bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial and temporal variability of aerobic anoxygenic photoheterotrophic bacteria along the east coast of Australia
Authors: Bibiloni‐Isaksson Jaime , Seymour Justin R. , Ingleton Tim , van de Kamp Jodie , Bodrossy Levente , Brown Mark V. 
Published: July 2016

SummaryAerobic Anoxygenic Phototrophic Bacteria (AAnPB) are ecologically important microorganisms, widespread in oceanic photic zones. However, the key environmental drivers underpinning AAnPB abundance and diversity are still largely undefined. The temporal patterns in AAnPB dynamics at three oceanographic reference stations spanning at approximately 15° latitude along the Australian east coast were examined. AAnPB abundance was highly variable, with pufM gene copies ranging from 1.1 × 102 to 1.4 × 105 ml−1 and positively correlated with day length and solar radiation. pufM gene Miseq sequencing revealed that the majority of sequences were closely related to those obtained previously, suggesting that key AAnPB groups are widely distributed across similar environments globally. Temperature was a major structuring factor for AAnPB assemblages across large spatial scales, correlating positively with richness and Gammaproteobacteria (phylogroup K) abundance but negatively with Roseobacter‐clade (phylogroup E) abundance, with temperatures between 16°C and 18°C identified as a potential transition zone between these groups. Network analysis revealed that discrete AAnPB populations exploit specific niches defined by varying temperature, light and nutrient conditions in the Tasman Sea system, with evidence for both niche sharing and partitioning amongst closely related operational taxonomic units.
Petroleum hydrocarbon contamination, plant identity and arbuscular mycorrhizal fungal (AMF) community determine assemblages of the AMF spore‐associated microbes
Authors: Iffis Bachir , St‐Arnaud Marc , Hijri Mohamed 
Published: July 2016

SummaryThe root‐associated microbiome is a key determinant of pollutant degradation, soil nutrient availability and plant biomass productivity, but could not be examined in depth prior to recent advances in high‐throughput sequencing. Arbuscular mycorrhizal fungi (AMF) form symbioses with the majority of vascular plants. They are known to enhance mineral uptake and promote plant growth and are postulated to influence the processes involved in phytoremediation. Amplicon sequencing approaches have previously shown that petroleum hydrocarbon pollutant (PHP) concentration strongly influences AMF community structure in in situ phytoremediation experiments. We examined how AMF communities and their spore‐associated microbiomes were structured within the rhizosphere of three plant species growing spontaneously in three distinct waste decantation basins of a former petrochemical plant. Our results show that the AMF community was only affected by PHP concentrations, while the AMF‐associated fungal and bacterial communities were significantly affected by both PHP concentrations and plant species identity. We also found that some AMF taxa were either positively or negatively correlated with some fungal and bacterial groups. Our results suggest that in addition to PHP concentrations and plant species identity, AMF community composition may also shape the community structure of bacteria and fungi associated with AMF spores.
Microbial biotechnology for the synthesis of (pro)vitamins, biopigments and antioxidants: challenges and opportunities
Authors: Revuelta Jose L. , Buey Ruben M. , Ledesma‐Amaro Rodrigo , Vandamme Erick J. 
Published: July 2016

SummaryVitamins and related compounds, such as provitamins, biopigments and antioxidants, belong to those few chemicals that appeal in a positive way to most people. These terms sound synonymous to vitality, good health and mental strenght, even to the layman. Everyone of us needs his/her daily intake of (pro)vitamins and antioxidants, normally provided by a balanced and varied diet. However, current food habits or preferences, food availabilities, as well as food processing, preservation or cooking methodologies and technologies, do not always assure a sufficient balanced natural daily (pro)vitamin supply to a healthy individual, and even more so for a stressed or sick human being. Today, modern society is seldom confronted with the notorious avitaminoses of the past, well known to the Western World, but they do still occur frequently in overpopulated, war‐ridden, poverty‐ or famine‐struck regions on our globe, as well as for surprisingly large population groups in developed countries.
A cost‐effective high‐throughput metabarcoding approach powerful enough to genotype ~44 000 year‐old rodent remains from Northern Africa
Authors: Guimaraes S. , Pruvost M. , Daligault J. , Stoetzel E. , Bennett E. A. , Côté N. M.‐L. , Nicolas V. , Lalis A. , Denys C. , Geigl E.‐M. , Grange T. 
Published: July 2016

