bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hot super-Earths stripped by their host stars
Authors: Lundkvist M. S. , Kjeldsen H. , Albrecht S. , Davies G. R. , Basu S. , Huber D. , Justesen A. B. , Karoff C. , Silva Aguirre V. , Van Eylen V. , Vang C. , Arentoft T. , Barclay T. , Bedding T. R. , Campante T. L. , Chaplin W. J. , Christensen-Dalsgaard J. , Elsworth Y. P. , Gilliland R. L. , Handberg R. , Hekker S. , Kawaler S. D. , Lund M. N. , Metcalfe T. S. , Miglio A. , Rowe J. F. , Stello D. , Tingley B. , White T. R. 
Published: April 2016

AbstractSimulations predict that hot super-Earth sized exoplanets can have their envelopes stripped by photoevaporation, which would present itself as a lack of these exoplanets. However, this absence in the exoplanet population has escaped a firm detection. Here we demonstrate, using asteroseismology on a sample of exoplanets and exoplanet candidates observed during the Kepler mission that, while there is an abundance of super-Earth sized exoplanets with low incident fluxes, none are found with high incident fluxes. We do not find any exoplanets with radii between 2.2 and 3.8 Earth radii with incident flux above 650 times the incident flux on Earth. This gap in the population of exoplanets is explained by evaporation of volatile elements and thus supports the predictions. The confirmation of a hot-super-Earth desert caused by evaporation will add an important constraint on simulations of planetary systems, since they must be able to reproduce the dearth of close-in super-Earths.
High-dimensional genomic data bias correction and data integration using MANCIE
Authors: Zang Chongzhi , Wang Tao , Deng Ke , Li Bo , Hu Sheng’en , Qin Qian , Xiao Tengfei , Zhang Shihua , Meyer Clifford A. , He Housheng Hansen , Brown Myles , Liu Jun S. , Xie Yang , Liu X. Shirley 
Published: April 2016

AbstractHigh-dimensional genomic data analysis is challenging due to noises and biases in high-throughput experiments. We present a computational method matrix analysis and normalization by concordant information enhancement (MANCIE) for bias correction and data integration of distinct genomic profiles on the same samples. MANCIE uses a Bayesian-supported principal component analysis-based approach to adjust the data so as to achieve better consistency between sample-wise distances in the different profiles. MANCIE can improve tissue-specific clustering in ENCODE data, prognostic prediction in Molecular Taxonomy of Breast Cancer International Consortium and The Cancer Genome Atlas data, copy number and expression agreement in Cancer Cell Line Encyclopedia data, and has broad applications in cross-platform, high-dimensional data integration.
Reference genotype and exome data from an Australian Aboriginal population for health-based research
Authors: Tang Dave , Anderson Denise , Francis Richard W. , Syn Genevieve , Jamieson Sarra E. , Lassmann Timo , Blackwell Jenefer M. 
Published: April 2016

AbstractGenetic analyses, including genome-wide association studies and whole exome sequencing (WES), provide powerful tools for the analysis of complex and rare genetic diseases. To date there are no reference data for Aboriginal Australians to underpin the translation of health-based genomic research. Here we provide a catalogue of variants called after sequencing the exomes of 72 Aboriginal individuals to a depth of 20X coverage in ∼80% of the sequenced nucleotides. We determined 320,976 single nucleotide variants (SNVs) and 47,313 insertions/deletions using the Genome Analysis Toolkit. We had previously genotyped a subset of the Aboriginal individuals (70/72) using the Illumina Omni2.5 BeadChip platform and found ~99% concordance at overlapping sites, which suggests high quality genotyping. Finally, we compared our SNVs to six publicly available variant databases, such as dbSNP and the Exome Sequencing Project, and 70,115 of our SNVs did not overlap any of the single nucleotide polymorphic sites in all the databases. Our data set provides a useful reference point for genomic studies on Aboriginal Australians.
PTH-dependence of the effectiveness of cinacalcet in hemodialysis patients with secondary hyperparathyroidism
Authors: Akizawa Tadao , Kurita Noriaki , Mizobuchi Masahide , Fukagawa Masafumi , Onishi Yoshihiro , Yamaguchi Takuhiro , Ellis Alan R. , Fukuma Shingo , Alan Brookhart M. , Hasegawa Takeshi , Kurokawa Kiyoshi , Fukuhara Shunichi 
Published: April 2016

