bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic structure and differentiation in Dendrocalamus sinicus (Poaceae: Bambusoideae) populations provide insight into evolutionary history and speciation of woody bamboos
Authors: Yang Jun Bo , Dong Yu Ran , Wong Khoon Meng , Gu Zhi Jia , Yang Han Qi , Li De Zhu 
Published: November 2018

AbstractEvolutionary processes, speciation in woody bamboos are presently little understood. Here we used Dendrocalamus sinicus Chia & J.L. Sun as a model species to investigate dispersal or vicariance speciation in woody bamboos. Variation in three chloroplast DNA (cpDNA) fragments and eight simple sequence repeat markers (SSR) among 232 individuals sampled from 18 populations across the known geographic range of D. sinicus was surveyed. D. sinicus populations exhibited a high level of genetic differentiation which divided them into two groups that are consistent with different culm types. Eleven haplotypes and two lineages (Straight-culm and Sinuous-culm lineages) were identified from phylogenetic analyses, and a strong phylogeographic structure across the distribution range was found. The demographic and spatial expansion times of the Straight-culm lineage were calculated as 11.3 Kya and 20.8 Kya, respectively. The populations of D. sinicus had experienced dispersal and long-term isolation, although this trace was diluted by contemporary gene flow revealed by SSR data. Our results provide an phylogeographic insight to better understand the speciation processes of woody bamboos.
Persistent metabolic changes in HIV-infected patients during the first year of combination antiretroviral therapy
Authors: Peltenburg N. Chantal , Schoeman Johannes C. , Hou Jun , Mora Fernando , Harms Amy C. , Lowe Selwyn H. , Bierau Jörgen , Bakker Jaap A. , Verbon Annelies , Hankemeier Thomas , Boonstra Andre 
Published: November 2018

AbstractThe HIV-human metabolic relationship is a complex interaction convoluted even more by antiretroviral therapy (cART) and comorbidities. The ability of cART to undo the HIV induced metabolic dysregulation is unclear and under-investigated. Using targeted metabolomics and multiplex immune biomarker analysis, we characterized plasma samples obtained from 18 untreated HIV-1-infected adult patients and compared these to a non-HIV infected (n = 23) control population. The biogenic amine perturbations during an untreated HIV infection implicated altered tryptophan- nitrogen- and muscle metabolism. Furthermore, the lipid profiles of untreated patients were also significantly altered compared to controls. In untreated HIV infection, the sphingomyelins and phospholipids correlated negatively to markers of infection IP-10 and sIL-2R whereas a strong association was found between triglycerides and MCP-1. In a second cohort, we characterized plasma samples obtained from 28 HIV-1-infected adult patients before and 12 months after the start of cART, to investigate the immune-metabolic changes associated with cART. The identified altered immune-metabolic pathways of an untreated HIV infection showed minimal change after 12 months of cART. In conclusion, 12 months of cART impacts only mildly on the metabolic dysregulation underlying an untreated HIV infection and provide insights into the comorbidities present in virally suppressed HIV patients.
Cued reactivation during slow-wave sleep induces brain connectivity changes related to memory stabilization
Authors: Berkers Ruud M. W. J. , Ekman Matthias , van Dongen Eelco. V. , Takashima Atsuko , Barth Markus , Paller Ken. A. , Fernández Guillén 
Published: November 2018

AbstractMemory reprocessing following acquisition enhances memory consolidation. Specifically, neural activity during encoding is thought to be ‘replayed’ during subsequent slow-wave sleep. Such memory replay is thought to contribute to the functional reorganization of neural memory traces. In particular, memory replay may facilitate the exchange of information across brain regions by inducing a reconfiguration of connectivity across the brain. Memory reactivation can be induced by external cues through a procedure known as “targeted memory reactivation”. Here, we analysed data from a published study with auditory cues used to reactivate visual object-location memories during slow-wave sleep. We characterized effects of memory reactivation on brain network connectivity using graph-theory. We found that cue presentation during slow-wave sleep increased global network integration of occipital cortex, a visual region that was also active during retrieval of object locations. Although cueing did not have an overall beneficial effect on the retention of cued versus uncued associations, individual differences in overnight memory stabilization were related to enhanced network integration of occipital cortex. Furthermore, occipital cortex displayed enhanced connectivity with mnemonic regions, namely the hippocampus, parahippocampal gyrus, thalamus and medial prefrontal cortex during cue sound presentation. Together, these results suggest a neural mechanism where cue-induced replay during sleep increases integration of task-relevant perceptual regions with mnemonic regions. This cross-regional integration may be instrumental for the consolidation and long-term storage of enduring memories.
Quenched Stochastic Optical Reconstruction Microscopy (qSTORM) with Graphene Oxide
Authors: Li Ruiheng , Georgiades Pantelis , Cox Henry , Phanphak Sorasak , Roberts Ian S. , Waigh Thomas A. , Lu Jian R. 
Published: November 2018

