bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metabarcoding of freshwater invertebrates to detect the effects of a pesticide spill
Authors: Andújar Carmelo , Arribas Paula , Gray Clare , Bruce Catherine , Woodward Guy , Yu Douglas W. , Vogler Alfried P. 
Published: November 2017

AbstractBiomonitoring underpins the environmental assessment of freshwater ecosystems and guides management and conservation. Current methodology for surveys of (macro)invertebrates uses coarse taxonomic identification where species‐level resolution is difficult to obtain. Next‐generation sequencing of entire assemblages (metabarcoding) provides a new approach for species detection, but requires further validation. We used metabarcoding of invertebrate assemblages with two fragments of the cox1 “barcode” and partial nuclear ribosomal (SSU) genes, to assess the effects of a pesticide spill in the River Kennet (southern England). Operational taxonomic unit (OTU) recovery was tested under 72 parameters (read denoising, filtering, pair merging and clustering). Similar taxonomic profiles were obtained under a broad range of parameters. The SSU marker recovered Platyhelminthes and Nematoda, missed by cox1, while Rotifera were only amplified with cox1. A reference set was created from all available barcode entries for Arthropoda in the BOLD database and clustered into OTUs. The River Kennet metabarcoding produced matches to 207 of these reference OTUs, five times the number of species recognized with morphological monitoring. The increase was due to the following: greater taxonomic resolution (e.g., splitting a single morphotaxon “Chironomidae” into 55 named OTUs); splitting of Linnaean binomials into multiple molecular OTUs; and the use of a filtration‐flotation protocol for extraction of minute specimens (meiofauna). Community analyses revealed strong differences between “impacted” vs. “control” samples, detectable with each gene marker, for each major taxonomic group, and for meio‐ and macrofaunal samples separately. Thus, highly resolved taxonomic data can be extracted at a fraction of the time and cost of traditional nonmolecular methods, opening new avenues for freshwater invertebrate biodiversity monitoring and molecular ecology.
Environmental filtering bypHand soil nutrients drives community assembly in fungi at fine spatial scales
Authors: Glassman Sydney I. , Wang Ian J. , Bruns Thomas D. 
Published: November 2017

AbstractWhether niche processes, like environmental filtering, or neutral processes, like dispersal limitation, are the primary forces driving community assembly is a central question in ecology. Here, we use a natural experimental system of isolated tree “islands” to test whether environment or geography primarily structures fungal community composition at fine spatial scales. This system consists of isolated pairs of two distantly related, congeneric pine trees established at varying distances from each other and the forest edge, allowing us to disentangle the effects of geographic distance vs. host and edaphic environment on associated fungal communities. We identified fungal community composition with Illumina sequencing ofITSamplicons, measured all relevant environmental parameters for each tree—including tree age, size and soil chemistry—and calculated geographic distances from each tree to all others and to the nearest forest edge. We applied generalized dissimilarity modelling to test whether total and ectomycorrhizal fungal (EMF) communities were primarily structured by geographic or environmental filtering. Our results provide strong evidence that as in many other organisms, niche and neutral processes both contribute significantly to turnover in community composition in fungi, but environmental filtering plays the dominant role in structuring both free‐living and symbiotic fungal communities at fine spatial scales. In our study system, we foundpHand organic matter primarily drive environmental filtering in total soil fungal communities and thatpHand cation exchange capacity—and, surprisingly, not host species—were the largest factors affectingEMFcommunity composition. These findings support an emerging paradigm thatpHmay play a central role in the assembly of all soil‐mediated systems.
Spatial variability of marine bacterial and archaeal communities along the particulate matter continuum
Authors: Mestre Mireia , Ferrera Isabel , Borrull Encarna , Ortega‐Retuerta Eva , Mbedi Susan , Grossart Hans‐Peter , Gasol Josep M. , Sala M. Montserrat 
Published: November 2017

AbstractBiotic and abiotic particles shape the microspatial architecture that defines the microbial aquatic habitat, being particles highly variable in size and quality along oceanic horizontal and vertical gradients. We analysed the prokaryotic (bacterial and archaeal) diversity and community composition present in six distinct particle size classes ranging from the pico‐ to the microscale (0.2 to 200 μm). Further, we studied their variations along oceanographic horizontal (from the coast to open oceanic waters) and vertical (from the ocean surface into the meso‐ and bathypelagic ocean) gradients. In general, prokaryotic community composition was more variable with depth than in the transition from the coast to the open ocean. Comparing the six size‐fractions, distinct prokaryotic communities were detected in each size‐fraction, and whereas bacteria were more diverse in the larger size‐fractions, archaea were more diverse in the smaller size‐fractions. Comparison of prokaryotic community composition among particle size‐fractions showed that most, but not all, taxonomic groups have a preference for a certain size‐fraction sustained with depth. Species sorting, or the presence of diverse ecotypes with distinct size‐fraction preferences, may explain why this trend is not conserved in all taxa.
Cultivation of Peptidiphaga gingivicola from subgingival plaque: The first representative of a novel genus of Actinomycetaceae
Authors: Beall C.J. , Mokrzan E.M. , Griffen A.L. , Leys E.J. 
Published: November 2017

