bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phase retrieval by coherent modulation imaging
Authors: Zhang Fucai , Chen Bo , Morrison Graeme R. , Vila-Comamala Joan , Guizar-Sicairos Manuel , Robinson Ian K. 
Published: November 2016

AbstractPhase retrieval is a long-standing problem in imaging when only the intensity of the wavefield can be recorded. Coherent diffraction imaging is a lensless technique that uses iterative algorithms to recover amplitude and phase contrast images from diffraction intensity data. For general samples, phase retrieval from a single-diffraction pattern has been an algorithmic and experimental challenge. Here we report a method of phase retrieval that uses a known modulation of the sample exit wave. This coherent modulation imaging method removes inherent ambiguities of coherent diffraction imaging and uses a reliable, rapidly converging iterative algorithm involving three planes. It works for extended samples, does not require tight support for convergence and relaxes dynamic range requirements on the detector. Coherent modulation imaging provides a robust method for imaging in materials and biological science, while its single-shot capability will benefit the investigation of dynamical processes with pulsed sources, such as X-ray free-electron lasers.
Lineage-specific roles of the cytoplasmic polyadenylation factor CPEB4 in the regulation of melanoma drivers
Authors: Pérez-Guijarro Eva , Karras Panagiotis , Cifdaloz Metehan , Martínez-Herranz Raúl , Cañón Estela , Graña Osvaldo , Horcajada-Reales Celia , Alonso-Curbelo Direna , Calvo Tonantzin G. , Gómez-López Gonzalo , Bellora Nicolas , Riveiro-Falkenbach Erica , Ortiz-Romero Pablo L. , Rodríguez-Peralto José L. , Maestre Lorena , Roncador Giovanna , de Agustín Asensio Juan C. , Goding Colin R. , Eyras Eduardo , Megías Diego , Méndez Raúl , Soengas María S. 
Published: November 2016

AbstractNuclear 3’-end-polyadenylation is essential for the transport, stability and translation of virtually all eukaryotic mRNAs. Poly(A) tail extension can also occur in the cytoplasm, but the transcripts involved are incompletely understood, particularly in cancer. Here we identify a lineage-specific requirement of the cytoplasmic polyadenylation binding protein 4 (CPEB4) in malignant melanoma. CPEB4 is upregulated early in melanoma progression, as defined by computational and histological analyses. Melanoma cells are distinct from other tumour cell types in their dependency on CPEB4, not only to prevent mitotic aberrations, but to progress through G1/S cell cycle checkpoints. RNA immunoprecipitation, sequencing of bound transcripts and poly(A) length tests link the melanoma-specific functions of CPEB4 to signalling hubs specifically enriched in this disease. Essential in these CPEB4-controlled networks are the melanoma drivers MITF and RAB7A, a feature validated in clinical biopsies. These results provide new mechanistic links between cytoplasmic polyadenylation and lineage specification in melanoma.
Interplay between past market correlation structure changes and future volatility outbursts
Authors: Musmeci Nicoló , Aste Tomaso , Di Matteo T. 
Published: November 2016

AbstractWe report significant relations between past changes in the market correlation structure and future changes in the market volatility. This relation is made evident by using a measure of “correlation structure persistence” on correlation-based information filtering networks that quantifies the rate of change of the market dependence structure. We also measured changes in the correlation structure by means of a “metacorrelation” that measures a lagged correlation between correlation matrices computed over different time windows. Both methods show a deep interplay between past changes in correlation structure and future changes in volatility and we demonstrate they can anticipate market risk variations and this can be used to better forecast portfolio risk. Notably, these methods overcome the curse of dimensionality that limits the applicability of traditional econometric tools to portfolios made of a large number of assets. We report on forecasting performances and statistical significance of both methods for two different equity datasets. We also identify an optimal region of parameters in terms of True Positive and False Positive trade-off, through a ROC curve analysis. We find that this forecasting method is robust and it outperforms logistic regression predictors based on past volatility only. Moreover the temporal analysis indicates that methods based on correlation structural persistence are able to adapt to abrupt changes in the market, such as financial crises, more rapidly than methods based on past volatility.
Fluorescence- and magnetic-activated cell sorting strategies to separate spermatozoa involving plural contributors from biological mixtures for human identification
Authors: Xu Yan , Xie Jianhui , Chen Ronghua , Cao Yu , Ping Yuan , Xu Qingwen , Hu Wei , Wu Dan , Gu Lihua , Zhou Huaigu , Chen Xin , Zhao Ziqin , Zhong Jiang , Li Rui 
Published: November 2016

