bluuebunny/crossref_metadata_2025_split huggingface dataset:
Flower colour and visitation rates of Costus arabicus support the ‘bee avoidance’ hypothesis for red‐reflecting hummingbird‐pollinated flowers
Authors: Bergamo Pedro J. , Rech André R. , Brito Vinícius L. G. , Sazima Marlies 
Published: August 2015

Summary

Floral colour mediates plant–pollinator interactions by often signalling floral resources. In this sense, hummingbird‐pollinated flowers are frequently red‐coloured, and there are two tentative hypotheses to explain this pattern: 1. hummingbirds are attracted to red due its easier detection and 2. bees are sensorially excluded from red flowers. The second hypothesis is based on bees’ red colour blindness, which lead them to be less frequent and less important than hummingbirds as pollinators of red‐reflecting flowers.

Here, we untangled the role of different flower traits mediating plant–pollinator interactions and empirically tested the above hypotheses. We chose Costus arabicus due to its synchronopatric white‐ and pink‐flowered individuals and its bee and hummingbird pollination system. Although pink flowers are not totally achromatic as pure red ones, they show an achromaticity degree that could drive bee exclusion. Specifically, we tested whether differences on red reflectance work attracting hummingbirds or excluding bees and the consequent implications for the plant's reproduction.

Flower colour morphs of C. arabicus do differ neither in morphology nor in nectar sugar content. Moreover, white and pink flowers can be discriminated by the bees’ and hummingbirds’ colour vision system. Both groups are able to discriminate the red colour variation morph on the flower petals, the white flowers being more easily detected by bees and the pink flowers by hummingbirds. Bees preferentially visited the white flowers, whereas hummingbirds visited both colours at the same rate – both patterns corroborating the second hypothesis.

Pollen loads deposited on stigmas did not differ between flower colour morphs, indicating that bees and hummingbirds play a similar role in the overall pollen deposition. However, bees are more likely to self‐pollinate than hummingbirds. Self‐pollination limits C. arabicus reproduction, and red‐reflecting flowers may be better pollinated by discouraging bee visitation. Therefore, the intraspecific colour variation is driving flowers to show colour‐related different levels of generalization.

Our results support the ‘bee avoidance’ rather than the ‘hummingbird preference’ hypothesis. Sensory exclusion of bees seems to be the pressure for red‐reflecting flowers evolution, driving specialization in hummingbird‐pollinated flowers due to the costs of bee pollination on plant reproduction.
Palate Shape and Depth: A Shape‐Matching and Machine Learning Method for Estimating Ancestry from Human Skeletal Remains
Authors: Maier Christopher A. , Zhang Kang , Manhein Mary H. , Li Xin 
Published: August 2015

AbstractIn the past, assessing ancestry relied on the naked eye and observer experience; however, replicability has become an important aspect of such analysis through the application of metric techniques. This study examines palate shape and assesses ancestry quantitatively using a 3D digitizer and shape‐matching and machine learning methods. Palate curves and depths were recorded, processed, and tested for 376 individuals. Palate shape was an accurate indicator of ancestry in 58% of cases. Cluster analysis revealed that the parabolic, hyperbolic, and elliptical shapes are discrete from one another. Preliminary results indicate that palate depth in Hispanic individuals is greatest. Palate shape appears to be a useful indicator of ancestry, particularly when assessed by a computer. However, these data suggest that palate shape is not useful for assessing ancestry in Hispanic individuals. Although ancestry may be determined from palate shape, the use of multiple features is recommended and more reliable.
Mining for Murder‐Suicide: An Approach to Identifying Cases of Murder‐Suicide in the National Violent Death Reporting System Restricted Access Database
Authors: McNally Matthew R. , Patton Christina L. , Fremouw William J. 
Published: August 2015

