bluuebunny/crossref_metadata_2025_split huggingface dataset:
High‐throughput identification and diagnostics of pathogens and pests: Overview and practical recommendations
Authors: Tedersoo Leho , Drenkhan Rein , Anslan Sten , Morales‐Rodriguez Carmen , Cleary Michelle 
Published: October 2018

AbstractHigh‐throughput identification technologies provide efficient tools for understanding the ecology and functioning of microorganisms. Yet, these methods have been only rarely used for monitoring and testing ecological hypotheses in plant pathogens and pests in spite of their immense importance in agriculture, forestry and plant community dynamics. The main objectives of this manuscript are the following: (a) to provide a comprehensive overview about the state‐of‐the‐art high‐throughput quantification and molecular identification methods used to address population dynamics, community ecology and host associations of microorganisms, with a specific focus on antagonists such as pathogens, viruses and pests; (b) to compile available information and provide recommendations about specific protocols and workable primers for bacteria, fungi, oomycetes and insect pests; and (c) to provide examples of novel methods used in other microbiological disciplines that are of great potential use for testing specific biological hypotheses related to pathology. Finally, we evaluate the overall perspectives of the state‐of‐the‐art and still evolving methods for diagnostics and population‐ and community‐level ecological research of pathogens and pests.
Promises and pitfalls of using high‐throughput sequencing for diet analysis
Authors: Alberdi Antton , Aizpurua Ostaizka , Bohmann Kristine , Gopalakrishnan Shyam , Lynggaard Christina , Nielsen Martin , Gilbert Marcus Thomas Pius 
Published: October 2018

AbstractThe application of high‐throughput sequencing‐based approaches to DNA extracted from environmental samples such as gut contents and faeces has become a popular tool for studying dietary habits of animals. Due to the high resolution and prey detection capacity they provide, both metabarcoding and shotgun sequencing are increasingly used to address ecological questions grounded in dietary relationships. Despite their great promise in this context, recent research has unveiled how a wealth of biological (related to the study system) and technical (related to the methodology) factors can distort the signal of taxonomic composition and diversity. Here, we review these studies in the light of high‐throughput sequencing‐based assessment of trophic interactions. We address how the study design can account for distortion factors, and how acknowledging limitations and biases inherent to sequencing‐based diet analyses are essential for obtaining reliable results, thus drawing appropriate conclusions. Furthermore, we suggest strategies to minimize the effect of distortion factors, measures to increase reproducibility, replicability and comparability of studies, and options to scale up DNA sequencing‐based diet analyses. In doing so, we aim to aid end‐users in designing reliable diet studies by informing them about the complexity and limitations of DNA sequencing‐based diet analyses, and encourage researchers to create and improve tools that will eventually drive this field to its maturity.
SNP‐based heritability and genetic architecture of tarsal osteochondrosis in North American Standardbred horses
Authors: McCoy A. M. , Norton E. M. , Kemper A. M. , Beeson S. K. , Mickelson J. R. , McCue M. E. 
Published: October 2018

SummaryOsteochondrosis is a common developmental orthopedic disease characterized by a failure of endochondral ossification. Standardbred horses are recognized as being predisposed to tarsal osteochondrosis. Prior heritability estimates for tarsal osteochondrosis in European Standardbreds and related trotting breeds have been based on pedigree data and range from 17–29%. Here, we report on genetic architecture and heritability based on high‐density genotyping data in a cohort of North American Standardbreds (n = 479) stringently phenotyped for tarsal osteochondrosis. Whole‐genome array genotyping data were imputed to ~2 million single nucleotide polymorphisms (SNPs).SNP‐based heritability of osteochondrosis in this population was explained by 2326SNPs. The majority of theseSNPs (86.6%) had small effects, whereas fewerSNPs had moderate or large effects (10% and 2.9% respectively), which is consistent with a polygenic/complex disease. Heritability was estimated at 0.24 ± 0.16 using two methods of restricted maximum likelihood analysis, as implemented ingcta(with and without a weighted relatedness matrix) andldaksoftware. Estimates were validated using bootstrapping. Heritability estimates were within the range previously reported and suggest that osteochondrosis is moderately heritable but that a significant portion of disease risk is due to environmental factors and/or genotype × environment interactions. Future identification of the genes/variants that have the most impact on disease risk may allow early recognition of high‐risk individuals.
Endotypes of chronic rhinitis: A cluster analysis study
Authors: Meng Yifan , Lou Hongfei , Wang Yang , Wang Xiaoyan , Cao Feifei , Wang Kuiji , Chu Xiaohan , Wang Chengshuo , Zhang Luo 
Published: October 2018

