bluuebunny/crossref_metadata_2025_split huggingface dataset:
The acetyllysine reader BRD3R promotes human nuclear reprogramming and regulates mitosis
Authors: Shao Zhicheng , Zhang Ruowen , Khodadadi-Jamayran Alireza , Chen Bo , Crowley Michael R. , Festok Muhamad A. , Crossman David K. , Townes Tim M. , Hu Kejin 
Published: March 2016

AbstractIt is well known that both recipient cells and donor nuclei demonstrate a mitotic advantage as observed in the traditional reprogramming with somatic cell nuclear transfer (SCNT). However, it is not known whether a specific mitotic factor plays a critical role in reprogramming. Here we identify an isoform of human bromodomain-containing 3 (BRD3), BRD3R (BRD3 with Reprogramming activity), as a reprogramming factor. BRD3R positively regulates mitosis during reprogramming, upregulates a large set of mitotic genes at early stages of reprogramming, and associates with mitotic chromatin. Interestingly, a set of the mitotic genes upregulated by BRD3R constitutes a pluripotent molecular signature. The two BRD3 isoforms display differential binding to acetylated histones. Our results suggest a molecular interpretation for the mitotic advantage in reprogramming and show that mitosis may be a driving force of reprogramming.
Data publication with the structural biology data grid supports live analysis
Authors: Meyer Peter A. , Socias Stephanie , Key Jason , Ransey Elizabeth , Tjon Emily C. , Buschiazzo Alejandro , Lei Ming , Botka Chris , Withrow James , Neau David , Rajashankar Kanagalaghatta , Anderson Karen S. , Baxter Richard H. , Blacklow Stephen C. , Boggon Titus J. , Bonvin Alexandre M. J. J. , Borek Dominika , Brett Tom J. , Caflisch Amedeo , Chang Chung-I , Chazin Walter J. , Corbett Kevin D. , Cosgrove Michael S. , Crosson Sean , Dhe-Paganon Sirano , Di Cera Enrico , Drennan Catherine L. , Eck Michael J. , Eichman Brandt F. , Fan Qing R. , Ferré-D'Amaré Adrian R. , Christopher Fromme J. , Garcia K. Christopher , Gaudet Rachelle , Gong Peng , Harrison Stephen C. , Heldwein Ekaterina E. , Jia Zongchao , Keenan Robert J. , Kruse Andrew C. , Kvansakul Marc , McLellan Jason S. , Modis Yorgo , Nam Yunsun , Otwinowski Zbyszek , Pai Emil F. , Pereira Pedro José Barbosa , Petosa Carlo , Raman C. S. , Rapoport Tom A. , Roll-Mecak Antonina , Rosen Michael K. , Rudenko Gabby , Schlessinger Joseph , Schwartz Thomas U. , Shamoo Yousif , Sondermann Holger , Tao Yizhi J. , Tolia Niraj H. , Tsodikov Oleg V. , Westover Kenneth D. , Wu Hao , Foster Ian , Fraser James S. , Maia Filipe R. N C. , Gonen Tamir , Kirchhausen Tom , Diederichs Kay , Crosas Mercè , Sliz Piotr 
Published: March 2016

AbstractAccess to experimental X-ray diffraction image data is fundamental for validation and reproduction of macromolecular models and indispensable for development of structural biology processing methods. Here, we established a diffraction data publication and dissemination system, Structural Biology Data Grid (SBDG; data.sbgrid.org), to preserve primary experimental data sets that support scientific publications. Data sets are accessible to researchers through a community driven data grid, which facilitates global data access. Our analysis of a pilot collection of crystallographic data sets demonstrates that the information archived by SBDG is sufficient to reprocess data to statistics that meet or exceed the quality of the original published structures. SBDG has extended its services to the entire community and is used to develop support for other types of biomedical data sets. It is anticipated that access to the experimental data sets will enhance the paradigm shift in the community towards a much more dynamic body of continuously improving data analysis.
Humans choose representatives who enforce cooperation in social dilemmas through extortion
Authors: Milinski Manfred , Hilbe Christian , Semmann Dirk , Sommerfeld Ralf , Marotzke Jochem 
Published: March 2016

