bluuebunny/crossref_metadata_2025_split huggingface dataset:
The H2A.Z histone variant integrates Wnt signaling in intestinal epithelial homeostasis
Authors: Rispal Jérémie , Baron Lucie , Beaulieu Jean-François , Chevillard-Briet Martine , Trouche Didier , Escaffit Fabrice 
Published: April 2019

AbstractThe Tip60/p400 chromatin-modifying complex, which is involved in the incorporation and post-translational modification of the H2A.Z histone variant, regulates cell proliferation and important signaling pathways, such as Wnt. Here, we study the involvement of H2A.Z in intestinal epithelial homeostasis, which is dependent on the finely-tuned equilibrium between stem cells renewal and differentiation, under the control of such pathway. We use cell models and inducible knock-out mice to study the impact of H2A.Z depletion on intestinal homeostasis. We show that H2A.Z is essential for the proliferation of human cancer and normal intestinal crypt cells and negatively controls the expression of a subset of differentiation markers, in cultured cells and mice. H2A.Z impairs the recruitment of the intestine-specific transcription factor CDX2 to chromatin, is itself a target of the Wnt pathway and thus, acts as an integrator for Wnt signaling in the control of intestinal epithelial cell fate and homeostasis.
The extracellular matrix protects Bacillus subtilis colonies from Pseudomonas invasion and modulates plant co-colonization
Authors: Molina-Santiago Carlos , Pearson John R. , Navarro Yurena , Berlanga-Clavero María Victoria , Caraballo-Rodriguez Andrés Mauricio , Petras Daniel , García-Martín María Luisa , Lamon Gaelle , Haberstein Birgit , Cazorla Francisco M. , de Vicente Antonio , Loquet Antoine , Dorrestein Pieter C. , Romero Diego 
Published: April 2019

AbstractBacteria of the genera Pseudomonas and Bacillus can promote plant growth and protect plants from pathogens. However, the interactions between these plant-beneficial bacteria are understudied. Here, we explore the interaction between Bacillus subtilis 3610 and Pseudomonas chlororaphis PCL1606. We show that the extracellular matrix protects B. subtilis colonies from infiltration by P. chlororaphis. The absence of extracellular matrix results in increased fluidity and loss of structure of the B. subtilis colony. The P. chlororaphis type VI secretion system (T6SS) is activated upon contact with B. subtilis cells, and stimulates B. subtilis sporulation. Furthermore, we find that B. subtilis sporulation observed prior to direct contact with P. chlororaphis is mediated by histidine kinases KinA and KinB. Finally, we demonstrate the importance of the extracellular matrix and the T6SS in modulating the coexistence of the two species on melon plant leaves and seeds.
Composite topological nodal lines penetrating the Brillouin zone in orthorhombic AgF2
Authors: Shao Dexi , Wang Huaiqiang , Chen Tong , Lu Pengchao , Gu Qinyan , Sheng Li , Xing Dingyu , Sun Jian 
Published: April 2019

AbstractIt has recently been found that nonsymmorphic symmetries can bring many exotic band crossings. Here, based on symmetry analysis, we predict that materials with time-reversal symmetry in the space group of Pbca (No. 61) possess rich symmetry-enforced band crossings, including nodal surfaces, fourfold degenerate nodal lines and hourglass Dirac loops, which appear in triplets as ensured by the cyclic permutation symmetry. We take Pbca AgF2 as an example in real systems and studied its band structures with ab initio calculations. Specifically, in the absence of spin-orbit coupling (SOC), besides the above-mentioned band degeneracies, this system features a nodal chain and a nodal armillary sphere penetrating the Brillouin zone (BZ). While with SOC, we find a new configuration of the hourglass Dirac loop/chain with the feature traversing the BZ, which originates from the splitting of a Dirac loop confined in the BZ. Furthermore, guided by the bulk-surface correspondence, we calculated the surface states to explore these bulk nodal phenomena. The evolution of these interesting nodal phenomena traversing the BZ under two specific uniaxial strains is also discussed.
Universal quantum control through deep reinforcement learning
Authors: Niu Murphy Yuezhen , Boixo Sergio , Smelyanskiy Vadim N. , Neven Hartmut 
Published: April 2019

