bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stable and luminescent halide perovskite fabricated in water
Authors: Na Guangren , Zhang Lijun 
Published: June 2020

AbstractLead bromide perovskite nanoparticles are fabricated in the water, which has been recognized previously as a severe source of damage to halide perovskite materials and devices. The perovskite nanoparticles exhibit a high photoluminescence quantum yield and excellent material stability.
Jellyfish genomes reveal distinct homeobox gene clusters and conservation of small RNA processing
Authors: Nong Wenyan , Cao Jianquan , Li Yiqian , Qu Zhe , Sun Jin , Swale Thomas , Yip Ho Yin , Qian Pei Yuan , Qiu Jian-Wen , Kwan Hoi Shan , Bendena William , Tobe Stephen , Chan Ting Fung , Yip Kevin Y. , Chu Ka Hou , Ngai Sai Ming , Tsim Karl Yk , Holland Peter W. H. , Hui Jerome H. L. 
Published: June 2020

AbstractThe phylum Cnidaria represents a close outgroup to Bilateria and includes familiar animals including sea anemones, corals, hydroids, and jellyfish. Here we report genome sequencing and assembly for true jellyfishSanderia malayensisandRhopilema esculentum. The homeobox gene clusters are characterised by interdigitation of Hox, NK, and Hox-like genes revealing an alternate pathway of ANTP class gene dispersal and an intact three gene ParaHox cluster. The mitochondrial genomes are linear but, unlike inHydra, we do not detect nuclear copies, suggesting that linear plastid genomes are not necessarily prone to integration. Genes for sesquiterpenoid hormone production, typical for arthropods, are also now found in cnidarians. Somatic and germline cells both express piwi-interacting RNAs in jellyfish revealing a conserved cnidarian feature, and evidence for tissue-specific microRNA arm switching as found in Bilateria is detected. Jellyfish genomes reveal a mosaic of conserved and divergent genomic characters evolved from a shared ancestral genetic architecture.
Piwi reduction in the aged niche eliminates germline stem cells via Toll-GSK3 signaling
Authors: Lin Kun-Yang , Wang Wen-Der , Lin Chi-Hung , Rastegari Elham , Su Yu-Han , Chang Yu-Tzu , Liao Yung-Feng , Chang Yi-Chieh , Pi Haiwei , Yu Bo-Yi , Chen Shu-Hwa , Lin Chung-Yen , Lu Mei-Yeh , Su Tsu-Yi , Tzou Fei-Yang , Chan Chih-Chiang , Hsu Hwei-Jan 
Published: June 2020

AbstractTransposons are known to participate in tissue aging, but their effects on aged stem cells remain unclear. Here, we report that in the Drosophila ovarian germline stem cell (GSC) niche, aging-related reductions in expression of Piwi (a transposon silencer) derepress retrotransposons and cause GSC loss. Suppression of Piwi expression in the young niche mimics the aged niche, causing retrotransposon depression and coincident activation of Toll-mediated signaling, which promotes Glycogen synthase kinase 3 activity to degrade β-catenin. Disruption of β-catenin-E-cadherin-mediated GSC anchorage then results in GSC loss. Knocking down gypsy (a highly active retrotransposon) or toll, or inhibiting reverse transcription in the piwi-deficient niche, suppresses GSK3 activity and β-catenin degradation, restoring GSC-niche attachment. This retrotransposon-mediated impairment of aged stem cell maintenance may have relevance in many tissues, and could represent a viable therapeutic target for aging-related tissue degeneration.
Regular-triangle trimer and charge order preserving the Anderson condition in the pyrochlore structure of CsW2O6
Authors: Okamoto Yoshihiko , Amano Haruki , Katayama Naoyuki , Sawa Hiroshi , Niki Kenta , Mitoka Rikuto , Harima Hisatomo , Hasegawa Takumi , Ogita Norio , Tanaka Yu , Takigawa Masashi , Yokoyama Yasunori , Takehana Kanji , Imanaka Yasutaka , Nakamura Yuto , Kishida Hideo , Takenaka Koshi 
Published: June 2020