SummaryA novel bacterium was isolated from the subgingival plaque of a patient with periodontal disease. Bacterial strain BA112T is a facultative Gram‐positive coccus. It metabolizes alanine, arginine, glycine, histidine, leucine, proline, serine and tyrosine, but does not appear to use carbohydrates. Urease, esculin, indole, catalase and nitrate reduction tests were all negative. Major cellular fatty acids were C18:0, C12:0, C16:0, C18:1 w9c and C20:0. The genome was sequenced and is 2.4 Mbp in length and has 64% GC content. Based on phylogenetics of the 16S rRNA sequence and concatenated alignments of 37 conserved proteins, BA112T belongs to the family Actinomycetaceae but is located on a branch of the tree without currently named members. Based on our phenotypic and phylogenetic studies, we propose that BA112T is the first known representative of a new genus, for which the name Peptidiphaga gingivicola gen. nov., sp. nov. is proposed. The type strain is BA112T.
Liver abnormalities and post‐transplant survival in pediatric Fontan patients
Authors: Hofferberth Sophie C. , Singh Tajinder P. , Bastardi Heather , Blume Elizabeth D. , Fynn‐Thompson Francis 
Published: November 2017

AbstractThe impact of liver parenchymal abnormalities on survival post‐heart transplant remains unknown in pediatric Fontan patients. We assessed pediatric Fontan patients who underwent heart transplant and had documented pretransplant hepatic ultrasound (U/S) studies. Liver U/S findings were classified as normal (Group 1), mildly abnormal (Group 2, hepatomegaly/vascular congestion), or severely abnormal (Group 3, heterogeneous echotexture/nodularity). Among 30 study patients, 8 were classified as Group 1, 14 as Group 2, while 8 met Group 3 criteria. Pretransplant liver biochemistry and synthetic function were similar in all groups. Six Group 3 patients underwent liver biopsy; 4 demonstrated perisinusoidal or centrilobular fibrosis, and 2 had cirrhosis. Overall mortality was 30% (n = 9). Median follow‐up was 5 years (range, 0.25‐13 years). One‐year survival was similar among all 3 groups (P = .37), with a trend toward higher cumulative 5‐year survival in Group 1 (100%). The majority of pediatric Fontan patients who underwent heart transplant demonstrated abnormal preoperative liver ultrasound findings. Heterogeneous echotexture or nodularity detected on U/S frequently indicates underlying liver parenchymal abnormalities. The presence of severe liver abnormalities was not associated with higher early mortality post‐heart transplant in pediatric Fontan patients; however, late outcomes must be further elucidated.
Mapping field photographs to textured surface meshes directly on mobile devices
Authors: Kehl Christian , Buckley Simon J. , Viseur Sophie , Gawthorpe Robert L. , Mullins James R. , Howell John A. 
Published: November 2017

AbstractThe mapping of photographs to surface geometry is an important procedure for many applications within the geosciences. This paper proposes an interactive framework for feature‐based image‐to‐geometry mapping that works directly on mobile devices, under challenging imaging conditions and with limited available hardware performance. The framework makes use of openly available digital elevation models (DEMs) together with mobile position‐and‐orientation sensor data. It integrates calculation heuristics for result evaluation and feedback, synthesising available knowledge in current registration literature. The approach is assessed on two image datasets captured on separate occasions. Their interpretations are mapped to one textured lidar surface model and the projection accuracy is qualitatively assessed. The experiments show a significant accuracy improvement in photograph registration results, as well as the faithful mapping of image interpretations on the underlying surface geometry. This semi‐automatic, user‐guided, interactive approach is superior to comparable fully automatic registration methods.
Unravelling the roles of innate lymphoid cells in cerebral malaria pathogenesis
Authors: Palomo J. , Quesniaux V. F. J. , Togbe D. , Reverchon F. , Ryffel B. 
Published: November 2017

SummaryCerebral malaria (CM) is one complication of Plasmodium parasite infection that can lead to strong inflammatory immune responses in the central nervous system (CNS), accompanied by lung inflammation and anaemia. Here, we focus on the role of the innate immune response in experimental cerebral malaria (ECM) caused by blood‐stage murine Plasmodium berghei ANKA infection. While T cells are important for ECM pathogenesis, the role of innate lymphoid cells (ILCs) is only emerging. The role of ILCs and non‐lymphoid cells, such as neutrophils and platelets, contributing to the host immune response and leading to ECM and human cerebral malaria (HCM) is reviewed.
Mind the Gap! Populism, Participation and Representation in Europe
Authors: Huber Robert A. , Ruth Saskia P. 
Published: November 2017

