bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microfluidic cytometric analysis of cancer cell transportability and invasiveness
Authors: Liu Zongbin , Lee Yeonju , Jang Joon hee , Li Ying , Han Xin , Yokoi Kenji , Ferrari Mauro , Zhou Ledu , Qin Lidong 
Published: September 2015

AbstractThe extensive phenotypic and functional heterogeneity of cancer cells plays an important role in tumor progression and therapeutic resistance. Characterizing this heterogeneity and identifying invasive phenotype may provide possibility to improve chemotherapy treatment. By mimicking cancer cell perfusion through circulatory system in metastasis, we develop a unique microfluidic cytometry (MC) platform to separate cancer cells at high throughput and further derive a physical parameter ‘transportability’ to characterize the ability to pass through micro-constrictions. The transportability is determined by cell stiffness and cell-surface frictional property and can be used to probe tumor heterogeneity, discriminate more invasive phenotypes and correlate with biomarker expressions in breast cancer cells. Decreased cell stiffness and cell-surface frictional force leads to an increase in transportability and may be a feature of invasive cancer cells by promoting cell perfusion through narrow spaces in circulatory system. The MC-Chip provides a promising microfluidic platform for studying cell mechanics and transportability could be used as a novel marker for probing tumor heterogeneity and determining invasive phenotypes.
Dynamic expression of chromatin modifiers during developmental transitions in mouse preimplantation embryos
Authors: Nestorov Peter , Hotz Hans-Rudolf , Liu Zichuan , Peters Antoine H.F.M. 
Published: September 2015

AbstractDuring mouse preimplantation development, major changes in cell fate are accompanied by extensive alterations of gene expression programs. Embryos first transition from a maternal to zygotic program and subsequently specify the pluripotent and the trophectodermal cell lineages. These processes are regulated by key transcription factors, likely in cooperation with chromatin modifiers that control histone and DNA methylation. To characterize the spatiotemporal expression of chromatin modifiers in relation to developmental transitions, we performed gene expression profiling of 156 genes in individual oocytes and single blastomeres of developing mouse embryos until the blastocyst stage. More than half of the chromatin modifiers displayed either maternal or zygotic expression. We also detected lineage-specific expression of several modifiers, including Ezh1, Prdm14, Scmh1 and Tet1 underscoring possible roles in cell fate decisions. Members of the SET-domain containing SMYD family showed differential gene expression during preimplantation development. We further observed co-expression of genes with opposing biochemical activities, such as histone methyltransferases and demethylases, suggesting the existence of a dynamic chromatin steady-state during preimplantation development.
Crystal structure of Streptococcus pneumoniae pneumolysin provides key insights into early steps of pore formation
Authors: Lawrence Sara L. , Feil Susanne C. , Morton Craig J. , Farrand Allison J. , Mulhern Terrence D. , Gorman Michael A. , Wade Kristin R. , Tweten Rodney K. , Parker Michael W. 
Published: September 2015

AbstractPore-forming proteins are weapons often used by bacterial pathogens to breach the membrane barrier of target cells. Despite their critical role in infection important structural aspects of the mechanism of how these proteins assemble into pores remain unknown. Streptococcus pneumoniae is the world’s leading cause of pneumonia, meningitis, bacteremia and otitis media. Pneumolysin (PLY) is a major virulence factor of S. pneumoniae and a target for both small molecule drug development and vaccines. PLY is a member of the cholesterol-dependent cytolysins (CDCs), a family of pore-forming toxins that form gigantic pores in cell membranes. Here we present the structure of PLY determined by X-ray crystallography and, in solution, by small-angle X-ray scattering. The crystal structure reveals PLY assembles as a linear oligomer that provides key structural insights into the poorly understood early monomer-monomer interactions of CDCs at the membrane surface.
Promoting the Adsorption of Metal Ions on Kaolinite by Defect Sites: A Molecular Dynamics Study
Authors: Li Xiong , Li Hang , Yang Gang 
Published: September 2015

