bluuebunny/crossref_metadata_2025 huggingface dataset:
What are the possible determinants of urinary incontinence during pregnancy? Results of a pilot study
Authors: Demircan Nejat , Özmen Ülkü , Köktürk Fürüzan , Küçük Hamdi , Ata Şevket , Harma Müge , Arıkan İnan İlker
Published: January 2018

Objectives: This study was conducted to determine the frequency, predisposing factors and impact of urinary incontinence (UI)during pregnancyon quality of life (QOL). Materials and Method: A preliminary cross-sectional survey was carried out among pregnant women from January to June of 2014. A total of 132 pregnant women were enrolled. We used a questionnaire form for sociodemographic features, ICIQ-SF-Turkish version to determine the occurrence and characteristics of UI and Wagner’s Quality of Life scale to assess impact on QOL. Results: Urinary incontinence was present in 56 out of 132 pregnant women (42.4%); these women were referred to as the UI-present group. The remaining 76 women comprised the UI-absent group. The overall mean age was 27.5 ± 5.1 y (p=0.780), median height in UI-present group was 160 cm (min-max: 153-176, p=0.037 <0.05) and median BMI was 28.7 kg/m2(min-max: 22.4-50.0, p=0.881).For women in the UI-present group, urine leakage occurred once a week (n=18, 32.1%) to twice or thrice a week (n=8, 14.3%), few times a day (n=14, 25%), once a day (n=5, 8.9%) and always (n=8, 14.3%). The pregnant women in the UI-present group mainly reported a small amount of urine leakage (n=33, 58.9%) or a moderate amount of leakage (n=4, 7.1%). There were statistically significant relationships between QOL scores and frequency of UI (p=0.002 <0.05) as well as the amount of leakage (p=0.002 <0.05). Impact on QOL scores ranged from mild (n=33, 58.9%) or moderate (n=4, 7.1%) to severe (n=4, 7.1%) levels. QOL has ‘mildly deteriorated’. The following features were found to favour the onset of UI: age of pregnant woman (OR= 0.845, 95% CI 0.268-2.669), occupational status (OR=1.800, 95% CI 0.850-3.810), anaemia (OR=0.939, 95% CI 0.464-1.901), parity (OR=0.519, 95% CI 0.325-0.829), miscarriage in previous pregnancies (OR=1.219, 95% CI 0.588-2.825) and living in rural vs urban settlement (OR=1.800, 95% CI 0.887-3.653).Heigt (p= 0,037<0.05), educational status (p=0.016 <0.05), miscarriage, parity and place of living (p=0.002, p=0.006, p=0.020 <0.05 respectively)were significant in favour of UI-present. Conclusions: Urinary incontinence was frequently encountered among pregnant women (42.1%). Urinary incontinence distorted the QOL in pregnant women at a mild level and caused life style changes. Frequency and amount of UI were the significant factors in deterioration. Age, parity, miscarriage, being housewife, place of living (rural) and anaemia were the factors in favour of onset of UI during pregnancy. Among them, height, educational status (primary-intermediate school graduate), place of living (rural), miscarriage and parity were statistically significant predictors. It is necessary to pay attention to UI and its impact on women’s health during pregnancy.
Multifarious native plant growth promoting fluorescent pseudomonads associated with rhizosphere of Aloe barbadensis miller
Authors: Rai Anuradha , Rai Pradeep K , Singh Jay S , Singh Surendra
Published: January 2018

Medicinal plants provide an enormous bioresource of potential use in modern medicine and agriculture. Phosphorous deficiency is a major constraint to plant production. Sustainable agriculture could be promoted by harnessing the plant beneficial bacteria particularly the fluorescent pseudomonads associated with the rhizosphere of plants, to mobilize soil inorganic phosphate and also to increase its bioavailability to the plants. Total five hundred seven fluorescent Pseudomonas isolates were obtained from four different Aloe barbadensis (Miller) growing locations of Varanasi. These Pseudomonas strains were further evaluated in vitro for their ability to solubilize phosphate and to produce indole acetic acid (IAA), hydrogen cyanide (HCN), siderophore and aminocyclopropane (ACC) deaminase. Total 119 fluorescent Pseudomonas isolates from the rhizospheric soil (RS) and 25 isolates from the endorhizosperic (ER) region solubilized phosphate.Whereas 53 (36.8%) Pseudomonas isolates produced IAA and siderophore, 36(25%) and 31 (21.5%) isolates, however, produced HCN and ACC deaminase. Out of 119 phosphate solubilizing bacteria (PSB) from RS region, 51 (42.9%) isolates and 9 (36%) isolates out of 25 PSBs from ER region lacked plant growth promoting traits (PGPTs). Among the phosphate solubilizing fluorescent pseudomonads showing PGPT, 59 isolates have multiple traits and showed more than two types of PGPT. A positive correlation exists between siderophore and ACC deaminase producers. Clustering by principal component analysis (PCA) showed that RS was the most important factor influencing the ecological distribution and physiological characterization of PGPT- possessing PSB. Geographical Information System (GIS) and Kriging Interpolation method was used to map and establish spatial variation of soil properties of the study site.
Deep learning for constructing microblog behavior representation to identify social media user's personality
Authors: Liu Xiaoqian , Zhu Tingshao
Published: January 2018

