bluuebunny/crossref_metadata_2025_split huggingface dataset:
Control of developmentally primed erythroid genes by combinatorial co-repressor actions
Authors: Stadhouders Ralph , Cico Alba , Stephen Tharshana , Thongjuea Supat , Kolovos Petros , Baymaz H. Irem , Yu Xiao , Demmers Jeroen , Bezstarosti Karel , Maas Alex , Barroca Vilma , Kockx Christel , Ozgur Zeliha , van Ijcken Wilfred , Arcangeli Marie-Laure , Andrieu-Soler Charlotte , Lenhard Boris , Grosveld Frank , Soler Eric 
Published: November 2015

AbstractHow transcription factors (TFs) cooperate within large protein complexes to allow rapid modulation of gene expression during development is still largely unknown. Here we show that the key haematopoietic LIM-domain-binding protein-1 (LDB1) TF complex contains several activator and repressor components that together maintain an erythroid-specific gene expression programme primed for rapid activation until differentiation is induced. A combination of proteomics, functional genomics and in vivo studies presented here identifies known and novel co-repressors, most notably the ETO2 and IRF2BP2 proteins, involved in maintaining this primed state. The ETO2–IRF2BP2 axis, interacting with the NCOR1/SMRT co-repressor complex, suppresses the expression of the vast majority of archetypical erythroid genes and pathways until its decommissioning at the onset of terminal erythroid differentiation. Our experiments demonstrate that multimeric regulatory complexes feature a dynamic interplay between activating and repressing components that determines lineage-specific gene expression and cellular differentiation.
Disinhibition of olfactory bulb granule cells accelerates odour discrimination in mice
Authors: Nunes Daniel , Kuner Thomas 
Published: November 2015

AbstractGranule cells are the dominant cell type of the olfactory bulb inhibiting mitral and tufted cells via dendrodendritic synapses; yet the factors regulating the strength of their inhibitory output, and, therefore, their impact on odour discrimination, remain unknown. Here we show that GABAAR β3-subunits are distributed in a somatodendritic pattern, mostly sparing the large granule cell spines also known as gemmules. Granule cell-selective deletion of β3-subunits nearly abolishes spontaneous and muscimol-induced currents mediated by GABAA receptors in granule cells, yet recurrent inhibition of mitral cells is strongly enhanced. Mice with disinhibited granule cells require less time to discriminate both dissimilar as well as highly similar odourants, while discrimination learning remains unaffected. Hence, granule cells are controlled by an inhibitory drive that in turn tunes mitral cell inhibition. As a consequence, the olfactory bulb inhibitory network adjusts the speed of early sensory processing.
The origin of electronic band structure anomaly in topological crystalline insulator group-IV tellurides
Authors: Ye Zhen-Yu , Deng Hui-Xiong , Wu Hui-Zhen , Li Shu-Shen , Wei Su-Huai , Luo Jun-Wei 
Published: November 2015

AbstractGroup-IV tellurides have exhibited exotic band structures. Specifically, despite the fact that Sn sits between Ge and Pb in the same column of the periodic table, cubic SnTe is a topological crystalline insulator with band inversion, but both isovalent GeTe and PbTe are trivial semiconductors with normal band order. By performing first-principles band structure calculations, we unravel the origin of this abnormal behaviour by using symmetry analysis and the atomic orbital energy levels and atomic sizes of these elements. In group-IV tellurides, the s lone pair band of the group-IV element is allowed by symmetry to couple with the anion valence p band at the L-point, and such s–p coupling leads to the occurrence of bandgap at the L-point. We find that such s–p coupling is so strong in SnTe that it inverts the band order near the bandgap; however, it is not strong enough in both GeTe and PbTe, so they remain normal semiconductors. The reason for this is the incomplete screening of the core of the relatively tight-binding Ge 4s orbital by its 3d orbitals and the large atomic size and strong relativistic effect in Pb, respectively. Interestingly, we also find that the rhombohedral distortion removes the inversion symmetry and the reduced s–p coupling transforms the α-SnTe back to a normal semiconductor. Our study demonstrates that, in addition to spin–orbital coupling, strain and interface dipole fields, inter-orbital coupling is another effective way to engineer the topological insulators.
An efficient descriptor model for designing materials for solar cells
Authors: Alharbi Fahhad H , Rashkeev Sergey N , El-Mellouhi Fedwa , Lüthi Hans P , Tabet Nouar , Kais Sabre 
Published: November 2015

