bluuebunny/crossref_metadata_2025 huggingface dataset:
Bone Marrow Mononuclear Cells Combined with Beta-Tricalcium Phosphate Granules for Alveolar Cleft Repair: A 12-Month Clinical Study
Authors: Du Fengzhou , Wu Huanhuan , Li Haidong , Cai Lei , Wang Qian , Liu Xia , Xiao Ran , Yin Ningbei , Cao Yilin
Published: October 2017

Alveolar cleft is the most common congenital bone defect. Autologous iliac crest bone graft (ICBG) is the most widely adopted procedure for alveolar cleft repair, but the condition is associated with door-site morbidities. For the first time, this study used bone marrow mononuclear cells (BMMNCs) combined with beta-tricalcium phosphate (β-TCP) granules to repair alveolar bone defect. The effectiveness of this technique was compared with autologous ICBG after 12 months of follow-up. The bone formation volume was quantitatively evaluated by three-dimensional computed tomography and computer aided engineering technology. BMMNCs/β-TCP granule grafting was radiographically equivalent to ICBG in alveolar cleft repair. Although considerable resorption was observed up to 6 months after surgery, no significant differences were noted in the Chelsea score and bone formation volume between groups. These finding indicate that BMMNCs/β-TCP grafting is a safe and effective approach for alveolar bone regeneration.
Site-selective spectroscopy with depth resolution using resonant x-ray reflectometry
Authors: Hamann-Borrero J. E. , Macke S. , Gray B. , Kareev M. , Schierle E. , Partzsch S. , Zwiebler M. , Treske U. , Koitzsch A. , Büchner B. , Freeland J. W. , Chakhalian J. , Geck J.
Published: October 2017

Combining dissimilar transition metal oxides (TMOs) into artificial heterostructures enables to create electronic interface systems with new electronic properties that do not exist in bulk. A detailed understanding of how such interfaces can be used to tailor physical properties requires characterization techniques capable to yield interface sensitive spectroscopic information with monolayer resolution. In this regard resonant x-ray reflectivity (RXR) provides a unique experimental tool to achieve exactly this. It yields the element specific electronic depth profiles in a non-destructive manner. Here, using a YBa2Cu3O7−δ
(YBCO) thin film, we demonstrate that RXR is further capable to deliver site selectivity. By applying a new analysis scheme to RXR, which takes the atomic structure of the material into account, together with information of the local charge anisotropy of the resonant ions, we obtained spectroscopic information from the different Cu sites (e.g., chain and plane) throughout the film profile. While most of the film behaves bulk-like, we observe that the Cu-chains at the surface show characteristics of electron doping, whereas the Cu-planes closest to the surface exhibit an orbital reconstruction similar to that observed at La1−x
Ca
x
MnO3/YBCO interfaces.
Quantum size effect on charges and phonons ultrafast dynamics in atomically controlled nanolayers of topological insulators Bi2Te3
Authors: Weis M. , Wilk B. , Vaudel G. , Balin K. , Rapacz R. , Bulou A. , Arnaud B. , Szade J. , Ruello P.
Published: October 2017

Heralded as one of the key elements for next generation spintronics devices, topological insulators (TIs) are now step by step envisioned as nanodevices like charge-to-spin current conversion or as Dirac fermions based nanometer Schottky diode for example. However, reduced to few nanometers, TIs layers exhibit a profound modification of the electronic structure and the consequence of this quantum size effect on the fundamental carriers and phonons ultrafast dynamics has been poorly investigated so far. Here, thanks to a complete study of a set of high quality molecular beam epitaxy grown nanolayers, we report the existence of a critical thickness of around ~6 nm, below which a spectacular reduction of the carrier relaxation time by a factor of ten is found in comparison to bulk Bi2 Te3 In addition, we also evidence an A1g optical phonon mode softening together with the appearance of a thickness dependence of the photoinduced coherent acoustic phonons signals. This drastic evolution of the carriers and phonons dynamics might be due an important electron-phonon coupling evolution due to the quantum confinement. These properties have to be taken into account for future TIs-based spintronic devices.
Genomics of extreme ecological specialists: multiple convergent evolution but no genetic divergence between ecotypes of Maculinea alcon butterflies
Authors: Koubínová Darina , Dincă Vlad , Dapporto Leonardo , Vodă Raluca , Suchan Tomasz , Vila Roger , Alvarez Nadir
Published: October 2017

Biotic interactions are often acknowledged as catalysers of genetic divergence and eventual explanation of processes driving species richness. We address the question, whether extreme ecological specialization is always associated with lineage sorting, by analysing polymorphisms in morphologically similar ecotypes of the myrmecophilous butterfly Maculinea alcon. The ecotypes occur in either hygric or xeric habitats, use different larval host plants and ant species, but no significant distinctive molecular traits have been revealed so far. We apply genome-wide RAD-sequencing to specimens originating from both habitats across Europe in order to get a view of the potential evolutionary processes at work. Our results confirm that genetic variation is mainly structured geographically but not ecologically — specimens from close localities are more related to each other than populations of each ecotype from distant localities. However, we found two loci for which the association with xeric versus hygric habitats is supported by segregating alleles, suggesting convergent evolution of habitat preference. Thus, ecological divergence between the forms probably does not represent an early stage of speciation, but may result from independent recurring adaptations involving few genes. We discuss the implications of these results for conservation and suggest preserving biotic interactions and main genetic clusters.
Resveratrol induces dephosphorylation of Tau by interfering with the MID1-PP2A complex
Authors: Schweiger Susann , Matthes Frank , Posey Karen , Kickstein Eva , Weber Stephanie , Hettich Moritz M. , Pfurtscheller Sandra , Ehninger Dan , Schneider Rainer , Krauß Sybille
Published: October 2017

