bluuebunny/crossref_metadata_2025_split huggingface dataset:
Did Sea-Level Changes Affect the Brazilian Amazon Forest during the Holocene?
Authors: Silva Mayra Nina Araujo , Cohen Marcelo C L , Rossetti Dilce F , Pessenda Luiz C R 
Published: August 2017

ABSTRACTIn order to contribute to the discussion of Holocene climate changes, four sediment cores were collected from the northern Brazilian Amazonia lowland. These cores were studied through pollen analysis and sedimentary features, and the results were discussed within a chronological framework provided by radiocarbon dating. The cores were sampled from fluvial terraces representative of channel, floodplain/lake and crevasse splay deposits formed since the mid-Holocene. The pollen samples derive from floodplain/lake deposits and the pollen grains are mainly composed by families Moraceae, Euphorbiaceae, Caesalpiniaceae, Fabaceae, Rubiaceae, Melastomataceae, Combretaceae, Sapindaceae, Poaceae, Cyperaceae, Aizoaceae, Apiaceae and genusSebastiana. The pollen data suggest no significant vegetation changes in the study area for the past 4808–4886 cal yr BP. This led to proposing stable climatic conditions since at least the middle Holocene. Such a finding is contrary to the occurrence of a dry period during the middle Holocene. The stabilization of the relative sea level about 6000 cal yr BP along the northern Brazilian littoral may have influenced the water table, and favored the establishment and maintenance of Amazonian lowland forest during the mid- and late Holocene. In addition, this process may have attenuated the impact of that dry period in areas under most fluvial influence.
The interaction between orientation and motion signals in moving oriented Glass patterns
Authors: PAVAN ANDREA , BIMSON LUCY M. , GALL MARTIN G. , GHIN FILIPPO , MATHER GEORGE 
Published: August 2017

AbstractPrevious psychophysical evidence suggests that motion and orientation processing systems interact asymmetrically in the human visual system, with orientation information having a stronger influence on the perceived motion direction thanvice versa. To investigate the mechanisms underlying this motion-form interaction we used moving and oriented Glass patterns (GPs), which consist of randomly distributed dot pairs (dipoles) that induce the percept of an oriented texture. In Experiment 1 we varied the angle between dipole orientation and motion direction (conflict angle). In separate sessions participants either judged the orientation or motion direction of the GP. In addition, the spatiotemporal characteristics of dipole motion were manipulated as a way to limit (Experiment 1) or favor (Experiment 2) the availability of orientation signals from motion (motion streaks). The results of Experiment 1 showed that apparent GP motion direction is attracted toward dipole orientation, and apparent GP orientation is repulsed from GP motion. The results of Experiment 2 showed stronger repulsion effects when judging the GP orientation, but stronger motion streaks from the GP motion can dominate over the signals provided by conflicting dipole orientation. These results are consistent with the proposal that two separate mechanisms contribute to our perception of stimuli which contain conflicting orientation and motion information: (i) perceived GP motion is mediated by spatial motion-direction sensors, in which signals from motion sensors are combined with excitatory input from orientation-tuned sensors tuned to orientations parallel to the axis of GP motion, (ii) perceived GP orientation is mediated by orientation-tuned sensors which mutually inhibit each other. The two mechanisms are revealed by the different effects of conflict angle and dipole lifetime on perceived orientation and motion direction.
Stereological analysis of gonads from diploid and triploid fish yellowtail tetra Astyanax altiparanae (Garutti & Britski) in laboratory conditions
Authors: Ferreira do Nascimento Nivaldo , de Siqueira-Silva Diógenes Henrique , Pereira-Santos Matheus , Fujimoto Takafumi , Senhorini José Augusto , Nakaghi Laura Satiko Okada , Yasui George Shigueki 
Published: August 2017

