bluuebunny/crossref_metadata_2025_split huggingface dataset:
Kant's wager. Kant's strong belief in extra-terrestrial life, the history of this question and its challenge for theology today
Authors: Losch Andreas 
Published: September 2016

AbstractKant was not the first in whom the ‘starry heavens’ above us inspired awe and wonder. For Kant, who was firmly convinced of the existence of inhabitants of other worlds, these heavens were inhabited. He is certain that ‘If it were possible to settle by any sort of experience whether there are inhabitants of at least some of the planets that we see, I might well bet everything that I have on it. Hence I say that it is not merely an opinion but a strong belief (on the correctness of which I would wager many advantages in life) that there are also inhabitants of other worlds.’ In this statement by Kant in no less a work than the Critique of Pure Reason one can, on the one hand, recognize a reflection of Kant's earlier convictions and expositions, on the other hand, the context of the citation and the contemporary background are, of course, relevant. Following the example of Kant, this paper investigates the meaning of such reflections about inhabitants of alien worlds, which due to advances in planetary astronomy are today again on the agenda. Consideration of this subject also represents a challenge for theology.
Gold nanocrystals with DNA-directed morphologies
Authors: Ma Xingyi , Huh June , Park Wounjhang , Lee Luke P. , Kwon Young Jik , Sim Sang Jun 
Published: September 2016

AbstractPrecise control over the structure of metal nanomaterials is important for developing advanced nanobiotechnology. Assembly methods of nanoparticles into structured blocks have been widely demonstrated recently. However, synthesis of nanocrystals with controlled, three-dimensional structures remains challenging. Here we show a directed crystallization of gold by a single DNA molecular regulator in a sequence-independent manner and its applications in three-dimensional topological controls of crystalline nanostructures. We anchor DNA onto gold nanoseed with various alignments to form gold nanocrystals with defined topologies. Some topologies are asymmetric including pushpin-, star- and biconcave disk-like structures, as well as more complex jellyfish- and flower-like structures. The approach of employing DNA enables the solution-based synthesis of nanocrystals with controlled, three-dimensional structures in a desired direction, and expands the current tools available for designing and synthesizing feature-rich nanomaterials for future translational biotechnology.
CDK1 phosphorylates WRN at collapsed replication forks
Authors: Palermo Valentina , Rinalducci Sara , Sanchez Massimo , Grillini Francesca , Sommers Joshua A. , Brosh Robert M. , Zolla Lello , Franchitto Annapaola , Pichierri Pietro 
Published: September 2016

AbstractRegulation of end-processing is critical for accurate repair and to switch between homologous recombination (HR) and non-homologous end joining (NHEJ). End resection is a two-stage process but very little is known about regulation of the long-range resection, especially in humans. WRN participates in one of the two alternative long-range resection pathways mediated by DNA2 or EXO1. Here we demonstrate that phosphorylation of WRN by CDK1 is essential to perform DNA2-dependent end resection at replication-related DSBs, promoting HR, replication recovery and chromosome stability. Mechanistically, S1133 phosphorylation of WRN is dispensable for relocalization in foci but is involved in the interaction with the MRE11 complex. Loss of WRN phosphorylation negatively affects MRE11 foci formation and acts in a dominant negative manner to prevent long-range resection altogether, thereby licensing NHEJ at collapsed forks. Collectively, we unveil a CDK1-dependent regulation of the WRN-DNA2-mediated resection and identify an undescribed function of WRN as a DSB repair pathway switch.
Capture of associated targets on chromatin links long-distance chromatin looping to transcriptional coordination
Authors: Bourgo Ryan J. , Singhal Hari , Greene Geoffrey L. 
Published: September 2016

