bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pesticide mixtures in the Swedish streams: environmental risks, contributions of individual compounds and consequences of single-substance oriented risk mitigation
Authors: Gustavsson Mikael B , Kreuger Jenny , Bundschuh Mirco , Backhaus Thomas 
Published: January 2018

The paper presents the ecotoxicological assessment and environmental risk evaluation of complex pesticide mixtures occurring in freshwater ecosystems in southern Sweden. The evaluation is based on the data collected between 2002 and 2013 by the Swedish pesticide monitoring program and includes 1308 individual samples, detecting mixtures of up to 54 pesticides (modal=8). The environmental risk of 77% of the samples exceeded acceptable levels, based on an assessment using Concentration-Addition and Swedish Water Quality Objectives (WQO) for the individual pesticides. Algae were the most sensitive organism group. However, the analytical detection limits, especially for insecticides, are currently insufficient to analyze concentrations at or near their WQO’s. Thus, the risk of the analyzed pesticide mixtures to crustaceans and fish is currently systematically underestimated.
Throughout the monitoring the risk associated with pesticide mixtures is often driven by only 1-3 compounds. However, the risk-drivers differ substantially between sites and samples, so that 83 of the 141 monitored pesticides need to be included in the assessment to account for 95% of the risk at all sites and years.
Single-substance oriented risk mitigation measures that would ensure that each individual pesticide is present at 95% of its individual WQO at maximum, would also reduce the mixture risk, from a median risk quotient of 2.7 to a median risk quotient of 2.3. However, acceptable total risk levels would still be exceeded in more than 70% of the samples.
Pesticide mixtures in the Swedish streams: environmental risks, contributions of individual compounds and consequences of single-substance oriented risk mitigation
Authors: Gustavsson Mikael B , Kreuger Jenny , Bundschuh Mirco , Backhaus Thomas 
Published: January 2018

This paper presents the ecotoxicological assessment and environmental risk evaluation of complex pesticide mixtures occurring in freshwater ecosystems in southern Sweden. The evaluation is based on exposure data collected between 2002 and 2013 by the Swedish pesticide monitoring program and includes 1308 individual samples, detecting mixtures of up to 53 pesticides (modal=8). Pesticide mixture risks were evaluated using three different scenarios for non-detects (best-case, worst-case and using the Kaplan-Meier method). The risk of each scenario was analyzed using Swedish Water Quality Objectives (WQO) and throphic-level specific environmental thresholds.
Using the Kaplan-Meier method the environmental risk of 73% of the samples exceeded acceptable levels, based on an assessment using Concentration-Addition and WQOs for the individual pesticides. Algae were the most sensitive organism group. However, analytical detection limits, especially for insecticides, were insufficient to analyze concentrations at or near their WQO’s. Thus, the risk of the analyzed pesticide mixtures to crustaceans and fish is systematically underestimated. Treating non-detects as being present at their individual limit of detection increased the estimated risk by a factor 100 or more, compared to the best-case or the Kaplan-Meier scenario.
Pesticide mixture risks are often driven by only 1-3 compounds. However, the risk-drivers (i.e., individual pesticides explaining the largest share of potential effects) differ substantially between sites and samples, and 83 of the 141 monitored pesticides need to be included in the assessment to account for 95% of the risk at all sites and years.
Single-substance oriented risk mitigation measures that would ensure that each individual pesticide is present at a maximum of 95% of its individual WQO, would also reduce the mixture risk, but only from a median risk quotient of 2.1 to a median risk quotient of 1.8. Also, acceptable total risk levels would still be exceeded in more than 70% of the samples.
Potential effects of climate change on the risk of accidents with poisonous species of the genusTityus (Scorpiones, Buthidae) in Argentina
Authors: Martinez Pablo , Andrade Mayane A , Bidau Claudio Juan 
Published: January 2018

BACKGROUND: The knowledge of the factors that affect the geographic distribution of species permits us to infer where they can be found. Human beings, through the expansion of their own distribution area and their contribution to climate alteration have modified the geographic distribution of other biological species. As a consequence, the temporal pattern of co-occurrence of human beings and venomous species (scorpions, spiders, snakes) is being modified. Thus, the temporal pattern of areas with risk of accidents with such species tends to become dynamic along time. The aim of this work was to analyze the areas of occurrence of species of Tityus in Argentina and assess the impact of global climate change on their area of distribution constructing risk maps.
METHODS: Using data of occurrence of the species and climatic variables, we constructed models of species distribution (SMDs) under current and future conditions. We also created maps that allow the detection of temporal shifts in the distribution patterns of each Tityus species. Finally, we constructed risk maps for the analyzed species.
RESULTS: Our results predict that climate change will have an impact on the distribution of Tityus species which will clearly expand to more southern latitudes, with the exception of T. argentinus. T. bahiensis, widely distributed in Brazil, showed a considerable increase of its potential area (ca. 37%) with future climate change. The species T. confluens and T. trivittatus that cause the highest number of accidents in Argentina, showed significant changes of their distributions in future scenarios. The former fact is worrying because Buenos Aires province is the more densely populated federal district in Argentina thus liable to become the one most affected by T. trivittatus.
DISCUSSION: Then, these alterations of distributional patterns can lead to amplify the accident risk zones of venomous species, becoming an important subject of concern for public health policies.
A review of R for Data Science: key elements and a critical analysis
Authors: Lortie Christopher J 
Published: January 2018

