bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fundamentals and applications of photocatalytic CO2 methanation
Authors: Ulmer Ulrich , Dingle Thomas , Duchesne Paul N. , Morris Robert H. , Tavasoli Alexandra , Wood Thomas , Ozin Geoffrey A. 
Published: July 2019

AbstractThe extraction and combustion of fossil natural gas, consisting primarily of methane, generates vast amounts of greenhouse gases that contribute to climate change. However, as a result of recent research efforts, “solar methane” can now be produced through the photocatalytic conversion of carbon dioxide and water to methane and oxygen. This approach could play an integral role in realizing a sustainable energy economy by closing the carbon cycle and enabling the efficient storage and transportation of intermittent solar energy within the chemical bonds of methane molecules. In this article, we explore the latest research and development activities involving the light-assisted conversion of carbon dioxide to methane.
Towards integrated tunable all-silicon free-electron light sources
Authors: Roques-Carmes Charles , Kooi Steven E. , Yang Yi , Massuda Aviram , Keathley Phillip D. , Zaidi Aun , Yang Yujia , Joannopoulos John D. , Berggren Karl K. , Kaminer Ido , Soljačić Marin 
Published: July 2019

AbstractExtracting light from silicon is a longstanding challenge in modern engineering and physics. While silicon has underpinned the past 70 years of electronics advancement, a facile tunable and efficient silicon-based light source remains elusive. Here, we experimentally demonstrate the generation of tunable radiation from a one-dimensional, all-silicon nanograting. Light is generated by the spontaneous emission from the interaction of these nanogratings with low-energy free electrons (2–20 keV) and is recorded in the wavelength range of 800–1600 nm, which includes the silicon transparency window. Tunable free-electron-based light generation from nanoscale silicon gratings with efficiencies approaching those from metallic gratings is demonstrated. We theoretically investigate the feasibility of a scalable, compact, all-silicon tunable light source comprised of a silicon Field Emitter Array integrated with a silicon nanograting that emits at telecommunication wavelengths. Our results reveal the prospects of a CMOS-compatible electrically-pumped silicon light source for possible applications in the mid-infrared and telecommunication wavelengths.
Strong and selective isotope effect in the vacuum ultraviolet photodissociation branching ratios of carbon monoxide
Authors: Jiang Pan , Chi Xiaoping , Zhu Qihe , Cheng Min , Gao Hong 
Published: July 2019

AbstractRare isotope (13C, 17O and 18O) substitutions can substantially change absorption line positions, oscillator strengths and photodissociation rates of carbon monoxide (CO) in the vacuum ultraviolet (VUV) region, which has been well accounted for in recent photochemical models for understanding the large isotopic fractionation effects that are apparent in carbon and oxygen in the solar system and molecular clouds. Here, we demonstrate a strong isotope effect associated with the VUV photodissociation of CO by measuring the branching ratios of 12C16O and 13C16O in the Rydberg 4p(2), 5p(0) and 5s(0) complex region. The measurements show that the quantum yields of electronically excited C atoms in the photodissociation of 13C16O are dramatically different from those of 12C16O, revealing strong isotope effect. This isotope effect strongly depends on specific quantum states of CO being excited, which implies that such effect must be considered in the photochemical models on a state by state basis.
Reconstitution of recombinant human CCR4-NOT reveals molecular insights into regulated deadenylation
Authors: Raisch Tobias , Chang Chung-Te , Levdansky Yevgen , Muthukumar Sowndarya , Raunser Stefan , Valkov Eugene 
Published: July 2019