AbstractDefect sites exist abundantly in minerals and play a crucial role for a variety of important processes. Here molecular dynamics simulations are used to comprehensively investigate the adsorption behaviors, stabilities and mechanisms of metal ions on defective minerals, considering different ionic concentrations, defect sizes and contents. Outer-sphere adsorbed Pb2+ ions predominate for all models (regular and defective), while inner-sphere Na+ ions, which exist sporadically only at concentrated solutions for regular models, govern the adsorption for all defective models. Adsorption quantities and stabilities of metal ions on kaolinite are fundamentally promoted by defect sites, thus explaining the experimental observations. Defect sites improve the stabilities of both inner- and outer-sphere adsorption and (quasi) inner-sphere Pb2+ ions emerge only at defect sites that reinforce the interactions. Adsorption configurations are greatly altered by defect sites but respond weakly by changing defect sizes or contents. Both adsorption quantities and stabilities are enhanced by increasing defect sizes or contents, while ionic concentrations mainly affect adsorption quantities. We also find that adsorption of metal ions and anions can be promoted by each other and proceeds in a collaborative mechanism. Results thus obtained are beneficial to comprehend related processes for all types of minerals.
High Confidence Fission Yeast SUMO Conjugates Identified by Tandem Denaturing Affinity Purification
Authors: Nie Minghua , Vashisht Ajay A. , Wohlschlegel James A. , Boddy Michael N. 
Published: September 2015

AbstractCovalent attachment of the small ubiquitin-like modifier (SUMO) to key targets in the proteome critically regulates the evolutionarily conserved processes of cell cycle control, transcription, DNA replication and maintenance of genome stability. The proteome-wide identification of SUMO conjugates in budding yeast has been invaluable in helping to define roles of SUMO in these processes. Like budding yeast, fission yeast is an important and popular model organism; however, the fission yeast Schizosaccharomyces pombe community currently lacks proteome-wide knowledge of SUMO pathway targets. To begin to address this deficiency, we adapted and used a highly stringent Tandem Denaturing Affinity Purification (TDAP) method, coupled with mass spectrometry, to identify fission yeast SUMO conjugates. Comparison of our data with that compiled in budding yeast reveals conservation of SUMO target enrichment in nuclear and chromatin-associated processes. Moreover, the SUMO “cloud” phenomenon, whereby multiple components of a single protein complex are SUMOylated, is also conserved. Overall, SUMO TDAP provides both a key resource of high confidence SUMO-modified target proteins in fission yeast and a robust method for future analyses of SUMO function.
Modulation of the optical transmittance in monolayer graphene oxide by using external electric field
Authors: Qiao Zhixing , Qin Chengbing , Gao Yan , Zhang Guofeng , Chen Ruiyun , Xiao Liantuan , Jia Suotang 
Published: September 2015

AbstractGraphene oxide (GO) emerges as a functional material in optoelectronic devices due to its broad spectrum response and abundant optical properties. In this article, it is demonstrated that the change of optical transmittance amplitude for monolayer GO (mGO) could be up to 24.8% by an external electric field. The frequency harmonics for transmittance spectra are analyzed by use of Fast Fourier Transforms to give an insight into the modulation mechanism. Two physical models, the electrical permittivity and the sheet conductivity which linearly vary as the electric field, are proposed to response for the transmittance modulation. The model-based simulations agree reasonable well with the experimental results.
Latitudinal variation of leaf stomatal traits from species to community level in forests: linkage with ecosystem productivity
Authors: Wang Ruili , Yu Guirui , He Nianpeng , Wang Qiufeng , Zhao Ning , Xu Zhiwei , Ge Jianping 
Published: September 2015

AbstractTo explore the latitudinal variation of stomatal traits from species to community level and their linkage with net primary productivity (NPP), we investigated leaf stomatal density (SDL) and stomatal length (SLL) across 760 species from nine forest ecosystems in eastern China and calculated the community-level SD (SDC) and SL (SLC) through species-specific leaf area index (LAI). Our results showed that latitudinal variation in species-level SDL and SLL was minimal, but community-level SDC and SLC decreased clearly with increasing latitude. The relationship between SD and SL was negative across species and different plant functional types (PFTs), but positive at the community level. Furthermore, community-level SDC correlated positively with forest NPP and explained 51% of the variation in NPP. These findings indicate that the trade-off by regulating SDL and SLL may be an important strategy for plant individuals to adapt to environmental changes and temperature acts as the main factor influencing community-level stomatal traits through alteration of species composition. Importantly, our findings provide new insight into the relationship between plant traits and ecosystem function.
Properties of Transmission and Leaky Modes in a Plasmonic Waveguide Constructed by Periodic Subwavelength Metallic Hollow Blocks
Authors: Jei Wu Jin , Jang Wu Chien , Qi Shen Jian , Hou Da Jun , Chen Lo Wen 
Published: September 2015