A detailed review of a recent data science book by Hadley Wickham and Garrett Grolemund is developed herein. Technical book reviews should provide a guide to the readers, a sense of the appropriate audience, the specifics of the software/language, and identify critical thinking questions that emerge through reading the specifics of these books. This is a pre-print, extended version of a review of 'R for Data Science', and it provides a relatively comprehensive framing of this particular book. The context and background of the authors is introduced, key elements of this book - primarily the workflow proposed and the value of the tidyverse - are summarized, and a critical analysis of the book was done. The following critical questions were addressed in the review.
(1) Does this book (or any data science book for that matter) effectively communicate basic versus advanced data science concepts to the reader?
(2) Does this book extend or improve upon previous resources particularly for the individual in- terested in using and learning data science to do statistics in R?
(3) Can this book be read as a general data science book and by extension how much is this an R versus RStudio book?
The importance of reading a book associated with tools one uses in computer science such as R versus rapid, online solution-based reading is very effectively established in 'R for Data Science'. Time spent with a technical book providing the big picture for the tools one uses to solve problems in R is important for deeper learning and insights.
Differentiation of Bifidobacterium longum subspecies longum and infantis by quantitative PCR using functional gene targets
Authors: Lawley Blair , Munro Karen , Hughes Alan , Hodgkinson Alison J , Prosser Colin G , Lowry Dianne , Zhou Shao J , Makrides Maria , Gibson Robert A , Lay Christophe , Chew Charmaine , Lee Pheng Soon , Wong Khai Hong , Tannock Gerald W 
Published: January 2018

Background. Members of the genus Bifidobacterium are abundant in the feces of babies during the exclusively-milk-diet period of life. Bifidobacterium longum is reported to be a common member of the infant fecal microbiota. However, B. longum is composed of three subspecies, two of which are represented in the bowel microbiota (B. longum subsp. longum; B. longum subsp. infantis). B. longum subspecies are not differentiated in many studies, so that their prevalence and relative abundances are not accurately known. This may largely be due to difficulty in assigning subspecies identity using DNA sequences of 16S rRNA or tuf genes that are commonly used in bacterial taxonomy.
Methods. We developed a qPCR method targeting the sialidase gene (subsp. infantis) and sugar kinase gene (subsp. longum) to differentiate the subspecies using specific primers and probes. Specificity of the primers/probes was tested by in silico, pangenomic search, and using DNA from standard cultures of bifidobacterial species. The utility of the method was further examined using DNA from feces that had been collected from infants inhabiting various geographical regions.
Results. A pangenomic search of the NCBI genomic database showed that the PCR primers/probes targeted only the respective genes of the two subspecies. The primers/probes showed total specificity when tested against DNA extracted from the gold standard strains (type cultures) of bifidobacterial species detected in infant feces. Use of the qPCR method with DNA extracted from the feces of infants of different ages, delivery method and nutrition, showed that subsp. infantis was detectable (0-32.4% prevalence) in the feces of Australian (n = 90), South-East Asian (n = 24), and Chinese babies (n = 91), but in all cases at low abundance (<0.01-4.6%) compared to subsp. longum (0.1-33.7% abundance; 21.4-100% prevalence).
Discussion. Our qPCR method differentiates B. longum subspecies longum and infantis using characteristic functional genes. It can be used as an identification aid for isolates of bifidobacteria, as well as in determining prevalence and abundance of the subspecies in feces. The method should thus be useful in ecological studies of the infant gut microbiota during early life where an understanding of the ecology of bifidobacterial species may be important in developing interventions to promote infant health.
Evidence based pathways to intervention for children with language disorders
Authors: Ebbels Susan H , McCartney Elspeth , Slonims Vicky , Dockrell Julie E , Norbury Courtenay 
Published: January 2018