AbstractCinacalcet lowers parathyroid hormone levels. Whether it can prolong survival of people with chronic kidney disease (CKD) complicated by secondary hyperparathyroidism (SHPT) remains controversial, in part because a recent randomized trial excluded patients with iPTH <300 pg/ml. We examined cinacalcet’s effects at different iPTH levels. This was a prospective case-cohort and cohort study involving 8229 patients with CKD stage 5D requiring maintenance hemodialysis who had SHPT. We studied relationships between cinacalcet initiation and important clinical outcomes. To avoid confounding by treatment selection, we used marginal structural models, adjusting for time-dependent confounders. Over a mean of 33 months, cinacalcet was more effective in patients with more severe SHPT. In patients with iPTH ≥500 pg/ml, the reduction in the risk of death from any cause was about 50% (Incidence Rate Ratio [IRR] = 0.49; 95% Confidence Interval [95% CI]: 0.29–0.82). For a composite of cardiovascular hospitalization and mortality, the association was not statistically significant, but the IRR was 0.67 (95% CI: 0.43–1.06). These findings indicate that decisions about using cinacalcet should take into account the severity of SHPT.
A stochastic model for immunotherapy of cancer
Authors: Baar Martina , Coquille Loren , Mayer Hannah , Hölzel Michael , Rogava Meri , Tüting Thomas , Bovier Anton 
Published: April 2016

AbstractWe propose an extension of a standard stochastic individual-based model in population dynamics which broadens the range of biological applications. Our primary motivation is modelling of immunotherapy of malignant tumours. In this context the different actors, T-cells, cytokines or cancer cells, are modelled as single particles (individuals) in the stochastic system. The main expansions of the model are distinguishing cancer cells by phenotype and genotype, including environment-dependent phenotypic plasticity that does not affect the genotype, taking into account the effects of therapy and introducing a competition term which lowers the reproduction rate of an individual in addition to the usual term that increases its death rate. We illustrate the new setup by using it to model various phenomena arising in immunotherapy. Our aim is twofold: on the one hand, we show that the interplay of genetic mutations and phenotypic switches on different timescales as well as the occurrence of metastability phenomena raise new mathematical challenges. On the other hand, we argue why understanding purely stochastic events (which cannot be obtained with deterministic models) may help to understand the resistance of tumours to therapeutic approaches and may have non-trivial consequences on tumour treatment protocols. This is supported through numerical simulations.
Large-deformation and high-strength amorphous porous carbon nanospheres
Authors: Yang Weizhu , Mao Shimin , Yang Jia , Shang Tao , Song Hongguang , Mabon James , Swiech Wacek , Vance John R. , Yue Zhufeng , Dillon Shen J. , Xu Hangxun , Xu Baoxing 
Published: April 2016

AbstractCarbon is one of the most important materials extensively used in industry and our daily life. Crystalline carbon materials such as carbon nanotubes and graphene possess ultrahigh strength and toughness. In contrast, amorphous carbon is known to be very brittle and can sustain little compressive deformation. Inspired by biological shells and honeycomb-like cellular structures in nature, we introduce a class of hybrid structural designs and demonstrate that amorphous porous carbon nanospheres with a thin outer shell can simultaneously achieve high strength and sustain large deformation. The amorphous carbon nanospheres were synthesized via a low-cost, scalable and structure-controllable ultrasonic spray pyrolysis approach using energetic carbon precursors. In situ compression experiments on individual nanospheres show that the amorphous carbon nanospheres with an optimized structure can sustain beyond 50% compressive strain. Both experiments and finite element analyses reveal that the buckling deformation of the outer spherical shell dominates the improvement of strength while the collapse of inner nanoscale pores driven by twisting, rotation, buckling and bending of pore walls contributes to the large deformation.
Hydrolases of the ILR1-like family of Arabidopsis thaliana modulate auxin response by regulating auxin homeostasis in the endoplasmic reticulum
Authors: Sanchez Carranza Ana Paula , Singh Aparajita , Steinberger Karoline , Panigrahi Kishore , Palme Klaus , Dovzhenko Alexander , Dal Bosco Cristina 
Published: April 2016

