bluuebunny/crossref_metadata_2025 huggingface dataset:
Single exponential decay waveform; a synergistic combination of electroporation and electrolysis (E2) for tissue ablation
Authors: Klein Nina , Guenther Enric , Mikus Paul , Stehling Michael K , Rubinsky Boris
Published: January 2018

Background: Electrolytic ablation and electroporation based ablation are minimally invasive, non-thermal surgical technologies that employ electrical currents and electric fields to ablate undesirable cells in a volume of tissue. In this study we explore the attributes of a new tissue ablation technology that simultaneously delivers a synergistic combination of electroporation and electrolysis (E2).

Method: A new device that delivers a controlled dose of electroporation field and electrolysis currents in the form of a single exponential decay waveform (EDW), was applied to the pig liver and the effect of various parameters on the extent of tissue ablation was examined with histology.

Results: Histological analysis shows that E2 delivered as EDW can produce tissue ablation in volumes of clinical significance, using electrical and temporal parameters which, if used in electroporation or electrolysis separately, cannot ablate the tissue

Discussion: The E2 combination has advantages over the three basic technologies of non-thermal ablation: electrolytic ablation, electrochemical ablation (reversible electroporation with injection of drugs) and irreversible electroporation. E2 ablates clinically relevant volumes of tissue in a shorter period of time than electrolysis and electroporation, without the need to inject drugs as in reversible electroporation or use paralyzing anesthesia as in irreversible electroporation.
A new correlation of the Cretaceous formations of the Western Interior of the United States, I: Santonian-Maastrichtian formations and dinosaur biostratigraphy
Authors: Fowler Denver W
Published: January 2018

Late Cretaceous deposits of the North American Western Interior represent the best, if not only, opportunity to construct a high-resolution chronostratigraphic framework within which to conduct continental-scale geological and paleontological analyses. This is due to the serendipitous combination of large areas of outcrop, interfingering marine units with biostratigraphically informative fossils, and a consistent scattering of radiometric dates due to synorogenic volcanic activity. Accurate correlation is essential for testing a large number of current geological and paleobiological hypotheses; however, despite the large amount of data available, many published correlations suffer from inaccuracies or are simply based on outdated information.

Here I present a comprehensive high-resolution stratigraphic chart for terrestrial Late Cretaceous units of North America, combining published chronostratigraphic, lithostratigraphic, and biostratigraphic data. For the first time, nearly two hundred 40Ar / 39Ar radiometric dates are recalibrated to both current standard and decay constant pairings, correcting errors in previous recalibrations. Revisions to the stratigraphic placement of most units are slight, but important changes are made to the proposed correlations of the Aguja and Javelina Formations, Texas, and miscalculations in recently published analyses are corrected which in particular affects the relative age positions of the Belly River Group, Alberta; Judith River Group, Montana, Kaiparowits Formation, Utah, and Fruitland and Kirtland Formations, New Mexico.

This work represents the most extensive and accurate interbasinal correlation currently available for the North American Western Interior and should replace all previously published similar works and diagrams.

The stratigraphic ranges of selected dinosaur clades are plotted on the chronostratigraphic framework, typically forming stacks of short-duration species which do not overlap stratigraphically with preceding or succeeding forms. This is the expected pattern which is produced by an anagenetic mode of evolution, suggesting that true branching (speciation) events were rare and may have geographic significance. Purported north-south provinciality of dinosaurs is shown to be mostly an artifact of stratigraphic miscorrelation. Rapid stepwise acquisition of display characters in many dinosaur clades, in particular chasmosaurine ceratopsids, suggests that they may represent the highest resolution biostratigraphic markers to be used where radiometric dates are not available.
Revised geochronology, correlation, and dinosaur stratigraphic ranges of the Santonian-Maastrichtian (Late Cretaceous) formations of the Western Interior of North America
Authors: Fowler Denver W
Published: January 2018

Interbasinal stratigraphic correlation provides the foundation for all consequent continental-scale geological and paleontological analyses. Correlation requires synthesis of lithostratigraphic, biostratigraphic and geochronologic data, and must be periodically updated to accord with advances in dating techniques, changing standards for radiometric dates, new stratigraphic concepts, hypotheses, fossil specimens, and field data. Outdated or incorrect correlation exposes geological and paleontological analyses to potential error.

The current work presents a high-resolution stratigraphic chart for terrestrial Late Cretaceous units of North America, combining published chronostratigraphic, lithostratigraphic, and biostratigraphic data. 40Ar / 39Ar radiometric dates are newly recalibrated to both current standard and decay constant pairings. Revisions to the stratigraphic placement of most units are slight, but important changes are made to the proposed correlations of the Aguja and Javelina Formations, Texas, and recalibration corrections in particular affect the relative age positions of the Belly River Group, Alberta; Judith River Formation, Montana; Kaiparowits Formation, Utah; and Fruitland and Kirtland formations, New Mexico.

