bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantifying shape, integration, and ecology in avian pedal claws: comparing geometric morphometric and traditional metric approaches
Authors: Hedrick Brandon P. , Cordero Samantha A. , Zanno Lindsay E. , Noto Christopher , Dodson Peter 
Published: April 2019

AbstractTerrestrial tetrapods use their claws to interact with their environments in a plethora of ways. Birds in particular have developed a diversity of claw shapes since they are not bound to terrestrial locomotion and have heterogeneous body masses ranging several orders of magnitude. Numerous previous studies have hypothesized a connection between pedal claw shape and ecological mode in birds, but have generated conflicting results, spanning from clear ecological groupings based on claw shape to a complete overlap of ecological modes. These studies have relied on traditional morphometric arc measurements of keratinous sheaths and have variably accounted for likely confounding factors such as body mass and phylogenetic relatedness. To better address the hypothesized relationship between ecology and claw shape in birds, 580 radiographs were collected allowing visualization of the bony core and keratinous sheath shape spanning 21 avian orders. A new method was used to quantify claw shape using geometric morphometrics and was compared to results using traditional arc measurements. Neither traditional nor geometric morphometrics are capable of significantly separating bird claws into coarse ecological categories after integrating body size and phylogenetic relatedness. Further, the bony claw core and keratinous sheath are significantly integrated with one another, suggesting that they function as a single unit. Therefore, it is likely possible to compare fossil bony cores with extant keratinous sheaths after applying corrections. Finally, traditional metrics and geometric morphometric shape are significantly, yet loosely correlated, and geometric morphometric data better distinguish ecological groups in morphospace than is possible with traditional metrics. Based on these results, future workers are encouraged to use geometric morphometric approaches to study claw geometry and account for confounding factors such as body size, phylogeny, and individual variation prior to predicting ecology in fossil taxa.
A novel phyllosphere residentProtomycesspecies that interacts with theArabidopsisimmune system
Authors: Wang Kai , Sipilä Timo , Rajaraman Sitaram , Safronov Omid , Laine Pia , Auzane Agate , Mari Alfredo , Auvinen Petri , Paulin Lars , Kemen Eric , Salojärvi Jarkko , Overmyer Kirk 
Published: April 2019

ABSTRACTWe describe the genome contents of sixProtomycesspp. that are pathogenic within the typical host range of the genus and a novelProtomycesstrain (SC29) that was previously isolated from the phylloplane of wildArabidopsis thaliana(Arabidopsis), an atypical or possible alternate host. Genome-wide phylogenetic analysis defined SC29 as a distinctProtomycessp. Analysis of gene family expansions, gene retention, and gene loss patterns among theseProtomycesspp. lead us to hypothesize that SC29 may have undergone a host jump. The role of phyllosphere residency in the lifecycle ofProtomycesspp. was previously unknown. Genomic changes in SC29 and all otherProtomycesspp. were consistent with adaptations to the plant phylloplane. As predicted by our analysis of its mating locus, SC29 did not cause disease onArabidopsisas a single strain, but could persist in its phylloplane, while the closely relatedP. inouyeidoes not. SC29 treatedArabidopsisexhibited enhanced immunity againstBotrytis cinereainfection, associated with activation of MAPK3/6, camalexin, and SA-signalling pathways. We conclude that SC29 is a novelProtomycessp. able to survive in theArabidopsisphylloplane and that phylloplane residency is an important element in the lifecycle ofProtomycesspp.
A three-sample test for introgression
Authors: Hahn Matthew W. , Hibbins Mark S. 
Published: April 2019

AbstractMany methods exist for detecting introgression between non-sister species, but the most commonly used require either a single sequence from four or more taxa or multiple sequences from each of three taxa. Here we present a test for introgression that uses only a single sequence from three taxa. This test, denoted D3, uses similar logic as the standard D-test for introgression, but by using pairwise distances instead of site patterns it is able to detect the same signal of introgression with fewer species. We use simulations to show that D3 has statistical power almost equal to D, demonstrating its use on a dataset of wild bananas (Musa). The new test is easy to apply and easy to interpret, and should find wide use among currently available datasets.
A vibrating mesh nebulizer as an alternative to the Collison 3-jet nebulizer for infectious disease aerobiology
Authors: Bowling Jennifer D. , O’ Malley Katherine J. , Klimstra William B. , Hartman Amy L. , Reed Douglas S. 
Published: April 2019