AbstractSince the discovery of the Verwey transition in magnetite, transition metal compounds with pyrochlore structures have been intensively studied as a platform for realizing remarkable electronic phase transitions. We report on a phase transition that preserves the cubic symmetry of the β-pyrochlore oxide CsW2O6, where each of W 5d electrons are confined in regular-triangle W3 trimers. This trimer formation represents the self-organization of 5d electrons, which can be resolved into a charge order satisfying the Anderson condition in a nontrivial way, orbital order caused by the distortion of WO6 octahedra, and the formation of a spin-singlet pair in a regular-triangle trimer. An electronic instability due to the unusual three-dimensional nesting of Fermi surfaces and the strong correlations of the 5d electrons characteristic of the pyrochlore oxides are both likely to play important roles in this charge-orbital-spin coupled phenomenon.
Topoisomerase 3β knockout mice show transcriptional and behavioural impairments associated with neurogenesis and synaptic plasticity
Authors: Joo Yuyoung , Xue Yutong , Wang Yue , McDevitt Ross A. , Sah Nirnath , Bossi Simone , Su Shuaikun , Lee Seung Kyu , Peng Wei , Xie Aoji , Zhang Yongqing , Ding Yi , Ku Wai Lim , Ghosh Soumita , Fishbein Kenneth , Shen Weiping , Spencer Richard , Becker Kevin , Zhao Keji , Mattson Mark P. , van Praag Henriette , Sharov Alexei , Wang Weidong 
Published: June 2020

AbstractTopoisomerase 3β (Top3β) is the only dual-activity topoisomerase in animals that can change topology for both DNA and RNA, and facilitate transcription on DNA and translation on mRNAs. Top3β mutations have been linked to schizophrenia, autism, epilepsy, and cognitive impairment. Here we show that Top3β knockout mice exhibit behavioural phenotypes related to psychiatric disorders and cognitive impairment. The mice also display impairments in hippocampal neurogenesis and synaptic plasticity. Notably, the brains of the mutant mice exhibit impaired global neuronal activity-dependent transcription in response to fear conditioning stress, and the affected genes include many with known neuronal functions. Our data suggest that Top3β is essential for normal brain function, and that defective neuronal activity-dependent transcription may be a mechanism by which Top3β deletion causes cognitive impairment and psychiatric disorders.
MLKL trafficking and accumulation at the plasma membrane control the kinetics and threshold for necroptosis
Authors: Samson Andre L. , Zhang Ying , Geoghegan Niall D. , Gavin Xavier J. , Davies Katherine A. , Mlodzianoski Michael J. , Whitehead Lachlan W. , Frank Daniel , Garnish Sarah E. , Fitzgibbon Cheree , Hempel Anne , Young Samuel N. , Jacobsen Annette V. , Cawthorne Wayne , Petrie Emma J. , Faux Maree C. , Shield-Artin Kristy , Lalaoui Najoua , Hildebrand Joanne M. , Silke John , Rogers Kelly L. , Lessene Guillaume , Hawkins Edwin D. , Murphy James M. 
Published: June 2020

AbstractMixed lineage kinase domain-like (MLKL) is the terminal protein in the pro-inflammatory necroptotic cell death program. RIPK3-mediated phosphorylation is thought to initiate MLKL oligomerization, membrane translocation and membrane disruption, although the precise choreography of events is incompletely understood. Here, we use single-cell imaging approaches to map the chronology of endogenous human MLKL activation during necroptosis. During the effector phase of necroptosis, we observe that phosphorylated MLKL assembles into higher order species on presumed cytoplasmic necrosomes. Subsequently, MLKL co-traffics with tight junction proteins to the cell periphery via Golgi-microtubule-actin-dependent mechanisms. MLKL and tight junction proteins then steadily co-accumulate at the plasma membrane as heterogeneous micron-sized hotspots. Our studies identify MLKL trafficking and plasma membrane accumulation as crucial necroptosis checkpoints. Furthermore, the accumulation of phosphorylated MLKL at intercellular junctions accelerates necroptosis between neighbouring cells, which may be relevant to inflammatory bowel disease and other necroptosis-mediated enteropathies.
Holistic engineering of cell-free systems through proteome-reprogramming synthetic circuits
Authors: Contreras-Llano Luis E. , Meyer Conary , Liu Yao , Sarker Mridul , Lim Sierin , Longo Marjorie L. , Tan Cheemeng 
Published: June 2020

AbstractSynthetic biology has focused on engineering genetic modules that operate orthogonally from the host cells. A synthetic biological module, however, can be designed to reprogram the host proteome, which in turn enhances the function of the synthetic module. Here, we apply this holistic synthetic biology concept to the engineering of cell-free systems by exploiting the crosstalk between metabolic networks in cells, leading to a protein environment more favorable for protein synthesis. Specifically, we show that local modules expressing translation machinery can reprogram the bacterial proteome, changing the expression levels of more than 700 proteins. The resultant feedback generates a cell-free system that can synthesize fluorescent reporters, protein nanocages, and the gene-editing nuclease Cas9, with up to 5-fold higher expression level than classical cell-free systems. Our work demonstrates a holistic approach that integrates synthetic and systems biology concepts to achieve outcomes not possible by only local, orthogonal circuits.
MeCP2 regulates gene expression through recognition of H3K27me3
Authors: Lee Wooje , Kim Jeeho , Yun Jung-Mi , Ohn Takbum , Gong Qizhi 
Published: June 2020