AbstractBased on the concept of low-frequency spoof surface plasmon polaritons (spoof SPPs), a kind of leaky mode is proposed in a waveguide made of a subwavelength metal-block array with open slots. Numerical results reveal that a new transmission mode is found in the periodic subwavelength metal open blocks. This modal field is located inside the interior of a hollow block compared with that in a solid metal block array. The dispersion curve shows that such a new SPPs mode has a negative slope, crossing the light line and then going into a zone of leaky mode at higher frequencies. The leaky mode has a wider frequency bandwidth and this can lead to a radiation scanning angle of 53° together with high radiation efficiency. Based on the individual characteristics exhibited by a frequency-dependent radiation pattern for the present leaky mode, the waveguide structure can have potential applications such as frequency dividers and demultiplexers. Experimental verification of such a leaky mode at microwave has been performed and the experimental results are found to be consistent with the theoretical analysis.
Enhancement of Chiroptical Signals by Circular Differential Mie Scattering of Nanoparticles
Authors: Yoo SeokJae , Park Q-Han 
Published: September 2015

AbstractWe enhance the weak optical signals of small chiral molecules via circular differential Mie scattering (CDMS) of nanoparticles immersed in them. CDMS is the preferential Mie scattering of left- and right-handed circularly polarized light by nanoparticles whose sizes are about the same as the wavelength of light. Solving the Mie scattering theory for chiral media, we find that the CDMS signal of the particle is linearly proportional to the chirality parameter κ of the molecules. This linear amplitude enhancement by CDMS of the particle holds, even for large particles, which have a retardation effect. We also demonstrate that the CDMS of a nanoparticle is sensitive to changes of molecular concentration and that the nanoparticle can be utilized as a chiroptical biosensor detecting the concentration of analyte. We expect that the enhancement of molecular chiroptical signals by CDMS will pave the way for novel chiroptical spectroscopy using nanostructures.
Auxenochlorella protothecoides and Prototheca wickerhamii plastid genome sequences give insight into the origins of non-photosynthetic algae
Authors: Yan Dong , Wang Yun , Murakami Tatsuya , Shen Yue , Gong Jianhui , Jiang Huifeng , Smith David R. , Pombert Jean-Francois , Dai Junbiao , Wu Qingyu 
Published: September 2015

AbstractThe forfeiting of photosynthetic capabilities has occurred independently many times throughout eukaryotic evolution. But almost all non-photosynthetic plants and algae still retain a colorless plastid and an associated genome, which performs fundamental processes apart from photosynthesis. Unfortunately, little is known about the forces leading to photosynthetic loss; this is largely because there is a lack of data from transitional species. Here, we compare the plastid genomes of two “transitional” green algae: the photosynthetic, mixotrophicAuxenochlorella protothecoidesand the non-photosynthetic, obligate heterotrophPrototheca wickerhamii. Remarkably, the plastid genome ofA. protothecoidesis only slightly larger than that ofP. wickerhamii, making it among the smallest plastid genomes yet observed from photosynthetic green algae. Even more surprising, both algae have almost identical plastid genomic architectures and gene compositions (with the exception of genes involved in photosynthesis), implying that they are closely related. This close relationship was further supported by phylogenetic and substitution rate analyses, which suggest that the lineages giving rise toA. protothecoidesandP. wickerhamiidiverged from one another around six million years ago.
The heptad repeat region is a major selection target in MERS-CoV and related coronaviruses
Authors: Forni Diego , Filippi Giulia , Cagliani Rachele , De Gioia Luca , Pozzoli Uberto , Al-Daghri Nasser , Clerici Mario , Sironi Manuela 
Published: September 2015

