bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic mapping and evolutionary analysis of human-expanded cognitive networks
Authors: Wei Yongbin , de Lange Siemon C. , Scholtens Lianne H. , Watanabe Kyoko , Ardesch Dirk Jan , Jansen Philip R. , Savage Jeanne E. , Li Longchuan , Preuss Todd M. , Rilling James K. , Posthuma Danielle , van den Heuvel Martijn P. 
Published: October 2019

AbstractCognitive brain networks such as the default-mode network (DMN), frontoparietal network, and salience network, are key functional networks of the human brain. Here we show that the rapid evolutionary cortical expansion of cognitive networks in the human brain, and most pronounced the DMN, runs parallel with high expression of human-accelerated genes (HAR genes). Using comparative transcriptomics analysis, we present that HAR genes are differentially more expressed in higher-order cognitive networks in humans compared to chimpanzees and macaques and that genes with high expression in the DMN are involved in synapse and dendrite formation. Moreover, HAR and DMN genes show significant associations with individual variations in DMN functional activity, intelligence, sociability, and mental conditions such as schizophrenia and autism. Our results suggest that the expansion of higher-order functional networks subserving increasing cognitive properties has been an important locus of genetic changes in recent human brain evolution.
Single-cell transcriptomic atlas of the human retina identifies cell types associated with age-related macular degeneration
Authors: Menon Madhvi , Mohammadi Shahin , Davila-Velderrain Jose , Goods Brittany A. , Cadwell Tanina D. , Xing Yu , Stemmer-Rachamimov Anat , Shalek Alex K. , Love John Christopher , Kellis Manolis , Hafler Brian P. 
Published: October 2019

AbstractGenome-wide association studies (GWAS) have identified genetic variants associated with age-related macular degeneration (AMD), one of the leading causes of blindness in the elderly. However, it has been challenging to identify the cell types associated with AMD given the genetic complexity of the disease. Here we perform massively parallel single-cell RNA sequencing (scRNA-seq) of human retinas using two independent platforms, and report the first single-cell transcriptomic atlas of the human retina. Using a multi-resolution network-based analysis, we identify all major retinal cell types, and their corresponding gene expression signatures. Heterogeneity is observed within macroglia, suggesting that human retinal glia are more diverse than previously thought. Finally, GWAS-based enrichment analysis identifies glia, vascular cells, and cone photoreceptors to be associated with the risk of AMD. These data provide a detailed analysis of the human retina, and show how scRNA-seq can provide insight into cell types involved in complex, inflammatory genetic diseases.
Extreme nonlinear strong-field photoemission from carbon nanotubes
Authors: Li Chi , Chen Ke , Guan Mengxue , Wang Xiaowei , Zhou Xu , Zhai Feng , Dai Jiayu , Li Zhenjun , Sun Zhipei , Meng Sheng , Liu Kaihui , Dai Qing 
Published: October 2019

AbstractStrong-field photoemission produces attosecond (10−18 s) electron pulses that are synchronized to the waveform of the incident light. This nonlinear photoemission lies at the heart of current attosecond technologies. Here we report a new nonlinear photoemission behaviour—the nonlinearity in strong-field regime sharply increases (approaching 40th power-law scaling), making use of sub-nanometric carbon nanotubes and 800 nm pulses. As a result, the carrier-envelope phase sensitive photoemission current shows a greatly improved modulation depth of up to 100% (with a total modulation current up to 2 nA). The calculations reveal that the behaviour is an interplay of valence band optical-field emission with charge interaction, and the nonlinear dynamics can be tunable by changing the bandgap of carbon nanotubes. The extreme nonlinear photoemission offers a new means of producing extreme temporal-spatial resolved electron pulses, and provides a new design philosophy for attosecond electronics and photonics.
Fungal-bacterial diversity and microbiome complexity predict ecosystem functioning
Authors: Wagg Cameron , Schlaeppi Klaus , Banerjee Samiran , Kuramae Eiko E. , van der Heijden Marcel G. A. 
Published: October 2019

