bluuebunny/crossref_metadata_2025_split huggingface dataset:
A time-resolved multi-omic atlas of the developing mouse stomach
Authors: Li Xianju , Zhang Chunchao , Gong Tongqing , Ni Xiaotian , Li Jin’e , Zhan Dongdong , Liu Mingwei , Song Lei , Ding Chen , Xu Jianming , Zhen Bei , Wang Yi , Qin Jun 
Published: November 2018

AbstractThe mammalian stomach is structurally highly diverse and its organ functionality critically depends on a normal embryonic development. Although there have been several studies on the morphological changes during stomach development, a system-wide analysis of the underlying molecular changes is lacking. Here, we present a comprehensive, temporal proteome and transcriptome atlas of the mouse stomach at multiple developmental stages. Quantitative analysis of 12,108 gene products allows identifying three distinct phases based on changes in proteins and RNAs and the gain of stomach functions on a longitudinal time scale. The transcriptome indicates functionally important isoforms relevant to development and identifies several functionally unannotated novel splicing junction transcripts that we validate at the peptide level. Importantly, many proteins differentially expressed in stomach development are also significantly overexpressed in diffuse-type gastric cancer. Overall, our study provides a resource to understand stomach development and its connection to gastric cancer tumorigenesis.
Pre-B acute lymphoblastic leukemia expresses cell surface nucleolin as a 9-O-acetylated sialoglycoprotein
Authors: Joo Eun Ji , Wasik Brian R , Parrish Colin , Paz Helicia , Mϋhlenhoff Martina , Abdel-Azim Hisham , Groffen John , Heisterkamp Nora 
Published: November 2018

AbstractPrecursor B acute lymphoblastic leukemias (pre-B ALLs) abnormally express a specific glycan structure, 9-O-acetylated sialic acid (9-O-Ac-Sia), on their cell surface, but glycoproteins that carry this modification have not been identified. Using three different lectins that specifically recognize this structure, we establish that nucleolin (NCL), a protein implicated in cancer, contains 9-O-Ac-Sia. Surprisingly, antibodies against the glycolipid 9-O-Ac-Sia GD3 also detected 9-O-Ac-Sia NCL. NCL is present on the surface of pre-B ALL cells as a sialoglycoprotein that is partly 9-O-acetylated and conversely, 9-O-Ac-Sia-containing structures other than NCL are present on these cells as well. Interestingly, NCL and the 9-O-Ac-Sia signal had less co-localization on normal pre-B cells. We also investigated regulation of NCL on the cell surface and found that sialidase treatment increased the percentage of cells positive for cell surface NCL, suggesting that sialylation of NCL promotes internalization. Treatment of pre-B ALL cells with the chemotherapy drug vincristine also increased the percentage of cells with surface NCL and correlated with increased 9-O-Ac-Sia expression. All tested leukemia cells including primary samples expressed NCL, suggesting it as a possible therapeutic target. We confirmed this by showing inhibition of cell proliferation in some pre-B ALLs by exposure to a NCL-specific aptamer AS1411.
Root Mean Square Minimum Distance as a Quality Metric for Stochastic Optical Localization Nanoscopy Images
Authors: Sun Yi 
Published: November 2018

AbstractA localization algorithm in stochastic optical localization nanoscopy plays an important role in obtaining a high-quality image. A universal and objective metric is crucial and necessary to evaluate qualities of nanoscopy images and performances of localization algorithms. In this paper, we propose root mean square minimum distance (RMSMD) as a quality metric for localization nanoscopy images. RMSMD measures an average, local, and mutual fitness between two sets of points. Its properties common to a distance metric as well as unique to itself are presented. The ambiguity, discontinuity, and inappropriateness of the metrics of accuracy, precision, recall, and Jaccard index, which are currently used in the literature, are analyzed. A numerical example demonstrates the advantages of RMSMD over the four existing metrics that fail to distinguish qualities of different nanoscopy images in certain conditions. The unbiased Gaussian estimator that achieves the Fisher information and Cramer-Rao lower bound (CRLB) of a single data frame is proposed to benchmark the quality of localization nanoscopy images and the performance of localization algorithms. The information-achieving estimator is simulated in an example and the result demonstrates the superior sensitivity of RMSMD over the other four metrics. As a universal and objective metric, RMSMD can be broadly employed in various applications to measure the mutual fitness of two sets of points.
The human olfactory cleft mucus proteome and its age-related changes
Authors: Yoshikawa Keiichi , Wang Hong , Jaen Cristina , Haneoka Mai , Saito Naoko , Nakamura Junji , Adappa Nithin D. , Cohen Noam A. , Dalton Pamela 
Published: November 2018