The stratigraphic ranges of selected clades of dinosaur species are plotted on the chronostratigraphic framework, with some clades comprising short-duration species that do not overlap stratigraphically with preceding or succeeding forms. This is the expected pattern that is produced by an anagenetic mode of evolution, suggesting that true branching (speciation) events were rare and may have geographic significance. The recent hypothesis of intracontinental latitudinal provinciality of dinosaurs is shown to be affected by previous stratigraphic miscorrelation. Rapid stepwise acquisition of display characters in many dinosaur clades, in particular chasmosaurine ceratopsids, suggests that they may be useful for high resolution biostratigraphy.
Condition dependence in animal colouration: tools for a comparative approach
Authors: Ethier Jessica , Despland Emma
Published: January 2018

The study of condition dependence in animal colour has undergone important changes in recent years. In particular, the focus on carotenoid-based colour traits is a thing of the past and a broader, comparative approach is becoming more common. Here, we refine a previously developed theoretical model describing pigment expression as a saturating function of resource intake and demonstrate its use as a tool to compare patterns of resource assimilation, resource allocation, and condition dependence between groups of organisms. Using a simple equation and non-linear regression analyses, we apply this saturating model to melanin-based colouration in a model insect species. We find that patterns of condition dependence differ between sexes, phenotypes, and populations, suggesting underlying differences in resource allocation priorities. Our results highlight both the usefulness of this method and the value of a comparative approach in identifying proximate mechanisms of condition dependence.
Sorting things out - assessing effects of unequal specimen biomass on DNA metabarcoding
Authors: Elbrecht Vasco , Peinert Bianca , Leese Florian
Published: January 2018

1) Environmental bulk samples often contain many taxa with biomass differences of several orders of magnitude. This can be problematic in DNA metabarcoding and metagenomic high throughput sequencing approaches, as large specimens contribute over proportionally much DNA template. Thus a few specimens of high biomass will dominate the dataset, potentially leading to smaller specimens remaining undetected. Sorting of samples and balancing the amounts of tissue used per size fraction should improve detection rates, but has not been systematically tested.

2) Here we tested the effects of size sorting on taxa detection using freshwater macroinvertebrates. Kick sampling was performed at two locations of a low-mountain stream in West Germany, specimens were morphologically identified and sorted into small, medium and large size classes (< 2.5x5, 5x10 and up to 10x20 mm). Tissue from the 3 size categories was extracted individually, and pooled to simulate bulk samples that were not sorted and samples which were sorted and then pooled proportionately by specimen size. DNA from all 5 extractions of both samples was amplified using 4 different freshwater primer sets for the COI gene and sequenced on a HiSeq Illumina sequencer.

3) Sorting taxa by size and pooling them proportionately according to their abundance lead to a more equal amplification compared to the processing of complete samples without sorting. The sorted samples recovered 30% more taxa than the unsorted samples, at the same sequencing depth. Our results imply that sequencing depth can be decreased ~ 5 fold when sorting the samples into three size classes.

4) Our results demonstrate that even a coarse size sorting can substantially improve detection rates. While high throughput sequencing will become more accessible and cheaper within the next years, sorting bulk samples by specimen biomass is a simple yet efficient method to reduce current sequencing costs.
The piglet case: commensalism as a new category of intraspecific animal relationships
Authors: Skok Janko
Published: January 2018

Relationships among organisms are separated into two main categories: interspecific (between species) and intraspecific (within species). Interspecific relationships, termed symbiosis, are considered very diverse, and include protocooperation (+/+; facultative, not obligatory, cooperation) and mutualism (+/+) – both represent cooperative relationships, antagonism (-/-), agonism (+/-; including parasitism and predation), amensalism (0/-), neutralism (0/0; if it exists in nature at all), and commensalism (+/0). Intraspecific relationships have just two categories: cooperation (+/+) and competition (+/-). Supporting my latest findings on the suckling behaviour of piglets, I propose an extension of the classification for existing intraspecific relationships by adding a new category: commensalism. The present classification fails to define all interactions among members of the same species, as demonstrated by observations of suckling behaviour in domestic pigs.
Comprehensive family-based SNV association analysis shows new alleles associated to mealy traits in Prunus persica
Authors: Vizoso Paula , Meneses Claudio , Campos Reinaldo , Orellana Ariel
Published: January 2018

