bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cross-depth analysis of marine bacterial networks suggests downward propagation of temporal changes
Authors: Cram Jacob A , Xia Li C , Needham David M , Sachdeva Rohan , Sun Fengzhu , Fuhrman Jed A 
Published: May 2015

Abstract
Interactions among microbes and stratification across depths are both believed to be important drivers of microbial communities, though little is known about how microbial associations differ between and across depths. We have monitored the free-living microbial community at the San Pedro Ocean Time-series station, monthly, for a decade, at five different depths: 5 m, the deep chlorophyll maximum layer, 150 m, 500 m and 890 m (just above the sea floor). Here, we introduce microbial association networks that combine data from multiple ocean depths to investigate both within- and between-depth relationships, sometimes time-lagged, among microbes and environmental parameters. The euphotic zone, deep chlorophyll maximum and 890 m depth each contain two negatively correlated ‘modules’ (groups of many inter-correlated bacteria and environmental conditions) suggesting regular transitions between two contrasting environmental states. Two-thirds of pairwise correlations of bacterial taxa between depths lagged such that changes in the abundance of deeper organisms followed changes in shallower organisms. Taken in conjunction with previous observations of seasonality at 890 m, these trends suggest that planktonic microbial communities throughout the water column are linked to environmental conditions and/or microbial communities in overlying waters. Poorly understood groups including Marine Group A, Nitrospina and AEGEAN-169 clades contained taxa that showed diverse association patterns, suggesting these groups contain multiple ecological species, each shaped by different factors, which we have started to delineate. These observations build upon previous work at this location, lending further credence to the hypothesis that sinking particles and vertically migrating animals transport materials that significantly shape the time-varying patterns of microbial community composition.
Long-term soil transplant simulating climate change with latitude significantly alters microbial temporal turnover
Authors: Liang Yuting , Jiang Yuji , Wang Feng , Wen Chongqing , Deng Ye , Xue Kai , Qin Yujia , Yang Yunfeng , Wu Liyou , Zhou Jizhong , Sun Bo 
Published: May 2015

Abstract
To understand soil microbial community stability and temporal turnover in response to climate change, a long-term soil transplant experiment was conducted in three agricultural experiment stations over large transects from a warm temperate zone (Fengqiu station in central China) to a subtropical zone (Yingtan station in southern China) and a cold temperate zone (Hailun station in northern China). Annual soil samples were collected from these three stations from 2005 to 2011, and microbial communities were analyzed by sequencing microbial 16S ribosomal RNA gene amplicons using Illumina MiSeq technology. Our results revealed a distinctly differential pattern of microbial communities in both northward and southward transplantations, along with an increase in microbial richness with climate cooling and a corresponding decrease with climate warming. The microbial succession rate was estimated by the slope (w value) of linear regression of a log-transformed microbial community similarity with time (time–decay relationship). Compared with the low turnover rate of microbial communities in situ (w=0.046, P&lt;0.001), the succession rate at the community level was significantly higher in the northward transplant (w=0.058, P&lt;0.001) and highest in the southward transplant (w=0.094, P&lt;0.001). Climate warming lead to a faster succession rate of microbial communities as well as lower species richness and compositional changes compared with in situ and climate cooling, which may be related to the high metabolic rates and intense competition under higher temperature. This study provides new insights into the impacts of climate change on the fundamental temporal scaling of soil microbial communities and microbial phylogenetic biodiversity.
Targeted DNA degradation using a CRISPR device stably carried in the host genome
Authors: Caliando Brian J. , Voigt Christopher A. 
Published: May 2015

AbstractOnce an engineered organism completes its task, it is useful to degrade the associated DNA to reduce environmental release and protect intellectual property. Here we present a genetically encoded device (DNAi) that responds to a transcriptional input and degrades user-defined DNA. This enables engineered regions to be obscured when the cell enters a new environment. DNAi is based on type-IE CRISPR biochemistry and a synthetic CRISPR array defines the DNA target(s). When the input is on, plasmid DNA is degraded 108-fold. When the genome is targeted, this causes cell death, reducing viable cells by a factor of 108. Further, the CRISPR nuclease can direct degradation to specific genomic regions (for example, engineered or inserted DNA), which could be used to complicate recovery and sequencing efforts. DNAi can be stably carried in an engineered organism, with no impact on cell growth, plasmid stability or DNAi inducibility even after passaging for >2 months.
C8orf4 negatively regulates self-renewal of liver cancer stem cells via suppression of NOTCH2 signalling
Authors: Zhu Pingping , Wang Yanying , Du Ying , He Lei , Huang Guanling , Zhang Geng , Yan Xinlong , Fan Zusen 
Published: May 2015