AbstractMeCP2 plays a multifaceted role in gene expression regulation and chromatin organization. Interaction between MeCP2 and methylated DNA in the regulation of gene expression is well established. However, the widespread distribution of MeCP2 suggests it has additional interactions with chromatin. Here we demonstrate, by both biochemical and genomic analyses, that MeCP2 directly interacts with nucleosomes and its genomic distribution correlates with that of H3K27me3. In particular, the methyl-CpG-binding domain of MeCP2 shows preferential interactions with H3K27me3. We further observe that the impact of MeCP2 on transcriptional changes correlates with histone post-translational modification patterns. Our findings indicate that MeCP2 interacts with genomic loci via binding to DNA as well as histones, and that interaction between MeCP2 and histone proteins plays a key role in gene expression regulation.
Rapid fast-delta decay following prolonged wakefulness marks a phase of wake-inertia in NREM sleep
Authors: Hubbard Jeffrey , Gent Thomas C. , Hoekstra Marieke M. B. , Emmenegger Yann , Mongrain Valerie , Landolt Hans-Peter , Adamantidis Antoine R. , Franken Paul 
Published: June 2020

AbstractSleep-wake driven changes in non-rapid-eye-movement sleep (NREM) sleep (NREMS) EEG delta (δ-)power are widely used as proxy for a sleep homeostatic process. Here, we noted frequency increases in δ-waves in sleep-deprived mice, prompting us to re-evaluate how slow-wave characteristics relate to prior sleep-wake history. We identified two classes of δ-waves; one responding to sleep deprivation with high initial power and fast, discontinuous decay during recovery sleep (δ2) and another unrelated to time-spent-awake with slow, linear decay (δ1). Reanalysis of previously published datasets demonstrates that δ-band heterogeneity after sleep deprivation is also present in human subjects. Similar to sleep deprivation, silencing of centromedial thalamus neurons boosted subsequent δ2-waves, specifically. δ2-dynamics paralleled that of temperature, muscle tone, heart rate, and neuronal ON-/OFF-state lengths, all reverting to characteristic NREMS levels within the first recovery hour. Thus, prolonged waking seems to necessitate a physiological recalibration before typical NREMS can be reinstated.
Phonon-exciton Interactions in WSe2 under a quantizing magnetic field
Authors: Li Zhipeng , Wang Tianmeng , Miao Shengnan , Li Yunmei , Lu Zhenguang , Jin Chenhao , Lian Zhen , Meng Yuze , Blei Mark , Taniguchi Takashi , Watanabe Kenji , Tongay Sefaattin , Yao Wang , Smirnov Dmitry , Zhang Chuanwei , Shi Su-Fei 
Published: June 2020

AbstractStrong many-body interaction in two-dimensional transitional metal dichalcogenides provides a unique platform to study the interplay between different quasiparticles, such as prominent phonon replica emission and modified valley-selection rules. A large out-of-plane magnetic field is expected to modify the exciton-phonon interactions by quantizing excitons into discrete Landau levels, which is largely unexplored. Here, we observe the Landau levels originating from phonon-exciton complexes and directly probe exciton-phonon interaction under a quantizing magnetic field. Phonon-exciton interaction lifts the inter-Landau-level transition selection rules for dark trions, manifested by a distinctively different Landau fan pattern compared to bright trions. This allows us to experimentally extract the effective mass of both holes and electrons. The onset of Landau quantization coincides with a significant increase of the valley-Zeeman shift, suggesting strong many-body effects on the phonon-exciton interaction. Our work demonstrates monolayer WSe2 as an intriguing playground to study phonon-exciton interactions and their interplay with charge, spin, and valley.
Scientists’ warning on affluence
Authors: Wiedmann Thomas , Lenzen Manfred , Keyßer Lorenz T. , Steinberger Julia K. 
Published: June 2020