AbstractQuenched Stochastic Optical Reconstruction Microscopy (qSTORM) was demonstrated with graphene oxide sheets, peptides and bacteria; a method of contrast enhancement with super-resolution fluorescence microscopy. Individual sheets of graphene oxide (GO) were imaged with a resolution of 16 nm using the quenching of fluorescence emission by GO via its large Resonant Energy Transfer (RET) efficiency. The method was then extended to image self-assembled peptide aggregates (resolution 19 nm) and live bacterial cells (resolution 55 nm, the capsular structure of E. coli from urinary tract infections) with extremely low backgrounds and high contrasts (between one and two orders of magnitude contrast factor improvements that depended on the thickness of the graphene oxide layer used). Graphene oxide films combined with STORM imaging thus provide an extremely convenient method to image samples with large backgrounds due to non-specifically bound fluorophores (either due to excess labelling or autofluorescent molecules), which is a common occurrence in studies of both biological cells and soft-condensed matter. The GO quenches the fluorescence across a thin layer at distances of less than 15 nm. Graphene oxide films coated with thin layers (≤15 nm) of polystyrene, polymethylmethacrylate and polylysine are shown to be effective in producing high contrast qSTORM images, providing a convenient modulation of sample/substrate interactions. The GO coatings can also provide an increased image resolution and a factor of 2.3 improvement was observed with the peptide fibres using a feature of interest metric,when there was a large non-specifically bound background.
A sixfold rise in concurrent day and night-time heatwaves in India under 2 °C warming
Authors: Mukherjee Sourav , Mishra Vimal 
Published: November 2018

AbstractHeatwaves with severe impacts have increased and projected to become more frequent under warming climate in India. Concurrent day and nighttime heatwaves can exacerbate human discomfort causing high morbidity and mortality; however, their changes in the observed and projected climate remain unrecognized. Here using observations and model simulations from climate of 20thcentury plus (C20C+) detection and attribution (D&A) and coupled model intercomparison project 5 (CMIP5) projects, we show that 1 and 3-day concurrent hot day and hot night (CHDHN) events have significantly increased during the observed climate in India. Our results show that the anthropogenic emissions contribute considerably to the increase of 1 and 3-day CHDHN events in India. The frequency of 3-day CHDHN events is projected to increase 12-fold of the current level by the end of 21stcentury and 4-fold by the mid 21stcentury under the high emission pathway of RCP 8.5. The increase in 3-day CHDHN events can be limited to only 2-fold by the end of 21stcentury under low emission scenario of RCP 2.6. One and 3-day CHDHN events are projected to increase by 4, 6, and 8 folds of the current level in India under the 1.5, 2, and 3 °C warming worlds, respectively. Restricting global mean temperature below 1.5° from the pre-industrial level can substantially reduce the risk of 1 and 3-day CHDHN events and associated implications in India.
Mycorrhizal fungi mediate the direction and strength of plant–soil feedbacks differently between arbuscular mycorrhizal and ectomycorrhizal communities
Authors: Kadowaki Kohmei , Yamamoto Satoshi , Sato Hirotoshi , Tanabe Akifumi S. , Hidaka Amane , Toju Hirokazu 
Published: November 2018