Due to the rapid development of information technology, Internet has become part of everyday life gradually. People would like to communicate with friends to share their opinions on social networks. The diverse social network behavior is an ideal users' personality traits reflection. Existing behavior analysis methods for personality prediction mostly extract behavior attributes with heuristic. Although they work fairly well, but it is hard to extend and maintain. In this paper, for personality prediction, we utilize deep learning algorithm to build feature learning model, which could unsupervised extract Linguistic Representation Feature Vector (LRFV) from text published on Sina Micro-blog actively. Compared with other feature extraction methods, LRFV, as an abstract representation of Micro-blog content, could describe use's semantic information more objectively and comprehensively. In the experiments, the personality prediction model is built using linear regression algorithm, and different attributes obtained through different feature extraction methods are taken as input of prediction model respectively. The results show that LRFV performs more excellently in micro-blog behavior description and improve the performance of personality prediction model.
Climate, topography and soil factors interact to drive community trait distributions in global drylands
Authors: Le Bagousse-Pinguet Yoann , Liancourt Pierre , Gross Nicolas , de Bello Francesco , Fonseca Carlos Roberto Carlos , Kattge Jens , Valencia Enrique , Leps Jan , Maestre Fernando T.
Published: January 2018

The skewness and kurtosis of community trait distributions (CTDs) can provide important insights on the mechanisms driving community assembly and species coexistence. However, they have not been considered yet when describing global patterns in CTDs. We aimed to do so by evaluating how environmental variables (mean annual temperature [MAT] and precipitation [MAP], precipitation seasonality [PS], slope angle and sand content) and their interactions affected the mean, variance, skewness, kurtosis of the plant CTDs in global drylands. We gathered specific leaf area and maximum plant height data from 130 dryland communities from all continents except Antarctica. Over 90% of the studied communities had skewed CTDs for SLA and height or had kurtosis values differing from those of normal distributions. Higher MAT and/or lower MAP led to a shift toward plant communities over-represented by “conservative” strategies, and a decrease in functional diversity. However, considering interactions among environmental drivers increased the explanatory power of our models by 20%. Sand content strongly altered the responses of height to changes in MAT and MAP (climate × topo-edaphic interactions). Increasing PS reversed the effects of MAT and MAP (climate × climate interactions) on the four moments of CTDs for SLA, particularly in dry-subhumid regions. Our results indicate that the increase in PS forecasted by climate change models will reduce the functional diversity of dry-subhumid communities. They also indicate that ignoring interactions among environmental drivers can lead to misleading conclusions when evaluating global patterns in CTDs, and thus may dramatically undermine our ability to predict the impact of global environmental change on plant communities and associated ecosystem functioning.
Longevity and personality in captive chimpanzees (Pan troglodytes)
Authors: Altschul Drew M , King James E , Inoue-Murayama Miho , Ross Stephen R , Weiss Alexander
Published: January 2018

Over the past 20 years, the study of personality has blossomed within primatology. Rating inventories have been extensively used across species to identify personality factor structures for different species. Chimpanzees share a common six-factor structure, composed of Dominance, Extraversion, Agreeableness, Conscientiousness, Neuroticism, and Openness. Conscientiousness, Agreeableness, and Extraversion, have been tied to positive effects on overall health and longevity in humans, while Neuroticism is associated with shorter life span. In captive gorillas, Extraversion alone is associated with longevity. We undertook a study of all captive, personality questionnaire-rated chimpanzees; the Chimpanzee and Hominoid Personality Questionnaires have been used to assess almost 600 chimpanzees from Europe, Australia, Japan, and the United States. With these data we investigated which personality dimensions and other life history characteristics might predict all-cause mortality. In an accelerated failure survival analysis, we found a strong effect of Extraversion (b = -4.74, p<0.0001), as well as lesser but significant effects of Agreeableness (b = 2.87, p<0.01) and Dominance (b = 1.64, p<0.05). Female and wild born chimpanzees appear to also live significantly longer (ps<0.01). The robustness of an animal's social network and the quality of its social interactions play a role in the health of social organisms. This is reflected in the importance of Extraversion for gorilla and chimpanzee health, and Agreeableness and Dominance for chimpanzees. Yet, the effect of Agreeableness is also similar to what has been found in humans.
Analysis of Test Driven Development on sentiment and coding activities in GitHub repositories
Authors: Borle Neil , Feghhi Meysam , Hindle Abram
Published: January 2018

This paper studies the relationship between Test Driven Development (TDD), productivity and developer sentiment in order to assess the impact of TDD on software development. We used a set of 256572 Java repositories archived from GitHub in September 2015 and made available through the Boa language and infrastructure. This research found that of these repositories, 9537 could be classified as using the TDD methodology. After obtaining these repositories we compared them to an equivalently sized set of control repositories. In general those repositories practicing TDD had fewer commits and a faster median rate of committing than did their control counterparts. We also found that TDD repositories generally contained fewer bug fixing commits. Finally, sentiment analysis was performed on both sets of repositories and it was determined that TDD repositories have a significantly (p-value 3.857e-12) more positive sentiment in comparison to the control repositories.
Is it safe to nest near bold neighbours? Spatial patterns in predation risk associated with the density of American Golden-Plover nest
Authors: Giroux Marie-Andrée , Trottier-Paquet Myriam , Bêty Joël , Lamarre Vincent , Lecomte Nicolas
Published: January 2018