Identification of DNA markers associated with mealiness trait is an important tool to agricultural industry. Many peach breeding initiatives have as aim to improve early selection of varieties with better postharvest performance. We present a family-based approach to identify and develop an association panel to evaluate potential varieties susceptible to mealiness induced by chilling. We used whole-genome sequencing and SNV genotyping of parents and ten contrasting siblings (Juicy and mealy) obtained from segregating population of self-cross ‘Venus’. Results show that there are differences regarding SNVs and structural variants (SVs) that could be associated with mealy to be contrasted with individuals without such damage phenotype. Preliminary results showed a total of 30.564 SNVs and 2.297 SVs having a non-synonymous change in genes. Comparison of SNVs between segregants and parental revealed 1.963 SNVs associated genes presents in juicy segregants and 6.162 SNVs associated genes in segregants mealiness. We found 230 and 244 SVs with functional impact in genomes mealy and juicy. As proof of concept, all SNVs obtained were correlated with the information published in peach related to chilling injury (QTL genomic region, dbSNP, SDR chillpeach, upeach and RNA-seq available). Guided by preliminary analysis, we selected pools of alleles that display a frequency difference between mealy and juicy fruit and a selective sweep is observed around those alleles. Some of the SNVs have been previously correlated with chilling injury through transcriptome analysis. Additionally, we identify new genome regions associated with mealy susceptibility. Most of these genes were related to negative regulation of programmed cell death, cell surface receptors signaling pathways and cell wall remodeling. On the other hand, the genes affected by SV in the juicy segregating are classified according to the biological process in metabolism of sugars and fatty acid biosynthetic process. These results provide insights into genetics determinants related with susceptibility to mealiness. Analysis of the sequences revealed the existence of a high polymorphism rate in nectarines, and statistical analysis showed that the segments could be used as genetic barcodes that should be informative enough to allow reliable identification of cultivars. This study proposes a predictive panel of biomarkers to identify varieties at susceptible for mealiness and identifies new candidates genes linked to mealiness in peach.
Quantitative and correlation analysis of the DNA methylation and expression of DAPK in breast cancer
Authors: Zhu Youzhi , Li Shuiqin , Wang Qingshui , Chen Ling , Wu Kunlin , Huang Yide , Chen Xiangjin , Lin Yao
Published: January 2018

Backgound. Death associated protein kinase 1 (DAPK) is an important tumor suppressor kinase involved in the regulation of multiple cellular activities such as apoptosis and autophagy. DNA methylation of DAPK gene was found in various types of cancers and often correlated with the clinicopathological characteristics. However, the mRNA and protein expression of DAPK in the same sample was rarely measured. Thus it was unclear if the correlation between DAPK gene methylation and clinicopathological parameters was due to the loss of DAPK expression.

Methods. In this study, the DNA methylation rate, mRNA and protein expression of DAPK was quantitatively detected in 15 pairs of breast cancer patient samples including tumor (T) and adjacent non-tumor (N) tissues. Results. The correlation between DNA methylation rate and mRNA expression, together with the correlation between mRNA and protein expression, was calculated. No correlation was observed between any levels using either the measurement value of each sample or the T/N ratio of each pair.

Discussion. These data suggested the DNA methylation status of DAPK did not correlate well with its mRNA or protein expression. Extra caution is needed when interpreting the DNA methylation data of DAPK gene in clinical studies.
Malaysia Biosafety Act 2007 and Cartagena Protocol on Biosafety: A critical comparative analysis
Authors: Chan Kok-Gan
Published: January 2018

Advancement of modern biotechnology has wide impact on various industries. Modern biotechnology in the past has gone unregulated but the responsible use of biotechnology is the main focus worldwide. The most important living modified organisms (LMOs) regulatory framework is the Cartagena Protocol on Biosafety. This Protocol provides guidelines for the national legal framework. This paper aimed to perform comparative studies on Malaysia Biosafety Act 2007 and the Cartagena Protocol on Biosafety. The results show that while certain clauses in the Protocol are highly similar, and some proviso in the Biosafety Act 2007 are broader in scope, and conversely, certain clauses of the Protocol are well reflected in the Biosafety Act 2007. It is submitted that in overall perspective, Biosafety Act 2007 is consistent with the Protocol. It is concluded that Malaysia biosafety regulation system satisfies this international requirement. However, with regards to enforcement of this Act, it remains unanswered, as no precedent has been reported. Interestingly, non-compliance of some proviso in the Biosafety Act 2007 will result in criminal penalty, and its impacts on the research and development in the biotechnology industry, commercial investment from abroad and domestic markets, and international trading of LMOs as food and feed, remain to be seen.
Introduction to special series on endocrine disruption: Chemical testing, risk assessment approaches and implications
Authors: Leopold Annegaaike , Coady Katherine
Published: January 2018

This special series of six papers (this introductory paper and 5 other papers) is about the Focused Topic Meeting on Endocrine Disruption Chemical Testing; Risk Assessment Approaches and Implications (4 – 6 February, 2014, Raleigh, North Carolina). The workshop was composed of five sessions that each dealt with a specific topic. Broadly speaking the following themes were addressed: a) the status of the USEPA Endocrine Disruptor Screening Program, b) how data from both EDSP-directed testing and other sources may be interpreted and applied in regulatory settings and c) approaches for moving beyond estrogen, androgen and thyroid pathways to address current challenges and expanding future approaches to EDC testing. The series of publications summarizes the knowledge presented and discussed at the Focused Topic Meeting and organizes the information by session. Where relevant, the summaries are enhanced beyond the original ideas of the presentations during the meeting. It is the intention of the Steering Committee that these publications will act not only as a record of the proceedings of the meeting, but also as a valuable resource.
Doctor safety in Australian after-hours house-call medical services: the use of chaperones and chauffeurs
Authors: Ifediora Chris Onyebuchi
Published: January 2018

Objectives: The use of escorts (chauffeurs and chaperones) while on duty in after-hours-house-call (AHHC) is one key protective option available to doctors in the service and has been linked to low burnout and increased satisfaction in AHHC. This study aims to explore the patterns of engagement of escorts in Australian AHHC.