AbstractFor over half a century, worldwide growth in affluence has continuously increased resource use and pollutant emissions far more rapidly than these have been reduced through better technology. The affluent citizens of the world are responsible for most environmental impacts and are central to any future prospect of retreating to safer environmental conditions. We summarise the evidence and present possible solution approaches. Any transition towards sustainability can only be effective if far-reaching lifestyle changes complement technological advancements. However, existing societies, economies and cultures incite consumption expansion and the structural imperative for growth in competitive market economies inhibits necessary societal change.
Nolz1 expression is required in dopaminergic axon guidance and striatal innervation
Authors: Soleilhavoup Clement , Travaglio Marco , Patrick Kieran , Garção Pedro , Boobalan Elangovan , Adolfs Youri , Spriggs Ruth V. , Moles-Garcia Emma , Dhiraj Dalbir , Oosterveen Tony , Ferri Sarah L. , Abel Ted , Brodkin Edward S. , Pasterkamp R. Jeroen , Brooks Brian P. , Panman Lia 
Published: June 2020

AbstractMidbrain dopaminergic (DA) axons make long longitudinal projections towards the striatum. Despite the importance of DA striatal innervation, processes involved in establishment of DA axonal connectivity remain largely unknown. Here we demonstrate a striatal-specific requirement of transcriptional regulator Nolz1 in establishing DA circuitry formation. DA projections are misguided and fail to innervate the striatum in both constitutive and striatal-specific Nolz1 mutant embryos. The lack of striatal Nolz1 expression results in nigral to pallidal lineage conversion of striatal projection neuron subtypes. This lineage switch alters the composition of secreted factors influencing DA axonal tract formation and renders the striatum non-permissive for dopaminergic and other forebrain tracts. Furthermore, transcriptomic analysis of wild-type and Nolz1−/− mutant striatal tissue led to the identification of several secreted factors that underlie the observed guidance defects and proteins that promote DA axonal outgrowth. Together, our data demonstrate the involvement of the striatum in orchestrating dopaminergic circuitry formation.
Eliminating the capsule-like layer to promote glucose uptake for hyaluronan production by engineered Corynebacterium glutamicum
Authors: Wang Yang , Hu Litao , Huang Hao , Wang Hao , Zhang Tianmeng , Chen Jian , Du Guocheng , Kang Zhen 
Published: June 2020

AbstractHyaluronan is widely used in cosmetics and pharmaceutics. Development of robust and safe cell factories and cultivation approaches to efficiently produce hyaluronan is of many interests. Here, we describe the metabolic engineering of Corynebacterium glutamicum and application of a fermentation strategy to manufacture hyaluronan with different molecular weights. C. glutamicum is engineered by combinatorial overexpression of type I hyaluronan synthase, enzymes of intermediate metabolic pathways and attenuation of extracellular polysaccharide biosynthesis. The engineered strain produces 34.2 g L−1 hyaluronan in fed-batch cultures. We find secreted hyaluronan encapsulates C. glutamicum, changes its cell morphology and inhibits metabolism. Disruption of the encapsulation with leech hyaluronidase restores metabolism and leads to hyper hyaluronan productions of 74.1 g L−1. Meanwhile, the molecular weight of hyaluronan is also highly tunable. These results demonstrate combinatorial optimization of cell factories and the extracellular environment is efficacious and likely applicable for the production of other biopolymers.
Substrate specificity of the TRAMP nuclear surveillance complexes
Authors: Delan-Forino Clémentine , Spanos Christos , Rappsilber Juri , Tollervey David 
Published: June 2020

AbstractDuring nuclear surveillance in yeast, the RNA exosome functions together with the TRAMP complexes. These include the DEAH-box RNA helicase Mtr4 together with an RNA-binding protein (Air1 or Air2) and a poly(A) polymerase (Trf4 or Trf5). To better determine how RNA substrates are targeted, we analyzed protein and RNA interactions for TRAMP components. Mass spectrometry identified three distinct TRAMP complexes formed in vivo. These complexes preferentially assemble on different classes of transcripts. Unexpectedly, on many substrates, including pre-rRNAs and pre-mRNAs, binding specificity is apparently conferred by Trf4 and Trf5. Clustering of mRNAs by TRAMP association shows co-enrichment for mRNAs with functionally related products, supporting the significance of surveillance in regulating gene expression. We compared binding sites of TRAMP components with multiple nuclear RNA binding proteins, revealing preferential colocalization of subsets of factors. TRF5 deletion reduces Mtr4 recruitment and increases RNA abundance for mRNAs specifically showing high Trf5 binding.
Combustible ice mimicking behavior of hydrogen-bonded organic framework at ambient condition
Authors: Wang Yang , Hou Xudong , Liu Congyan , Albolkany Mohamed K. , Wang Yan , Wu Niannian , Chen Chunhui , Liu Bo 
Published: June 2020

