bluuebunny/crossref_metadata_2025 huggingface dataset:
Contrasting Global Patterns of Spatially Periodic Fairy Circles and Regular Insect Nests in Drylands
Authors: Getzin Stephan , Yizhaq Hezi , Cramer Michael D. , Tschinkel Walter R.
Published: November 2019

Numerical analysis of spatial pattern is widely used in ecology to describe the characteristics of floral and faunal distributions. These methods allow attribution of pattern to causal mechanisms by uncovering the specific signatures of patterns and causal agents. For example, grassland‐gap patterns called fairy circles (FCs) in Namibia and Australia are characterized by highly regular and homogenous distributions across landscapes that show spatially periodic ordering. These FCs have been suggested to be caused by both social insects and competitive plant interactions. We compared eight Namibian and Australian FC patterns and also modeled FCs to 16 patterns of social insect nests in Africa, Australia, and America that include the most regular termite mound patterns known. For pattern‐process inference, we used spatial statistics based on both nearest‐neighbor analysis and neighborhood‐density functions. None of the analyzed insect‐nest distributions attain the spatially periodic ordering that is typical of FCs. The inherently more variable patterns of termite and ant nests are commonly attributable to well documented aspects of the faunal life‐history. Our quantitative evidence from drylands shows that the more variable insect‐nest distributions in water‐limited environments cannot explain the characteristic spatial signature of FCs. The analysis demonstrates the interpretation of scale‐dependent neighborhood‐density functions and that it is the identification of unique spatial signatures in regular patterns that need to be linked to process. While our results cannot verify a specific hypothesis, they support the hypothesis that FCs in these drylands are more likely an emergent vegetation pattern caused by strong plant competition for water.
Scalable Flux Metrics at the Channel‐Floodplain Interface as Indicators of Lateral Surface Connectivity During Flood Events
Authors: Byrne C. F. , Stone M. C. , Morrison R. R.
Published: November 2019

Lateral surface connectivity (LSC), defined here as the surficial component of hydrologic exchange flows perpendicular to longitudinal flow, is vital to biogeochemical, geomorphological, and ecological processes on floodplains. Because rivers throughout much of the world have been subjected to anthropogenic manipulation, LSC has been greatly altered. While qualitative descriptions of LSC exist, only a limited number of studies quantify this process. The objective of this study was to quantify mass and momentum flux as proxies for LSC. This objective was met through the analysis of hydrodynamic model outputs along a 10‐km reach of the Middle Rio Grande near Albuquerque, New Mexico, USA. Mass and momentum fluxes were quantified for two synthetic floods across three spatial scales: geomorphic sub‐units, units, and reaches. In addition, three floodplain surface elevations were defined: inset, restored, and historical. Mass and momentum fluxes displayed distinct hydrodynamic signatures at each floodplain surface elevation. Inset floodplains were subjected to the greatest and most widely distributed flux magnitudes, an indication of the anthropogenic alteration along the reach. Flux heterogeneity on inset surfaces was also greatest, and increased flood magnitude did not result in comparable heterogeneity at higher floodplain elevations. Unsteady results showed that peak flux magnitudes can occur on the rising and falling limbs of a flood hydrograph, providing evidence of hysteresis in channel‐floodplain connections. Ultimately, the results are indicative of complexities associated with LSC processes along geomorphologically altered channel‐floodplain systems. The scalable methods are applicable to a wide variety of river‐floodplain systems and are complementary to empirical flux measurements.
Illusory sound texture reveals multi-second statistical completion in auditory scene analysis
Authors: McWalter Richard , McDermott Josh H.
Published: November 2019

Sound sources in the world are experienced as stable even when intermittently obscured, implying perceptual completion mechanisms that “fill in” missing sensory information. We demonstrate a filling-in phenomenon in which the brain extrapolates the statistics of background sounds (textures) over periods of several seconds when they are interrupted by another sound, producing vivid percepts of illusory texture. The effect differs from previously described completion effects in that 1) the extrapolated sound must be defined statistically given the stochastic nature of texture, and 2) the effect lasts much longer, enabling introspection and facilitating assessment of the underlying representation. Illusory texture biases subsequent texture statistic estimates indistinguishably from actual texture, suggesting that it is represented similarly to actual texture. The illusion appears to represent an inference about whether the background is likely to continue during concurrent sounds, providing a stable statistical representation of the ongoing environment despite unstable sensory evidence.
Author Correction: Metal-coordinated sub-10 nm membranes for water purification
Authors: You Xinda , Wu Hong , Zhang Runnan , Su Yanlei , Cao Li , Yu Qianqian , Yuan Jinqiu , Xiao Ke , He Mingrui , Jiang Zhongyi
Published: November 2019

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Nature of excitations and defects in structural glasses
Authors: Scalliet Camille , Berthier Ludovic , Zamponi Francesco
Published: November 2019

The nature of defects in amorphous materials, analogous to vacancies and dislocations in crystals, remains elusive. Here, we explore their nature in a three-dimensional microscopic model glass-former that describes granular, colloidal, atomic and molecular glasses by changing the temperature and density. We find that all glasses evolve in a very rough energy landscape, with a hierarchy of barrier sizes corresponding to both localized and delocalized excitations. Collective excitations dominate in the jamming regime relevant for granular and colloidal glasses. By moving gradually to larger densities describing atomic and molecular glasses, the system crosses over to a regime dominated by localized defects and relatively simpler landscapes. We quantify the energy and temperature scales associated to these defects and their evolution with density. Our results pave the way to a systematic study of low-temperature physics in a broad range of physical conditions and glassy materials.
Control of the temporal and polarization response of a multimode fiber
Authors: Mounaix Mickael , Carpenter Joel
Published: November 2019