AbstractThe National Violent Death Reporting System (NVDRS) is a United States Centers for Disease Control and Prevention (CDC) database of violent deaths from 2003 to the present. TheNVDRScollects information from 32 states on several types of violent deaths, including suicides, homicides, homicides followed by suicides, and deaths resulting from child maltreatment or intimate partner violence, as well as legal intervention and accidental firearm deaths. Despite the availability of data from police narratives, medical examiner reports, and other sources, reliably finding the cases of murder‐suicide in theNVDRShas proven problematic due to the lack of a unique code for murder‐suicide incidents and outdated descriptions of case‐finding procedures from previous researchers. By providing a description of the methods used to access to theNVDRSand coding procedures used to decipher these data, the authors seek to assist future researchers in correctly identifying cases of murder‐suicide deaths while avoiding false positives.
Detection of Traces of Ovalbumin and Casein in White and Red Wines by Quantitative Western Blotting
Authors: Meyer Philippe , Zanetti Simone 
Published: August 2015

AbstractFining of wine with agents containing cow's milk or hen's egg white is a common and traditional procedure. In light of increasing food allergies all over the world, the presence of fining residues has been subject of intense debate. Switzerland does not make exception, and since 2009 the Federal Department of Home Affairs has modified its food regulations stating that the labels must show if traces of fining agents are present. Nevertheless, the application of this regulation is not based on an official analytical method. In this study we show that immunoblotting is an efficient technique to detect and quantify ovalbumin and casein residues in bottled wine. We showed that final filtration is an essential step to remove finings in red wine, and that overfining of white wine may result in fining residues in finished products. Finally, for the first time in Switzerland, 22 samples were taken by food safety inspectors and officially analyzed for the regional food control authority of the Canton of Vaud. These samples were allergen free, but a larger study is currently planned in collaboration with other regional authorities of Switzerland to complete these results and make a complete picture of the Swiss wine production.
Pathway Analysis for RNA-Seq Data Using a Score-Based Approach
Authors: Zhou Yi-Hui 
Published: August 2015

SummaryA variety of pathway/gene-set approaches have been proposed to provide evidence of higher-level biological phenomena in the association of expression with experimental condition or clinical outcome. Among these approaches, it has been repeatedly shown that resampling methods are far preferable to approaches that implicitly assume independence of genes. However, few approaches have been optimized for the specific characteristics of RNA-Seq transcription data, in which mapped tags produce discrete counts with varying library sizes, and with potential outliers or skewness patterns that violate parametric assumptions. We describe transformations to RNA-Seq data to improve power for linear associations with outcome and flexibly handle normalization factors. Using these transformations or alternate transformations, we apply recently developed null approximations to quadratic form statistics for both self-contained and competitive pathway testing. The approach provides a convenient integrated platform for RNA-Seq pathway testing. We demonstrate that the approach provides appropriate type I error control without actual permutation and is powerful under many settings in comparison to competing approaches. Pathway analysis of data from a study of F344 vs. HIV1Tg rats, and of sex differences in lymphoblastoid cell lines from humans, strongly supports the biological interpretability of the findings.
Editorial: Evidence‐guided interventions and optimising outcomes in routine clinical care of children and young people's mental health
Authors: Sayal Kapil 
Published: August 2015

AbstractThis Editorial reflects on several articles in this issue of the journal that focus on evidence‐based interventions in routine clinical care. In particular, it highlights the approaches advocated in the review by Bearman & Weisz into overcoming barriers to the implementation of research findings into routine clinical care: conceptually unified treatments that acknowledge the overlap and comorbidity between presenting problems; modular approaches to co‐ordinate and combine treatment approaches to improve the fit for young people presenting with multiple problems; and approaches to monitoring and feedback of progress and outcomes to aid clinical review and decision‐making. Issues of access, stigma and measurement of meaningful outcomes in routine clinical practice are also considered.
An Image Degradation Model for Depth‐augmented Image Editing
Authors: Hennessey James W. , Mitra Niloy J. 
Published: August 2015

AbstractImages remain the most popular medium to capture our surroundings. Although significant advances have been made in developing image editing tools, the key challenge is to intelligently account for missing depth information. The growing popularity of depth images offers a new avenue to revisit image editing tasks. In this work, we investigate how even coarse depth information can be exploited to address some of the fundamental challenges in image editing namely producing correct perspective, handling occlusion, and obtaining segmentation. To this end, we propose a novel image degradation model that predicts how well an image edit can be performed in presence of coarse depth information. Technically, we create proxy geometry to summarize available depth information, and use it to predict occlusions and ordering between image patches, complete occluded regions, and anticipate image‐level changes under camera movement. We evaluate the proposed image degradation model in the context of parallax photography from single depth images.
Risks and benefits in treatment of mediastinal abscess by endobronchial ultrasound‐guided transbronchial needle aspiration
Authors: Tian Lei , Krimsky William S. , Wu Qingchen , Sun Jiayuan 
Published: August 2015