AbstractHere we describe a sensitive and novel method of identifying endogenous DNA–DNA interactions. Capture of Associated Targets on CHromatin (CATCH) uses efficient capture and enrichment of specific genomic loci of interest through hybridization and subsequent purification via complementary biotinylated oligonucleotide. The CATCH assay requires no enzymatic digestion or ligation, requires little starting material, provides high-quality data, has excellent reproducibility and is completed in less than 24 h. Efficacy is demonstrated through capture of three disparate loci, which demonstrate unique subsets of long-distance chromatin interactions enriched for both enhancer marks and oestrogen receptor-binding sites. In each experiment, CATCH-seq peaks representing long-distance chromatin interactions were centred near the TSS of genes, and, critically, the genes identified as physically interacting are shown to be transcriptionally coexpressed. These interactions could potentially create transcriptional hubs for the regulation of gene expression programmes.
Genetic and environmental factors strongly influence risk, severity and progression of age-related macular degeneration
Authors: Wang Wenqiu , Gawlik Katarzyna , Lopez Joe , Wen Cindy , Zhu Jie , Wu Frances , Shi William , Scheibler Samuel , Cai Huimin , Vairavan Ram , Shi Alexander , Haw Weldon , Ferreyra Henry , Zhang Ming , Chang Sherman , Zhang Kang 
Published: September 2016

AbstractAge-related macular degeneration (AMD) is characterized by complex interactions between genetic and environmental factors. Here we genotyped the selected 25 single-nucleotide polymorphisms (SNPs) in 983 cases with advanced AMD and 271 cases with intermediate AMD and build an AMD life-risk score model for assessment of progression from intermediate to advanced AMD. We analyzed the performance of the prediction model for geographic atrophy progressors or choroidal neovascularization progressors versus non-progressors based on the 25 SNPs plus body mass index and smoking status. Our results suggest that a class prediction algorithm can be used for the risk assessment of progression from intermediate to late AMD stages. The algorithm could also be potentially applied for therapeutic response, and toward personalized care and precision medicine.
Modification of Susceptible and Toxic Herbs on Grassland Disease
Authors: Yao Xiang , Fan Yubing , Chai Qing , Johnson Richard D. , Nan Zhibiao , Li Chunjie 
Published: September 2016

AbstractRecent research shows that continuous overgrazing not only causes grassland biodiversity to decline, but also causes light fungal disease. Achnatherum inebrians is susceptible to fungal diseases and increases in prevalence during over grazing due its toxicity to livestock. This study aimed to examine the effects of A. inebrians on biological control organisms and levels of plant diseases in overgrazed grasslands in northwestern China. The results showed that A. inebrians plants were seriously infected by fungal diseases and that this led to a high incidence of the mycoparasitic species Ampelomyces quisqualis and Sphaerellopsis filum. In addition, the fungivore, Aleocharinae, was found only in the soil growing A. inebrians rather than in the overgrazed area without A. inebrians. Overall, in an overgrazed grassland fenced for one year, disease levels in blocks without A. inebrians were significantly higher than those in blocks with A. inebrians. Our findings indicated that the disease susceptible, toxic A. inebrians can help control plant disease levels in overgrazed grasslands.
Comparison of research methods for functional characterization of insect olfactory receptors
Authors: Wang Bing , Liu Yang , He Kang , Wang Guirong 
Published: September 2016

AbstractInsect olfactory receptors (ORs) in the peripheral olfactory system play an important role detecting elements of information from the environment. At present, various approaches are used for deorphanizing of ORs in insect. In this study, we compared methods for functional analysis of ORs in vitro and in vivo taking the candidate pheromone receptor OR13 of Helicoverpa assulta (HassOR13) as the object of our experiments. We found that the natural system was more sensitive than those utilizing transgenic Drosophila. The two-electrode voltage-clamp recording is more suitable for functional screening of large numbers of ORs, while the in vivo transgenic Drosophila system could prove more accurate to further validate the function of a specific OR. We also found that, among the different solvents used to dissolve pheromones and odorants, hexane offered good reproducibility and high sensitivity. Finally, the function of ORs was indirectly confirmed in transgenic Drosophila, showing that odor-activation of ORs-expressing olfactory receptor neurons (ORNs) can mediate behavioral choices. In summary, our results compare advantages and drawbacks of different approaches, thus helping in the choice of the method most suitable, in each specific situation, for deorphanizing insect ORs.
Mitigation of soil N2O emission by inoculation with a mixed culture of indigenous Bradyrhizobium diazoefficiens
Authors: Akiyama Hiroko , Hoshino Yuko Takada , Itakura Manabu , Shimomura Yumi , Wang Yong , Yamamoto Akinori , Tago Kanako , Nakajima Yasuhiro , Minamisawa Kiwamu , Hayatsu Masahito 
Published: September 2016