AbstractAge-related decreases in olfactory sensitivity are often accompanied by a decrease in the quality of life. However, the molecular mechanisms underlying these changes are not well described. Inhaled substances including odorants are detected by sensory neurons in the olfactory cleft covered with a layer of mucus. This olfactory mucus is the first molecular machinery responsible for tissue protection and for detection of environmental odorants. Yet, little is known about the molecular identities of the actors because of the lack of information on the mucus proteome and its age-related changes. Here, we sampled human mucus from different nasal locations and from young and elderly subjects. The composition of the mucus was extensively analyzed by shotgun proteomic analysis for a vast array of proteins. We also explored correlations between the levels of each mucus proteins with the olfactory sensitivity of subjects. This analysis revealed previously unrecognized proteins with potentially important functions in olfaction. Taken together, this report describes the most comprehensive catalogue of the nasal mucus proteins to date, their positional and age-related differences, and candidate proteins associated with olfaction. This catalogue will provide fundamental information useful for future studies, such as identification of olfactory auxiliary proteins, causes of age-related declines in olfaction, and biomarkers for neurodegenerative disorders.
Generation of uniform-sized multicellular tumor spheroids using hydrogel microwells for advanced drug screening
Authors: Lee Jong Min , Park Da Yeon , Yang Letao , Kim Eun-Joong , Ahrberg Christian D. , Lee Ki-Bum , Chung Bong Geun 
Published: November 2018

AbstractEven though in vitro co-culture tumor spheroid model plays an important role in screening drug candidates, its wide applications are currently limited due to the lack of reliable and high throughput methods for generating well-defined and 3D complex co-culture structures. Herein, we report the development of a hydrogel microwell array to generate uniform-sized multicellular tumor spheroids. Our developed multicellular tumor spheroids are structurally well-defined, robust and can be easily transferred into the widely used 2D culture substrates while maintaining our designed multicellular 3D-sphere structures. Moreover, to develop effective anti-cancer therapeutics we integrated our recently developed gold-graphene hybrid nanomaterial (Au@GO)-based photothermal cancer therapy into a series of multicellular tumor spheroid co-culture system. The multicellular tumor spheroids were harvested onto a two-dimensional (2D) substrate, under preservation of their three-dimensional (3D) structure, to evaluate the photothermal therapy effectiveness of graphene oxide (GO)-wrapped gold nanoparticles (Au@GO). From the model of co-culture spheroids of HeLa/Ovarian cancer and HeLa/human umbilical vein endothelial cell (HUVEC), we observed that Au@GO nanoparticles displayed selectivity towards the fast-dividing HeLa cells, which could not be observed to this extent in 2D cultures. Overall, our developed uniform-sized 3D multicellular tumor spheroid could be a powerful tool for anticancer drug screening applications.
Single-cell imaging of phosphorus uptake shows that key harmful algae rely on different phosphorus sources for growth
Authors: Schoffelen Niels J. , Mohr Wiebke , Ferdelman Timothy G. , Littmann Sten , Duerschlag Julia , Zubkov Mikhail V. , Ploug Helle , Kuypers Marcel M. M. 
Published: November 2018

AbstractSingle-cell measurements of biochemical processes have advanced our understanding of cellular physiology in individual microbes and microbial populations. Due to methodological limitations, little is known about single-cell phosphorus (P) uptake and its importance for microbial growth within mixed field populations. Here, we developed a nanometer-scale secondary ion mass spectrometry (nanoSIMS)-based approach to quantify single-cell P uptake in combination with cellular CO2 and N2 fixation. Applying this approach during a harmful algal bloom (HAB), we found that the toxin-producer Nodularia almost exclusively used phosphate for growth at very low phosphate concentrations in the Baltic Sea. In contrast, the non-toxic Aphanizomenon acquired only 15% of its cellular P-demand from phosphate and ~85% from organic P. When phosphate concentrations were raised, Nodularia thrived indicating that this toxin-producer directly benefits from phosphate inputs. The phosphate availability in the Baltic Sea is projected to rise and therefore might foster more frequent and intense Nodularia blooms with a concomitant rise in the overall toxicity of HABs in the Baltic Sea. With a projected increase in HABs worldwide, the capability to use organic P may be a critical factor that not only determines the microbial community structure, but the overall harmfulness and associated costs of algal blooms.
Bone histology provides insights into the life history mechanisms underlying dwarfing in hipparionins
Authors: Orlandi-Oliveras Guillem , Nacarino-Meneses Carmen , Koufos George D. , Köhler Meike 
Published: November 2018

