bluuebunny/crossref_metadata_2025_split huggingface dataset:
The whale shark genome reveals how genomic and physiological properties scale with body size
Authors: Park Seung Gu , Luria Victor , Weber Jessica A. , Jeon Sungwon , Kim Hak-Min , Jeon Yeonsu , Bhak Youngjune , Jun Jehun , Kim Sang Wha , Hong Won Hee , Lee Semin , Cho Yun Sung , Karger Amir , Cain John W. , Manica Andrea , Kim Soonok , Kim Jae-Hoon , Edwards Jeremy S. , Bhak Jong , Church George M. 
Published: October 2018

AbstractThe endangered whale shark (Rhincodon typus) is the largest fish on Earth and is a long-lived member of the ancient Elasmobranchii clade. To characterize the relationship between genome features and biological traits, we sequenced and assembled the genome of the whale shark and compared its genomic and physiological features to those of 81 animals and yeast. We examined scaling relationships between body size, temperature, metabolic rates, and genomic features and found both general correlations across the animal kingdom and features specific to the whale shark genome. Among animals, increased lifespan is positively correlated to body size and metabolic rate. Several genomic features also significantly correlated with body size, including intron and gene length. Our large-scale comparative genomic analysis uncovered general features of metazoan genome architecture: GC content and codon adaptation index are negatively correlated, and neural connectivity genes are longer than average genes in most genomes. Focusing on the whale shark genome, we identified multiple features that significantly correlate with lifespan. Among these were very long gene length, due to large introns highly enriched in repetitive elements such as CR1-like LINEs, and considerably longer neural genes of several types, including connectivity, activity, and neurodegeneration genes. The whale shark’s genome had an expansion of gene families related to fatty acid metabolism and neurogenesis, with the slowest evolutionary rate observed in vertebrates to date. Our comparative genomics approach uncovered multiple genetic features associated with body size, metabolic rate, and lifespan, and showed that the whale shark is a promising model for studies of neural architecture and lifespan.
A robust nonlinear low-dimensional manifold for single cell RNA-seq data
Authors: Verma Archit , Engelhardt Barbara E. 
Published: October 2018

AbstractModern developments in single cell sequencing technologies enable broad insights into cellular state. Single cell RNA sequencing (scRNA-seq) can be used to explore cell types, states, and developmental trajectories to broaden understanding of cell heterogeneity in tissues and organs. Analysis of these sparse, high-dimensional experimental results requires dimension reduction. Several methods have been developed to estimate low-dimensional embeddings for filtered and normalized single cell data. However, methods have yet to be developed for unfiltered and unnormalized count data. We present a nonlinear latent variable model with robust, heavy-tailed error and adaptive kernel learning to estimate low-dimensional nonlinear structure in scRNA-seq data. Gene expression in a single cell is modeled as a noisy draw from a Gaussian process in high dimensions from low-dimensional latent positions. This model is called the Gaussian process latent variable model (GPLVM). We model residual errors with a heavy-tailed Student’s t-distribution to estimate a manifold that is robust to technical and biological noise. We compare our approach to common dimension reduction tools to highlight our model’s ability to enable important downstream tasks, including clustering and inferring cell developmental trajectories, on available experimental data. We show that our robust nonlinear manifold is well suited for raw, unfiltered gene counts from high throughput sequencing technologies for visualization and exploration of cell states.
On the unfounded enthusiasm for soft selective sweeps II: examining recent evidence from humans, flies, and viruses
Authors: Harris Rebecca B. , Sackman Andrew , Jensen Jeffrey D. 
Published: October 2018