AbstractThis article assesses the influence of populist parties on two central aspects of democracy – participation and representation. In line with traditional theories on populism and democracy, we argue that populist parties have a positive effect on electoral turnout and the equality of participation. This effect, however, is moderated by the party's role in government or opposition as well as their host‐ideology, i.e. left, centre or right. We argue that populist parties also have a positive effect on substantive representation, but that this effect is strongly dependent on their host‐ideology. We test these arguments with lagged dependent variable models using data from 31 European countries from 1990 until 2014. We find mixed support for our theoretical expectations.
A Study on Methodology to Make Team: Methodology — Phase II
Authors: Sugimoto Yoichi , Arakawa Masao , Ishimaru Masahiko 
Published: November 2017

Improvement in labor productivity is a common problem in each country. In particular, in Japan where the productive age population is decreasing, it is necessary to steadily advance efforts for the improvement at various sites throughout the entire society. In doing so, in order to make it prevail over broad areas, it is necessary to consider that on-site holding resources can be utilized, that it can be easily introduced, and that it will surely be effective. Therefore, we have focused on improving the way of collaboration from an angle of “person’s personality”. Specifically, we have aimed to build a methodology, for a “team” that is a collaborative form widely introduced and utilized at companies and educational sites, which enhances the effectiveness of team activities. As for the overall structure of the methodology, we have designed it with a three-layer structure in order to clarify separation from other intellectual properties and consideration to ethical aspects. That is, the designed methodology comprises the following three phases. Phase I: a team formation methodology; Phase II: a team management methodology; and Phase III: a team development support methodology.
Study results of Phase I were presented at the 26th Design Engineering and System Division Lecture by the Japan Society of Mechanical Engineers (JSME). In this study, we have used the methodology of Phase I to devise, as a method included in Phase II, three Rules for creating a team environment that makes it easy for “introverted” persons in Jungian psychology to express their opinions. Then, we have conducted parallel group randomized trials comparing an intervention group with a control group, analyzed the results by an analysis method such as Data Envelopment Analysis (DEA), and verified the effectiveness of the devised method. As a result, the findings have revealed that teams in which the team management was carried out according to the devised method tends to be more effective and prone to excellent effectiveness.
A Method of Utilizing Digital Manikins to Assist Passenger Vehicle Design
Authors: Wan Jian , Wang Nanxin , Kozak Ksenia , Gomez-levi Gianna , Mikulionis Linas 
Published: November 2017

Most occupant accommodation assessments of a new vehicle design currently still utilize human appraisal. That is, human subjects experience the new design physically and provide feedback including a numerical rating or verbatim description. There are two drawbacks with this type of assessment: 1) the outcome is subjective. They are likely affected by other factors such as the vehicle’s appearance or brand and the individual’s own bias; 2) the outcome may not be able to reveal where the issues are nor how to resolve them.
The digital manikin technology has been widely used in different areas: starting from movie and video gaming industries, and getting more and more involved in the product life circle of manufacture industries. Human motions are captured, and the digital manikin is utilized to present these motions virtually. This paper introduces a method that uses digital manikins to assist the process of vehicle design. Subjects’ motions interacting with a vehicle, which are related to a new design change, are captured. These motions are used to drive digital manikins that represent their respective subjects in size and body shape. A software system that animates the digital manikin according to the motions and creates swept volumes of selected body segments was created. The collection of the swept volumes of all subjects represents the space that is occupied by the human body during the motion. This space can be used to assess the design changes by indicating the minimum clearance between the swept volume and vehicle components or the interference between the human body with the components. In addition, the space described by the swept volumes provides a guideline or space limit for any future design changes.
This method is objective. It not only pin-points the locations that cause discomfort or inconvenience by the new design, but also provides quantitative suggestions on how much improvement is needed for a better design.
An Exploration Study for Augmented and Virtual Reality Enhancing Situation Awareness for Plant Teleanalysis
Authors: Aschenbrenner Doris , Maltry Nicolas , Schilling Klaus , Verlinden Jouke 
Published: November 2017

