bluuebunny/crossref_metadata_2025_split huggingface dataset:
Involvement of PARP1 in the regulation of alternative splicing
Authors: Matveeva Elena , Maiorano John , Zhang Qingyang , Eteleeb Abdallah M , Convertini Paolo , Chen Jing , Infantino Vittoria , Stamm Stefan , Wang Jiping , Rouchka Eric C , Fondufe-Mittendorf Yvonne N 
Published: February 2016

AbstractSpecialized chromatin structures such as nucleosomes with specific histone modifications decorate exons in eukaryotic genomes, suggesting a functional connection between chromatin organization and the regulation of pre-mRNA splicing. Through profiling the functional location of Poly (ADP) ribose polymerase, we observed that it is associated with the nucleosomes at exon/intron boundaries of specific genes, suggestive of a role for this enzyme in alternative splicing. Poly (ADP) ribose polymerase has previously been implicated in the PARylation of splicing factors as well as regulation of the histone modification H3K4me3, a mark critical for co-transcriptional splicing. In light of these studies, we hypothesized that interaction of the chromatin-modifying factor, Poly (ADP) ribose polymerase with nucleosomal structures at exon–intron boundaries, might regulate pre-mRNA splicing. Using genome-wide approaches validated by gene-specific assays, we show that depletion of PARP1 or inhibition of its PARylation activity results in changes in alternative splicing of a specific subset of genes. Furthermore, we observed that PARP1 bound to RNA, splicing factors and chromatin, suggesting that Poly (ADP) ribose polymerase serves as a gene regulatory hub to facilitate co-transcriptional splicing. These studies add another function to the multi-functional protein, Poly (ADP) ribose polymerase, and provide a platform for further investigation of this protein’s function in organizing chromatin during gene regulatory processes.
Thermal and quantum depletion of superconductivity in narrow junctions created by controlled electromigration
Authors: Baumans Xavier D. A. , Cerbu Dorin , Adami Obaïd-Allah , Zharinov Vyacheslav S. , Verellen Niels , Papari Gianpaolo , Scheerder Jeroen E. , Zhang Gufei , Moshchalkov Victor V. , Silhanek Alejandro V. , Van de Vondel Joris 
Published: February 2016

AbstractSuperconducting nanowires currently attract great interest due to their application in single-photon detectors and quantum-computing circuits. In this context, it is of fundamental importance to understand the detrimental fluctuations of the superconducting order parameter as the wire width shrinks. In this paper, we use controlled electromigration to narrow down aluminium nanoconstrictions. We demonstrate that a transition from thermally assisted phase slips to quantum phase slips takes place when the cross section becomes less than ∼150 nm2. In the regime dominated by quantum phase slips the nanowire loses its capacity to carry current without dissipation, even at the lowest possible temperature. We also show that the constrictions exhibit a negative magnetoresistance at low-magnetic fields, which can be attributed to the suppression of superconductivity in the contact leads. These findings reveal perspectives of the proposed fabrication method for exploring various fascinating superconducting phenomena in atomic-size contacts.
Near-island biological hotspots in barren ocean basins
Authors: Gove Jamison M. , McManus Margaret A. , Neuheimer Anna B. , Polovina Jeffrey J. , Drazen Jeffrey C. , Smith Craig R. , Merrifield Mark A. , Friedlander Alan M. , Ehses Julia S. , Young Charles W. , Dillon Amanda K. , Williams Gareth J. 
Published: February 2016

AbstractPhytoplankton production drives marine ecosystem trophic-structure and global fisheries yields. Phytoplankton biomass is particularly influential near coral reef islands and atolls that span the oligotrophic tropical oceans. The paradoxical enhancement in phytoplankton near an island-reef ecosystem—Island Mass Effect (IME)—was first documented 60 years ago, yet much remains unknown about the prevalence and drivers of this ecologically important phenomenon. Here we provide the first basin-scale investigation of IME. We show that IME is a near-ubiquitous feature among a majority (91%) of coral reef ecosystems surveyed, creating near-island ‘hotspots’ of phytoplankton biomass throughout the upper water column. Variations in IME strength are governed by geomorphic type (atoll vs island), bathymetric slope, reef area and local human impacts (for example, human-derived nutrient input). These ocean oases increase nearshore phytoplankton biomass by up to 86% over oceanic conditions, providing basal energetic resources to higher trophic levels that support subsistence-based human populations.
Negative global phosphorus budgets challenge sustainable intensification of grasslands
Authors: Sattari S. Z. , Bouwman A. F. , Martinez Rodríguez R. , Beusen A. H. W. , van Ittersum M. K. 
Published: February 2016