AbstractCCR4-NOT is a conserved multiprotein complex which regulates eukaryotic gene expression principally via shortening of poly(A) tails of messenger RNA or deadenylation. Here, we reconstitute a complete, recombinant human CCR4-NOT complex. Our reconstitution strategy permits strict compositional control to test mechanistic hypotheses with purified component variants. CCR4-NOT is more active and selective for poly(A) than the isolated exonucleases, CCR4a and CAF1, which have distinct deadenylation profiles in vitro. The exonucleases require at least two out of three conserved non-enzymatic modules (CAF40, NOT10:NOT11 or NOT) for full activity in CCR4-NOT. CAF40 and the NOT10:NOT11 module both bind RNA directly and stimulate deadenylation in a partially redundant manner. Linear motifs from different RNA-binding factors that recruit CCR4-NOT to specific mRNAs via protein-protein interactions with CAF40 can inhibit bulk deadenylation. We reveal an additional layer of regulatory complexity to the human deadenylation machinery, which may prime it either for general or target-specific degradation.
Whole-genome landscape of mucosal melanoma reveals diverse drivers and therapeutic targets
Authors: Newell Felicity , Kong Yan , Wilmott James S. , Johansson Peter A. , Ferguson Peter M. , Cui Chuanliang , Li Zhongwu , Kazakoff Stephen H. , Burke Hazel , Dodds Tristan J. , Patch Ann-Marie , Nones Katia , Tembe Varsha , Shang Ping , van der Weyden Louise , Wong Kim , Holmes Oliver , Lo Serigne , Leonard Conrad , Wood Scott , Xu Qinying , Rawson Robert V. , Mukhopadhyay Pamela , Dummer Reinhard , Levesque Mitchell P. , Jönsson Göran , Wang Xuan , Yeh Iwei , Wu Hong , Joseph Nancy , Bastian Boris C. , Long Georgina V. , Spillane Andrew J. , Shannon Kerwin F. , Thompson John F. , Saw Robyn P. M. , Adams David J. , Si Lu , Pearson John V. , Hayward Nicholas K. , Waddell Nicola , Mann Graham J. , Guo Jun , Scolyer Richard A. 
Published: July 2019

AbstractKnowledge of key drivers and therapeutic targets in mucosal melanoma is limited due to the paucity of comprehensive mutation data on this rare tumor type. To better understand the genomic landscape of mucosal melanoma, here we describe whole genome sequencing analysis of 67 tumors and validation of driver gene mutations by exome sequencing of 45 tumors. Tumors have a low point mutation burden and high numbers of structural variants, including recurrent structural rearrangements targeting TERT, CDK4 and MDM2. Significantly mutated genes are NRAS, BRAF, NF1, KIT, SF3B1, TP53, SPRED1, ATRX, HLA-A and CHD8. SF3B1 mutations occur more commonly in female genital and anorectal melanomas and CTNNB1 mutations implicate a role for WNT signaling defects in the genesis of some mucosal melanomas. TERT aberrations and ATRX mutations are associated with alterations in telomere length. Mutation profiles of the majority of mucosal melanomas suggest potential susceptibility to CDK4/6 and/or MEK inhibitors.
Identifying surface reaction intermediates with photoemission tomography
Authors: Yang Xiaosheng , Egger Larissa , Hurdax Philipp , Kaser Hendrik , Lüftner Daniel , Bocquet François C. , Koller Georg , Gottwald Alexander , Tegeder Petra , Richter Mathias , Ramsey Michael G. , Puschnig Peter , Soubatch Serguei , Tautz F. Stefan 
Published: July 2019

AbstractThe determination of reaction pathways and the identification of reaction intermediates are key issues in chemistry. Surface reactions are particularly challenging, since many methods of analytical chemistry are inapplicable at surfaces. Recently, atomic force microscopy has been employed to identify surface reaction intermediates. While providing an excellent insight into the molecular backbone structure, atomic force microscopy is less conclusive about the molecular periphery, where adsorbates tend to react with the substrate. Here we show that photoemission tomography is extremely sensitive to the character of the frontier orbitals. Specifically, hydrogen abstraction at the molecular periphery is easily detected, and the precise nature of the reaction intermediates can be determined. This is illustrated with the thermally induced reaction of dibromo-bianthracene to graphene which is shown to proceed via a fully hydrogenated bisanthene intermediate. We anticipate that photoemission tomography will become a powerful companion to other techniques in the study of surface reaction pathways.
Activation of neuronal genes via LINE-1 elements upon global DNA demethylation in human neural progenitors
Authors: Jönsson Marie E , Ludvik Brattås Per , Gustafsson Charlotte , Petri Rebecca , Yudovich David , Pircs Karolina , Verschuere Shana , Madsen Sofia , Hansson Jenny , Larsson Jonas , Månsson Robert , Meissner Alexander , Jakobsson Johan 
Published: July 2019