AbstractSocial dilemmas force players to balance between personal and collective gain. In many dilemmas, such as elected governments negotiating climate-change mitigation measures, the decisions are made not by individual players but by their representatives. However, the behaviour of representatives in social dilemmas has not been investigated experimentally. Here inspired by the negotiations for greenhouse-gas emissions reductions, we experimentally study a collective-risk social dilemma that involves representatives deciding on behalf of their fellow group members. Representatives can be re-elected or voted out after each consecutive collective-risk game. Selfish players are preferentially elected and are hence found most frequently in the ‘representatives’ treatment. Across all treatments, we identify the selfish players as extortioners. As predicted by our mathematical model, their steadfast strategies enforce cooperation from fair players who finally compensate almost completely the deficit caused by the extortionate co-players. Everybody gains, but the extortionate representatives and their groups gain the most.
The use of low-calorie sweeteners is associated with self-reported prior intent to lose weight in a representative sample of US adults
Authors: Drewnowski A , Rehm C D 
Published: March 2016

AbstractBackground:Low-calorie sweeteners (LCSs) are said to be a risk factor for obesity and diabetes. Reverse causality may be an alternative explanation.Methods:Data on LCS use, from a single 24-h dietary recall, for a representative sample of 22 231 adults were obtained from 5 cycles of the National Health and Nutrition Examination Survey (1999–2008 NHANES). Retrospective data on intent to lose or maintain weight during the prior 12-months and 10-year weight history were obtained from the weight history questionnaire. Objectively measured heights and weights were obtained from the examination. Primary analyses evaluated the association between intent to lose/maintain weight and use of LCSs and specific LCS product types using survey-weighted generalized linear models. We further evaluated whether body mass index (BMI) may mediate the association between weight loss intent and use of LCSs. The association between 10-year weight history and current LCS use was evaluated using restricted cubic splines.Results:In cross-sectional analyses, LCS use was associated with a higher prevalence of obesity and diabetes. Adults who tried to lose weight during the previous 12 months were more likely to consume LCS beverages (prevalence ratio=1.64, 95% confidence interval (CI) 1.54–1.75), tabletop LCS (prevalence ratio=1.68, 95% CI 1.47–1.91) and LCS foods (prevalence ratio=1.93, 95% CI 1.60–2.33) as compared with those who did not. In mediation analyses, BMI only partially mediated the association between weight control history and the use of LCS beverages, tabletop LCS, but not LCS foods. Current LCS use was further associated with a history of prior weight change (for example, weight loss and gain).Conclusions:LCS use was associated with self-reported intent to lose weight during the previous 12 months. This association was only partially mediated by differences in BMI. Any inference of causality between attempts at weight control and LCS use is tempered by the cross-sectional nature of these data and retrospective self-reports of prior weight loss/maintenance intent.
Death receptor 6 (DR6) is required for mouse B16 tumor angiogenesis via the NF-κB, P38 MAPK and STAT3 pathways
Authors: Yang X , Shi B , Li L , Xu Z , Ge Y , Shi J , Liu Y , Zheng D 
Published: March 2016

AbstractAlthough death receptor 6 (DR6) is aberrantly expressed in certain cancer cell lines, its function, signaling pathway and potential clinical significance in tumor progression are not well characterized. We report here that knocking down DR6 in the mouse B16 cell line has no effect on B16 cell death in vitro but suppresses xenograft B16 tumor growth by preventing tumor blood vessel formation in vivo. Deficiency of DR6 changes cytokine expression and secretion; in particular, it inhibits the proinflammatory cytokine interleukin-6 (IL-6), which is able to induce the expression of the angiogenesis-related factors: vascular endothelial growth factor-A, platelet-derived growth factor-β, vascular endothelial growth factor-D and platelet-derived growth factor receptor-α. Further experiments demonstrate that DR6-dependent angiogenesis is involved in the IL-6/P38 MAPK and IL-6/STAT3 pathways. Our novel findings demonstrate for the first time that DR6 expression in B16 cells facilitates tumor growth by accelerating tumor angiogenesis. Moreover, these results suggest that DR6 is involved in three important intracellular pathways that lead to homeostatic angiogenesis in tumor growth.
Second magnetization peak effect, vortex dynamics and flux pinning in 112-type superconductor Ca0.8La0.2Fe1−xCoxAs2
Authors: Zhou Wei , Xing Xiangzhuo , Wu Wenjuan , Zhao Haijun , Shi Zhixiang 
Published: March 2016