AbstractWe present a cost‐effective metabarcoding approach, aMPlex Torrent, which relies on an improved multiplex PCR adapted to highly degraded DNA, combining barcoding and next‐generation sequencing to simultaneously analyse many heterogeneous samples. We demonstrate the strength of these improvements by generating a phylochronology through the genotyping of ancient rodent remains from a Moroccan cave whose stratigraphy covers the last 120 000 years. Rodents are important for epidemiology, agronomy and ecological investigations and can act as bioindicators for human‐ and/or climate‐induced environmental changes. Efficient and reliable genotyping of ancient rodent remains has the potential to deliver valuable phylogenetic and paleoecological information. The analysis of multiple ancient skeletal remains of very small size with poor DNA preservation, however, requires a sensitive high‐throughput method to generate sufficient data. We show this approach to be particularly adapted at accessing this otherwise difficult taxonomic and genetic resource. As a highly scalable, lower cost and less labour‐intensive alternative to targeted sequence capture approaches, we propose the aMPlex Torrent strategy to be a useful tool for the genetic analysis of multiple degraded samples in studies involving ecology, archaeology, conservation and evolutionary biology.
Binge Drinking Decreases Corticotropin‐Releasing Factor‐Binding Protein Expression in the Medial Prefrontal Cortex of Mice
Authors: Ketchesin Kyle D. , Stinnett Gwen S. , Seasholtz Audrey F. 
Published: July 2016

BackgroundDysregulation of the corticotropin‐releasing factor (CRF) system has been observed in rodent models of binge drinking, with a large focus on CRF receptor 1 (CRF‐R1). The role of CRF‐binding protein (CRF‐BP), a key regulator of CRF activity, in binge drinking is less well understood. In humans, single‐nucleotide polymorphisms in CRHBP are associated with alcohol use disorder and stress‐induced alcohol craving, suggesting a role for CRF‐BP in vulnerability to alcohol addiction.MethodsThe role and regulation of CRF‐BP in binge drinking were examined in mice exposed to the drinking in the dark (DID) paradigm. Using in situ hybridization, the regulation of CRF‐BP, CRF‐R1, and CRF mRNA expression was determined in the stress and reward systems of C57BL/6J mice after repeated cycles of DID. To determine the functional role of CRF‐BP in binge drinking, CRF‐BP knockout (CRF‐BP KO) mice were exposed to 6 cycles of DID, during which alcohol consumption was measured and compared to wild‐type mice.ResultsCRF‐BP mRNA expression was significantly decreased in the prelimbic (PL) and infralimbic medial prefrontal cortex (mPFC) of C57BL/6J mice after 3 cycles and in the PL mPFC after 6 cycles of DID. No significant changes in CRF or CRF‐R1 mRNA levels were observed in mPFC, ventral tegmental area, bed nucleus of the stria terminalis, or amygdala after 3 cycles of DID. CRF‐BP KO mice do not show significant alterations in drinking compared to wild‐type mice across 6 cycles of DID.ConclusionsThese results reveal that repeated cycles of binge drinking alter CRF‐BP mRNA expression in the mPFC, a region responsible for executive function and regulation of emotion and behavior, including responses to stress. We observed a persistent decrease in CRF‐BP mRNA expression in the mPFC after 3 and 6 DID cycles, which may allow for increased CRF signaling at CRF‐R1 and contribute to excessive binge‐like ethanol consumption.
Alcohol Vapor Inhalation as a Model of Alcohol‐Induced Organ Disease
Authors: Mouton Alan J. , Maxi John K. , Souza‐Smith Flavia , Bagby Gregory J. , Gilpin Nicholas W. , Molina Patricia E. , Gardner Jason D. 
Published: July 2016