AbstractExperimental infection of animals via inhalation containing pathogenic agents is essential to understanding the natural history and pathogenesis of infectious disease as well as evaluation of potential medical countermeasures. We evaluated whether the Aeroneb, a vibrating mesh nebulizer, would serve as an alternative to the Collison, the ‘gold standard’ for generating infectious bioaerosols. While the Collison possesses desirable properties that have contributed to its longevity in infectious disease aerobiology, concerns have lingered about the volume and concentration of agent required to cause disease and the damage that jet nebulization causes to the agent. For viruses, the ratio of aerosol concentration to nebulizer concentration (spray factor, SF), the Aeroneb was superior to the Collison for four different viruses in a nonhuman primate head-only exposure chamber. Aerosol concentration of influenza was higher relative to fluorescein for the Aeroneb compared to the Collison, suggesting that the Aeroneb was less harsh to viral pathogens than the Collison when generating aerosols. The Aeroneb did not improve the aerosol SF for a vegetative bacterium,Francisella tularensis.Environmental parameters collected during the aerosols indicated that the Aeroneb generated a higher relative humidity in exposure chambers while not affecting other environmental parameters. Aerosol mass median aerodynamic diameter was generally larger and more disperse for aerosols generated by the Aeroneb than what is seen with the Collison but ≥80% were within the range that would reach the lower respiratory tract and alveolar regions. These data suggest that for viral pathogens, the Aeroneb is a suitable alternative to the Collison 3-jet nebulizer.ImportanceThe threat of aerosolization is often not the natural method of transmission. While selection of an appropriate animal model is vital for these types of experiments, other confounding factors can be controlled through a thorough understanding of experimental design and the effects that different parameters can have on disease outcome. Route of administration, particle size, and dose are all factors which can affect disease progression and need to be controlled. Aerosol research methods and equipment need to be well characterized to optimize the development of animal models for bioterrorism agents.
Three new integration vectors and fluorescent proteins for use in the opportunistic human pathogenStreptococcus pneumoniae
Authors: Keller Lance E. , Rueff Anne-Stéphanie , Kurushima Jun , Veening Jan-Willem 
Published: April 2019

AbstractHere we describe the creation of three integration vectors, pPEPX, pPEPY and pPEPZ, for use with the opportunistic human pathogenStreptococcus pneumoniae. The constructed vectors, named PEP for Pneumococcal Engineering Platform, employ an IPTG-inducible promoter and BglBrick and BglFusion compatible multiple cloning sites allowing for fast and interchangeable cloning. PEP plasmids replicate inEscherichia coliand harbor integration sites that have homology in a large set of pneumococcal strains, including recent clinical isolates. In addition, several options of antibiotic resistance markers are available, even allowing for selection in multidrug resistant clinical isolates. The transformation efficiency of these PEP vectors as well as their ability to be expressed simultaneously were tested. Two of the three PEP vectors share homology of the integration regions with over half of theS. pneumoniaegenomes examined. Transformation efficiency varied among PEP vectors based on the length of the homology regions, but all were highly transformable and can be integrated simultaneously in strain D39V. Vectors used for pneumococcal cloning are an important tool for researchers for a wide range of uses. The PEP vectors described are of particular use because they have been designed to allow for easy transfer of genes between vectors as well as integrating into transcriptionally silent areas of the chromosome. In addition, we demonstrate the successful production of several new spectrally distinct fluorescent proteins (mTurquoise2, mNeonGreen and mScarlet-I) from the PEP vectors. The PEP vectors and newly described fluorescent proteins will expand the genetic toolbox for pneumococcal researchers and aid future discoveries.
Classification of Neurons in the Adult Mouse Cochlear Nucleus: Linear Discriminant Analysis
Authors: Manis Paul B. , Kasten Michael R. , Xie Ruili 
Published: April 2019