AbstractIntroduction: Mediastinal abscess is a fatal condition, treatment of mediastinal abscess is with antibiotics and sometimes surgery for debridement and drainage. Endobronchial ultrasound‐guided transbronchial needle aspiration (EBUS‐TBNA) is a safe assessment and candidate treatment method of mediastinal lesions.Objectives: This study aimed to HYPERLINK “javascript:void(0);” discuss risks and benefits in treatment of mediastinal abscess by EBUS‐TBNA.Methods: We noticed a 56‐year‐old man with developed bilateral pneumonia and sepsis after puncture of mediastinal abscess by EBUS‐TBNA. The patient was successfully treated with a combination of systemic anti‐infection treatment and intracavitary administration of antibiotics, antifungal and repeated drainage and lavage via EBUS‐TBNA, in 1 year follow‐up without recurrence.Results: This study indicated infection spread risk of mediastinal abscess after EBUS‐TBNA, and mediastinal abscess was successfully cured by combination of systemic anti‐infection and local intervention through EBUS‐TBNA.Conclusion: EBUS‐TBNA is a potential effective minimally invasive treatment for mediastinal abscess, and it is necessary to be aware of clinical complications after puncture of mediastinal infectious lesions by EBUS‐TBNA.
Principles of cooperation across systems: from human sharing to multicellularity and cancer
Authors: Aktipis Athena 
Published: August 2015

AbstractFrom cells to societies, several general principles arise again and again that facilitate cooperation and suppress conflict. In this study, I describe three general principles of cooperation and how they operate across systems including human sharing, cooperation in animal and insect societies and the massively large‐scale cooperation that occurs in our multicellular bodies. The first principle is that of Walk Away: that cooperation is enhanced when individuals can leave uncooperative partners. The second principle is that resource sharing is often based on the need of the recipient (i.e., need‐based transfers) rather than on strict account‐keeping. And the last principle is that effective scaling up of cooperation requires increasingly sophisticated and costly cheater suppression mechanisms. By comparing how these principles operate across systems, we can better understand the constraints on cooperation. This can facilitate the discovery of novel ways to enhance cooperation and suppress cheating in its many forms, from social exploitation to cancer.
A software tool for tomographic axial superresolution in STED microscopy
Authors: KOHO S. , DEGUCHI T. , HÄNNINEN P. E. 
Published: August 2015

SummaryA method for generating three‐dimensional tomograms from multiple three‐dimensional axial projections in STimulated Emission Depletion (STED) superresolution microscopy is introduced. Our STED< method, based on the use of a micromirror placed on top of a standard microscopic sample, is used to record a three‐dimensional projection at an oblique angle in relation to the main optical axis. Combining the STED< projection with the regular STED image into a single view by tomographic reconstruction, is shown to result in a tomogram with three‐to‐four‐fold improved apparent axial resolution. Registration of the different projections is based on the use of a mutual‐information histogram similarity metric. Fusion of the projections into a single view is based on Richardson‐Lucy iterative deconvolution algorithm, modified to work with multiple projections. Our tomographic reconstruction method is demonstrated to work with real biological STED superresolution images, including a data set with a limited signal‐to‐noise ratio (SNR); the reconstruction software (SuperTomo) and its source code will be released under BSD open‐source license.
Begomoviruses Infecting Tomato Crops in Panama
Authors: Herrera‐Vásquez José Angel , Ortega Deibis , Romero Ana Belkis , Davino Salvatore , Mejía Luis Carlos , Panno Stefano , Davino Mario 
Published: August 2015