AbstractEmerging reinforcement learning techniques using deep neural networks have shown great promise in control optimization. They harness non-local regularities of noisy control trajectories and facilitate transfer learning between tasks. To leverage these powerful capabilities for quantum control optimization, we propose a new control framework to simultaneously optimize the speed and fidelity of quantum computation against both leakage and stochastic control errors. For a broad family of two-qubit unitary gates that are important for quantum simulation of many-electron systems, we improve the control robustness by adding control noise into training environments for reinforcement learning agents trained with trusted-region-policy-optimization. The agent control solutions demonstrate a two-order-of-magnitude reduction in average-gate-error over baseline stochastic-gradient-descent solutions and up to a one-order-of-magnitude reduction in gate time from optimal gate synthesis counterparts. These significant improvements in both fidelity and runtime are achieved by combining new physical understandings and state-of-the-art machine learning techniques. Our results open a venue for wider applications in quantum simulation, quantum chemistry and quantum supremacy tests using near-term quantum devices.
Measuring holographic entanglement entropy on a quantum simulator
Authors: Li Keren , Han Muxin , Qu Dongxue , Huang Zichang , Long Guilu , Wan Yidun , Lu Dawei , Zeng Bei , Laflamme Raymond 
Published: April 2019

AbstractQuantum simulation promises to have wide applications in many fields where problems are hard to model with classical computers. Various quantum devices of different platforms have been built to tackle the problems in, say, quantum chemistry, condensed matter physics, and high-energy physics. Here, we report an experiment towards the simulation of quantum gravity by simulating the holographic entanglement entropy. On a six-qubit nuclear magnetic resonance quantum simulator, we demonstrate a key result of Anti-de Sitter/conformal field theory (AdS/CFT) correspondence—the Ryu-Takayanagi formula is demonstrated by measuring the relevant entanglement entropies on the perfect tensor state. The fidelity of our experimentally prepared the six-qubit state is 85.0% via full state tomography and reaches 93.7% if the signal-decay due to decoherence is taken into account. Our experiment serves as the basic module of simulating more complex tensor network states that exploring AdS/CFT correspondence. As the initial experimental attempt to study AdS/CFT via quantum information processing, our work opens up new avenues exploring quantum gravity phenomena on quantum simulators.
Real-space observation of charge ordering in epitaxial La2−xSrxCuO4 films
Authors: Wang Yang , Zhong Yong , Luo Zhiling , Liao Menghan , Wang Ruifeng , Dou Ziyuan , Zhang Qinghua , Zhang Ding , Gu Lin , Song Can-Li , Ma Xu-Cun , Xue Qi-Kun 
Published: April 2019

AbstractThe cuprate superconductors exhibit ubiquitous instabilities toward charge-ordered states. These unusual electronic states break the spatial symmetries of the host crystal, and have been widely appreciated as essential ingredients for constructing a theory for high-temperature superconductivity in cuprates. Here, we report real-space imaging of the doping-dependent charge orders in the epitaxial thin films of a canonical cuprate compound La2–xSrxCuO4 using scanning tunneling microscopy. As the films are moderately doped, we observe a crossover from incommensurate to commensurate (4a0, where a0 is the Cu–O–Cu distance) stripes. Furthermore, at lower and higher doping levels, the charge orders occur in the form of distorted Wigner crystal and grid phase of crossed vertical and horizontal stripes. We discuss how the charge orders are stabilized, and their interplay with superconductivity.
Extended regions of suspected mis-assembly in the rat reference genome
Authors: Ramdas Shweta , Ozel Ayse Bilge , Treutelaar Mary K. , Holl Katie , Mandel Myrna , Woods Leah C. Solberg , Li Jun Z. 
Published: April 2019

AbstractWe performed whole-genome sequencing for eight inbred rat strains commonly used in genetic mapping studies. They are the founders of the NIH heterogeneous stock (HS) outbred colony. We provide their sequences and variant calls to the rat genomics community. When analyzing the variant calls we identified regions with unusually high levels of heterozygosity. These regions are consistent across the eight inbred strains, including Brown Norway, which is the basis of the rat reference genome. These regions show higher read depths than other regions in the genome and contain higher rates of apparent tri-allelic variant sites. The evidence suggests that these regions may correspond to duplicated segments that were incorrectly overlaid as a single segment in the reference genome. We provide masks for these regions of suspected mis-assembly as a resource for the community to flag potentially false interpretations of mapping or functional results.
Atlas of RNA sequencing profiles for normal human tissues
Authors: Suntsova Maria , Gaifullin Nurshat , Allina Daria , Reshetun Alexey , Li Xinmin , Mendeleeva Larisa , Surin Vadim , Sergeeva Anna , Spirin Pavel , Prassolov Vladimir , Morgan Alexander , Garazha Andrew , Sorokin Maxim , Buzdin Anton 
Published: April 2019

