bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-resolution imaging and near-infrared spectroscopy of penumbral decay
Authors: Verma M. , Denker C. , Balthasar H. , Kuckein C. , Rezaei R. , Sobotka M. , Deng N. , Wang H. , Tritschler A. , Collados M. , Diercke A. , González Manrique S. J. 
Published: January 2018

Aims. Combining high-resolution spectropolarimetric and imaging data is key to understanding the decay process of sunspots as it allows us to scrutinize the velocity and magnetic fields of sunspots and their surroundings.
Methods. Active region NOAA 12597 was observed on 2016 September 24 with the 1.5-meter GREGOR solar telescope using high-spatial-resolution imaging as well as imaging spectroscopy and near-infrared (NIR) spectropolarimetry. Horizontal proper motions were estimated with local correlation tracking, whereas line-of-sight (LOS) velocities were computed with spectral line fitting methods. The magnetic field properties were inferred with the “Stokes Inversions based on Response functions” (SIR) code for the Si I and Ca I NIR lines.
Results. At the time of the GREGOR observations, the leading sunspot had two light bridges indicating the onset of its decay. One of the light bridges disappeared, and an elongated, dark umbral core at its edge appeared in a decaying penumbral sector facing the newly emerging flux. The flow and magnetic field properties of this penumbral sector exhibited weak Evershed flow, moat flow, and horizontal magnetic field. The penumbral gap adjacent to the elongated umbral core and the penumbra in that penumbral sector displayed LOS velocities similar to granulation. The separating polarities of a new flux system interacted with the leading and central part of the already established active region. As a consequence, the leading spot rotated 55° clockwise over 12 h.
Conclusions. In the high-resolution observations of a decaying sunspot, the penumbral filaments facing the flux emergence site contained a darkened area resembling an umbral core filled with umbral dots. This umbral core had velocity and magnetic field properties similar to the sunspot umbra. This implies that the horizontal magnetic fields in the decaying penumbra became vertical as observed in flare-induced rapid penumbral decay, but on a very different time-scale.
Global convergence of a class of networks on time scales
Authors: Bin Honghua , Wang Boyu , Huang Zhenkun 
Published: January 2018

Abstract
In this paper, we propose a class of simplified background neural networks model with two subnetworks on time scales. Some basic dynamic properties including positive invariance, boundedness, global attractivity and complete convergence of networks are analyzed. The main contributions in this paper are listed as follows: (1) the global attractive set of the model is verified and conditions for global attractivity are derived. (2) Complete convergence for the new networks are proved by constructing a novel energy function on time scales. Finally, three simulation examples are presented to illustrate the feasibility and effectiveness of the obtained results.
Safeguarding China's water resources
Authors: Qiu Jane 
Published: January 2018

Abstract
Water is scarce in China. The country ekes by with only one-quarter of the global average for water per person. The scarcity is exacerbated by rampant pollution—with devastating consequences on ecosystems, food supply and public health. In the face of growing population, water pollution threatens the very survival of the Chinese nation.
In his speech at the 19th National Congress of the Communist Party of China last October, President Xi Jinping repeatedly emphasized the importance to redress the balance between economic development and environmental protection. One of his most frequently cited phrases is ‘clean waters and lush mountains are gold and silver’. And he has matched his rhetoric with action. In April 2015, the State Council, China's cabinet, issued the Water Pollution and Control Action Plan (known as Shuishitiao or Water Ten Plan)—widely hailed as the toughest and most comprehensive water policy to date. Last October, it announced a five-year plan to tackle water pollution, with a budget of 700 billion yuan (US$106 billion). The country's top legislature has also revised the Water Prevention and Control Law, which will go into effect in early 2018.
In a forum chaired by National Science Review’s Executive Editor-in-Chief Mu-ming Poo, a panel of experts of diverse backgrounds and perspectives discussed the current status of China's water resources, their views on the comprehensive policy package, how national initiatives have been going, what the challenges are and why information transparency and public participation are absolutely essential in environmental protection.