Control of the spatial and temporal properties of light propagating in disordered media have been demonstrated over the last decade using spatial light modulators. Most of the previous studies demonstrated spatial focusing to the speckle grain size, and manipulation of the temporal properties of the achieved focus. In this work, we demonstrate an approach to control the total temporal impulse response, not only at a single speckle grain but over all spatial degrees of freedom (spatial and polarization modes) at any arbitrary delay time through a multimode fiber. Global enhancement or suppression of the total light intensity exiting a multimode fibre is shown for arbitrary delays and polarization states. This work could benefit to applications that require pulse delivery in disordered media.
From small-scale forest structure to Amazon-wide carbon estimates
Authors: Rödig Edna , Knapp Nikolai , Fischer Rico , Bohn Friedrich J. , Dubayah Ralph , Tang Hao , Huth Andreas
Published: November 2019

Tropical forests play an important role in the global carbon cycle. High-resolution remote sensing techniques, e.g., spaceborne lidar, can measure complex tropical forest structures, but it remains a challenge how to interpret such information for the assessment of forest biomass and productivity. Here, we develop an approach to estimate basal area, aboveground biomass and productivity within Amazonia by matching 770,000 GLAS lidar (ICESat) profiles with forest simulations considering spatial heterogeneous environmental and ecological conditions. This allows for deriving frequency distributions of key forest attributes for the entire Amazon. This detailed interpretation of remote sensing data improves estimates of forest attributes by 20–43% as compared to (conventional) estimates using mean canopy height. The inclusion of forest modeling has a high potential to close a missing link between remote sensing measurements and the 3D structure of forests, and may thereby improve continent-wide estimates of biomass and productivity.
WUSCHEL acts as an auxin response rheostat to maintain apical stem cells in Arabidopsis
Authors: Ma Yanfei , Miotk Andrej , Šutiković Zoran , Ermakova Olga , Wenzl Christian , Medzihradszky Anna , Gaillochet Christophe , Forner Joachim , Utan Gözde , Brackmann Klaus , Galván-Ampudia Carlos S. , Vernoux Teva , Greb Thomas , Lohmann Jan U.
Published: November 2019

To maintain the balance between long-term stem cell self-renewal and differentiation, dynamic signals need to be translated into spatially precise and temporally stable gene expression states. In the apical plant stem cell system, local accumulation of the small, highly mobile phytohormone auxin triggers differentiation while at the same time, pluripotent stem cells are maintained throughout the entire life-cycle. We find that stem cells are resistant to auxin mediated differentiation, but require low levels of signaling for their maintenance. We demonstrate that the WUSCHEL transcription factor confers this behavior by rheostatically controlling the auxin signaling and response pathway. Finally, we show that WUSCHEL acts via regulation of histone acetylation at target loci, including those with functions in the auxin pathway. Our results reveal an important mechanism that allows cells to differentially translate a potent and highly dynamic developmental signal into stable cell behavior with high spatial precision and temporal robustness.
Regulation of CHD2 expression by the Chaserr long noncoding RNA gene is essential for viability
Authors: Rom Aviv , Melamed Liliya , Gil Noa , Goldrich Micah Jonathan , Kadir Rotem , Golan Matan , Biton Inbal , Perry Rotem Ben-Tov , Ulitsky Igor
Published: November 2019

Chromodomain helicase DNA binding protein 2 (Chd2) is a chromatin remodeller implicated in neurological disease. Here we show that Chaserr, a highly conserved long noncoding RNA transcribed from a region near the transcription start site of Chd2 and on the same strand, acts in concert with the CHD2 protein to maintain proper Chd2 expression levels. Loss of Chaserr in mice leads to early postnatal lethality in homozygous mice, and severe growth retardation in heterozygotes. Mechanistically, loss of Chaserr leads to substantially increased Chd2 mRNA and protein levels, which in turn lead to transcriptional interference by inhibiting promoters found downstream of highly expressed genes. We further show that Chaserr production represses Chd2 expression solely in cis, and that the phenotypic consequences of Chaserr loss are rescued when Chd2 is perturbed as well. Targeting Chaserr is thus a potential strategy for increasing CHD2 levels in haploinsufficient individuals.
Early life stress alters transcriptomic patterning across reward circuitry in male and female mice
Authors: Peña Catherine Jensen , Smith Milo , Ramakrishnan Aarthi , Cates Hannah M. , Bagot Rosemary C. , Kronman Hope G. , Patel Bhakti , Chang Austin B. , Purushothaman Immanuel , Dudley Joel , Morishita Hirofumi , Shen Li , Nestler Eric J.
Published: November 2019

Abuse, neglect, and other forms of early life stress (ELS) significantly increase risk for psychiatric disorders including depression. In this study, we show that ELS in a postnatal sensitive period increases sensitivity to adult stress in female mice, consistent with our earlier findings in male mice. We used RNA-sequencing in the ventral tegmental area, nucleus accumbens, and prefrontal cortex of male and female mice to show that adult stress is distinctly represented in the brain’s transcriptome depending on ELS history. We identify: 1) biological pathways disrupted after ELS and associated with increased behavioral stress sensitivity, 2) putative transcriptional regulators of the effect of ELS on adult stress response, and 3) subsets of primed genes specifically associated with latent behavioral changes. We also provide transcriptomic evidence that ELS increases sensitivity to future stress through enhancement of known programs of cortical plasticity.
Non-noble metal-nitride based electrocatalysts for high-performance alkaline seawater electrolysis
Authors: Yu Luo , Zhu Qing , Song Shaowei , McElhenny Brian , Wang Dezhi , Wu Chunzheng , Qin Zhaojun , Bao Jiming , Yu Ying , Chen Shuo , Ren Zhifeng
Published: November 2019