ABSTRACTSince the initial description of the genomic patterns expected under models of positive selection acting on standing genetic variation and on multiple beneficial mutations—so-called soft selective sweeps—researchers have sought to identify these patterns in natural population data. Indeed, over the past two years, large-scale data analyses have argued that soft sweeps are pervasive across organisms of very different effective population size and mutation rate—humans, Drosophila, and HIV. Yet, others have evaluated the relevance of these models to natural populations, as well as the identifiability of the models relative to other known population-level processes, arguing that soft sweeps are likely to be rare. Here, we look to reconcile these opposing results by carefully evaluating three recent studies and their underlying methodologies. Using population genetic theory, as well as extensive simulation, we find that all three examples are prone to extremely high false-positive rates, incorrectly identifying soft sweeps under both hard sweep and neutral models. Furthermore, we demonstrate that well-fit demographic histories combined with rare hard sweeps serve as the more parsimonious explanation. These findings represent a necessary response to the growing tendency of invoking parameter-heavy, assumption-laden models of pervasive positive selection, and neglecting best practices regarding the construction of proper demographic null models.
Screening performance of abbreviated versions of the UPSIT smell test
Authors: Joseph Theresita , Auger Stephen D. , Peress Luisa , Rack Daniel , Cuzick Jack , Giovannoni Gavin , Lees Andrew , Schrag Anette E. , Noyce Alastair J. 
Published: October 2018

ABSTRACTBackgroundHyposmia features in several neurodegenerative conditions, including Parkinson’s disease (PD). The University of Pennsylvania Smell Identification Test (UPSIT) is a widely used screening tool for detecting hyposmia, but is time-consuming and expensive when used on a large scale.MethodsWe assessed shorter subsets of UPSIT items for their ability to detect hyposmia in 891 healthy participants from the PREDICT-PD study. Established shorter tests included Versions A and B of both the 4-item Pocket Smell Test (PST) and 12-item Brief Smell Identification Test (BSIT). Using a data-driven approach, we evaluated screening performances of 23,231,378 combinations of 1-7 smell items from the full UPSIT.ResultsPST Versions A and B achieved sensitivity/specificity of 76.8%/64.9% and 86.6%/45.9% respectively, whilst BSIT Versions A and B achieved 83.1%/79.5% and 96.5%/51.8% for detecting hyposmia defined by the longer UPSIT. From the data-driven analysis, two optimised sets of 7 smells surpassed the screening performance of the 12 item BSITs (with validation sensitivity/specificities of 88.2%/85.4% and 100%/53.5%). A set of 4 smells (Menthol, Clove, Gingerbread and Orange) had higher sensitivity for hyposmia than PST-A, -B and even BSIT-A (with validation sensitivity 91.2%). The same 4 smells also featured amongst those most commonly misidentified by 44 individuals with PD compared to 891 PREDICT-PD controls and a screening test using these 4 smells would have identified all hyposmic patients with PD.ConclusionUsing abbreviated smell tests could provide a cost-effective means of screening for hyposmia in large cohorts, allowing more targeted administration of the UPSIT or similar smell tests.
A multi-parent recombinant inbred line population ofCaenorhabditis elegansenhances mapping resolution and identification of novel QTLs for complex life-history traits
Authors: Snoek Basten L. , Volkers Rita J.M. , Nijveen Harm , Petersen Carola , Dirksen Philipp , Sterken Mark G. , Nakad Rania , Riksen Joost , Rosenstiel Philip , Stastna Jana J. , Braeckman Bart P. , Harvey Simon C. , Schulenburg Hinrich , Kammenga Jan E. 
Published: October 2018

AbstractLocal populations of the bacterivorous nematodeCaenorhabditis eleganscan be genetically almost as diverse as global populations. To investigate the effect of local genetic variation on heritable traits, we developed a new recombinant inbred line (RIL) population derived from four wild isolates. The wild isolates were collected from two closely located sites in France: Orsay and Santeuil. By crossing these four genetically diverse parental isolates a population of 200 RILs was constructed. RNA-seq was used to obtain sequence polymorphisms identifying almost 9000 SNPs variable between the four genotypes with an average spacing of 11 kb, possibly doubling the mapping resolution relative to currently available RIL panels. The SNPs were used to construct a genetic map to facilitate QTL analysis. Life history traits, such as lifespan, stress resistance, developmental speed and population growth were measured in different environments. For most traits substantial variation was found, and multiple QTLs could be detected, including novel QTLs not found in previous QTL analysis, for example for lifespan or pathogen responses. This shows that recombining genetic variation acrossC. eleganspopulations that are in geographical close proximity provides ample variation for QTL mapping. Taken together, we show that RNA-seq can be used for genotyping, that using more parents than the classical two parental genotypes to construct a RIL population facilitates the detection of QTLs and that the use of wild isolates permits analysis of local adaptation and life history trade-offs.
Dynamics of spontaneous alpha activity correlate with language ability in young children
Authors: Kwok Elaine Y. L. , Cardy Janis Oram , Allman Brian L. , Allen Prudence , Herrmann Björn 
Published: October 2018