BackgroundChronic intermittent ethanol vapor (CIEV) exposure has been used extensively to produce rodent models of alcohol dependence, but unlike other models of alcohol abuse, CIEV has not been assessed as a model of end‐organ damage. The purpose of this study was to characterize the effects of CIEV on peripheral organ systems affected by alcohol abuse, including the liver, lungs, and cardiovascular system.MethodsAdult male Sprague‐Dawley rats were exposed to daily CIEV for a period of 8 weeks (14HR ON/10HR OFF), producing blood alcohol levels of ~200 mg/dl. Controls were exposed to room air. After 8 weeks, echocardiography was performed to assess cardiac function. Indices of liver injury (alanine and aspartate aminotransferases [ALT and AST]; cytochrome p450 2E1 [CYP2E1]; alcohol dehydrogenase [ADH]; Oil Red O and triglyceride content; lipid peroxidation; inflammatory cytokine expression; and macrophage infiltration), and lung inflammatory cell count, proinflammatory cytokine expression, and lipid peroxidation were measured.ResultsLeft ventricular posterior wall thickness was significantly decreased, and systolic blood pressure was significantly elevated by CIEV compared with air controls. CIEV led to a significant increase in plasma ALT and triglycerides compared with room air controls. CIEV did not affect liver triglyceride content, lipid staining or peroxidation, but increased CYP2E1 and chemokine (C‐C motif) ligand 2 (CCL2) protein expression, while decreasing ADH expression. CIEV significantly increased numbers of both polymorphonuclear neutrophils and lymphocytes in the bronchoalveolar lavage fluid, indicative of pulmonary inflammation. However, CIEV did not produce significant changes in lung mass, pulmonary lipid peroxidation, inflammatory cytokine expression, or edema.ConclusionsThese results show that CIEV produces hepatic, pulmonary, and cardiovascular effects in rats similar to those found in other models of chronic alcohol administration. Alcohol vapor administration is a novel method of alcohol‐induced tissue injury with high potential for widespread use in alcohol toxicology research.
Improving Connectivity in Indonesia: The Challenges of Better Infrastructure, Better Regulations, and Better Coordination
Authors: Sandee Henry 
Published: July 2016

AbstractThis paper presents and discusses the main challenges that an archipelago like Indonesia is facing in improving its connectivity. Distinguishing between intra‐island, inter‐island, and international connectivity is essential in order to understand the nature of the challenges and causes behind the bottlenecks. High domestic shipping costs are identified as one key challenge. The Government of Indonesia has identified improved connectivity as a key issue in promoting economic growth, especially in the manufacturing sector, now that Indonesia can no longer rely on commodities as a driver of growth. Better infrastructure, regulations, and coordination among stakeholders are crucial components in promoting improved connectivity for manufacturing growth. Promoting investment in infrastructure is necessary, including both hard and soft infrastructure. However, Indonesian experience highlights that without regulatory reform and improved policy coordination, infrastructure investment will continue to lag behind. There is a need for an improved and empowered governance structure to turn investment plans into reality.
A Bootstrap Likelihood Approach to Bayesian Computation
Authors: Zhu Weixuan , Marin J. Miguel , Leisen Fabrizio 
Published: July 2016

SummaryThere is an increasing amount of literature focused on Bayesian computational methods to address problems with intractable likelihood. One approach is a set of algorithms known as Approximate Bayesian Computational (ABC) methods. One of the problems with these algorithms is that their performance depends on the appropriate choice of summary statistics, distance measure and tolerance level. To circumvent this problem, an alternative method based on the empirical likelihood has been introduced. This method can be easily implemented when a set of constraints, related to the moments of the distribution, is specified. However, the choice of the constraints is sometimes challenging. To overcome this difficulty, we propose an alternative method based on a bootstrap likelihood approach. The method is easy to implement and in some cases is actually faster than the other approaches considered. We illustrate the performance of our algorithm with examples from population genetics, time series and stochastic differential equations. We also test the method on a real dataset.
Steroid dependency and trends in prescribing for inflammatory bowel disease – a 20‐year national population‐based study
Authors: Chhaya V. , Saxena S. , Cecil E. , Subramanian V. , Curcin V. , Majeed A. , Pollok R. C. 
Published: July 2016