Weijiang Liu
Hydrologist at the Chinese Academy for Environmental Planning, Ministry of Environmental Protection, Beijing, China

Ji Shen
Environment scientist at Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China

Chunmiao Zheng
Hydrologist at Southern University of Science and Technology, Shenzhen, China

Jun Ma
Founder and director of the non-governmental organization Institute of Public and Environmental Affairs, Beijing, China

Tao Tao
Environment scientist at the College of Environmental Science and Engineering and the Key Laboratory of Yangtze River Water Environment at Tongji University, Shanghai, China

Mu-ming Poo (Chair)
Director, Institute of Neuroscience, Chinese Academy of Sciences, Shanghai, China
Case Report: Facial Nerve Bifurcation Noted During Resection of Vestibular Schwannoma
Authors: Sokolowski Jennifer D , Ruhl Douglas S , Kesser Bradley W , Asthagiri Ashok R 
Published: January 2018

Abstract

BACKGROUND AND IMPORTANCE
Resection of cerebellopontine angle tumors is challenging because the proximity of the facial nerve puts it at risk of inadvertent injury and subsequent dysfunction. It is critical to consider variations in anatomy and be aware of the potential deviations in the course of the nerve in order to avoid damage.

CLINICAL PRESENTATION
We present a case of a facial nerve bifurcation identified during resection of a vestibular schwannoma.

CONCLUSION
This is the only reported case of proximal facial nerve bifurcation. We review what is known about variations in proximal facial nerve anatomy, the rates of facial nerve injury after schwannoma resection, and the importance of neuromonitoring in identifying the nerve and predicting function postoperatively. Ultimately, understanding possible anatomic variations in the nerve is critical to minimize iatrogenic injury during surgery.
In-flight calibration of Hitomi Soft X-ray Spectrometer. (3) Effective area
Authors: Tsujimoto Masahiro , Okajima Takashi , Eckart Megan E , Hayashi Takayuki , Hoshino Akio , Iizuka Ryo , Kelley Richard L , Kilbourne Caroline A , Leutenegger Maurice A , Maeda Yoshitomo , Mori Hideyuki , Porter Frederick S , Sato Kosuke , Sato Toshiki , Serlemitsos Peter J , Szymkowiak Andrew , Yaqoob Tahir 
Published: January 2018

Abstract
We present the result of the in-flight calibration of the effective area of the Soft X-ray Spectrometer (SXS) on board the Hitomi X-ray satellite using an observation of the Crab nebula. We corrected for artifacts when observing high count rate sources with the X-ray microcalorimeter. We then constructed a spectrum in the 0.5–20 keV band, which we modeled with a single power-law continuum attenuated by interstellar extinction. We evaluated the systematic uncertainty of the spectral parameters by various calibration items. In the 2–12 keV band, the SXS result is consistent with the literature values in flux (2.20 ± 0.08 × 10−8 erg s−1 cm−2 with a 1 σ statistical uncertainty) but is softer in the power-law index (2.19 ± 0.11). The discrepancy is attributable to the systematic uncertainty of about +6%/−7% and +2%/−5% respectively for the flux and the power-law index. The softer spectrum is affected primarily by the systematic uncertainty of the Dewar gate valve transmission and the event screening.
Balance sheets after the EMU: an assessment of the redenomination risk
Authors: Durand Cédric , Villemot Sébastien 
Published: January 2018

Abstract
The probability of a partial or complete break-up of the euro has risen over the last years. Such an event could create a balance sheet problem for economic agents, if the redenomination process introduced significant currency mismatches between the asset and liability sides. We propose a new assessment of this redenomination risk, by country and by main institutional sector, for two scenarios: a single country exit and a complete break-up. Our main conclusion is that, even though the problem has to be taken seriously, its order of magnitude should not be exaggerated. Only a few sectors are at significant risk: public debts of Greece and Portugal, financial sectors of Greece, Ireland and Luxembourg. In particular, the balance sheet exposure of the non-financial private sector to the redenomination risk appears to be limited.
Fast automated reconstruction of genome-scale metabolic models for microbial species and communities
Authors: Machado Daniel , Andrejev Sergej , Tramontano Melanie , Patil Kiran Raosaheb 
Published: January 2018