AbstractEarly childhood is a period of tremendous growth in both language ability and brain maturation. To understand the dynamic interplay between neural activity and spoken language development, we used resting-state EEG recordings to explore the relation between alpha oscillations (7–10 Hz) and oral language ability in 4- to 6-year-old children with typical development (N=41). Three properties of alpha oscillations were investigated: a) alpha power using spectral analysis, b) flexibility of the alpha frequency quantified via the oscillation’s moment-to-moment fluctuations, and c) scaling behavior of the alpha oscillator investigated via the long-range temporal correlation in the alpha-amplitude time course. All three properties of the alpha oscillator correlated with children’s oral language abilities. Higher language scores were correlated with lower alpha power, greater flexibility of the alpha frequency, and longer temporal correlations in the alpha-amplitude time course. Our findings demonstrate a cognitive role of several properties of the alpha oscillator that has largely been overlooked in the literature.
Graphical Abstract
Social isolation-induced epigenetic and transcriptional changes inDrosophiladopaminergic neurons
Authors: Agarwal Pavan , Chung Phuong , Heberlein Ulrike , Kent Clement 
Published: October 2018

AbstractEpigenetic mechanisms play fundamental roles in brain function and behavior and stressors such as social isolation can alter animal behavior via epigenetic mechanisms. However, due to cellular heterogeneity, identifying cell-type-specific epigenetic changes in the brain is challenging. Here we report first use of a modified INTACT method in behavioral epigenetics ofDrosophila: a method we call mini-INTACT. Using ChIP-seq on mini-INTACT purified dopaminergic nuclei, we identified epigenetic signatures in socially-isolated and socially-enrichedDrosophilamales. Social experience altered the epigenetic landscape in clusters of genes involved in transcription and neural function. Some of these alterations were predicted by expression changes of four transcription factors and the prevalence of their binding sites in several clusters. These transcription factors were previously identified as activity-regulated genes and their knockdown in dopaminergic neurons reduced the effects of social experience on sleep. Our work enables the use ofDrosophilaas a model for cell-type-specific behavioral epigenetics.
Foreign R&D satellites as a medium for the international diffusion of knowledge
Authors: Blit Joel 
Published: October 2018

AbstractI examine the extent to which foreign R&D satellites of multinational firms act as a medium for the international diffusion of knowledge. Using patents from the United States Patent and Trademark Office, I compare the frequency with which headquarters patents are cited by third‐party firms in the satellite's host country relative to a control group of patents, and this both before and after the establishment of the satellite (using a difference‐in‐differences approach). The results suggest that the satellite increases the flow of knowledge from the multinational's headquarters to firms in the satellite's host country. This satellite effect on knowledge diffusion is largest in host countries and sectors with strong but not world‐class capabilities that have both the motivation and absorptive capacity to learn from foreign parties. The findings also suggest that knowledge diffusion is greatest when satellites are staffed with inventors that have previously either patented with other local firms (thus having stronger local social networks) or with the headquarters (thus having headquarters knowledge).
An economic and environment friendly way of recycling boron carbide waste to prepare B4C/Al composite ceramic
Authors: Gao Shuaibo , Dong Kaizhao , Li Xin , Kong Jian , Wang Shuai , Xing Pengfei , Li Pan 
Published: October 2018