AbstractDNA methylation contributes to the maintenance of genomic integrity in somatic cells, in part through the silencing of transposable elements. In this study, we use CRISPR-Cas9 technology to delete DNMT1, the DNA methyltransferase key for DNA methylation maintenance, in human neural progenitor cells (hNPCs). We observe that inactivation of DNMT1 in hNPCs results in viable, proliferating cells despite a global loss of DNA CpG-methylation. DNA demethylation leads to specific transcriptional activation and chromatin remodeling of evolutionarily young, hominoid-specific LINE-1 elements (L1s), while older L1s and other classes of transposable elements remain silent. The activated L1s act as alternative promoters for many protein-coding genes involved in neuronal functions, revealing a hominoid-specific L1-based transcriptional network controlled by DNA methylation that influences neuronal protein-coding genes. Our results provide mechanistic insight into the role of DNA methylation in silencing transposable elements in somatic human cells, as well as further implicating L1s in human brain development and disease.
Signal integration and information transfer in an allosterically regulated network
Authors: Shockley Erin M. , Rouzer Carol A. , Marnett Lawrence J. , Deeds Eric J. , Lopez Carlos F. 
Published: July 2019

AbstractA biological reaction network may serve multiple purposes, processing more than one input and impacting downstream processes via more than one output. These networks operate in a dynamic cellular environment in which the levels of network components may change within cells and across cells. Recent evidence suggests that protein concentration variability could explain cell fate decisions. However, systems with multiple inputs, multiple outputs, and changing input concentrations have not been studied in detail due to their complexity. Here, we take a systems biochemistry approach, combining physiochemical modeling and information theory, to investigate how cyclooxygenase-2 (COX-2) processes simultaneous input signals within a complex interaction network. We find that changes in input levels affect the amount of information transmitted by the network, as does the correlation between those inputs. This, and the allosteric regulation of COX-2 by its substrates, allows it to act as a signal integrator that is most sensitive to changes in relative input levels.
Simulation of heterosis in a genome-scale metabolic network provides mechanistic explanations for increased biomass production rates in hybrid plants
Authors: Vacher Michael , Small Ian 
Published: July 2019

AbstractHeterosis, or hybrid vigour, is said to occur when F1 individuals exhibit increased performance for a number of traits compared to their parental lines. Improved traits can include increased size, better yield, faster development and a higher tolerance to pathogens or adverse conditions. The molecular basis for the phenomenon remains disputed, despite many decades of theorising and experimentation. In this study, we add a genetics layer to a constraint-based model of plant (Arabidopsis) primary metabolism and show that we can realistically reproduce and quantify heterosis in a highly complex trait (the rate of biomass production). The results demonstrate that additive effects coupled to the complex patterns of epistasis generated by a large metabolic network are sufficient to explain most or all the heterosis seen in typical F1 hybrids. Such models provide a simple approach to exploring and understanding heterosis and should assist in designing breeding strategies to exploit this phenomenon in the future.
Transcriptome analysis and codominant markers development in caper, a drought tolerant orphan crop with medicinal value
Authors: Mercati Francesco , Fontana Ignazio , Gristina Alessandro Silvestre , Martorana Adriana , El Nagar Mahran , De Michele Roberto , Fici Silvio , Carimi Francesco 
Published: July 2019

AbstractCaper (Capparis spinosa L.) is a xerophytic shrub cultivated for its flower buds and fruits, used as food and for their medicinal properties. Breeding programs and even proper taxonomic classification of the genus Capparis has been hampered so far by the lack of reliable genetic information and molecular markers. Here, we present the first genomic resource for C. spinosa, generated by transcriptomic approach and de novo assembly. The sequencing effort produced nearly 80 million clean reads assembled into 124,723 unitranscripts. Careful annotation and comparison with public databases revealed homologs to genes with a key role in important metabolic pathways linked to abiotic stress tolerance and bio-compounds production, such purine, thiamine and phenylpropanoid biosynthesis, α-linolenic acid and lipid metabolism. Additionally, a panel of genes involved in stomatal development/distribution and encoding for Stress Associated Proteins (SAPs) was also identified. We also used the transcriptomic data to uncover novel molecular markers for caper. Out of 50 SSRs tested, 14 proved polymorphic and represent the first set of SSR markers for the genus Capparis. This transcriptome will be an important contribution to future studies and breeding programs for this orphan crop, aiding to the development of improved varieties to sustain agriculture in arid conditions.
Host specificity drives genetic structure in a freshwater mussel
Authors: Wacker Sebastian , Larsen Bjørn Mejdell , Karlsson Sten , Hindar Kjetil 
Published: July 2019