AbstractThe soil microbiome is highly diverse and comprises up to one quarter of Earth’s diversity. Yet, how such a diverse and functionally complex microbiome influences ecosystem functioning remains unclear. Here we manipulated the soil microbiome in experimental grassland ecosystems and observed that microbiome diversity and microbial network complexity positively influenced multiple ecosystem functions related to nutrient cycling (e.g. multifunctionality). Grassland microcosms with poorly developed microbial networks and reduced microbial richness had the lowest multifunctionality due to fewer taxa present that support the same function (redundancy) and lower diversity of taxa that support different functions (reduced functional uniqueness). Moreover, different microbial taxa explained different ecosystem functions pointing to the significance of functional diversity in microbial communities. These findings indicate the importance of microbial interactions within and among fungal and bacterial communities for enhancing ecosystem performance and demonstrate that the extinction of complex ecological associations belowground can impair ecosystem functioning.
A general synthesis approach for amorphous noble metal nanosheets
Authors: Wu Geng , Zheng Xusheng , Cui Peixin , Jiang Hongyu , Wang Xiaoqian , Qu Yunteng , Chen Wenxing , Lin Yue , Li Hai , Han Xiao , Hu Yanmin , Liu Peigen , Zhang Qinghua , Ge Jingjie , Yao Yancai , Sun Rongbo , Wu Yuen , Gu Lin , Hong Xun , Li Yadong 
Published: October 2019

AbstractNoble metal nanomaterials have been widely used as catalysts. Common techniques for the synthesis of noble metal often result in crystalline nanostructures. The synthesis of amorphous noble metal nanostructures remains a substantial challenge. We present a general route for preparing dozens of different amorphous noble metal nanosheets with thickness less than 10 nm by directly annealing the mixture of metal acetylacetonate and alkali salts. Tuning atom arrangement of the noble metals enables to optimize their catalytic properties. Amorphous Ir nanosheets exhibit a superior performance for oxygen evolution reaction under acidic media, achieving 2.5-fold, 17.6-fold improvement in mass activity (at 1.53 V vs. reversible hydrogen electrode) over crystalline Ir nanosheets and commercial IrO2 catalyst, respectively. In situ X-ray absorption fine structure spectra indicate the valance state of Ir increased to less than + 4 during the oxygen evolution reaction process and recover to its initial state after the reaction.
Structural variants exhibit widespread allelic heterogeneity and shape variation in complex traits
Authors: Chakraborty Mahul , Emerson J. J. , Macdonald Stuart J. , Long Anthony D. 
Published: October 2019

AbstractIt has been hypothesized that individually-rare hidden structural variants (SVs) could account for a significant fraction of variation in complex traits. Here we identified more than 20,000 euchromatic SVs from 14Drosophila melanogastergenome assemblies, of which ~40% are invisible to high specificity short-read genotyping approaches. SVs are common, with 31.5% of diploid individuals harboring a SV in genes larger than 5kb, and 24% harboring multiple SVs in genes larger than 10kb. SV minor allele frequencies are rarer than amino acid polymorphisms, suggesting that SVs are more deleterious. We show that a number of functionally important genes harbor previously hidden structural variants likely to affect complex phenotypes. Furthermore, SVs are overrepresented in candidate genes associated with quantitative trait loci mapped using the Drosophila Synthetic Population Resource. We conclude that SVs are ubiquitous, frequently constitute a heterogeneous allelic series, and can act as rare alleles of large effect.
Feature integration within discrete time windows
Authors: Drissi-Daoudi Leila , Doerig Adrien , Herzog Michael H. 
Published: October 2019

AbstractSensory information must be integrated over time to perceive, for example, motion and melodies. Here, to study temporal integration, we used the sequential metacontrast paradigm in which two expanding streams of lines are presented. When a line in one stream is offset observers perceive all other lines to be offset too, even though they are straight. When more lines are offset the offsets integrate mandatorily, i.e., observers cannot report the individual offsets. We show that mandatory integration lasts for up to 450 ms, depending on the observer. Importantly, integration occurs only when offsets are presented within a discrete window of time. Even stimuli that are in close spatio-temporal proximity do not integrate if they are in different windows. A window of integration starts with stimulus onset and integration in the next window has similar characteristics. We present a two-stage computational model based on discrete time windows that captures these effects.
Reverse diauxie phenotype in Pseudomonas aeruginosa biofilm revealed by exometabolomics and label-free proteomics
Authors: Yung Yeni P. , McGill S. Lee , Chen Hui , Park Heejoon , Carlson Ross P. , Hanley Luke 
Published: October 2019