AbstractComprehensive analysis of molecular pathology requires a collection of reference samples representing normal tissues from healthy donors. For the available limited collections of normal tissues from postmortal donors, there is a problem of data incompatibility, as different datasets generated using different experimental platforms often cannot be merged in a single panel. Here, we constructed and deposited the gene expression database of normal human tissues based on uniformly screened original sequencing data. In total, 142 solid tissue samples representing 20 organs were taken from post-mortal human healthy donors of different age killed in road accidents no later than 36 hours after death. Blood samples were taken from 17 healthy volunteers. We then compared them with the 758 transcriptomic profiles taken from the other databases. We found that overall 463 biosamples showed tissue-specific rather than platform- or database-specific clustering and could be aggregated in a single database termed Oncobox Atlas of Normal Tissue Expression (ANTE). Our data will be useful to all those working with the analysis of human gene expression.
Mice lacking Casp1, Ifngr and Nos2 genes exhibit altered depressive- and anxiety-like behaviour, and gut microbiome composition
Authors: Inserra Antonio , Choo Jocelyn M. , Lewis Martin D. , Rogers Geraint B. , Wong Ma-Li , Licinio Julio 
Published: April 2019

AbstractConverging evidence supports the involvement of pro-inflammatory pathways and the gut microbiome in major depressive disorder (MDD). Pre-clinical and clinical studies suggest that decreasing pro-inflammatory signaling may provide clinical benefit in MDD. In this study, we used the chronic unpredictable stress (CUS) paradigm to assess whether mice lacking the pro-inflammatory caspase 1, interferon gamma-receptor, and nitric oxide synthase (Casp1, Ifngr, Nos2)−/− present altered depressive- and anxiety-like behaviour at baseline and in response to CUS. In comparison to wild-type (wt) mice, (Casp1, Ifngr, Nos2)−/− mice displayed decreased depressive- and anxiety-like behaviour, and increased hedonic-like behaviour and locomotor activity at baseline, and resistance to developing anhedonic-like behaviour and a heightened emotional state following stress. Plasma levels of ACTH and CORT did not differ between the triple knockout and wt mice following stress. The faecal microbiome of (Casp1, Ifngr, Nos2)−/− mice differed from that of wt mice at baseline and displayed reduced changes in response to chronic stress. Our results demonstrate that simultaneous deficit in multiple pro-inflammatory pathways has antidepressant-like effects at baseline, and confers resilience to stress-induced anhedonic-like behaviour. Moreover, accompanying changes in the gut microbiome composition suggest that CASP1, IFNGR and NOS2 play a role in maintaining microbiome homeostasis.
The serum level of irisin, but not asprosin, is abnormal in polycystic ovary syndrome patients
Authors: Chang Chia Lin , Huang Shang Yu , Hsu Ya Chiung , Chin Tzu Hsuan , Soong Yung Kuei 
Published: April 2019

AbstractPolycystic ovary syndrome (PCOS) is a disorder characterized by hyperandrogenism, oligo- or anovulation, and/or polycystic ovary. It frequently presents with dyslipidemia and insulin resistance. Recent studies have shown that the white adipose tissue-derived asprosin is elevated in humans with insulin resistance. Because many PCOS patients have a propensity to develop dyslipidemia and/or insulin resistance, asprosin metabolism could be dysregulated in PCOS patients. Accordingly, we investigated serum levels of asprosin, irisin, GIP, androgens, LH, glucose, insulin, and lipids as well as HOMA-IR, QUICKI and ISI Matsuda in a cohort of 444 PCOS patients and 156 controls. Patients were stratified based on metabolic syndrome risk factors (ATPIII [+] and [−] groups), or BMI (overweight and lean groups). The irisin level was significantly correlated with body weight, SBP, DBP, Ferriman–Gallwey score, and levels of TSH, triglycerides, glucose and insulin in the overall population, and was elevated in ATPIII(+) and overweight PCOS patients compared to corresponding controls. By contrast, asprosin levels in PCOS, ATPIII(+), or overweight patients were similar to those of corresponding controls. This finding indicated that the regulation of irisin, but not asprosin, metabolism is abnormal in PCOS patients, and this metabolic characteristic is distinctly different from that of diabetes patients.
Gestational exposure to an epidemiologically defined mixture of phthalates leads to gonadal dysfunction in mouse offspring of both sexes
Authors: Repouskou Anastasia , Panagiotidou Emily , Panagopoulou Lydia , Bisting Pernilla Larsdotter , Tuck Astrud R. , Sjödin Marcus O. D. , Lindberg Johan , Bozas Evangelos , Rüegg Joëlle , Gennings Chris , Bornehag Carl-Gustaf , Damdimopoulou Pauliina , Stamatakis Antonios , Kitraki Efthymia 
Published: April 2019

