bluuebunny/crossref_metadata_2025_split huggingface dataset:
Net carbon emissions from African biosphere dominate pan-tropical atmospheric CO2 signal
Authors: Palmer Paul I. , Feng Liang , Baker David , Chevallier Frédéric , Bösch Hartmut , Somkuti Peter 
Published: August 2019

AbstractTropical ecosystems are large carbon stores that are vulnerable to climate change. The sparseness of ground-based measurements has precluded verification of these ecosystems being a net annual source (+ve) or sink (−ve) of atmospheric carbon. We show that two independent satellite data sets of atmospheric carbon dioxide (CO2), interpreted using independent models, are consistent with the land tropics being a net annual carbon emission of $$({\mathrm{median}}_{{\mathrm{minimum}}}^{{\mathrm{maximum}}})$$

(

median

minimum

maximum

)

$$1.03_{ - 0.20}^{ + 1.73}$$
1.0

3

-
0.20

+
1.73

and $$1.60_{ + 1.39}^{ + 2.11}$$
1.6

0

+
1.39

+
2.11

petagrams (PgC) in 2015 and 2016, respectively. These pan-tropical estimates reflect unexpectedly large net emissions from tropical Africa of $$1.48_{ + 0.80}^{ + 1.95}$$
1.4

8

+
0.80

+
1.95

PgC in 2015 and $$1.65_{ + 1.14}^{ + 2.42}$$
1.6

5

+
1.14

+
2.42

PgC in 2016. The largest carbon uptake is over the Congo basin, and the two loci of carbon emissions are over western Ethiopia and western tropical Africa, where there are large soil organic carbon stores and where there has been substantial land use change. These signals are present in the space-borne CO2 record from 2009 onwards.
RIG-I-like receptors direct inflammatory macrophage polarization against West Nile virus infection
Authors: Stone Amy E. L. , Green Richard , Wilkins Courtney , Hemann Emily A. , Gale Michael 
Published: August 2019

AbstractRIG-I-Like Receptors (RLRs) RIG-I, MDA5, and LGP2, are vital pathogen recognition receptors in the defense against RNA viruses. West Nile Virus (WNV) infections continue to grow in the US. Here, we use a systems biology approach to define the contributions of each RLR in the innate immune response to WNV. Genome-wide RNAseq and bioinformatics analyses of macrophages from mice lacking either RLR reveal that the RLRs drive distinct immune gene activation and response polarization to mediate an M1/inflammatory signature while suppressing the M2/wound healing phenotype. While LGP2 functions to modulate inflammatory signaling, RIG-I and MDA5 together are essential for M1 macrophage polarization in vivo and the control of WNV infection through potential downstream control of ATF4 and SMAD4 to regulate target gene expression for cell polarization. These analyses reveal the RLR-driven signature of macrophage polarization, innate immune protection, and immune programming against WNV infection.
Smu1 and RED are required for activation of spliceosomal B complexes assembled on short introns
Authors: Keiper Sandra , Papasaikas Panagiotis , Will Cindy L. , Valcárcel Juan , Girard Cyrille , Lührmann Reinhard 
Published: August 2019

AbstractHuman pre-catalytic spliceosomes contain several proteins that associate transiently just prior to spliceosome activation and are absent in yeast, suggesting that this critical step is more complex in higher eukaryotes. We demonstrate via RNAi coupled with RNA-Seq that two of these human-specific proteins, Smu1 and RED, function both as alternative splicing regulators and as general splicing factors and are required predominantly for efficient splicing of short introns. In vitro splicing assays reveal that Smu1 and RED promote spliceosome activation, and are essential for this step when the distance between the pre-mRNA’s 5′ splice site (SS) and branch site (BS) is sufficiently short. This Smu1-RED requirement can be bypassed when the 5′ and 3′ regions of short introns are physically separated. Our observations suggest that Smu1 and RED relieve physical constraints arising from a short 5′SS-BS distance, thereby enabling spliceosomes to overcome structural challenges associated with the splicing of short introns.
Local orbital degeneracy lifting as a precursor to an orbital-selective Peierls transition
Authors: Bozin E. S. , Yin W. G. , Koch R. J. , Abeykoon M. , Hor Y. S. , Zheng H. , Lei H. C. , Petrovic C. , Mitchell J. F. , Billinge S. J. L. 
Published: August 2019