Method: A questionnaire-based, electronic survey of all 300 doctors involved in AHHC through the National Home Doctor Service (NHDS), Australia’s largest providers of the service.

Results: A total of 168 valid responses (56.0%) were received. 60.8% of the doctors engaged escorts. Of the doctors that engage chauffeurs, three-quarters do so “all or most times”, while only one-quarter engage chaperones to the same degree of frequency. Hiring escorts is very popular among Brisbane (91.7%) and Sydney-based (88.2%) practitioners, but is unpopular in the City of Gold Coast (26.1%). There were moderate patronages in Adelaide (52.9%) and Melbourne (46.4%).

Compared to females, males were more likely to drive themselves (OR 5.34; P=0.001; CI 2.08 to 13.74) and less likely to use chauffeurs (OR 0.19; p<0.001; CI 0.07 to 0.51). Doctors in legally recognized social unions (OR 0.24; p=0.03; CI 0.07 to 0.83) and those that have attained the postgraduate fellowships (OR 0.43; p=0.02; CI 0.21 to 0.87) were both less likely to work without escorts.

Conclusion: More needs to be done to increase the engagement of escorts by doctors involved in the Australian AHHC, particularly given their proven benefits in the service. Future studies may be needed to fully explore the real reasons behind the significant associations identified in this study.
Introduction to the science and regulation concerning endocrine disrupting chemicals: the challenges ahead
Authors: Leopold Annegaaike , Van Der Kraak Glen , Manibusan Mary K. , Andersson Niklas , Wheeler James R.
Published: January 2018

Presentations in session one of the Society of Environmental Toxicology and Chemistry (SETAC) North America Focused Topic Meeting: Endocrine Disruption (February 4 – 6, 2014) described where the science and the regulations have arrived and identified the key challenges that lie ahead. The first presentation gave an overview of where the endocrine disrupting chemical (EDC) issue currently stands in terms of science and policy. It introduced the significant debate about whether suspected EDCs should be evaluated using a hazard-based or a risk-based approach. Subsequent presentations provided a synopsis of the US-EPA Endocrine Disruption Screening Program (EDSP), including a description of the legislative origins of the program, its risk-based nature, its evolution and its future through the input of multi-stakeholder advisory groups. A presentation was given about the current status of potential regulatory activities in the European Union (EU) relative to EDCs and the fact that it is a highly political subject in Europe was highlighted. Finally an EU- industry perspective was given on the repercussions of hazard versus risk-based approaches for EDCs. Both European speakers noted that the regulatory situation in the EU is not set and that at present it is not possible to predict exactly how EDCs will be addressed.
Influence of different types of sessile epibionts on the community structure of mobile invertebrates in an eelgrass bed
Authors: Momota Kyosuke , Nakaoka Masahiro
Published: January 2018

The variation in the biomass, abundance and diversity of mobile invertebrates in eelgrass (Zostera marina) beds has been examined in relation to various abiotic and biotic factors, such as water temperature, salinity, eelgrass biomass and epiphytic microalgae presence. However, the importance of sessile epibionts, such as macroalgae and calcific spirorbid polychaetes attached to eelgrass blades, has not been the focus of previous studies. In the present study, we examined the effects of three different sessile epibionts, namely, branched red algae, filamentous green algae, and calcific spirorbid polychaetes, on the biomass and diversity of mobile invertebrates in the eelgrass beds of Akkeshi in Northeastern Japan. The relationships of the dominant mobile invertebrate biomass, the total biomass of mobile invertebrates and the species diversity to multiple abiotic and biotic variables were analyzed using a linear mixed model. Our results show that large-sized epibiotic organisms can be good predictors of the variation in the total biomass, species richness and species diversity of mobile invertebrates and the biomass of major dominant species, especially for species that have a relatively high dependency on eelgrass blades. These results suggest that the different functional groups of sessile epibionts have significant roles in determining the biomass and diversity of mobile invertebrates in eelgrass beds.
Somatic inhibition controls dendritic selectivity in a sparse coding network of spiking neurons
Authors: Drix Damien
Published: January 2018