AbstractPlants influence their soil environment, which affects the next generation of seedlings that can be established. While research has shown that such plant–soil feedbacks occur in the presence of mycorrhizal fungi, it remains unclear when and how mycorrhizal fungi mediate the direction and strength of feedbacks in tree communities. Here we show that arbuscular mycorrhizal and ectomycorrhizal fungal guilds mediate plant–soil feedbacks differently to influence large-scale patterns such as tree species coexistence and succession. When seedlings are grown under the same mycorrhizal type forest, arbuscular mycorrhizal plant species exhibit negative or neutral feedbacks and ectomycorrhizal plant species do neutral or positive feedbacks. In contrast, positive and neutral feedbacks dominate when seedlings are grown in associations within the same versus different mycorrhizal types. Thus, ectomycorrhizal communities show more positive feedbacks than arbuscular mycorrhizal communities, potentially explaining why most temperate forests are ectomycorrhizal.
An improved genome assembly for Larimichthys crocea reveals hepcidin gene expansion with diversified regulation and function
Authors: Mu Yinnan , Huo Jieying , Guan Yanyun , Fan Dingding , Xiao Xiaoqiang , Wei Jingguang , Li Qiuhua , Mu Pengfei , Ao Jingqun , Chen Xinhua 
Published: November 2018

AbstractLarimichthys crocea(large yellow croaker) is a type of perciform fish well known for its peculiar physiological properties and economic value. Here, we constructed an improved version of theL. croceagenome assembly, which contained 26,100 protein-coding genes. Twenty-four pseudo-chromosomes ofL. croceawere also reconstructed, comprising 90% of the genome assembly. This improved assembly revealed several expansions in gene families associated with olfactory detection, detoxification, and innate immunity. Specifically, six hepcidin genes (LcHamps) were identified inL. crocea, possibly resulting from lineage-specific gene duplication. All LcHamps possessed similar genomic structures and functional domains, but varied substantially with respect to expression pattern, transcriptional regulation, and biological function. LcHamp1 was associated specifically with iron metabolism, while LcHamp2s were functionally diverse, involving in antibacterial activity, antiviral activity, and regulation of intracellular iron metabolism. This functional diversity among gene copies may have allowedL. croceato adapt to diverse environmental conditions.
Early Motor and Communicative Development in Infants With an Older Sibling With Autism Spectrum Disorder
Authors: Iverson Jana M. 
Published: November 2018

PurposeA recent approach to identifying early markers of risk for autism spectrum disorder (ASD) has been to study infants who have an older sibling with ASD. These infants are at heightened risk (HR) for ASD and for other developmental difficulties, and even those who do not receive an eventual ASD diagnosis manifest a high degree of variability in trajectories of development. The primary goal of this review is to summarize findings from research on early motor and communicative development in these HR infants.MethodThis review focuses on 2 lines of inquiry. The first assesses whether delays and atypicalities in early motor abilities and in the development of early communication provide an index of eventual ASD diagnosis. The second asks whether such delays also influence infants' interactions with objects and people in ways that exert far-reaching, cascading effects on development.ResultsHR infants who do and who do not receive a diagnosis of ASD vary widely in motor and communicative development. In addition, variation in infant motor and communicative development appears to have cascading effects on development, both on the emergence of behavior in other domains and on the broader learning environment.ConclusionsAdvances in communicative and language development are supported by advances in motor skill. When these advances are slowed and/or when new skills are not consolidated and remain challenging for the infant, the enhanced potential for exploration afforded by new abilities and the concomitant increase in opportunities for learning are reduced. Improving our understanding of communicative delays of the sort observed in ASD and developing effective intervention methods requires going beyond the individual to consider the constant, complex interplay between developing communicators and their environments.Presentation Videohttps://doi.org/10.23641/asha.7299308
Modeling ionized gas in low-metallicity environments: the Local Group dwarf galaxy IC 10
Authors: Polles F. L. , Madden S. C. , Lebouteiller V. , Cormier D. , Abel N. , Galliano F. , Hony S. , Karczewski O. Ł. , Lee M.-Y. , Chevance M. , Galametz M. , Lianou S. 
Published: November 2018