AbstractAdsorption of guest molecules by porous materials proceeds in a spontaneous exothermic way, whereas desorption usually requires external energy input as an endothermic process. Reducing such energy consumption makes great sense in practice. Here we report the reversible and automatic methanol (MeOH) adsorption/release in an ionic hydrogen-bonded organic framework (iHOF) constructed from guanidinium cation and borate anion ([B(OCH3)4]3[C(NH2)3]4Cl•4CH3OH, termed Gd-B) at ambient condition. The metastable Gd-B automatically releases all sixteen MeOH molecules (63.4 wt%) via desorption and tetra-methyl borate hydrolysis at ambient atmosphere and the structure can be recovered when re-exposed to MeOH vapor or liquid, mimicking combustible ice behavior but at ambient condition. Reversible capture/release of four guest MeOH molecules is also realized without destroying its crystal structure. The combustible Gd-B paves a way for exploring metastable iHOF materials as carrier for alternative energy source and drug delivery etc.
Quantum Monte Carlo study of lattice polarons in the two-dimensional three-orbital Su–Schrieffer–Heeger model
Authors: Li Shaozhi , Johnston Steven 
Published: June 2020

AbstractThe electron–lattice interaction gives rise to a rich set of phenomena in quantum materials. Microscopically, this interaction often arises from the modulation of orbital overlaps; however, many theoretical studies neglect such couplings. Here, we present an exact diagonalization and determinant quantum Monte Carlo study of a three-orbital Su–Schrieffer–Heeger (SSH) model, on a two-dimensional Lieb lattice and in the negative charge transfer regime. At half-filling (one hole/unit cell), we observe a bipolaron insulating phase with a bond-disproportionate lattice. This phase is robust against moderate hole doping but is suppressed at large hole concentrations, leading to a metallic polaron-liquid-like state with fluctuating patches of local distortions. We also find an s-wave superconducting state at large hole doping that primarily appears on the oxygen sublattice. Our work provides a non-perturbative view of SSH-type couplings in two dimensions with implications for materials where such couplings are dominant.
CODC: a Copula-based model to identify differential coexpression
Authors: Ray Sumanta , Lall Snehalika , Bandyopadhyay Sanghamitra 
Published: June 2020

AbstractDifferential coexpression has recently emerged as a new way to establish a fundamental difference in expression pattern among a group of genes between two populations. Earlier methods used some scoring techniques to detect changes in correlation patterns of a gene pair in two conditions. However, modeling differential coexpression by means of finding differences in the dependence structure of the gene pair has hitherto not been carried out. We exploit a copula-based framework to model differential coexpression between gene pairs in two different conditions. The Copula is used to model the dependency between expression profiles of a gene pair. For a gene pair, the distance between two joint distributions produced by copula is served as differential coexpression. We used five pan-cancer TCGA RNA-Seq data to evaluate the model that outperforms the existing state of the art. Moreover, the proposed model can detect a mild change in the coexpression pattern across two conditions. For noisy expression data, the proposed method performs well because of the popular scale-invariant property of copula. In addition, we have identified differentially coexpressed modules by applying hierarchical clustering on the distance matrix. The identified modules are analyzed through Gene Ontology terms and KEGG pathway enrichment analysis.
Adipose tissue morphology, imaging and metabolomics predicting cardiometabolic risk and family history of type 2 diabetes in non-obese men
Authors: Rawshani Aidin , Eliasson Björn , Rawshani Araz , Henninger Josefin , Mardinoglu Adil , Carlsson Åsa , Sohlin Maja , Ljungberg Maria , Hammarstedt Ann , Rosengren Annika , Smith Ulf 
Published: June 2020

AbstractWe evaluated the importance of body composition, amount of subcutaneous and visceral fat, liver and heart ectopic fat, adipose tissue distribution and cell size as predictors of cardio-metabolic risk in 53 non-obese male individuals. Known family history of type 2 diabetes was identified in 25 individuals. The participants also underwent extensive phenotyping together with measuring different biomarkers and non-targeted serum metabolomics. We used ensemble learning and other machine learning approaches to identify predictors with considerable relative importance and their intricate interactions. Visceral fat and age were strong individual predictors of ectopic fat accumulation in liver and heart along with markers of lipid oxidation and reduced glucose tolerance. Subcutaneous adipose cell size was the strongest individual predictor of whole-body insulin sensitivity and also a marker of visceral and ectopic fat accumulation. The metabolite 3-MOB along with related branched-chain amino acids demonstrated strong predictability for family history of type 2 diabetes.