The formation of paired helical filaments (PHF), which are composed of hyperphosphorylated Tau protein dissociating from microtubules, is one of the pathological hallmarks of Alzheimer’s disease (AD) and other tauopathies. The most important phosphatase that is capable of dephosphorylating Tau at AD specific phospho-sites is protein phosphatase 2 A (PP2A). Here we show that resveratrol, a polyphenol, significantly induces PP2A activity and reduces Tau phosphorylation at PP2A-dependent epitopes. The increase in PP2A activity is caused by decreased expression of the MID1 ubiquitin ligase that mediates ubiquitin-specific modification and degradation of the catalytic subunit of PP2A when bound to microtubules. Interestingly, we further show that MID1 expression is elevated in AD tissue. Our data suggest a key role of MID1 in the pathology of AD and related tauopathies. Together with previous studies showing that resveratrol reduces β-amyloid toxicity they also give evidence of a promising role for resveratrol in the prophylaxis and therapy of AD.
One-step growth of multilayer-graphene hollow nanospheres via the self-elimination of SiC nuclei templates
Authors: Kim Byeong Geun , Nam Deok-Hui , Jeong Seong-Min , Lee Myung-Hyun , Seo Won-Seon , Choi Soon-Mok
Published: October 2017

We introduce a one-step growth method for producing multilayer-graphene hollow nanospheres via a high-temperature chemical vapor deposition process using tetramethylsilane as an organic precursor. When the SiC nuclei were grown under an excess carbon atmosphere, they were surrounded via desorption of the hydrocarbon gas species, and graphene layers formed on the surface of the SiC nuclei via the rearrangement of solid carbon during the heating and cooling. The core SiC nuclei were spontaneously removed by the subsequent thermal decomposition, which also supplied the carbon for the graphene layers. Hence, multilayer-graphene hollow nanospheres were acquired via a one-step process, which was simply controlled by the growth temperature. In this growth process, the SiC nuclei acted as both the template and carbon source for the formation of multilayer-graphene hollow nanospheres.
Live cell X-ray imaging of autophagic vacuoles formation and chromatin dynamics in fission yeast
Authors: Strelnikova Natalja , Sauter Nora , Guizar-Sicairos Manuel , Göllner Michael , Diaz Ana , Delivani Petrina , Chacón Mariola , Tolić Iva M. , Zaburdaev Vasily , Pfohl Thomas
Published: October 2017

Seeing physiological processes at the nanoscale in living organisms without labeling is an ultimate goal in life sciences. Using X-ray ptychography, we explored in situ the dynamics of unstained, living fission yeast Schizosaccharomyces pombe cells in natural, aqueous environment at the nanoscale. In contrast to previous X-ray imaging studies on biological matter, in this work the eukaryotic cells were alive even after several ptychographic X-ray scans, which allowed us to visualize the chromatin motion as well as the autophagic cell death induced by the ionizing radiation. The accumulated radiation of the sequential scans allowed for the determination of a characteristic dose of autophagic vacuole formation and the lethal dose for fission yeast. The presented results demonstrate a practical method that opens another way of looking at living biological specimens and processes in a time-resolved label-free setting.
Genetic Characterization of Chinese fir from Six Provinces in Southern China and Construction of a Core Collection
Authors: Duan Hongjing , Cao Sen , Zheng Huiquan , Hu Dehuo , Lin Jun , Cui Binbin , Lin Huazhong , Hu Ruiyang , Wu Bo , Sun Yuhan , Li Yun
Published: October 2017

Large ex situ germplasm collections of plants generally contain significant diversity. A set of 700 well-conserved Chinese fir (Cunninghamia lanceolata (Lamb.) Hook) clones from six provinces in southern China in the ex situ gene bank of Longshan State Forest, was analyzed using 21 simple sequence repeat markers, with the aim of assessing the genetic diversity of these germplasm resources. Genetic analysis revealed extensive genetic variation among the accessions, with an average of 8.31 alleles per locus and a mean Shannon index of 1.331. Excluding loci with null alleles, we obtained a low level of genetic differentiation among provinces, consistent with the interpopulation genetic variation (1%). Three clusters were identified by STRUCTURE, which did not match the individuals’ geographical provenances. Ten traits related to growth and wood properties were quantified in these individuals, and there was substantial variation in all traits across individuals, these provide a potential source of variation for genetic improvement of the Chinese fir. Screening large collections for multiple-trait selective breeding programs is laborious and expensive; a core collection of 300 accessions, representative of the germplasm, was established, based on genotypic and phenotypic data. The identified small, but diverse, collections will be useful for further genome-wide association studies.
hiPSC-CM Monolayer Maturation State Determines Drug Responsiveness in High Throughput Pro-Arrhythmia Screen
Authors: da Rocha André Monteiro , Campbell Katherine , Mironov Sergey , Jiang Jiang , Mundada Lakshmi , Guerrero-Serna Guadalupe , Jalife José , Herron Todd J.
Published: October 2017