Predation is one of the main factors explaining nesting mortality in most bird species. Birds can avoid nest predation or reduce predation pressure by breeding at higher latitude, showing anti-predator behaviour, and nesting in association with protective species. Plovers actively defend their territory by displaying early warning and aggressive/mobbing behaviour, potentially benefiting the neighbouring nests by decreasing their predation risk. To test for the existence of such a protective effect, we studied the influence of proximity to plover nests on predation risk of artificial nests on Igloolik Island (Nunavut, Canada) in July 2014. We predicted that the predation risk of artificial nests increases and decreases with the distance to and the density of plover nests, respectively. We monitored 18 plover nests and set 35 artificial nests at 30, 50, 100, 200 and 500 m from seven of those plover nests. Surprisingly, we showed that predation risk of artificial nests increases with the density of active plover nests. We also found a significant negative effect of the distance to the nearest active protector nest on predation risk of artificial nests. Understanding how the composition and structure of shorebird communities generate spatial patterns in predation risks represent a key step to better understand the importance of these species of conservation concern in tundra food webs.
Does ecophysiology mediate reptile responses to fire regimes? Evidence from Iberian lizards
Authors: Ferreira Catarina C , Santos Xavier , Carretero Miguel A.
Published: January 2018

Background. Reptiles are sensitive to habitat disturbance induced by wildfires but species frequently show opposing responses. Functional causes of such variability have been scarcely explored. In the northernmost limit of the Mediterranean bioregion, lizard species of Mediterranean affinity (Psammodromus algirus and Podarcis guadarramae) increase in abundance in burnt areas whereas Atlantic species (Lacerta schreiberi and Podarcis bocagei) decrease. Timon lepidus, the largest Mediterranean lizard in the region, show mixed responses depending on the locality and fire history. We tested if such interspecific differences are of functional nature, namely, if lizard ecophysiological traits may determine their response to fire. Based on the variation in habitat structure between burnt and unburnt sites, we hypothesise that Mediterranean species increasing density in open habitats promoted by frequent fire regimes should be more thermophile and suffer lower water losses than Atlantic species. Methods. We submitted 6-10 adult males of the five species to standard experiments for assessing preferred body temperatures (Tp) and evaporative water loss rates (EWL), and examined the variation among species and along time by means of repeated-measures AN(C)OVAs. Results. Results only partially supported our initial expectations, since the medium-sized P. algirus clearly attained higher Tp and lower EWL. The two small wall lizards (P. bocagei and P. guadarramae) displayed low Tp and high EWL while the two large green lizards (T. lepidus and L. schreiberi) displayed intermediate values for both parameters. Discussion. The predicted differences according to the biogeographic affinities within each pair were not fully confirmed. We conclude that ecophysiology may help to understand functional reptile responses to fire but other biological traits are also to be considered.
Managing wolves to benefit woodland caribou populations in northeast British Columbia: what we know and what we need
Authors: Wilson Steven F
Published: January 2018

Predator-prey systems are complex and attempts to manage them to benefit woodland caribou populations have generated mixed results. Despite limited success, calls for wolf control continue because of the urgent need to reverse the decline of woodland caribou populations, and because there are so few management options available that have the potential to demonstrate immediate benefits. I present the results of a policy analysis that reviews the potential role of wolf control within the ecological, social and political context of northeast British Columbia (BC). The scale and scope of a wolf control program is ultimately limited by the economic and ethical support of the public, while the program’s effectiveness is governed by the conditional dependencies among the major factors effecting woodland caribou declines. The policy analysis suggests that the contribution of wolf control programs to caribou conservation efforts in northeast BC will be limited, but that significant uncertainties in the causal pathways resulting in caribou population declines limit our ability to propose alternative management policies that have a high confidence of success.
Compensation and density dependence
Authors: Boyce Mark S. , Merrill Evelyn H.
Published: January 2018

Compensatory mortality is a key concept in sustainable resource development and predator-prey theory. Two driving mechanisms underlie compensatory mortality: seasonality and density dependence. Indeed, density dependence is fundamental to being able to achieve a sustainable harvest policy and is also central to stabilizing predator-prey systems. An intuitive view of compensatory mortality promoted by Paul Errington is the notion of an annual doomed surplus of recruits produced each year that can be harvested or killed by predators with no consequence to the spring breeding densities. An interaction between density dependence and harvest or predation mortality can result in overcompensation or the Hydra Effect where survival and/or population size is actually increased by low to moderate removals.
Boa: a link between worlds
Authors: Romansky Stephen , Charmchi Sadegh , Hindle Abram
Published: January 2018