AbstractBackgroundChronic rhinitis (CR) is currently regarded as a syndrome, which presents as several endotypes. The aim of this study was to identify the CR endotype clusters and investigate the inflammatory patterns associated with the different endotypes.MethodsA total of 259 CR patients and 20 control subjects were enrolled in this prospective study. Twelve clinical variables were analyzed using cluster analysis and five inflammatory variables were measured to investigate the inflammatory patterns associated with the different clusters.ResultsSix endotype clusters of CR were defined in the Chinese CR patients. Patients in cluster 1 (38.6%) were diagnosed as allergic rhinitis (AR) without asthma, and in cluster 2 (13.5%) as AR with asthma, with all demonstrating positive results for local eosinophils and high levels of local and serum IgE. Similarly, patients in cluster 3 (18.6%) were diagnosed as nonallergic rhinitis with eosinophilia syndrome (NARES) without asthma and in cluster 5 (5.0%) as NARES with asthma, with all demonstrating positive results for local eosinophils, and negative results for both local and serum IgE. Patients in cluster 4 (4.6%) were diagnosed as local allergic rhinitis and showed positive results for local eosinophils and local IgE, but negative results for serum IgE, whereas patients in cluster 6 (19.7%) were diagnosed as idiopathic rhinitis because of high symptoms scores, but negative findings for local eosinophils, local IgE, and serum IgE.ConclusionsChinese CR patients may be clustered into six endotypes with different inflammatory patterns, which may help in delivering individualized treatment.
Informality Materialised: Long‐term Temporariness as a Mode of Informal Urbanism
Authors: Moatasim Faiza 
Published: October 2018

AbstractThis paper establishes an important link between the architectural strategies and long‐term sustenance of “ordinary” informal spaces in the planned modernist city of Islamabad. By focusing on the modalities of street hawking in Islamabad, this paper demonstrates that the architecture of ordinary informality follows an aesthetic and materiality of temporariness, and invokes design criteria based on the rituals of daily assembly and disassembly, and shared customs involving “temporary” claims to immediate public space. The paper uses the concept of “long‐term temporariness” to argue that the sustained existence of street hawking depends upon the routine maintenance of the relationship between its temporality and materiality, evident in both the everyday spatial practices and official procedures concerning informal street commerce. The paper thus situates street hawking within the realms of both formal and informal processes, and highlights the role of provisionality in urban transformations in the global South.
Sex‐biased dispersal: a review of the theory
Authors: Li Xiang‐Yi , Kokko Hanna 
Published: October 2018