Human induced pluripotent stem cell derived cardiomyocytes (hiPSC-CMs) offer a novel in vitro platform for pre-clinical cardiotoxicity and pro-arrhythmia screening of drugs in development. To date hiPSC-CMs used for cardiotoxicity testing display an immature, fetal-like cardiomyocyte structural and electrophysiological phenotype which has called into question the applicability of hiPSC-CM findings to the adult heart. The aim of the current work was to determine the effect of cardiomyocyte maturation state on hiPSC-CM drug responsiveness. To this end, here we developed a high content pro-arrhythmia screening platform consisting of either fetal-like or mature hiPSC-CM monolayers. Compounds tested in the screen were selected based on the pro-arrhythmia risk classification (Low risk, Intermediate risk, or High risk) established recently by the FDA and major stakeholders in the Drug Discovery field for the validation of the Comprehensive In vitro Pro-Arrhythmia Assay (CiPA). Here we show that maturation state of hiPSC-CMs determines the absolute pro-arrhythmia risk score calculated for these compounds. Thus, the maturation state of hiPSC-CMs should be considered prior to pro-arrhythmia and cardiotoxicity screening in drug discovery programs.
White matter microstructure is associated with functional, cognitive and emotional symptoms 12 months after mild traumatic brain injury
Authors: Hellstrøm Torgeir , Westlye Lars T. , Kaufmann Tobias , Trung Doan Nhat , Søberg Helene L. , Sigurdardottir Solrun , Nordhøy Wibeke , Helseth Eirik , Andreassen Ole A. , Andelic Nada
Published: October 2017

Identifying patients at risk of poor outcome after mild traumatic brain injury (MTBI) is essential to aid prognostics and treatment. Diffuse axonal injury (DAI) may be the primary pathologic feature of MTBI but is normally not detectable by conventional imaging technology. This lack of sensitivity of clinical imaging techniques has impeded a pathophysiologic understanding of the long-term cognitive and emotional consequences of MTBI, which often remain unnoticed and are attributed to factors other than the injury. Diffusion tensor imaging (DTI) is sensitive to microstructural properties of brain tissue and has been suggested to be a promising candidate for the detection of DAIin vivo. In this study, we report strong associations between brain white matter DTI and self-reported cognitive, somatic and emotional symptoms at 12 months post-injury in 134 MTBI patients. The anatomical distribution suggested global associations, in line with the diffuse symptomatology, although the strongest effects were found in frontal regions including the genu of the corpus callosum and the forceps minor. These findings support the hypothesis that DTI may provide increased sensitivity to the diffuse pathophysiology of MTBI and suggest an important role of advanced Magnetic Resonance Imaging (MRI) in trauma care.
Arrhythmogenic cardiomyopathy related DSG2 mutations affect desmosomal cadherin binding kinetics
Authors: Dieding Mareike , Debus Jana Davina , Kerkhoff Raimund , Gaertner-Rommel Anna , Walhorn Volker , Milting Hendrik , Anselmetti Dario
Published: October 2017

Cadherins are calcium dependent adhesion proteins that establish the intercellular mechanical contact by bridging the gap to adjacent cells. Desmoglein-2 (Dsg2) is a specific cadherin of the cell-cell contact in cardiac desmosomes. Mutations in the DSG2-gene are regarded to cause arrhythmogenic (right ventricular) cardiomyopathy (ARVC) which is a rare but severe heart muscle disease. The molecular pathomechanisms of the vast majority of DSG2 mutations, however, are unknown. Here, we investigated the homophilic binding of wildtype Dsg2 and two mutations which are associated with ARVC. Using single molecule force spectroscopy and applying Jarzynski’s equality we determined the kinetics and thermodynamics of Dsg2 homophilic binding. Notably, the free energy landscape of Dsg2 dimerization exposes a high activation barrier which is in line with the proposed strand-swapping binding motif. Although the binding motif is not directly affected by the mutations the binding kinetics differ significantly from the wildtype. Furthermore, we applied a dispase based cell dissociation assay using HT1080 cell lines over expressing Dsg2 wildtype and mutants, respectively. Our molecular and cellular results consistently demonstrate that Dsg2 mutations can heavily affect homophilic Dsg2 interactions. Furthermore, the full thermodynamic and kinetic description of Dsg2 dimerization provides a consistent model of the so far discussed homophilic cadherin binding.
Palaeobiology of red and white blood cell-like structures, collagen and cholesterol in an ichthyosaur bone
Authors: Plet Chloé , Grice Kliti , Pagès Anais , Verrall Michael , Coolen Marco J. L. , Ruebsam Wolfgang , Rickard William D. A. , Schwark Lorenz
Published: October 2017

Carbonate concretions are known to contain well-preserved fossils and soft tissues. Recently, biomolecules (e.g. cholesterol) and molecular fossils (biomarkers) were also discovered in a 380 million-year-old concretion, revealing their importance in exceptional preservation of biosignatures. Here, we used a range of microanalytical techniques, biomarkers and compound specific isotope analyses to report the presence of red and white blood cell-like structures as well as platelet-like structures, collagen and cholesterol in an ichthyosaur bone encapsulated in a carbonate concretion from the Early Jurassic (~182.7 Ma). The red blood cell-like structures are four to five times smaller than those identified in modern organisms. Transmission electron microscopy (TEM) analysis revealed that the red blood cell-like structures are organic in composition. We propose that the small size of the blood cell-like structures results from an evolutionary adaptation to the prolonged low oxygen atmospheric levels prevailing during the 70 Ma when ichthyosaurs thrived. The δ13C of the ichthyosaur bone cholesterol indicates that it largely derives from a higher level in the food chain and is consistent with a fish and cephalopod diet. The combined findings above demonstrate that carbonate concretions create isolated environments that promote exceptional preservation of fragile tissues and biomolecules.
Association between post-transplant red cell distribution width and prognosis of kidney transplant recipients
Authors: Park Sehoon , Kim Young Hoon , Kim Yong Chul , Yu Mi-Yeon , Lee Jung Pyo , Han Duck Jong , Kim Yon Su , Park Su-Kil
Published: October 2017