AbstractSize shifts may be a by-product of alterations in life history traits driven by natural selection. Although this approach has been proposed for islands, it has not yet been explored in continental faunas. The trends towards size decrease experienced by some hipparionins constitute a good case study for the application of a life history framework to understand the size shifts on the continent. Here, we analysed bone microstructure to reconstruct the growth of some different-sized hipparionins from Greece and Spain. The two dwarfed lineages studied show different growth strategies. The Greek hipparions ceased growth early at a small size thus advancing maturity, whilst the slower-growing Spanish hipparion matured later at a small size. Based on predictive life history models, we suggest that high adult mortality was the likely selective force behind early maturity and associated size decrease in the Greek lineage. Conversely, we infer that resource limitation accompanied by high juvenile mortality triggered decrease in growth rate and a relative late maturity in the Spanish lineage. Our results provide evidence that different selective pressures can precipitate different changes in life history that lead to similar size shifts.
Kinetic Equilibrium of Dipolarization Fronts
Authors: Ganguli Gurudas , Crabtree Chris , Fletcher Alex C. , Tejero Erik , Malaspina David , Cohen Ian 
Published: November 2018

AbstractThe unprecedented high-resolution data from the Magnetospheric Multi-Scale (MMS) satellites is revealing the physics of dipolarization fronts created in the aftermath of magnetic reconnection in extraordinary detail. The data shows that the fronts contain structures on small spatial scales beyond the scope of fluid framework. A new kinetic analysis, applied to MMS data here, predicts that global plasma compression produces a unique particle distribution in a narrow boundary layer with separation of electron and ion scale physics. Layer widths on the order of an ion gyro-diameter lead to an ambipolar potential across the magnetic field resulting in strongly sheared flows. Gradients along the magnetic field lines create a potential difference, which can accelerate ions and electrons into beams. These small-scale kinetic effects determine the plasma dynamics in dipolarization fronts, including the origin of the distinctive broadband emissions.
Neurofilament heavy polypeptide protects against reduction in synaptopodin expression and prevents podocyte detachment
Authors: Wang Juan , Hidaka Teruo , Sasaki Yu , Tanaka Eriko , Takagi Miyuki , Shibata Terumi , Kubo Ayano , Trejo Juan Alejandro Oliva , Wang Lining , Asanuma Katsuhiko , Tomino Yasuhiko 
Published: November 2018

AbstractPodocytes are highly specialized cells that line the glomerulus of the kidney and play a role in filtration. Podocyte injury plays a critical role in the development of many kidney diseases, but the underlying mechanisms remain unclear. In this study, we identified that neurofilament heavy polypeptide (NEFH), an intermediate filament component, protects podocyte from injury. We observed that NEFH was upregulated after ADRIAMYCIN(ADR)-induced podocyte injury in both mice and cultured murine podocytes. Immunofluorescence and co-immunoprecipitation analyses revealed that NEFH was colocalized with synaptopodin, a podocyte-specific marker. High NEFH expression in podocytes prevented the Adriamycin-induced reduction in synaptopodin expression. The siRNA-mediated knockdown of NEFH in podocytes reduced the number of vinculin-containing focal contacts, thereby reducing adhesion to the extracellular matrix and increasing podocyte detachment. In addition, NEFH expression was significantly increased in renal biopsy specimens from patients with focal segmental glomerulosclerosis and membranous nephropathy, but in those with minimal change disease. These findings indicate that NEFH is expressed in podocytes during the disease course and that it prevents the reduction in synaptopodin expression and detachment of podocytes.
Another view on Gilbert damping in two-dimensional ferromagnets
Authors: Pervishko Anastasiia A. , Baglai Mikhail I. , Eriksson Olle , Yudin Dmitry 
Published: November 2018