AbstractAn efficient descriptor model for fast screening of potential materials for solar cell applications is presented. It works for both excitonic and non-excitonic solar cells materials, and in addition to the energy gap it includes the absorption spectrum (α(E)) of the material. The charge transport properties of the explored materials are modelled using the characteristic diffusion length (Ld) determined for the respective family of compounds. The presented model surpasses the widely used Scharber model developed for bulk heterojunction solar cells. Using published experimental data, we show that the presented model is more accurate in predicting the achievable efficiencies. To model both excitonic and non-excitonic systems, two different sets of parameters are used to account for the different modes of operation. The analysis of the presented descriptor model clearly shows the benefit of including α(E) and Ld in view of improved screening results.
Onshore industrial wind turbine locations for the United States up to March 2014
Authors: Diffendorfer Jay E. , Kramer Louisa A. , Ancona Zach H. , Garrity Christopher P. 
Published: November 2015

AbstractWind energy is a rapidly growing form of renewable energy in the United States. While summary information on the total amounts of installed capacity are available by state, a free, centralized, national, turbine-level, geospatial dataset useful for scientific research, land and resource management, and other uses did not exist. Available in multiple formats and in a web application, these public domain data provide industrial-scale onshore wind turbine locations in the United States up to March 2014, corresponding facility information, and turbine technical specifications. Wind turbine records have been collected and compiled from various public sources, digitized or position verified from aerial imagery, and quality assured and quality controlled. Technical specifications for turbines were assigned based on the wind turbine make and model as described in public literature. In some cases, turbines were not seen in imagery or turbine information did not exist or was difficult to obtain. Uncertainty associated with these is recorded in a confidence rating.
A collection of Australian Drosophila datasets on climate adaptation and species distributions
Authors: Hangartner Sandra B. , Hoffmann Ary A. , Smith Ailie , Griffin Philippa C. 
Published: November 2015

AbstractThe Australian Drosophila Ecology and Evolution Resource (ADEER) collates Australian datasets on drosophilid flies, which are aimed at investigating questions around climate adaptation, species distribution limits and population genetics. Australian drosophilid species are diverse in climatic tolerance, geographic distribution and behaviour. Many species are restricted to the tropics, a few are temperate specialists, and some have broad distributions across climatic regions. Whereas some species show adaptability to climate changes through genetic and plastic changes, other species have limited adaptive capacity. This knowledge has been used to identify traits and genetic polymorphisms involved in climate change adaptation and build predictive models of responses to climate change. ADEER brings together 103 datasets from 39 studies published between 1982–2013 in a single online resource. All datasets can be downloaded freely in full, along with maps and other visualisations. These historical datasets are preserved for future studies, which will be especially useful for assessing climate-related changes over time.
Biochar as an electron shuttle for reductive dechlorination of pentachlorophenol by Geobacter sulfurreducens
Authors: Yu Linpeng , Yuan Yong , Tang Jia , Wang Yueqiang , Zhou Shungui 
Published: November 2015

AbstractThe reductive dechlorination of pentachlorophenol (PCP) by Geobacter sulfurreducens in the presence of different biochars was investigated to understand how biochars affect the bioreduction of environmental contaminants. The results indicated that biochars significantly accelerate electron transfer from cells to PCP, thus enhancing reductive dechlorination. The promotion effects of biochar (as high as 24-fold) in this process depend on its electron exchange capacity (EEC) and electrical conductivity (EC). A kinetic model revealed that the surface redox-active moieties (RAMs) and EC of biochar (900 °C) contributed to 56% and 41% of the biodegradation rate, respectively. This work demonstrates that biochars are efficient electron mediators for the dechlorination of PCP and that both the EC and RAMs of biochars play important roles in the electron transfer process.
High-throughput transcriptome sequencing of the cold seep mussel Bathymodiolus platifrons
Authors: Wong Yue Him , Sun Jin , He Li Sheng , Chen Lian Guo , Qiu Jian-Wen , Qian Pei-Yuan 
Published: November 2015