The role of elevated post-transplant red cell distribution width (RDW) as a predictive factor for graft loss remains unclear, although RDW was reported to be significantly associated with poor prognosis in various clinical fields. We performed a retrospective cohort study with 2,939 kidney transplant patients from two tertiary teaching hospitals in Korea. RDW level at transplantation and 3-months post-transplantation were collected. Those with RDW in the upper quartile range were considered to have increased RDW (>14.9%). Death-with-graft-function (DWGF), death-censored graft failure (DCGF), and composite graft loss were assessed as the study outcomes, using multivariable cox proportional hazard model. At the median follow-up duration of 6.6 (3.6–11.4) years, 336 patients experienced graft loss. There were 679 patients with elevated RDW at 3-months post-transplant. Elevated RDW was associated with composite graft loss (adjusted hazard ratio, 1.60, 95% confidence interval, 1.23–2.07, P < 0.001), even after adjusted for hemoglobin and various clinical factors. The 1% increment of post-transplant RDW was also significantly associated with the outcome, regardless of the presence of anemia. The worst prognosis was seen in patients with elevated RDW after transplantation, but not at baseline. Therefore, post-transplant RDW level may be significantly associated with patient prognosis, independent of hemoglobin values.
Tunable two-dimensional assembly of colloidal particles in rotating electric fields
Authors: Yakovlev Egor V. , Komarov Kirill A. , Zaytsev Kirill I. , Kryuchkov Nikita P. , Koshelev Kirill I. , Zotov Arsen K. , Shelestov Dmitry A. , Tolstoguzov Victor L. , Kurlov Vladimir N. , Ivlev Alexei V. , Yurchenko Stanislav O.
Published: October 2017

Tunable interparticle interactions in colloidal suspensions are of great interest because of their fundamental and practical significance. In this paper we present a new experimental setup for self-assembly of colloidal particles in two-dimensional systems, where the interactions are controlled by external rotating electric fields. The maximal magnitude of the field in a suspension is 25 V/mm, the field homogeneity is better than 1% over the horizontal distance of 250 μm, and the rotation frequency is in the range of 40 Hz to 30 kHz. Based on numerical electrostatic calculations for the developed setup with eight planar electrodes, we found optimal experimental conditions and performed demonstration experiments with a suspension of 2.12 μm silica particles in water. Thanks to its technological flexibility, the setup is well suited for particle-resolved studies of fundamental generic phenomena occurring in classical liquids and solids, and therefore it should be of interest for a broad community of soft matter, photonics, and material science.
Long-lived laser-induced arc discharges for energy channeling applications
Authors: Point Guillaume , Arantchouk Leonid , Thouin Emmanuelle , Carbonnel Jérôme , Mysyrowicz André , Houard Aurélien
Published: October 2017

Laser filamentation offers a promising way for the remote handling of large electrical power in the form of guided arc discharges. We here report that it is possible to increase by several orders of magnitude the lifetime of straight plasma channels from filamentation-guided sparks in atmospheric air. A 30 ms lifetime can be reached using a low-intensity, 100 mA current pulse. Stability of the plasma shape is maintained over such a timescale through a continuous Joule heating from the current. This paves the way for applications based on the generation of straight, long duration plasma channels, like virtual plasma antennas or contactless transfer of electric energy.
Active modulation of the calcifying fluid carbonate chemistry (δ11B, B/Ca) and seasonally invariant coral calcification at sub-tropical limits
Authors: Ross Claire L. , Falter James L. , McCulloch Malcolm T.
Published: October 2017

Coral calcification is dependent on both the supply of dissolved inorganic carbon (DIC) and the up-regulation of pH in the calcifying fluid (cf). Using geochemical proxies (δ11B, B/Ca, Sr/Ca, Li/Mg), we show seasonal changes in the pHcf and DICcf for Acropora yongei and Pocillopora damicornis growing in-situ at Rottnest Island (32°S) in Western Australia. Changes in pHcf range from 8.38 in summer to 8.60 in winter, while DICcf is 25 to 30% higher during summer compared to winter (×1.5 to ×2 seawater). Thus, both variables are up-regulated well above seawater values and are seasonally out of phase with one another. The net effect of this counter-cyclical behaviour between DICcf and pHcf is that the aragonite saturation state of the calcifying fluid (Ωcf) is elevated ~4 times above seawater values and is ~25 to 40% higher during winter compared to summer. Thus, these corals control the chemical composition of the calcifying fluid to help sustain near-constant year-round calcification rates, despite a seasonal seawater temperature range from just ~19° to 24 °C. The ability of corals to up-regulate Ωcf is a key mechanism to optimise biomineralization, and is thus critical for the future of coral calcification under high CO2 conditions.
Optogenetic Neuronal Silencing in Drosophila during Visual Processing
Authors: Mauss Alex S. , Busch Christian , Borst Alexander
Published: October 2017