Seawater is one of the most abundant natural resources on our planet. Electrolysis of seawater is not only a promising approach to produce clean hydrogen energy, but also of great significance to seawater desalination. The implementation of seawater electrolysis requires robust and efficient electrocatalysts that can sustain seawater splitting without chloride corrosion, especially for the anode. Here we report a three-dimensional core-shell metal-nitride catalyst consisting of NiFeN nanoparticles uniformly decorated on NiMoN nanorods supported on Ni foam, which serves as an eminently active and durable oxygen evolution reaction catalyst for alkaline seawater electrolysis. Combined with an efficient hydrogen evolution reaction catalyst of NiMoN nanorods, we have achieved the industrially required current densities of 500 and 1000 mA cm−2 at record low voltages of 1.608 and 1.709 V, respectively, for overall alkaline seawater splitting at 60 °C. This discovery significantly advances the development of seawater electrolysis for large-scale hydrogen production.
Author Correction: c-Met activation leads to the establishment of a TGFβ-receptor regulatory network in bladder cancer progression
Authors: Sim Wen Jing , Iyengar Prasanna Vasudevan , Lama Dilraj , Lui Sarah Kit Leng , Ng Hsien Chun , Haviv-Shapira Lior , Domany Eytan , Kappei Dennis , Tan Tuan Zea , Saei Azad , Jaynes Patrick William , Verma Chandra Shekhar , Kumar Alan Prem , Rouanne Mathieu , Ha Hong Koo , Radulescu Camelia , ten Dijke Peter , Eichhorn Pieter Johan Adam , Thiery Jean Paul
Published: November 2019

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
CDK2-mediated site-specific phosphorylation of EZH2 drives and maintains triple-negative breast cancer
Authors: Nie Lei , Wei Yongkun , Zhang Fei , Hsu Yi-Hsin , Chan Li-Chuan , Xia Weiya , Ke Baozhen , Zhu Cihui , Deng Rong , Tang Jun , Yao Jun , Chu Yu-Yi , Zhao Xixi , Han Ye , Hou Junwei , Huo Longfei , Ko How-Wen , Lin Wan-Chi , Yamaguchi Hirohito , Hsu Jung-Mao , Yang Yi , Pan Dean N. , Hsu Jennifer L. , Kleer Celina G. , Davidson Nancy E. , Hortobagyi Gabriel N. , Hung Mien-Chie
Published: November 2019

Triple-negative breast cancer (TNBC), which lacks estrogen receptor α (ERα), progesterone receptor, and human epidermal growth factor receptor 2 (HER2) expression, is closely related to basal-like breast cancer. Previously, we and others report that cyclin E/cyclin-dependent kinase 2 (CDK2) phosphorylates enhancer of zeste homolog 2 (EZH2) at T416 (pT416-EZH2). Here, we show that transgenic expression of phospho-mimicking EZH2 mutant EZH2T416D in mammary glands leads to tumors with TNBC phenotype. Coexpression of EZH2T416D in mammary epithelia of HER2/Neu transgenic mice reprograms HER2-driven luminal tumors into basal-like tumors. Pharmacological inhibition of CDK2 or EZH2 allows re-expression of ERα and converts TNBC to luminal ERα-positive, rendering TNBC cells targetable by tamoxifen. Furthermore, the combination of either CDK2 or EZH2 inhibitor with tamoxifen effectively suppresses tumor growth and markedly improves the survival of the mice bearing TNBC tumors, suggesting that the mechanism-based combination therapy may be an alternative approach to treat TNBC.
Cr-spinel records metasomatism not petrogenesis of mantle rocks
Authors: Gamal El Dien Hamed , Arai Shoji , Doucet Luc-Serge , Li Zheng-Xiang , Kil Youngwoo , Fougerouse Denis , Reddy Steven M. , Saxey David W. , Hamdy Mohamed
Published: November 2019

Mantle melts provide a window on processes related to global plate tectonics. The composition of chromian spinel (Cr-spinel) from mafic-ultramafic rocks has been widely used for tracing the geotectonic environments, the degree of mantle melting and the rate of mid-ocean ridge spreading. The assumption is that Cr-spinel’s core composition (Cr# = Cr/(Cr + Al)) is homogenous, insensitive to post-formation modification and therefore a robust petrogenetic indicator. However, we demonstrate that the composition of Cr-spinel can be modified by fluid/melt-rock interactions in both sub-arc and sub-mid oceanic mantle. Metasomatism can produce Al-Cr heterogeneity in Cr-spinel that lowers the Cr/Al ratio, and therefore modifies the Cr#, making Cr# ineffective as a geotectonic and mantle melting indicator. Our analysis also demonstrates that Cr-spinel is a potential sink for fluid-mobile elements, especially in subduction zone environments. The heterogeneity of Cr# in Cr-spinel can, therefore, be used as an excellent tracer for metasomatic processes.
Regulation of priming effect by soil organic matter stability over a broad geographic scale
Authors: Chen Leiyi , Liu Li , Qin Shuqi , Yang Guibiao , Fang Kai , Zhu Biao , Kuzyakov Yakov , Chen Pengdong , Xu Yunping , Yang Yuanhe
Published: November 2019

