bluuebunny/crossref_metadata_2025_split huggingface dataset:
State-dependent differences in the frequency of TMS-evoked potentials between resting and active states
Authors: Stanfield Candice T. , Wiener Martin 
Published: April 2019

AbstractPrevious evidence suggests different cortical areas naturally oscillate at distinct frequencies, reflecting tuning properties of each region. The concurrent use of transcranial magnetic stimulation (TMS) and electroencephalography (EEG) has been used to perturb cortical regions, resulting in an observed post-stimulation response that is maximal at the natural frequency of that region. However, little is known about the spatial extent of TMS-induced activation differences in cortical regions when comparing resting state (passive) versus active task performance. Here, we employed TMS-EEG to directly perturb three cortical areas in the right hemisphere while measuring the resultant changes in maximal evoked frequency in healthy human subjects during a resting state (N=12) and during an active sensorimotor task (N=12). Our results revealed that the brain engages a higher dominant frequency mode when actively engaged in a task, such that the frequency evoked during a task is consistently higher across cortical regions, regardless of the region stimulated. These findings suggest that a distinct characteristic of active performance versus resting state is a higher state of natural cortical frequencies.
Direct Comparative Analysis of 10X Genomics Chromium and Smart-seq2
Authors: Wang Xiliang , He Yao , Zhang Qiming , Ren Xianwen , Zhang Zemin 
Published: April 2019

AbstractSingle cell RNA sequencing (scRNA-seq) is widely used for profiling transcriptomes of individual cells. The droplet-based 10X Genomics Chromium (10X) approach and the plate-based Smart-seq2 full-length method are two frequently-used scRNA-seq platforms, yet there are only a few thorough and systematic comparisons of their advantages and limitations. Here, by directly comparing the scRNA-seq data by the two platforms from the same samples of CD45-cells, we systematically evaluated their features using a wide spectrum of analysis. Smart-seq2 detected more genes in a cell, especially low abundance transcripts as well as alternatively spliced transcripts, but captured higher proportion of mitochondrial genes. The composite of Smart-seq2 data also resembled bulk RNA-seq data better. For 10X-based data, we observed higher noise for mRNA in the low expression level. Despite the poly(A) enrichment, approximately 10-30% of all detected transcripts by both platforms were from non-coding genes, with lncRNA accounting for a higher proportion in 10X. 10X-based data displayed more severe dropout problem, especially for genes with lower expression levels. However, 10X-data can better detect rare cell types given its ability to cover a large number of cells. In addition, each platform detected different sets of differentially expressed genes between cell clusters, indicating the complementary nature of these technologies. Our comprehensive benchmark analysis offers the basis for selecting the optimal scRNA-seq strategy based on the objectives of each study.
A weighted sequence alignment strategy for gene structure annotation lift over from reference genome to a newly sequenced individual
Authors: Song Baoxing , Sang Qing , Wang Hai , Pei Huimin , Wang Fen , Gan XiangChao 
Published: April 2019

AbstractGenome sequences and gene structure annotation are very important for genomic analysis, while only the reference gene structure annotation is widely used for a wide range of investigations of different natural variation individuals. Herein, we are reporting the software GEAN which could lift over the reference gene structure annotation to other individuals belonging to the same or closely related species whose genome sequence was determined by whole-genome resequencing or de novo assembly. We found that inconsistent sequence alignment makes the coordinate lift over between different individual genomes unreliable, thus obscuring the lift over of gene structure annotations and genomic variants functional prediction. We designed a zebraic dynamic programming (ZDP) algorithm by providing different weights to different genetic features to refine the gene structure lift over. Using the lift over gene structure annotation as anchors, a base-pair resolution whole-genome-wide sequence alignment and variant calling pipeline for de novo assembly have been implemented. Taking Arabidopsis thaliana as example, we show that the natural variation alleles expression level of apoptosis death and defence response related genes might could be better quantified using GEAN. And GEAN could be used to refine the functional annotation of genetic variants, annotate de novo assembly genome sequence, detect syntenic blocks, improve the quantification of gene expression levels using RNA-seq data and genomic variants encoding for population genetic analysis. We expect that GEAN will be a standard gene structure annotation lift over and genome sequence alignment tool for the coming age of de novo assembly population genetics analysis.
Brown Adipose Tissue Remodeling Precedes Cardiometabolic Abnormalities Independent of Overweight in Fructose-Feed Mice
Authors: Machado Thaissa Queiroz , Pereira-Silva Debora Cristina , Gonçalves Leidyanne Ferreira , Fernandes-Santos Caroline 
Published: April 2019