AbstractA keen interest towards technological implications of spin-orbit driven magnetization dynamics requests a proper theoretical description, especially in the context of a microscopic framework, to be developed. Indeed, magnetization dynamics is so far approached within Landau-Lifshitz-Gilbert equation which characterizes torques on magnetization on purely phenomenological grounds. Particularly, spin-orbit coupling does not respect spin conservation, leading thus to angular momentum transfer to lattice and damping as a result. This mechanism is accounted by the Gilbert damping torque which describes relaxation of the magnetization to equilibrium. In this study we work out a microscopic Kubo-Středa formula for the components of the Gilbert damping tensor and apply the elaborated formalism to a two-dimensional Rashba ferromagnet in the weak disorder limit. We show that an exact analytical expression corresponding to the Gilbert damping parameter manifests linear dependence on the scattering rate and retains the constant value up to room temperature when no vibrational degrees of freedom are present in the system. We argue that the methodology developed in this paper can be safely applied to bilayers made of non- and ferromagnetic metals, e.g., CoPt.
Seasonal succession of ciliate Mesodinium spp. with red, green, or mixed plastids and their association with cryptophyte prey
Authors: Nishitani Goh , Yamaguchi Mineo 
Published: November 2018

AbstractMesodinium spp. are commonly found in marine and brackish waters, and several species are known to contain red, green, or both plastids that originate from cryptophyte prey. We observed the seasonal succession of Mesodinium spp. in a Japanese brackish lake, and we analysed the origin and diversity of the various coloured plastids within the cells of Mesodinium spp. using a newly developed primer set that specifically targets the cryptophyte nuclear 18S rRNA gene. Mesodinium rubrum isolated from the lake contained only red plastids originating from cryptophyte Teleaulax amphioxeia. We identified novel Mesodinium sp. that contained only green plastids or both red and green plastids originating from cryptophytes Hemiselmis sp. and Teleaulax acuta. Although the morphology of the newly identified Mesodinium sp. was indistinguishable from that of M. rubrum under normal light microscopy, phylogenetic analysis placed this species between the M. rubrum/major species complex and a well-supported lineage of M. chamaeleon and M. coatsi. Close associations were observed in cryptophyte species composition within cells of Mesodinium spp. and in ambient water samples. The appearance of suitable cryptophyte prey is probably a trigger for succession of Mesodinium spp., and the subsequent abundance of Mesodinium spp. appears to be influenced by water temperature and dissolved inorganic nutrients.
Preparation of Lauroyl Grafted Alginate-Psyllium Husk Gel Composite Film with Enhanced Physicochemical, Mechanical and Antimicrobial Properties
Authors: Fernandes Clara , Acharya Pratap Chandra , Bhatt Shikha 
Published: November 2018

AbstractIn this study, a lauroyl grafted hydrophobic glycolipid derivative of alginate has been successfully synthesized and characterized. This glycolipid has been incorporated into Psyllium husk gel-alginate composite films and compared with the films containing only Psyllim husk gel and Psyllim husk gel-alginate for its mechanical and physicochemical properties. Additionally, the composite film has also been evaluated for protein adsorption and antimicrobial property to verify its utility in biomedical applications. The results showed that the composite films have enhanced physicochemical and mechanical properties. The film produced better swelling characteristic and lower protein adsorption property indicating the usefulness of the film in wound care dressing, particularly for low suppurating wounds. Incorporation of the synthesised glycolipid derivative also imparts antimicrobial activity to the composite film. Therefore, the developed film is capable of sustaining the microbial contamination during the storage and also valuable in the biomedical utility including wound dressings.
Analysis of Zika virus neutralizing antibodies in normal healthy Thais
Authors: Sornjai Wannapa , Jaratsittisin Janejira , Auewarakul Prasert , Wikan Nitwara , Smith Duncan R. 
Published: November 2018