The modification of soil organic matter (SOM) decomposition by plant carbon (C) input (priming effect) represents a critical biogeochemical process that controls soil C dynamics. However, the patterns and drivers of the priming effect remain hidden, especially over broad geographic scales under various climate and soil conditions. By combining systematic field and laboratory analyses based on multiple analytical and statistical approaches, we explore the determinants of priming intensity along a 2200 km grassland transect on the Tibetan Plateau. Our results show that SOM stability characterized by chemical recalcitrance and physico-chemical protection explains more variance in the priming effect than plant, soil and microbial properties. High priming intensity (up to 137% of basal respiration) is associated with complex SOM chemical structures and low mineral-organic associations. The dependence of priming effect on SOM stabilization mechanisms should be considered in Earth System Models to accurately predict soil C dynamics under changing environments.
Author Correction: Transcriptional read-through of the long non-coding RNA SVALKA governs plant cold acclimation
Authors: Kindgren Peter , Ard Ryan , Ivanov Maxim , Marquardt Sebastian
Published: November 2019

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Gamma-aminobutyric acid-producing lactobacilli positively affect metabolism and depressive-like behaviour in a mouse model of metabolic syndrome
Authors: Patterson E. , Ryan P. M. , Wiley N. , Carafa I. , Sherwin E. , Moloney G. , Franciosi E. , Mandal R. , Wishart D. S. , Tuohy K. , Ross R. P. , Cryan J. F. , Dinan T. G. , Stanton C.
Published: November 2019

Metabolic and neuroactive metabolite production represents one of the mechanisms through which the gut microbiota can impact health. One such metabolite, gamma-aminobutyric acid (GABA), can modulate glucose homeostasis and alter behavioural patterns in the host. We previously demonstrated that oral administration of GABA-producing Lactobacillus brevis DPC6108 has the potential to increase levels of circulating insulin in healthy rats. Therefore, the objective of this study was to assess the efficacy of endogenous microbial GABA production in improving metabolic and behavioural outcomes in a mouse model of metabolic dysfunction. Diet-induced obese and metabolically dysfunctional mice received one of two GABA-producing strains, L. brevis DPC6108 or L. brevis DSM32386, daily for 12 weeks. After 8 and 10 weeks of intervention, the behavioural and metabolic profiles of the mice were respectively assessed. Intervention with both L. brevis strains attenuated several abnormalities associated with metabolic dysfunction, causing a reduction in the accumulation of mesenteric adipose tissue, increased insulin secretion following glucose challenge, improved plasma cholesterol clearance and reduced despair-like behaviour and basal corticosterone production during the forced swim test. Taken together, this exploratory dataset indicates that intervention with GABA-producing lactobacilli has the potential to improve metabolic and depressive- like behavioural abnormalities associated with metabolic syndrome in mice.
Hierarchically Ordered α-Zirconium Phosphate Platelets in Aqueous Phase with Empty Liquid
Authors: Lin Xi , Schmelter Dirk , Imanian Sadaf , Hintze-Bruening Horst
Published: November 2019

Platelets of α-zirconium phosphate (α-ZrP) obtained from the reflux method in H3PO4 are successfully exfoliated into water via the intercalation of alkanol amines. With volume fractions greater than 0.02 they are stacked into tactoids of few layers with a repeat distance in the order of 10 nm. The tactoids align into nematic liquid crystalline phases with irregularly wide interstices of empty liquid. Colloidal processing involves the freeze-drying of such anisotropic fluids and the dispersion of the restacked tacoids into aqueous dispersions of colloidal polymer particles of largely varying size which occupy the otherwise empty liquid between the α-ZrP tactoids and induce piling of the tactoids into columns. Real-time SAXS on drying films and TEM of the obtained coatings demonstrate that the stacked α-ZrP platelets and the polymer particles comprising liquid dry separately without polymer intercalation, while the morphology of the obtained composites can be tuned primarily by the size of the polymer colloids. Concomitant α-ZrP hydrolysis in the exfoliation step is scrutinized as a function of amine basicity and temperature. The role of zirconium based hydrolysis products in the hierarchical α-ZrP assembly is indirectly though consistently confirmed by opposing impacts of ultra-filtration and added oxoanions on the platelets’ spacing, smoothness and aggregation. HAADF-TEM imaging of scattered, singular platelets and XRD peak analysis of the pristine solid shed light on the α-ZrP synthesis. Coexisting flakes and lacunae, both similar in size to the intra-layer crystal domains, suggest the stitching of proto-α-ZrP flakes into extended layers in accordance with our observations on the aging behaviour of α-ZrP dispersions as well as with literature data on related systems.
Statin Short-term Inhibition of Insulin Sensitivity and Secretion During Acute Phase of ST-Elevation Myocardial Infarction
Authors: Sposito Andrei C. , Carvalho Luiz Sergio F. , Moura Filipe A. , Campos-Staffico Alessandra M. , Cintra Riobaldo M. R. , Nadruz Wilson , Almeida Osorio R. , Quinaglia e Silva Jose C.
Published: November 2019