AbstractLiver cancer stem cells (CSCs) harbour self-renewal and differentiation properties, accounting for chemotherapy resistance and recurrence. However, the molecular mechanisms to sustain liver CSCs remain largely unknown. In this study, based on analysis of several hepatocellular carcinoma (HCC) transcriptome datasets and our experimental data, we find that C8orf4 is weakly expressed in HCC tumours and liver CSCs. C8orf4 attenuates the self-renewal capacity of liver CSCs and tumour propagation. We show that NOTCH2 is activated in liver CSCs. C8orf4 is located in the cytoplasm of HCC tumour cells and associates with the NOTCH2 intracellular domain, which impedes the nuclear translocation of N2ICD. C8orf4 deletion causes the nuclear translocation of N2ICD that triggers the NOTCH2 signalling, which sustains the stemness of liver CSCs. Finally, NOTCH2 activation levels are consistent with clinical severity and prognosis of HCC patients. Altogether, C8orf4 negatively regulates the self-renewal of liver CSCs via suppression of NOTCH2 signalling.
The production of information in the attention economy
Authors: Ciampaglia Giovanni Luca , Flammini Alessandro , Menczer Filippo 
Published: May 2015

AbstractOnline traces of human activity offer novel opportunities to study the dynamics of complex knowledge exchange networks, in particular how emergent patterns of collective attention determine what new information is generated and consumed. Can we measure the relationship between demand and supply for new information about a topic? We propose a normalization method to compare attention bursts statistics across topics with heterogeneous distribution of attention. Through analysis of a massive dataset on traffic to Wikipedia, we find that the production of new knowledge is associated to significant shifts of collective attention, which we take as proxy for its demand. This is consistent with a scenario in which allocation of attention toward a topic stimulates the demand for information about it and in turn the supply of further novel information. However, attention spikes only for a limited time span, during which new content has higher chances of receiving traffic, compared to content created later or earlier on. Our attempt to quantify demand and supply of information and our finding about their temporal ordering, may lead to the development of the fundamental laws of the attention economy and to a better understanding of social exchange of knowledge information networks.
Structure of Slitrk2–PTPδ complex reveals mechanisms for splicing-dependent trans-synaptic adhesion
Authors: Yamagata Atsushi , Sato Yusuke , Goto-Ito Sakurako , Uemura Takeshi , Maeda Asami , Shiroshima Tomoko , Yoshida Tomoyuki , Fukai Shuya 
Published: May 2015

AbstractSelective binding between pre- and postsynaptic adhesion molecules can induce synaptic differentiation. Here we report the crystal structure of a synaptogenic trans-synaptic adhesion complex between Slit and Trk-like family member 2 (Slitrk2) and receptor protein tyrosine phosphatase (RPTP) δ. The structure and site-directed mutational analysis revealed the structural basis of splicing-dependent adhesion between Slitrks and type IIa RPTPs for inducing synaptic differentiation.
In Vivo Two-Photon Imaging of Axonal Dieback, Blood Flow and Calcium Influx withMethylprednisolone Therapy after Spinal Cord Injury
Authors: Tang Peifu , Zhang Yiling , Chen Chao , Ji Xinran , Ju Furong , Liu Xingyu , Gan Wen-Biao , He Zhigang , Zhang Shengxiang , Li Wei , Zhang Lihai 
Published: May 2015