AbstractObjectivesTo investigate the early cardiometabolic abnormalities along with WAT and BAT remodeling in short-term fructose feeding mice model.MethodsMice (n=10-11/group) were fed for four weeks with control diet (AIN93-M) or experimental diets rich in glucose or fructose. We investigated body weight, body adiposity, blood glucose, lipid and hepatic parameters, and white (WAT) and brown adipose tissue (BAT) histopathology.ResultsFructose feeding promoted neither weight gain nor hypertrophy of visceral and subcutaneous WAT depots, but the fat was redistributed toward visceral depots. Glucose, lipid and hepatic metabolic dysfunction were not yet noticed in fructose-fed mice, with the exception for an elevation in total cholesterol and hepatic weight without steatosis. BAT mass did not increase, and it was proportionally reduced compared with visceral WAT in fructose feed mice. BAT suffered premature adverse morphological remodeling, characterized by increased lipid deposition per tissue area in enlarged intracellular lipid droplets.ConclusionShort-term fructose feeding redistributes body fat, changes the proportion of BAT to visceral fat, and promotes BAT adverse remodeling, characterized by enlarged intracellular lipid droplets.
Structures of a highly variable cell‐wall anchored protein‐encoding the spj gene from ST8/SCCmecIVl community‐associated methicillin‐resistant Staphylococcus aureus (CA‐MRSA/J) isolated from 2003 onwards: An indicator of a strongly invasive pathotype
Authors: Wan Tsai‐Wen , Teng Lee‐Jene , Yamamoto Tatsuo 
Published: April 2019

AbstractThe cell wall‐anchored protein‐encoding spj gene on staphylococcal cassette chromosome mec IVl (SCCmecIVl) was found to vary in size because of its 22‐ and 86‐aa repeat domains. The 22‐aa repeats are the more flexible of the two repeats, comprising three 11‐aa units, and were classified into three groups with eleven types. The 11/22‐aa repeats are longer in individuals with bullous impetigo, shorter in those with invasive disease and were absent in a fatal case, this last one having been rapidly diagnosed by PCR. IS431‐flanking pUB110 (bleO, aadD) is present on SCCmecIVl at 90%. The bacterial surface has the spj product and a unique surface layer.
A fast and robust two‐point ray tracing method in layered media with constant or linearly varying layer velocity
Authors: Fang Xinding , Chen Xiaofei 
Published: April 2019

ABSTRACTA fast and robust method for two‐point ray tracing in one‐dimensional layered media is presented. This method is applicable to layered models with constant or linearly varying isotropic layer velocity. For given model properties and source and receiver positions, a ray path can be uniquely determined once its ray parameter (i.e. horizontal slowness) is known. The ray parameter can be obtained by numerically solving the nonlinear offset (i.e. source–receiver horizontal distance) equation using Newton's method, which generally works well at near and mid offsets. However, Newton's method becomes hard to converge at large offsets due to the oversensitivity of offset to ray parameter. Based on the analysis of the characteristic of the offset equation, a modified ray parameter is proposed and used to replace the generic ray parameter in numerical calculation. Numerical experiments show that the iteration process becomes stable and converges rapidly with the modified ray parameter. Moreover, a rational function that asymptotically approximates the shape of the offset equation is introduced for obtaining good initial estimates of the modified ray parameter. Numerical tests show that this method is robust in any situation, and an accurate ray parameter can be obtained within two or three iterations for a wide range of model velocity structure and source–receiver distance. Furthermore, the proposed two‐point ray tracing method is easy to implement.
Real‐time compensation of magnetic data acquired by a single‐rotor unmanned aircraft system
Authors: Tuck L. , Samson C. , Polowick C. , Laliberté J. 
Published: April 2019

