bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome-Wide Genotype-Expression Relationships Reveal Both Copy Number and Single Nucleotide Differentiation Contribute to Differential Gene Expression between Stickleback Ecotypes
Authors: Huang Yun , Feulner Philine G D , Eizaguirre Christophe , Lenz Tobias L , Bornberg-Bauer Erich , Milinski Manfred , Reusch Thorsten B H , Chain Frédéric J J 
Published: July 2019

Abstract
Repeated and independent emergence of trait divergence that matches habitat differences is a sign of parallel evolution by natural selection. Yet, the molecular underpinnings that are targeted by adaptive evolution often remain elusive. We investigate this question by combining genome-wide analyses of copy number variants (CNVs), single nucleotide polymorphisms (SNPs), and gene expression across four pairs of lake and river populations of the three-spined stickleback (Gasterosteus aculeatus). We tested whether CNVs that span entire genes and SNPs occurring in putative cis-regulatory regions contribute to gene expression differences between sticklebacks from lake and river origins. We found 135 gene CNVs that showed a significant positive association between gene copy number and gene expression, suggesting that CNVs result in dosage effects that can fuel phenotypic variation and serve as substrates for habitat-specific selection. Copy number differentiation between lake and river sticklebacks also contributed to expression differences of two immune-related genes in immune tissues, cathepsin A and GIMAP7. In addition, we identified SNPs in cis-regulatory regions (eSNPs) associated with the expression of 1,865 genes, including one eSNP upstream of a carboxypeptidase gene where both the SNP alleles differentiated and the gene was differentially expressed between lake and river populations. Our study highlights two types of mutations as important sources of genetic variation involved in the evolution of gene expression and in potentially facilitating repeated adaptation to novel environments.
Genome Resequencing Reveals Congenital Causes of Embryo and Nestling Death in Crested Ibis (Nipponia nippon)
Authors: Fu Chun-Zheng , Guang Xuan-Min , Wan Qiu-Hong , Fang Sheng-Guo 
Published: July 2019

AbstractThe crested ibis (Nipponia nippon) is endangered worldwide. Although a series of conservation measures have markedly increased the population size and distribution area of these birds, the high mortality of embryos and nestlings considerably decreases the survival potential of this bird species. High-throughput sequencing technology was utilized to compare whole genomes between ten samples from dead crested ibises (including six dead embryos and four dead nestlings aged 0–45 days) and 32 samples from living birds. The results indicated that the dead samples all shared the genetic background of a specific ancestral subpopulation. Furthermore, the dead individuals were less genetically diverse and suffered higher degrees of inbreeding compared with these measures in live birds. Several candidate genes (KLHL3, SETDB2, TNNT2, PKP1, AK1, and EXOSC3) associated with detrimental diseases were identified in the genomic regions that differed between the alive and dead samples, which are likely responsible for the death of embryos and nestlings. In addition, in these regions, we also found several genes involved in the protein catabolic process (UBE4A and LONP1), lipid metabolism (ACOT1), glycan biosynthesis and metabolism (HYAL1 and HYAL4), and the immune system (JAM2) that are likely to promote the normal development of embryos and nestlings. The aberrant conditions of these genes and biological processes may contribute to the death of embryos and nestlings. Our data identify congenital factors underlying the death of embryos and nestlings at the whole genome level, which may be useful toward informing more effective conservation efforts for this bird species.
Phenotypic and Genomic Local Adaptation across Latitude and Altitude in Populus trichocarpa
Authors: Zhang Man , Suren Haktan , Holliday Jason A 
Published: July 2019