AbstractBathymodiolid mussels dominate hydrothermal vents, cold methane/sulfide-hydrocarbon seeps and other sites of organic enrichment. Here, we aimed to explore the innate immune system and detoxification mechanism of the deep sea mussel Bathymodiolus platifrons collected from a methane seep in the South China Sea. We sequenced the transcriptome of the mussels’ gill, foot and mantle tissues and generated a transcriptomic database containing 96,683 transcript sequences. Based on GO and KEGG annotations, we reported transcripts that were related to the innate immune system, heavy metal detoxification and sulfide metabolic genes. Our in-depth analysis on the isoforms of peptidoglycan recognition protein (PGRP) that have different cellular location and potentially differential selectivity towards peptidoglycan (PGN) from gram-positive and gram-negative bacteria were differentially expressed in different tissues. We also reported a potentially novel form of metallothionein and the production of phytochelatin in B. platifrons, which has not been reported in any of its coastal relative Mytilus mussel species. Overall, the present study provided new insights into heavy metal and sulfide metabolism in B. platifrons and can be served as the basis for future molecular studies on host-symbiont interactions in cold seep mussels.
Oral iron acutely elevates bacterial growth in human serum
Authors: Cross James H. , Bradbury Richard S. , Fulford Anthony J. , Jallow Amadou T. , Wegmüller Rita , Prentice Andrew M. , Cerami Carla 
Published: November 2015

AbstractIron deficiency is the most common nutrient deficiency worldwide and routine supplementation is standard policy for pregnant mothers and children in most low-income countries. However, iron lies at the center of host-pathogen competition for nutritional resources and recent trials of iron administration in African and Asian children have resulted in significant excesses of serious adverse events including hospitalizations and deaths. Increased rates of malaria, respiratory infections, severe diarrhea and febrile illnesses of unknown origin have all been reported, but the mechanisms are unclear. We here investigated the ex vivo growth characteristics of exemplar sentinel bacteria in adult sera collected before and 4 h after oral supplementation with 2 mg/kg iron as ferrous sulfate. Escherichia coli, Yersinia enterocolitica and Salmonella enterica serovar Typhimurium (all gram-negative bacteria) and Staphylococcus epidermidis (gram-positive) showed markedly elevated growth in serum collected after iron supplementation. Growth rates were very strongly correlated with transferrin saturation (p < 0.0001 in all cases). Growth of Staphylococcus aureus, which preferentially scavenges heme iron, was unaffected. These data suggest that even modest oral supplements with highly soluble (non-physiological) iron, as typically used in low-income settings, could promote bacteremia by accelerating early phase bacterial growth prior to the induction of immune defenses.
Epstein-Barr virus from Burkitt Lymphoma biopsies from Africa and South America share novel LMP-1 promoter and gene variations
Authors: Lei Haiyan , Li Tianwei , Li Bingjie , Tsai Shien , Biggar Robert J. , Nkrumah Francis , Neequaye Janet , Gutierrez Marina , Epelman Sidnei , Mbulaiteye Sam M. , Bhatia Kishor , Lo Shyh-Ching 
Published: November 2015

AbstractEpstein Barr virus (EBV) sequence variation is thought to contribute to Burkitt lymphoma (BL), but lack of data from primary BL tumors hampers efforts to test this hypothesis. We directly sequenced EBV from 12 BL biopsies from Ghana, Brazil and Argentina, aligned the obtained reads to the wild-type (WT) EBV reference sequence and compared them with 100 published EBV genomes from normal and diseased people from around the world. The 12 BL EBVs were Type 1. Eleven clustered close to each other and to EBV from Raji BL cell line, but away from 12 EBVs reported from other BL-derived cell lines and away from EBV from NPC and healthy people from Asia. We discovered 23 shared novel nucleotide-base changes in the latent membrane protein (LMP)-1 promoter and gene (associated with 9 novel amino acid changes in the LMP-1 protein) of the 11 BL EBVs. Alignment of this region for the 112 EBV genomes revealed four distinct patterns, tentatively termed patterns A to D. The distribution of BL EBVs was 48%, 8%, 24% and 20% for patterns A to D, respectively; the NPC EBV’s were Pattern B and EBV-WT was pattern D. Further work is needed to investigate the association between EBV LMP-1 patterns with BL.
Structural insights into YfiR sequestering by YfiB in Pseudomonas aeruginosa PAO1
Authors: Li Shanshan , Li Tingting , Xu Yueyang , Zhang Qionglin , Zhang Wei , Che Shiyou , Liu Ruihua , Wang Yingying , Bartlam Mark 
Published: November 2015