SummaryThis study aimed to examine the gonadal morphology of diploid and triploid fish through stereological analysis. Triploid individuals were obtained after temperature shock (40°C for 2 min) at 2 min post-fertilization and reared until 175 days post-fertilization (dpf). Intact eggs were used to obtain the diploids. Gonads were collected for histological analysis at 83, 114, 144 and 175 dpf. Diploid females and males presented normal oogenesis and spermatogenesis through all the experimental period. Conversely, stereological analysis revealed that triploid females were sterile and oogonia were the prevalent cell type in the ovaries. Triploid males presented increased amounts of spermatocyte cysts and a large area of lumen when compared with diploids and in addition the amount of spermatozoa was lower than that observed for diploids. However, some triploid males presented spermatogenesis similar to diploids. Therefore, we concluded that triploidization is an interesting alternative to produce sterile individuals in A. altiparanae.
Tales Bent Backward: Early Modern Local History in Persianate Transregional Contexts
Authors: MANCINI-LANDER DEREK J. 
Published: August 2017

AbstractThis article contributes to a growing body of scholarship on immigrants from Safavid Iran who travelled back and forth between their home cities and Hind during the early modern period. Intending to better comprehend some of the key mentalities and social practices of these cosmopolitan Persianate communities, I explore the literary strategies by which migrants worked to negotiate their place in rapidly transforming and highly competitive political environments in both Hind and Iran. Focusing on migration narratives that were commonly embedded in Persian historical works, I examine a cluster of local and dynastic histories that were composed in dialogue with one another and that emerged around a particular corridor of migration linking the Iranian city of Yazd with various cities in the Deccan. Previous scholarship has argued that immigrants could acquire social capital in their new environments by commemorating ties to Iranian cities through narratives of migration. I demonstrate that migrants also brought migration stories they had found in the Deccan back to their hometowns in Iran, where they redeployed them for similar political ends in new works of history.
Interactions between International Law and Private Fisheries Certification
Authors: Karavias Markos 
Published: August 2017

AbstractThe management of fisheries at the international level is no longer the exclusive preserve of states and international organizations. The proliferation of private certification initiatives – the reach of which defies territorial boundaries – has heralded an era of transnational fisheries governance. Whereas the interactions between private standards and national regulation have attracted scholarly attention, the function of international law in the context of transnational fisheries governance is largely unexplored. This article maps the interactions between international fisheries law and the most prominent among private certification standards, namely the Marine Stewardship Council Fisheries Standard and Guidance (MSC FSG). The article proposes a methodology to assess such interactions at the stage of norm development and argues that the interactions between the two regimes are multidirectional and complex. International law serves as a model for private standard setting and as a yardstick for private decision making. Conversely, the MSC FSG has acted as a model for the Food and Agriculture Organization of the United Nations Ecolabelling Guidelines. Moreover, the MSC FSG may constitute a benchmark for resolutions adopted by regional fisheries management organizations. The MSC FSG, in incorporating international fisheries law, affirms the latter’s resilience as a global point of reference for the management of fisheries globally. Yet, at the same time, by prompting states to comply with their international obligations in order to secure market access for their fishing industry, the MSC FSG may be exposing the inability of international law to generate compliance autonomously.
Focal cortical seizures start as standing waves and propagate respecting homotopic connectivity
Authors: Rossi L. Federico , Wykes Robert C. , Kullmann Dimitri M. , Carandini Matteo 
Published: August 2017

AbstractFocal epilepsy involves excessive cortical activity that propagates both locally and distally. Does this propagation follow the same routes as normal cortical activity? We pharmacologically induced focal seizures in primary visual cortex (V1) of awake mice, and compared their propagation to the retinotopic organization of V1 and higher visual areas. We used simultaneous local field potential recordings and widefield imaging of a genetically encoded calcium indicator to measure prolonged seizures (ictal events) and brief interictal events. Both types of event are orders of magnitude larger than normal visual responses, and both start as standing waves: synchronous elevated activity in the V1 focus and in homotopic locations in higher areas, i.e. locations with matching retinotopic preference. Following this common beginning, however, seizures persist and propagate both locally and into homotopic distal regions, and eventually invade all of visual cortex and beyond. We conclude that seizure initiation resembles the initiation of interictal events, and seizure propagation respects the connectivity underlying normal visual processing.
Plasmonic silver nanoshells for drug and metabolite detection
Authors: Huang Lin , Wan Jingjing , Wei Xiang , Liu Yu , Huang Jingyi , Sun Xuming , Zhang Ru , Gurav Deepanjali D. , Vedarethinam Vadanasundari , Li Yan , Chen Ruoping , Qian Kun 
Published: August 2017