AbstractThe key regions in Panama involved in open field‐ and greenhouse‐grown commercial tomato production, including the Chiriquí, Veraguas, Herrera, Los Santos, Coclé and Panama Oeste provinces, were surveyed for the incidence and distribution of begomoviruses in the growing seasons of 2011 and 2012. The surveys took place in 14 of the 51 districts of the above‐mentioned provinces and comprised all relevant tomato production areas of the provinces. A total of 28 tomato plots were surveyed. The exact location of each plot was geo‐referenced using a hand‐held Global Positioning System unit. In total, 319 individual tomato plants (181 in 2011 and 138 in 2012) were sampled. Plants displayed diverse combinations of virus‐like symptoms of different severity, including necrosis, yellowing, mosaic, mottling, rolling, curling, distortion and puckering of leaves, reduced leaf size, and stunted growth. DNA was extracted from each plant for a subsequent polymerase chain reaction (PCR) analysis, using two sets of degenerate primers able to detect members of the genus Begomovirus. The samples displaying a positive reaction were subsequently analysed with specific primer pairs to identify the affecting begomoviruses. A total of 42.3% of all collected samples showed a positive signal to PCRs. Three begomovirus species were detected with the species‐specific set of primers; in particular, in the samples obtained in 2011, Potato yellow mosaic Panama virus (PYMPV), Tomato leaf curl Sinaloa virus (ToLCSiV) and Tomato yellow mottle virus (TYMoV) were detected, while in the 2012 samples, only PYMPV and ToLCSiV were found. To our knowledge, this is the first reported incidence of ToLCSiV and TYMoV in Panamanian tomato crops.
New hosts for the mite Ornithonyssus bursa in Argentina
Authors: SANTILLÁN M. Á. , GRANDE J. M. , LIÉBANA M. S. , MARTÍNEZ P. , DÍAZ L. A. , BRAGAGNOLO L. A. , SOLARO C. , GALMES M. A. , SARASOLA J. H. 
Published: August 2015

AbstractThe mite Ornithonyssus bursa (Berlese) (Mesostigmata: Macronyssidae) is considered a poultry pest causing important infestations in chickens and it is considered a potential vector of arbovirus. Despite being considered a common parasite in wild birds, there is scarce published information about its potential hosts and effects on them. Here we present new bird hosts for O. bursa, assess the presence of Alphavirus, Flavivirus and Bunyavirus in mites from three host species, and discuss its potential impact on wild bird populations. We found O. bursa infecting five raptor and six passerine wild bird species. For nine of these species, this is the first record of infection by O. bursa. Although all analysed mites were negative for the examined arboviruses, the small sample size of mites does not allow further conclusions at the present moment. Because of the general nature of this ectoparasite, its presence in migratory long dispersal and endangered bird species, and the seropositivity for arboviruses in some of the species studied here, we consider it critical to assess the role of O. bursa and other ectoparasites as vectors and reservoirs of pathogens and as potential deleterious agents in wild bird populations.
Effect of Aggregatibacter actinomycetemcomitans from Aggressive Periodontitis patients on Streptococcus mutans
Authors: Kozlovsky A , Wolff A , Saminsky M , Mazor Y , Venezia E , Bar‐Ness Greenstein R 
Published: August 2015

ObjectivesTo determine in vivo association between Aggregatibacter actinomycetemcomitans (Aa) and Streptococcus mutans (Sm) in aggressive periodontitis patients (AgP) and the in vitro influence on Sm of saliva and of Aa strains isolated from individual Aa‐positive patients.Materials and MethodsClinical indices and saliva samples were taken from 30 AgP patients. Aa and mutans streptococci levels were determined. Antibacterial effect of saliva from 12 Aa‐positive patients, and their individual Aa strain, was checked turbidimetrically in vitro on Sm.ResultsAa salivary level was inversely correlated with levels of mutans streptococci and directly correlated with pockets of ≥7 mm. During exponential growth phase: (i) All Aa‐positive and Aa‐negative saliva samples showed no significant influence on Sm growth. (ii) Each individually isolated Aa strain presented significant inhibitory effect on Sm growth. During stationary growth phase, all the above demonstrated an inhibitory effect on Sm growth, with significantly greater influence of Aa individual strains.ConclusionSaliva of each AgP Aa‐positive subject had an inhibitory effect on Sm growth, which is most likely derived from Aa bacterial physiology. This research raises the possibility that suppression of Aa due to periodontal treatment may increase Sm levels and hence caries incidence.
Nationwide survey of Streptococcus pneumoniae drug resistance in the pediatric field in Japan
Authors: Okada Takafumi , Sato Yoshitake , Toyonaga Yoshikiyo , Hanaki Hideaki , Sunakawa Keisuke 
Published: August 2015