AbstractFundamental electronic principles underlying all transition metal compounds are the symmetry and filling of the d-electron orbitals and the influence of this filling on structural configurations and responses. Here we use a sensitive local structural technique, x-ray atomic pair distribution function analysis, to reveal the presence of fluctuating local-structural distortions at high temperature in one such compound, CuIr2S4. We show that this hitherto overlooked fluctuating symmetry-lowering is electronic in origin and will modify the energy-level spectrum and electronic and magnetic properties. The explanation is a local, fluctuating, orbital-degeneracy-lifted state. The natural extension of our result would be that this phenomenon is likely to be widespread amongst diverse classes of partially filled nominally degenerate d-electron systems, with potentially broad implications for our understanding of their properties.
GWAS for urinary sodium and potassium excretion highlights pathways shared with cardiovascular traits
Authors: Pazoki Raha , Evangelou Evangelos , Mosen-Ansorena David , Pinto Rui Climaco , Karaman Ibrahim , Blakeley Paul , Gill Dipender , Zuber Verena , Elliott Paul , Tzoulaki Ioanna , Dehghan Abbas 
Published: August 2019

AbstractUrinary sodium and potassium excretion are associated with blood pressure (BP) and cardiovascular disease (CVD). The exact biological link between these traits is yet to be elucidated. Here, we identify 50 loci for sodium and 13 for potassium excretion in a large-scale genome-wide association study (GWAS) on urinary sodium and potassium excretion using data from 446,237 individuals of European descent from the UK Biobank study. We extensively interrogate the results using multiple analyses such as Mendelian randomization, functional assessment, co localization, genetic risk score, and pathway analyses. We identify a shared genetic component between urinary sodium and potassium expression and cardiovascular traits. Ingenuity pathway analysis shows that urinary sodium and potassium excretion loci are over-represented in behavioural response to stimuli. Our study highlights pathways that are shared between urinary sodium and potassium excretion and cardiovascular traits.
Mutations in topoisomerase IIβ result in a B cell immunodeficiency
Authors: Broderick Lori , Yost Shawn , Li Dong , McGeough Matthew D. , Booshehri Laela M. , Guaderrama Marisela , Brydges Susannah D. , Kucharova Karolina , Patel Niraj C. , Harr Margaret , Hakonarson Hakon , Zackai Elaine , Cowell Ian G. , Austin Caroline A. , Hügle Boris , Gebauer Corinna , Zhang Jianguo , Xu Xun , Wang Jian , Croker Ben A. , Frazer Kelly A. , Putnam Christopher D. , Hoffman Hal M. 
Published: August 2019

AbstractB cell development is a highly regulated process involving multiple differentiation steps, yet many details regarding this pathway remain unknown. Sequencing of patients with B cell-restricted immunodeficiency reveals autosomal dominant mutations in TOP2B. TOP2B encodes a type II topoisomerase, an essential gene required to alleviate topological stress during DNA replication and gene transcription, with no previously known role in B cell development. We use Saccharomyces cerevisiae, and knockin and knockout murine models, to demonstrate that patient mutations in TOP2B have a dominant negative effect on enzyme function, resulting in defective proliferation, survival of B-2 cells, causing a block in B cell development, and impair humoral function in response to immunization.
Population dynamics of an Escherichia coli ST131 lineage during recurrent urinary tract infection
Authors: Forde Brian M. , Roberts Leah W. , Phan Minh-Duy , Peters Kate M. , Fleming Brittany A. , Russell Colin W. , Lenherr Sara M. , Myers Jeremy B. , Barker Adam P. , Fisher Mark A. , Chong Teik-Min , Yin Wai-Fong , Chan Kok-Gan , Schembri Mark A. , Mulvey Matthew A. , Beatson Scott A. 
Published: August 2019

AbstractRecurrent urinary tract infections (rUTIs) are extremely common, with ~ 25% of all women experiencing a recurrence within 1 year of their original infection. Escherichia coli ST131 is a globally dominant multidrug resistant clone associated with high rates of rUTI. Here, we show the dynamics of an ST131 population over a 5-year period from one elderly woman with rUTI since the 1970s. Using whole genome sequencing, we identify an indigenous clonal lineage (P1A) linked to rUTI and persistence in the fecal flora, providing compelling evidence of an intestinal reservoir of rUTI. We also show that the P1A lineage possesses substantial plasmid diversity, resulting in the coexistence of antibiotic resistant and sensitive intestinal isolates despite frequent treatment. Our longitudinal study provides a unique comprehensive genomic analysis of a clonal lineage within a single individual and suggests a population-wide resistance mechanism enabling rapid adaptation to fluctuating antibiotic exposure.
Cellular internalization of bystander nanomaterial induced by TAT-nanoparticles and regulated by extracellular cysteine
Authors: Wei Yushuang , Tang Tang , Pang Hong-Bo 
Published: August 2019