AbstractIn-vitro metabolite and drug detection rely on designed materials-based analytical platforms, which are universally used in biomedical research and clinical practice. However, metabolic analysis in bio-samples needs tedious sample preparation, due to the sample complexity and low molecular abundance. A further challenge is to construct diagnostic tools. Herein, we developed a platform using silver nanoshells. We synthesized SiO2@Ag with tunable shell structures by multi-cycled silver mirror reactions. Optimized nanoshells achieved direct laser desorption/ionization mass spectrometry in 0.5 μL of bio-fluids. We applied these nanoshells for disease diagnosis and therapeutic evaluation. We identified patients with postoperative brain infection through daily monitoring and glucose quantitation in cerebrospinal fluid. We measured drug distribution in blood and cerebrospinal fluid systems and validated the function of blood-brain/cerebrospinal fluid-barriers for pharmacokinetics. Our work sheds light on the design of materials for advanced metabolic analysis and precision diagnostics.
Nanogrid single-nucleus RNA sequencing reveals phenotypic diversity in breast cancer
Authors: Gao Ruli , Kim Charissa , Sei Emi , Foukakis Theodoros , Crosetto Nicola , Chan Leong-Keat , Srinivasan Maithreyan , Zhang Hong , Meric-Bernstam Funda , Navin Nicholas 
Published: August 2017

AbstractSingle cell RNA sequencing has emerged as a powerful tool for resolving transcriptional diversity in tumors, but is limited by throughput, cost and the ability to process archival frozen tissue samples. Here we develop a high-throughput 3′ single-nucleus RNA sequencing approach that combines nanogrid technology, automated imaging, and cell selection to sequence up to ~1800 single nuclei in parallel. We compare the transcriptomes of 485 single nuclei to 424 single cells in a breast cancer cell line, which shows a high concordance (93.34%) in gene levels and abundance. We also analyze 416 nuclei from a frozen breast tumor sample and 380 nuclei from normal breast tissue. These data reveal heterogeneity in cancer cell phenotypes, including angiogenesis, proliferation, and stemness, and a minor subpopulation (19%) with many overexpressed cancer genes. Our studies demonstrate the utility of nanogrid single-nucleus RNA sequencing for studying the transcriptional programs of tumor nuclei in frozen archival tissue samples.
Activated NK cells cause placental dysfunction and miscarriages in fetal alloimmune thrombocytopenia
Authors: Yougbaré Issaka , Tai Wei-She , Zdravic Darko , Oswald Brigitta Elaine , Lang Sean , Zhu Guangheng , Leong-Poi Howard , Qu Dawei , Yu Lisa , Dunk Caroline , Zhang Jianhong , Sled John G. , Lye Stephen J. , Brkić Jelena , Peng Chun , Höglund Petter , Croy B. Anne , Adamson S. Lee , Wen Xiao-Yan , Stewart Duncan J. , Freedman John , Ni Heyu 
Published: August 2017

AbstractMiscarriage and intrauterine growth restriction (IUGR) are devastating complications in fetal/neonatal alloimmune thrombocytopenia (FNAIT). We previously reported the mechanisms for bleeding diatheses, but it is unknown whether placental, decidual immune cells or other abnormalities at the maternal–fetal interface contribute to FNAIT. Here we show that maternal immune responses to fetal platelet antigens cause miscarriage and IUGR that are associated with vascular and immune pathologies in murine FNAIT models. Uterine natural killer (uNK) cell recruitment and survival beyond mid-gestation lead to elevated NKp46 and CD107 expression, perforin release and trophoblast apoptosis. Depletion of NK cells restores normal spiral artery remodeling and placental function, prevents miscarriage, and rescues hemorrhage in neonates. Blockade of NK activation receptors (NKp46, FcɣRIIIa) also rescues pregnancy loss. These findings shed light on uNK antibody-dependent cell-mediated cytotoxicity of invasive trophoblasts as a pathological mechanism in FNAIT, and suggest that anti-NK cell therapies may prevent immune-mediated pregnancy loss and ameliorate FNAIT.
Structural and functional insights into the lipopolysaccharide ABC transporter LptB2FG
Authors: Dong Haohao , Zhang Zhengyu , Tang Xiaodi , Paterson Neil G. , Dong Changjiang 
Published: August 2017