AbstractSevere spinal cord injury (SCI) can cause neurological dysfunction and paralysis.However, the early dynamic changes of neurons and their surrounding environmentafter SCI are poorly understood. Although methylprednisolone (MP) is currently thestandard therapeutic agent for treating SCI, its efficacy remains controversial. Thepurpose of this project was to investigate the early dynamic changes andMP's efficacy on axonal damage, blood flow and calcium influx into axonsin a mouse SCI model. YFP H-line and Thy1-GCaMP transgenic mice were used in thisstudy. Two-photon microscopy was used for imaging of axonal dieback, blood flow, andcalcium influx post-injury. We found that MP treatment attenuated progressive damageof axons, increased blood flow and reduced calcium influx post-injury. Furthermore,microglia/macrophages accumulated in the lesion site after SCI and expressed theproinflammatory mediators iNOS, MCP-1 and IL-1β. MP treatment markedlyinhibited the accumulation of microglia/macrophages and reduced the expression ofthe proinflammatory mediators. MP treatment also improved the recovery of behavioralfunction post-injury. These findings suggest that MP exerts a neuroprotective effecton SCI treatment by attenuating progressive damage of axons, increasing blood flow,reducing calcium influx and inhibiting the accumulation of microglia/macrophagesafter SCI.
Do deposit-feeders compete? Isotopic niche analysis of an invasion in a species-poor system
Authors: Karlson Agnes M. L. , Gorokhova Elena , Elmgren Ragnar 
Published: May 2015

AbstractSuccessful establishment of invasive species is often related to the existence of vacant niches. Competition occurs when invaders use the same limiting resources as members of the recipient community, which will be reflected in some overlap of their trophic niches. The concept of isotopic niche has been used to study trophic niche partitioning among species. Here, we present a two-year field study comparing isotopic niches of the deposit-feeding community in a naturally species-poor system. The isotopic niche analyses showed no overlap between a recent polychaete invader and any of the native species suggesting that it has occupied a vacant niche. Its narrow isotopic niche suggests specialized feeding, however, the high δ15N values compared to natives are most likely due to isotope fractionation effects related to nitrogen recycling and a mismatch between biological stoichiometry of the polychaete and the sediment nitrogen content. Notably, highly overlapping isotopic niches were inferred for the native species, which is surprising in a food-limited system. Therefore, our results demonstrate that invaders may broaden the community trophic diversity and enhance resource utilization, but also raise questions about the congruence between trophic and isotopic niche concepts and call for careful examination of assumptions underlying isotopic niche interpretation.
Enhanced emission of charged-exciton polaritons from colloidal quantum dots on a SiN/SiO2 slab waveguide
Authors: Xu Xingsheng , Li Xingyun 
Published: May 2015

AbstractWe investigate the photoluminescence (PL) spectra and the time-resolved PL decay process from colloidal quantum dots on SiN/SiO2 wet etched via BOE (HF:NH4F:H2O). The spectrum displays multi-peak shapes that vary with irradiation time. The evolution of the spectral peaks with irradiation time and collection angle demonstrates that the strong coupling of the charged-exciton emission to the leaky modes of the SiN/SiO2 slab waveguide predominantly produces short-wavelength spectral peaks, resulting in multi-peak spectra. We conclude that BOE etching enhances the charged-exciton emission efficiency and its contribution to the total emission compared with the unetched case. BOE etching smoothes the electron confinement potential, thus decreasing the Auger recombination rate. Therefore, the charged-exciton emission efficiency is high and the charged-exciton-polariton emission can be further enhanced through strong coupling to the leaky mode of the slab waveguide.
Triplex real-time PCR–an improved method to detect a wide spectrum of mitochondrial DNA deletions in single cells
Authors: Rygiel Karolina A. , Grady John P. , Taylor Robert W. , Tuppen Helen A. L. , Turnbull Doug M. 
Published: May 2015

AbstractMitochondrial DNA (mtDNA) mutations are commonly found in the skeletal muscle of patients with mitochondrial disease, inflammatory myopathies and sarcopenia. The majority of these mutations are mtDNA deletions, which accumulate to high levels in individual muscle fibres causing a respiratory defect. Most mtDNA deletions are major arc deletions with breakpoints located between the origin of light strand (OL) and heavy strand (OH) replication within the major arc. However, under certain disease conditions, rarer, minor arc deletions are detected. Currently, there are few techniques which would allow the detection and quantification of both types of mtDNA deletions in single muscle fibres. We have designed a novel triplex real-time PCR assay which simultaneously amplifies the MT-ND4 gene in the major arc, the MT-ND1 gene in the minor arc and the non-coding D-Loop region. We demonstrate that this assay is a highly sensitive and reliable tool for the detection and quantification of a broad range of major and minor arc mtDNA deletions with the potential to investigate the molecular pathogenesis in both research and diagnostic settings.
New ambuic acid derivatives from the solid culture of Pestalotiopsis neglecta and their nitric oxide inhibitory activity
Authors: Qi Qiu-Yue , Li Er-Wei , Han Jun-Jie , Pei Yun-Fei , Ma Ke , Bao Li , Huang Ying , Zhao Feng , Liu Hong-Wei 
Published: May 2015