AbstractNo effective method has been developed to distinguish sperm cells originating from different men in multi-suspect sexual assault cases. Here we combined MACS and FACS to isolate single donor sperm cells from forensic mixture samples including female vaginal epithelial cells and sperm cells from multiple contributors. Sperms from vaginal swab were isolated by MACS using FITC-conjugated A kinase anchor protein 3 (AKAP3) antibody; target individual sperm cells involving two or three donors were separated by FACS using FITC-labeled blood group A/B antigen antibody. This procedure was further tested in two mock multi-suspect sexual assault samples and one practical casework sample. Our results showed that complete single donor STR profiles could be successfully obtained from sperm/epithelial cell and sperm mixtures from two contributors. For unbalanced sperm/epithelial cells and sperm cells mixtures, sensitivity results revealed that target cells could be detected at as low as 1:32 and 1:8 mixed ratios, respectively. Although highly relies on cell number and blood types or secretor status of the individuals, this procedure would still be useful tools for forensic DNA analysis of multi-suspect sexual assault cases by the combined use of FACS and MACS based on sperm-specific AKAP3 antigen and human blood type antigen.
miRNAsong: a web-based tool for generation and testing of miRNA sponge constructs in silico
Authors: Barta Tomas , Peskova Lucie , Hampl Ales 
Published: November 2016

AbstractMicroRNA (miRNA) sponges are RNA transcripts containing multiple high-affinity binding sites that associate with and sequester specific miRNAs to prevent them from interacting with their target messenger (m)RNAs. Due to the high specificity of miRNA sponges and strong inhibition of target miRNAs, these molecules have become increasingly applied in miRNA loss-of-function studies. However, improperly designed sponge constructs may sequester off-target miRNAs; thus, it has become increasingly important to develop a tool for miRNA sponge construct design and testing. In this study, we introducemicroRNA spongegenerator and tester (miRNAsong), a freely available web-based tool for generation andin silicotesting of miRNA sponges. This tool generates miRNA sponge constructs for specific miRNAs and miRNA families/clusters and tests them for potential binding to miRNAs in selected organisms. Currently, miRNAsong allows for testing of sponge constructs in 219 species covering 35,828 miRNA sequences. Furthermore, we also provide an example, supplemented with experimental data, of how to use this tool. Using miRNAsong, we designed and tested a sponge for miR-145 inhibition, and cloned the sequence into an inducible lentiviral vector. We found that established cell lines expressing miR-145 sponge strongly inhibited miR-145, thus demonstrating the usability of miRNAsong tool for sponge generation. URL:http://www.med.muni.cz/histology/miRNAsong/.
Genomic contributors to atrial electroanatomical remodeling and atrial fibrillation progression: Pathway enrichment analysis of GWAS data
Authors: Husser Daniela , Ueberham Laura , Dinov Borislav , Kosiuk Jedrzej , Kornej Jelena , Hindricks Gerhard , Shoemaker M. Benjamin , Roden Dan M. , Bollmann Andreas , Büttner Petra 
Published: November 2016