AbstractThe cell surface of most Gram-negative bacteria contains lipopolysaccharide that is essential for their viability and drug resistance. A 134-kDa protein complex LptB2FG is unique among ATP-binding cassette transporters because it extracts lipopolysaccharide from the external leaflet of the inner membrane and propels it along a filament that extends across the periplasm to directly deliver lipopolysaccharide into the external leaflet of the outer membrane. Here we report the crystal structure of the lipopolysaccharide transporter LptB2FG from Klebsiella pneumoniae, in which both LptF and LptG are composed of a β-jellyroll-like periplasmic domain and six α-helical segments in the transmembrane domain. LptF and LptG form a central cavity containing highly conserved hydrophobic residues. Structural and functional studies suggest that LptB2FG uses an alternating lateral access mechanism to extract lipopolysaccharide and traffic it along the hydrophobic cavity toward the transporter’s periplasmic domains.
Structure of the magnetic excitations in the spin-1/2 triangular-lattice Heisenberg antiferromagnet Ba3CoSb2O9
Authors: Ito Saya , Kurita Nobuyuki , Tanaka Hidekazu , Ohira-Kawamura Seiko , Nakajima Kenji , Itoh Shinichi , Kuwahara Keitaro , Kakurai Kazuhisa 
Published: August 2017

AbstractA spin-1/2 triangular-lattice Heisenberg antiferromagnet (TLHAF) is a prototypical frustrated quantum magnet, which exhibits remarkable quantum many-body effects that arise from the synergy between spin frustration and quantum fluctuation. The ground-state properties of a spin-1/2 TLHAF are theoretically well understood. However, the theoretical consensus regarding the magnetic excitations is limited. The experimental study of the magnetic excitations in spin-1/2 TLHAFs has also been limited. Here we show the structure of magnetic excitations in the spin-1/2 TLHAF Ba3CoSb2O9 investigated by inelastic neutron scattering. Significantly different from theoretical expectations, the excitation spectrum has a three-stage energy structure. The lowest-energy first stage is composed of dispersion branches of single-magnon excitations. The second and third stages are dispersive continua accompanied by a columnar continuum extending above 10 meV, which is six times larger than the exchange interaction J = 1.67 meV. Our results indicate the shortcomings of the current theoretical framework.
Performance of objective functions and optimisation procedures for parameter estimation in system biology models
Authors: Degasperi Andrea , Fey Dirk , Kholodenko Boris N. 
Published: August 2017

AbstractMathematical modelling of signalling pathways aids experimental investigation in system and synthetic biology. Ever increasing data availability prompts the development of large dynamic models with numerous parameters. In this paper, we investigate how the number of unknown parameters affects the convergence of three frequently used optimisation algorithms and four objective functions. We compare objective functions that use data-driven normalisation of the simulations with those that use scaling factors. The data-driven normalisation of the simulation approach implies that simulations are normalised in the same way as the data, making both directly comparable. The scaling factor approach, which is commonly used for parameter estimation in dynamic systems, introduces scaling factors that multiply the simulations to convert them to the scale of the data. Here we show that the scaling factor approach increases, compared to data-driven normalisation of the simulations, the degree of practical non-identifiability, defined as the number of directions in the parameter space, along which parameters are not identifiable. Further, the results indicate that data-driven normalisation of the simulations greatly improve the speed of convergence of all tested algorithms when the overall number of unknown parameters is relatively large (74 parameters in our test problems). Data-driven normalisation of the simulations also markedly improve the performance of the non-gradient-based algorithm tested even when the number of unknown parameters is relatively small (10 parameters in our test problems). As the models and the unknown parameters increase in size, the data-driven normalisation of the simulation approach can be the preferred option, because it does not aggravate non-identifiability and allows for obtaining parameter estimates in a reasonable amount of time.
Statistical analysis of mutant allele frequency level of circulating cell-free DNA and blood cells in healthy individuals
Authors: Xia Ligang , Li Zhoufang , Zhou Bo , Tian Geng , Zeng Lidong , Dai Hongyu , Li Xiaohua , Liu Chaoyu , Lu Shixin , Xu Feiyue , Tu Xiaonian , Deng Fang , Xie Yuancai , Huang Weiren , He Jiankui 
Published: August 2017