AbstractGenome-scale metabolic models are instrumental in uncovering operating principles of cellular metabolism and model-guided re-engineering. Recent applications of metabolic models have also demonstrated their usefulness in unraveling cross-feeding within microbial communities. Yet, the application of genome-scale models, especially to microbial communities, is lagging far behind the availability of sequenced genomes. This is largely due to the time-consuming steps of manual cura-tion required to obtain good quality models and thus physiologically meaningful simulation results. Here, we present an automated tool – CarveMe – for reconstruction of species and community level metabolic models. We introduce the concept of a universal model, which is manually curated and simulation-ready. Starting with this universal model and annotated genome sequences, CarveMe uses a top-down approach to build single-species and community models in a fast and scalable manner. We build reconstructions for two model organisms, Escherichia coli and Bacillus subtillis, as well as a collection of human gut bacteria, and show that CarveMe models perform similarly to manually curated models in reproducing experimental phenotypes. Finally, we demonstrate the scalability of CarveMe through reconstructing 5587 bacterial models. Overall, CarveMe provides an open-source and user-friendly tool towards broadening the use of metabolic modeling in studying microbial species and communities.
Wnt signalling drives context-dependent differentiation or proliferation in neuroblastoma
Authors: Szemes Marianna , Greenhough Alexander , Melegh Zsombor , Malik Sally , Yuksel Aysen , Catchpoole Daniel , Gallacher Kelli , Kollareddy Madhu , Park Ji Hyun , Malik Karim 
Published: January 2018

AbstractNeuroblastoma is one of the commonest and deadliest solid tumours of childhood, and is thought to result from disrupted differentiation of the developing sympathoadrenergic lineage of the neural crest. Neuroblastoma exhibits intra-and intertumoural heterogeneity, with high risk tumours characterised by poor differentiation, which can be attributable to MYCN-mediated repression of genes involved in neuronal differentiation. MYCN is known to co-operate with oncogenic signalling pathways such as Alk, Akt and MEK/ERK signalling, and, together with c-MYC has been shown to be activated by Wnt signalling in various tissues. However, our previous work demonstrated that Wnt3a/Rspo2 treatment of some neuroblastoma cell lines can, paradoxically, decrease c-MYC and MYCN proteins. This prompted us to define the neuroblastoma-specific Wnt3a/Rspo2-driven transcriptome using RNA sequencing, and characterise the accompanying changes in cell biology.Here we report the identification of ninety Wnt target genes, and show that Wnt signalling is upstream of numerous transcription factors and signalling pathways in neuroblastoma. Using live-cell imaging, we show that Wnt signalling can drive differentiation of SK-N-BE(2)-C and SH-SY5Y cell-lines, but, conversely, proliferation of SK-N-AS cells. We show that cell-lines that differentiate show induction of pro-differentiation BMP4 and EPAS1 proteins, which is not apparent in the SK-N-AS cells. In contrast, SK-N-AS cells show increased CCND1, phosphorylated RB and E2F1 in response to Wnt3a/Rspo2, consistent with their proliferative response, and these proteins are not increased in differentiating lines. By meta-analysis of the expression of our 90 genes in primary tumour gene expression databases, we demonstrate discrete expression patterns of our Wnt genes in patient cohorts with different prognosis. Furthermore our analysis reveals interconnectivity within subsets of our Wnt genes, with one subset comprised of novel putative drivers of neuronal differentiation repressed by MYCN. Assessment of β-catenin immunohistochemistry shows high levels of β-catenin in tumours with better differentiation, further supporting a role for canonical Wnt signalling in neuroblastoma differentiation.
Mathematical modelling elucidates core mechanisms underpinning GnRH pulse generation
Authors: Voliotis Margaritis , Li Xiao Feng , De Burgh Ross , Lass Geffen , Lightman Stafford L , O’Byrne Kevin T. , Tsaneva-Atanasova Krasimira 
Published: January 2018