Background: Paediatric SLT roles often involve planning individualised intervention for specific children (provided directly by SLTs or indirectly through non-SLTs), working collaboratively with families and education staff and providing advice and training. A tiered approach to service delivery is currently recommended, whereby services become increasingly specialised and individualised for children with greater needs.
Aims: To examine 1) evidence of intervention effectiveness for children with language disorders at different tiers and 2) evidence regarding SLT roles; and to propose an evidence-based model of SLT service delivery.
Methods: Controlled, peer-reviewed studies, meta-analyses and systematic reviews of interventions for children with language disorders are reviewed and their outcomes discussed, alongside the differing roles SLTs play in these interventions. We indicate where gaps in the evidence base exist and present a possible model of service delivery consistent with current evidence, and a flowchart to aid clinical decision making.
Main Contribution: The service delivery model presented resembles the tiered model commonly used in education services, but divides individualised (Tier 3) services into Tier3A: indirect intervention delivered by non-SLTs, and Tier 3B: direct intervention by an SLT. We report the evidence for intervention effectiveness and which children might best be served by each tier, the role SLTs could take within each, and the evidence of effectiveness of these roles. Regarding universal interventions provided to all children (Tier 1) and those targeted at children with language weaknesses (Tier 2), there is growing evidence that approaches led by education services can be effective when staff are highly trained and well-supported. There is currently limited evidence regarding additional benefit of SLT-specific roles at Tiers 1 and 2. With regard to individualised intervention (Tier 3): children with complex or pervasive language disorders progress significantly following direct individualised intervention (Tier 3B), whereas children with milder or less pervasive difficulties can make progress when intervention is managed by an SLT, but delivered indirectly by others (Tier 3A), provided they are well-trained, -supported and -monitored.
Conclusions: SLTs have a contribution to make at all tiers, but where prioritisation for clinical services is a necessity, we need to establish the benefits and cost-effectiveness of each contribution. Good evidence exists for SLTs delivering direct individualised intervention, and we should ensure that this is available to those children with pervasive and/or complex language impairments. In cases where service models are being provided which lack evidence, we strongly recommend that SLTs investigate the effectiveness of their approaches.
Microbiome succession during ammonification in eelgrass bed sediments
Authors: Ettinger Cassandra L , Williams Susan L , Abbott Jessica M , Stachowicz John J , Eisen Jonathan A 
Published: January 2018

Background. Eelgrass (Zostera marina) is a marine angiosperm and foundation species that plays an important ecological role in primary production, food web support, and elemental cycling in coastal ecosystems. As with other plants, the microbial communities living in, on, and near eelgrass are thought to be intimately connected to the ecology and biology of eelgrass. Here we characterized the microbial communities in eelgrass sediments throughout an experiment to quantify the rate of ammonification, the first step in early remineralization of organic matter, or diagenesis, from plots at a field site in Bodega Bay, CA.
Methods. Sediment was collected from 72 plots from a 15 month long field experiment in which eelgrass genotypic richness and relatedness were manipulated. In the laboratory, we placed sediment samples (n= 4 per plot) under a N2 atmosphere, incubated them at in situ temperatures (15 oC) and sampled them initially and after 4, 7, 13, and 19 days to determine the ammonification rate. Comparative microbiome analysis using high throughput sequencing of 16S rRNA genes was performed on sediment samples taken initially and at 7, 13 and 19 days to characterize the relative abundances of microbial taxa and how they changed throughout early diagenesis.
Results. Within-sample diversity of the sediment microbial communities across all plots decreased after the initial timepoint using both richness based (observed number of OTUs, Chao1) and richness and evenness based diversity metrics (Shannon, Inverse Simpson). Additionally, microbial community composition changed across the different timepoints. Many of the observed changes in relative abundance of taxonomic groups between timepoints appeared driven by sulfur cycling with observed decreases in sulfur reducers (Desulfobacterales) and corresponding increases in sulfide oxidizers (Alteromonadales and Thiotrichales). None of these changes in composition or richness were associated with ammonification rates.
Discussion. Overall, our results showed that the microbiome of sediment from different plots followed similar successional patterns, which we surmise to be due to changes related to sulfur metabolism. These large changes likely overwhelmed any potential changes in sediment microbiome related to ammonification rate. We found no relationship between eelgrass presence or genetic composition and the microbiome. This was likely due to our sampling of bulk sediments to measure ammonification rates rather than sampling microbes in sediment directly in contact with the plants and suggests that eelgrass influence on the sediment microbiome may be limited in spatial extent. More in-depth functional studies associated with eelgrass microbiome will be required in order to fully understand the implications of these microbial communities in broader host-plant and ecosystem functions (e.g. elemental cycling and eelgrass-microbe interactions).
Body and skull morphometric variations between two shovel-headed species of Amphisbaenia (Reptilia: Squamata) with morphofunctional inferences on burrowing
Authors: Hohl Leandro , Loguercio Mariana , Sicuro Fernando , Barros-Filho José , Rocha-Barbosa Oscar 
Published: January 2018

