bluuebunny/crossref_metadata_2025_split huggingface dataset:
miRNA-205 targets VEGFA and FGF2 and regulates resistance to chemotherapeutics in breast cancer
Authors: Hu Y , Qiu Y , Yagüe E , Ji W , Liu J , Zhang J 
Published: June 2016

AbstractMicroRNAs (miRNAs) have critical roles in regulating cancer cell survival, proliferation and sensitivity to chemotherapy. The potential application of using miRNAs to predict chemotherapeutic response to cancer treatment is highly promising. However, the underlying mechanisms of chemotherapy response control by miRNAs remain to be fully identified and their prognostic value has not been fully evaluated. Here we show a strong correlation between miR-205 expression and chemosensitivtiy to TAC (docetaxol, doxorubicin plus cyclophosphamide), a widely-used neoadjuvant chemotherapy (NAC) regimen, for breast cancer patients. High level of miR-205 predicted better response to TAC regimen NAC in breast cancer patients. We found miR-205 downregulated in both MCF-7/A02 and CALDOX cells, two drug-resistant derivatives of MCF-7 and Cal51 cells, and its ectopic expression led to an increase in apoptosis resensitization of both drug-resistant cell lines to doxorubicin and taxol. We further show that miR-205 directly binds VEGFA and FGF2 mRNA 3′-UTRs and confirm that miR-205 levels are negatively correlated with VEGFA and FGF2 mRNA expression in breast cancer patients. Adding VEGFA and FGF2 exogenously to chemosensitive breast cancer cells and chemoresistant cells with miR-205 overexpression led to drug resistance. Consistently, low VEGFA and FGF2 expression correlated with better response to NAC in breast cancer patients. In addition, inhibition of tumor growth and resensitization to doxorubicin were also observed in mouse tumor xenografts from cells overexpressing miR-205. Taken together, our data suggest that miR-205 enhances chemosensitivity of breast cancer cells to TAC chemotherapy by suppressing both VEGFA and FGF2, leading to evasion of apoptosis. MiR-205 may serve as a predictive biomarker and a potential therapeutic target in breast cancer treatment.
Mpath maps multi-branching single-cell trajectories revealing progenitor cell progression during development
Authors: Chen Jinmiao , Schlitzer Andreas , Chakarov Svetoslav , Ginhoux Florent , Poidinger Michael 
Published: June 2016

AbstractSingle-cell RNA-sequencing offers unprecedented resolution of the continuum of state transition during cell differentiation and development. However, tools for constructing multi-branching cell lineages from single-cell data are limited. Here we present Mpath, an algorithm that derives multi-branching developmental trajectories using neighborhood-based cell state transitions. Applied to mouse conventional dendritic cell (cDC) progenitors, Mpath constructs multi-branching trajectories spanning from macrophage/DC progenitors through common DC progenitor to pre-dendritic cells (preDC). The Mpath-generated trajectories detect a branching event at the preDC stage revealing preDC subsets that are exclusively committed to cDC1 or cDC2 lineages. Reordering cells along cDC development reveals sequential waves of gene regulation and temporal coupling between cell cycle and cDC differentiation. Applied to human myoblasts, Mpath recapitulates the time course of myoblast differentiation and isolates a branch of non-muscle cells involved in the differentiation. Our study shows that Mpath is a useful tool for constructing cell lineages from single-cell data.
Coronary vasculature patterning requires a novel endothelial ErbB2 holoreceptor
Authors: Aghajanian Haig , Cho Young Kuk , Manderfield Lauren J. , Herling Madison R. , Gupta Mudit , Ho Vivienne C. , Li Li , Degenhardt Karl , Aharonov Alla , Tzahor Eldad , Epstein Jonathan A. 
Published: June 2016