AbstractEntry into cells is necessary for many nanomaterial applications, and a common solution is to functionalize nanoparticles (NPs) with cell-penetrating ligands. Despite intensive studies on these functionalized NPs, little is known about their effect on cellular activities to engulf other cargo from the nearby environment. Here, we use NPs functionalized with TAT (transactivator of transcription) peptide (T-NPs) as an example to investigate their impact on cellular uptake of bystander cargo. We find that T-NP internalization enables cellular uptake of bystander NPs, but not common fluid markers, through a receptor-dependent macropinocytosis pathway. Moreover, the activity of this bystander uptake is stimulated by cysteine presence in the surrounding solution. The cargo selectivity and cysteine regulation are further demonstrated ex vivo and in vivo. These findings reveal another mechanism for NP entry into cells and open up an avenue of studying the interplay among endocytosis, amino acids, and nanomaterial delivery.
PlatformTM, a standards-based data custodianship platform for translational medicine research
Authors: Emam Ibrahim , Elyasigomari Vahid , Matthews Alex , Pavlidis Stelios , Rocca-Serra Philippe , Guitton Florian , Verbeeck Denny , Grainger Lucinda , Borgogni Erica , Del Giudice Giuseppe , Saqi Mansoor , Houston Paul , Guo Yike 
Published: August 2019

AbstractBiomedical informatics has traditionally adopted a linear view of the informatics process (collect, store and analyse) in translational medicine (TM) studies; focusing primarily on the challenges in data integration and analysis. However, a data management challenge presents itself with the new lifecycle view of data emphasized by the recent calls for data re-use, long term data preservation, and data sharing. There is currently a lack of dedicated infrastructure focused on the ‘manageability’ of the data lifecycle in TM research between data collection and analysis. Current community efforts towards establishing a culture for open science prompt the creation of a data custodianship environment for management of TM data assets to support data reuse and reproducibility of research results. Here we present the development of a lifecycle-based methodology to create a metadata management framework based on community driven standards for standardisation, consolidation and integration of TM research data. Based on this framework, we also present the development of a new platform (PlatformTM) focused on managing the lifecycle for translational research data assets.
Glioblastoma multiforme restructures the topological connectivity of cerebrovascular networks
Authors: Hahn Artur , Bode Julia , Krüwel Thomas , Solecki Gergely , Heiland Sabine , Bendszus Martin , Tews Björn , Winkler Frank , Breckwoldt Michael O. , Kurz Felix T. 
Published: August 2019

AbstractGlioblastoma multiforme alters healthy tissue vasculature by inducing angiogenesis and vascular remodeling. To fully comprehend the structural and functional properties of the resulting vascular network, it needs to be studied collectively by considering both geometric and topological properties. Utilizing Single Plane Illumination Microscopy (SPIM), the detailed capillary structure in entire healthy and tumor-bearing mouse brains could be resolved in three dimensions. At the scale of the smallest capillaries, the entire vascular systems of bulk U87- and GL261-glioblastoma xenografts, their respective cores, and healthy brain hemispheres were modeled as complex networks and quantified with fundamental topological measures. All individual vessel segments were further quantified geometrically and modular clusters were uncovered and characterized as meta-networks, facilitating an analysis of large-scale connectivity. An inclusive comparison of large tissue sections revealed that geometric properties of individual vessels were altered in glioblastoma in a relatively subtle way, with high intra- and inter-tumor heterogeneity, compared to the impact on the vessel connectivity. A network topology analysis revealed a clear decomposition of large modular structures and hierarchical network organization, while preserving most fundamental topological classifications, in both tumor models with distinct growth patterns. These results augment our understanding of cerebrovascular networks and offer a topological assessment of glioma-induced vascular remodeling. The findings may help understand the emergence of hypoxia and necrosis, and prove valuable for therapeutic interventions such as radiation or antiangiogenic therapy.
High-throughput metagenome analysis of the Sarcoptes scabiei internal microbiota and in-situ identification of intestinal Streptomyces sp.
Authors: Swe Pearl M. , Zakrzewski Martha , Waddell Rebecca , Sriprakash Kadaba S. , Fischer Katja 
Published: August 2019