AbstractFour new ambuic acid derivatives (1–4) and four known derivatives (5–8), were isolated from the solid culture of a plant pathogenic fungus Pestalotiopsis neglecta. Their structures were elucidated by extensive NMR experiments. The absolute configuration of the C-16 secondary alcohol in 1 was deduced via the CD data of the in situ formed [Rh2(OCOCF3)4] complex with the acetonide derivative of 1. The absolute configuration in 3 was assigned by comparison of the experimental and simulated electronic circular dichroism (ECD) spectrum. The NMR data of compound 5 was reported for the first time. In the nitric oxide (NO) inhibition assay, compounds 4, 6 and 7 showed inhibitory activity against the NO production in the lipopolysaccharide (LPS)-induced macrophage with IC50 values of 88.66, 11.20 and 20.80 µM, respectively.
PALM-IST: Pathway Assembly from Literature Mining - an Information Search Tool
Authors: Mandloi Sapan , Chakrabarti Saikat 
Published: May 2015

AbstractManual curation of biomedical literature has become extremely tedious process due to its exponential growth in recent years. To extract meaningful information from such large and unstructured text, newer and more efficient mining tool is required. Here, we introduce PALM-IST, a computational platform that not only allows users to explore biomedical abstracts using keyword based text mining but also extracts biological entity (e.g., gene/protein, drug, disease, biological processes, cellular component, etc.) information from the extracted text and subsequently mines various databases to provide their comprehensive inter-relation (e.g., interaction, expression, etc.). PALM-IST constructs protein interaction network and pathway information data relevant to the text search using multiple data mining tools and assembles them to create a meta-interaction network. It also analyzes scientific collaboration by extraction and creation of “co-authorship network,” for a given search context. Hence, this useful combination of literature and data mining provided in PALM-IST can be used to extract novel protein-protein interaction (PPI), to generate meta-pathways and further to identify key crosstalk and bottleneck proteins. PALM-IST is available at www.hpppi.iicb.res.in/ctm.
Punitive preferences, monetary incentives and tacit coordination in the punishment of defectors promote cooperation in humans
Authors: Diekmann Andreas , Przepiorka Wojtek 
Published: May 2015

AbstractPeer-punishment is effective in promoting cooperation, but the costs associated with punishing defectors often exceed the benefits for the group. It has been argued that centralized punishment institutions can overcome the detrimental effects of peer-punishment. However, this argument presupposes the existence of a legitimate authority and leaves an unresolved gap in the transition from peer-punishment to centralized punishment. Here we show that the origins of centralized punishment could lie in individuals’ distinct ability to punish defectors. In our laboratory experiment, we vary the structure of the punishment situation to disentangle the effects of punitive preferences, monetary incentives and individual punishment costs on the punishment of defectors. We find that actors tacitly coordinate on the strongest group member to punish defectors, even if the strongest individual incurs a net loss from punishment. Such coordination leads to a more effective and more efficient provision of a cooperative environment than we observe in groups of all equals. Our results show that even an arbitrary assignment of an individual to a focal position in the social hierarchy can trigger the endogenous emergence of more centralized forms of punishment.
Action observation: mirroring across our spontaneous movement tempo
Authors: Avanzino Laura , Lagravinese Giovanna , Bisio Ambra , Perasso Luisa , Ruggeri Piero , Bove Marco 
Published: May 2015

AbstractDuring action observation (AO), the activity of the “mirror system” is influenced by the viewer’s expertise in the observed action. A question that remains open is whether the temporal aspects of the subjective motor repertoire can influence the “mirror system” activation.
15-year incidence of diabetic ketoacidosis at onset of type 1 diabetes in children from a regional setting (Auckland, New Zealand)
Authors: Jefferies Craig , Cutfield Samuel W. , Derraik José G. B. , Bhagvandas Jignal , Albert Benjamin B. , Hofman Paul L. , Gunn Alistair J. , Cutfield Wayne S. 
Published: May 2015