AbstractRecently, with the rapid growth of sapphire wafer applications, boron carbide as abrasive, has shown an increasing demand. Great amounts of boron carbide waste (low purity and small grain size with D50 ≈ 1 μm) are therefore produced during the production of boron carbide abrasives and barely recovered and utilized. This paper is aimed at developing an economic and environment friendly process to recycle the boron carbide waste through adding a certain amount of Al powder to prepare B4C/Al composite ceramic. Prior to the sintering process, samples were firstly mixed with different Al powder and then pelleted and dehydrated. The effects of the pelletizing factors on performances of the pellets and the ceramics were optimized as binder hydroxypropyl methylcellulose addition 0.4%, pelleting pressure 30 MPa, Al addition 9 wt%, sintering time 90 minutes. Under these conditions, the apparent porosity, bulk density, compressive strength and flexural strength of the sintered B4C/Al are 19.08%, 1.84 g/cm3, 246.88 MPa and 71.10 MPa respectively. Al addition can not only attribute to the low‐temperature liquid sintering and densification of the product, but also generation of some stable phases including AlB12, AlB12C2 and Al3BC, which in turn increase the performance of the ceramic composite.
Modification of commercial boron carbide powder using Rapid Carbothermal Reduction
Authors: Toksoy Muhammet Fatih , Haber Richard A. 
Published: October 2018

AbstractNon‐uniform morphology and existence of free carbon are two main problems for commercial boron carbide powders. This work proposes a method for eliminating free carbon and changing the morphology of commercial powders using Rapid Carbothermal Reduction (RCR) process. Free carbon is eliminated from commercial boron carbide powders and morphology is evolved to less angular shapes with limited particle size growth. Commercial and modified powders were densified by Spark Plasma Sintering at 1900°C with 0, 5, and 20 minutes dwell. Despite the particle size growth, modified boron carbide powders reached >99%TDwith shorter dwell times compared with commercial starting powders. Improved microhardness observed with dense modified samples as a result of enhanced morphology and increased twinning.
Electrically conductive SiC ceramics processed by pressureless sintering
Authors: Kim Yong‐Hyeon , Kim Young‐Wook , Kim Kwang Joo 
Published: October 2018

AbstractPolycrystalline SiC ceramics with 10 vol% Y2O3‐AlN additives were sintered without any applied pressure at temperatures of 1900‐2050°C in nitrogen. The electrical resistivity of the resulting SiC ceramics decreased from 6.5 × 101 to 1.9 × 10−2 Ω·cm as the sintering temperature increased from 1900 to 2050°C. The average grain size increased from 0.68 to 2.34 μm with increase in sintering temperature. A decrease in the electrical resistivity with increasing sintering temperature was attributed to the grain‐growth‐induced N‐doping in the SiC grains, which is supported by the enhanced carrier density. The electrical conductivity of the SiC ceramic sintered at 2050°C was ~53 Ω−1·cm−1 at room temperature. This ceramic achieved the highest electrical conductivity among pressureless liquid‐phase sintered SiC ceramics.
Assembly of β‐SiC Nanowires film and humidity sensing performance
Authors: Shen Xiulin , Liu Haitao , Liu Silin , Huang Zhaohui , Liu Yangai , Fang Minghao , Wu Xiaowen , Min Xin 
Published: October 2018

Abstractβ‐SiC materials have been seen as the third‐generation semiconductor widely used in kinds of photoelectric device, high temperature electronics, and other fields. Compared with ordinary semiconductors, β‐SiC materials have huge potential application in replacing monocrystalline silicon in extreme environments because of their numerals extraordinary chemical and physical properties. Based on this, β‐SiC nanowires obviously are more desirable in any way. Here, we present a modified chemical vapor deposition (CVD) method to synthesis β‐SiC nanowires, which needs no protect gas, and transfer it to Si/SiO2 substrates equipped with Au electrodes. The microstructure of the as‐prepared samples is tested by field emission scanning electron microscopy (FESEM). The humidity sensing performance of electronic device is measured by electrochemical workstation test equipment. It shows that the resistance of β‐SiC nanowires increases with increasing environment humidity within very short response/recovery time‐0.5 seconds/0.5 seconds and also performs excellent cycling stability. Such advantage superiorities make it highly possible to apply β‐SiC nanowires into various environments.
Systems vaccinology and big data in the vaccine development chain
Authors: Raeven René H. M. , van Riet Elly , Meiring Hugo D. , Metz Bernard , Kersten Gideon F. A. 
Published: October 2018