AbstractMultiple parasitic arthropods of medical importance depend on symbiotic bacteria. While the link between scabies and secondary bacterial infections causing post infective complications of Group A streptococcal and staphylococcal pyoderma is increasingly recognized, very little is known about the microbiota of Sarcoptes scabiei. Here we analyze adult female mite and egg metagenome datasets. The majority of adult mite bacterial reads matched with Enterobacteriaceae (phylum Proteobacteria), followed by Corynebacteriaceae (phylum Actinobacteria). Klebsiella was the most dominant genus (78%) and Corynebacterium constituted 9% of the assigned sequences. Scabies mite eggs had a more diverse microbial composition with sequences from Proteobacteria being the most dominant (75%), while Actinobacteria, Bacteroidetes and Firmicutes accounted for 23% of the egg microbiome sequences. DNA sequences of a potential endosymbiont, namely Streptomyces, were identified in the metagenome sequence data of both life stages. The presence of Streptomyces was confirmed by conventional PCR. Digital droplet PCR indicated higher Streptomyces numbers in adult mites compared to eggs. Streptomyces were localized histologically in the scabies mite gut and faecal pellets by Fluorescent In Situ Hybridization (FISH). Streptomyces may have essential symbiotic roles in the scabies parasite intestinal system requiring further investigation.
Synthesis of centimeter-size free-standing perovskite nanosheets from single-crystal lead bromide for optoelectronic devices
Authors: Zheng Jian-Yao , Manning Hugh G. , Zhang Yanhui , Wang Jing Jing , Purcell-Milton Finn , Pokle Anuj , Porter Stephen-Barry , Zhong Chuan , Li Jing , O’Reilly Meehan Rudi , Enright Ryan , Gun’ko Yurii K. , Nicolosi Valeria , Boland John J. , Sanvito Stefano , Donegan John F. 
Published: August 2019

AbstractConsiderable attention has been drawn to the lead halide perovskites (LHPs) because of their outstanding optoelectronic characteristics. LHP nanosheets (NSs) grown from single crystalline lead halide possess advantages in device applications as they provide the possibility for control over morphology, composition, and crystallinity. Here, free-standing lead bromide (PbBr2) single-crystalline NSs with sizes up to one centimeter are synthesized from solution. These NSs can be converted to LHP while maintaining the NS morphology. We demonstrate that these perovskite NSs can be processed directly for fabrication of photodetector and laser arrays on a large scale. This strategy will allow high-yield synthesis of large-size perovskite NSs for functional devices in an integrated photonics platform.
Metataxonomic analyses reveal differences in aquifer bacterial community as a function of creosote contamination and its potential for contaminant remediation
Authors: Júlio Aline Daniela Lopes , de Cássia Mourão Silva Ubiana , Medeiros Julliane Dutra , Morais Daniel Kumazawa , dos Santos Vera Lúcia 
Published: August 2019

AbstractMetataxonomic approach was used to describe the bacterial community from a creosote-contaminated aquifer and to access the potential for in situ bioremediation of the polycyclic aromatic hydrocarbons (PAHs) by biostimulation. In general, the wells with higher PAH contamination had lower richness and diversity than others, using the Shannon and Simpson indices. By the principal coordinate analysis (PCoA) it was possible to observe the clustering of the bacterial community of most wells in response of the presence of PAH contamination. The significance analysis using edgeR package of the R program showed variation in the abundance of some Operational Taxonomic Units (OTUs) of contaminated wells compared to uncontaminated ones. Taxons enriched in the contaminated wells were correlated positively (p < 0.05) with the hydrocarbons, according to redundancy analysis (RDA). All these enriched taxa have been characterized as PAH degrading agents, such as the genus Comamonas, Geobacter, Hydrocarboniphaga, Anaerolinea and Desulfomonile. Additionally, it was possible to predict, with the PICRUSt program, a greater proportion of pathways and genes related to the degradation of PAHs in the wells with higher contamination levels. We conclude that the contaminants promoted the enrichment of several groups of degrading bacteria in the area, which strengthens the feasibility of applying biostimulation as an aquifer remediation strategy.
The role of surface air temperature over the east Asia on the early and late Indian Summer Monsoon Onset over Kerala
Authors: Choudhury Devanil , Nath Debashis , Wen Chen 
Published: August 2019