Optogenetic channels and ion pumps have become indispensable tools in neuroscience to manipulate neuronal activity and thus to establish synaptic connectivity and behavioral causality. Inhibitory channels are particularly advantageous to explore signal processing in neural circuits since they permit the functional removal of selected neurons on a trial-by-trial basis. However, applying these tools to study the visual system poses a considerable challenge because the illumination required for their activation usually also stimulates photoreceptors substantially, precluding the simultaneous probing of visual responses. Here, we explore the utility of the recently discovered anion channelrhodopsins GtACR1 and GtACR2 for application in the visual system of Drosophila. We first characterized their properties using a larval crawling assay. We further obtained whole-cell recordings from cells expressing GtACR1, which mediated strong and light-sensitive photocurrents. Finally, using physiological recordings and a behavioral readout, we demonstrate that GtACR1 enables the fast and reversible silencing of genetically targeted neurons within circuits engaged in visual processing.
Cytolytic toxin production by Staphylococcus aureus is dependent upon the activity of the protoheme IX farnesyltransferase
Authors: Stevens Emily , Laabei Maisem , Gardner Stewart , Somerville Greg A. , Massey Ruth C.
Published: October 2017

Staphylococcus aureus is a medically important pathogen with an abundance of virulence factors that are necessary for survival within a host, including the production of cytolytic toxins. The regulation of toxin production is mediated by the Agr quorum sensing system, and a poorly defined post-exponential growth phase signal independent of Agr. As part of a recent genome wide association study (GWAS) to identify novel loci that alter the expression of cytolytic toxins, a polymorphism in the cyoE gene, which encodes a protoheme IX farnesyltransferase, was identified. This enzyme is essential for processing heme into the electron transport chain for use as an electron acceptor. Interestingly, without this enzyme S. aureus were repressed in their ability to secrete cytolytic toxins, and this appears to be mediated through repression of the Agr quorum sensing system. We hypothesize that the loss of electron transport is inducing feedback inhibition of metabolic capabilities that suppress the TCA cycle, and that this coupled with decreased RNAIII transcription prevents synthesis of cytolytic toxins.
FTY720-induced endocytosis of yeast and human amino acid transporters is preceded by reduction of their inherent activity and TORC1 inhibition
Authors: Barthelemy Céline , Barry Abdoulaye Oury , Twyffels Laure , André Bruno
Published: October 2017

FTY720 is a sphingoid base analog that acts as an anticancer agent in animal models. Its effect on tumor cells stems largely from its ability to trigger endocytosis of several nutrient transporters. The observation that FTY720 similarly stimulates downregulation of amino acid permeases in yeast suggests that the cellular mechanisms it targets, which are still poorly characterized, are evolutionarily conserved. We here report that adding FTY720 to yeast cells results in rapid inhibition of the intrinsic activity of multiple permeases. This effect is associated with inhibition of the TORC1 kinase complex, which in turn promotes ubiquitin-dependent permease endocytosis. Further analysis of the Gap1 permease showed that FTY720 elicits its ubiquitylation via the same factors that promote this modification when TORC1 is inhibited by rapamycin. We also show that FTY720 promotes endocytosis of the LAT1/SLC7A5 amino acid transporter in HeLa cells, this being preceded by loss of its transport activity and by mTORC1 inhibition. Our data suggest that in yeast, TORC1 deactivation resulting from FTY720-mediated inhibition of membrane transport elicits permease endocytosis. The same process seems to occur in human cells even though our data and previous reports suggest that FTY720 promotes transporter endocytosis via an additional mechanism insensitive to rapamycin.
Deciphering pore-level precipitation mechanisms
Authors: Prasianakis N. I. , Curti E. , Kosakowski G. , Poonoosamy J. , Churakov S. V.
Published: October 2017

Mineral precipitation and dissolution in aqueous solutions has a significant effect on solute transport and structural properties of porous media. The understanding of the involved physical mechanisms, which cover a large range of spatial and temporal scales, plays a key role in several geochemical and industrial processes. Here, by coupling pore scale reactive transport simulations with classical nucleation theory, we demonstrate how the interplay between homogeneous and heterogeneous precipitation kinetics along with the non-linear dependence on solute concentration affects the evolution of the system. Such phenomena are usually neglected in pure macroscopic modelling. Comprehensive parametric analysis and comparison with laboratory experiments confirm that incorporation of detailed microscale physical processes in the models is compulsory. This sheds light on the inherent coupling mechanisms and bridges the gap between atomistic processes and macroscopic observations.
Transcriptomics and proteomics reveal genetic and biological basis of superior biomass crop Miscanthus
Authors: Sheng Jiajing , Zheng Xingfei , Wang Jia , Zeng Xiaofei , Zhou Fasong , Jin Surong , Hu Zhongli , Diao Ying
Published: October 2017

Miscanthus is a rhizomatous C4 grass which is considered as potential high-yielding energy crop with the low-nutrient requirements, high water-use efficiency, and capability of C mitigation. To better understand the genetic basis, an integrative analysis of the transcriptome and proteome was performed to identify important genes and pathways involved in Miscanthus leaves. At the transcript level, 64,663 transcripts in M. lutarioriparius, 97,043 in M. sacchariflorus, 97,043 in M. sinensis, 67,323 in M. floridulus and 70,021 in M. × giganteus were detected by an RNA sequencing approach. At the protein level, 1964 peptide-represented proteins were identified and 1933 proteins differed by 1.5-fold or more in their relative abundance, as indicated by iTRAQ (isobaric tags for relative and absolute quantitation) analysis. Phylogenies were constructed from the nearly taxa of Miscanthus. A large number of genes closely related to biomass production were found. And SSR markers and their corresponding primers were derived from Miscanthus transcripts and 90% of them were successfully detected by PCR amplification among Miacanthus species. These similarities and variations on the transcriptional and proteomic level between Miscanthus species will serve as a resource for research in Miscanthus and other lignocellulose crops.
Spatial Heterogeneity of SOM Concentrations Associated with White-rot Versus Brown-rot Wood Decay
Authors: Bai Zhen , Ma Qiang , Dai Yucheng , Yuan Haisheng , Ye Ji , Yu Wantai
Published: October 2017