AbstractMicroorganisms enhance fitness by prioritizing catabolism of available carbon sources using a process known as carbon catabolite repression (CCR). Planktonically grown Pseudomonas aeruginosa is known to prioritize the consumption of organic acids including lactic acid over catabolism of glucose using a CCR strategy termed “reverse diauxie.” P. aeruginosa is an opportunistic pathogen with well-documented biofilm phenotypes that are distinct from its planktonic phenotypes. Reverse diauxie has been described in planktonic cultures, but it has not been documented explicitly in P. aeruginosa biofilms. Here a combination of exometabolomics and label-free proteomics was used to analyze planktonic and biofilm phenotypes for reverse diauxie. P. aeruginosa biofilm cultures preferentially consumed lactic acid over glucose, and in addition, the cultures catabolized the substrates completely and did not exhibit the acetate secreting “overflow” metabolism that is typical of many model microorganisms. The biofilm phenotype was enabled by changes in protein abundances, including lactate dehydrogenase, fumarate hydratase, GTP cyclohydrolase, L-ornithine N(5)-monooxygenase, and superoxide dismutase. These results are noteworthy because reverse diauxie-mediated catabolism of organic acids necessitates a terminal electron acceptor like O2, which is typically in low supply in biofilms due to diffusion limitation. Label-free proteomics identified dozens of proteins associated with biofilm formation including 16 that have not been previously reported, highlighting both the advantages of the methodology utilized here and the complexity of the proteomic adaptation for P. aeruginosa biofilms. Documenting the reverse diauxic phenotype in P. aeruginosa biofilms is foundational for understanding cellular nutrient and energy fluxes, which ultimately control growth and virulence.
Insights into flagellar function and mechanism from the squid–vibrio symbiosis
Authors: Aschtgen Marie-Stephanie , Brennan Caitlin A. , Nikolakakis Kiel , Cohen Stephanie , McFall-Ngai Margaret , Ruby Edward G. 
Published: October 2019

AbstractFlagella are essential and multifunctional nanomachines that not only move symbionts towards their tissue colonization site, but also play multiple roles in communicating with the host. Thus, untangling the activities of flagella in reaching, interacting, and signaling the host, as well as in biofilm formation and the establishment of a persistent colonization, is a complex problem. The squid–vibrio system offers a unique model to study the many ways that bacterial flagella can influence a beneficial association and, generally, other bacteria–host interactions.Vibrio fischeriis a bioluminescent bacterium that colonizes the Hawaiian bobtail squid,Euprymna scolopes. Over the last 15 years, the structure, assembly, and functions ofV. fischeriflagella, including not only motility and chemotaxis, but also biofilm formation and symbiotic signaling, have been revealed. Here we discuss these discoveries in the perspective of other host–bacteria interactions.
Wnt5a induces ROR1 to recruit cortactin to promote breast-cancer migration and metastasis
Authors: Hasan Md Kamrul , Widhopf George F. , Zhang Suping , Lam Sharon M. , Shen Zhouxin , Briggs Steven P. , Parker Barbara A. , Kipps Thomas J. 
Published: October 2019

AbstractROR1 is a conserved oncoembryonic surface protein expressed in breast cancer. Here we report that ROR1 associates with cortactin in primary breast-cancer cells or in MCF7 transfected to express ROR1. Wnt5a also induced ROR1-dependent tyrosine phosphorylation of cortactin (Y421), which recruited ARHGEF1 to activate RhoA and promote breast-cancer-cell migration; such effects could be inhibited by cirmtuzumab, a humanized mAb specific for ROR1. Furthermore, treatment of mice bearing breast-cancer xenograft with cirmtuzumab inhibited cortactin phosphorylation in vivo and impaired metastatic development. We established that the proline at 841 of ROR1 was required for it to recruit cortactin and ARHGEF1, activate RhoA, and enhance breast-cancer-cell migration in vitro or development of metastases in vivo. Collectively, these studies demonstrate that the interaction of ROR1 with cortactin plays an important role in breast-cancer-cell migration and metastasis.
Environmental transcriptomes of invasive dreissena, a model species in ecotoxicology and invasion biology
Authors: Péden Romain , Poupin Pascal , Sohm Bénédicte , Flayac Justine , Giambérini Laure , Klopp Christophe , Louis Fanny , Pain-Devin Sandrine , Potet Marine , Serre Rémy-Félix , Devin Simon 
Published: October 2019