The business models of software/platform as a service have contributed to developers dependence on the Internet. Developers can rapidly point each other and consumers to the newest software changes with the power of the hyper link. But, developers are not limited to referencing software changes to one another through the web. Other shared hypermedia might include links to: Stack Overflow, Twitter, and issue trackers. This work explores the software traceability of Uniform Resource Locators (URLs) which software developers leave in commit messages and software repositories. URLs are easily extracted from commit messages and source code. Therefore, it would be useful to researchers if URLs provide additional insight on project development. To assess traceability, manual topic labelling is evaluated against automated topic labelling on URL data sets. This work also shows differences between URL data collected from commit messages versus URL data collected from source code. As well, this work explores outlying software projects with many URLs in case these projects do not provide meaningful software relationship information. Results from manual topic labelling show promise under evaluation while automated topic labelling did not yield precise topics. Further investigation of manual and automated topic analysis would be useful.
Longitudinal and seasonal succession of algal periphyton colonization in lowland river (Tundzha River Part of Turkey)
Authors: Öterler Burak
Published: January 2018

The aim of this paper is to determine and compare the environmental factors controlling longitudinal colonisation of periphytic algae in agricultural and urbanization effects of a lowland river, the Tundzha River, located in Turkish Tunca. To investigate the effect of the environmental factors on periphyton colonization at the river, 6 stations were selected and samples were collected between April 2012 and March 2013. Canonical correspondence analyses have been applied to clarify relationships between environmental variables and periphytic algae. During the study, the Shannon-Wiener diversity index (H′) varied from 1.62 to 3.91. The phytoplankton biovolume was positively related to pH, temperature, salinity, chlorophyll- a and nutrients, and was negatively correlated with dissolved oxygen, turbidity, and silicate. Out of the 5 divisions and of 73 identified species of phytoplankton, the diatoms, namely Fragilaria ulna, Cymbella tumida, Cocconeis placentula, Gomphonema acuminatum and Cymbella cystula were found to be dominant. In addition to these species, the biovolumes of filamentous diatom Melosira varians, filamentous blue-green algae Oscillatoria limosa, and placcoderm desmids Cosmarium botrytis were determined to be at high levels during the year. The euglenoid blooms in St.5 showed many times during the study period.
A review of KDD99 dataset usage in intrusion detection and machine learning between 2010 and 2015
Authors: Özgür Atilla , Erdem Hamit
Published: January 2018

Although KDD99 dataset is more than 15 years old, it is still widely used in academic research. To investigate wide usage of this dataset in Machine Learning Research (MLR) and Intrusion Detection Systems (IDS); this study reviews 149 research articles from 65 journals indexed in Science Citation In- dex Expanded and Emerging Sources Citation Index during the last six years (2010–2015). If we include papers presented in other indexes and conferences, number of studies would be tripled. The number of published studies shows that KDD99 is the most used dataset in IDS and machine learning areas, and it is the de facto dataset for these research areas. To show recent usage of KDD99 and the related sub-dataset (NSL-KDD) in IDS and MLR, the following de- scriptive statistics about the reviewed studies are given: main contribution of articles, the applied algorithms, compared classification algorithms, software toolbox usage, the size and type of the used dataset for training and test- ing, and classification output classes (binary, multi-class). In addition to these statistics, a checklist for future researchers that work in this area is provided.
The XL-mHG test for enrichment: Algorithms, bounds, and power
Authors: Wagner Florian
Published: January 2018

The XL-mHG test is a semiparametric test for enrichment in ranked lists with Boolean (0/1-valued) entries. It is a generalization of the nonparametric mHG test, designed to provide some control over the kind of enrichment that is being tested for, and to allow a flexible trade-off between the sensitivity and robustness of the test. Here, I describe an improved algorithm to efficiently calculate the XL-mHG p-value p, and discuss upper and lower bounds for p. Furthermore, I perform simulations to show that the mHG test is a significantly more powerful alternative to the Kolmogorov-Smirnov (KS) test for detecting enrichment in scenarios that are frequently encountered in biological applications. An open-source Python/Cython implementation of the XL-mHG test is provided in the xlmhg package, which is available from PyPI and GitHub (https://github.com/flo-compbio/xlmhg) under an OSI-approved license.
The devastating impact of an invasive ambrosia beetle on the riparian habitats of the Tijuana River Valley, California
Authors: Boland John M
Published: January 2018