AbstractGrasslands provide grass and fodder to sustain the growing need for ruminant meat and milk. Soil nutrients in grasslands are removed through withdrawal in these livestock products and through animal manure that originates from grasslands and is spread in croplands. This leads to loss of soil fertility, because globally most grasslands receive no mineral fertilizer. Here we show that phosphorus (P) inputs (mineral and organic) in global grasslands will have to increase more than fourfold in 2050 relative to 2005 to achieve an anticipated 80% increase in grass production (for milk and meat), while maintaining the soil P status. Combined with requirements for cropland, we estimate that mineral P fertilizer use must double by 2050 to sustain future crop and grassland production. Our findings point to the need to better understand the role of grasslands and their soil P status and their importance for global food security.
Spatiotemporal patterns of population in mainland China, 1990 to 2010
Authors: Gaughan Andrea E. , Stevens Forrest R. , Huang Zhuojie , Nieves Jeremiah J. , Sorichetta Alessandro , Lai Shengjie , Ye Xinyue , Linard Catherine , Hornby Graeme M. , Hay Simon I. , Yu Hongjie , Tatem Andrew J. 
Published: February 2016

AbstractAccording to UN forecasts, global population will increase to over 8 billion by 2025, with much of this anticipated population growth expected in urban areas. In China, the scale of urbanization has, and continues to be, unprecedented in terms of magnitude and rate of change. Since the late 1970s, the percentage of Chinese living in urban areas increased from ~18% to over 50%. To quantify these patterns spatially we use time-invariant or temporally-explicit data, including census data for 1990, 2000, and 2010 in an ensemble prediction model. Resulting multi-temporal, gridded population datasets are unique in terms of granularity and extent, providing fine-scale (~100 m) patterns of population distribution for mainland China. For consistency purposes, the Tibet Autonomous Region, Taiwan, and the islands in the South China Sea were excluded. The statistical model and considerations for temporally comparable maps are described, along with the resulting datasets. Final, mainland China population maps for 1990, 2000, and 2010 are freely available as products from the WorldPop Project website and the WorldPop Dataverse Repository.
Transcriptome regulation and chromatin occupancy by E2F3 and MYC in mice
Authors: Tang Xing , Liu Huayang , Srivastava Arunima , Pécot Thierry , Chen Zhong , Wang Qianben , Huang Kun , Sáenz-Robles Maria Teresa , Cantalupo Paul , Pipas James , Leone Gustavo 
Published: February 2016

AbstractE2F3 and MYC are transcription factors that control cellular proliferation. To study their mechanism of action in the context of a regenerating tissue, we isolated both proliferating (crypts) and non-dividing (villi) cells from wild-type and Rb depleted small intestines of mice and performed ChIP-exo-seq (chromatin immunoprecipitation combined with lambda exonuclease digestion followed by high-throughput sequencing). The genome-wide chromatin occupancy of E2F3 and MYC was determined by mapping sequence reads to the genome and predicting preferred binding sites (peaks). Binding sites could be accurately identified within small regions of only 24 bp-28 bp long, highlighting the precision to which binding peaks can be identified by ChIP-exo-seq. Forty randomly selected E2F3- and MYC-specific binding sites were validated by ChIP-PCR. In addition, we also presented gene expression data sets from wild type, Rb-, E2f3- and Myc-depleted crypts and villi within this manuscript. These represent comprehensive and validated datasets that can be integrated to identify putative direct targets of E2F3 and MYC involved in the control of cellular proliferation in normal and Rb-deficient small intestines.
Associations of Plasma FGF2 Levels and Polymorphisms in the FGF2 Gene with Obesity Phenotypes in Han Chinese Population
Authors: Hao Ruo-Han , Guo Yan , Dong Shan-Shan , Weng Gai-Zhi , Yan Han , Zhu Dong-Li , Chen Xiao-Feng , Chen Jia-Bin , Yang Tie-Lin 
Published: February 2016