SummaryBackgroundIt is unclear whether adherence to prescribing standards has been achieved in inflammatory bowel disease (IBD).AimTo determine how prescribing of 5‐aminosalicylates (5‐ASAs), steroids and thiopurines has changed in response to emerging evidence.MethodsWe examined trends in oral and topical therapies in 23 509 incident IBD cases (6997 with Crohn's disease and 16 512 with ulcerative colitis) using a nationally representative sample between 1990 and 2010. We created five eras according to the year of diagnosis: era 1 (1990–1993), era 2 (1994–1997), era 3 (1998–2001), era 4 (2002–2005) and era 5 (2006–2010). We calculated the proportion of patients treated with prolonged 5‐ASAs (>12 months) and steroid dependency, defined as prolonged steroids (>3 months) or recurrent (restarting within 3 months) steroid exposure. We calculated the cumulative probability of receiving each medication using survival analysis.ResultsHalf of the Crohn's disease patients were prescribed prolonged oral 5‐ASAs during the study, although this decreased between era 3 and 5 from 61.8% to 56.4% (P = 0.002). Thiopurine use increased from 14.0% to 47.1% (P < 0.001) between era 1 and 5. This coincided with a decrease in steroid dependency from 36.5% to 26.8% (P < 0.001) between era 1 and 2 and era 4 and 5 respectively.In ulcerative colitis, 49% of patients were maintained on prolonged oral 5‐ASAs. Despite increasing thiopurine use, repeated steroid exposure increased from 15.3% to 17.8% (P = 0.02) between era 1 and 2 and era 4 and 5 respectively.ConclusionsPrescribing in clinical practice insufficiently mirrors the evidence base. Physicians should direct management towards reducing steroid dependency and optimising 5‐ASA use in patients with IBD.
Socioeconomic factors and penile cancer risk and mortality; a population‐based study
Authors: Torbrand Christian , Wigertz Annette , Drevin Linda , Folkvaljon Yasin , Lambe Mats , Håkansson Ulf , Kirrander Peter 
Published: July 2016

ObjectiveTo investigate possible associations between socioeconomic status (SES) and penile cancer risk, stage at diagnosis, and mortality.Patients/subjects and methodsA population‐based register study including men in Sweden diagnosed with penile cancer between 2000 and 2012 (1676 men) and randomly chosen controls (9872 men). Data were retrieved from the National Penile Cancer Register (NPECR) and several other population‐based healthcare and sociodemographic registers. Educational level, disposable income, marital status, and number of individuals in the household, were assessed as indicators of SES. The risk of penile cancer and penile cancer death in relation to SES were estimated using logistic regression and proportional hazards models, respectively. Cumulative cause‐specific mortality (CSM) estimates by SES were calculated using the Kaplan–Meier method.ResultsA low educational level and low disposable income were associated with an increased risk of invasive penile cancer. Furthermore, low educational level was associated with more advanced primary tumour stage. Divorced and never married men had a generally increased risk of penile cancer and were diagnosed with more advanced primary tumour stages. However, neither educational level nor marital status was associated with lymph node or distant metastases. Also, men in single‐person households had an increased risk of both non‐invasive and invasive disease. In men with invasive penile cancer, there were no significant associations of indicators of SES and CSM.ConclusionsLow educational level, low disposable income, being divorced or never married, and living in a single‐person household, all increase the risk of advanced stage penile cancer, but not lymph node or distant metastases. The assessed indicators of SES did not influence penile CSM. In conclusion, our findings indicates that SES influences the risk and stage of penile cancer, but not survival.
Exploring and Comparing Clusterings of Multivariate Data Sets Using Persistent Homology
Authors: Rieck B. , Leitte H. 
Published: July 2016