AbstractAmide-linked conjugates of indole-3-acetic acid (IAA) have been identified in most plant species. They function in storage, inactivation or inhibition of the growth regulator auxin. We investigated how the major known endogenous amide-linked IAA conjugates with auxin-like activity act in auxin signaling and what role ILR1-like proteins play in this process in Arabidopsis. We used a genetically encoded auxin sensor to show that IAA-Leu, IAA-Ala and IAA-Phe act through the TIR1-dependent signaling pathway. Furthermore, by using the sensor as a free IAA reporter, we followed conjugate hydrolysis mediated by ILR1, ILL2 and IAR3 in plant cells and correlated the activity of the hydrolases with a modulation of auxin response. The conjugate preferences that we observed are in agreement with available in vitro data for ILR1. Moreover, we identified IAA-Leu as an additional substrate for IAR3 and showed that ILL2 has a more moderate kinetic performance than observed in vitro. Finally, we proved that IAR3, ILL2 and ILR1 reside in the endoplasmic reticulum, indicating that in this compartment the hydrolases regulate the rates of amido-IAA hydrolysis which results in activation of auxin signaling.
Generation of Hprt-disrupted rat through mouse←rat ES chimeras
Authors: Isotani Ayako , Yamagata Kazuo , Okabe Masaru , Ikawa Masahito 
Published: April 2016

AbstractWe established rat embryonic stem (ES) cell lines from a double transgenic rat line which harboursCAG-GFPfor ubiquitous expression of GFP in somatic cells andAcr3-EGFPfor expression in sperm (green body and green sperm: GBGS rat). By injecting the GBGS rat ES cells into mouse blastocysts and transplanting them into pseudopregnant mice, rat spermatozoa were produced in mouse←rat ES chimeras. Rat spermatozoa from the chimeric testis were able to fertilize eggs by testicular sperm extraction combined with intracytoplasmic sperm injection (TESE-ICSI). In the present paper, we disrupted rat hypoxanthine-guanine phosphoribosyl transferase (Hprt) gene in ES cells and produced aHprt-disrupted rat line using the mouse←rat ES chimera system. The mouse←rat ES chimera system demonstrated the dual advantages of space conservation and a clear indication of germ line transmission in knockout rat production.
Wettability of partially suspended graphene
Authors: Ondarçuhu Thierry , Thomas Vincent , Nuñez Marc , Dujardin Erik , Rahman Atikur , Black Charles T. , Checco Antonio 
Published: April 2016

AbstractThe dependence of the wettability of graphene on the nature of the underlying substrate remains only partially understood. Here, we systematically investigate the role of liquid-substrate interactions on the wettability of graphene by varying the area fraction of suspended graphene from 0 to 95% by means of nanotextured substrates. We find that completely suspended graphene exhibits the highest water contact angle (85° ± 5°) compared to partially suspended or supported graphene, regardless of the hydrophobicity (hydrophilicity) of the substrate. Further, 80% of the long-range water-substrate interactions are screened by the graphene monolayer, the wettability of which is primarily determined by short-range graphene-liquid interactions. By its well-defined chemical and geometrical properties, supported graphene therefore provides a model system to elucidate the relative contribution of short and long range interactions to the macroscopic contact angle.
Visualization of neonatal lung injury associated with mechanical ventilation using x-ray dark-field radiography
Authors: Yaroshenko Andre , Pritzke Tina , Koschlig Markus , Kamgari Nona , Willer Konstantin , Gromann Lukas , Auweter Sigrid , Hellbach Katharina , Reiser Maximilian , Eickelberg Oliver , Pfeiffer Franz , Hilgendorff Anne 
Published: April 2016

AbstractMechanical ventilation (MV) and supplementation of oxygen-enriched gas, often needed in postnatal resuscitation procedures, are known to be main risk factors for impaired pulmonary development in the preterm and term neonates. Unfortunately, current imaging modalities lack in sensitivity for the detection of early stage lung injury. The present study reports a new imaging approach for diagnosis and staging of early lung injury induced by MV and hyperoxia in neonatal mice. The imaging method is based on the Talbot-Lau x-ray grating interferometry that makes it possible to quantify the x-ray small-angle scattering on the air-tissue interfaces. This so-called dark-field signal revealed increasing loss of x-ray small-angle scattering when comparing images of neonatal mice undergoing hyperoxia and MV-O2 with animals kept at room air. The changes in the dark field correlated well with histologic findings and provided superior differentiation than conventional x-ray imaging and lung function testing. The results suggest that x-ray dark-field radiography is a sensitive tool for assessing structural changes in the developing lung. In the future, with further technical developments x-ray dark-field imaging could be an important tool for earlier diagnosis and sensitive monitoring of lung injury in neonates requiring postnatal oxygen or ventilator therapy.
Histone H4 lysine 20 acetylation is associated with gene repression in human cells
Authors: Kaimori Jun-Ya , Maehara Kazumitsu , Hayashi-Takanaka Yoko , Harada Akihito , Fukuda Masafumi , Yamamoto Satoko , Ichimaru Naotsugu , Umehara Takashi , Yokoyama Shigeyuki , Matsuda Ryo , Ikura Tsuyoshi , Nagao Koji , Obuse Chikashi , Nozaki Naohito , Takahara Shiro , Takao Toshifumi , Ohkawa Yasuyuki , Kimura Hiroshi , Isaka Yoshitaka 
Published: April 2016