AbstractThis study investigates the physical mechanism for late Indian Summer Monsoon onset over Kerala (MOK). 14 early and 9 late onset years are selected based on the criteria when the onset is 5 days or more prior and after normal onset date (i.e 1st June according to India Meteorological Department) respectively. Then, we perform composite analyses of mean May monthly and daily evolution during early and late onset years to examine the differences in monsoon circulation features prior to the MOK. We find that advection of Surface Air Temperature (SAT) from the northern to the southern China and the eastern Tibetan Plateau (TP) plays an important role to modulate the MOK processes. In the late onset years, more low-level jet (LLJ) from the Bay of Bengal (BOB) divert towards the east Asia before the onset, which is due to an extension of the low sea level pressure and high SAT over the east Asia (eastern TP, east-central China). This strengthens the low-level convergence and upper level divergence over the eastern TP and southern China. As a result, a significant amount of moisture from the BOB is transported towards the eastern TP and southern China. Thereby, a comparatively weaker LLJ and deficit low-level moisture supply over the eastern BOB maintain the key roles in modulating the MOK processes.
A chromosome-anchored eggplant genome sequence reveals key events in Solanaceae evolution
Authors: Barchi Lorenzo , Pietrella Marco , Venturini Luca , Minio Andrea , Toppino Laura , Acquadro Alberto , Andolfo Giuseppe , Aprea Giuseppe , Avanzato Carla , Bassolino Laura , Comino Cinzia , Molin Alessandra Dal , Ferrarini Alberto , Maor Louise Chappell , Portis Ezio , Reyes-Chin-Wo Sebastian , Rinaldi Riccardo , Sala Tea , Scaglione Davide , Sonawane Prashant , Tononi Paola , Almekias-Siegl Efrat , Zago Elisa , Ercolano Maria Raffaella , Aharoni Asaph , Delledonne Massimo , Giuliano Giovanni , Lanteri Sergio , Rotino Giuseppe Leonardo 
Published: August 2019

AbstractWith approximately 450 species, spiny Solanum species constitute the largest monophyletic group in the Solanaceae family, but a high-quality genome assembly from this group is presently missing. We obtained a chromosome-anchored genome assembly of eggplant (Solanum melongena), containing 34,916 genes, confirming that the diploid gene number in the Solanaceae is around 35,000. Comparative genomic studies with tomato (S. lycopersicum), potato (S. tuberosum) and pepper (Capsicum annuum) highlighted the rapid evolution of miRNA:mRNA regulatory pairs and R-type defense genes in the Solanaceae, and provided a genomic basis for the lack of steroidal glycoalkaloid compounds in the Capsicum genus. Using parsimony methods, we reconstructed the putative chromosomal complements of the key founders of the main Solanaceae clades and the rearrangements that led to the karyotypes of extant species and their ancestors. From 10% to 15% of the genes present in the four genomes were syntenic paralogs (ohnologs) generated by the pre-γ, γ and T paleopolyploidy events, and were enriched in transcription factors. Our data suggest that the basic gene network controlling fruit ripening is conserved in different Solanaceae clades, and that climacteric fruit ripening involves a differential regulation of relatively few components of this network, including CNR and ethylene biosynthetic genes.
Cost-effective sol-gel synthesis of porous CuO nanoparticle aggregates with tunable specific surface area
Authors: Dörner Lars , Cancellieri Claudia , Rheingans Bastian , Walter Marc , Kägi Ralf , Schmutz Patrik , Kovalenko Maksym V. , Jeurgens Lars P. H. 
Published: August 2019

AbstractCuO nanoparticles (NPs) are applied in various key technologies, such as catalysis, energy conversion, printable electronics and nanojoining. In this study, an economic, green and easy-scalable sol-gel synthesis method was adopted to produce submicron-sized nanoporous CuO NP aggregates with a specific surface area > 18 m²/g. To this end, a copper-carbonate containing precursor was precipitated from a mixed solution of copper acetate and ammonia carbonate and subsequently calcinated at T ≥ 250 °C. The thus obtained CuO nanopowder is composed of weakly-bounded agglomerates, which are constituted of aggregated CuO NPs with a tunable size in the range of 100–140 nm. The CuO aggregates, in turn, are composed of equi-axed primary crystallites with a tunable crystallite size in the range of 20–40 nm. The size and shape of the primary CuO crystallites, as well as the nanoporosity of their fused CuO aggregates, can be tuned by controlled variation of the degree of supersaturation of the solution via the pH and the carbonate concentration. The synthesized submicron-sized CuO aggregates can be more easily and safely processed in the form of a solution, dispersion or paste than individual NPs, while still offering the same enhanced reactivity due to their nanoporous architecture.