AbstractZika virus (ZIKV) infections have been reported from all over Thailand, but the number of reported cases remains low, suggesting a degree of immune protection against ZIKV infection. To address this possibility, the presence of ZIKV neutralizing antibodies was determined in serum from 135 healthy Thai adults with a plaque reduction neutralization test (PRNT), and a number of samples were subsequently analyzed for the presence of neutralizing antibodies to dengue virus (DENV) and Japanese encephalitis virus (JEV). Results showed that 70.4% (PRNT50 ≥ 10), 55.6 (PRNT50 ≥ 20) or 22.2% (PRNT90 ≥ 20) of the samples showed neutralizing antibodies to ZIKV. Detailed analysis showed no association between the presence of neutralizing antibodies to other flaviviruses (DENV, JEV) and the presence of ZIKV neutralizing antibodies. These results suggest that the level of ZIKV neutralizing antibodies in the Thai population is enough to dampen the transmission of the virus in Thailand.
Biological activity of PtIV prodrugs triggered by riboflavin-mediated bioorthogonal photocatalysis
Authors: Alonso-de Castro Silvia , Terenzi Alessio , Hager Sonja , Englinger Bernhard , Faraone Adriana , Martínez Javier Calvo , Galanski Mathea Sophia , Keppler Bernhard K. , Berger Walter , Salassa Luca 
Published: November 2018

AbstractWe have recently demonstrated that riboflavin (Rf) functions as unconventional bioorthogonal photocatalyst for the activation of PtIV prodrugs. In this study, we show how the combination of light and Rf with two PtIV prodrugs is a feasible strategy for light-mediated pancreatic cancer cell death induction. In Capan-1 cells, which have high tolerance against photodynamic therapy, Rf-mediated activation of the cisplatin and carboplatin prodrugs cis,cis,trans-[Pt(NH3)2(Cl)2(O2CCH2CH2CO2H)2] (1) and cis,cis,trans-[Pt(NH3)2(CBDCA)(O2CCH2CH2CO2H)2] (2, where CBDCA = cyclobutane dicarboxylate) resulted in pronounced reduction of the cell viability, including under hypoxia conditions. Such photoactivation mode occurs to a considerable extent intracellularly, as demonstrated for 1 by uptake and cell viability experiments. 195Pt NMR, DNA binding studies using circular dichroism, mass spectrometry and immunofluorescence microscopy were performed using the Rf-1 catalyst-substrate pair and indicated that cell death is associated with the efficient light-induced formation of cisplatin. Accordingly, Western blot analysis revealed signs of DNA damage and activation of cell death pathways through Rf-mediated photochemical activation. Phosphorylation of H2AX as indicator for DNA damage, was detected for Rf-1 in a strictly light-dependent fashion while in case of free cisplatin also in the dark. Photochemical induction of nuclear pH2AX foci by Rf-1 was confirmed in fluorescence microscopy again proving efficient light-induced cisplatin release from the prodrug system.
Self-Transforming Configuration Based on Atmospheric-Adaptive Materials for Solid Oxide Cells
Authors: Kim Seona , Lee Seungtae , Kim Junyoung , Shin Jeeyoung , Kim Guntae 
Published: November 2018

AbstractSolid oxide cells (SOC) with a symmetrical configuration have been focused due to the practical benefits of such configurations, such as minimized compatibility issues, a simple fabrication process and reduced cost compared to SOCs with the asymmetrical configuration. However, the performance of SOCs using a single type of electrode material (symmetrical configuration) is lower than the performance of those using the dissimilar electrode materials (asymmetrical configuration). Therefore, to achieve a high-performance cell, we design a ‘self-transforming cell’ with the asymmetric configuration using only materials of the single type, one based on atmospheric adaptive materials. Atmospheric-adaptive perovskite Pr0.5Ba0.5Mn0.85Co0.15O3-δ (PBMCo) was used for the so-called self-transforming cell electrodes, which changed to layered perovskite and metal in the fuel atmosphere and retained its original structure in the air atmosphere. In fuel cell mods, the self-transforming cell shows excellent electrochemical performance of 1.10 W cm−2 at 800 °C and good stability for 100 h without any catalyst. In electrolysis mode, the moderate current densities of −0.42 A cm−2 for 3 vol.% H2O and −0.62 A cm−2 for 10 vol.% H2O, respectively, were observed at a cell voltage of 1.3 V at 800 °C. In the reversible cycling test, the transforming cell maintains the constant voltages for 30 h at +/− 0.2 A cm−2 under 10 vol. % H2O.