watching boats and research boat during focal group following.
Experimental evidence that habitat-specific chemical cues influence fish preference patterns
Authors: Martin Charles W
Published: January 2018

Vegetated habitats provide numerous benefits to nekton, including structural refuge from predators and food sources. However, the sensory mechanisms by which fishes locate these habitats remain unclear for many species, especially when environmental conditions (such as increased turbidity) are unfavorable for visual identification of habitats. Here, a series of laboratory experiments test whether three species of adult fish (golden topminnow Fundulus chrysotus Günther 1866, sailfin molly Poecilia latipinna Lesueur 1821, and western mosquitofish Gambusia affinis Baird and Girard 1853) use plant chemical cues to orient to one of two habitats (hydrilla Hydrilla verticillata (L.f.) Royle or water hyacinth Eichhornia crassipes (Mart.) Solms). First, experiments in aquaria were conducted offering fish a choice of the two habitats to determine preference patterns. Next, a two-channel flume, with each side containing flow originating in one of the two habitats, was used to determine if preferences were still exhibited when fish could only detect habitats through olfactory means. While patterns among the three fish species tested here were variable, results did indicate consistent habitat preferences despite the lack of cues other than olfactory, suggesting that these organisms are capable of discriminating habitats via chemical exudates from plants. As such, olfactory mechanisms likely provide vital information about the surrounding environment and future work should be directed at determining how anthropogenic inputs such as eutrophication and sediment runoff affect the physiology of these sensory capabilities.
Probabilistic programming in Python using PyMC3
Authors: Salvatier John , Wiecki Thomas V , Fonnesbeck Christopher
Published: January 2018

Probabilistic Programming allows for automatic Bayesian inference on user-defined probabilistic models. Recent advances in Markov chain Monte Carlo (MCMC) sampling allow inference on increasingly complex models. This class of MCMC, known as Hamliltonian Monte Carlo, requires gradient information which is often not readily available. PyMC3 is a new open source Probabilistic Programming framework written in Python that uses Theano to compute gradients via automatic differentiation as well as compile probabilistic programs on-the-fly to C for increased speed. Contrary to other Probabilistic Programming languages, PyMC3 allows model specification directly in Python code. The lack of a domain specific language allows for great flexibility and direct interaction with the model. This paper is a tutorial-style introduction to this software package.
Similarity to a single set
Authors: Naish Lee
Published: January 2018

Identifying patterns and associations in data is fundamental to discovery in science. This work investigates a very simple instance of the problem, where each data point consists of a vector of binary attributes, and attributes are treated equally. For example, each data point may correspond to a person and the attributes may be their sex, whether they smoke cigarettes, whether they have been diagnosed with lung cancer, etc. Measuring similarity of attributes in the data is equivalent to measuring similarity of sets - an attribute can be mapped to the set of data points which have the attribute. Furthermore, there is one identified base set (or attribute) and only similarity to that set is considered - the other sets are just ranked according to how similar they are to the base set. For example, if the base set is lung cancer sufferers, the set of smokers may well be high in the ranking. Identifying set similarity or correlation has many uses and is often the first step in determining causality. Set similarity is also the basis for comparing binary classifiers such as diagnostic tests for any data set. More than a hundred set similarity measures have been proposed in the literature is but there is very little understanding of how best to choose a similarity measure for a given domain. This work discusses numerous properties that similarity measures can have, weakening some previously proposed definitions so they are no longer incompatible, and identifying important forms of symmetry which have not previously been considered. It defines ordering relations over similarity measures and shows how some properties of a domain can be used to help choose a similarity measure which will perform well for that domain.