AbstractCell-free DNA (cfDNA) in plasma has emerged as a potential important biomarker in clinical diagnostics, particularly in cancer. However, somatic mutations are also commonly found in healthy individuals, which interfere with the effectiveness for cancer diagnostics. This study examined the background somatic mutations in white blood cells (WBC) and cfDNA in healthy controls based on sequencing data from 821 non-cancer individuals and several cancer samples with the aim of understanding the patterns of mutations detected in cfDNA. We determined the mutation allele frequencies in both WBC and cfDNA using a panel of 50 cancer-associated genes that covers 20 K-nucleotide region and ultra-deep sequencing with average depth >40000-fold. Our results showed that most of the mutations in cfDNA were highly correlated to WBC. We also observed that the NPM1 gene was the most frequently mutated gene in both WBC and cfDNA. Our study highlighted the importance of sequencing both cfDNA and WBC to improve the sensitivity and accuracy for calling cancer-related mutations from circulating tumour DNA, and shedded light on developing a strategy for early cancer diagnosis by cfDNA sequencing.
Horizontal mantle flow controls subduction dynamics
Authors: Ficini E. , Dal Zilio L. , Doglioni C. , Gerya T. V. 
Published: August 2017

AbstractIt is generally accepted that subduction is driven by downgoing-plate negative buoyancy. Yet plate age –the main control on buoyancy– exhibits little correlation with most of the present-day subduction velocities and slab dips. “West”-directed subduction zones are on average steeper (~65°) than “East”-directed (~27°). Also, a “westerly”-directed net rotation of the lithosphere relative to the mantle has been detected in the hotspot reference frame. Thus, the existence of an “easterly”-directed horizontal mantle wind could explain this subduction asymmetry, favouring steepening or lifting of slab dip angles. Here we test this hypothesis using high-resolution two-dimensional numerical thermomechanical models of oceanic plate subduction interacting with a mantle flow. Results show that when subduction polarity is opposite to that of the mantle flow, the descending slab dips subvertically and the hinge retreats, thus leading to the development of a back-arc basin. In contrast, concordance between mantle flow and subduction polarity results in shallow dipping subduction, hinge advance and pronounced topography of the overriding plate, regardless of their age-dependent negative buoyancy. Our results are consistent with seismicity data and tomographic images of subduction zones. Thus, our models may explain why subduction asymmetry is a common feature of convergent margins on Earth.
Fabrication of Water Jet Resistant and Thermally Stable Superhydrophobic Surfaces by Spray Coating of Candle Soot Dispersion
Authors: Qahtan Talal F. , Gondal Mohammed A. , Alade Ibrahim O. , Dastageer Mohammed A. 
Published: August 2017

AbstractA facile synthesis method for highly stable carbon nanoparticle (CNP) dispersion in acetone by incomplete combustion of paraffin candle flame is presented. The synthesized CNP dispersion is the mixture of graphitic and amorphous carbon nanoparticles of the size range of 20–50 nm and manifested the mesoporosity with an average pore size of 7 nm and a BET surface area of 366 m2g−1. As an application of this material, the carbon nanoparticle dispersion was spray coated (spray-based coating) on a glass surface to fabricate superhydrophobic (water contact angle > 150° and sliding angle < 10 °) surfaces. The spray coated surfaces were found to exhibit much improved water jet resistance and thermal stability up to 400 °C compared to the surfaces fabricated from direct candle flame soot deposition (candle-based coating). This study proved that water jet resistant and thermally stable superhydrophobic surfaces can be easily fabricated by simple spray coating of CNP dispersion gathered from incomplete combustion of paraffin candle flame and this technique can be used for different applications with the potential for the large scale fabrication.