AbstractInvestigation of vortex pinning and its relaxation is of great importance for both basic physics and technological applications in the field of superconductivity. We report a great improvement of superconducting properties in the recently discovered 112-type superconductors (Ca, La)FeAs2 through Co co-doping. High critical current density Js(5 K) > 2*106 A/cm2 is obtained and pronounced second peak effect is observed in magnetization hysteresis loops. Both the dynamic and static relaxation studies result in comparable and sizable relaxation rates S or Q, indicating a fast vortex creep. The second magnetization peak (SMP) is found to be strongly associated with a crossover from elastic to plastic vortex creep. Above the crossover, plastic vortex creep governs the vortex dynamics in a wide range of temperatures and fields. A good scaling behavior of the normalized pinning force density fp by formula fp = hp(1−h)q (p = 1.44, q = 1.66, h = 0.44) is revealed, which demonstrates an important contribution from core normal point-like pinning sites. To better understand the SMP phenomenon, we discuss the related physical scenario as well as the affecting factors in the SMP occurrence.
3D Binder-free MoSe2 Nanosheets/Carbon Cloth Electrodes for Efficient and Stable Hydrogen Evolution Prepared by Simple Electrophoresis Deposition Strategy
Authors: Liu Yundan , Ren Long , Zhang Zhen , Qi Xiang , Li Hongxing , Zhong Jianxin 
Published: March 2016

AbstractWe successfully developed a simple electrophoretic deposition (EPD) method to decorate the MoSe2 nanosheets on the carbon fiber surface of carbon cloth (MoSe2/CC). With this process, MoSe2 nanosheets can be uniformly and tightly deposited on this flexible conductor to form a 3D binder-free electrode for hydrogen evolution reaction (HER). The film thickness can also be controlled by the EPD time. Directly used as binder-free electrodes for hydrogen evolution reaction, the as-prepared 3D MoSe2/CC samples exhibit excellent catalytic activity in an acidic electrolyte (21 mA/cm2 at an over-potential of 250 mV). Variation of MoSe2 nanosheets film thickness in the electrodes could affect the catalytic activity and it was found that the MoSe2/CC sample prepared with 60 min EPD time shows the highest HER activity amongst these different thickness samples. Moreover, stability tests though long-term potential cycles (no degradation after 1000 continuous potential cycles) and extended electrolysis confirm the exceptional durability of the catalyst. This development offers us an attractive and active 3D electrode for electrochemical water splitting.
Experimental and theoretical thermal equations of state of MgSiO3 post-perovskite at multi-megabar pressures
Authors: Sakai Takeshi , Dekura Haruhiko , Hirao Naohisa 
Published: March 2016

AbstractThe MgSiO3 post-perovskite phase is the most abundant silicate phase in a super-Earth’s mantle, although it only exists within the Earth’s lowermost mantle. In this study, we established the thermal equation of state (EoS) of the MgSiO3 post-perovskite phase, which were determined by using both laser-heated diamond anvil cell and density-functional theoretical techniques, within a multi-megabar pressure range, corresponding to the conditions of a super-Earth’s mantle. The Keane and AP2 EoS models were adopted for the first time to extract meaningful physical properties. The experimentally determined Grüneisen parameter, which is one of the thermal EoS parameters and its volume dependence were found to be consistent with their theoretically obtained values. This reduced the previously reported discrepancy observed between experiment and theory. Both the experimental and theoretical EoS were also found to be in very good agreement for volumes at pressures and temperatures of up to 300 GPa and 5000 K, respectively. Our newly developed EoS should be applicable to a super-Earth’s mantle, as well as the Earth’s core-mantle boundary region.
Simultaneous expression and transportation of insulin by supramolecular polysaccharide nanocluster
Authors: Zhang Yu-Hui , Zhang Ying-Ming , Zhao Qi-Hui , Liu Yu 
Published: March 2016