AbstractThe increasing concern for the reproductive toxicity of abundantly used phthalates requires reliable tools for exposure risk assessment to mixtures of chemicals, based on real life human exposure and disorder-associated epidemiological evidence. We herein used a mixture of four phthalate monoesters (33% mono-butyl phthalate, 16% mono-benzyl phthalate, 21% mono-ethyl hexyl phthalate, and 30% mono-isononyl phthalate), detected in 1st trimester urine of 194 pregnant women and identified as bad actors for a shorter anogenital distance (AGD) in their baby boys. Mice were treated with 0, 0.26, 2.6 and 13 mg/kg/d of the mixture, corresponding to 0x, 10x, 100x, 500x levels detected in the pregnant women. Adverse outcomes detected in the reproductive system of the offspring in pre-puberty and adulthood included reduced AGD index and gonadal weight, changes in gonadal histology and altered expression of key regulators of gonadal growth and steroidogenesis. Most aberrations were apparent in both sexes, though more pronounced in males, and exhibited a non-monotonic pattern. The phthalate mixture directly affected expression of steroidogenesis as demonstrated in a relevant in vitro model. The detected adversities at exposures close to the levels detected in pregnant women, raise concern on the existing safety limits for early-life human exposures and emphasizes the need for re-evaluation of the exposure risk.
The Piezo2 ion channel is mechanically activated by low-threshold positive pressure
Authors: Shin Kyung Chul , Park Hyun Ji , Kim Jae Gon , Lee In Hwa , Cho Hawon , Park Chanjae , Sung Tae Sik , Koh Sang Don , Park Sang Woong , Bae Young Min 
Published: April 2019

AbstractRecent parallel studies clearly indicated that Merkel cells and the mechanosensitive piezo2 ion channel play critical roles in the light-touch somatosensation. Moreover, piezo2 was suggested to be a light-touch sensing ion channel without a role in pain sensing in mammals. However, biophysical characteristics of piezo2, such as single channel conductance and sensitivities to various mechanical stimuli, are unclear, hampering a precise understanding of its role in touch sensation. Here, we describe the biophysical properties of piezo2 in human Merkel cell carcinoma (MCC)-13 cells; piezo2 is a low-threshold, positive pressure-specific, curvature-sensitive, mechanically activated cation channel with a single channel conductance of ~28.6 pS. Application of step indentations under the whole-cell mode of the patch-clamp technique, and positive pressures ≥5 mmHg under the cell-attached mode, activated piezo2 currents in MCC-13 and human embryonic kidney 293 T cells where piezo2 was overexpressed. By contrast, application of a negative pressure failed to activate piezo2 in these cells, whereas both positive and negative pressure activated piezo1 in a similar manner. Our results are the first to demonstrate single channel recordings of piezo2. We anticipate that our findings will be a starting point for a more sophisticated understanding of piezo2 roles in light-touch sensation.
Low-temperature microstructural studies on superconducting CaFe2As2
Authors: Huyan S. , Deng L. Z. , Wu Z. , Zhao K. , Sun J. Y. , Wu L. J. , Zhao Y. Y. , Yuan H. M. , Gooch M. , Lv B. , Zhu Y. , Chen S. , Chu C. W. 
Published: April 2019