AbstractOrganogenesis and regeneration require coordination of cellular proliferation, regulated in part by secreted growth factors and cognate receptors, with tissue nutrient supply provided by expansion and patterning of blood vessels. Here we reveal unexpected combinatorial integration of a growth factor co-receptor with a heterodimeric partner and ligand known to regulate angiogenesis and vascular patterning. We show that ErbB2, which can mediate epidermal growth factor (EGF) and neuregulin signalling in multiple tissues, is unexpectedly expressed by endothelial cells where it partners with neuropilin 1 (Nrp1) to form a functional receptor for the vascular guidance molecule semaphorin 3d (Sema3d). Loss of Sema3d leads to improper patterning of the coronary veins, a phenotype recapitulated by endothelial loss of ErbB2. These findings have implications for possible cardiovascular side-effects of anti-ErbB2 therapies commonly used for cancer, and provide an example of integration at the molecular level of pathways involved in tissue growth and vascular patterning.
Long-read sequencing and de novo assembly of a Chinese genome
Authors: Shi Lingling , Guo Yunfei , Dong Chengliang , Huddleston John , Yang Hui , Han Xiaolu , Fu Aisi , Li Quan , Li Na , Gong Siyi , Lintner Katherine E. , Ding Qiong , Wang Zou , Hu Jiang , Wang Depeng , Wang Feng , Wang Lin , Lyon Gholson J. , Guan Yongtao , Shen Yufeng , Evgrafov Oleg V. , Knowles James A. , Thibaud-Nissen Francoise , Schneider Valerie , Yu Chack-Yung , Zhou Libing , Eichler Evan E. , So Kwok-Fai , Wang Kai 
Published: June 2016

AbstractShort-read sequencing has enabled the de novo assembly of several individual human genomes, but with inherent limitations in characterizing repeat elements. Here we sequence a Chinese individual HX1 by single-molecule real-time (SMRT) long-read sequencing, construct a physical map by NanoChannel arrays and generate a de novo assembly of 2.93 Gb (contig N50: 8.3 Mb, scaffold N50: 22.0 Mb, including 39.3 Mb N-bases), together with 206 Mb of alternative haplotypes. The assembly fully or partially fills 274 (28.4%) N-gaps in the reference genome GRCh38. Comparison to GRCh38 reveals 12.8 Mb of HX1-specific sequences, including 4.1 Mb that are not present in previously reported Asian genomes. Furthermore, long-read sequencing of the transcriptome reveals novel spliced genes that are not annotated in GENCODE and are missed by short-read RNA-Seq. Our results imply that improved characterization of genome functional variation may require the use of a range of genomic technologies on diverse human populations.
Impeding 99Tc(IV) mobility in novel waste forms
Authors: Lee Mal-Soon , Um Wooyong , Wang Guohui , Kruger Albert A. , Lukens Wayne W. , Rousseau Roger , Glezakou Vassiliki-Alexandra 
Published: June 2016

AbstractTechnetium (99Tc) is an abundant, long-lived radioactive fission product whose mobility in the subsurface is largely governed by its oxidation state. Tc immobilization is crucial for radioactive waste management and environmental remediation. Tc(IV) incorporation in spinels has been proposed as a novel method to increase Tc retention in glass waste forms during vitrification. However, experiments under high-temperature and oxic conditions show reoxidation of Tc(IV) to volatile pertechnetate, Tc(VII). Here we examine this problem withab initiomolecular dynamics simulations and propose that, at elevated temperatures, doping with first row transition metal can significantly enhance Tc retention in magnetite in the order Co>Zn>Ni. Experiments with doped spinels at 700 °C provide quantitative confirmation of the theoretical predictions in the same order. This work highlights the power of modern, state-of-the-art simulations to provide essential insights and generate theory-inspired design criteria of complex materials at elevated temperatures.
MCOLN1 is a ROS sensor in lysosomes that regulates autophagy
Authors: Zhang Xiaoli , Cheng Xiping , Yu Lu , Yang Junsheng , Calvo Raul , Patnaik Samarjit , Hu Xin , Gao Qiong , Yang Meimei , Lawas Maria , Delling Markus , Marugan Juan , Ferrer Marc , Xu Haoxing 
Published: June 2016

AbstractCellular stresses trigger autophagy to remove damaged macromolecules and organelles. Lysosomes ‘host’ multiple stress-sensing mechanisms that trigger the coordinated biogenesis of autophagosomes and lysosomes. For example, transcription factor (TF)EB, which regulates autophagy and lysosome biogenesis, is activated following the inhibition of mTOR, a lysosome-localized nutrient sensor. Here we show that reactive oxygen species (ROS) activate TFEB via a lysosomal Ca2+-dependent mechanism independent of mTOR. Exogenous oxidants or increasing mitochondrial ROS levels directly and specifically activate lysosomal TRPML1 channels, inducing lysosomal Ca2+ release. This activation triggers calcineurin-dependent TFEB-nuclear translocation, autophagy induction and lysosome biogenesis. When TRPML1 is genetically inactivated or pharmacologically inhibited, clearance of damaged mitochondria and removal of excess ROS are blocked. Furthermore, TRPML1’s ROS sensitivity is specifically required for lysosome adaptation to mitochondrial damage. Hence, TRPML1 is a ROS sensor localized on the lysosomal membrane that orchestrates an autophagy-dependent negative-feedback programme to mitigate oxidative stress in the cell.
Cortical idiosyncrasies predict the perception of object size
Authors: Moutsiana Christina , de Haas Benjamin , Papageorgiou Andriani , van Dijk Jelle A. , Balraj Annika , Greenwood John A. , Schwarzkopf D. Samuel 
Published: June 2016