AbstractDrug/gene transportation systems with stimuli-responsive release behaviors are becoming research hotspots in biochemical and biomedical fields. In this work, a glucose-responsive supramolecular nanocluster was successfully constructed by the intermolecular complexation of phenylboronic acid modified β-cyclodextrin with adamantane modified polyethylenimine, which could be used as a biocompatible carrier for insulin and pCMV3-C-GFPSpark-Ins DNA which could express insulin co-delivery. Benefiting from the response capability of phenylboronic acid moiety toward glucose, the encapsulated insulin could be specifically released and the corresponding targeted DNA could efficiently express insulin in HepG2 cell, accompanied by the high-level insulin release in vitro. Our results demonstrate that the simultaneous insulin drug delivery and insulin gene transfection in a controlled mode may have great potential in the clinical diabetes treatments.
A systematic method to identify modulation of transcriptional regulation via chromatin activity reveals regulatory network during mESC differentiation
Authors: Duren Zhana , Wang Yong 
Published: March 2016

AbstractChromatin regulators (CRs) are crucial for connecting the chromatin level and transcriptome level by modulating chromatin structures, establishing and maintaining epigenetic modifications. We present a systematic method to identify MOdulation of transcriptional regulation via CHromatin Activity (MOCHA) from gene expression data and demonstrate its advantage in associating CRs to their chromatin localization and understand CRs’ function. We first re-construct the CRs modulation network by integrating the correlation and conditional correlation concepts. Then we quantify the chromatin activity as hidden variable in network by integrating the upstream and downstream information. We applied MOCHA to systematically explore the interplay of CRs, TFs and target genes in mouse embryonic stem cells (ESC). As a result, MOCHA identified 420 chromatin regulators with modulation preference, including Pou5f1 and Eed. We found that BAF complex, NuRD complex and polycomb-group proteins, regulate the delicate balance between pluripotency and differentiation by modulating key TFs including Klf4, Tcf3 and Max; NuRD complex members Mbd3 and Hdac1 may modulate Klf4 to achieve its dual functional roles in pluripotent and differentiation stages;Imprinted gene H19 and Igf2 are modulated by DNA methylation, histone acetylation and insulator CTCF. Finally, we analyzed CR’s combinational modulation pattern by constructing a CR-CR interaction network.
Discovery of a Biological Mechanism of Active Transport through the Tympanic Membrane to the Middle Ear
Authors: Kurabi Arwa , Pak Kwang K. , Bernhardt Marlen , Baird Andrew , Ryan Allen F. 
Published: March 2016

AbstractOtitis media (OM) is a common pediatric disease for which systemic antibiotics are often prescribed. While local treatment would avoid the systemic treatment side-effects, the tympanic membrane (TM) represents an impenetrable barrier unless surgically breached. We hypothesized that the TM might harbor innate biological mechanisms that could mediate trans-TM transport. We used two M13-bacteriophage display biopanning strategies to search for mediators of trans-TM transport. First, aliquots of linear phage library displaying 1010th 12mer peptides were applied on the TM of rats with active bacterial OM. The middle ear (ME) contents were then harvested, amplified and the preparation re-applied for additional rounds. Second, the same naïve library was sequentially screened for phage exhibiting TM binding, internalization and then transit. Results revealed a novel set of peptides that transit across the TM to the ME in a time and temperature dependent manner. The peptides with highest transport capacities shared sequence similarities. Historically, the TM was viewed as an impermeable barrier. However, our studies reveal that it is possible to translocate peptide-linked small particles across the TM. This is the first comprehensive biopanning for the isolation of TM transiting peptidic ligands. The identified mechanism offers a new drug delivery platform into the ME.
In-situ Observation of Cross-Sectional Microstructural Changes and Stress Distributions in Fracturing TiN Thin Film during Nanoindentation
Authors: Zeilinger Angelika , Todt Juraj , Krywka Christina , Müller Martin , Ecker Werner , Sartory Bernhard , Meindlhumer Michael , Stefenelli Mario , Daniel Rostislav , Mitterer Christian , Keckes Jozef 
Published: March 2016