Background. The Tijuana River Valley is the first natural habitat in California to be substantially invaded by the Kuroshio Shot Hole Borer (KSHB, Euwallacea sp.), an invasive ambrosia beetle native to Southeast Asia. This paper documents the distribution of the KSHB in the riparian vegetation in the valley and assesses the damage done to the vegetation as of early 2016, approximately six months after the beetle was first observed in the valley. Methods. I divided the riparian habitats in the valley into 29 survey units such that the vegetation within each was relatively homogenous in terms of species composition, age and density. From a random point within each unit, I examined approximately 60 individuals of the dominant plant species for evidence of KSHB infection and evidence of major damage such as limb breakage. In the 22 forested units, I examined the dominant arroyo and black willows (Salix lasiolepis and S. gooddingii), and in the seven scrub units, I examined mule fat (Baccharis salicifolia). In addition, I recorded evidence of infection in other common species as they were encountered. Results. Evidence of KSHB infection was found in 25 of the 29 units. In the forest units, infection rates ranged from 0 to 100% and were high (>60%) in 16 of the units. In the scrub units, infection rates ranged from 0 to 33%. Infection rates were significantly negatively correlated with the dryness of a unit; drier units had lower infection rates. Evidence of physical damage was found in 24 units, and dense stands of willows were reduced to broken trunks in several areas. Overall, I estimated that more than 280,000 (70%) of the willows in the valley were infected, and more than 140,000 had suffered major limb damage. Of the 23 species examined, 14 showed evidence of beetle attack. The four species with the highest rates of infection were native riparian trees in the Salicaeae family. The three species considered to be the worst invasive plants in the valley, Ricinus communis, Tamarix ramosissima and Arundo donax, had low rates of infection. Discussion. The KSHB has substantially infected and damaged the dominant native trees in the riparian forests of the Tijuana River Valley, and this has led to a drastic alteration in the structure of the canopy of the forests. The loss of canopy is likely to promote the growth and spread of invasive plant species that were relatively inconspicuous in the forests prior to the beetle attack. The beetle’s impacts are a novel disturbance, and it remains to be seen whether the affected forests can recover. If resource managers are to control the spread of the beetle, they will need to develop an effective early detection and rapid response program. Because infection rates in the valley varied along a gradient of dryness, resource managers trying to detect the KSHB in other areas should thoroughly search trees near surface water.
Association of potential salivary biomarkers with diabetic retinopathy and its severity in type-2 diabetes mellitus: a proteomic analysis by mass spectrometry
Authors: Chee Chin Soon , Chang Khai Meng , Loke Mun Fai , Angela Loo Voon Pei , Subrayan Visvaraja
Published: January 2018

Aim/hypothesis The aim of our study was to characterize the human salivary proteome and determine the changes in protein expression in 2 different stages of diabetic retinopathy with type-2 diabetes mellitus: (1) with non-proliferative diabetic retinopathy (NPDR) and (2) with proliferative diabetic retinopathy (PDR). Type-2 diabetes without diabetic retinopathy (XDR) was designated as control. Method In this study, 45 saliva samples were collected (15 samples from XDR control group, 15 samples from NPDR disease group and 15 samples from PDR disease group). Salivary proteins were extracted, reduced, alkylated, trypsin digested and labeled with iTRAQ before analyzing by Orbitrap fusion tribrid mass spectrometer. Proteins annotation, fold change calculation and statistical analysis were interrogated by Proteome Discoverer. Biological pathway analysis was performed by Ingenuity Pathway Analysis. Data are available via ProteomeXchange with identifiers PXD003723-PX003725. Results A total of 315 proteins were identified from the salivary proteome and 119 proteins were found to be differentially expressed. The differentially expressed proteins from the NPDR disease group and the PDR disease group were assigned to respective canonical pathways indicating increased LXR/RXR activation, FXR/RXR activation, acute phase response signaling, sucrose degradation V and regulation of actin-based motility by Rho in the PDR disease group compared to the NPDR disease group Conclusions/Interpretation Progression from non-proliferative to proliferative retinopathy in type-2 diabetic patients is a complex multi-mechanism and systemic process. Furthermore, saliva was shown to be a feasible alternative sample source for diabetic retinopathy biomarkers.
The health care and life sciences community profile for dataset descriptions
Authors: Dumontier Michel , Gray Alasdair J G , Marshall M. Scott , Alexiev Vladimir , Ansell Peter , Bader Gary , Baran Joachim , Bolleman Jerven T , Callahan Alison , Cruz-Toledo José , Gaudet Pascale , Gombocz Erich A , Gonzalez Beltran Alejandra N , Groth Paul , Haendel Melissa Melissa , Ito Maori , Jupp Simon , Juty Nick , Katayama Toshiaki , Kobayashi Norio , Krishnaswami Kalpana , Laibe Camille , Le Novère Nicolas , Lin Simon , Malone James , Miller Michael , Mungall Christopher J , Rietveld Laurens , Wimalaratne Sarala M , Yamaguchi Atsuko
Published: January 2018

Access to consistent, high-quality metadata is critical to finding, understanding, and reusing scientific data. However, while there are many relevant vocabularies for the annotation of a dataset, none sufficiently captures all the necessary metadata. This prevents uniform indexing and querying of dataset repositories. Towards providing a practical guide for producing a high quality description of biomedical datasets, the W3C Semantic Web for Health Care and the Life Sciences Interest Group (HCLSIG) identified Resource Description Framework (RDF) vocabularies that could be used to specify common metadata elements and their value sets. The resulting guideline covers elements of description, identification, attribution, versioning, provenance, and content summarization. This guideline reuses existing vocabularies, and is intended to meet key functional requirements including indexing, discovery, exchange, query, and retrieval of datasets, thereby enabling the publication of FAIR data. The resulting metadata profile is generic and could be used by other domains with an interest in providing machine readable descriptions of versioned datasets.
BioMine-DB: A database for metazoan biomineralization proteins
Authors: Kamel Bishoy S , Voolstra Christian R , Medina Mónica
Published: January 2018