ABSTRACTDispersal is ubiquitous throughout the tree of life: factors selecting for dispersal include kin competition, inbreeding avoidance and spatiotemporal variation in resources or habitat suitability. These factors differ in whether they promote male and female dispersal equally strongly, and often selection on dispersal of one sex depends on how much the other disperses. For example, for inbreeding avoidance it can be sufficient that one sex disperses away from the natal site. Attempts to understand sex‐specific dispersal evolution have created a rich body of theoretical literature, which we review here. We highlight an interesting gap between empirical and theoretical literature. The former associates different patterns of sex‐biased dispersal with mating systems, such as female‐biased dispersal in monogamous birds and male‐biased dispersal in polygynous mammals. The predominant explanation is traceable back to Greenwood's () ideas of how successful philopatric or dispersing individuals are at gaining mates or the resources required to attract them. Theory, however, has developed surprisingly independently of these ideas: models typically track how immigration and emigration change relatedness patterns and alter competition for limiting resources. The limiting resources are often considered sexually distinct, with breeding sites and fertilizable females limiting reproductive success for females and males, respectively. We show that the link between mating system and sex‐biased dispersal is far from resolved: there are studies showing that mating systems matter, but the oft‐stated association between polygyny and male‐biased dispersal is not a straightforward theoretical expectation. Here, an important understudied factor is the extent to which movement is interpretable as an extension of mate‐searching (e.g. are matings possibleen routeor do they only happen after settling in new habitat – or can females perhaps move with stored sperm). We also point out other new directions for bridging the gap between empirical and theoretical studies: there is a need to build Greenwood's influential yet verbal explanation into formal models, which also includes the possibility that an individual benefits from mobility as it leads to fitness gains in more than one final breeding location (a possibility not present in models with a very rigid deme structure). The order of life‐cycle events is likewise important, as this impacts whether a departing individual leaves behind important resources for its female or male kin, or perhaps both, in the case of partially overlapping resource use.
Factors affecting mode choice for the home–elementary school journey: Evidence from Halifax, Canada
Authors: Spinney Jamie E. L. , Maoh Hanna , Millward Hugh 
Published: October 2018

AbstractThis research investigates personal, school, neighbourhood, and weather characteristics that are associated with travel mode choices for children's direct journeys between home and school. Travel diary and socio‐demographic data were collected from elementary school students aged 5 to 11 years in Halifax, Nova Scotia, and were joined with characteristics about their respective school, neighbourhood, and weather. Multinomial and mixed logistic regression were used to examine the relationships between these characteristics and choices between car, bus, and walk travel modes. Results indicate that personal, school, neighbourhood, and weather characteristics all impact mode choice decisions, yet distance between home and school is among the most significant. To promote active travel between home and school, our findings suggest that smaller elementary schools should be sited centrally within compact, high‐density neighbourhoods that are designed for active travel, thereby minimizing school travel distances and maximizing the practicality of active travel modes.
Phase 1 study of olaratumab plus doxorubicin in Japanese patients with advanced soft‐tissue sarcoma
Authors: Yonemori Kan , Kodaira Makoto , Satoh Taroh , Kudo Toshihiro , Takahashi Shunji , Nakano Kenji , Ando Yuichi , Shimokata Tomoya , Mori Joji , Inoue Koichi , Oakley Gerard J. , Sakaguchi Sachi , Tamura Kenji 
Published: October 2018

Olaratumab, a monoclonal antibody targeting human platelet‐derived growth factor receptor α, plus doxorubicin significantly improved overall survival in patients with advanced soft‐tissue sarcoma (STS) in a prior phase 1b/2 randomized trial. Subsequent exposure‐response analysis suggested that higher olaratumab exposures earlier might improve outcomes in patients at risk of early disease progression. This phase 1 study (3 treatment cohorts; minimum 6 patients each) investigated the safety, pharmacokinetics and antitumor activity of olaratumab plus doxorubicin in Japanese patients with STS. Patients received olaratumab 15 mg/kg on Days 1 and 8 during each 21‐day cycle until disease progression. Patients in Cohort 3 received a 20 mg/kg loading dose of olaratumab in Cycle 1. Doxorubicin was administered for up to 6 cycles. Patients in Cohort 1 received doxorubicin 25 mg/m2 on Days 1, 2 and 3. Patients in Cohorts 2 and 3 received doxorubicin 75 mg/m2 on Day 1. One patient in Cohort 2 experienced a dose‐limiting toxicity of Grade 3 febrile neutropenia. Most treatment‐emergent adverse events were of mild and moderate severity, and were known doxorubicin toxicities. Olaratumab serum concentrations in Cohort 3 reached a steady‐state exceeding the target level in Cycle 1. Partial response was confirmed in 4 patients (2 each in Cohorts 2 and 3). Olaratumab plus doxorubicin had an acceptable safety profile in patients with STS. A loading dose of olaratumab 20 mg/kg was effective for achieving minimum serum concentrations above the target trough level in Cycle 1.
Inhibition and Mathematical Performance: Poorly Correlated, Poorly Measured, or Poorly Matched?
Authors: Lee Kerry , Lee Hon Wah 
Published: October 2018