AbstractHistone acetylation is generally associated with gene activation and chromatin decondensation. Recent mass spectrometry analysis has revealed that histone H4 lysine 20, a major methylation site, can also be acetylated. To understand the function of H4 lysine 20 acetylation (H4K20ac), we have developed a specific monoclonal antibody and performed ChIP-seq analysis using HeLa-S3 cells. H4K20ac was enriched around the transcription start sites (TSSs) of minimally expressed genes and in the gene body of expressed genes, in contrast to most histone acetylation being enriched around the TSSs of expressed genes. The distribution of H4K20ac showed little correlation with known histone modifications, including histone H3 methylations. A motif search in H4K20ac-enriched sequences, together with transcription factor binding profiles based on ENCODE ChIP-seq data, revealed that most transcription activators are excluded from H4K20ac-enriched genes and a transcription repressor NRSF/REST co-localized with H4K20ac. These results suggest that H4K20ac is a unique acetylation mark associated with gene repression.
Spironolactone promotes autophagy via inhibiting PI3K/AKT/mTOR signalling pathway and reduce adhesive capacity damage in podocytes under mechanical stress
Authors: Li Dong , Lu Zhenyu , Xu Zhongwei , Ji Junya , Zheng Zhenfeng , Lin Shan , Yan Tiekun 
Published: April 2016

Mechanical stress which would cause deleterious adhesive effects on podocytes is considered a major contributor to the early progress of diabetic nephropathy (DN). Our previous study has shown that spironolactone could ameliorate podocytic adhesive capacity in diabetic rats. Autophagy has been reported to have a protective role against renal injury. The present study investigated the underlying mechanisms by which spironolactone reduced adhesive capacity damage in podocytes under mechanical stress, focusing on the involvement of autophagy. Human conditional immortalized podocytes exposed to mechanical stress were treated with spironolactone, LY294002 or rapamycin for 48 h. The accumulation of LC3 puncta was detected by immunofluorescence staining. Podocyte expression of mineralocorticoid receptor (MR), integrin β1, LC3, Atg5, p85-PI3K, p-Akt, p-mTOR were detected by Western blotting. Podocyte adhesion to collagen type IV was also performed with spectrophotometry. Immunofluorescence staining showed that the normal level of autophagy was reduced in podocytes under mechanical stress. Decreased integrin β1, LC3, Atg5 and abnormal activation of the PI3K/Akt/mTOR pathway were also detected in podocytes under mechanical stress. Spironolactone up-regulated integrin β1, LC3, Atg5 expression, down-regulated p85-PI3K, p-Akt, p-mTOR expression and reduced podocytic adhesive capacity damage. Our data demonstrated that spironolactone inhibited mechanical-stress-induced podocytic adhesive capacity damage through blocking PI3K/Akt/mTOR pathway and restoring autophagy activity.
The complexity of signalling mediated by the glucagon-like peptide-1 receptor
Authors: Fletcher Madeleine M. , Halls Michelle L. , Christopoulos Arthur , Sexton Patrick M. , Wootten Denise 
Published: April 2016

The glucagon-like peptide-1 receptor (GLP-1R) is a class B GPCR that is a major therapeutic target for the treatment of type 2 diabetes. The receptor is activated by the incretin peptide GLP-1 promoting a broad range of physiological effects including glucose-dependent insulin secretion and biosynthesis, improved insulin sensitivity of peripheral tissues, preservation of β-cell mass and weight loss, all of which are beneficial in the treatment of type 2 diabetes. Despite this, existing knowledge surrounding the underlying signalling mechanisms responsible for the physiological actions downstream of GLP-1R activation is limited. Here, we review the current understanding around GLP-1R-mediated signalling, in particular highlighting recent contributions to the field on biased agonism, the spatial and temporal aspects for the control of signalling and how these concepts may influence future drug development.
Lipid transfer proteins do their thing anchored at membrane contact sites… but what is their thing?
Authors: Wong Louise H. , Levine Tim P. 
Published: April 2016