Context. Star formation activity is an important driver of galaxy evolution and is influenced by the physical properties of the interstellar medium. Dwarf galaxies allow us to understand how the propagation of radiation and the physical conditions of the different ISM phases are affected by the low-metallicity environment.
Aims. Our objective is to investigate the physical properties of the ionized gas of the low-metallicity dwarf galaxy, IC 10, at various spatial scales: from individual H II regions to the entire galaxy scale and examine whether diagnostics for integrated measurements introduce bias in the results.
Methods. We modeled the ionized gas combining the mid- and far-infrared fine-structure cooling lines observed with Spitzer/IRS and Herschel/PACS, with the photoionization code CLOUDY. The free parameters of the models are the age of the stellar cluster, the density, and the ionization parameter of the ionized gas as well as the depth of the cloud. The latter is used to investigate the leakage of the ionizing photons from the analyzed regions of IC 10. We investigated H II regions in the main star-forming body, on scales of ~25 pc, three in the main star-forming region in the center of the galaxy and two on the first arc. We then considered larger sizes on the scale of ~200 pc.
Results. Most clumps have almost-identical properties, density ~102–102.6 cm−3, ionization parameter between 10−2.2 and 10−1.6, and age of the stellar cluster ~5.5 Myr. All of them are matter-bounded regions, allowing ionizing photons to leak. The relatively uniform physical properties of the clumps suggest a common origin for their star formation activity, which could be related to the feedback from stellar winds or supernovae of a previous generation of stars. The properties derived for ~200 pc size “zones” have similar properties as the H II regions they encompass, but with the larger regions tending to be more radiation bounded. Finally, we investigated the fraction of [CII] 157.7 μm, [SiII] 34.8 μm and [FeII] 25.9 μm emission arising from the ionized gas phase and we find that most of the emission originates from the neutral gas, not from the ionized gas.
Selection functions of large spectroscopic surveys
Authors: Mints Alexey , Hekker Saskia 
Published: November 2018

Context. Large spectroscopic surveys open the way to explore our Galaxy. In order to use the data from these surveys to understand the Galactic stellar population, we need to be sure that stars contained in a survey are a representative sub-set of the underlying population. Without the selection function taken into account, the results might reflect the properties of the selection function rather than those of the underlying stellar population.
Aims. In this work, we introduce a method to estimate the selection function for a given spectroscopic survey. We aim to apply this method to a large sample of public spectroscopic surveys.
Methods. We have applied a median division binning algorithm to bin observed stars in the colour–magnitude space. This approach produces lower uncertainties and lower biases of the selection function estimate as compared to traditionally used 2D-histograms. We ran a set of simulations to verify the method and calibrate the one free parameter it contains. These simulations allow us to test the precision and accuracy of the method.
Results. We produce and publish estimated values and uncertainties of selection functions for a large sample of public spectroscopic surveys. We publicly release the code used to produce the selection function estimates.
Conclusions. The effect of the selection function on distance modulus and metallicity distributions of stars in surveys is important for surveys with small and largely inhomogeneous spatial coverage. For surveys with contiguous spatial coverage the effect of the selection function is almost negligible.
Properties of the inner penumbral boundary and temporal evolution of a decaying sunspot
Authors: Benko M. , González Manrique S. J. , Balthasar H. , Gömöry P. , Kuckein C. , Jurčák J. 
Published: November 2018

Context. It has been empirically determined that the umbra-penumbra boundaries of stable sunspots are characterized by a constant value of the vertical magnetic field.
Aims. We analyzed the evolution of the photospheric magnetic field properties of a decaying sunspot belonging to NOAA 11277 between August 28–September 3, 2011. The observations were acquired with the spectropolarimeter on-board of the Hinode satellite. We aim to prove the validity of the constant vertical magnetic-field boundary between the umbra and penumbra in decaying sunspots.
Methods. A spectral-line inversion technique was used to infer the magnetic field vector from the full-Stokes profiles. In total, eight maps were inverted and the variation of the magnetic properties in time were quantified using linear or quadratic fits.
Results. We find a linear decay of the umbral vertical magnetic field, magnetic flux, and area. The penumbra showed a linear increase of the vertical magnetic field and a sharp decay of the magnetic flux. In addition, the penumbral area quadratically decayed. The vertical component of the magnetic field is weaker on the umbra-penumbra boundary of the studied decaying sunspot compared to stable sunspots. Its value seem to be steadily decreasing during the decay phase. Moreover, at any time of the sunspot decay shown, the inner penumbra boundary does not match with a constant value of the vertical magnetic field, contrary to what is seen in stable sunspots.
Conclusions. During the decaying phase of the studied sunspot, the umbra does not have a sufficiently strong vertical component of the magnetic field and is thus unstable and prone to be disintegrated by convection or magnetic diffusion. No constant value of the vertical magnetic field is found for the inner penumbral boundary.
Whole-Body CT in Multiple Trauma Patients: Clinically Adapted Usage of Differently Weighted CT Protocols
Authors: Reske Stefan , Braunschweig Rainer , Reske Andreas , Loose Reinhard , Wucherer Michael 
Published: November 2018