AbstractObesity is highly heritable, but the specific genes influencing obesity related traits are largely unknown. Fibroblast growth factor 2 (FGF2) could influence adipocyte differentiation. However, the association of FGF2 polymorphisms and obesity remains unclear. This study aimed to investigate the associations of both the plasma FGF2 levels and SNPs in FGF2 gene with obesity phenotypes in Han Chinese populations. Plasma FGF2 levels were measured and subjected to association analyses in 62 subjects. Eleven SNPs in FGF2 were genotyped and tested for associations in a discovery sample of 1,300 subjects. SNPs significantly associated with obesity were subjected to replication in another independent sample of 1,035 subjects. We found that plasma FGF2 levels were positively correlated with fat mass (P = 0.010). Association analyses in the discovery sample identified three SNPs (rs1449683, rs167428, rs308442) significantly associated with fat mass after multiple testing adjustments (P < 0.0045). Subsequent replication study successfully validated one SNP (rs167428) associated with fat mass (Pcombine = 3.46 × 10−5). eQTL analyses revealed that SNPs associated with obesity also affected FGF2 expression. Our findings suggested that high plasma FGF2 level correlated with increased risk of obesity and FGF2 gene polymorphisms could affect individual variances of obesity in Han Chinese population.
Phenotypic and functional alterations of pDCs in lupus-prone mice
Authors: Zhou Zhenyuan , Ma Jianyang , Xiao Chunyuan , Han Xiao , Qiu Rong , Wang Yan , Zhou Yingying , Wu Li , Huang Xinfang , Shen Nan 
Published: February 2016

AbstractPlasmacytoid dendritic cells (pDCs) were considered to be the major IFNα source in systemic lupus erythematosus (SLE) but their phenotype and function in different disease status have not been well studied. To study the function and phenotype of pDCs in lupus-prone mice we used 7 strains of lupus-prone mice including NZB/W F1, NZB, NZW, NZM2410, B6.NZMSle1/2/3, MRL/lpr and BXSB/Mp mice and C57BL/6 as control mice. Increased spleen pDC numbers were found in most lupus mice compared to C57BL/6 mice. The IFNα-producing ability of BM pDCs was similar between lupus and C57BL/6 mice, whereas pDCs from the spleens of NZB/W F1 and NZB mice produced more IFNα than pDCs from the spleens of C57BL/6 mice. Furthermore, spleen pDCs from MRL-lpr and NZM2410 mice showed increased responses to Tlr7 and Tlr9, respectively. As the disease progressed, IFN signature were evaluated in both BM and spleen pDC from lupus prone mice and the number of BM pDCs and their ability to produce IFNα gradually decreased in lupus-prone mice. In conclusion, pDC are activated alone with disease development and its phenotype and function differ among lupus-prone strains and these differences may contribute to the development of lupus in these mice.
The heterogeneous energy landscape expression of KWW relaxation
Authors: Wu J. H. , Jia Q. 
Published: February 2016

AbstractHere we show a heterogeneous energy landscape approach to describing the Kohlrausch-Williams-Watts (KWW) relaxation function. For a homogeneous dynamic process, the distribution of free energy landscape is first proposed, revealing the significance of rugged fluctuations. In view of the heterogeneous relaxation given in two dynamic phases and the transmission coefficient in a rate process, we obtain a general characteristic relaxation time distribution equation for the KWW function in a closed, analytic form. Analyses of numerical computation show excellent accuracy, both in time and frequency domains, in the convergent performance of the heterogeneous energy landscape expression and shunning the catastrophic truncations reported in the previous work. The stretched exponential β, closely associated to temperature and apparent correlation with one dynamic phase, reveals a threshold value of 1/2 defining different behavior of the probability density functions. Our work may contribute, for example, to in-depth comprehension of the dynamic mechanism of glass transition, which cannot be provided by existing approaches.
Ab initio molecular dynamics simulation of the effects of stacking faults on the radiation response of 3C-SiC
Authors: Jiang M. , Peng S. M. , Zhang H. B. , Xu C. H. , Xiao H. Y. , Zhao F. A. , Liu Z. J. , Zu X. T. 
Published: February 2016