AbstractClustering algorithms support exploratory data analysis by grouping inputs that share similar features. Especially the clustering of unlabelled data is said to be a fiendishly difficult problem, because users not only have to choose a suitable clustering algorithm but also a suitable number of clusters. The known issues of existing clustering validity measures comprise instabilities in the presence of noise and restrictive assumptions about cluster shapes. In addition, they cannot evaluate individual clusters locally. We present a new measure for assessing and comparing different clusterings both on a global and on a local level. Our measure is based on the topological method of persistent homology, which is stable and unbiased towards cluster shapes. Based on our measure, we also describe a new visualization that displays similarities between different clusterings (using a global graph view) and supports their comparison on the individual cluster level (using a local glyph view). We demonstrate how our visualization helps detect different—but equally valid—clusterings of data sets from multiple application domains.
Space‐Time Bifurcation Lines for Extraction of 2D Lagrangian Coherent Structures
Authors: Machado Gustavo , Boblest Sebastian , Ertl Thomas , Sadlo Filip 
Published: July 2016

AbstractWe present a novel and efficient technique to extract Lagrangian coherent structures in two‐dimensional time‐dependent vector fields. We show that this can be achieved by employing bifurcation line extraction in the space‐time representation of the vector field, and generating space‐time bifurcation manifolds therefrom. To show the utility and applicability of our approach, we provide an evaluation of existing extraction techniques for Lagrangian coherent structures, and compare them to our approach.
Visualizing the Impact of Geographical Variations on Multivariate Clustering
Authors: Zhang Y. , Luo W. , Mack E. A. , Maciejewski R. 
Published: July 2016

AbstractTraditional multivariate clustering approaches are common in many geovisualization applications. These algorithms are used to define geodemographic profiles, ecosystems and various other land use patterns that are based on multivariate measures. Cluster labels are then projected onto a choropleth map to enable analysts to explore spatial dependencies and heterogeneity within the multivariate attributes. However, local variations in the data and choices of clustering parameters can greatly impact the resultant visualization. In this work, we develop a visual analytics framework for exploring and comparing the impact of geographical variations for multivariate clustering. Our framework employs a variety of graphical configurations and summary statistics to explore the spatial extents of clustering. It also allows users to discover patterns that can be concealed by traditional global clustering via several interactive visualization techniques including a novel drag & drop clustering difference view. We demonstrate the applicability of our framework over a demographics dataset containing quick facts about counties in the continental United States and demonstrate the need for analytical tools that can enable users to explore and compare clustering results over varying geographical features and scales.
Visibility Equalizer Cutaway Visualization of Mesoscopic Biological Models
Authors: Le Muzic M. , Mindek P. , Sorger J. , Autin L. , Goodsell D. S. , Viola I. 
Published: July 2016

AbstractIn scientific illustrations and visualization, cutaway views are often employed as an effective technique for occlusion management in densely packed scenes. We propose a novel method for authoring cutaway illustrations of mesoscopic biological models. In contrast to the existing cutaway algorithms, we take advantage of the specific nature of the biological models. These models consist of thousands of instances with a comparably smaller number of different types. Our method constitutes a two stage process. In the first step, clipping objects are placed in the scene, creating a cutaway visualization of the model. During this process, a hierarchical list of stacked bars inform the user about the instance visibility distribution of each individual molecular type in the scene. In the second step, the visibility of each molecular type is fine‐tuned through these bars, which at this point act as interactive visibility equalizers. An evaluation of our technique with domain experts confirmed that our equalizer‐based approach for visibility specification is valuable and effective for both, scientific and educational purposes.
Cytosplore: Interactive Immune Cell Phenotyping for Large Single‐Cell Datasets
Authors: Höllt T. , Pezzotti N. , van Unen V. , Koning F. , Eisemann E. , Lelieveldt B. , Vilanova A. 
Published: July 2016

AbstractTo understand how the immune system works, one needs to have a clear picture of its cellular compositon and the cells' corresponding properties and functionality. Mass cytometry is a novel technique to determine the properties of single‐cells with unprecedented detail. This amount of detail allows for much finer differentiation but also comes at the cost of more complex analysis. In this work, we present Cytosplore, implementing an interactive workflow to analyze mass cytometry data in an integrated system, providing multiple linked views, showing different levels of detail and enabling the rapid definition of known and unknown cell types. Cytosplore handles millions of cells, each represented as a high‐dimensional data point, facilitates hypothesis generation and confirmation, and provides a significant speed up of the current workflow. We show the effectiveness of Cytosplore in a case study evaluation.