White- and brown-rot fungal decay via distinct pathways imparts characteristic molecular imprints on decomposing wood. However, the effect that a specific wood-rotting type of fungus has on proximal soil organic matter (SOM) accumulation remains unexplored. We investigated the potential influence of white- and brown-rot fungi-decayedAbies nephrolepislogs on forest SOM stocks (i.e., soil total carbon (C) and nitrogen (N)) and the concentrations of amino sugars (microbial necromass) at different depths and horizontal distances from decaying woody debris. The brown-rot fungal wood decay resulted in higher concentrations of soil C and N and a greater increase in microbial necromass (i.e., 1.3- to 1.7-fold greater) than the white-rot fungal wood decay. The white-rot sets were accompanied by significant differences in the proportions of the bacterial residue index (muramic acid%) with soil depth; however, the brown-rot-associated soils showed complementary shifts, primarily in fungal necromass, across horizontal distances. Soil C and N concentrations were significantly correlated with fungal rather than bacterial necromass in the brown-rot systems. Our findings confirmed that the brown-rot fungi-dominated degradation of lignocellulosic residues resulted in a greater SOM buildup than the white-rot fungi-dominated degradation.
A chloroquine-induced macrophage-preconditioning strategy for improved nanodelivery
Authors: Wolfram Joy , Nizzero Sara , Liu Haoran , Li Feng , Zhang Guodong , Li Zheng , Shen Haifa , Blanco Elvin , Ferrari Mauro
Published: October 2017

Site-specific localization is critical for improving the therapeutic efficacy and safety of drugs. Nanoparticles have emerged as promising tools for localized drug delivery. However, over 90% of systemically injected nanocarriers typically accumulate in the liver and spleen due to resident macrophages that form the mononuclear phagocyte system. In this study, the clinically approved antimalarial agent chloroquine was shown to reduce nanoparticle uptake in macrophages by suppressing endocytosis. Pretreatment of mice with a clinically relevant dose of chloroquine substantially decreased the accumulation of liposomes and silicon particles in the mononuclear phagocyte system and improved tumoritropic and organotropic delivery. The novel use of chloroquine as a macrophage-preconditioning agent presents a straightforward approach for addressing a major barrier in nanomedicine. Moreover, this priming strategy has broad applicability for improving the biodistribution and performance of particulate delivery systems. Ultimately, this study defines a paradigm for the combined use of macrophage-modulating agents with nanotherapeutics for improved site-specific delivery.
Dimethyl pyrazol-based nitrification inhibitors effect on nitrifying and denitrifying bacteria to mitigate N2O emission
Authors: Torralbo Fernando , Menéndez Sergio , Barrena Iskander , Estavillo José M. , Marino Daniel , González-Murua Carmen
Published: October 2017

Nitrous oxide (N2O) emissions have been increasing as a result of intensive nitrogen (N) fertilisation. Soil nitrification and denitrification are the main sources of N2O, and the use of ammonium-based fertilisers combined with nitrification inhibitors (NIs) could be useful in mitigating N2O emissions from agricultural systems. In this work we looked at the N2O mitigation capacity of two dimethylpyrazol-based NIs, 3,4-dimethylpyrazole phosphate (DMPP) and 2-(N-3,4-dimethyl-1H-pyrazol-1-yl) succinic acid isomeric mixture (DMPSA), on soil nitrifying and denitrifying microbial populations under two contrasting soil water contents (40% and 80% soil water filled pore space; WFPS). Our results show that DMPP and DMPSA are equally efficient at reducing N2O emissions under 40% WFPS conditions by inhibiting bacterial ammonia oxidation. In contrast, at 80% WFPS DMPSA was less efficient than DMPP at reducing N2O emissions. Interestingly, at 80% WFPS, where lowered oxygen availability limits nitrification, both DMPP and DMPSA not only inhibited nitrification but also stimulated N2O reduction to molecular nitrogen (N2) via nitrous oxide reductase activity (Nos activity). Therefore, in this work we observed that DMP-based NIs stimulated the reduction of N2O to N2by nitrous oxide reductase during the denitrification process.
Near-simultaneous intravital microscopy of glucose uptake and mitochondrial membrane potential, key endpoints that reflect major metabolic axes in cancer
Authors: Zhu Caigang , Martinez Amy F. , Martin Hannah L. , Li Martin , Crouch Brian T. , Carlson David A. , Haystead Timothy A. J. , Ramanujam Nimmi
Published: October 2017