AbstractPerception is subjective. Even basic judgments, like those of visual object size, vary substantially between observers and also across the visual field within the same observer. The way in which the visual system determines the size of objects remains unclear, however. We hypothesize that object size is inferred from neuronal population activity in V1 and predict that idiosyncrasies in cortical functional architecture should therefore explain individual differences in size judgments. Here we show results from novel behavioural methods and functional magnetic resonance imaging (fMRI) demonstrating that biases in size perception are correlated with the spatial tuning of neuronal populations in healthy volunteers. To explain this relationship, we formulate a population read-out model that directly links the spatial distribution of V1 representations to our perceptual experience of visual size. Taken together, our results suggest that the individual perception of simple stimuli is warped by idiosyncrasies in visual cortical organization.
Array of nanosheets render ultrafast and high-capacity Na-ion storage by tunable pseudocapacitance
Authors: Chao Dongliang , Zhu Changrong , Yang Peihua , Xia Xinhui , Liu Jilei , Wang Jin , Fan Xiaofeng , Savilov Serguei V. , Lin Jianyi , Fan Hong Jin , Shen Ze Xiang 
Published: June 2016

AbstractSodium-ion batteries are a potentially low-cost and safe alternative to the prevailing lithium-ion battery technology. However, it is a great challenge to achieve fast charging and high power density for most sodium-ion electrodes because of the sluggish sodiation kinetics. Here we demonstrate a high-capacity and high-rate sodium-ion anode based on ultrathin layered tin(II) sulfide nanostructures, in which a maximized extrinsic pseudocapacitance contribution is identified and verified by kinetics analysis. The graphene foam supported tin(II) sulfide nanoarray anode delivers a high reversible capacity of ∼1,100 mAh g−1 at 30 mA g−1 and ∼420 mAh g−1 at 30 A g−1, which even outperforms its lithium-ion storage performance. The surface-dominated redox reaction rendered by our tailored ultrathin tin(II) sulfide nanostructures may also work in other layered materials for high-performance sodium-ion storage.
FRESH AIR: an implementation research project funded through Horizon 2020 exploring the prevention, diagnosis and treatment of chronic respiratory diseases in low-resource settings
Authors: Cragg Liza , Williams Siân , Chavannes Niels H ,   On behalf of the FRESH AIR Group
Published: June 2016

AbstractThis protocol describes FRESH AIR, an implementation science project exploring how to improve the prevention, diagnosis and treatment of chronic lung diseases in contexts with limited healthcare resources. It consists of inter-related studies that take place in four countries that are part of the International Primary Care Respiratory Group’s (IPCRG) global network: Uganda, the Kyrgyz Republic, Vietnam and Greece. The project has been funded by the European Commission Horizon 2020 research programme and runs from October 2015 until September 2018.
Human GV oocytes generated by mitotically active germ cells obtained from follicular aspirates
Authors: Ding Xinbao , Liu Guishu , Xu Bo , Wu Changqing , Hui Ning , Ni Xin , Wang Jian , Du Meirong , Teng Xiaoming , Wu Ji 
Published: June 2016

AbstractHuman female germline stem cells (FGSCs) have opened new opportunities for understanding human oogenesis, delaying menopause, treating infertility and providing a new strategy for preserving fertility. However, the shortage of adult human ovaries tissues available impedes their future investigations and clinical applications. Here, we have established FGSC lines from scarce ovarian cortical tissues that exist in follicular aspirates (faFGSCs), which are produced and discarded in in vitro fertilization centers worldwide. The faFGSCs have characteristics of germline stem cells involved in the gene expression profile, growth characteristics and a normal karyotype consistent with that of FGSCs obtained from ovarian cortexes surgically removed from patients (srFGSCs). Furthermore, faFGSCs have developmental potentials including spontaneous differentiation into oocytes under feeder-free conditions, communicating with granulosa cells by gap junctions and paracrine factors, entering meiosis after RA induction, as well as forming follicles after injection into human ovarian cortical tissues xenografted into adult immunodeficient female mice. Lastly, we developed a strategy guiding FGSCs differentiated into germinal vesicle (GV) stage oocytes in vitro and revealed their developmental mechanisms. Our study not only provides a new approach to obtain human FGSCs for medical treatment, but also opens several avenues to investigate human oogenesis in vitro.
Exploring pig trade patterns to inform the design of risk-based disease surveillance and control strategies
Authors: Guinat C. , Relun A. , Wall B. , Morris A. , Dixon L. , Pfeiffer D. U. 
Published: June 2016