AbstractDreissenids are established model species for ecological and ecotoxicological studies, since they are sessile and filter feeder organisms and reflect in situ freshwater quality. Despite this strong interest for hydrosystem biomonitoring, omics data are still scarce. In the present study, we achieved full de novo assembly transcriptomes of digestive glands to gain insight into Dreissena polymorpha and D. rostriformis bugensis molecular knowledge. Transcriptomes were obtained by Illumina RNA sequencing of seventy-nine organisms issued from fifteen populations inhabiting sites that exhibits multiple freshwater contamination levels and different hydrosystem topographies (open or closed systems). Based on a recent de novo assembly algorithm, we carried out a complete, quality-checked and annotated transcriptomes. The power of the present study lies in the completeness of transcriptomes gathering multipopulational organisms sequencing and its full availability through an open access interface that gives a friendly and ready-to-use access to data. The use of such data for proteogenomic and targeted biological pathway investigations purpose is promising as they are first full transcriptomes for this two Dreissena species.
Gas Diffusion Electrodes on the Electrosynthesis of Controllable Iron Oxide Nanoparticles
Authors: Prato Rafael A. , Van Vught Vincent , Eggermont Sam , Pozo Guillermo , Marin Pilar , Fransaer Jan , Dominguez-Benetton Xochitl 
Published: October 2019

AbstractThe electrosynthesis of iron oxide nanoparticles offers a green route, with significant energy and environmental advantages. Yet, this is mostly restricted by the oxygen solubility in the electrolyte. Gas-diffusion electrodes (GDEs) can be used to overcome that limitation, but so far they not been explored for nanoparticle synthesis. Here, we develop a fast, environmentally-friendly, room temperature electrosynthesis route for iron oxide nanocrystals, which we term gas-diffusion electrocrystallization (GDEx). A GDE is used to generate oxidants and hydroxide in-situ, enabling the oxidative synthesis of a single iron salt (e.g., FeCl2) into nanoparticles. Oxygen is reduced to reactive oxygen species, triggering the controlled oxidation of Fe2+ to Fe3+, forming Fe3−xO4−x (0 ≤ x ≤ 1). The stoichiometry and lattice parameter of the resulting oxides can be controlled and predictively modelled, resulting in highly-defective, strain-heavy nanoparticles. The size of the nanocrystals can be tuned from 5 nm to 20 nm, with a large saturation magnetization range (23 to 73 A m2 kg−1), as well as minimal coercivity (~1 kA m−1). Using only air, NaCl, and FeCl2, a biocompatible approach is achieved, besides a remarkable level of control over key parameters, with a view on minimizing the addition of chemicals for enhanced production and applications.
Highly Plasmonic Titanium Nitride by Room-Temperature Sputtering
Authors: Chang Chun-Chieh , Nogan John , Yang Zu-Po , Kort-Kamp Wilton J. M. , Ross Willard , Luk Ting S. , Dalvit Diego A. R. , Azad Abul K. , Chen Hou-Tong 
Published: October 2019

AbstractTitanium nitride (TiN) has recently emerged as an attractive alternative material for plasmonics. However, the typical high-temperature deposition of plasmonic TiN using either sputtering or atomic layer deposition has greatly limited its potential applications and prevented its integration into existing CMOS device architectures. Here, we demonstrate highly plasmonic TiN thin films and nanostructures by a room-temperature, low-power, and bias-free reactive sputtering process. We investigate the optical properties of the TiN films and their dependence on the sputtering conditions and substrate materials. We find that our TiN possesses one of the largest negative values of the real part of the dielectric function as compared to all other plasmonic TiN films reported to date. Two-dimensional periodic arrays of TiN nanodisks are then fabricated, from which we validate that strong plasmonic resonances are supported. Our room-temperature deposition process can allow for fabricating complex plasmonic TiN nanostructures and be integrated into the fabrication of existing CMOS-based photonic devices to enhance their performance and functionalities.
Pop-in behavior and elastic-to-plastic transition of polycrystalline pure iron during sharp nanoindentation
Authors: Pöhl Fabian 
Published: October 2019