Purpose Whole-body CT (wbCT) has been established as an internationally accepted diagnostic modality in multiple trauma. Until 2011, a uniform CT scanning protocol was used for all multiple trauma patients (pat.) at our hospital (OLD protocol = OP). In 2011, 2 new differently weighted protocols were introduced: TIME protocol (TP) for hemodynamically unstable pat. and DOSE protocol (DP) for pat. with stable vital parameters. The aim of this study was to compare the original “One-fits-all-concept” with the new, clinically oriented approach to wbCT.
Materials and Methods This study retrospectively evaluated 3 distinct wbCT protocols, looking at automatic exposure control variation (AEC; OP/TP) and arm positioning close to the body/overhead (TP/DP). The analysis included waist circumference (WC, cm), injury severity score (ISS), examination time (ET, min), image noise (IN), and effective dose (E, mSv). Normality of distribution was assessed with the Kolmogorov-Smirnov test. Data are given as median and range. Test of significance with Kruskal-Wallis test or Mann-Whitney-U-test. Level of significance: 0.05.
Results 308 pat. were included in the study (77 % m; age: 46 a, 18 – 90 a; WC: 93 cm, 66 – 145 cm). ISS was 14 (OP; n = 104; 0 – 75), 18 (TP; n = 102; 0 – 75) and 9 (DP; n = 102; 0 – 50). ET was 3.9 min (OP; 3.3 – 5.6 min), 4.1 min (TP; 2.8 – 7.2 min) and 7.7 min (DP; 6 – 10 min). IN showed no significant differences when comparing OP/TP but was significantly reduced in DP. For a wbCT (vertex to ischium), E could be reduced from 49.7 mSv to 35.4 mSv by optimizing AEC (OP/TP). Through the overhead repositioning of the arms in DP, a further reduction to 28.2 mSv was achieved.
Conclusion AEC and arm repositioning have a crucial influence on image quality and dose. The presented clinical approach is superior to the original concept.
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Impact Loading During Distracted Running Before and After Auditory Gait Retraining
Authors: Ching Eric , An Winko , Au Ivan , Zhang Janet , Chan Zoe , Shum Gary , Cheung Roy 
Published: November 2018

AbstractVisual feedback gait retraining has been reported to successfully reduce impact loading in runners, even when the runners were distracted. However, auditory feedback is more feasible in real life application. Hence, this study compared the peak positive acceleration (PPA), vertical average (VALR) and instantaneous (VILR) loading rate during distracted running before and after a course of auditory feedback gait retraining in 16 runners. The runners were asked to land with softer footfalls with and without auditory feedback. Low or high sound pitch was generated according to the impact of particular footfall, when compared with the preset target. Runners then received a course of auditory gait retraining, and after the gait retraining, runners completed a reassessment. Runners before gait retraining exhibited lower PPA, VALR and VILR with augmented auditory feedback (p<0.049). We found a reduction in PPA, VALR and VILR after gait retraining, regardless of the presence of feedback (p<0.018). However, runners after gait retraining did not demonstrate further reduction in PPA and VALR with auditory feedback (p>0.104). A small effect of auditory feedback on VILR in runners after gait retraining was observed (p=0.032). Real time auditory feedback gait retraining is effective in impact loading reduction, even when the runners were distracted.