AbstractAgricultural soil is the largest source of nitrous oxide (N2O), a greenhouse gas. Soybean is an important leguminous crop worldwide. Soybean hosts symbiotic nitrogen-fixing soil bacteria (rhizobia) in root nodules. In soybean ecosystems, N2O emissions often increase during decomposition of the root nodules. Our previous study showed that N2O reductase can be used to mitigate N2O emission from soybean fields during nodule decomposition by inoculation with nosZ++ strains [mutants with increased N2O reductase (N2OR) activity] of Bradyrhizobium diazoefficiens. Here, we show that N2O emission can be reduced at the field scale by inoculation with a mixed culture of indigenous nosZ+ strains of B. diazoefficiens USDA110 group isolated from Japanese agricultural fields. Our results also suggested that nodule nitrogen is the main source of N2O production during nodule decomposition. Isolating nosZ+ strains from local soybean fields would be more applicable and feasible for many soybean-producing countries than generating mutants.
Integrated stress response of vertebrates is regulated by four eIF2α kinases
Authors: Taniuchi Shusuke , Miyake Masato , Tsugawa Kazue , Oyadomari Miho , Oyadomari Seiichi 
Published: September 2016

AbstractThe integrated stress response (ISR) is a cytoprotective pathway initiated upon phosphorylation of the eukaryotic translation initiation factor 2 (eIF2α) residue designated serine-51, which is critical for translational control in response to various stress conditions. Four eIF2α kinases, namely heme-regulated inhibitor (HRI), protein kinase R (PKR), PKR-like endoplasmic reticulum kinase, (PERK) and general control non-depressible 2 (GCN2), have been identified thus far, and they are known to be activated by heme depletion, viral infection, endoplasmic reticulum stress, and amino acid starvation, respectively. Because eIF2α is phosphorylated under various stress conditions, the existence of an additional eIF2α kinase has been suggested. To validate the existence of the unidentified eIF2α kinase, we constructed an eIF2α kinase quadruple knockout cells (4KO cells) in which the four known eIF2α kinase genes were deleted using the CRISPR/Cas9-mediated genome editing. Phosphorylation of eIF2α was completely abolished in the 4KO cells by various stress stimulations. Our data suggests that the four known eIF2α kinases are sufficient for ISR and that there are no additional eIF2α kinases in vertebrates.
Genome-wide association analysis reveals variants on chromosome 19 that contribute to childhood risk of chronic otitis media with effusion
Authors: Einarsdottir Elisabet , Hafrén Lena , Leinonen Eira , Bhutta Mahmood F. , Kentala Erna , Kere Juha , Mattila Petri S. 
Published: September 2016

AbstractTo identify genetic risk factors of childhood otitis media (OM), a genome-wide association study was performed on Finnish subjects, 829 affected children, and 2118 randomly selected controls. The most significant and validated finding was an association with an 80 kb region on chromosome 19. It includes the variants rs16974263 (P = 1.77 × 10−7, OR = 1.59), rs268662 (P = 1.564 × 10−6, OR = 1.54), and rs4150992 (P = 3.37 × 10−6, OR = 1.52), and harbors the genes PLD3, SERTAD1, SERTAD3, HIPK4, PRX, and BLVRB, all in strong linkage disequilibrium. In a sub-phenotype analysis of the 512 patients with chronic otitis media with effusion, one marker reached genome-wide significance (rs16974263, P = 2.92 × 10−8). The association to this locus was confirmed but with an association signal in the opposite direction, in a UK family cohort of 4860 subjects (rs16974263, P = 3.21 × 10−4, OR = 0.72; rs4150992, P = 1.62 × 10−4, OR = 0.71). Thus we hypothesize that this region is important for COME risk in both the Finnish and UK populations, although the precise risk variants or haplotype background remain unclear. Our study suggests that the identified region on chromosome 19 includes a novel and previously uncharacterized risk locus for OM.
A diverse virome in kidney transplant patients contains multiple viral subtypes with distinct polymorphisms
Authors: Rani Asha , Ranjan Ravi , McGee Halvor S. , Metwally Ahmed , Hajjiri Zahraa , Brennan Daniel C. , Finn Patricia W. , Perkins David L. 
Published: September 2016