AbstractYfiBNR is a tripartite signalling system in Pseudomonas aeruginosa that modulates intracellular c-di-GMP levels in response to signals received in the periplasm. YfiB is an outer membrane lipoprotein and presumed sensor protein that sequesters the repressor protein YfiR. To provide insights into YfiBNR function, we have determined three-dimensional crystal structures of YfiB and YfiR from P. aeruginosa PAO1 alone and as a 1:1 complex. A YfiB(27–168) construct is predominantly dimeric, whereas a YfiB(59–168) is monomeric, indicating that YfiB can dimerize via its N-terminal region. YfiR forms a stable complex with YfiB(59–168), while the YfiR binding interface is obstructed by the N-terminal region in YfiB(27–168). The YfiB-YfiR complex reveals a conserved interaction surface on YfiR that overlaps with residues predicted to interact with the periplasmic PAS domain of YfiN. Comparison of native and YfiR-bound structures of YfiB suggests unwinding of the N-terminal linker region for attachment to the outer membrane. A model is thus proposed for YfiR sequestration at the outer membrane by YfiB. Our work provides the first detailed insights into the interaction between YfiB and YfiR at the molecular level and is a valuable starting point for further functional and mechanistic studies of the YfiBNR signalling system.
P2×7 purinergic signaling in dilated cardiomyopathy induced by auto-immunity against muscarinic M2 receptors: autoantibody levels, heart functionality and cytokine expression
Authors: Martinez Camila Guerra , Zamith-Miranda Daniel , da Silva Marcia Gracindo , Ribeiro Karla Consort , Brandão Izaíra Trincani , Silva Celio Lopes , Diaz Bruno Lourenço , Bellio Maria , Persechini Pedro Muanis , Kurtenbach Eleonora 
Published: November 2015

AbstractAutoantibodies against the M2 receptors (M2AChR) have been associated with Dilated Cardiomyopathy (DCM). In the heart, P2×7 receptors influence electrical conduction, coronary circulation and response to ischemia. They can also trigger pro-inflammatory responses and the development of neurological, cardiac and renal disorders. Here, P2×7−/− mice displayed an increased heart rate and ST segment depression, but similar exercise performance when compared to wild type (WT) animals. After immunization with plasmid containing M2AChR cDNA sequence, WT mice produced anti-M2AChR antibodies, while P2×7−/− mice showed an attenuated production. Despite this, WT and P2×7−/− showed left ventricle cavity enlargement and decreased exercise tolerance. Transfer of serum from M2AChR WT immunized mice to näive recipients led to an alteration in heart shape. P2×7−/− mice displayed a significant increase in the frequency of spleen regulatory T cells population, which is mainly composed by the FoxP3+CD25− subset. M2AChR WT immunized mice showed an increase in IL-1β, IFNγ and IL-17 levels in the heart, while P2×7−/− group produced lower amounts of IL-1β and IL-17 and higher amounts of IFNγ. These results pointed to previously unnoticed roles of P2×7 in cardiovascular and immune systems and underscored the participation of IL-17 and IFNγ in the progress of autoimmune DCM.
Mimosoid legume plastome evolution: IR expansion, tandem repeat expansions and accelerated rate of evolution in clpP
Authors: Dugas Diana V. , Hernandez David , Koenen Erik J.M. , Schwarz Erika , Straub Shannon , Hughes Colin E. , Jansen Robert K. , Nageswara-Rao Madhugiri , Staats Martijn , Trujillo Joshua T. , Hajrah Nahid H. , Alharbi Njud S. , Al-Malki Abdulrahman L. , Sabir Jamal S. M. , Bailey C. Donovan 
Published: November 2015