While the demand for metabolic imaging has increased in recent years, simultaneous in vivo measurement of multiple metabolic endpoints remains challenging. Here we report on a novel technique that provides in vivo high-resolution simultaneous imaging of glucose uptake and mitochondrial metabolism within a dynamic tissue microenvironment. Two indicators were leveraged; 2-[N-(7-nitrobenz-2-oxa-1, 3-diazol-4-yl) amino]-2-deoxy-D-glucose (2-NBDG) reports on glucose uptake and Tetramethylrhodamine ethyl ester (TMRE) reports on mitochondrial membrane potential. Although we demonstrated that there was neither optical nor chemical crosstalk between 2-NBDG and TMRE, TMRE uptake was significantly inhibited by simultaneous injection with 2-NBDG in vivo. A staggered delivery scheme of the two agents (TMRE injection was followed by 2-NBDG injection after a 10-minute delay) permitted near-simultaneous in vivo microscopy of 2-NBDG and TMRE at the same tissue site by mitigating the interference of 2-NBDG with normal glucose usage. The staggered delivery strategy was evaluated under both normoxic and hypoxic conditions in normal tissues as well as in a murine breast cancer model. The results were consistent with those expected for independent imaging of 2-NBDG and TMRE. This optical imaging technique allows for monitoring of key metabolic endpoints with the unique benefit of repeated, non-destructive imaging within an intact microenvironment.
Mobile fluxons as coherent probes of periodic pinning in superconductors
Authors: Dobrovolskiy Oleksandr V. , Huth Michael , Shklovskij Valerij A. , Vovk Ruslan V.
Published: October 2017

The interaction of (quasi)particles with a periodic potential arises in various domains of science and engineering, such as solid-state physics, chemical physics, and communication theory. An attractive test ground to investigate this interaction is represented by superconductors with artificial pinning sites, where magnetic flux quanta (Abrikosov vortices) interact with the pinning potential U(r) = U(r + R) induced by a nanostructure. At a combination of microwave and dc currents, fluxons act as mobile probes of U(r): The ac component shakes the fluxons in the vicinity of their equilibrium points which are unequivocally determined by the local pinning force counterbalanced by the Lorentz force induced by the dc current, linked to the curvature of U(r) which can then be used for a successful fitting of the voltage responses. A good correlation of the deduced dependences U(r) with the cross sections of the nanostructures points to that pinning is primarily caused by vortex length reduction. Our findings pave a new route to a non-destructive evaluation of periodic pinning in superconductor thin films. The approach should also apply to a broad class of systems whose evolution in time can be described by the coherent motion of (quasi)particles in a periodic potential.
3D Printing Bioinspired Ceramic Composites
Authors: Feilden Ezra , Ferraro Claudio , Zhang Qinghua , García-Tuñón Esther , D’Elia Eleonora , Giuliani Finn , Vandeperre Luc , Saiz Eduardo
Published: October 2017

Natural structural materials like bone and shell have complex, hierarchical architectures designed to control crack propagation and fracture. In modern composites there is a critical trade-off between strength and toughness. Natural structures provide blueprints to overcome this, however this approach introduces another trade-off between fine structural manipulation and manufacturing complex shapes in practical sizes and times. Here we show that robocasting can be used to build ceramic-based composite parts with a range of geometries, possessing microstructures unattainable by other production technologies. This is achieved by manipulating the rheology of ceramic pastes and the shear forces they experience during printing. To demonstrate the versatility of the approach we have fabricated highly mineralized composites with microscopic Bouligand structures that guide crack propagation and twisting in three dimensions, which we have followed using an original in-situ crack opening technique. In this way we can retain strength while enhancing toughness by using strategies taken from crustacean shells.
Contributions of MyD88-dependent receptors and CD11c-positive cells to corneal epithelial barrier function against Pseudomonas aeruginosa
Authors: Metruccio Matteo M. E. , Tam Connie , Evans David J. , Xie Anna L. , Stern Michael E. , Fleiszig Suzanne M. J.
Published: October 2017

Previously we reported that corneal epithelial barrier function against Pseudomonas aeruginosa was MyD88-dependent. Here, we explored contributions of MyD88-dependent receptors using vital mouse eyes and confocal imaging. Uninjured IL-1R (−/−) or TLR4 (−/−) corneas, but not TLR2 (−/−), TLR5 (−/−), TLR7 (−/−), or TLR9 (−/−), were more susceptible to P. aeruginosa adhesion than wild-type (3.8-fold, 3.6-fold respectively). Bacteria adherent to the corneas of IL-1R (−/−) or TLR5 (−/−) mice penetrated beyond the epithelial surface only if the cornea was superficially-injured. Bone marrow chimeras showed that bone marrow-derived cells contributed to IL-1R-dependent barrier function. In vivo, but not ex vivo, stromal CD11c+ cells responded to bacterial challenge even when corneas were uninjured. These cells extended processes toward the epithelial surface, and co-localized with adherent bacteria in superficially-injured corneas. While CD11c+ cell depletion reduced IL-6, IL-1β, CXCL1, CXCL2 and CXCL10 transcriptional responses to bacteria, and increased susceptibility to bacterial adhesion (>3-fold), the epithelium remained resistant to bacterial penetration. IL-1R (−/−) corneas also showed down-regulation of IL-6 and CXCL1 genes with and without bacterial challenge. These data show complex roles for TLR4, TLR5, IL-1R and CD11c+ cells in constitutive epithelial barrier function against P. aeruginosa, with details dependent upon in vivo conditions.
Genetic Variants Associated with Episodic Ataxia in Korea
Authors: Choi Kwang-Dong , Kim Ji-Soo , Kim Hyo-Jung , Jung Ileok , Jeong Seong-Hae , Lee Seung-Han , Kim Dong Uk , Kim Sang-Ho , Choi Seo Young , Shin Jin-Hong , Kim Dae-Seong , Park Kyung-Pil , Kim Hyang-Sook , Choi Jae-Hwan
Published: October 2017