AbstractLocal adaptation to climate allows plants to cope with temporally and spatially heterogeneous environments, and parallel phenotypic clines provide a natural experiment to uncover the genomic architecture of adaptation. Though extensive effort has been made to investigate the genomic basis of local adaptation to climate across the latitudinal range of tree species, less is known for altitudinal clines. We used exome capture to genotype 451 Populus trichocarpa genotypes across altitudinal and latitudinal gradients spanning the natural species range, and phenotyped these trees for a variety of adaptive traits in two common gardens. We observed clinal variation in phenotypic traits across the two transects, which indicates climate-driven selection, and coupled gene-based genotype–phenotype and genotype–environment association scans to identify imprints of climatic adaptation on the genome. Although many of the phenotype- and climate-associated genes were unique to one transect, we found evidence of parallelism between latitude and altitude, as well as significant convergence when we compared our outlier genes with those putatively involved in climatic adaptation in two gymnosperm species. These results suggest that not only genomic constraint during adaptation to similar environmental gradients in poplar but also different environmental contexts, spatial scale, and perhaps redundant function among potentially adaptive genes and polymorphisms lead to divergent adaptive architectures.
Upper mantle shear velocity structure beneath the equatorial East Pacific Rise from array-based teleseismic surface-wave dispersion analysis
Authors: Zhai Qiushi , Yao Huajian , Peng Zhigang 
Published: July 2019

Summary
The Discovery/Gofar transform faults system is associated with a fast-spreading center on the equatorial East Pacific Rise. Most previous studies focus on its regular seismic cycle and crustal fault zone structure, but the characteristics of the upper mantle structure beneath this mid-ocean ridge system are not well known. Here we invert upper mantle shear velocity structure in this region using both teleseismic surface waves and ambient seismic noise from 24 ocean bottom seismometers (OBSs) deployed in this region in 2008. We develop an array analysis method with multi-dimensional stacking and tracing to determine the average fundamental mode Rayleigh wave phase-velocity dispersion curve (period band 20–100 s) for 94 teleseismic events distributed along the E-W array direction. Then, we combine with the previously measured Rayleigh wave phase-velocity dispersion (period band 2–25 s) from ambient seismic noise to obtain the average fundamental mode (period band 2–100 s) and the first-higher mode (period band 3–7 s) Rayleigh wave phase-velocity dispersion. The average dispersion data are inverted for the 1-D average shear wave velocity (Vs) structure from crust to 200-km depth in the upper mantle beneath our study region. The average Vs between the Moho and 200-km depth of the final model is about 4.18 km/s. There exists an ∼5-km thickness high-velocity lid (LID) beneath the Moho with the maximum Vs of 4.37 km/s. Below the LID, the Vs of a pronounced low-velocity zone (LVZ) in the uppermost mantle (15–60 km depth) is 4.03–4.23 km/s (∼10 per cent lower than the global average). This pronounced LVZ is thinner and shallower than the LVZs beneath other oceanic areas with older lithospheric ages. We infer that partial melting (0.5–5 per cent) mainly occurs in the shallow upper mantle zone beneath this young (0–2 Myr) oceanic region. In the deeper portion (60–200 km depth), the Vs of a weak LVZ is 4.15–4.27 km/s (∼5 per cent lower than the global average). Furthermore, the inferred lithosphere-asthenosphere boundary (LAB) with ∼15-km thickness can fit well with the conductive cooling model. These results are useful for understanding the depth distribution and melting characteristics of the upper mantle lithosphere and asthenosphere in this active ridge-transform fault region.
Data-oriented constraint on the interpretation of S receiver function and its application to observations of seismic discontinuities in the lithosphere–asthenosphere system
Authors: Shen Xuzhang , Kim YoungHee , Song Teh-Ru Alex , Lim Hobin 
Published: July 2019