Sparse coding is an effective operating principle for the brain, one that can guide the discovery of features and support the learning of assocations. Here we show how spiking neurons with discrete dendrites can learn sparse codes via an online, nonlinear Hebbian rule based on the concept of somato-dendritic mismatch. The rule gives lateral inhibition direct control over the selectivity of dendritic receptive fields, without the need for a sliding threshold. The network discovers independent components that are similar to the features learned by a sparse autoencoder. This improves the linear decodability of the input: combined with a linear readout, our single-layer network performs as well as a deeper multi-layer Perceptron on the MNIST dataset. It can also produce topographic feature maps when the lateral connections are organised in a center-surround pattern, although this does not improve the quality of the encoding.
Endocrine disruption: where have we been, interpretation of data, and lessons learned from Tier 1
Authors: Staveley Jane P , Touart Leslie W , Solomon Keith , Mihaich Ellen , Blankinship Amy , Ankley Gerald
Published: January 2018

In response to the requirements of the US EPA’s Endocrine Disruptor Screening Program, Tier 1 assays have been performed with a number of pesticides over the past several years. These assays are designed to be used in concert as a screen for potential interactions with vertebrate estrogen, androgen, and thyroid systems. The results of the 11 assays in the Tier 1 battery are then used, along with other lines of evidence, to determine whether a chemical is endocrine-active and, as a consequence, might be a candidate for Tier 2 testing. An overview of the Tier-1 testing program was presented in Session Two of the Society of Environmental Toxicology and Chemistry (SETAC) North America Focused Topic Meeting: Endocrine Disruption Chemical Testing: Risk Assessment Approaches and Implications (February 4 – 6, 2014). Subsequent presentations discussed the concept of weight-of-evidence (WoE) and assessment of Tier 1 results in a WoE framework. The importance of scientifically credible, transparent approaches for conducting WoE analyses was recognized, and approaches for framing the hypotheses, evaluating the data, assigning weight to different endpoints relative to their diagnostic effectiveness, and assessing confounding factors were presented. In recognition of the cross-species conservation of the hypothalamic-pituitary-gonadal axis among vertebrates, a subset of the Tier-1 in vivo assays may be useful for more rapidly screening chemicals for potential endocrine activity.
General purpose medical digital library definition
Authors: Rocha-Pereira Tiago , Lopes-Santos Jose A , Martins Antonio Constantion L
Published: January 2018

The need of an approach for the definition of a platform-independent medical digital library, using only open-source tools, will be described. To test the need and the success of such an approach, a library will be created, which can later be used in a larger scale as a general purpose digital medical tool, when comes the need to evaluate an image. As a first test, the library will be used in the development of a tool aimed to aid doctors in otoplasty candidates’ evaluation. This tool shall be developed and tested first on a mobile platform, so the potential of the developed library can be tested on the most adverse situation. Also, the resulting library will be license free, making easier the collaboration of others in development and integration with other software, translating in a better spread of the library in medical practice
New data towards the development of a comprehensive taphonomic framework for the Cleveland-Lloyd Dinosaur Quarry
Authors: Peterson Joseph E , Warnock Jonathan P , Eberhart Shawn L , Clawson Steven R , Noto Christopher R
Published: January 2018

The Cleveland-Lloyd Dinosaur Quarry (CLDQ) is the densest deposit of Jurassic theropod dinosaurs discovered to date. Unlike typical Jurassic bone deposits, it is dominated by the presence of Allosaurus fragilis. Since excavation began in the 1920’s numerous hypotheses have been put forward to explain the taphonomy of CLDQ, including a predator trap, a drought assemblage, and a poison spring. In an effort to reconcile the various interpretations of the quarry and reach a consensus on the depositional history of CLDQ, new data is required to develop a robust taphonomic framework congruent with all available data. Here we present two new data sets which aid in the development of such a robust taphonomic framework for CLDQ. First, x-ray fluorescence of CLDQ sediments indicate elevated barite and sulfide minerals relative to other sediments from the Morrison Formation, suggesting an ephemeral environment dominated by periods of hypereutrophic conditions during bone accumulation. Second, the degree of weathering and hydraulic equivalency of small bone fragments dispersed throughout the matrix were analyzed from CLDQ. Results of these analyses suggest that bone fragments are autochthonous or parautochthonous and are derived from bones deposited in the assemblage. The variability in abrasion exhibited by the fragments is most parsimoniously explained by periodic reworking and redeposition during seasonal fluctuations throughout the duration of the quarry assemblage. Collectively, these data support some previous interpretations that the CLDQ represents an attritional assemblage in a poorly-drained overbank deposit where vertebrate remains were introduced post-mortem to an ephemeral pond during flood conditions. Furthermore, elevated heavy metals and rare earth elements detected at the quarry are likely a diagenetic signal, potentially produced in part from an abundance of vertebrate remains, and not the primary driver for the accumulation of carcasses. These new data help to explain the specific depositional environment of the quarry, and represent a significant step in understanding the taphonomy of the bone bed and late Jurassic paleoecology.
Anatomy of a crash repository
Authors: Campbell Joshua C , Santos Eddie Antonio , Hindle Abram
Published: January 2018