AbstractThis study analyzes the elastic-to-plastic transition during nanoindentation of polycrystalline iron. We conduct nanoindentation (Berkovich indenter) experiments and electron backscatter diffraction analysis to investigate the initiation of plasticity by the appearance of the pop-in phenomenon in the loading curves. Numerous load–displacement curves are statistically analyzed to identify the occurrence of pop-ins. A first pop-in can result from plasticity initiation caused by homogeneous dislocation nucleation and requires shear stresses in the range of the theoretical strength of a defect-free iron crystal. The results also show that plasticity initiation in volumes with preexisting dislocations is significantly affected by small amounts of interstitially dissolved atoms (such as carbon) that are segregated into the stress fields of dislocations, impeding their mobility. Another strong influence on the pop-in behavior is grain boundaries, which can lead to large pop-ins at relatively high indentation loads. The pop-in behavior appears to be a statistical process affected by interstitial atoms, dislocation density, grain boundaries, and surface roughness. No effect of the crystallographic orientation on the pop-in behavior can be observed.
Integrin α11 cytoplasmic tail is required for FAK activation to initiate 3D cell invasion and ERK-mediated cell proliferation
Authors: Erusappan Pugazendhi , Alam Jahedul , Lu Ning , Zeltz Cédric , Gullberg Donald 
Published: October 2019

AbstractIntegrin α11β1 is a collagen-binding integrin, which is receiving increasing attention in the context of wound healing and fibrosis. Although α11β1 integrin displays similar collagen specificity to α2β1 integrin, both integrins have distinct in vivo functions. In this context, the contribution of α11 subunit cytoplasmic tail interactions to diverse molecular signals and biological functions is largely unknown. In the current study, we have deleted the α11 cytoplasmic tail and studied the effect of this deletion on α11 integrin function. Compared to wild-type cells, C2C12 cells expressing tail-less α11 attached normally to collagen I, but formed fewer focal contacts. α11-tail-less cells furthermore displayed a reduced capacity to invade and reorganize a 3D collagen matrix and to proliferate. Analysis of cell signaling showed that FAK and ERK phosphorylation was reduced in cells expressing tail-less α11. Inhibition of ERK and FAK activation decreased α11-mediated cell proliferation, whereas α11-mediated cell invasion was FAK-dependent and occurred independently of ERK signaling. In summary, our data demonstrate that the integrin α11 cytoplasmic tail plays a central role in α11 integrin-specific functions, including FAK-dependent ERK activation to promote cell proliferation.
A new approach to study the Zeno effect for a macroscopic quantum system under frequent interactions with a harmonic environment
Authors: Ghasemi Fatemeh , Shafiee Afshin 
Published: October 2019

AbstractQuantum Zeno and anti-Zeno behaviors of a two-level macroscopic quantum system in interaction with a harmonic environment are studied using the perturbation theory. The system-environment interactions are applied in a successive and step-by-step way. A new expression for the probability of surviving the macrosystem in its initial state, after the Nth interaction step, is derived through a different method of calculation. It is shown that multiple transitions between Zeno and anti-Zeno behaviors can be found in our approach. We have shown that in addition to the environmental parameters like the Ohmicity, the macroscopic trait of the system also has a notable effect on the decay rate Γ(τ). Moreover, we have investigated how the decay rate Γ(τ) varies as the parameter of the macroscopicity of the system $$\tilde{{\boldsymbol{h}}}$$

h
˜

changes continuously in a given domain.
Millimeter-wave pulsed heating in vitro: cell mortality and heat shock response
Authors: Orlacchio Rosa , Le Page Yann , Le Dréan Yves , Le Guével Rémy , Sauleau Ronan , Alekseev Stanislav , Zhadobov Maxim 
Published: October 2019

AbstractMillimeter wave (MMW)-induced heating represents a promising alternative for non-invasive hyperthermia of superficial skin cancer, such as melanoma. Pulsed MMW-induced heating of tumors allows for reaching high peak temperatures without overheating surrounding tissues. Herein, for the first time, we evaluate apoptotic and heat shock responses of melanoma cells exposed in vitro to continuous (CW) or pulsed-wave (PW) amplitude-modulated MMW at 58.4 GHz with the same average temperature rise. Using an ad hoc exposure system, we generated 90 min pulse train with 1.5 s pulse duration, period of 20 s, amplitude of 10 °C, and steady-state temperature at the level of cells of 49.2 °C. The activation of Caspase-3 and phosphorylation of HSP27 were investigated using fluorescence microscopy to monitor the spatial variation of cellular response. Our results demonstrate that, under the considered exposure conditions, Caspase-3 activation was almost 5 times greater following PW exposure compared to CW. The relationship between the PW-induced cellular response and SAR-dependent temperature rise was non-linear. Phosphorylation of HSP27 was 58% stronger for PW compared to CW. It exhibits a plateau for the peak temperature ranging from 47.7 to 49.2 °C. Our results provide an insight into understanding of the cellular response to MMW-induced pulsed heating.