AbstractLoad-displacement curves measured during indentation experiments on thin films depend on non-homogeneous intrinsic film microstructure and residual stress gradients as well as on their changes during indenter penetration into the material. To date, microstructural changes and local stress concentrations resulting in plastic deformation and fracture were quantified exclusively using numerical models which suffer from poor knowledge of size dependent material properties and the unknown intrinsic gradients. Here, we report the first in-situ characterization of microstructural changes and multi-axial stress distributions in a wedge-indented 9 μm thick nanocrystalline TiN film volume performed using synchrotron cross-sectional X-ray nanodiffraction. During the indentation, needle-like TiN crystallites are tilted up to 15 degrees away from the indenter axis in the imprint area and strongly anisotropic diffraction peak broadening indicates strain variation within the X-ray nanoprobe caused by gradients of giant compressive stresses. The morphology of the multiaxial stress distributions with local concentrations up to −16.5 GPa correlate well with the observed fracture modes. The crack growth is influenced decisively by the film microstructure, especially by the micro- and nano-scopic interfaces. This novel experimental approach offers the capability to interpret indentation response and indenter imprint morphology of small graded nanostructured features.
Formation and Geological Sequestration of Uranium Nanoparticles in Deep Granitic Aquifer
Authors: Suzuki Yohey , Mukai Hiroki , Ishimura Toyoho , Yokoyama Takaomi D. , Sakata Shuhei , Hirata Takafumi , Iwatsuki Teruki , Mizuno Takashi 
Published: March 2016

AbstractThe stimulation of bacterial activities that convert hexavalent uranium, U(VI), to tetravalent uranium, U(IV), appears to be feasible for cost-effective remediation of contaminated aquifers. However, U(VI) reduction typically results in the precipitation of U(IV) particles less than 5 nanometers in diameter, except for environmental conditions enriched with iron. Because these tiny particles are mobile and susceptible to oxidative dissolution after the termination of nutrient injection, in situ bioremediation remains to be impractical. Here we show that U(IV) nanoparticles of coffinite (U(SiO4)1−x(OH)4x) formed in fracture-filling calcium carbonate in a granitic aquifer. In situ U-Pb isotope dating demonstrates that U(IV) nanoparticles have been sequestered in the calcium carbonate for at least 1 million years. As the microbiologically induced precipitation of calcium carbonate in aquifer systems worldwide is extremely common, we anticipate simultaneous stimulation of microbial activities for precipitation reactions of calcium carbonate and U(IV) nanoparticles, which leads to long-term sequestration of uranium and other radionuclides in contaminated aquifers and deep geological repositories.
Controllable chaos in hybrid electro-optomechanical systems
Authors: Wang Mei , Lü Xin-You , Ma Jin-Yong , Xiong Hao , Si Liu-Gang , Wu Ying 
Published: March 2016

AbstractWe investigate the nonlinear dynamics of a hybrid electro-optomechanical system (EOMS) that allows us to realize the controllable opto-mechanical nonlinearity by driving the microwave LC resonator with a tunable electric field. A controllable optical chaos is realized even without changing the optical pumping. The threshold and lifetime of the chaos could be optimized by adjusting the strength, frequency, or phase of the electric field. This study provides a method of manipulating optical chaos with an electric field. It may offer the prospect of exploring the controllable chaos in on-chip optoelectronic devices and its applications in secret communication.
Mechanical insights into ribosomal progression overcoming RNA G-quadruplex from periodical translation suppression in cells
Authors: Endoh Tamaki , Sugimoto Naoki 
Published: March 2016

AbstractG-quadruplexes formed on DNA and RNA can be roadblocks to movement of polymerases and ribosome on template nucleotides. Although folding and unfolding processes of the G-quadruplexes are deliberately studiedin vitro, how the mechanical and physical properties of the G-quadruplexes affect intracellular biological systems is still unclear. In this study, mRNAs with G-quadruplex forming sequences located either in the 5′ untranslated region (UTR) or in the open reading frame (ORF) were constructed to evaluate positional effects of the G-quadruplex on translation suppression in cells. Periodic fluctuation of translation suppression was observed at every three nucleotides within the ORF but not within the 5′ UTR. The results suggested that difference in motion of ribosome at the 5′ UTR and the ORF determined the ability of the G-quadruplex structure to act as a roadblock to translation in cells and provided mechanical insights into ribosomal progression to overcome the roadblock.