AbstractWe assessed the incidence of diabetic ketoacidosis (DKA) in children aged <15 years with newly diagnosed type 1 diabetes mellitus (T1DM) in the Auckland Region (New Zealand) in 1999–2013, in a retrospective review of a complete regional cohort. DKA and its severity were classified according to ISPAD 2014 guidelines. Of 730 children presenting with new-onset T1DM over the 15-year time period, 195 cases had DKA of any severity (27%). There was no change in the incidence of DKA or the proportion of children with severe DKA at presentation. The incidence of DKA among children aged <2.0 years (n = 40) was 53% compared to 25% for those aged 2–14 years (n = 690; p = 0.005). In children aged 2–14 years, increasing age at diagnosis was associated with greater likelihood of DKA at presentation (p = 0.025), with the odds of DKA increasing 1.06 times with each year increase in age. Non-Europeans were more likely to present in DKA than New Zealand Europeans (OR 1.52; p = 0.048). Despite a consistent secular trend of increasing incidence of T1DM, there was no reduction in the incidence of DKA in new-onset T1DM in the Auckland Region over time. Thus, it is important to explore ways to reduce DKA risk.
Hydrothermally Grown In-doped ZnO Nanorods on p-GaN Films for Color-tunable Heterojunction Light-emitting-diodes
Authors: Park Geun Chul , Hwang Soo Min , Lee Seung Muk , Choi Jun Hyuk , Song Keun Man , Kim Hyun You , Kim Hyun-Suk , Eum Sung-Jin , Jung Seung-Boo , Lim Jun Hyung , Joo Jinho 
Published: May 2015

AbstractThe incorporation of doping elements in ZnO nanostructures plays an important role in adjusting the optical and electrical properties in optoelectronic devices. In the present study, we fabricated 1-D ZnO nanorods (NRs) doped with different In contents (0% ~ 5%) on p-GaN films using a facile hydrothermal method and investigated the effect of the In doping on the morphology and electronic structure of the NRs and the electrical and optical performances of the n-ZnO NRs/p-GaN heterojunction light emitting diodes (LEDs). As the In content increased, the size (diameter and length) of the NRs increased and the electrical performance of the LEDs improved. From the electroluminescence (EL) spectra, it was found that the broad green-yellow-orange emission band significantly increased with increasing In content due to the increased defect states (oxygen vacancies) in the ZnO NRs and consequently, the superposition of the emission bands centered at 415 nm and 570 nm led to the generation of white-light. These results suggest that In doping is an effective way to tailor the morphology and the optical, electronic and electrical properties of ZnO NRs, as well as the EL emission property of heterojunction LEDs.
A high-performance white-light-emitting-diodes based on nano-single crystal divanadates quantum dots
Authors: Yang Weiqing , Liu Zhongli , Chen Jun , Huang Li , Zhang Lei , Pan Hong , Wu Bo , Lin Yuan 
Published: May 2015

AbstractWe report a high-performance phosphors-free white light-emitting-diodes (w-LEDs) using Ba2V2O7 or Sr2V2O7 quantum dots that directly heteroepitaxially grown on common quartz substrates by polymer assisted deposition (PAD). The quantum efficiency of quantum dots is as high as 95%. More importantly, electronic local functions, band structure and partial density of states have been firstly calculated to study the luminescent and heteroepitaxial growth mechanisms by the Ab-initio Simulation. Additionally, the glaring white light excited at a wavelength of 325 nm was experimentally observed, which unambiguously demonstrated that such quantum dots can be efficient w-LEDs for solid state lighting.
The autism-associated gene chromodomain helicase DNA-binding protein 8 (CHD8) regulates noncoding RNAs and autism-related genes
Authors: Wilkinson B , Grepo N , Thompson B L , Kim J , Wang K , Evgrafov O V , Lu W , Knowles J A , Campbell D B 
Published: May 2015

AbstractChromodomain helicase DNA-binding protein 8 (CHD8) was identified as a leading autism spectrum disorder (ASD) candidate gene by whole-exome sequencing and subsequent targeted-sequencing studies. De novo loss-of-function mutations were identified in 12 individuals with ASD and zero controls, accounting for a highly significant association. Small interfering RNA-mediated knockdown of CHD8 in human neural progenitor cells followed by RNA sequencing revealed that CHD8 insufficiency results in altered expression of 1715 genes, including both protein-coding and noncoding RNAs. Among the 10 most changed transcripts, 4 (40%) were noncoding RNAs. The transcriptional changes among protein-coding genes involved a highly interconnected network of genes that are enriched in neuronal development and in previously identified ASD candidate genes. These results suggest that CHD8 insufficiency may be a central hub in neuronal development and ASD risk.