AbstractIn this study, an ab initio molecular dynamics method is employed to investigate how the existence of stacking faults (SFs) influences the response of SiC to low energy irradiation. It reveals that the C and Si atoms around the SFs are generally more difficult to be displaced than those in unfaulted SiC, and the corresponding threshold displacement energies for them are generally larger, indicative of enhanced radiation tolerance caused by the introduction of SFs, which agrees well with the recent experiment. As compared with the unfaulted state, more localized point defects are generated in faulted SiC. Also, the efficiency of damage production for Si recoils is generally higher than that of C recoils. The calculated potential energy increases for defect generation in SiC with intrinsic and extrinsic SFs are found to be higher than those in unfaulted SiC, due to the stronger screen-Coulomb interaction between the PKA and its neighbors. The presented results provide a fundamental insight into the underlying mechanism of displacement events in faulted SiC and will help to advance the understanding of the radiation response of SiC with and without SFs.
Albuminuria, Cerebrovascular Disease and Cortical Atrophy: among Cognitively Normal Elderly Individuals
Authors: Cho Eun Bin , Shin Hee-Young , Park Sang Eon , Chun Phillip , Jang Hye Ryoun , Yang Jin-ju , Kim Hee Jin , Kim Yeo Jin , Jung Na-Yeon , Lee Jin San , Lee Juyoun , Jang Young Kyoung , Jang Eun Young , Kang Mira , Lee Jong-Min , Kim Changsoo , Min Ju-Hong , Ryu Seungho , Na Duk L. , Seo Sang Won 
Published: February 2016

AbstractWe tested the hypothesis that decreased glomerular filtration rate and albuminuria have different roles in brain structure alterations. We enrolled 1,215 cognitively normal individuals, all of whom underwent high-resolution T1-weighted volumetric magnetic resonance imaging scans. The cerebral small vessel disease burdens were assessed with white matter hyperintensities (WMH), lacunes, and microbleeds. Subjects were considered to have an abnormally elevated urine albumin creatinine ratio if the value was ≥17 mg/g for men and ≥25 mg/g for women. Albuminuria, but not estimated glomerular filtration rate (eGFR), was associated with increased WMH burdens (p = 0.002). The data was analyzed after adjusting for age, sex, education, history of hypertension, diabetes mellitus, hyperlipidemia, ischemic heart disease, stroke, total cholesterol level, body mass index, status of smoking and alcohol drinking, and intracranial volume. Albuminuria was also associated with cortical thinning, predominantly in the frontal and occipital regions (both p < 0.01) in multiple linear regression analysis. However, eGFR was not associated with cortical thickness. Furthermore, path analysis for cortical thickness showed that albuminuria was associated with frontal thinning partially mediated by WMH burdens. The assessment of albuminuria is needed to improve our ability to identify individuals with high risk for cognitive impairments, and further institute appropriate preventive measures.
Nanoscale optical interferometry with incoherent light
Authors: Li Dongfang , Feng Jing , Pacifici Domenico 
Published: February 2016

AbstractOptical interferometry has empowered an impressive variety of biosensing and medical imaging techniques. A widely held assumption is that devices based on optical interferometry require coherent light to generate a precise optical signature in response to an analyte. Here we disprove that assumption. By directly embedding light emitters into subwavelength cavities of plasmonic interferometers, we demonstrate coherent generation of surface plasmons even when light with extremely low degrees of spatial and temporal coherence is employed. This surprising finding enables novel sensor designs with cheaper and smaller light sources and consequently increases accessibility to a variety of analytes, such as biomarkers in physiological fluids, or even airborne nanoparticles. Furthermore, these nanosensors can now be arranged along open detection surfaces and in dense arrays, accelerating the rate of parallel target screening used in drug discovery, among other high volume and high sensitivity applications.
Diagnostic Accuracy of Transcranial Sonography of the Substantia Nigra in Parkinson’s disease: A Systematic Review and Meta-analysis
Authors: Li Dun-Hui , He Ya-Chao , Liu Jun , Chen Sheng-Di 
Published: February 2016