Membrane contact sites are structures where two organelles come close together to regulate flow of material and information between them. One type of inter-organelle communication is lipid exchange, which must occur for membrane maintenance and in response to environmental and cellular stimuli. Soluble lipid transfer proteins have been extensively studied, but additional families of transfer proteins have been identified that are anchored into membranes by transmembrane helices so that they cannot diffuse through the cytosol to deliver lipids. If such proteins target membrane contact sites they may be major players in lipid metabolism. The eukaryotic family of so-called Lipid transfer proteins Anchored at Membrane contact sites (LAMs) all contain both a sterol-specific lipid transfer domain in the StARkin superfamily (related to StART/Bet_v1), and one or more transmembrane helices anchoring them in the endoplasmic reticulum (ER), making them interesting subjects for study in relation to sterol metabolism. They target a variety of membrane contact sites, including newly described contacts between organelles that were already known to make contact by other means. Lam1–4p target punctate ER–plasma membrane contacts. Lam5p and Lam6p target multiple contacts including a new category: vacuolar non-NVJ cytoplasmic ER (VancE) contacts. These developments confirm previous observations on tubular lipid-binding proteins (TULIPs) that established the importance of membrane anchored proteins for lipid traffic. However, the question remaining to be solved is the most difficult of all: are LAMs transporters, or alternately are they regulators that affect traffic more indirectly?
Theoretical and experimental analyses of a hybrid excitation synchronous generator with integrated brushless excitation
Authors: Zhu Shushu , Liu Chuang , Wang Kai , Hu Yaohua , Ning Yinhang 
Published: April 2016

This paper proposes a novel integrated brushless excitation method (IBEM) for a rotor‐excited generator. IBEM is applied to a rotor‐excited hybrid excitation synchronous generator (HESG) to realise brushless excitation while the key features of the rotor‐excited generator are maintained. The new generator is referred as IBE HESG here. The stator excitation windings are buried in the stator slots. The static excitation field is established in the air gap when there is dc excitation current in the stator excitation windings. The three‐phase armature coils of the rotor induce the static excitation field and provide the dc excitation current for the rotor excitation windings via a rotating rectifier. The operating principles are discussed theoretically. The magnetic field distribution and the operating characteristics are studied by finite‐element analysis. The no‐load, external, regulation and excitation characteristics are analysed. Compared with the brush excitation HESG, the rotor excitation current is able to meet the requirement and the output voltage is conveniently regulated by the stator excitation current. Finally, a 1.5 kVA prototype is fabricated to test the operating characteristics of IBE HESG. It demonstrates that the brushless excitation is realised and the output voltage is regulated by the stator excitation current.
Integrated radial/thrust magnetic bearing without thrust disk for a high‐speed driving system
Authors: Han Bangcheng , Xu Qinjie , Zheng Shiqiang 
Published: April 2016

In this paper, the authors present a novel compact structure of an integrated radial/thrust magnetic bearing (IRTMB) without thrust disk. The structure without thrust disk can further reduce the frictional and windage loss for a high‐speed driving system. At the same time the rotor supported by the two IRTMBs can further reduce its axial size, and improve rotor dynamic performance. The axially magnetised magnet forms a cylindrical magnet sandwiched between a four‐leg laminated radial stator and a solid return pole piece. On the basis of the return pole, a novel air gap, called the return air gap, is constructed between the rotor and the return pole. The bias flux produced by the permanent magnet and the control flux produced by the thrust magnetic bearing (TMB) unit are conducted by this return pole. The magnet produces the bias flux for radial and TMB units, and separates the control flux loops of radial and TMB units. The IRTMB structure and its analytical models are deduced using equivalent magnetic circuit method. To study the performances of the IRTMB, another IRTMB with thrust disk used in a high‐speed motor with power of 45 kW at 60,000 rev/min has been fabricated and is chosen as the comparison target.
Ultrasonic Degradation of Biologically Active Polysaccharide Produced by Serratia piscatorum
Authors: Kita Yasuo , Igarasi Seizi , Nakanishi Itaru , Isono Masao 
Published: April 2016

Abstract
Changes in chemical, physicochemical and biological properties of Serratia piscatorum polysaccharide, PLS N–I, by ultrasonic irradiation were investigated. Ultrasonication decreased the viscosity of an aqueous solution of PLS N–I to give two degraded polysaccharide fractions, PLS F–I and PLS F-II, as separated each other by column chromatography on Sepharose 4B. PLS F–I was different from PLS F–II in their physicochemical and biological properties as well as in their chemical compositions.