ABSTRACTTwo methods for low‐altitude calibration of a single‐rotor unmanned aircraft system using a real‐time compensator are tested: (1) a stationary calibration where the unmanned aircraft system executes manoeuvres while hovering in order to minimize ambient field changes due to the local geology; and (2) an adapted box calibration flown in four orthogonal directions. Both methods use two compensator‐specific limits derived from established methods for manned airborne calibration: the lowest frequency used by the compensator for the calibration algorithm and the maximum variation of the ambient magnetic intensity experienced by the unmanned aircraft system during calibration. Prior to flying, the unmanned aircraft system was magnetically characterized using the heading error and fourth difference. Magnetic interference was mitigated by extending the magnetometer‐unmanned aircraft system separation distance to 1.7 m, shielding, and demagnetization. The stationary calibration yielded an improvement ratio of 8.595 and a standard deviation of the compensated total magnetic intensity of 0.075 nT (estimated Figure‐of‐Merit of 3.8 nT). The box calibration also yielded an improvement ratio of 3.989 and a standard deviation of the compensated total magnetic intensity of 0.083 nT (estimated Figure‐of‐Merit of 4.2 nT). The stationary and box calibration solutions were robust with low cross‐correlation indexes (1.090 and 1.048, respectively) when applied to a non‐native data set.
Root‐feeding larvae increase their performance by inducing leaf volatiles that attract above‐ground conspecific adults
Authors: Sun Xiao , Siemann Evan , Liu Zhen , Wang Qiyun , Wang Dingli , Huang Wei , Zhang Chujun , Ding Jianqing 
Published: April 2019

Abstract

Herbivore‐induced changes in plant volatile emissions mediate above–below‐ground interactions by determining host plant colonization of different herbivores. By changing shoot‐emitted volatiles, below‐ground herbivores may use the plant to extend their capacity to interact with above‐ground con‐ and heterospecifics.

We investigated the attractiveness of Triadica sebifera plants infested by larvae of a specialist beetle or root‐knot nematodes to above‐ground herbivores. We then determined the contribution of leaf volatiles to the observed recruitment patterns using olfactometer experiments. We also identified volatiles through gas chromatography–mass spectrometry (GC–MS) and electroantennography, and conducted field experiments to confirm their effects.

Leaf volatiles induced by the root‐feeding larvae attracted above‐ground conspecific adults in laboratory and field experiments, but repelled a heterospecific specialist weevil, whereas induction by root‐knot nematodes had no effects on either. Greater leaf consumption by conspecific adults increased root nutrients, decreased root defences and facilitated root feeding larval performance. Thus, larvae and adults appear to manipulate their host plant, which increases aggregation above‐ground and feeding below‐ground.

Synthesis. The resulting colonization dynamics may shape the composition of plant rhizosphere and phyllosphere herbivore communities by enhancing conspecific establishment and reducing colonization by other herbivores. By modifying above‐ground volatiles and above‐ground herbivore behaviour, root feeders could mediate plant and leaf herbivore interactions and benefit via plant responses to above‐ground feeding.
Optimal Monetary Policy in China with Money as Not Redundant
Authors: Zhang Guoxiong 
Published: April 2019

AbstractThis article provides three pieces of evidence to show that money is not redundant in China: aggregate real money balance can affect aggregate demand even when its effect through short‐term interest rates is controlled. I estimate a DSGE model using Chinese data. With the estimated model, I find that monetary policy that controls the money supply (the quantity rule) is better than the one that controls the short‐term interest rate (the price rule) in terms of minimising welfare loss. I then discuss the optimal monetary policy that combines both the price rule and the quantity rule.
Organisational culture and enterprise risk management: The Australian not‐for‐profit context
Authors: Chen Jinhua , Jiao Lu , Harrison Graeme 
Published: April 2019