AbstractThe Leguminosae has emerged as a model for studying angiosperm plastome evolution because of its striking diversity of structural rearrangements and sequence variation. However, most of what is known about legume plastomes comes from few genera representing a subset of lineages in subfamily Papilionoideae. We investigate plastome evolution in subfamily Mimosoideae based on two newly sequenced plastomes (Inga and Leucaena) and two recently published plastomes (Acacia and Prosopis) and discuss the results in the context of other legume and rosid plastid genomes. Mimosoid plastomes have a typical angiosperm gene content and general organization as well as a generally slow rate of protein coding gene evolution, but they are the largest known among legumes. The increased length results from tandem repeat expansions and an unusual 13 kb IR-SSC boundary shift in Acacia and Inga. Mimosoid plastomes harbor additional interesting features, including loss of clpP intron1 in Inga, accelerated rates of evolution in clpP for Acacia and Inga and dN/dS ratios consistent with neutral and positive selection for several genes. These new plastomes and results provide important resources for legume comparative genomics, plant breeding and plastid genetic engineering, while shedding further light on the complexity of plastome evolution in legumes and angiosperms.
Selection of best-performing reference gene products for investigating transcriptional regulation across silvering in the European eel (Anguilla anguilla)
Authors: Franzellitti Silvia , Kiwan Alisar , Valbonesi Paola , Fabbri Elena 
Published: November 2015

AbstractThe focus of the present study was to set a methodological approach for evaluating molecular mechanisms underlying silvering transformation in the European eel, Anguilla anguilla. Silvering is a tightly controlled process during which eels undergo significant morphological, physiological and behavioral changes, pre-adapting for the oceanic spawning migration. Female eels showing different silver indexes were caught in different seasons in the Comacchio Lagoon (North Adriatic Sea, Italy). Isolated hepatocytes from these eels were selected as the experimental model given the relevant role of these cells in metabolic functions potentially altered during silvering. Expression profiles of 7 candidate reference transcripts were analyzed seeking the most viable and robust strategies for accurate qPCR data normalization during silvering. Stability analysis and further statistical validation identified transcripts encoding the ribosomal proteins L13 and ARP as the appropriate reference genes in studies on A. anguilla through silvering. The identified reference transcripts were further used to evaluate expression profiles of target transcripts encoding the thyroid hormone receptor β (THRβ) and vitellogenin (vtg), known to be involved in silvering processes. To the best of our knowledge, this is the first study comparing THRβ expression in European eels across silvering.
Experiments and Model for Serration Statistics in Low-Entropy, Medium-Entropy and High-Entropy Alloys
Authors: Carroll Robert , Lee Chi , Tsai Che-Wei , Yeh Jien-Wei , Antonaglia James , Brinkman Braden A. W. , LeBlanc Michael , Xie Xie , Chen Shuying , Liaw Peter K. , Dahmen Karin A. 
Published: November 2015

AbstractHigh-entropy alloys (HEAs) are new alloys that contain five or more elements in roughly-equal proportion. We present new experiments and theory on the deformation behavior of HEAs under slow stretching (straining) and observe differences, compared to conventional alloys with fewer elements. For a specific range of temperatures and strain-rates, HEAs deform in a jerky way, with sudden slips that make it difficult to precisely control the deformation. An analytic model explains these slips as avalanches of slipping weak spots and predicts the observed slip statistics, stress-strain curves and their dependence on temperature, strain-rate and material composition. The ratio of the weak spots’ healing rate to the strain-rate is the main tuning parameter, reminiscent of the Portevin-LeChatellier effect and time-temperature superposition in polymers. Our model predictions agree with the experimental results. The proposed widely-applicable deformation mechanism is useful for deformation control and alloy design.
Tunable zero-field ferromagnetic resonance frequency from S to X band in oblique deposited CoFeB thin films
Authors: Li Chengyi , Chai Guozhi , Yang Chengcheng , Wang Wenfeng , Xue Desheng 
Published: November 2015

AbstractTunable zero-field ferromagnetic resonance frequency in wide range is very useful for the application of microwave devices. We performed an investigation of the static and high frequency magnetic properties for oblique sputtered CoFeB thin films. The static magnetic results revealed that oblique sputtered CoFeB thin films possess well defined in-plane uniaxial magnetic anisotropy, which increases monotonically from 50.1 to 608.8 Oe with the increasing of deposition angle from 10° to 70°. Continuous modification of the resonance frequency of CoFeB thin films in a range of 2.83–9.71 GHz (covers three microwave bands including S, C and X bands) has been achieved. This behavior can be explained as the result of the microstructure due to the self-shadowing effect mainly. These CoFeB thin films with tunable magnetic properties may be good candidates for usage in microwave devices.