SUMMARYThis paper aims to improve the robustness of interpretation in the S receiver function (SRF), a technique commonly used to retrieve forward scattering of S-to-P converted waves (Sdp) originated from the lithosphere–asthenosphere system (LAS) beneath the stations. Although the SRF does not suffer interferences from backward scattering waves such as the first multiples from the Moho, one major drawback in the method is that Sdp phases can interfere with P coda waves and it is conceivable that these signal-generated noise may be misinterpreted as Sdp phase from the LAS beneath seismic stations. Through systematic analysis of full-waveform synthetics and SRFs from catalogued source parameters, we find that the strong P coda waves before the S wave in the longitudinal-component waveforms result in unwanted signal-generated noise before the S wave in the synthetic SRFs. If the mean amplitude of SRFs after the S wave is large, dubious signal-generated noise before the S arrival are strong as well. In this study, we honor the level of these unwanted signal-generated noise and devise data-oriented screening criteria to minimize the interference between P coda waves and genuine S-to-P converted waves. The first criterion is LQR, a direct measure of the amplitude ratio between longitudinal P coda waves and radial S wave in the waveform data. The second criterion is AMP, the amplitude of SRFs after the S arrival. We illustrate that these criteria effectively measure the energy level of mantle waves such as the SP wave. With synthetics and real data, we demonstrate the effectiveness of LQR and AMP criteria in minimizing these unwanted signal-generated noise in the stacked SRFs down to 1–2 per cent, improving detection threshold and interpretation of Sdp phases from seismic discontinuities in the LAS.
Changes of energy fluxes in marine animal forests of the Anthropocene: factors shaping the future seascape
Authors: Rossi Sergio , Isla Enrique , Bosch-Belmar Mar , Galli Giovanni , Gori Andrea , Gristina Michele , Ingrosso Gianmarco , Milisenda Giacomo , Piraino Stefano , Rizzo Lucia , Schubert Nadine , Soares Marcelo , Solidoro Cosimo , Thurstan Ruth H , Viladrich Núria , Willis Trevor J , Ziveri Patrizia 
Published: July 2019

AbstractClimate change is already transforming the seascapes of our oceans by changing the energy availability and the metabolic rates of the organisms. Among the ecosystem-engineering species that structure the seascape, marine animal forests (MAFs) are the most widespread. These habitats, mainly composed of suspension feeding organisms, provide structural complexity to the sea floor, analogous to terrestrial forests. Because primary and secondary productivity is responding to different impacts, in particular to the rapid ongoing environmental changes driven by climate change, this paper presents some directions about what could happen to different MAFs depending on these fast changes. Climate change could modify the resistance or resilience of MAFs, potentially making them more sensitive to impacts from anthropic activities (i.e. fisheries and coastal management), and vice versa, direct impacts may amplify climate change constraints in MAFs. Such changes will have knock-on effects on the energy budgets of active and passive suspension feeding organisms, as well as on their phenology, larval nutritional condition, and population viability. How the future seascape will be shaped by the new energy fluxes is a crucial question that has to be urgently addressed to mitigate and adapt to the diverse impacts on natural systems.
The ‘Chinese Dream’ and the ‘Belt and Road Initiative’: narratives, practices, and sub-state actors
Authors: Loh Dylan M H 
Published: July 2019

Abstract
The ‘Chinese Dream’ (CD) and the ‘Belt Road Initiative’ (BRI) are signature programs of President Xi Jinping. Much of the scholarships on these two projects have concerned itself with either domestic propagandistic effects or external foreign policy impact. These concerns have underpinned the literature’s focus on material expressions of such projects, be it through infrastructural construction in the case of the BRI or propaganda tools in the example of the CD. Yet, an important but understudied element of these two projects is the narratives that they tell and the impact of these narratives. In that regard, this article complements existing studies of the CD and the BRI by reading the projects as grand narratives. Drawing on international practice theory, I trace an explicit link between narratives and practices to demonstrate how narratives activate, anchor, produces and contest political practices of some sub-state actors in China. That is to say narratives: (i) serve as signposts for sub-state actors’ orientations in clarifying what are relevant/irrelevant and appropriate/inappropriate practices; (ii) provide ‘background’ stock of information where actors draw on to legitimize their practices when they speak of the BRI and CD; and (iii) create conditions for both the creation of new practices and contestation of existing ones. I then argue that four narrative-practice processes are seen in the Chinese example: contestation, sustenance, activation, and production.
4-Fluoromethylphenidate: Fatal Intoxication Involving a Previously Unreported Novel Psychoactive Substance in the USA
Authors: Shoff Elisa N , Kahl Joseph H , Hime George W , Coburn Marta , Boland Diane M 
Published: July 2019