AbstractAn understanding of the patterns of animal contact networks provides essential information for the design of risk-based animal disease surveillance and control strategies. This study characterises pig movements throughout England and Wales between 2009 and 2013 with a view to characterising spatial and temporal patterns, network topology and trade communities. Data were extracted from the Animal and Plant Health Agency (APHA)’s RADAR (Rapid Analysis and Detection of Animal-related Risks) database, and analysed using descriptive and network approaches. A total of 61,937,855 pigs were moved through 872,493 movements of batches in England and Wales during the 5-year study period. Results show that the network exhibited scale-free and small-world topologies, indicating the potential for diseases to quickly spread within the pig industry. The findings also provide suggestions for how risk-based surveillance strategies could be optimised in the country by taking account of highly connected holdings, geographical regions and time periods with the greatest number of movements and pigs moved, as these are likely to be at higher risk for disease introduction. This study is also the first attempt to identify trade communities in the country, information which could be used to facilitate the pig trade and maintain disease-free status across the country in the event of an outbreak.
Inhomogeneous Point-Processes to Instantaneously Assess Affective Haptic Perception through Heartbeat Dynamics Information
Authors: Valenza G. , Greco A. , Citi L. , Bianchi M. , Barbieri R. , Scilingo E. P. 
Published: June 2016

AbstractThis study proposes the application of a comprehensive signal processing framework, based on inhomogeneous point-process models of heartbeat dynamics, to instantaneously assess affective haptic perception using electrocardiogram-derived information exclusively. The framework relies on inverse-Gaussian point-processes with Laguerre expansion of the nonlinear Wiener-Volterra kernels, accounting for the long-term information given by the past heartbeat events. Up to cubic-order nonlinearities allow for an instantaneous estimation of the dynamic spectrum and bispectrum of the considered cardiovascular dynamics, as well as for instantaneous measures of complexity, through Lyapunov exponents and entropy. Short-term caress-like stimuli were administered for 4.3–25 seconds on the forearms of 32 healthy volunteers (16 females) through a wearable haptic device, by selectively superimposing two levels of force, 2 N and 6 N and two levels of velocity, 9.4 mm/s and 65 mm/s. Results demonstrated that our instantaneous linear and nonlinear features were able to finely characterize the affective haptic perception, with a recognition accuracy of 69.79% along the force dimension and 81.25% along the velocity dimension.
Polarity protein Crumbs homolog-3 (CRB3) regulates ectoplasmic specialization dynamics through its action on F-actin organization in Sertoli cells
Authors: Gao Ying , Lui Wing-yee , Lee Will M. , Cheng C. Yan 
Published: June 2016

AbstractCrumbs homolog 3 (or Crumbs3, CRB3) is a polarity protein expressed by Sertoli and germ cells at the basal compartment in the seminiferous epithelium. CRB3 also expressed at the blood-testis barrier (BTB), co-localized with F-actin, TJ proteins occludin/ZO-1 and basal ES (ectoplasmic specialization) proteins N-cadherin/β-catenin at stages IV-VII only. The binding partners of CRB3 in the testis were the branched actin polymerization protein Arp3, and the barbed end-capping and bundling protein Eps8, illustrating its possible role in actin organization. CRB3 knockdown (KD) by RNAi in Sertoli cells with an established tight junction (TJ)-permeability barrier perturbed the TJ-barrier via changes in the distribution of TJ- and basal ES-proteins at the cell-cell interface. These changes were the result of CRB3 KD-induced re-organization of actin microfilaments, in which actin microfilaments were truncated, and extensively branched, thereby destabilizing F-actin-based adhesion protein complexes at the BTB. Using Polyplusin vivo-jetPEI as a transfection medium with high efficiency for CRB3 KD in the testis, the CRB3 KD testes displayed defects in spermatid and phagosome transport, and also spermatid polarity due to a disruption of F-actin organization. In summary, CRB3 is an actin microfilament regulator, playing a pivotal role in organizing actin filament bundles at the ES.
Four-junction superconducting circuit
Authors: Qiu Yueyin , Xiong Wei , He Xiao-Ling , Li Tie-Fu , You J. Q. 
Published: June 2016