AbstractWith the increasing emphasis on risk management in not‐for‐profit organisations, this study is timely in its examination of risk management practices in the Australian not‐for‐profit sector. Specifically, the study investigates the relation between not‐for‐profits’ organisational culture and the maturity of enterprise risk management (ERM) practices. The results show that the organisational culture factors of Outcome Orientation (valuing achievements and results) and Innovation (valuing receptivity and adaptability to change) are associated with the maturity of not‐for‐profits’ ERM. This finding demonstrates the important role that organisational culture plays in shaping ERM practices in not‐for‐profit organisations and the crucial role that leaders play in creating and nurturing such a culture within their organisations. The results also have implications for regulatory policy‐making in, and for, the not‐for‐profit sector.
Survey mode effects and insurance coverage estimates in the redesigned Gallup well‐being index
Authors: Sommers Benjamin D. , Goldman Anna L. , Lee Dennis , Epstein Arnold M. 
Published: April 2019

AbstractObjectiveTo test whether a change from a telephone to mail and Internet survey in January 2018 affected the sample composition and uninsured estimates in the Gallup‐Sharecare Well‐Being Index.Data SourcesGallup‐Sharecare Well‐Being Index (2013‐2018).Study DesignRegression discontinuity analysis identified changes after the survey redesign in the estimated U.S. uninsured rate (adults 18‐64) and in the sample's demographic composition.Principal FindingsAfter the survey redesign, the estimated uninsured rate fell 5.3 percentage points (P < 0.001), respondents were older and disproportionately white, more likely to have a college degree, and had higher average incomes. These changes were modestly reduced by survey weights.ConclusionsThe shift to a mail survey (with a web option) led to an older, more educated sample with fewer minorities, and a significant break in trend in the estimated uninsured rate.
Conservation and the Environment in US Farm Legislation
Authors: Lichtenberg Erik 
Published: April 2019

SummaryConservation programmes have been a feature of US agricultural policy since the 1930s. Farmers are paid to take farmland out of production and to install or maintain farming practices to reduce erosion and runoff or to protect wildlife habitat. Budgets for these programmes have grown substantially over the past two decades and they have become major vehicles for making payments to farmers. The goals are to promote agricultural sustainability and to enhance environmental quality. Providing income support to farmers is an explicit goal of some of the programmes and an implicit function of others. They operate by paying farmers to convert environmentally sensitive land to more sustainable uses; to adopt or maintain runoff‐ and erosion‐reducing practices on working farmland; or to preserve land of environmental or cultural importance in its current condition. The benefits of conserving agriculture's natural resource base are largely private while the benefits of environmental quality improvements are largely public. Income support (and thus political) considerations have dominated the geographic distribution of spending, to the detriment of potential achievements in environmental quality improvement. These programmes remain important as virtually the only means by which non‐point source pollution from agriculture is addressed in the United States.
EU and US Agricultural Policies: Commonalities and Contrasts
Authors: Blandford David , Matthews Alan 
Published: April 2019

SummaryThe fact that the EU and the United States are revising their farm legislation at the same time provides a good opportunity to compare the direction of farm policy in the two jurisdictions. In both cases policy developments are required to satisfy budgetary constraints, which on this occasion appear to be more stringent for the EU. Farm‐oriented spending in both regions continues to be largely directed to farm income support – the farm safety net in the US and direct payments in the EU. Policy changes in the US have aimed to increase the likelihood that financial support will be provided to farmers. The EU, at least in the rhetorical justification for its legal proposal, gives greater priority to incentivising farmers to adopt practices friendlier to the environment and is more focused on climate mitigation and adaptation. However, the key innovation in the EU proposal revolves around the management of the policy, with the aim of steering the decisions of Member States through a results‐based rather than compliance‐based approach. This introduction highlights some background and context for the articles to follow that explore these themes in greater depth.
Environment and Climate in the Common Agricultural Policy
Authors: Dupraz Pierre , Guyomard Hervé 
Published: April 2019