AbstractThe cochlear nucleus (CN) transforms the spike trains of spiral ganglion cells into a new set of sensory representations that are essential for auditory discriminations and perception. These transformations require the coordinated activity of different classes of neurons that are embryologically derived from distinct sets of precursors. Decades of investigation have shown that the neurons of the CN are differentiated by their ion channel expression and intrinsic excitability. In the present study we have used linear discriminant analysis (LDA) to perform an unbiased analysis of measures of the responses of CN neurons to current injections to mathematically separate cells on the basis of both morphology and physiology. Recordings were made from cells in brain slices from CBA mice and a transgenic mouse line, NF107, crossed against the Ai32 line. For each cell, responses to current injections were analyzed for spike rate, spike shape (action potential height, afterhyperpolarization depth, first spike half-width), input resistance, resting membrane potential, membrane time constant, hyperpolarization-activated sag and time constant. Cells were filled with dye for morphological classification, and visually classified according to published accounts. The different morphological classes of cells were separated with the LDA. Ventral cochlear nucleus (VCN) bushy cells, planar multipolar (T-stellate) cells, and radiate multipolar (D-stellate) cells were in separate clusters, and were also separated from all of the neurons from the dorsal cochlear nucleus (DCN). Within the DCN, the pyramidal cells and tuberculoventral cells were largely separated from a distinct clusters of cartwheel cells. DCN cells fell largely within a plane in the first 3 principal axes, whereas VCN cells were in 3 clouds approximately orthogonal to this plane. VCN neurons from the two mouse strains were slightly separated, indicating either a strain dependence or the differences in slice preparation methods. We conclude that cochlear nucleus neurons can be objectively distinguished based on their intrinsic electrical properties, but that such distinctions are still best aided by morphological identification.
Early Reactivation of Emotion in ERPs to Neutral Retrieval Cues
Authors: Bowen Holly J. , Fields Eric C. , Kensinger Elizabeth A. 
Published: April 2019

AbstractMemory retrieval is thought to involve the reactivation of encoding processes. Previous fMRI work has indicated that reactivation processes are modulated by the residual effects of the prior emotional encoding context; different spatial patterns emerge during retrieval of memories previously associated with negative compared to positive or neutral context. Other research suggests that ERP indicators of memory retrieval processes, like the left parietal old/new effect, can also be modulated by emotion, but the spatial distribution and temporal dynamics of these effects is unclear. In the current study, we examinedwhenemotion affects memory reactivation and whether that timing reflects processes that come before and may guide successful retrieval or post-recollection recovery of emotional episodic detail. While recording EEG, participants (N = 25) viewed neutral words paired with negative, positive or neutral pictures during encoding, followed by a recognition test for the words. Analyses focused on ERPs during the recognition test. In line with prior ERP studies, we found an early positive-going parietally distributed effect starting around 200 ms post retrieval-cue onset. This effect emerged for words that had been encoded in an emotional compared to neutral context (no valence differences), before the general old/new effect. This emotion-dependent effect occurred in an early time window, suggesting emotion-related reactivation is a precursor to successful recognition.
Integrating case studies into graduate teaching assistant training to improve instruction in biology laboratory courses
Authors: Kraft Jelena , Walck-Shannon Elise , Reilly Colleen , Stapleton Ann E 
Published: April 2019

AbstractToday’s biology laboratory courses are primarily instructed by graduate teaching assistants (GTAs) working toward their own graduate degrees in a science field. Even though GTAs are the driving instructional force in biology laboratories, they receive little to no training in pedagogical principles and applications. Here, we present the GTAs’ self-reported unmet training needs with respect to teaching biology laboratory courses. To address these needs, we developed three training cases along with instructions for implementation in online and in-person GTA trainings. We piloted our training materials for GTA training in person at Iowa State University and in a Center for the Integration of Research, Teaching, and Learning three-part online workshop. Upon completion of these training sessions, GTAs reported an increase in both their confidence and knowledge of student-centered instructional approaches. Furthermore, examination of the online workshop participants’ lesson plans demonstrated that GTAs were able to implement effective teaching practices in their own lesson plans. For brief training sessions, these are positive outcomes suggesting these cases are effective tools that could be incorporated into a variety of GTA training programs to improve instruction in biology laboratory courses.
Mini-barcodes are equally useful for species identification and more suitable for large-scale species discovery in Metazoa than full-length barcodes
Authors: Yeo Darren , Srivathsan Amrita , Meier Rudolf 
Published: April 2019