Background. Morphological descriptions comparing Leposternon microcephalum and L. scutigerum are known. However, these taxa lack of a formal quantitative morphological characterization and comparison between their morphometric patterns. Studies suggest that morphology and burrowing performance seem to be related. For example, the robustness of the head in L. microcephalum is positively associated to the digging force. The excavatory movements of this species were described in detail. However, there is a lack of studies comparing locomotor patterns and/or performance among different amphisbaenids sharing the same skull pattern. Likewise, morphofunctional interpretations of the morphological variations are scarce. This paper presents the first study of comparative morphometric variations between two adaptively close amphisbaenid species,L. microcephalum and L. scutigerum, with functional inferences of fossorial locomotion efficiency.
Methods. Inter-specific morphometric variations were verified through statistical analyses of body and cranial measures of L. microcephalum and L. scutigerum specimens. Their burrowing activity was assessed through X-ray videoflouroscopy and then compared. The influence of morphological variations on the speed of the digging performance was tested among Leposternon individuals.
Results. Leposternon microcephalum and L. scutigerum are morphometrically distinct species. The first is shorter and robust with a wider head while the other is more elongated and slim with a narrower head. They seem to share the same excavatory movements. However, L. scutigerum presented higher averages for speed, travel distance and frequency of excavatory cycles, and lower values for cycle duration in relation to that found for L. microcephalum. The animals analyzed reached relatively high speeds, but individuals with narrower skulls dig faster. A negative correlation between the speed and the width of skull was determined, but not with total length or diameter of the body.
Discussion. The morphometric differences between L. microcephalum and L. scutigerum are in accord with morphological variations previously described. Since these species performed the same excavation pattern, we may infer that adaptively close amphisbaenids with the same skull type would exhibit the same excavatory pattern. The locomotor performance values suggested that L. scutigerum is a faster digger than L. microcephalum. Such differences are supported by morphometric and morphological features. The negatively correlation between head width and excavation speed is also observed in others fossorial squamates. The robustness of the skull is also related to compression force in L. microcephalum. Individuals with wider heads are stronger. Thus, we suggested trade-offs between excavation speed and compression force during burrowing activity for this species.
bioPDFX: preparing PDF scientific articles for biomedical text mining
Authors: Bhargava Shitij , Kuo Tsung-Ting , Goyal Ankit , Kuri Vincent , Lin Gordon , Hsu Chun-Nan 
Published: January 2018

Background. There is huge amount of full-text biomedical literatures available in public repositories like PubMed Central (PMC). However, a substantial number of the papers are in Portable Document Format (PDF) and do not provide plain text format ready for text mining and natural language processing (NLP). Although there exist many PDF-to-text converters, they still suffer from several challenges while processing biomedical PDFs, such as the correct transcription of titles/abstracts, segmenting references/acknowledgements, special characters, jumbling errors (the wrong order of the text), and word boundaries.
Methods. In this paper, we present bioPDFX, a novel tool which complements weaknesses with strengths of multiple state-of-the-art methods and then applies machine learning methods to address all issues above
Results. The experiment results on publications of Genome Wide Association Studies (GWAS) demonstrated that bioPDFX significantly improved the quality of XML comparing to state-of-the-art PDF-to-XML converter, leading to a biomedical database more suitable for text mining.
Discussion. Overall, the whole pipeline developed in this paper makes the published literature in form of PDF files much better suited for text mining tasks, while slightly improving the overall text quality as well. The service is open to access freely at URL: http://textmining.ucsd.edu:9000 . A list of PubMed Central IDs of the 941 articles (see Supplemental File 1) used in this study is available for download at the same URL. The instructions of how to run the service with a PubMed ID are described in Supplemental File 2.
Region level risk factors for the Ebola virus disease in West Africa
Authors: Levy Benjamin , Odoi Agricola 
Published: January 2018

Background. The Ebola Virus Disease (EVD) is a highly infectious disease that has claimed over 25,000 cases in the past 50 years. While many past outbreaks of EVD resulted in relatively few incidents, the 2014 outbreak in West Africa was the most deadly occurrence of EVD to date producing over 15,000 confirmed cases.
Objective. In this study we relate total confirmed case counts of EVD to predictor variables at the region level in Sierra Leone, Liberia, and Guinea.
Methods. We used a Poisson framework and negative binomial framework to relate the predictors to the outcome. A spatial analysis was conducted to further our understanding and help interpret results.
Results. Results indicate that the percent of the population living in urban areas, percent of household with a bad quality or no toilet, and percent of married men working in blue collar jobs protect against the transmission of EVD. Our study also shows that mean years of education contributes to increased case counts of the disease.
Conclusions. Each significant predictor are associated with the types of dynamics that either protect against, or exacerbate, the spread of EVD. While having limited contact with the bodily fluids of others, reduced person-to-person contact, and isolated population clusters protect against the spread of EVD, the types of daily interactions an educated individual will experience leads to higher incidence rates. This information can be used to identify potential transmission routes and prevent future outbreak of this deadly disease.