SummaryIn the 2014–20 CAP, environment is targeted through a combination of measures in both Pillar 1, through cross‐compliance and green payments, and Pillar 2, mainly through voluntary measures with compensation for cost incurred and income forgone. The European Commission's legislative proposals for the CAP after 2020 would suppress green payments but their objectives would be retained as part of new conditionality requirements. A new environmental instrument would be introduced in Pillar 1, the ‘eco‐scheme’, and the CAP would be implemented through national strategic plans offering Member States large room for manoeuvre in application of the principle of subsidiarity. This article explains the weak environmental effectiveness of the CAP until now. It then analyses the extent to which the European Commission's proposals could improve the regulation of the environment and climate impacts of European agriculture. Pillar 2 measures are largely unchanged with their strengths and weaknesses. There is a risk that short‐run political pressures will lead numerous countries to opt for limited ambition in their eco‐schemes. However, there is an urgent need to tackle climate and biodiversity issues seriously. This could be done following the principles of public economics and environmental federalism. In that perspective, defining simple and robust agri‐environmental indicators is crucial.
New evolving strategies revealed by transcriptomic analysis of a fur− mutant of the cyanotrophic bacterium Pseudomonas pseudoalcaligenes CECT 5344
Authors: Becerra Gracia , Igeño María Isabel , Merchán Faustino , Sánchez‐Clemente Rubén , Blasco Rafael 
Published: April 2019

SummaryThe transcriptomic analysis (RNA‐seq) of a fur mutant of P. pseudoalcaligenes CECT 5344 has revealed that Fur regulates the expression of more than 100 genes in this bacterial strain, most of them negatively. The highest upregulated genes in response to fur deletion, with respect to the wild type, both cultivated in LB medium, corresponded to genes implicated in iron uptake. They include both TonB‐dependent siderophore transporters for the active transport across the outer membrane, and ABC‐type and MSF‐type transporters for the active transport across the cytoplasmic membrane. Therefore, the main response of this bacterium to iron limitation is expressing genes necessary for metabolism of Fe siderophores produced by other microorganisms (xenosiderophores). The number of genes whose expression decreased in the fur− mutant, as well as its normalized expression (fold change), was lower. Among them, it is remarkable the presence of one of the two cas operons of the two CRISP/Cas clusters was detected in the genome of this bacterium. The transcriptome was validated by qPCR, including the decrease in the expression of cas genes (cse1). The expression of cse1 was also decreased by limiting the amount of iron, carbon or nitrogen in the medium, or by adding menadione, a compound that causes oxidative stress. The higher decrease in cse1 expression was triggered by the addition of cyanide in minimal medium. These results suggest that this bacterium responds to stress conditions, and especially to cyanide, taking a reasonable risk with respect to both the uptake of (TonB‐dependent receptors gates) and the tolerance to (reduced immunity) foreign nucleic acids. In conjunction, this can be considered a yet unknown molecular mechanism forcing bacterial evolution.
A Rapid Response Survey to Characterize the Impacts of the 2017 High Water Event on Lake Ontario
Authors: Steinschneider Scott , Styler Alex , Stedman Richard , Austerman Mary 
Published: April 2019

AbstractIn the spring and summer of 2017, communities along the Lake Ontario shoreline suffered from the worst flood event on record. In late May, daily water levels reached their highest point in over 100 years, and flooding continued throughout much of the summer as lake levels slowly declined, with inundation and erosion significantly impacting shoreline homes and businesses. In this work, we present results from a rapid response online survey of property owners along the New York Lake Ontario shoreline to quantify the perceived flood impacts of the 2017 extended high water event. The survey focused on the degree and spatial distribution of inundation and erosion; the duration and drivers of inundation; the associated damages to different property features, with an emphasis on shoreline protection; and the degree of disruption to business and other activities and services. Photographic documentation of inundation extent and property damage also was provided by survey respondents. We demonstrate the potential utility of this dataset by characterizing key features of inundation and erosion impacts across the shoreline, and by using classification and regression trees to explore the predictability of inundation and erosion based on property characteristics. This work is part of a larger effort to develop models of inundation and erosion that can support flood impact assessments across the shoreline and help communities better prepare for future extended high water events.