AbstractIn atrial fibrillation (AF), left atrial diameter (LAD) and low voltage area (LVA) are intermediate phenotypes that are associated with AF type and progression. In this study, we tested the hypothesis, that these phenotypes share common, genetically-determined pathways using pathway enrichment analysis of GWAS data. Samples from 660 patients with paroxysmal (n = 370) or persistent AF (n = 290) were genotyped for ~1,000,000 SNPs. SNPs found significantly associated with LAD, LVA or AF type were used for gene-based association tests in a systematic biological Knowledge-based mining system for Genome-wide Genetic studies (KGG). Associated genes were tested for pathway enrichment using two enrichment tools (WebGestalt and GATHER) and the databases provided by Kyoto Encyclopedia of Genes and Genomes. The calcium signaling pathway (hsa04020) was the only pathway that reached statistical significance for LAD and LVA in both enrichment tools and was also significantly associated with AF type. Within this pathway, there were 39 genes (i.e. CACNA1C, RyR2) that were associated with LAD, LVA and AF type. In conclusion, there is a genomic contribution to electroanatomical remodeling (LAD, LVA) and AF type via the calcium signaling pathway. Future and larger studies are necessary to replicate and apply these findings.
Gene expression profiling of breast cancer in Lebanese women
Authors: Makoukji Joelle , Makhoul Nadine J. , Khalil Maya , El-Sitt Sally , Aldin Ehab Saad , Jabbour Mark , Boulos Fouad , Gadaleta Emanuela , Sangaralingam Ajanthah , Chelala Claude , Boustany Rose-Mary , Tfayli Arafat 
Published: November 2016

AbstractBreast cancer is commonest cancer in women worldwide. Elucidation of underlying biology and molecular pathways is necessary for improving therapeutic options and clinical outcomes. Molecular alterations in breast cancer are complex and involve cross-talk between multiple signaling pathways. The aim of this study is to extract a unique mRNA fingerprint of breast cancer in Lebanese women using microarray technologies. Gene-expression profiles of 94 fresh breast tissue samples (84 cancerous/10 non-tumor adjacent samples) were analyzed using GeneChip Human Genome U133 Plus 2.0 arrays. Quantitative real-time PCR was employed to validate candidate genes. Differentially expressed genes between breast cancer and non-tumor tissues were screened. Significant differences in gene expression were established for COL11A1/COL10A1/MMP1/COL6A6/DLK1/S100P/CXCL11/SOX11/LEP/ADIPOQ/OXTR/FOSL1/ACSBG1 and C21orf37. Pathways/diseases representing these genes were retrieved and linked using PANTHER®/Pathway Studio®. Many of the deregulated genes are associated with extracellular matrix, inflammation, angiogenesis, metastasis, differentiation, cell proliferation and tumorigenesis. Characteristics of breast cancers in Lebanese were compared to those of women from Western populations to explain why breast cancer is more aggressive and presents a decade earlier in Lebanese victims. Delineating molecular mechanisms of breast cancer in Lebanese women led to key genes which could serve as potential biomarkers and/or novel drug targets for breast cancer.
Significant Phylogenetic Signal and Climate-Related Trends in Leaf Caloric Value from Tropical to Cold-Temperate Forests
Authors: Song Guangyan , Li Ying , Zhang Jiahui , Li Meiling , Hou Jihua , He Nianpeng 
Published: November 2016

AbstractLeaf caloric value (LCV) is a useful index to represent the conversion efficiency of leaves for solar energy. We investigated the spatial pattern of LCV and explored the factors (phylogeny, climate, and soil) that influence them at a large scale by determining LCV standardized by leaf area in 920 plant species from nine forest communities along the 3700 km North-South Transect of Eastern China. LCV ranged from 0.024 to 1.056 kJ cm−2 with an average of 0.151 kJ cm−2. LCV declined linearly with increasing latitude along the transect. Altogether, 57.29% of the total variation in LCV was explained by phylogenetic group (44.03% of variation), climate (1.27%), soil (0.02%) and their interacting effects. Significant phylogenetic signals in LCV were observed not only within forest communities but also across the whole transect. This phylogenetic signal was higher at higher latitudes, reflecting latitudinal change in the species composition of forest communities from complex to simple. We inferred that climate influences the spatial pattern of LCV through directly regulating the species composition of plant communities, since most plant species might tolerate only a limited temperature range. Our findings provide new insights into the adaptive mechanisms in plant traits in future studies.
Generalised monogamy relation of convex-roof extended negativity in multi-level systems
Authors: Tian Tian , Luo Yu , Li Yongming 
Published: November 2016