AbstractParasites often depend on their hosts for long distance transport, and genetic population structure can be strongly affected by host specificity and dispersal. Freshwater pearl mussel (Margaritifera margaritifera) populations have previously been found to naturally infest either primarily Atlantic salmon (‘salmon-mussel’) or exclusively brown trout (‘trout-mussel’) across a wide geographic range. Here, we experimentally test whether this intraspecific variation in natural infestation can be explained by host specificity in freshwater pearl mussel. Our experiments show that when both host species were exposed to larvae from salmon- and trout-mussel respectively, salmon-mussel larvae almost never infested brown trout and vice versa. This suggests that host specificity can explain variation in natural infestation among the studied freshwater pearl mussel populations. Host specificity provides a link to the species’ variable population genetic structure, as mussel populations limited to Atlantic salmon, the host with stronger dispersal, show higher genetic diversity and weaker differentiation than populations limited to brown trout as host.
Insufficient evidence for BMAA transfer in the pelagic and benthic food webs in the Baltic Sea
Authors: Zguna Nadezda , Karlson Agnes M. L. , Ilag Leopold L. , Garbaras Andrius , Gorokhova Elena 
Published: July 2019

AbstractThe evidence regarding BMAA occurrence in the Baltic Sea is contradictory, with benthic sources appearing to be more important than pelagic ones. The latter is counterintuitive considering that the identified sources of this compound in the food webs are pelagic primary producers, such as diatoms, dinoflagellates, and cyanobacteria. To elucidate BMAA distribution, we analyzed BMAA in the pelagic and benthic food webs in the Northern Baltic Proper. As potential sources, phytoplankton communities were used. Pelagic food chain was represented by zooplankton, mysids and zooplanktivorous fish, whereas benthic invertebrates and benthivorous fish comprised the benthic chain. The trophic structure of the system was confirmed by stable isotope analysis. Contrary to the reported ubiquitous occurrence of BMAA in the Baltic food webs, only phytoplankton, zooplankton and mysids tested positive, whereas no measurable levels of this compound occurred in the benthic invertebrates and any of the tested fish species. These findings do not support the widely assumed occurrence and transfer of BMAA to the top consumers in the Baltic food webs. More controlled experiments and field observations are needed to understand the transfer and possible transformation of BMAA in the food web under various environmental settings.
Ferromagnetic-like behavior of Bi0.9La0.1FeO3–KBr nanocomposites
Authors: Karpinsky Dmitry V. , Fesenko Olena M. , Silibin Maxim V. , Dubkov Sergei V. , Chaika Mykola , Yaremkevich Andrii , Lukowiak Anna , Gerasymchuk Yuri , Stręk Wiesław , Pakalniškis Andrius , Skaudzius Ramunas , Kareiva Aivaras , Fomichov Yevhen M. , Shvartsman Vladimir V. , Kalinin Sergei V. , Morozovsky Nicholas V. , Morozovska Anna N. 
Published: July 2019