Biomineralization is the process by which living organisms construct hard skeletons creating complex structures that range from specialized tissues such as bone or teeth to ecosystems such as coral reefs. Biominerals are composed of both inorganic minerals and proteins, which give them extra hardness and special attributes. Biomineralization proteins are also known to be associated with multiple bone disorders and are therefore of biomedical importance. Herein we describe BioMine-DB, a biomineralization centric protein database. Availability and implementation: BioMine-DB can be accessed at http://biomine.net, SQL dump, FASTA files and source code are available for download as well at https://github.com/bishoyh/biomineDB "
Design of an open source framework for oil spill decision support system
Authors: Mokhtari Sahar , Kadlec Jiri
Published: January 2018

Oil spill in marine ecosystems have serious short term and long term effects on aquatics lifecycle and on social and economic activities. A Decision Support System (DSS) can assist environmental managers to visualize the distribution of oil pollution, identify sensitive areas that are likely to be exposed to oil pollutions, and assess vulnerable resources. This paper describes the design of an open source software framework and a prototype desktop software application of a DSS for oil spill management. This system can be connected to an open source oil spill simulation model. We also present a user interface for selecting the properties, time and location of a potential oil spill and for visualizing the oil spill affected area and its impact on coastal zone.
Behavioral flexibility in an invasive bird is independent of other behaviors
Authors: Logan Corina J
Published: January 2018

Behavioral flexibility is considered important for a species to adapt to environmental change. Yet behavioral flexibility relates to problem solving ability and speed in unpredictable ways. This leaves an open question of whether behavioral flexibility instead varies with differences in individual behaviors, such as neophobia or exploration. If present, such correlations would mask which behavior causes individual variation. I investigated whether behavioral flexibility (reversal learning) performances were linked with other behaviors in great-tailed grackles, an invasive bird. I found that behavioral flexibility did not significantly correlate with neophobia, exploration, risk aversion, persistence, or motor diversity. This suggests that great-tailed grackle performance in behavioral flexibility tasks reflect a distinct source of individual variation. Maintaining multiple distinct sources of individual variation, and particularly variation in behavioral flexibility, may be a mechanism for this species’ invasion success by permitting populations to cope with the diversity of novel elements in their environments.
Understanding the functional components of predator-prey response to habitat restoration: A Bayesian approach
Authors: McNay Robert , Sutherland Glenn D , Anderson Meghan S , Brumovsky Viktor , Giguere Line , Dickie Melanie , Cody Michael
Published: January 2018

Effective action planning for recovering endangered populations of boreal caribou (Rangifer tarandus caribou) requires an understanding of the functional interactions between: (1) responses by predators to current and prospective future habitat conditions, (2) responses of prey to population and habitat conditions influencing apparent competition, and (3) residual effects of past population bottlenecks. Monitoring recovery trajectories when human-altered habitats are restored requires consideration of many cause-effect linkages operating among multiple species and across multiple ecological scales. We developed a Bayesian Belief Network (BBN) to help frame potential functional responses of 2 predators (wolves, bears) and 2 prey (moose, caribou) to a large-scaled, silviculturally-based, habitat restoration experiment conducted within the Cold Lake caribou herd area in the Alberta oil sands. The full BBN consists of three general components: (1) those related to predator and prey movements, including use of non-restored and restored habitat features as those opposed conditions affect travel speed and search rates of predators; (2) those related to daily and seasonal use of habitat and how that may affect encounter probabilities between predators and prey; and (3) those related to the probability of kill given an encounter between predator and prey. These components structured in a BBN architecture support the application of the basic parameters in Holling’s disc equation, particularly: seasonal predator search rates and probability of a kill given an encounter (i.e., the area of effective search). We used the BBN to map the functional response spatially and to assess the dynamics of the predators and prey (demographics and response to restoration treatments). Our understanding of these hypothetical responses will, in the future, help shape management actions designed to reduce predator density and prey risk. To demonstrate the management utility of this approach, we plan to set BBN prior probabilities for each model component using 4 types of data: (1) habitat conditions measured semi-annually; (2) GPS relocation data from 128 individual predators (77 wolves; 51 bears) and 34 prey (25 moose and 9 caribou); (3) kill site investigations; and (4) DNA analyses of prey species density.
Climate induced wolf prey selection in Yellowstone National Park, 1995-2015
Authors: Smith Douglas W , Metz Matthew , Wilmers Chris , Stahler Daniel , Geremia Chris
Published: January 2018

Prey selection by wolves has been a fundamental and long-term topic of interest for wolf-prey studies. Virtually all studies conclude the selectivity of wolf predation and typically identify what made an individual vulnerable. Vulnerability, however, varies for multiple reasons and emerging research is discovering climate induced effects on prey forage altering condition and selective advantage of migration. We present data from a twenty year study of wolf-elk predation in Yellowstone National Park (YNP) which found bull elk killed more frequently in early winter after years with less snowfall compared to years with normal snowfall. Snowfall impacted summer forage, which impacted bull elk condition going into the autumn rut, which weakened elk prematurely post-rut causing them to be selected by wolves in early rather than late winter, and possibly caused more bulls to be killed overall. Bull elk ratios have declined over the last 20 years (from 40-60 to 10-15 bulls/100 cows; lower outside YNP), which has led to calls for a reduced human harvest on bulls which has been met with significant resistance. Understanding the interaction between climate, forage and wolf predation on bull elk (and other sex/age classes) will help guide management decisions and potentially sustain hunting of bulls in the long term as well as protect natural management objectives within YNP. Results will be of widespread value as they may suggest changing predator-prey dynamics across North America by making some otherwise healthy prey vulnerable to predation.
Hypothesis: A new anteroposterior axis for non-radiate early echinoderms
Authors: de Lussanet Marc HE
Published: January 2018