AbstractWe develop a theory for the quantum circuit consisting of a superconducting loop interrupted by four Josephson junctions and pierced by a magnetic flux (either static or time-dependent). In addition to the similarity with the typical three-junction flux qubit in the double-well regime, we demonstrate the difference of the four-junction circuit from its three-junction analogue, including its advantages over the latter. Moreover, the four-junction circuit in the single-well regime is also investigated. Our theory provides a tool to explore the physical properties of this four-junction superconducting circuit.
Chemically driven negative linear compressibility in sodium amidoborane, Na(NH2BH3)
Authors: Magos-Palasyuk Ewelina , Fijalkowski Karol J. , Palasyuk Taras 
Published: June 2016

AbstractOver the past few years we have been witnessing a surge of scientific interest to materials exhibiting a rare mechanical effect such as negative linear compressibility (NLC). Here we report on strong NLC found in an ionic molecular crystal of sodium amidoborane (NaAB) – easily-accessible, optically transparent material. In situ Raman measurements revealed abnormal elongation of B-N and N-H bonds of NaAB at pressure about 3 GPa. Ab initio calculations indicate the observed spectroscopic changes are due to an isostructural phase transition accompanied by a stepwise expansion of the crystal along c axis. Analysis of calculated charge density distribution and geometry of molecular species (NH2BH3) univocally points to a chemically driven mechanism of NLC – pressure-induced formation of hydrogen bonds. The new H-bond acts as a “pivot screw” coupling N-H covalent bonds of neighbor molecular species – a system resembling a two-lever “jack device” on a molecular scale. A mechanism based on formation of new bonds stands in apparent contrast to mechanisms so far reported in majority of NLC materials where no significant alteration of chemical bonding was observed. The finding therefore suggests a qualitatively new direction in exploration the field towards rational design of incompressible materials.
Catalytic Hydrodeoxygenation of Bio-oil Model Compounds over Pt/HY Catalyst
Authors: Lee Heejin , Kim Hannah , Yu Mi Jin , Ko Chang Hyun , Jeon Jong-Ki , Jae Jungho , Park Sung Hoon , Jung Sang-Chul , Park Young-Kwon 
Published: June 2016

AbstractThe hydrodeoxygenation of a model compound of lignin-derived bio-oil, guaiacol, which can be obtained from the pyrolysis of biomass to bio-oil, has attracted considerable research attention because of its huge potential as a substitute for conventional fuels. In this study, platinum-loaded HY zeolites (Pt/HY) with different Si/Al molar ratios were used as catalysts for the hydrodeoxygenation of guaiacol, anisole, veratrole, and phenol to a range of hydrocarbons, such as cyclohexane. The cyclohexane (major product) yield increased with increasing number of acid sites. To produce bio-oil with the maximum level of cyclohexane and alkylated cyclohexanes, which would be suitable as a substitute for conventional transportation fuels, the Si/Al molar ratio should be optimized to balance the Pt particle-induced hydrogenation with acid site-induced methyl group transfer. The fuel properties of real bio-oil derived from the fast pyrolysis of cork oak was improved using the Pt/HY catalyst.
Unlocking the bacterial and fungal communities assemblages of sugarcane microbiome
Authors: de Souza Rafael Soares Correa , Okura Vagner Katsumi , Armanhi Jaderson Silveira Leite , Jorrín Beatriz , Lozano Núria , da Silva Márcio José , González-Guerrero Manuel , de Araújo Laura Migliorini , Verza Natália Cristina , Bagheri Homayoun Chaichian , Imperial Juan , Arruda Paulo 
Published: June 2016

AbstractPlant microbiome and its manipulation herald a new era for plant biotechnology with the potential to benefit sustainable crop production. However, studies evaluating the diversity, structure and impact of the microbiota in economic important crops are still rare. Here we describe a comprehensive inventory of the structure and assemblage of the bacterial and fungal communities associated with sugarcane. Our analysis identified 23,811 bacterial OTUs and an unexpected 11,727 fungal OTUs inhabiting the endophytic and exophytic compartments of roots, shoots and leaves. These communities originate primarily from native soil around plants and colonize plant organs in distinct patterns. The sample type is the primary driver of fungal community assemblage and the organ compartment plays a major role in bacterial community assemblage. We identified core bacterial and fungal communities composed of less than 20% of the total microbial richness but accounting for over 90% of the total microbial relative abundance. The roots showed 89 core bacterial families, 19 of which accounted for 44% of the total relative abundance. Stalks are dominated by groups of yeasts that represent over 12% of total relative abundance. The core microbiome described here comprise groups whose biological role underlies important traits in plant growth and fermentative processes.