Episodic ataxia (EA) is a rare neurological condition characterized by recurrent spells of truncal ataxia and incoordination. Five genes (KCNA1, CACNA1A, CACNB4, SLC1A3, and UBR4) have been linked to EA. Despite extensive efforts to genetically diagnose EA, many patients remain still undiagnosed. Whole-exome sequencing was carried out in 39 Korean patients with EA to identify pathogenic mutations of the five known EA genes. We also evaluated 40 candidate genes that cause EA as a secondary phenotype or cerebellar ataxia. Eighteen patients (46%) revealed genetic information useful for establishing a molecular diagnosis of EA. In 11 patients, 16 pathogenic mutations were detected in three EA genes. These included nine mutations in CACNA1A, three in SLC1A3, and four in UBR4. Three patients had mutations in two genes, either CACNA1A and SLC1A3 or CACNA1A and UBR4, suggesting that SLC1A3 and UBR4 may act as genetic modifiers with synergic effects on the abnormal presynaptic activity caused by CACNA1A mutations. In seven patients with negative results for screening of EA genes, potential pathogenic mutations were identified in the candidate genes ATP1A2, SCN1A, TTBK2, TGM6, FGF14, and KCND3. This study demonstrates the genetic heterogeneity of Korean EA, and indicates that whole-exome sequencing may be useful for molecular genetic diagnosis of EA.
Evidence of Reproductive Stress in Titanosaurian Sauropods Triggered by an Increase in Ecological Competition
Authors: Sellés Albert G. , Vila Bernat , Galobart Àngel
Published: October 2017

The occurrence of dinosaur pathologic eggs in the Late Cretaceous of Europe is well known, but their origin remains unclear. Here we expose the results of a detailed sampling of the conspicuous fossil record of Late Cretaceous titanosaurian eggs (oogenus Megaloolithius) from several southwestern Europe basins. After examining more than 450 samples, we observed a remarkable and statistically supported occurrence of multiple pathologic eggs in a relatively short stratigraphic range at the end of the early Maastrichtian, circa 71-70 Ma. All pathologic specimens exhibit multi-layered eggshell condition, a characteristic related to dystocia, or egg retention within the female uterus for an abnormal prolonged period of time. After exploring various scenarios, the occurrence of pathologic eggs is strongly correlated with an intense dinosaur faunal replacement that occurred during the early Maastrichtian in the Ibero-Armorican Island. Given that inter-species competiveness is proved to produce major affects in ecological communities, our results suggest that pathologies in the eggs of European titanosaurians could be a consequence of an increase in reproductive stress triggered by direct ecological competition between different dinosaurs. Thus, the present study provides a new perspective of how dinosaurs might have been affected by ecological/environmental disturbance.
Female alcohol consumption and fecundability: a systematic review and dose-response meta-analysis
Authors: Fan Dazhi , Liu Li , Xia Qing , Wang Wen , Wu Shuzhen , Tian Guo , Liu Ying , Ni Jing , Wu Song , Guo Xiaoling , Liu Zhengping
Published: October 2017

To what extent could alcohol consumption affects female fertility is still unclear. The aim of this study was to quantitatively summarize the dose-response relation between total and specific types of alcohol beverage (beer, wine, and spirits) consumption in female and the fecundability. Four electronic databases were searched. Observational studies (cohort and case-control) that provided female alcohol consumption and fecundity were eligible. Nineteen studies, involving 98657 women, were included in this study. Compared to non-drinkers, the combined estimate (with relative risk, RR) of alcohol consumers on fecundability was 0.87 (95% CI 0.78–0.95) for overall 19 studies. Compared to non-drinkers, the pooled estimates were 0.89 (95% CI 0.82–0.97) for light drinkers (≤12.5 g/day of ethanol) and 0.77 (95% CI 0.61–0.94) for moderate-heavy drinkers (>12.5 g/day of ethanol). Moreover, compared to non-drinkers, the corresponding estimates on fecundability were 0.98 (95% CI 0.85–1.11), 1.02 (95% CI 0.99–1.05), and 0.92 (95% CI 0.83–1.01) for studies focused on wine, beer and spirits, respectively. Dose-response meta-analysis suggested a linear association between decreased fecundability and every 12.5 g/d increasing in alcohol consumption with a RR 0.98 (95% CI 0.97–0.99). This first systematic review and meta-analysis suggested that female alcohol consumption was associated with a reduced fecundability.
Comparing crop rotations between organic and conventional farming
Authors: Barbieri Pietro , Pellerin Sylvain , Nesme Thomas
Published: October 2017

Cropland use activities are major drivers of global environmental changes and of farming system resilience. Rotating crops is a critical land-use driver, and a farmers’ key strategy to control environmental stresses and crop performances. Evidence has accumulated that crop rotations have been dramatically simplified over the last 50 years. In contrast, organic farming stands as an alternative production way that promotes crop diversification. However, our understanding of crop rotations is surprisingly limited. In order to understand if organic farming would result in more diversified and multifunctional landscapes, we provide here a novel, systematic comparison of organic-to-conventional crop rotations at the global scale based on a meta-analysis of the scientific literature, paired with an independent analysis of organic-to-conventional land-use. We show that organic farming leads to differences in land-use compared to conventional: overall, crop rotations are 15% longer and result in higher diversity and evener crop species distribution. These changes are driven by a higher abundance of temporary fodders, catch and cover-crops, mostly to the detriment of cereals. We also highlighted differences in organic rotations between Europe and North-America, two leading regions for organic production. This increased complexity of organic crop rotations is likely to enhance ecosystem service provisioning to agroecosystems.