AbstractMiddle East respiratory syndrome coronavirus (MERS-CoV) originated in bats and spread to humans via zoonotic transmission from camels. We analyzed the evolution of the spike (S) gene in betacoronaviruses (betaCoVs) isolated from different mammals, in bat coronavirus populations, as well as in MERS-CoV strains from the current outbreak. Results indicated several positively selected sites located in the region comprising the two heptad repeats (HR1 and HR2) and their linker. Two sites (R652 and V1060) were positively selected in the betaCoVs phylogeny and correspond to mutations associated with expanded host range in other coronaviruses. During the most recent evolution of MERS-CoV, adaptive mutations in the HR1 (Q/R/H1020) arose in camels or in a previous host and spread to humans. We determined that different residues at position 1020 establish distinct inter- and intra-helical interactions and affect the stability of the six-helix bundle formed by the HRs. A similar effect on stability was observed for a nearby mutation (T1015N) that increases MERS-CoV infection efficiency in vitro. Data herein indicate that the heptad repeat region was a major target of adaptive evolution in MERS-CoV-related viruses; these results are relevant for the design of fusion inhibitor peptides with antiviral function.
Optofluidic analysis system for amplification-free, direct detection of Ebola infection
Authors: Cai H. , Parks J. W. , Wall T. A. , Stott M. A. , Stambaugh A. , Alfson K. , Griffiths A. , Mathies R. A. , Carrion R. , Patterson J. L. , Hawkins A. R. , Schmidt H. 
Published: September 2015

AbstractThe massive outbreak of highly lethal Ebola hemorrhagic fever in West Africa illustrates the urgent need for diagnostic instruments that can identify and quantify infections rapidly, accurately and with low complexity. Here, we report on-chip sample preparation, amplification-free detection and quantification of Ebola virus on clinical samples using hybrid optofluidic integration. Sample preparation and target preconcentration are implemented on a PDMS-based microfluidic chip (automaton), followed by single nucleic acid fluorescence detection in liquid-core optical waveguides on a silicon chip in under ten minutes. We demonstrate excellent specificity, a limit of detection of 0.2 pfu/mL and a dynamic range of thirteen orders of magnitude, far outperforming other amplification-free methods. This chip-scale approach and reduced complexity compared to gold standard RT-PCR methods is ideal for portable instruments that can provide immediate diagnosis and continued monitoring of infectious diseases at the point-of-care.
Molecular portraits revealing the heterogeneity of breast tumor subtypes defined using immunohistochemistry markers
Authors: Dai Xiaofeng , Li Yang , Bai Zhonghu , Tang Xu-Qing 
Published: September 2015

AbstractBreast cancer is highly heterogeneous. The subtypes defined using immunohistochemistry markers and gene expression profilings (GEP) are related but not equivalent, with inter-connections under investigated. Our previous study revealed a set of differentially expressed genes (diff-genes), containing 1015 mRNAs and 69 miRNAs, which characterize the immunohistochemistry-defined breast tumor subtypes at the GEP level. However, they may convey redundant information due to the large amount of genes included. By reducing the dimension of the diff-genes, we identified 119 mRNAs and 20 miRNAs best explaining breast tumor heterogeneity with the most succinct number of genes found using hierarchical clustering and nearest-to-center principle. The final signature panel contains 119 mRNAs, whose superiority over diff-genes was replicated in two independent public datasets. The comparison of our signature with two pioneering signatures, the Sorlie’s signature and PAM50, suggests a novel marker, FOXA1, in breast cancer classification. Subtype-specific feature genes are reported to characterize each immunohistochemistry-defined subgroup. Pathway and network analysis reveal the critical roles of Notch signalings in [ER+|PR+]HER2− and cell cycle in [ER+|PR+]HER2+ tumors. Our study reveals the primary differences among the four immunohistochemistry-defined breast tumors at the mRNA and miRNA levels and proposes a novel signature for breast tumor subtyping given GEP data.
Many Atolls May be Uninhabitable Within Decades Due to Climate Change
Authors: Storlazzi Curt D. , Elias Edwin P.L. , Berkowitz Paul 
Published: September 2015