This work investigates the properties of crash reports collected from Ubuntu Linux users. Understanding crash reports is important to better store, categorize, prioritize, parse, triage, assign bugs to, and potentially synthesize them. Understanding what is in a crash report, and how the metadata and stack traces in crash reports vary will help solve, debug, and prevent the causes of crashes. 10 different aspects of 40,592 crash reports about 1,921 pieces of software submitted by users and developers to the Ubuntu project were analyzed, plotted, and statistical distributions were fitted to some of them. We investigated the structure and properties of crash reports. Crashes have many properties that seem to have distributions similar to standard statistical distributions, but with even longer tails than expected. These aspects of crash reports have not been analyzed statistically before. We found that many applications only had a single crash, while a few applications had a large number of crashes reported. Crash bucket size (clusters of similar crashes) also followed a Zipf-like distribution. The lifespan of buckets ranged from less than an hour to over four years. Some stack traces were short, and some were so long they were truncated by the tool that produced them. Many crash reports had no recursion, some contained recursion, and some displayed evidence of unbounded recursion. Linguistics literature hinted that sentence length follows a gamma distribution; this is not the case for function name length. Additionally, only two hardware architectures, and a few signals are reported for almost all of the crashes in the Ubuntu dataset. Many crashes were similar but there were also many unique crashes. This study of crashes from 1,921 projects will be valuable for anyone who wishes to: cluster or deduplicate crash reports, synthesize or simulate crash reports, store or triage crash reports, or data-mine crash reports.
Tracheophyte phylogeny poster - Vascular plants: systematics and characteristics
Authors: Cole Theodor C H , Hilger Hartmut H
Published: January 2018

The "Tracheophyte Phylogeny Poster – Vascular Plants: Systematics and Characteristics" is an educational tool presenting an overview of the evolutionary relationships among vascular plants as of 2016. The phylogenetic tree depicts orders and families (incl. genera in gymnosperms), listing the main apomorphies and plesiomorphies as well as diagnostic and nondiagnostic anatomical and morphological features. The intuitive color-coding facilitates memorization and teaching. Translations of the poster into various languages are being made available. The recommendations of the Pteridophyte Phylogeny Group (PPG) are followed here. This is one in a series of three educational posters on the phylogeny of land plants: Poster 1: "Angiosperms", Poster 2: "Tracheophytes: Lycophytes, Ferns, Gymnosperms", Poster 3: "Bryophytes: Liverworts, Mosses, Hornworts".
Challenges as enablers for high quality linked data: Insights from the semantic publishing challenge
Authors: Dimou Anastasia , Vahdati Sahar , Di Iorio Angelo , Lange Christoph , Verborgh Ruben , Mannens Erik
Published: January 2018

While most challenges organized so far in the Semantic Web domain are focused on comparing tools with respect to different criteria such as their features and competencies, or exploiting semantically enriched data, the Semantic Web Evaluation Challenges series, co-located with the ESWC Semantic Web Conference, aims to compare them based on their output, namely the produced dataset. The Semantic Publishing Challenge is one of these challenges. Its goal is to involve participants in extracting data from heterogeneous sources on scholarly publications, and producing Linked Data that can be exploited by the community itself. This paper reviews lessons learned from both (i) the overall organization of the Semantic Publishing Challenge, regarding the definition of the tasks, building the input dataset and forming the evaluation, and (ii) the results produced by the participants, regarding the proposed approaches, the used tools, the preferred vocabularies and the results produced in the three editions of 2014, 2015 and 2016. We compared these lessons to other Semantic Web Evaluation challenges. In this paper, we (i) distill best practices for organizing such challenges that could be applied to similar events, and (ii) report observations on Linked Data publishing derived from the submitted solutions. We conclude that higher quality may be achieved when Linked Data is produced as a result of a challenge, because the competition becomes an incentive, while solutions become better with respect to Linked Data publishing best practices when they are evaluated against the rules of the challenge.
Curating GitHub for engineered software projects
Authors: Munaiah Nuthan , Kroh Steven , Cabrey Craig , Nagappan Meiyappan
Published: January 2018