SummaryFertility critically depends on the gonadotropin-releasing hormone (GnRH) pulse generator, a neural construct comprised of hypothalamic neurons co-expressing kisspeptin, neurokoinin-B and dynorphin that drives the pulsatile release of GnRH. How this neural network generates and controls the appropriate ultradian frequency essential for gametogenesis and ovulation is unknown. Here, we present a mathematical model of the GnRH pulse generator with theoretical evidence and in vivo experimental data showing that robust pulsatile release of luteinizing hormone, a proxy for GnRH, emerges abruptly as we increase the basal activity of the neuronal network using continuous low frequency optogenetic stimulation of the neural construct. Further increases in basal activity markedly increase pulse frequency. Model predictions that such behaviors are concomitant of non-linear positive and negative feedback interactions mediated through neurokinin-B and dynorphin signaling respectively are confirmed neuropharmacologically. Our mathematical model sheds light on the long-elusive GnRH pulse generator offering new horizons for fertility regulation.
Assembly of Long Error-Prone Reads Using Repeat Graphs
Authors: Kolmogorov Mikhail , Yuan Jeffrey , Lin Yu , Pevzner Pavel. A. 
Published: January 2018

ABSTRACTThe problem of genome assembly is ultimately linked to the problem of the characterization of all repeat families in a genome as a repeat graph. The key reason the de Bruijn graph emerged as a popular short read assembly approach is because it offered an elegant representation of all repeats in a genome that reveals their mosaic structure. However, most algorithms for assembling long error-prone reads use an alternative overlap-layout-consensus (OLC) approach that does not provide a repeat characterization. We present the Flye algorithm for constructing the A-Bruijn (assembly) graph from long error-prone reads, that, in contrast to the k-mer-based de Bruijn graph, assembles genomes using an alignment-based A-Bruijn graph. In difference from existing assemblers, Flye does not attempt to construct accurate contigs (at least at the initial assembly stage) but instead simply generates arbitrary paths in the (unknown) assembly graph and further constructs an assembly graph from these paths. Counter-intuitively, this fast but seemingly reckless approach results in the same graph as the assembly graph constructed from accurate contigs. Flye constructs (overlapping) contigs with possible assembly errors at the initial stage, combines them into an accurate assembly graph, resolves repeats in the assembly graph using small variations between various repeat instances that were left unresolved during the initial assembly stage, constructs a new, less tangled assembly graph based on resolved repeats, and finally outputs accurate contigs as paths in this graph. We benchmark Flye against several state-of-the-art Single Molecule Sequencing assemblers and demonstrate that it generates better or comparable assemblies for all analyzed datasets.
Genome-wide gene-environment analyses of depression and reported lifetime traumatic experiences in UK Biobank
Authors: Coleman Jonathan R.I. , Purves Kirstin L. , Davis Katrina A.S. , Rayner Christopher , Choi Shing Wan , Hübel Christopher , Gaspar Héléna A. , Kan Carol , Van der Auwera Sandra , Adams Mark James , Lyall Donald M. , Peyrot Wouter J. ,   Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium, Dunn Erin C. , Vassos Evangelos , Danese Andrea , Grabe Hans J. , Lewis Cathryn M. , O’Reilly Paul F. , McIntosh Andrew M. , Smith Daniel J. , Wray Naomi R. , Hotopf Matthew , Eley Thalia C. , Breen Gerome 
Published: January 2018

AbstractDepression is more frequently observed among individuals exposed to traumatic events. The relationship between trauma exposure and depression, including the role of genetic variation, is complex and poorly understood. The UK Biobank concurrently assessed depression and reported trauma exposure in 126,522 genotyped individuals of European ancestry. We compared the shared aetiology of depression and a range of phenotypes, contrasting individuals reporting trauma exposure with those who did not (final sample size range: 24,094-92,957). Depression was heritable in participants reporting trauma exposure and in unexposed individuals, and the genetic correlation between the groups was substantial and not significantly different from 1. Genetic correlations between depression and psychiatric traits were strong regardless of reported trauma exposure, whereas genetic correlations between depression and body mass index (and related phenotypes) were observed only in trauma exposed individuals. The narrower range of genetic correlations in trauma unexposed depression and the lack of correlation with BMI echoes earlier ideas of endogenous depression.
De novo origins of multicellularity in response to predation
Authors: Herron Matthew D. , Borin Joshua M. , Boswell Jacob C. , Walker Jillian , Chen I-Chen Kimberly , Knox Charles A. , Boyd Margrethe , Rosenzweig Frank , Ratcliff William C. 
Published: January 2018