AbstractObservations show global sea level is rising due to climate change, with the highest rates in the tropical Pacific Ocean where many of the world’s low-lying atolls are located. Sea-level rise is particularly critical for low-lying carbonate reef-lined atoll islands; these islands have limited land and water available for human habitation, water and food sources and ecosystems that are vulnerable to inundation from sea-level rise. Here we demonstrate that sea-level rise will result in larger waves and higher wave-driven water levels along atoll islands’ shorelines than at present. Numerical model results reveal waves will synergistically interact with sea-level rise, causing twice as much land forecast to be flooded for a given value of sea-level rise than currently predicted by current models that do not take wave-driven water levels into account. Atolls with islands close to the shallow reef crest are more likely to be subjected to greater wave-induced run-up and flooding due to sea-level rise than those with deeper reef crests farther from the islands’ shorelines. It appears that many atoll islands will be flooded annually, salinizing the limited freshwater resources and thus likely forcing inhabitants to abandon their islands in decades, not centuries, as previously thought.
Coordinated vigilance provides evidence for direct reciprocity in coral reef fishes
Authors: Brandl Simon J. , Bellwood David R. 
Published: September 2015

AbstractReciprocity is frequently assumed to require complex cognitive abilities. Therefore, it has been argued that reciprocity may be restricted to animals that can meet these demands. Here, we provide evidence for the potential presence of direct reciprocity in teleost fishes. We demonstrate that in pairs of coral reef rabbitfishes (f. Siganidae), one fish frequently assumes an upright vigilance position in the water column, while the partner forages in small crevices in the reef substratum. Both behaviours are strongly coordinated and partners regularly alternate their positions, resulting in a balanced distribution of foraging activity. Compared to solitary individuals, fishes in pairs exhibit longer vigilance bouts, suggesting that the help provided to the partner is costly. In turn, fishes in pairs take more consecutive bites and penetrate deeper into crevices than solitary individuals, suggesting that the safety provided by a vigilant partner may outweigh initial costs by increasing foraging efficiency. Thus, the described system appears to meet all of the requirements for direct reciprocity. We argue that the nature of rabbitfish pairs provides favourable conditions for the establishment of direct reciprocity, as continuous interaction with the same partner, simultaneous needs, interdependence and communication relax the cognitive demands of reciprocal cooperation.
Improving the power efficiency of enhanced unipolar OFDM for optical wireless communication
Authors: Dang Jian , Zhang Zaichen , Wu Liang 
Published: September 2015

Enhanced unipolar orthogonal frequency division multiplexing (eU‐OFDM) is a novel unipolar multicarrier modulation scheme used in intensity modulation and direct detection systems for optical wireless communication. It improves the spectral efficiency of unipolar OFDM at the expense of lower power efficiency. A novel symbol detection method exploiting the intrinsic signal structure of the received signal is proposed. Analysis and simulations show that the power efficiency of eU‐OFDM could be improved up to 3 dB in the high signal‐to‐noise ratio regime using the proposed method.
Liquid‐metal frequency‐reconfigurable slot antenna using air‐bubble actuation
Authors: Dang J.H. , Gough R.C. , Morishita A.M. , Ohta A.T. , Shiroma W.A. 
Published: September 2015

Liquid metal actuated by pressure‐driven air bubbles is guided within channels to dynamically reconfigure the length of the radiating aperture and feed line of a slot antenna. The gallium‐based liquid metal is held in position by air bubbles, and liquid‐metal motion is induced when a pressure differential is created. In contrast to conventional hydraulic or pneumatic actuation of gallium‐based liquid metal, the pressure actuation described here is reversible and repeatable, as the liquid metal is enveloped by a thin layer of NaOH solution, which acts as a slip layer and reduces any metal oxidation. The slot antenna achieves a 26% tunable bandwidth with a contiguous range from 1.42 to 1.84 GHz for which the S11 is <−10 dB. The peak gain ranges from 4.8 dBi in its lowest‐frequency state to 4.1 dBi in its highest‐frequency state.