Software forges like GitHub host millions of repositories. Software engineering researchers have been able to take advantage of such a large corpora of potential study subjects with the help of tools like GHTorrent and Boa. However, the simplicity in querying comes with a caveat: there are limited means of separating the signal (e.g. repositories containing engineered software projects) from the noise (e.g. repositories containing home work assignments). The proportion of noise in a random sample of repositories could skew the study and may lead to researchers reaching unrealistic, potentially inaccurate, conclusions. We argue that it is imperative to have the ability to sieve out the noise in such large repository forges. We propose a framework, and present a reference implementation of the framework as a tool called reaper, to enable researchers to select GitHub repositories that contain evidence of an engineered software project. We identify software engineering practices (called dimensions) and propose means for validating their existence in a GitHub repository. We used reaper to measure the dimensions of 1,994,977 GitHub repositories. We then used the data set train classifiers capable of predicting if a given GitHub repository contains an engineered software project. The performance of the classifiers was evaluated using a set of 200 repositories with known ground truth classification. We also compared the performance of the classifiers to other approaches to classification (e.g. number of GitHub Stargazers) and found our classifiers to outperform existing approaches. We found stargazers-based classifier to exhibit high precision (96%) but an inversely proportional recall (27%). On the other hand, our best classifier exhibited a high precision (82%) and a high recall (83%). The stargazer-based criteria offers precision but fails to recall a significant potion of the population.
Semi-automatic wavelet soft-thresholding applied to digital image error level analysis
Authors: Jeronymo Daniel C
Published: January 2018

In this paper a method for detection of image forgery in lossy compressed digital images known as error level analysis (ELA) is presented and it's noisy components are filtered with automatic wavelet soft-thresholding. With ELA, a lossy compressed image is recompressed at a known error rate and the absolute differences between these images, known as error levels, are computed. This method might be weakened if the image noise generated by the compression scheme is too intense, creating the necessity of noise filtering. Wavelet thresholding is a proven denoising technique which is capable of removing an image's noise avoiding altering other components, like high frequencies regions, by thresholding the wavelet transform coefficients, thus not causing blurring. Despite its effectiveness, the choice of the threshold is a known issue. However there are some approaches to select it automatically. In this paper, a lowpass filter is implemented through wavelet thresholding, attenuating error level noises. An efficient method to automatically determine the threshold level is used, showing good results in threshold selection for the presented problem. Standard test images have been doctored to simulate image tampering, error levels for these images are computed and wavelet thresholding is performed to attenuate noise. Results are presented, confirming the method's efficiency at noise filtering while preserving necessary error levels.
Genome sequencing and analysis of the genome of Acidithiobacillus ferrooxidans strain DLC-5, a heavy metal resistant strain from acid mine drainage in northeast China
Authors: Chen Peng , Xu Ruixiang , Yan Zheng , Yan Lei , Wu Zhengrong , Wei Yan , Zhao Wenbin , Li Hongyu
Published: January 2018

Acidithiobacillus ferrooxidans ( A. ferrooxidans ) is a gram-negative, extremely acidophilic, mesophilic, chemolithotrophic bacterium and the most well-studied acidophilic organism which is usually found in acid environments such as acid mine drainage. The draft genome sequence of A. ferrooxidans ATCC 23270 was first reported in 2000, fourteen years ago. Here we describe the features of this organism, together with the draft genome sequence, and annotation. This is the draft genome sequence from the A. ferrooxidans, and the 3,142,890 bp long single replicon genome with its 32,719 protein-coding and 64 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Bacterial project.
A probabilistic model to recover individual genomes from metagenomes
Authors: Dröge Johannes , Schönhuth Alexander , McHardy Alice C
Published: January 2018

Shotgun metagenomics of microbial communities reveals information about strains of relevance for applications in medicine, biotechnology and ecology. Recovering their genomes is a crucial, but very challenging step, due to the complexity of the underlying biological system and technical factors. Microbial communities are heterogeneous, with oftentimes hundreds of present genomes deriving from different species or strains, all at varying abundances and with different degrees of similarity to each other and reference data. We present a versatile probabilistic model for genome recovery and analysis, which aggregates three types of information that are commonly used for genome recovery from metagenomes. As potential applications we showcase metagenome contig classification, genome sample enrichment and genome bin comparisons. The open source implementation MGLEX is available via the Python Package Index and on GitHub and can be embedded into metagenome analysis workflows and programs.
Software vs. data in the context of citation
Authors: Katz Daniel S , Niemeyer Kyle E , Smith Arfon M , Anderson William L , Boettiger Carl , Hinsen Konrad , Hooft Rob , Hucka Michael , Lee Allen , Löffler Frank , Pollard Tom , Rios Fernando
Published: January 2018

Software is data, but it is not just data. While "data" in computing and information science can refer to anything that can be processed by a computer, software is a special kind of data that can be a creative, executable tool that operates on data. However, software and data are similar in that they both traditionally have not been cited in publications. This paper discusses the differences between software and data in the context of citation, by providing examples and referring to evidence in the form of citations.
The qPMO network: quality management tools to improve research efficiency, reproducibility, data management and dissemination
Authors: Bongiovanni Antonella , Liguori Giovanna Lucia , Colotti Gianni , Cirafici Anna Maria , Di Carlo Marta , Digilio Filomena Anna , Lacerra Giuseppina , Lanati Antonella , Mascia Anna , Kisslinger Annamaria
Published: January 2018