SummarySystems vaccinology has proven a fascinating development in the last decade. Where traditionally vaccine development has been dominated by trial and error, systems vaccinology is a tool that provides novel and comprehensive understanding if properly used. Data sets retrieved from systems‐based studies endorse rational design and effective development of safe and efficacious vaccines. In this review we first describe different omics‐techniques that form the pillars of systems vaccinology. In the second part, the application of systems vaccinology in the different stages of vaccine development is described. Overall, this review shows that systems vaccinology has become an important tool anywhere in the vaccine development chain.
No evidence of quantitative signal honesty across species of aposematic burnet moths (Lepidoptera: Zygaenidae)
Authors: Briolat Emmanuelle S. , Zagrobelny Mika , Olsen Carl E. , Blount Jonathan D. , Stevens Martin 
Published: October 2018

AbstractMany defended species use conspicuous visual warning signals to deter potential predators from attacking. Traditional theory holds that these signals should converge on similar forms, yet variation in visual traits and the levels of defensive chemicals is common, both within and between species. It is currently unclear how the strength of signals and potency of defences might be related: conflicting theories suggest that aposematic signals should be quantitatively honest, or, in contrast, that investment in one component should be prioritized over the other, while empirical tests have yielded contrasting results. Here, we advance this debate by examining the relationship between defensive chemicals and signal properties in a family of aposematic Lepidoptera, accounting for phylogenetic relationships and quantifying coloration from the perspective of relevant predators. We test for correlations between toxin levels and measures of wing colour across 14 species of day‐flying burnet and forester moths (Lepidoptera: Zygaenidae), protected by highly aversive cyanogenic glucosides, and find no clear evidence of quantitative signal honesty. Significant relationships between toxin levels and coloration vary between sexes and sampling years, and several trends run contrary to expectations for signal honesty. Although toxin concentration is positively correlated with increasing luminance contrast in forewing pattern in 1 year, higher toxin levels are also associated with paler and less chromatically salient markings, at least in females, in another year. Our study also serves to highlight important factors, including sex‐specific trends and seasonal variation, that should be accounted for in future work on signal honesty in aposematic species.
Cargo‐dependent and cell wall‐associated xylem transport in Arabidopsis
Authors: Endo Satoshi , Iwai Yumi , Fukuda Hiroo 
Published: October 2018

Summary

Sap molecules are transported by xylem flow throughout the whole plant body. Factors regulating the xylem transport of different molecules remain to be identified.

We used fluorophores to visualize xylem transport from roots to leaves in Arabidopsis thaliana. Several previously established Arabidopsis lines with modified xylem cell walls were used to determine the contribution of xylem cell walls to xylem transport.

Fluorophores underwent xylem flow‐dependent transport from roots to leaves within 20 min. A comparison of rhodamine, fluorescein and three fluorescently labeled CLV3/ESR‐related (CLE) peptides revealed cargo‐dependent xylem transport patterns in terms of leaf position and vein order. Only minor changes in amino acid sequence were sufficient to alter the xylem transport patterns of the labeled CLE peptides. We found that the xylem transport pattern of fluorescein was affected in Arabidopsis lines with modified AtXYN1, LAC4 or CCoAOMT1 expression. In these lines, application of a defense inducer, pipecolic acid, to roots resulted in altered defense response patterns in leaves, whereas all the lines showed wild‐type‐like responses when pipecolic acid was sprayed onto leaves.

The combined results reveal a finely controlled cargo‐dependent xylem transport and suggest that the xylem cell wall structure is crucial for this transport system.