AbstractNew techniques for the species-level sorting of millions of specimens are needed in order to accelerate species discovery, determine how many species live on earth, and develop efficient biomonitoring techniques. These sorting methods should be reliable, scalable and cost-effective, as well as being largely insensitive to low-quality genomic DNA, given that this is usually all that can be obtained from museum specimens. Mini-barcodes seem to satisfy these criteria, but it is unclear how well they perform for species-level sorting when compared to full-length barcodes. This is here tested based on 20 empirical datasets covering ca. 30,000 specimens and 5,500 species, as well as six clade-specific datasets from GenBank covering ca. 98,000 specimens for over 20,000 species. All specimens in these datasets had full-length barcodes and had been sorted to species-level based on morphology. Mini-barcodes of different lengths and positions were obtainedin silicofrom full-length barcodes using a sliding window approach (3 windows: 100-bp, 200-bp, 300-bp) and by excising nine mini-barcodes with established primers (length: 94 – 407-bp). We then tested whether barcode length and/or position reduces species-level congruence between morphospecies and molecular Operational Taxonomic Units (mOTUs) that were obtained using three different species delimitation techniques (PTP, ABGD, objective clustering). Surprisingly, we find no significant differences in performance for both species- or specimen-level identification between full-length and mini-barcodes as long as they are of moderate length (>200-bp). Only very short mini-barcodes (<200-bp) perform poorly, especially when they are located near the 5’ end of the Folmer region. The mean congruence between morphospecies and mOTUs is ca. 75% for barcodes >200-bp and the congruent mOTUs contain ca. 75% of all specimens. Most conflict is caused by ca. 10% of the specimens that can be identified and should be targeted for re-examination in order to efficiently resolve conflict. Our study suggests that large-scale species discovery, identification, and metabarcoding can utilize mini-barcodes without any demonstrable loss of information compared to full-length barcodes.
Optimal policy for multi-alternative decisions
Authors: Tajima Satohiro , Drugowitsch Jan , Patel Nisheet , Pouget Alexandre 
Published: April 2019

AbstractEvery-day decisions frequently require choosing among multiple alternatives. Yet, the optimal policy for such decisions is unknown. Here we derive the normative policy for general multi-alternative decisions. This strategy requires evidence accumulation to nonlinear, time-dependent bounds, that trigger choices. A geometric symmetry in those boundaries allows the optimal strategy to be implemented by a simple neural circuit involving a normalization with fixed decision bounds and an urgency signal. The model captures several key features of the response of decision-making neurons as well as the increase in reaction time as a function of the number of alternatives, known as Hick’s law. In addition, we show that, in the presence of divisive normalization and internal variability, our model can account for several so called ‘irrational’ behaviors such as the similarity effect as well as the violation of both the independent irrelevant alternative principle and the regularity principle.
Weighted burden analysis of exome-sequenced late onset Alzheimer’s cases and controls provides further evidence for a role for PSEN1 and suggests involvement of the PI3K/Akt/GSK-3β and WNT signalling pathways
Authors: Curtis David , Bakaya Kaushiki , Sharma Leona , Bandyopadhyay Sreejan 
Published: April 2019