AbstractIn this paper, we investigate the generalised monogamy inequalities of convex-roof extended negativity (CREN) in multi-level systems. The generalised monogamy inequalities provide the upper and lower bounds of bipartite entanglement, which are obtained by using CREN and the CREN of assistance (CRENOA). Furthermore, we show that the CREN of multi-qubit pure states satisfies some monogamy relations. Additionally, we test the generalised monogamy inequalities for qudits by considering the partially coherent superposition of a generalised W-class state in a vacuum and show that the generalised monogamy inequalities are satisfied in this case as well.
Managing peatland vegetation for drinking water treatment
Authors: Ritson Jonathan P. , Bell Michael , Brazier Richard E. , Grand-Clement Emilie , Graham Nigel J. D. , Freeman Chris , Smith David , Templeton Michael R. , Clark Joanna M. 
Published: November 2016

AbstractPeatland ecosystem services include drinking water provision, flood mitigation, habitat provision and carbon sequestration. Dissolved organic carbon (DOC) removal is a key treatment process for the supply of potable water downstream from peat-dominated catchments. A transition from peat-forming Sphagnum moss to vascular plants has been observed in peatlands degraded by (a) land management, (b) atmospheric deposition and (c) climate change. Here within we show that the presence of vascular plants with higher annual above-ground biomass production leads to a seasonal addition of labile plant material into the peatland ecosystem as litter recalcitrance is lower. The net effect will be a smaller litter carbon pool due to higher rates of decomposition, and a greater seasonal pattern of DOC flux. Conventional water treatment involving coagulation-flocculation-sedimentation may be impeded by vascular plant-derived DOC. It has been shown that vascular plant-derived DOC is more difficult to remove via these methods than DOC derived from Sphagnum, whilst also being less susceptible to microbial mineralisation before reaching the treatment works. These results provide evidence that practices aimed at re-establishing Sphagnum moss on degraded peatlands could reduce costs and improve efficacy at water treatment works, offering an alternative to ‘end-of-pipe’ solutions through management of ecosystem service provision.
Endotoxemia contributes to CD27+ memory B-cell apoptosis via enhanced sensitivity to Fas ligation in patients with Cirrhosis
Authors: Chang Li-Yuan , Li Yonghai , Kaplan David E. 
Published: November 2016

AbstractPeripheral CD27+ memory B-cells become quantitatively reduced and dysfunctional in patients with cirrhosis through poorly characterized mechanisms. We hypothesized that the disappearance of CD27+ memory B-cells results from enhanced sensitivity to apoptosis caused by exposure to gut microbial translocation products. Using isolated naïve and memory B-cells from patients with cirrhosis and age-matched controls, ex vivo and activation-induced sensitivity to Fas-mediated apoptosis was assessed under relevant experimental conditions. We observed differential expression of CD95(Fas) in CD27+ B-cells from cirrhotic patients that was inversely correlated with peripheral CD27+ B-cell frequency. While memory B-cells from cirrhotic patients were resistant to Fas-mediated apoptosis ex vivo, Toll-like receptor 4(TLR4)-ligation restored Fas-sensitivity. Sensitivity to Fas-mediated apoptosis could be transferred to healthy donor memory B-cells by co-culturing these cells with plasma from cirrhotic patients, a sensitivity partially mediated by Fas and TLR4 signaling, and partially rescued via B-cell receptor crosslinking. We conclude that peripheral CD27+ memory B-cells in cirrhosis exhibit increased sensitivity to Fas-induced apoptosis in an activation-dependent manner to which endotoxin contributes, associated with reduced frequency of circulating memory B-cells. Destruction of this critical cell subset may contribute to the cirrhotic immunodeficiency state and heightened risk of systemic infections in advanced liver disease.
Dramatic undercutting of piedmont rivers after the 2008 Wenchuan Ms 8.0 Earthquake
Authors: Fan Niannian , Nie Ruihua , Wang Qiang , Liu Xingnian 
Published: November 2016