Abstract
The (±)-threo-4-fluoromethylphenidate (4F-MPH) is a fluorinated analog of the prescription central nervous system stimulant medication, methylphenidate. This novel psychoactive substance was first detected in drug paraphernalia at the Miami-Dade County Medical Examiner Department Toxicology Laboratory in 2016 but was not detected in a biological specimen until 2018. Limited literature is available on 4F-MPH, with predominate literature being published out of Europe, and no known toxicities reported in the USA. Post-mortem specimens were screened using both gas chromatography mass spectrometry and liquid chromatography ion trap mass spectrometry (LC–Ion Trap-MSn). In addition, a validated method for the quantification of 4F-MPH was developed using liquid chromatography–tandem mass spectrometry (LC–MS-MS), with a linear range of 0.01–0.500 mg/L and acceptable validation criteria including precision, bias, carry-over, linearity and endogenous/exogenous interferences. In addition to the detection of 4F-MPH, 3-methoxy-PCP, amphetamine, methamphetamine, 6-monoacetylmorphine, morphine, codeine and tetrahydrocannabinol were also identified in the decedent. A single source of blood was collected (femoral vein) and quantified in all blood tubes used for collection, with concentrations varying from 0.012 to 0.05 mg/L. Additional specimens available for screening included gastric contents and urine. An additional peak having the same targeted ions and transitions as 4F-MPH was identified in both the LC–Ion Trap-MSn screening procedure and the LC–MS-MS quantitative procedure. This peak suggests the presence of a structural isomer, possibly (±)-erythro-4-fluoromethylphenidate, which cannot be confirmed due to there being no available certified reference material. This case report presents the first time that 4F-MPH was detected in a decedent, as well as the first time 4F-MPH has been listed in the official cause of death of a decedent in Florida.
On the Frequency of Voluntary Martyrdom in the Patristic Era
Authors: Vincelette Alan 
Published: July 2019

Abstract
Contemporary scholarship on early Christian martyrdom has tended to accept the position of G. E. M. de Ste. Croix that voluntary martyrdom, or handing oneself over to the authorities prior to being sought out or arrested, was quite common. This view falls apart, however, if we avoid an overly broad definition of voluntary martyrdom, a problem common to Ste. Croix and contemporaries such as Arthur Droge, Paul Middleton, and Candida Moss, who count various political protestors, public edifiers, and comforters and aiders as voluntary martyrs. In fact, if we carefully examine the accounts of martyrdom that took place in the first four centuries, voluntary martyrdom, though not unknown, makes up a small percentage of the whole, around 12 per cent instead of the 50 per cent described by Ste. Croix and others.
Shocks in relativistic viscous accretion flows around Kerr black holes
Authors: Dihingia Indu K , Das Santabrata , Maity Debaprasad , Nandi Anuj 
Published: July 2019