Homalozoa are a weird group of echinoderms, for their complete lack of radiate symmetry. Indeed, they are typified by their tendency to marked asymmetric body forms. It has been proposed that they asymmetric forms evolved from bilaterally symmetric ones, but so far, only approximately bilaterally symmetric forms have been described (Robinson & Sprinkle 1969;Zamora 2012). Hypothesis: Homalozoans developed from bilaterally symmetric, tropartite larvae, by adopting a secondary anteroposterior axis.
Managing raptors to reduce wildlife strikes at Chicago’s O’Hare International Airport
Authors: Pullins Craig K. , Guerrant Travis L. , Beckerman Scott F. , Washburn Brian E.
Published: January 2018

Nationally, wildlife-aircraft collisions (wildlife strikes) have been increasing over the past 25 years; denoted in the National Wildlife Strike Database that has been maintained by the Federal Aviation Administration (FAA) since 1990. Increasing wildlife populations and air traffic coupled with quieter, faster aircraft create a significant risk to aviation safety; the cost to the civil aviation industry is an estimated $937 million dollars annually. USDA/APHIS/Wildlife Services (WS) provides technical and direct assistance to over 850 airports and airbases around the United States, including Chicago’s O’Hare International Airport (ORD). At ORD, raptors are one of the most commonly struck bird guild and accounted for at least 25% of damaging strikes from 2010-2013. An Integrated Wildlife Damage Management (IWDM) program is implemented at ORD to reduce the presence of wildlife on the airfield, consequently lowering the risk of wildlife strikes. Professional airport wildlife biologists at ORD concentrate much of their efforts on raptor management due to the high strike risk these birds pose to aircraft on the airfield itself. A variety of techniques are currently used to manage raptor populations at ORD. Concurrently, research is being conducted to evaluate the efficacy of the Red-tailed Hawk relocation program at the airport, as well as to assess their movements within the airfield environment.
­Bcl-2 homologue debcl enhances α-synuclein-induced phenotypes in Drosophila
Authors: M'Angale Peter G , Staveley Brian E
Published: January 2018

Background Parkinson disease (PD) is a debilitating movement disorder that afflicts 1 to 2% of the population over 50 years of age. The common hallmark for both sporadic and familial forms of PD is mitochondrial dysfunction. Mammals have at least twenty proapoptotic and antiapoptotic Bcl-2 family members, in contrast, only two Bcl-2 family genes have been identified in Drosophila melanogaster, the proapoptotic mitochondrial localized debcl and the antiapoptotic Buffy. The expression of α-synuclein, the first gene identified to contribute to inherited forms of PD, in the dopaminergic neurons (DA) of flies has provided a robust and well-studied Drosophila model of PD complete with the loss of neurons and accompanying motor defects. The altered expression of debcl in the DA neurons and neuron-rich eye and along with the expression of α-synuclein offers an opportunity to highlight the role of debcl in mitochondrial-dependent neuronal degeneration and death. Results The directed overexpression of debcl using the Ddc-Gal4 transgene in the dopaminergic neurons of Drosophila resulted in flies with severely decreased survival and a premature age-dependent loss in climbing ability. The inhibition of debcl resulted in enhanced survival and improved climbing ability whereas the overexpression of debcl in the α-synuclein-induced Drosophila model of PD resulted in more severe phenotypes. In addition, the co-expression of debcl along with Buffy partially counteracts the debcl-induced phenotypes, to improve the lifespan and the associated loss of locomotor ability observed. In complementary experiments, the overexpression of debcl along with the expression of α-synuclein in the eye, enhanced the eye ablation that results from the overexpression of debcl. The co-expression of Buffy along with debcl overexpression results in the rescue of the moderate developmental eye defects. The co-expression of Buffy along with inhibition of debcl partially restores the eye to a roughened eye phenotype. Discussion The overexpression of debcl in DA neurons produces flies with shortened lifespan and impaired locomotor ability, phenotypes that are strongly associated with models of PD in Drosophila. The co-expression of debcl along with α-synuclein enhanced the Parkinson disease-like phenotypes. The co-expression of debcl along with Buffy suppresses these phenotypes. Complementary experiments in the Drosophila eye show similar trends during development. Taken all together these results suggest a role for debcl in neurodegenerative disorders.
Automated annotation of corals in natural scene images using multiple texture representations
Authors: Blanchet Jean-Nicola , Déry Sébastien , Landry Jacques-André , Osborne Kate
Published: January 2018