Hyperglycemia during myocardial infarction (MI) has a strong and direct association with mortality. In stable patients and experimental models, statins favor the elevation of glycaemia. The present study investigated whether short-course treatment with statins during MI can influence glucose homeostasis and thus the clinical outcome. In this prospective study, euglycemic hyperinsulinemic clamp (EHC) was performed at second (D2) and sixth (D6) day after MI in patients randomized to simvastatin (S)10 or 80 mg/day during hospitalization (n = 27). In addition, patients (n = 550) were treated without (WS) or with simvastatin (S) at 20, 40 or 80 mg/day had HOMA2S on admission (D1) and fifth (D5) day after MI. According to EHC, insulin sensitivity increased by 20 ± 60% in S10 and decreased by −6 ± 28% in S80 (p = 0.025). Consistently, the changes in HOMA2S between D1 and D5 were 40 ± 145% (WS), 22 ± 117% (S20), 16 ± 61% (S40) and −2% ± 88% (S80) (p = 0.001). In conclusion, statin during the acute phase of MI reduces insulin sensitivity in a dose-dependent manner.
Differential allosteric modulation within dopamine D2R - neurotensin NTS1R and D2R - serotonin 5-HT2AR receptor complexes gives bias to intracellular calcium signalling
Authors: Plach Michael , Schäfer Thorsten , Borroto-Escuela Dasiel Oscar , Weikert Dorothée , Gmeiner Peter , Fuxe Kjell , Friedland Kristina
Published: November 2019

Proceeding investigations of G protein-coupled receptor (GPCR) heterocomplexes have demonstrated that the dopamine D2 receptor (D2R), one of the hub receptors in the physiology of schizophrenia, interacts with both the neurotensin NTS1 (NTS1R) and the serotonin 5-HT2A receptor (5-HT2AR) in cell lines and rodent brain tissue. In situ proximity ligation assay and BRET-based saturation experiments confirmed interacting receptor assemblies in HEK293T and neuronal HT22 cells. The NTS1R agonist NT(8-13) reduces the Gαq-mediated calcium signal in the NTS1R-D2R complex compared to the NTS1R monomer which could be reversed by D2R antagonists. The bivalent ligand CS148 (NTS1R-agonistic, D2R-antagonistic) increased the calcium response addressing the dimer, consistent with the effect of the monovalent ligands suggesting an allosteric D2R-mediated modulation. In contrast, the 5-HT2AR-D2R heteromer did not show a calcium-altering receptor-receptor interaction. Despite their common coupling-preference for Gαq, 5-HT2AR and NTS1R supposedly interact with D2R each in a unique mode. This remarkably diverse ligand-mediated signalling in two different D2R heteroreceptor complexes illustrates the complexity of receptor-receptor interactions and their potential of modifying cell responses to external stimuli. Therefore, GPCR heteromers may provide a very promising novel target for the therapy of neuropsychiatric disorders.
Bacillus velezensis 5113 Induced Metabolic and Molecular Reprogramming during Abiotic Stress Tolerance in Wheat
Authors: Abd El-Daim Islam A. , Bejai Sarosh , Meijer Johan
Published: November 2019

Abiotic stresses are main limiting factors for agricultural production around the world. Plant growth promoting rhizobacteria (PGPR) have been shown to improve abiotic stress tolerance in several plants. However, the molecular and physiological changes connected with PGPR priming of stress management are poorly understood. The present investigation aimed to explore major metabolic and molecular changes connected with the ability of Bacillus velezensis 5113 to mediate abiotic stress tolerance in wheat. Seedlings treated with Bacillus were exposed to heat, cold/freezing or drought stress. Bacillus improved wheat survival in all stress conditions. SPAD readings showed higher chlorophyll content in 5113-treated stressed seedlings. Metabolite profiling using NMR and ESI-MS provided evidences for metabolic reprograming in 5113-treated seedlings and showed that several common stress metabolites were significantly accumulated in stressed wheat. Two-dimensional gel electrophoresis of wheat leaves resolved more than 300 proteins of which several were differentially expressed between different treatments and that cold stress had a stronger impact on the protein pattern compared to heat and drought. Peptides maps or sequences were used for database searches which identified several homologs. The present study suggests that 5113 treatment provides systemic effects that involve metabolic and regulatory functions supporting both growth and stress management.
FRD-CNN: Object detection based on small-scale convolutional neural networks and feature reuse
Authors: Li Wei , Liu Kai , Yan Lin , Cheng Fei , Lv YunQiu , Zhang LiZhe
Published: November 2019

Most of the recent successful object detection methods have been based on convolutional neural networks (CNNs). From previous studies, we learned that many feature reuse methods improve the network performance, but they increase the number of parameters. DenseNet uses thin layers that have fewer channels to alleviate the increase in parameters. This motivated us to find other methods for solving the increase in model size problems introduced by feature reuse methods. In this work, we employ different feature reuse methods on fire units and mobile units. We solved the problem and constructed two novel neural networks, fire-FRD-CNN and mobile-FRD-CNN. We conducted experiments with the proposed neural networks on KITTI and PASCAL VOC datasets.
Swimming capability of zebrafish is governed by water temperature, caudal fin length and genetic background
Authors: Wakamatsu Yuma , Ogino Kazutoyo , Hirata Hiromi
Published: November 2019

Several zebrafish strains such as AB, Tübingen (TU), Wild India Kolkata (WIK) and Tupfel long fin (TL) have been established for genetic study. Each strain has its morphological and behavioral traits. Motor traits, however, have not been explored in zebrafish strains. We here applied a treadmill for fish (swimmill) and measured swimming capability of adult zebrafish by critical swimming speed, which is the maximum water velocity in which fish can keep swimming. First, we confirmed that swimming capability does not vary between female and male. Second, we found that the appropriate water temperature for swimming was between 16 and 30 °C. Third, our fin clip experiments using long-finned zebrafish revealed that they can exhibit high swimming capability when the caudal fin length was set between 3 and 10 mm, implying that long-finned zebrafish are unfavorable for fast swimming. Finally, we compared swimming capability of several zebrafish strains and demonstrated that WIK fish was significantly less capable of swimming despite that they have short caudal fin (~9 mm). The offspring of WIK fish were less capable of swimming, while hybrids of WIK and TU showed high swimming performance comparable to TU. Thus, lower swimming capability of WIK strain is inheritable as a motor trait.
Mutation of the PTCH1 gene predicts recurrence of breast cancer
Authors: Wang Chih-Yang , Chang Yung-Chieh , Kuo Yao-Lung , Lee Kuo-Ting , Chen Pai-Sheng , Cheung Chun Hei Antonio , Chang Chih-Peng , Phan Nam Nhut , Shen Meng-Ru , Hsu Hui-Ping
Published: November 2019