AbstractInhibition is an important aspect of executive functioning (EF) that refers to a cognitive mechanism that blocks or suppresses irrelevant stimuli, memory, habitual responses, or automatized processes from interrupting the desired response. Researchers have found weak and inconsistent relations between inhibitory abilities and mathematics performance (Bull & Lee, 2014). Given anecdotal evidence of the effects of external distraction or intruding thoughts on the ability to stay on task, it is surprising that inhibitory abilities do not have a more prominent role. In this article, we argue that this lower‐than‐expected association is due to (a) age‐related changes in EF, (b) the sensitivity of inhibitory tasks commonly used in studies, (c) a mismatch in how susceptibility to interference and mathematical performance are measured, and (d) the choice of criterion measures, with some mathematical tasks imposing less inhibitory demands than others.
Assessment of macular ganglion cell complex using optical coherence tomography: Impact of a paediatric reference database in clinical practice
Authors: Muñoz‐Gallego Alicia , De la Cruz Javier , Rodríguez‐Salgado Martín , Torres‐Peña José L. , de‐Lucas‐Viejo Beatriz , Ortueta‐Olartecoechea Ana , Tejada‐Palacios Pilar 
Published: October 2018

ImportanceOptical coherence tomography software classifies abnormality of macular ganglion cell‐inner plexiform layer thickness and macular retinal nerve fibre layer thickness based on adult series.BackgroundWe assessed the impact of using paediatric reference macular ganglion cell complex values instead of adult reference values.DesignCross‐sectional study. Primary and tertiary health‐care setting.ParticipantsOut of 140 healthy participants aged 5 to 18 years, 90% were eligible.MethodsFollowing a dilated eye examination and cycloplegic refraction, participants underwent optical coherence tomography ganglion cell scans (Topcon 3D OCT‐2000; Topcon Corporation, Tokyo, Japan). Right eye measurements for superior, inferior, and total layer thickness and spherical equivalent were reported, together with age, sex and origin.Main Outcome MeasuresPaediatric reference values by age and spherical equivalent were produced, and the specific agreement between paediatric and adult ganglion cell complex reference values below or equal to percentile 5 was estimated.ResultsThe multivariate analysis confirmed a positive association between spherical equivalent and macular ganglion cell‐inner plexiform layer thickness, and between age and macular retinal nerve fibre layer (five out of six regression coefficients P values were ≤ 0.03). Specific agreement was 25% for ganglion cell‐inner plexiform layer thickness and > 80% for macular retinal nerve fibre layer. Adult‐based software identified low ganglion cell values in one in seven children compared to paediatric reference values (0.8% vs 5.5%, P = 0.031).Conclusions and RelevanceThe availability of optical coherence tomography ganglion cell complex reference values for paediatric age and spherical equivalent groups can be used to improve detection of children with low cell layer thickness.
Online Global Non‐rigid Registration for 3D Object Reconstruction Using Consumer‐level Depth Cameras
Authors: Xu Jiamin , Xu Weiwei , Yang Yin , Deng Zhigang , Bao Hujun 
Published: October 2018

AbstractWe investigate how to obtain high‐quality 360‐degree 3D reconstructions of small objects using consumer‐level depth cameras. For many homeware objects such as shoes and toys with dimensions around 0.06 – 0.4 meters, their whole projections, in the hand‐held scanning process, occupy fewer than 20% pixels of the camera's image. We observe that existing 3D reconstruction algorithms like KinectFusion and other similar methods often fail in such cases even under the close‐range depth setting. To achieve high‐quality 3D object reconstruction results at this scale, our algorithm relies on an online global non‐rigid registration, where embedded deformation graph is employed to handle the drifting of camera tracking and the possible nonlinear distortion in the captured depth data. We perform an automatic target object extraction from RGBD frames to remove the unrelated depth data so that the registration algorithm can focus on minimizing the geometric and photogrammetric distances of the RGBD data of target objects. Our algorithm is implemented using CUDA for a fast non‐rigid registration. The experimental results show that the proposed method can reconstruct high‐quality 3D shapes of various small objects with textures.
FashionGAN: Display your fashion design using Conditional Generative Adversarial Nets
Authors: Cui Y. R. , Liu Q. , Gao C. Y. , Su Z. 
Published: October 2018