This work wants to investigate which visualization method is able to support remote teleanalysis of industrial plants best regarding comprehension, usability and situation awareness. The application goal is the remote optimization of an industrial plant and the examined scenario was generated out of a large data set of a real production entity. The plant consists of an industrial manipulator, a molding machine and a montage system. Prior studies on the same plant with video based visualization explored by remote experts showed a large potential for optimization, but indicated a higher demand for situation awareness.
In order to test the influence of the visualization method, a user study has been carried out with 60 student participants with six different visualization methods, including various VR and AR implementations. Overall, our used AR environment performed significantly better than the used VR and video implementations, but the VR implementation surpasses AR regarding situation awareness.
Basic Study on Development of Delight Design Method: Proposal and Application of Beer Cup Design Based on Value Model and Evaluation Model of KANSEI
Authors: Tanaka Yukako , Misaka Mai , Aoyama Hideki 
Published: November 2017

Customers with diversified tastes have come to expect more than high product quality and performance. A high level of added value is required, and the provision for products that meet the individual requirements customers has become important. In recent years, delight design has attracted attention as a method for enhancing customer satisfaction. Delight design describes a design that offers attractive qualities beyond the required performance and quality requirements. However, attractiveness depends on the quality of the designer; furthermore, there are difficulties associated with the definition and expression based on similarities between the actual design and the original idea.
Therefore, in this study, we have proposed two methods for constructing neural network models: one for a value model using customer KANSEI data and one for an evaluation model for customers (designed as an inverse model). The customer value model creates the required product design from KANSEI. The evaluation model analyzes KANSEI for the individual customer and creates a design (delight design) according to KANSEI engineering and the preferences of the individual customer. The method proposed in this study was applied to the crack pattern seen on ceramic surfaces.
Invasive Disease Caused Simultaneously by Dual Serotypes of Streptococcus pneumoniae
Authors: Ndlangisa Kedibone , du Plessis Mignon , Allam Mushal , Wolter Nicole , de Gouveia Linda , Klugman Keith P. , Cohen Cheryl , Gladstone Rebecca A. , von Gottberg Anne 
Published: November 2017

ABSTRACT
There are at least 98 known pneumococcal serotypes. Invasive pneumococcal disease (IPD) is usually caused by a single serotype, and dual-serotype IPD is rare. To assess factors associated with dual-serotype IPD, patient information obtained through laboratory-based surveillance for IPD from 2005 through 2014 in South Africa was reviewed. Genomes of isolate pairs from coinfected individuals were sequenced to determine their molecular characteristics. For 30 (91%) of 33 patients with dual serotypes, one or both isolates were a pneumococcal conjugate vaccine (PCV13) serotype. Dual-serotype IPD was associated with children <5 years of age (adjusted odds ratio [aOR], 4.7; 95% confidence interval [95% CI], 1.8 to 11.7), underlying illness (other than HIV) (aOR, 2.8; 95% CI, 1.1 to 6.6) and death (aOR, 2.5; 95% CI, 1.08 to 6.09). For each coinfecting pair, isolates were genotypically unrelated, and their genotypes were common among isolates of the same serotype in South Africa. Of 701 accessory genes identified among dual-serotype IPD isolates, four were common between isolate pairs. Coinfecting isolate pairs had different genotypic backgrounds. The association of dual serotypes with death warrants increased awareness of IPD coinfection caused by two or more serotypes.
Assessment of Chronic Wasting Disease Prion Shedding in Deer Saliva with Occupancy Modeling
Authors: Davenport Kristen A. , Mosher Brittany A. , Brost Brian M. , Henderson Davin M. , Denkers Nathaniel D. , Nalls Amy V. , McNulty Erin , Mathiason Candace K. , Hoover Edward A. 
Published: November 2017

ABSTRACT
The detection of prions is difficult due to the peculiarity of the pathogen, which is a misfolded form of a normal protein. The specificity and sensitivity of detection methods are imperfect in complex samples, including in excreta. Here, we combined optimized prion amplification procedures with a statistical method that accounts for false-positive and false-negative errors to test deer saliva for chronic wasting disease (CWD) prions. This approach enabled us to discriminate the shedding of prions in saliva and the detection of prions in saliva—a distinction crucial to understanding the role of prion shedding in disease transmission and for diagnosis. We found that assay sensitivity and specificity were indeed imperfect, and we were able to draw several conclusions pertinent to CWD biology from our analyses: (i) the shedding of prions in saliva increases with time postinoculation, but is common throughout the preclinical phase of disease; (ii) the shedding propensity is influenced neither by sex nor by prion protein genotype at codon 96; and (iii) the source of prion-containing inoculum used to infect deer affects the likelihood of prion shedding in saliva; oral inoculation of deer with CWD-positive saliva resulted in 2.77 times the likelihood of prion shedding in saliva compared to that from inoculation with CWD-positive brain. These results are pertinent to horizontal CWD transmission in wild cervids. Moreover, the approach described is applicable to other diagnostic assays with imperfect detection.