Breast cancer is the most common cancer in women, and some patients develop recurrence after standard therapy. Effective predictors are urgently needed to detect recurrence earlier. The activation of Hedgehog signaling in breast cancer is correlated with poor prognosis. PTCH1 is an essential membrane receptor of Hedgehog. However, there are few reports about mutations in Hedgehog genes in breast cancer. We conducted a comprehensive study via an experimental and bioinformatics approach to detect mutated genes in breast cancer. Twenty-two breast cancer patients who developed recurrence within 24 months postoperatively were enrolled with 22 control cancer patients. Targeted deep sequencing was performed to assess the mutations among individuals with breast cancer using a panel of 143 cancer-associated genes. Bioinformatics and public databases were used to predict the protein functions of the mutated genes. Mutations were identified in 44 breast cancer specimens, and the most frequently mutated genes were BRCA2, APC, ATM, BRCA1, NF1, TET2, TSC1, TSC2, NOTCH1, MSH2, PTCH1, TP53, PIK3CA, FBXW7, and RB1. Mutation of these genes was correlated with protein phosphorylation and autophosphorylation, such as peptidyl-tyrosine and protein kinase C phosphorylation. Among these highly mutated genes, mutations of PTCH1 were associated with poor prognosis and increased recurrence of breast cancer, especially mutations in exons 22 and 23. The public sequencing data from the COSMIC database were exploited to predict the functions of the mutations. Our findings suggest that mutation of PTCH1 is correlated with early recurrence of breast cancer patients and will become a powerful predictor for recurrence of breast cancer.
The citrus flavonoid naringenin impairs the in vitro infection of human cells by Zika virus
Authors: Cataneo Allan Henrique Depieri , Kuczera Diogo , Koishi Andrea Cristine , Zanluca Camila , Silveira Guilherme Ferreira , Arruda Thais Bonato de , Suzukawa Andréia Akemi , Bortot Leandro Oliveira , Dias-Baruffi Marcelo , Verri Waldiceu Aparecido , Robert Anny Waloski , Stimamiglio Marco Augusto , Duarte dos Santos Claudia Nunes , Wowk Pryscilla Fanini , Bordignon Juliano
Published: November 2019

The Zika virus (ZIKV) is an arthropod-borne virus that belongs to theFlaviviridaefamily. The ZIKV infection is usually asymptomatic or is associated with mild clinical manifestations; however, increased numbers of cases of microcephaly and birth defects have been recently reported. To date, neither a vaccine nor an antiviral treatment has become available to control ZIKV replication. Among the natural compounds recognized for their medical properties, flavonoids, which can be found in fruits and vegetables, have been found to possess biological activity against a variety of viruses. Here, we demonstrate that the citrus flavanone naringenin (NAR) prevented ZIKV infection in human A549 cells in a concentration-dependent and ZIKV-lineage independent manner. NAR antiviral activity was also observed when primary human monocyte-derived dendritic cells were infected by ZIKV. NAR displayed its antiviral activity when the cells were treated after infection, suggesting that NAR acts on the viral replication or assembly of viral particles. Moreover, a molecular docking analysis suggests a potential interaction between NAR and the protease domain of the NS2B-NS3 protein of ZIKV which could explain the anti-ZIKV activity of NAR. Finally, the results support the potential of NAR as a suitable candidate molecule for developing anti-ZIKV treatments.
Re-sequencing and optical mapping reveals misassemblies and real inversions on Corynebacterium pseudotuberculosis genomes
Authors: Sousa Thiago de Jesus , Parise Doglas , Profeta Rodrigo , Parise Mariana Teixeira Dornelles , Gomide Anne Cybelle Pinto , Kato Rodrigo Bentos , Pereira Felipe Luiz , Figueiredo Henrique Cesar Pereira , Ramos Rommel , Brenig Bertram , Costa da Silva Artur Luiz da , Ghosh Preetam , Barh Debmalya , Góes-Neto Aristóteles , Azevedo Vasco
Published: November 2019

The number of draft genomes deposited in Genbank from the National Center for Biotechnology Information (NCBI) is higher than the complete ones. Draft genomes are assemblies that contain fragments of misassembled regions (gaps). Such draft genomes present a hindrance to the complete understanding of the biology and evolution of the organism since they lack genomic information. To overcome this problem, strategies to improve the assembly process are developed continuously. Also, the greatest challenge to the assembly progress is the presence of repetitive DNA regions. This article highlights the use of optical mapping, to detect and correct assembly errors in Corynebacterium pseudotuberculosis. We also demonstrate that choosing a reference genome should be done with caution to avoid assembly errors and loss of genetic information.
Structural insights into mutagenicity of anticancer nucleoside analog cytarabine during replication by DNA polymerase η
Authors: Rechkoblit Olga , Johnson Robert E. , Buku Angeliki , Prakash Louise , Prakash Satya , Aggarwal Aneel K.
Published: November 2019