AbstractChanges in river channel erosion or deposition affect the geomorphic evolution, aquatic ecosystems, and river regulation strategies. Fluvial processes are determined by the flow, sediment and boundary conditions, and it has long been expected that increasing sediment supply will induce aggradation. Here, based on thorough field surveys, we show the unexpected undercutting of the piedmont rivers influenced by the 2008 Wenchuan (Ms 8.0) Earthquake. The rivers flow from the Longmen Mountain with significant topographic relief to the flat Chengdu plain. In the upstreams, sediment supply increased because of the landslides triggered by the earthquake, causing deposition in the upstream mountain reaches. However, the downstream plain reaches suffered undercutting instead of deposition, and among those rivers, Shiting River was the most seriously affected, with the largest undercutting depth exceeding 20 m. The reasons for this unexpected undercutting are proposed herein and relate to both natural and anthropogenic causes. In addition, we also demonstrate, at least for certain conditions, such as rivers flowing from large-gradient mountain regions to low-gradient plain regions, that upstream sediment pulses may induce aggradation in upstream and degradation in downstream, causing the longitudinal profile to steepen to accommodate the increasing sediment flux.
Stent revascularization versus bypass surgery for peripheral artery disease in type 2 diabetic patients – an instrumental variable analysis
Authors: Chang Chia-Hsuin , Lin Jou-Wei , Hsu Jiun , Wu Li-Chiu , Lai Mei-Shu 
Published: November 2016

AbstractThe objective of this study was to use instrumental variable (IV) analyses to evaluate the clinical effectiveness of percutaneous stent revascularization versus bypass surgery in the treatment of peripheral artery disease (PAD) among type 2 diabetic patients. Type 2 diabetic patients who received peripheral artery bypass surgery (n = 5,652) or stent revascularization (n = 659) for lower extremity arterial stenosis between 2000 and 2007 were identified from the Taiwan National Health Insurance claims database. Patients were followed from the date of index hospitalization for 2 years for lower-extremity amputation, revascularization, and hospitalization for medical treatment. Analysis using treatment year, patients’ monthly income level, and regional difference as IVs were conducted to reduce unobserved treatment selection bias. The crude analysis showed a statistically significant risk reduction in favor of stent placement in lower extremity amputation and in the composite endpoint of amputation, revascularization, or hospitalization for medical treatment. However, peripheral artery stent revascularization and bypass surgery had similar risk of lower limb amputation and composite endpoints in the analyses using calendar year or patients’ monthly income level as IVs. These two treatment modalities had similar risk of lower limb amputation among DM patients with PAD.
Laser controlled atom source for optical clocks
Authors: Kock Ole , He Wei , Świerad Dariusz , Smith Lyndsie , Hughes Joshua , Bongs Kai , Singh Yeshpal 
Published: November 2016

AbstractPrecision timekeeping has been a driving force in innovation, from defining agricultural seasons to atomic clocks enabling satellite navigation, broadband communication and high-speed trading. We are on the verge of a revolution in atomic timekeeping, where optical clocks promise an over thousand-fold improvement in stability and accuracy. However, complex setups and sensitivity to thermal radiation pose limitations to progress. Here we report on an atom source for a strontium optical lattice clock which circumvents these limitations. We demonstrate fast (sub 100 ms), cold and controlled emission of strontium atomic vapours from bulk strontium oxide irradiated by a simple low power diode laser. Our results demonstrate that millions of strontium atoms from the vapour can be captured in a magneto-optical trap (MOT). Our method enables over an order of magnitude reduction in scale of the apparatus. Future applications range from satellite clocks testing general relativity to portable clocks for inertial navigation systems and relativistic geodesy.
Giant frequency down-conversion of the dancing acoustic bubble
Authors: Deymier P. A. , Keswani M. , Jenkins N. , Tang C. , Runge K. 
Published: November 2016

AbstractWe have demonstrated experimentally the existence of a giant frequency down-conversion of the translational oscillatory motion of individual submillimeter acoustic bubbles in water in the presence of a high frequency (500 kHz) ultrasonic standing wave. The frequency of the translational oscillations (~170 Hz) is more than three orders of magnitude smaller than that of the driving acoustic wave. We elucidate the mechanism of this very slow oscillation with an analytical model leading to an equation of translational motion of a bubble taking the form of Mathieu’s equation. This equation illuminates the origin of the giant down conversion in frequency as arising from an unstable equilibrium. We also show that bubbles that form chains along the direction of the acoustic standing wave due to radiation interaction forces exhibit also translation oscillations that form a spectral band. This band extends approximately from 130 Hz up to nearly 370 Hz, a frequency range that is still at least three orders of magnitude lower than the frequency of the driving acoustic wave.