AbstractBackgroundStreptococcus pneumoniae is a major causative pathogen of pneumonia in children. The Drug‐Resistant Pathogen Surveillance Group in Pediatric Infectious Disease conducted a nationwide surveillance of S. pneumoniae in 2000–2001, 2004, 2007, 2010 and 2012, and investigated changes in drug resistance of S. pneumoniae.MethodsAll strains of S. pneumoniae were isolated from clinical specimens collected from pediatric patients. The minimun inhibitory concentration was measured and the strains were classified according to the Clinical Laboratory Standards Institute criteria. The isolation rates of penicillin‐intermediate resistant S. pneumoniae (PISP) and penicillin‐resistant S. pneumoniae (PRSP) were compared based on seven patient factors. Logistic regression analysis was also performed.ResultsThe sum of the isolation rates for PISP and PRSP for each period was 64.6%, 67.0%, 56.2%, 76.9% and 49.5%, respectively. Among the patient factors, age category 1 (<3 years, ≥3 years), age category 2 (infant, toddler and preschooler, schoolchild), siblings (absence, presence), and pre‐treatment with antimicrobial agents (absence, presence) were associated with significant differences in the isolation rate of PISP + PRSP. An interaction was observed between pre‐treatment with antimicrobial agents and schoolchild, and the isolation rate of PISP + PRSP was higher in patients with both pre‐treatment with antimicrobial agents and schoolchild.ConclusionAlthough some changes were observed in the rate of resistance of S. pneumoniae, an increasing trend was not observed. Both pre‐treatment with antimicrobial agents and age were associated with resistance, and an interaction was observed between pre‐treatment with antimicrobial agents and schoolchild.
Joint Models for Discrete Longitudinal Outcomes in Aging Research
Authors: van den Hout Ardo , Muniz-Terrera Graciela 
Published: August 2015

SummaryGiven the aging population in the UK, statistical modelling of cognitive function in the older population is of interest. Joint models are formulated for survival and cognitive function in the older population. Because tests of cognitive function often result in discrete outcomes, binomial and beta–binomial mixed effects regression models are applied to analyse longitudinal measurements. Dropout due to death is accounted for by parametric survival models, where the choice of a Gompertz baseline hazard and the specification of the random-effects structure are of specific interest. The measurement model and the survival model are combined in a shared parameter joint model. Estimation is by marginal likelihood. The methods are used to analyse data from the Cambridge City over-75s cohort study and the English Longitudinal Study of Ageing.
Trends in Moderate Rainfall Extremes: A Regional Monotone Regression Approach
Authors: Roth M. , Buishand T. A. , Jongbloed G. 
Published: August 2015

Abstract
Rainfall extremes are thought to have increased over recent years. Typically linear trends have been considered to describe the temporal evolution of high quantiles of the daily rainfall distribution. For long records it is important to allow more flexibility. Quantile regression methods are available to estimate monotone trends for single stations. Having multiple stations in a region, the significance of the trend at the regional scale is often of interest. From this perspective the authors propose a regression approach that can be used to estimate a common monotone trend for the site-specific quantiles. Moreover, the method allows for the construction of confidence bands and testing the hypothesis of an existing nondecreasing trend against the null hypothesis of no trend. The approach is applied to 102 series of daily rainfall over the Netherlands for the period 1910–2009. The results are compared with those from a (regional) Mann–Kendall test. Significantly increasing trends are found for the winter season and for the whole year. In the summer season trends are less consistent over the region and are only significant in the western part of the Netherlands. For the summer season, linearity of the trend seems less apparent than for winter and for the whole year. However, the deviation from linearity is not significant.