AbstractRecent studies have established that the human urine contains a complex microbiome, including a virome about which little is known. Following immunosuppression in kidney transplant patients, BK polyomavirus (BKV) has been shown to induce nephropathy (BKVN), decreasing graft survival. In this study we investigated the urine virome profile of BKV+ and BKV− kidney transplant recipients. Virus-like particles were stained to confirm the presence of VLP in the urine samples. Metagenomic DNA was purified, and the virome profile was analyzed using metagenomic shotgun sequencing. While the BK virus was predominant in the BKV+ group, it was also found in the BKV− group patients. Additional viruses were also detected in all patients, notably including JC virus (JCV) and Torque teno virus (TTV) and interestingly, we detected multiple subtypes of the BKV, JCV and TTV. Analysis of the BKV subtypes showed that nucleotide polymorphisms were detected in the VP1, VP2 and Large T Antigen proteins, suggesting potential functional effects for enhanced pathogenicity. Our results demonstrate a complex urinary virome in kidney transplant patients with multiple viruses with several distinct subtypes warranting further analysis of virus subtypes in immunosuppressed hosts.
Mechanisms Responsible for the Large Piezoelectricity at the Tetragonal-Orthorhombic Phase Boundary of (1-x)BaZr0.2Ti0.8O3-xBa0.7Ca0.3TiO3 System
Authors: Yang Tao , Ke Xiaoqin , Wang Yunzhi 
Published: September 2016

AbstractRecently it was found that in the lead-free (1-x)BaZr0.2Ti0.8O3-xBa0.7Ca0.3TiO3 (BZT-xBCT) system, the highest piezoelectric d33 coefficient appears at the tetragonal (T) – orthorhombic (O) phase boundary rather than the O – rhombohedral (R) phase boundary, but the physical origin of it is still unclear. In this work we construct the phase diagram of the BZT-xBCT system using a generic sixth-order Landau free energy polynomial and calculate the energy barrier (EB) for direct domain switching between two variants of the stable low-symmetry ferroelectric phase. We find that the EB at the T-O phase boundary is lower than that at the O-R phase boundary and EB may serve as a rigorous quantitative measure of the degree of polarization anisotropy through Landau potential. The calculations may shed some light on the physical origin of the highest piezoelectric coefficients as well as the softest elastic compliance at the T-O phase boundary observed in experiments.
Direct theoretical evidence for weaker correlations in electron-doped and Hg-based hole-doped cuprates
Authors: Jang Seung Woo , Sakakibara Hirofumi , Kino Hiori , Kotani Takao , Kuroki Kazuhiko , Han Myung Joon 
Published: September 2016

AbstractMany important questions for high-Tc cuprates are closely related to the insulating nature of parent compounds. While there has been intensive discussion on this issue, all arguments rely strongly on, or are closely related to, the correlation strength of the materials. Clear understanding has been seriously hampered by the absence of a direct measure of this interaction, traditionally denoted by U. Here, we report a first-principles estimation of U for several different types of cuprates. The U values clearly increase as a function of the inverse bond distance between apical oxygen and copper. Our results show that the electron-doped cuprates are less correlated than their hole-doped counterparts, which supports the Slater picture rather than the Mott picture. Further, the U values significantly vary even among the hole-doped families. The correlation strengths of the Hg-cuprates are noticeably weaker than that of La2CuO4. Our results suggest that the strong correlation enough to induce Mott gap may not be a prerequisite for the high-Tc superconductivity.
An integrative and comparative study of pan-cancer transcriptomes reveals distinct cancer common and specific signatures
Authors: Cao Zhen , Zhang Shihua 
Published: September 2016

AbstractTo investigate the commonalities and specificities across tumor lineages, we perform a systematic pan-cancer transcriptomic study across 6744 specimens. We find six pan-cancer subnetwork signatures which relate to cell cycle, immune response,Sp1regulation, collagen, muscle system and angiogenesis. Moreover, four pan-cancer subnetwork signatures demonstrate strong prognostic potential. We also characterize 16 cancer type-specific subnetwork signatures which show diverse implications to somatic mutations, somatic copy number aberrations, DNA methylation alterations and clinical outcomes. Furthermore, some of them are strongly correlated with histological or molecular subtypes, indicating their implications with tumor heterogeneity. In summary, we systematically explore the pan-cancer common and cancer type-specific gene subnetwork signatures across multiple cancers, and reveal distinct commonalities and specificities among cancers at transcriptomic level.
Long-term exposure to microgravity impairs vestibulo-cardiovascular reflex
Authors: Morita Hironobu , Abe Chikara , Tanaka Kunihiko 
Published: September 2016