SummaryThe transition from unicellular to multicellular life was one of a few major events in the history of life that created new opportunities for more complex biological systems to evolve. Predation is hypothesized as one selective pressure that may have driven the evolution of multicellularity. Here we show that de novo origins of simple multicellularity can evolve in response to predation. We subjected outcrossed populations of the unicellular green alga Chlamydomonas reinhardtii to selection by the filter-feeding predator Paramecium tetraurelia. Two of five experimental populations evolved multicellular structures not observed in unselected control populations within ~750 asexual generations. Considerable variation exists in the evolved multicellular life cycles, with both cell number and propagule size varying among isolates. Survival assays show that evolved multicellular traits provide effective protection against predation. These results support the hypothesis that selection imposed by predators may have played a role in some origins of multicellularity.
MITOMIX, an Algorithm to Reconstruct Population Admixture Histories Indicates Ancient European Ancestry of Modern Hungarians
Authors: Maróti Zoltán , Török Tibor , Neparáczki Endre , Raskó István , Nagy István , Maróti Miklós , Varga Tamás , Bihari Péter , Boldogkői Zsolt , Tombácz Dóra , Kalmár Tibor 
Published: January 2018

AbstractBy making use of the increasing number of available mitogenomes we propose a novel population genetic distance metric, named Shared Haplogroup Distance (SHD). Unlike FST, SHD is a true mathematical distance that complies with all metric axioms, which enables our new algorithm (MITOMIX) to detect population-level admixture based on SHD minimum optimization. In order to demonstrate the effectiveness of our methodology we analyzed the relation of 62 modern and 25 ancient Eurasian human populations, and compared our results with the most widely used FSTcalculation. We also sequenced and performed an in-depth analysis of 272 modern Hungarian mtDNA genomes to shed light on the genetic composition of modern Hungarians. MITOMIX analysis showed that in general admixture occurred between neighboring populations, but in some cases it also indicated admixture with migrating populations. SHD and MITOMIX analysis comply with known genetic data and shows that in case of closely related and/or admixing populations, SHD gives more realistic results and provides better resolution than FST. Our results suggest that the majority of modern Hungarian maternal lineages have Late Neolith/Bronze Age European origins (partially shared also with modern Danish, Belgian/Dutch and Basque populations), and a smaller fraction originates from surrounding (Serbian, Croatian, Slovakian, Romanian) populations. However only a minor genetic contribution (<3%) was identified from the IXthHungarian Conquerors whom are deemed to have brought Hungarians to the Carpathian Basin. Our analysis shows that SHD and MITOMIX can augment previous methods by providing novel insights into past population processes.
Small interfering RNAs based on huntingtin trinucleotide repeats are highly toxic to cancer cells
Authors: Murmann Andrea E. , Gao Quan Q. , Putzbach William , Patel Monal , Bartom Elizabeth T. , Law Calvin , Bridgeman Bryan , Chen Siquan , McMahon Kaylin M. , Thaxton C. Shad , Peter Marcus E. 
Published: January 2018

AbstractTrinucleotide repeat (TNR) expansions in the genome cause a number of degenerative diseases. A prominent TNR expansion involves the triplet CAG in the huntingtin (HTT) gene responsible for Huntington’s disease (HD). Pathology is caused by protein and RNA generated from the TNR regions including small siRNA-sized repeat fragments. An inverse correlation between the length of the repeats in HTT and cancer incidence has been reported for HD patients. We now show that siRNAs based on the CAG TNR are toxic to cancer cells by targeting genes that contain long reverse complimentary TNRs in their open reading frames. Of the 60 siRNAs based on the different TNRs, the 6 members in the CAG/CUG family of related TNRs are the most toxic to both human and mouse cancer cells. siCAG/CUG TNR-based siRNAs induce cell deathin vitroin all tested cancer cell lines and slow down tumor growth in a preclinical mouse model of ovarian cancer with no signs of toxicity to the mice. We propose to explore TNR-based siRNAs as a novel form of anti-cancer reagents.