Quality disciplines have been widely used for decades in industrial and business fields. It is only in recent times, however, that Quality management and approaches have received proper attention in life science. In particular, the need for Quality standards in non-regulated research is a matter of considerable current debate inside international research community. The Quality and Project Management OpenLab (qPMO) is a research network involving 5 different Institutes and two Departmentes of the Italian National Research Council (CNR), aimed at realizing a Total Quality Management (TQM) model for Life Sciences laboratories. This TQM OpenLab model will act as a uniform environment in which strong, innovation-oriented research projects can be designed and developed according to international Quality standards and with the planning of Horizon 2020. Our experience demonstrates that Quality management tools can strongly support the management of scientific research through disseminating knowledge, best practice and interoperability and enhance of the economic value of project and research outcomes.
Local genes for local bacteria: evidence of allopatry in the genomes of transatlantic Campylobacter populations
Authors: Pascoe Ben , Meric Guillaume , Yahara Koji , Wimalarathna Helen , Murray Susan , Hitchings Matthew D , Sproston Emma L , Carrillo Catherine D , Taboada Eduardo N , Cooper Kerry K , Huynh Steven , Cody Alison J , Jolley Keith A , Maiden Martin CJ , McCarthy Noel D , Didelot Xavier , Parker Craig , Sheppard Samuel K
Published: January 2018

The genetic structure of bacterial populations can be related to geographical locations of isolation. In some species, there is a strong correlation between geographical distance and genetic distance, which can be caused by different evolutionary mechanisms. Patterns of ancient admixture in Helicobacter pylori can be reconstructed in concordance with past human migration, whereas in Mycobacterium tuberculosis it is the lack of recombination that causes allopatric clusters. In Campylobacter , analyses of genomic data and molecular typing have been successful in determining the reservoir host species, but not geographical origin. We investigated biogeographical variation in highly recombining genes to determine the extent of clustering between genomes from geographically distinct Campylobacter populations. Whole genome sequences from 294 Campylobacter isolates from North America and the UK were analysed. Isolates from within the same country shared more recently recombined DNA than isolates from different countries. Using 15 UK/American closely matched pairs of isolates that shared ancestors, we identify regions that have frequently and recently recombined to test their correlation with geographical origin. The seven genes that demonstrated the greatest clustering by geography were used in an attribution model to infer geographical origin which was tested using a further 383 UK clinical isolates to detect signatures of recent foreign travel. Patient records indicated that in 46 cases travel abroad had occurred less than two weeks prior to sampling and genomic analysis identified that 34 (74%) of these isolates were of a non-UK origin. Identification of biogeographical markers in Campylobacter genomes will contribute to improved source attribution of clinical Campylobacter infection and inform intervention strategies to reduce campylobacteriosis.
Species-specific pharmacology of maximakinin, an amphibian homologue of bradykinin: putative prodrug activity at the human B2 receptor and peptidase resistance in rat
Authors: Charest-Morin Xavier , Bachelard Hélène , Jean Melissa , Marceau Francois
Published: January 2018

Maximakinin (MK), an amphibian peptide possessing the C-terminal sequence of bradykinin (BK), is a BK B2 receptor (B2R) agonist eliciting prolonged signaling. We reinvestigated this 19-mer for species-specific pharmacologic profile, in vivo confirmation of resistance to inactivation by angiotensin converting enzyme (ACE), value as a module for the design of fusion proteins that bind to the B2R in mammalian species and potential activity as a histamine releaser. Competition of the binding of [3H]BK to recombinant human myc-B2Rs in cells that express these receptors revealed that MK possessed a tenuous fraction (<0.1%) of the affinity of BK, despite being only ~10-fold less potent than BK in a contractility assay based on the human isolated umbilical vein. These findings are reconciled by the generation of C-terminal fragments, like Lys-Gly-Pro-BK and Gly-Pro-BK, when the latent MK is incubated with human venous tissue (LC-MS), supporting activation via hydrolysis upstream of the BK sequence. At the rat recombinant myc-B2R, MK had a lesser affinity than that of BK, but with a narrower margin (6.2-fold, radioligand binding competition). Accordingly, MK (10 nM) stimulated calcium transients in cells that expressed the rat receptors, but not the human B2R. Recombinant MRGPRX2, a receptor that mediates cationic peptide-induced mast cell secretion, minimally responded by increased [Ca+2]i to MK at 10 μM. Enhanced green fluorescent protein fused to MK (EGFP-MK) labeled cells that expressed rat, but not human B2Rs. Intravenous MK induced dose-dependent hypotensive, vasodilator and tachycardic responses in anesthetized rats and the effects were antagonized by pretreatment with icatibant but not modified by pyrilamine or enalaprilat. Strong species-specific responses to the toxin-derived peptide MK and its prodrug status in the isolated human vein were evidenced. Accordingly, MK in the EGFP-MK fusion protein is a pharmacophore module that confers affinity for the rat B2R, but not for the human form of the B2R. MK is unlikely to be an efficient mast cell activator, but its resistance to inactivation by ACE was confirmed in vivo.