AbstractUndoped CaFe2As2 (Ca122) can be stabilized in two slightly different non-superconducting tetragonal phases, PI and PII, through thermal treatments. Upon proper annealing, superconductivity with a Tc up to 25 K emerges in the samples with an admixture of PI and PII phases. Systematic low-temperature X-ray diffraction studies were conducted on undoped Ca122 samples annealed at 350 °C over different time periods. In addition to the diffraction peaks associated with the single-phase aggregation of PI and PII, a broad intermediate peak that shifts with annealing time was observed in the superconducting samples only. Our simulation of phase distribution suggests that the extra peak is associated with the admixture of PI and PII on the nanometer scale. High-resolution transmission electron microscopy confirms the existence of these nano-scale phase admixtures in the superconducting samples. These experimental results and simulation analyses lend further support for our conclusion that interfacial inducement is the most reasonable explanation for the emergence of superconductivity in undoped Ca122 single crystals.
Preparation of a magnetic reduced-graphene oxide/tea waste composite for high-efficiency sorption of uranium
Authors: Yang Aili , Zhu Yukuan , Li Ping , Huang C. P. 
Published: April 2019

AbstractThe preparation and application of adsorptive materials with low cost and high-efficiency recovery of uranium from nuclear waste is necessary for the development of sustainable, clean energy resources and to avoid nuclear pollution. In this work, the capacity of tea waste and tea waste hybrids as inexpensive sorbents for uranium removal from water solutions was investigated. Composites of graphene oxide (GO) and tea waste (TW) exhibited a promising adsorption performance for uranium from aqueous solutions. The composites GOTW and magnetic rGO/Fe3O4/TW show high adsorption capacities (Qm (TW) = 91.72 mg/g, Qm (GOTW) = 111.61 mg/g and Qm (rGO/Fe3O4/TW) = 104.95 mg/g) and removal rates (~99%) for U(VI). The equilibrium sorption of the adsorbents fitted well to the Langmuir model, and the sorption rate fitted well to a pseudo-second-order kinetic model. The thermodynamic parameters indicated that sorption was spontaneous and favourable. The prepared adsorbents were used for the removal of uranium from real water samples as well. The results revealed that GOTW and rGO/Fe3O4/TW can be used to remediate nuclear industrial effluent as a potential adsorbent.
Novel DNA Biosensor for Direct Determination of Carrageenan
Authors: Hassan Riyadh Abdulmalek , Heng Lee Yook , Tan Ling Ling 
Published: April 2019

AbstractA novel disposable electrochemical biosensor based on immobilized calf thymus double-stranded DNA (dsDNA) on the carbon-based screen-printed electrode (SPE) is developed for rapid biorecognition of carrageenan by using methylene blue (MB) redox indicator. The biosensor protocol for the detection of carrageenan is based on the concept of competitive binding of positively charged MB to the negatively charged dsDNA and carrageenan. The decrement in the MB cathodic peak current (ipc) signal as a result of the released MB from the immobilized dsDNA, and attracted to the carrageenan can be monitored via differential pulse voltammetry (DPV). The biosensor showed high sensitivity and selectivity to carrageenan at low concentration without interference from other polyanions such as alginate, gum arabic and starch. Calibration of the biosensor with carrageenan exhibited an excellent linear dependence from 1–10 mg L−1 (R2 = 0.98) with a detection limit of 0.08 mg L−1. The DNA-based carrageenan biosensor showed satisfactory reproducibility with 5.6–6.9% (n = 3) relative standard deviations (RSD), and possessing several advantages such as simplicity, fast and direct application to real sample analysis without any prior extensive sample treatments, particularly for seaweeds and food analyses.
Adding a new dimension to investigations of early radiolarian evolution
Authors: Kachovich Sarah , Sheng Jiani , Aitchison Jonathan C. 
Published: April 2019

AbstractKnowledge of the detailed architecture of the earliest radiolarian microfossils is key to resolving the evolution and systematics of this important group of marine protozoans. Non-destructive methods for observing the complexity within the internal structures of their siliceous skeletons have long eluded paleontologists. By developing methodologies that overcome some limitations of existing micro-computed tomography (micro-CT) we demonstrate a technique with potential to provide new insight into their evolution. Using 3D micro-CT data to generate models for six well-preserved siliceous radiolarian skeletons from the Middle Cambrian Inca Formation in far north Queensland, Australia and the Middle Ordovician Piccadilly Formation, in western Newfoundland, Canada, we can reconstruct phylogenetic relationships amongst some of the earliest radiolarians. Better knowledge of early radiolarian morphologies clarifies the vital function of internal structures and hierarchical diagnosis across a range of taxonomic affiliations.