ABSTRACT
We study the relativistic viscous accretion flows around the Kerr black holes. We present the governing equations that describe the steady-state flow motion in full general relativity and solve them in 1.5D to obtain the complete set of global transonic solutions in terms of the flow parameters, namely specific energy (${\mathcal E}$), specific angular momentum (${\mathcal L}$), and viscosity (α). We obtain a new type of accretion solution which was not reported earlier. Further, we show for the first time to the best of our knowledge that viscous accretion solutions may contain shock waves particularly when flow simultaneously passes through both inner critical point (rin) and outer critical point (rout) before entering into the Kerr black holes. We examine the shock properties, namely shock location (rs) and compression ratio (R, the measure of density compression across the shock front) and show that shock can form for a large region of parameter space in ${\cal L}\!-\!{\cal E}$ plane. We study the effect of viscous dissipation on the shock parameter space and find that parameter space shrinks as α is increased. We also calculate the critical viscosity parameter (αcri) beyond which standing shock solutions disappear and examine the correlation between the black hole spin (ak) and αcri. Finally, the relevance of our work is conferred where, using rs and R, we empirically estimate the oscillation frequency of the shock front (νQPO) when it exhibits quasi-periodic (QP) variations. The obtained results indicate that the present formalism seems to be potentially viable to account for the QPO frequency in the range starting from milli-Hz to kilo-Hz as $0.386~{\rm Hz}\le \nu _{\mathrm{ QPO}} (\frac{10\, \mathrm{M}_\odot }{M_{\mathrm{ BH}}}) \le 1312$ Hz for ak = 0.99, where MBH stands for the black hole mass.
The effect of telescope aperture, scattered light and human vision on early measurements of sunspot and group numbers
Authors: Karachik Nina V , Pevtsov Alexei A , Nagovitsyn Yury A 
Published: July 2019

ABSTRACT
Early telescopic observations of sunspots were conducted with instruments of relatively small aperture. These instruments also suffered from a higher level of scattered light, and the human eye served as a ‘detector’. The eye’s ability to resolve small details depends on image contrast, and on average intensity variations smaller than ≈3 per cent contrast relative to background are not detected even if they are resolved by the telescope. Here we study the effect of these three parameters (telescope aperture, scattered light and detection threshold of human vision) on sunspot number, group number and area of sunspots. As an ‘ideal’ dataset, we employ white-light (pseudo-continuum) observations from the Helioseismic and Magnetic Imager (HMI) on board the Solar Dynamics Observatory, and we model the appearance of sunspots by degrading the HMI images to corresponding telescope apertures with added scattered light. We discuss the effects of different parameters on sunspot counts and derive functional dependences, which could be used to normalize historical observations of sunspot counts to a common denominator.
Not Quite What You Expected: The Curious Case of Brexit Scrutiny in the Czech Parliament
Authors: Kaniok Petr , Brusenbauch Meislova Monika 
Published: July 2019

AbstractThe aim of the article is to explore how the Czech bicameral parliament has reacted to the process of the United Kingdom's (UK's) withdrawal from the European Union (EU). Drawing upon insights from the theoretical expectations of parliamentary power, the inquiry researches the ways that Czech legislatures have developed in terms of engaging with and influencing the Brexit process. In this regard, the Czech case is exceptionally interesting and worth exploring, since the EU agenda has become a highly politicised issue within the Czech context. The significance of this inquiry has been further highlighted by the high level of party-based Euroscepticism typical of Czech politics as well as the frequent changes that the Czech party system has been undergoing in recent years. Throughout the in-depth analysis of parliamentary scrutiny activities—conceptualised as comprising four aspects: (i) the institutional adjustment; (ii) articulation of priorities; (iii) interactions with the government and (iv) parliamentary party politics—the article considers how these activities compare between both chambers of the Czech Parliament.
The Polls—Trends
Authors: Krause Nicole M , Brossard Dominique , Scheufele Dietram A , Xenos Michael A , Franke Keith 
Published: July 2019

AbstractEvents such as the 2017 “March for Science” have brought greater attention to public attitudes toward science and scientists. Our analyses of recent poll data show that Americans’ confidence in scientists has been high for roughly 40 years (relative to other institutions), and that it is high even for controversial topics such as global warming and nuclear energy. International comparisons show broad similarities with individuals in Germany and the UK, including that trust in scientists can fluctuate depending on who employs them and what topic is under discussion. Finally, more granular analyses in the United States reveal large divides in trust based on geographic location and religious identification (i.e., rural residents exhibit comparatively low trust and the nonreligious comparatively high trust), while the gap between political partisans has been relatively small but has spiked in recent years.