Cytarabine (AraC) is the mainstay chemotherapy for acute myeloid leukemia (AML). Whereas initial treatment with AraC is usually successful, most AML patients tend to relapse, and AraC treatment-induced mutagenesis may contribute to the development of chemo-resistant leukemic clones. We show here that whereas the high-fidelity replicative polymerase Polδ is blocked in the replication of AraC, the lower-fidelity translesion DNA synthesis (TLS) polymerase Polη is proficient, inserting both correct and incorrect nucleotides opposite a template AraC base. Furthermore, we present high-resolution crystal structures of human Polη with a template AraC residue positioned opposite correct (G) and incorrect (A) incoming deoxynucleotides. We show that Polη can accommodate local perturbation caused by the AraC via specific hydrogen bonding and maintain a reaction-ready active site alignment for insertion of both correct and incorrect incoming nucleotides. Taken together, the structures provide a novel basis for the ability of Polη to promote AraC induced mutagenesis in relapsed AML patients.
On the possibility of a terahertz light emitting diode based on a dressed quantum well
Authors: Mandal S. , Dini K. , Kibis O. V. , Liew T. C. H.
Published: November 2019

We consider theoretically the realization of a tunable terahertz light emitting diode from a quantum well with dressed electrons placed in a highly doped p-n junction. In the considered system the strong resonant dressing field forms dynamic Stark gaps in the valence and conduction bands and the electric field inside the p-n junction makes the QW asymmetric. It is shown that the electrons transiting through the light induced Stark gaps in the conduction band emit photons with energy directly proportional to the dressing field. This scheme is tunable, compact, and shows a fair efficiency.
Deciphering phylogenetic relationships and delimiting species boundaries using a Bayesian coalescent approach in protists: A case study of the ciliate genus Spirostomum (Ciliophora, Heterotrichea)
Authors: Shazib Shahed Uddin Ahmed , Vďačný Peter , Slovák Marek , Gentekaki Eleni , Shin Mann Kyoon
Published: November 2019

The ciliate genus Spirostomum comprises eight morphospecies, inhabiting diverse aquatic environments worldwide, where they can be used as water quality indicators. Although Spirostomum species are relatively easily identified using morphological methods, the previous nuclear rDNA-based phylogenies indicated several conflicts in morphospecies delineation. Moreover, the single locus phylogenies and previous analytical approaches could not unambiguously resolve phylogenetic relationships among Spirostomum morphospecies. Here, we attempt to investigate species boundaries and evolutionary history of Spirostomum taxa, using 166 new sequences from multiple populations employing one mitochondrial locus (CO1 gene) and two nuclear loci (rRNA operon and alpha-tubulin gene). In accordance with previous studies, relationships among the eight Spirostomum morphospecies were poorly supported statistically in individual gene trees. To overcome this problem, we utilised for the first time in ciliates the Bayesian coalescent approach, which accounts for ancestral polymorphisms, incomplete lineage sorting, and recombination. This strategy enabled us to robustly resolve deep relationships between Spirostomum species and to support the hypothesis that taxa with compact macronucleus and taxa with moniliform macronucleus each form a distinct lineage. Bayesian coalescent-based delimitation analyses strongly statistically supported the traditional morphospecies concept but also indicated that there are two S. minus-like cryptic species and S. teres is non-monophyletic. Spirostomum teres was very likely defined by a set of ancestral features of lineages that also gave rise to S. yagiui and S. dharwarensis. However, molecular data from type populations of the morphospecies S. minus and S. teres are required to unambiguously resolve the taxonomic problems.
Optimal environmental and culture conditions allow the in vitro coexistence of Pseudomonas aeruginosa and Staphylococcus aureus in stable biofilms
Authors: Cendra Maria del Mar , Blanco-Cabra Núria , Pedraz Lucas , Torrents Eduard
Published: November 2019

The coexistence between species that occurs in some infections remains hard to achieve in vitro since bacterial fitness differences eventually lead to a single organism dominating the mixed culture. Pseudomonas aeruginosa and Staphylococcus aureus are major pathogens found growing together in biofilms in disease-affected lungs or wounds. Herein, we tested and analyzed different culture media, additives and environmental conditions to support P. aeruginosa and S. aureus coexistence in vitro. We have unraveled the potential of DMEM to support the growth of these two organisms in mature cocultured biofilms (three days old) in an environment that dampens the pH rise. Our conditions use equal initial inoculation ratios of both strains and allow the stable formation of separate S. aureus microcolonies that grow embedded in a P. aeruginosa biofilm, as well as S. aureus biofilm overgrowth when bovine serum albumin is added to the system. Remarkably, we also found that S. aureus survival is strictly dependent on a well-characterized phenomenon of oxygen stratification present in the coculture biofilm. An analysis of differential tolerance to gentamicin and ciprofloxacin treatment, depending on whether P. aeruginosa and S. aureus were growing in mono- or coculture biofilms, was used to validate our in vitro coculture conditions.
Aberrant DNA methylation of miRNAs in Fuchs endothelial corneal dystrophy
Authors: Pan Peipei , Weisenberger Daniel J. , Zheng Siyu , Wolf Marie , Hwang David G. , Rose-Nussbaumer Jennifer R. , Jurkunas Ula V. , Chan Matilda F.
Published: November 2019