AbstractVirtual garment display plays an important role in fashion design for it can directly show the design effect of the garment without having to make a sample garment like traditional clothing industry. In this paper, we propose an end‐to‐end virtual garment display method based on Conditional Generative Adversarial Networks. Different from existing 3D virtual garment methods which need complex interactions and domain‐specific user knowledge, our method only need users to input a desired fashion sketch and a specified fabric image then the image of the virtual garment whose shape and texture are consistent with the input fashion sketch and fabric image can be shown out quickly and automatically. Moreover, it can also be extended to contour images and garment images, which further improves the reuse rate of fashion design. Compared with the existing image‐to‐image methods, the quality of images generated by our method is better in terms of color and shape.
Single Image Surface Appearance Modeling with Self‐augmented CNNs and Inexact Supervision
Authors: Ye Wenjie , Li Xiao , Dong Yue , Peers Pieter , Tong Xin 
Published: October 2018

AbstractThis paper presents a deep learning based method for estimating the spatially varying surface reflectance properties from a single image of a planar surface under unknown natural lighting trained using only photographs of exemplar materials without referencing any artist generated or densely measured spatially varying surface reflectance training data. Our method is based on an empirical study of Li et al.'s [LDPT17] self‐augmentation training strategy that shows that the main role of the initial approximative network is to provide guidance on the inherent ambiguities in single image appearance estimation. Furthermore, our study indicates that this initial network can be inexact (i.e., trained from other data sources) as long as it resolves the inherent ambiguities. We show that the single image estimation network trained without manually labeled data outperforms prior work in terms of accuracy as well as generality.
Deep Video Stabilization Using Adversarial Networks
Authors: Xu Sen‐Zhe , Hu Jun , Wang Miao , Mu Tai‐Jiang , Hu Shi‐Min 
Published: October 2018

AbstractVideo stabilization is necessary for many hand‐held shot videos. In the past decades, although various video stabilization methods were proposed based on the smoothing of 2D, 2.5D or 3D camera paths, hardly have there been any deep learning methods to solve this problem. Instead of explicitly estimating and smoothing the camera path, we present a novel online deep learning framework to learn the stabilization transformation for each unsteady frame, given historical steady frames. Our network is composed of a generative network with spatial transformer networks embedded in different layers, and generates a stable frame for the incoming unstable frame by computing an appropriate affine transformation. We also introduce an adversarial network to determine the stability of apiece of video. The network is trained directly using the pair of steady and unsteady videos. Experiments show that our method can produce similar results as traditional methods, moreover, it is capable of handling challenging unsteady video of low quality, where traditional methods fail, such as video with heavy noise or multiple exposures. Our method runs in real time, which is much faster than traditional methods.
Local and Hierarchical Refinement for Subdivision Gradient Meshes
Authors: Verstraaten T. W. , Kosinka J. 
Published: October 2018

AbstractGradient mesh design tools allow users to create detailed scalable images, traditionally through the creation and manipulation of a (dense) mesh with regular rectangular topology. Through recent advances it is now possible to allow gradient meshes to have arbitrary manifold topology, using a modified Catmull‐Clark subdivision scheme to define the resultant geometry and colour [LKSD17]. We present two novel methods to allow local and hierarchical refinement of both colour and geometry for such subdivision gradient meshes. Our methods leverage the mesh properties that the particular subdivision scheme ensures. In both methods, the artists enjoy all the standard capabilities of manipulating the mesh and the associated colour gradients at the coarsest level as well as locally at refined levels. Further novel features include interpolation of both position and colour of the vertices of the input meshes, local detail follows coarser‐level edits, and support for sharp colour transitions, all at any level in the hierarchy offered by subdivision.