AbstractThe vestibular system is known to have an important role in controlling blood pressure upon posture transition (vestibulo-cardiovascular reflex, VCR). However, under a different gravitational environment, the sensitivity of the vestibular system may be altered. Thus, the VCR may become less sensitive after spaceflight because of orthostatic intolerance potentially induced by long-term exposure to microgravity. To test this hypothesis in humans, we investigated the ability of the VCR to maintain blood pressure upon head-up tilt before and after a 4–6 months stay on the International Space Station. To detect the functional state of the VCR, galvanic vestibular stimulation (GVS) was applied. As GVS transiently interrupts the vestibular-mediated pressor response, impaired VCR is detected when the head-up tilt-induced blood pressure response does not depend on GVS. During the first 20 s of head-up tilt, a transient blood pressure increase (11.9 ± 1.6 mmHg) was observed at pre-spaceflight but not at 1–4 days after return from spaceflight. The magnitude of VCR recovered to the pre-spaceflight levels within 2 months after return. These results indicate that long-term exposure to microgravity induces VCR impairment, which may be involved in a mechanism of spaceflight-induced orthostatic intolerance.
Chiral Antioxidant-based Gold Nanoclusters Reprogram DNA Epigenetic Patterns
Authors: Ma Yue , Fu Hualin , Zhang Chunlei , Cheng Shangli , Gao Jie , Wang Zhen , Jin Weilin , Conde João , Cui Daxiang 
Published: September 2016

AbstractEpigenetic modifications sit ‘on top of’ the genome and influence DNA transcription, which can force a significant impact on cellular behavior and phenotype and, consequently human development and disease. Conventional methods for evaluating epigenetic modifications have inherent limitations and, hence, new methods based on nanoscale devices are needed. Here, we found that antioxidant (glutathione) chiral gold nanoclusters induce a decrease of 5-hydroxymethylcytosine (5hmC), which is an important epigenetic marker that associates with gene transcription regulation. This epigenetic change was triggered partially through ROS activation and oxidation generated by the treatment with glutathione chiral gold nanoclusters, which may inhibit the activity of TET proteins catalyzing the conversion of 5-methylcytosine (5mC) to 5hmC. In addition, these chiral gold nanoclusters can downregulate TET1 and TET2 mRNA expression. Alteration of TET-5hmC signaling will then affect several downstream targets and be involved in many aspects of cell behavior. We demonstrate for the first time that antioxidant-based chiral gold nanomaterials have a direct effect on epigenetic process of TET-5hmC pathways and reveal critical DNA demethylation patterns.
The hidden hyperbolic geometry of international trade: World Trade Atlas 1870–2013
Authors: García-Pérez Guillermo , Boguñá Marián , Allard Antoine , Serrano M. Ángeles 
Published: September 2016

AbstractHere, we present the World Trade Atlas 1870–2013, a collection of annual world trade maps in which distance combines economic size and the different dimensions that affect international trade beyond mere geography. Trade distances, based on a gravity model predicting the existence of significant trade channels, are such that the closer countries are in trade space, the greater their chance of becoming connected. The atlas provides us with information regarding the long-term evolution of the international trade system and demonstrates that, in terms of trade, the world is not flat but hyperbolic, as a reflection of its complex architecture. The departure from flatness has been increasing since World War I, meaning that differences in trade distances are growing and trade networks are becoming more hierarchical. Smaller-scale economies are moving away from other countries except for the largest economies; meanwhile those large economies are increasing their chances of becoming connected worldwide. At the same time, Preferential Trade Agreements do not fit in perfectly with natural communities within the trade space and have not necessarily reduced internal trade barriers. We discuss an interpretation in terms of globalization, hierarchization, and localization; three simultaneous forces that shape the international trade system.