SummaryPrevious studies have implicated common and rare genetic variants as risk factors for late onset Alzheimer’s disease (AD, LOAD). Here, weighted burden analysis was applied to over 10,000 exome sequenced subjects from the Alzheimer’s Disease Sequencing Project. Analyses were carried out to investigate whether rare variants predicted to have a functional effect within a gene were more commonly seen in cases or in controls. Confirmatory results were obtained for TREM2, ABCA7 and SORL1. Additional support was provided for PSEN1 (p = 0.0002), which previously had been only weakly implicated in LOAD. There was suggestive evidence that functional variants in PIK3R1, WNT7A, C1R and EXOC5 might increase risk and that variants in TIAF1 and/or NDRG2 might have a protective effect. Overall, there was strong evidence (p = 5 × 10−6) that variants in tyrosine phosphatase genes reduce the risk of developing LOAD. Since PIK3R1 variants are expected to impair PI3K/Akt/GSK-3β signalling while variants in tyrosine phosphatase genes would enhance it, these findings are in line with those from animal models suggesting that this pathway is protective against AD.
Managing congestion at visitor hotspots using park-level use level data: Case study of a Chinese World Heritage site
Authors: Guo Jin-Hui , Guo Tian , Lin Kai-Miao , Leung Yu-Fai , Chen Qiu-Hua 
Published: April 2019

AbstractTourist congestion at hot spots has been a major management concern for UNESCO World Heritage Sites and other iconic protected areas. A growing number of heritage sites employ technologies, such as cameras and electronic ticket-checking systems, to monitor user levels, but data collected by these monitoring technologies are often under-utilize. In this study, we illustrated how to integrate data from hot spots by camera-captured monitoring and entrance counts to manage use levels at a World Heritage Site in southeastern China. 6,930 photos of a congestion hotspot (scenic outlook on a trail) were collected within the park at a 10-minute interval over 105 days from January to November 2017. The entrance counts were used to predict daily average and maximum use level at the hotspot Average use level at the congestion hotspot did not exceed the use limit mandated by the Chinese park administration agency. However, from 9:20 am to 12:00 pm, the use level at hotspots exceeded visitor preferred use level. Visitor use level was significantly higher at the hotspot during a major Chinese “golden week” holiday. The daily entrance counts significantly predicted the average and maximum use level at the hotspot. Based on our findings, we recommend that the number of visitors entering the gate on each day should be less than 28,764 for the hotspots to meet use level mandates, while less than 6,245 to meet visitor preference. The gap manifested the complexity in visitor capacity management at high-use World Heritage Sites and other protected areas and calls for innovative monitoring and management strategies.
Understanding patterns of abiotic and biotic stress resilience to unleash the potential of crop wild relatives for climate-smart legume breeding
Authors: van Zonneveld Maarten , Rakha Mohamed , Tan Shin-yee , Chou Yu-yu , Chang Ching-huan , Yen Joyce , Schafleitner Roland , Nair Ramakrishnan , Naito Ken , Solberg Svein Ø. 
Published: April 2019

AbstractAlthough new varieties are urgently needed for climate-smart legume production, legume breeding lags behind with cereals and underutilizes wild relatives. This paper provides insights in patterns of abiotic and biotic stress resilience of legume crops and wild relatives to enhance the use and conservation of these genetic resources for climate-smart legume breeding. We focus onVigna, a pantropical genus with more than 88 taxa including important crops such as cowpea and mung bean. Sources of pest and disease resistance occur in more than 50 percent of theVignataxa, which were screened while sources of abiotic stress resilience occur in less than 20 percent of the taxa, which were screened. This difference suggests thatVignataxa co-evolve with pests and diseases while taxa are more conservative to adapt to climatic changes and salinization. Twenty-twoVignataxa are poorly conserved in genebanks or not at all. This germplasm is not available for legume breeding and requires urgent germplasm collecting before these taxa extirpate on farm and in the wild.Vignataxa, which tolerate heat and drought stress are rare compared with taxa, which escape these stresses or tolerate salinity. These rareVignataxa should be prioritized for conservation and screening for multifunctional traits of combined abiotic and biotic stress resilience. The high presence of salinity tolerance compared with drought stress tolerance, suggests thatVignataxa are good at developing salt-tolerant traits compared with drought-tolerant traits.Vignataxa are therefore of high value for legume production in areas that suffer from salinization.