Current coral reef health monitoring programs rely on biodiversity data obtained through the acquisition and annotation of underwater photographs. Manual annotation of these photographs is a necessary step, but has become problematic due to the high volume of images and the high cost of human resources. While automated and reliable multi-spectral annotation methods exist, coral reef images are often limited to visible light, which makes automation difficult. Much of the previous work has focused on popular texture recognition methods, but the results remain unsatisfactory when compared to human performance for the same task. In this work, we present an improved automatic method for coral image annotation that yields consistent accuracy improvements over existing methods. Our method builds on previous work by combining multiple feature representations. We demonstrate that the aggregation of multiple methods outperforms any single method. Furthermore, our proposed system requires virtually no parameter tuning, and supports rejection for improved results. Firstly, the complex texture diversity of corals is handled by combining multiple feature representations: local binary patterns, hue and opponent angle histograms, textons, and deep convolutional activation feature. Secondly, these multiple representations are aggregated using a score-level fusion of multiple support vector machines. Thirdly, rejection can optionally be applied to enhance classification results, and allows efficient semi-supervised image annotation in collaboration with human experts.
Balancing under the high wire; a study into PTT antenna effects on the Common Guillemot Uria aalge
Authors: Vandenabeele Sylvie P , Shepard Emily LC , Grogan Adam , Thompson Richard , Gleiss Adrian C , Wilson Rory P
Published: January 2018

External tags fitted to diving birds can affect them in many ways with the most critical effect being an increase in drag. The effects of transmitters can be even more acute due to the presence of a protruding aerial. The study assesses the impact of PTT antenna on the behaviour and energetics of device-equipped guillemots (Uria aalge) in captivity. Birds with antenna-devices appeared to consume about 20% more energy than non-antenna birds during the descent phase of the dive. The balance of the birds while diving or resting on the water also appeared to be compromised by the presence of an antenna. Based on these first results and because transmitters are one of the most common methods used to track animals, it appears critical to determine what impact these devices, and particularly antenna, can have on their bearers and try minimize it.
Validation and development of COI metabarcoding primers for freshwater macroinvertebrate bioassessment
Authors: Elbrecht Vasco , Leese Florian
Published: January 2018

A central challenge in the present era of biodiversity loss is to assess and manage human impacts on freshwater ecosystems. Macroinvertebrates are an important group for bioassessment as many taxa show specific responses to environmental conditions. However, generating accurate macroinvertebrate inventories based on larval morphology is difficult and error-prone. Here, DNA metabarcoding provides new opportunities. Its potential to accurately identify invertebrates in bulk samples to the species level, has been demonstrated in several case studies. However, DNA based identification is often limited by primer bias, potentially leading to taxa in the sample remaining undetected. Thus, the success of DNA metabarcoding as an emerging technique for bioassessment critically relies on carefully evaluating primers.

We used the R package PrimerMiner to obtain and process cytochrome c oxidase I (COI) sequence data for the 15 most globally relevant freshwater invertebrate groups for stream assessment. Using these sequence alignments, we developed four primer combinations optimized for freshwater macrozoobenthos. All primers were evaluated by sequencing ten mock community samples, each consisting of 52 freshwater invertebrate taxa. Additionally, popular metabarcoding primers from the literature and the developed primers were tested in silico against the 15 relevant invertebrate groups.

The developed primers varied in amplification efficiency and the number of detected taxa, yet all detected more taxa than standard ‘Folmer’ barcoding primers. Two new primer combinations showed more consistent amplification than a previously tested ribosomal marker (16S) and detected all 42 insect taxa present in the mock community samples. In silico evaluation revealed critical design flaws in some commonly used primers from the literature.

We demonstrate a reliable strategy to develop optimized primers using the tool PrimerMiner. The developed primers detected almost all taxa present in the mock samples, and we argue that high base degeneracy is necessary to decrease primer bias as confirmed by experimental results and in silico primer evaluation. We further demonstrate that some primers currently used in metabarcoding studies may not be suitable for amplification of freshwater macroinvertebrates. Therefore, careful primer evaluation and more region / ecosystem specific primers are needed before DNA metabarcoding can be used for routine bioassessment of freshwater ecosystems.
Uncertainty modeling process for semantic technology
Authors: Carvalho Rommel N , Laskey Kathryn B , Costa Paulo C. G. Da
Published: January 2018

The ubiquity of uncertainty across application domains generates a need for principled support for uncertainty management in semantically aware systems. A probabilistic ontology provides constructs for representing uncertainty in domain ontologies. While the literature has been growing on formalisms for representing uncertainty in ontologies, there remains little guidance in the knowledge engineering literature for how to design probabilistic ontologies. To address the gap, this paper presents the Uncertainty Modeling Process for Semantic Technology (UMP-ST), a new methodology for modeling probabilistic ontologies. To explain how the methodology works and to verify that it can be applied to different scenarios, this paper describes step-by-step the construction of a proof-of-concept probabilistic ontology. The resulting domain model is intended to support identification of fraud in public procurements in Brazil. While the case study illustrates the development of a probabilistic ontology in the PR-OWL probabilistic ontology language, the methodology is applicable to any ontology formalism that properly integrates uncertainty with domain semantics.