AbstractA large number of articles have reported substantia nigra hyperechogenicity in Parkinson’s disease (PD) and have assessed the diagnostic accuracy of transcranial sonography (TCS); however, the conclusions are discrepant. Consequently, this systematic review and meta-analysis aims to consolidate the available observational studies and provide a comprehensive evaluation of the clinical utility of TCS in PD. Totally, 31 studies containing 4,386 participants from 13 countries were included. A random effects model was utilized to pool the effect sizes. Meta-regression and sensitivity analysis were performed to explore potential heterogeneity. Overall diagnostic accuracy of TCS in differentiating PD from normal controls was quite high, with a pooled sensitivity of 0.83 (95% CI: 0.81–0.85) and a pooled specificity of 0.87 (95% CI: 0.85–0.88). The positive likelihood ratio, the negative likelihood ratio and diagnostic odds ratio were calculated 6.94 (95% CI: 5.09–9.48), 0.19 (95% CI: 0.16–0.23) and 42.89 (95% CI: 30.03–61.25) respectively. Our systematic review of the literature and meta-analysis suggest that TCS has high diagnostic accuracy in the diagnosis of PD when compared to healthy control.
Post-illumination activity of SnO2 nanoparticle-decorated Cu2O nanocubes by H2O2 production in dark from photocatalytic “memory”
Authors: Liu Lingmei , Sun Wuzhu , Yang Weiyi , Li Qi , Shang Jian Ku 
Published: February 2016

AbstractMost photocatalysts only function under illumination, while many potential applications require continuous activities in dark. Thus, novel photocatalysts should be developed, which could store part of their photoactivity in “memory” under illumination and then be active from this “memory” after the illumination is turned off for an extended period of time. Here a novel composite photocatalyst of SnO2 nanoparticle-decorated Cu2O nanocubes is developed. Their large conduction band potential difference and the inner electrostatic field formed in the p-n heterojunction provide a strong driving force for photogenerated electrons to move from Cu2O to SnO2 under visible light illumination, which could then be released to react with O2 in dark to produce H2O2 for its post-illumination activity. This work demonstrates that the selection of decoration components for photocatalysts with the post-illumination photocatalytic “memory” could be largely expanded to semiconductors with conduction band potentials less positive than the two-electron reduction potential of O2.
Local electron-electron interaction strength in ferromagnetic nickel determined by spin-polarized positron annihilation
Authors: Ceeh Hubert , Weber Josef Andreas , Böni Peter , Leitner Michael , Benea Diana , Chioncel Liviu , Ebert Hubert , Minár Jan , Vollhardt Dieter , Hugenschmidt Christoph 
Published: February 2016

AbstractWe employ a positron annihilation technique, the spin-polarized two-dimensional angular correlation of annihilation radiation (2D-ACAR), to measure the spin-difference spectra of ferromagnetic nickel. The experimental data are compared with the theoretical results obtained within a combination of the local spin density approximation (LSDA) and the many-body dynamical mean-field theory (DMFT). We find that the self-energy defining the electronic correlations in Ni leads to anisotropic contributions to the momentum distribution. By direct comparison of the theoretical and experimental results we determine the strength of the local electronic interaction U in ferromagnetic Ni as 2.0 ± 0.1 eV.
Whole genome resequencing of the human parasite Schistosoma mansoni reveals population history and effects of selection
Authors: Crellen Thomas , Allan Fiona , David Sophia , Durrant Caroline , Huckvale Thomas , Holroyd Nancy , Emery Aidan M. , Rollinson David , Aanensen David M. , Berriman Matthew , Webster Joanne P. , Cotton James A. 
Published: February 2016

AbstractSchistosoma mansoniis a parasitic fluke that infects millions of people in the developing world. This study presents the first application of population genomics toS. mansonibased on high-coverage resequencing data from 10 global isolates and an isolate of the closely-relatedSchistosoma rodhaini, which infects rodents. Using population genetic tests, we document genes under directional and balancing selection inS. mansonithat may facilitate adaptation to the human host. Coalescence modeling reveals the speciation ofS. mansoniandS. rodhainias 107.5–147.6KYA, a period which overlaps with the earliest archaeological evidence for fishing in Africa. Our results indicate thatS. mansonioriginated in East Africa and experienced a decline in effective population size 20–90KYA, before dispersing across the continent during the Holocene. In addition, we find strong evidence thatS. mansonimigrated to the New World with the 16–19thCentury Atlantic Slave Trade.