Homeostatic maintenance of corneal endothelial cells is essential for maintenance of corneal deturgescence and transparency. In Fuchs endothelial corneal dystrophy (FECD), an accelerated loss and dysfunction of endothelial cells leads to progressively severe visual impairment. An abnormal accumulation of extracellular matrix (ECM) is a distinctive hallmark of the disease, however the molecular pathogenic mechanisms underlying this phenomenon are not fully understood. Here, we investigate genome-wide and sequence-specific DNA methylation changes of miRNA genes in corneal endothelial samples from FECD patients. We discover that miRNA gene promoters are frequent targets of aberrant DNA methylation in FECD. More specifically,miR-199Bis extensively hypermethylated and its mature transcript miR-199b-5p was previously found to be almost completely silenced in FECD. Furthermore, we find that miR-199b-5p directly and negatively regulates Snai1 and ZEB1, two zinc finger transcription factors that lead to increased ECM deposition in FECD. Taken together, these findings suggest a novel epigenetic regulatory mechanism of matrix protein production by corneal endothelial cells in whichmiR-199Bhypermethylation leads to miR-199b-5p downregulation and thereby the increased expression of its target genes, includingSnai1andZEB1. Our results support miR-199b-5p as a potential therapeutic target to prevent or slow down the progression of FECD disease.
Correlation between macular vessel density and number of intravitreal anti-VEGF agents for macular edema associated with branch retinal vein occlusion
Authors: Tomita Ryo , Iwase Takeshi , Goto Kensuke , Yamamoto Kentaro , Ra Eimei , Terasaki Hiroko
Published: November 2019

We evaluated whether the reduction of macular vessel density was correlated with the number of intravitreal injections of anti-vascular endothelial growth factor (VEGF) agents in eyes with a branch retinal vein occlusion (BRVO). The mean vessel density was determined by optical coherence tomography angiography in 29 eyes with macular edema associated with a BRVO. Our results showed that the mean vessel density in the group that had a resolution of the macular edema after one anti-VEGF injection was significantly higher than group that had a recurrence of the macular edema (P = 0.028). Single regression analysis showed that the number of intravitreal injections was significantly correlated with the reduction of the modified vessel density (r = −0.421, P = 0.023) and systemic hypertension (r = 0.377, P = 0.044). Multiple stepwise regression analysis showed that the reduction of the modified vessel density (β = −0.442, P = 0.009) and hypertension (β = 0.403, P = 0.016) were independent factors associated with the number of intravitreal injections. We conclude that the vessel density reduction can be used to predict whether recurrences of the macular edema will develop after the initial anti-VEGF injection in eyes with macular edema associated with a BRVO.
Gradual and selective trace-element enrichment in slab-released fluids at sub-arc depths
Authors: Ferrando Simona , Petrelli Maurizio , Frezzotti Maria Luce
Published: November 2019

The geochemical signature of magmas generated at convergent margins greatly depends on the nature of fluids and melts released during subduction. While major- and trace-elements transport capacity of ultrahigh pressure (UHP) hydrous-silicate melts has been investigated, little is known about solute enrichment and fractionation in UHP (>3.5–4 GPa) solute-rich aqueous fluids released along colder geothermal gradients. Here, we performed in situ LA-ICP-MS trace-element analyses on selected UHP prograde-to-peak fluid inclusions trapped in a kyanite-bearing quartzite from Sulu (China). The alkali-aluminosilicate-rich aqueous fluid released from the meta-sediments by dehydration reactions is enriched in LILE, U, Th, Sr, and REE. Inclusions trapped at increasing temperature (and pressure) preserve a gradual and selective trace-element enrichment resulting from the progressive dissolution of phengite and carbonate and the partial dissolution of allanite/monazite. We show that, at the investigated P-T conditions, aqueous fluids generated by dissolution of volatile-bearing minerals fractionate trace-element distinctly from hydrous-silicate melts, regardless of the source lithology. The orogenic/post-orogenic magmas generated in a mantle enriched by metasomatic processes involving either solute-rich aqueous fluids or hydrous-silicate melts released by the slab at UHP conditions can preserve evidence of the nature of these agents.
Exfoliative toxin E, a new Staphylococcus aureus virulence factor with host-specific activity
Authors: Imanishi Ichiro , Nicolas Aurélie , Caetano Ana-Carolina Barbosa , Castro Thiago Luiz de Paula , Tartaglia Natayme Rocha , Mariutti Ricardo , Guédon Eric , Even Sergine , Berkova Nadia , Arni Raghuvir K. , Seyffert Nubia , Azevedo Vasco , Nishifuji Koji , Le Loir Yves
Published: November 2019

Exfoliative toxins (ETs) are secreted virulence factors produced by staphylococci. These serine proteases specifically cleave desmoglein 1 (Dsg1) in mammals and are key elements in staphylococcal skin infections. We recently identified a newetgene inS. aureusO46, a strain isolated from ovine mastitis. In the present study, we characterized the newetgene at a genetic level and the enzymatic activity of the deduced protein. TheS. aureusO46 genome was re-assembled, annotated and compared with other publicly availableS. aureusgenomes. The deduced amino acid sequence of the newetgene shared 40%, 53% and 59% sequence identity to those of ETA, ETB and ETD, respectively. The newetgene shared the same genetic vicinity and was similar in otherS. aureusstrains bearing this gene. The recombinant enzyme of the newetgene caused skin exfoliationin vivoin neonatal mice. The newet-gene was thus namedete, encoding a new type (type E) of exfoliative toxin. We showed that ETE degraded the extracellular segments of Dsg1 in murine, ovine and caprine epidermis, as well as in ovine teat canal epithelia, but not that in bovine epidermis. We further showed that it directly hydrolyzed human and swine Dsg1 as well as murine Dsg1α and Dsg1β, but not canine Dsg1 or murine Dsg1γ. Molecular modeling revealed a correlation between the preferred orientation of ETE docking on its Dsg1 cleavage site and species-specific cleavage activity, suggesting that the docking step preceding cleavage accounts for the ETE species-specificity. This new virulence factor may contribute to the bacterial colonization on the stratified epithelia in certain ruminants with mastitis.