AbstractWe studied magnetostatic response of the Bi0.9La0.1FeO3– KBr composites (BLFO-KBr) consisting of nanosized (≈100 nm) ferrite Bi0.9La0.1FeO3(BLFO) conjugated with fine grinded ionic conducting KBr. When the fraction of KBr is rather small (less than 15 wt%) the magnetic response of the composite is very weak and similar to that observed for the BLFO (pure KBr matrix without Bi1-xLaxFeO3has no magnetic response as anticipated). However, when the fraction of KBr increases above 15%, the magnetic response of the composite changes substantially and the field dependence of magnetization reveals ferromagnetic-like hysteresis loop with a remanent magnetization about 0.14 emu/g and coercive field about 1.8 Tesla (at room temperature). Nothing similar to the ferromagnetic-like hysteresis loop can be observed in Bi1-zLazFeO3ceramics with z ≤ 0.15, which magnetization quasi-linearly increases with magnetic field. Different physical mechanisms were considered to explain the unusual experimental results for BLFO-KBr nanocomposites, but only those among them, which are highly sensitive to the interaction of antiferromagnetic Bi0.9La0.1FeO3with ionic conductor KBr, can be relevant.
Role of intravenous immunoglobulin therapy in the survival rate of pediatric patients with acute myocarditis: A systematic review and meta-analysis
Authors: Yen Chun-Yu , Hung Miao-Chiu , Wong Ying-Chi , Chang Chia-Yuan , Lai Chou-Cheng , Wu Keh-Gong 
Published: July 2019

AbstractThe treatment of pediatric myocarditis is controversial, and the benefits of intravenous immunoglobulin (IVIG) are inconclusive due to limited data. We searched studies from PubMed, MEDLINE, Embase, and Cochrane Library databases since establishment until October 1st, 2018. Thirteen studies met the inclusion criteria. We included a total of 812 patients with IVIG treatment and 592 patients without IVIG treatment. The meta-analysis showed that the survival rate in the IVIG group was higher than that in the non-IVIG group (odds ratio = 2.133, 95% confidence interval (CI): 1.32–3.43, p = 0.002). There was moderate statistical heterogeneity among the included studies (I2 = 35%, p = 0.102). However, after adjustment using Duval and Tweedie’s trim and fill method, the point estimate of the overall effect size was 1.40 (95% CI 0.83, 2.35), which became insignificant. Moreover, the meta-regression revealed that age (coefficient = −0.191, 95% CI (−0.398, 0.015), p = 0.069) and gender (coefficient = 0.347, 95% CI (−7.586, 8.279), p = 0.93) were not significantly related to the survival rate. This meta-analysis showed that IVIG treatment was not associated with better survival. The use of IVIG therapy in acute myocarditis in children cannot be routinely recommended based on current evidence. Further prospective and randomized controlled studies are needed to elucidate the effects of IVIG treatment.
Systematic Review of Somatic Mutations in Splenic Marginal Zone Lymphoma
Authors: Jaramillo Oquendo Carolina , Parker Helen , Oscier David , Ennis Sarah , Gibson Jane , Strefford Jonathan C. 
Published: July 2019

AbstractThe aims of this systematic review are to refine the catalogue of somatic variants in splenic marginal zone lymphoma (SMZL) and to provide a well-annotated, manually curated database of high-confidence somatic mutations to facilitate variant interpretation for further biological studies and future clinical implementation. Two independent reviewers systematically searched PubMed and Ovid in January 2019 and included studies that sequenced SMZL cases with confirmed diagnosis. The database included fourteen studies, comprising 2817 variants in over 1000 genes from 475 cases. We confirmed the high prevalence of NOTCH2, KLF2 and TP53 mutations and analysis of targeted genes further implicated TNFAIP3, KMT2D, and TRAF3 as recurrent targets of somatic mutation based on their high incidence across studies. The major limitations we encountered were the low number of patients with whole-genome, unbiased analysis and the relative sensitivities of differing sequencing approaches. Overall, we showed that there is little concordance between whole exome sequencing studies of SMZL. We strongly support the continuing unbiased analysis of the SMZL genome for mutations in all protein-coding genes and provide a valuable database resource to facilitate this endeavour that will ultimately improve our understanding of SMZL pathobiology.
Emergence of hierarchical organization in memory for random material
Authors: Naim Michelangelo , Katkov Mikhail , Recanatesi Stefano , Tsodyks Misha 
Published: July 2019

AbstractStructured information is easier to remember and recall than random one. In real life, information exhibits multi-level hierarchical organization, such as clauses, sentences, episodes and narratives in language. Here we show that multi-level grouping emerges even when participants perform memory recall experiments with random sets of words. To quantitatively probe brain mechanisms involved in memory structuring, we consider an experimental protocol where participants perform ‘final free recall’ (FFR) of several random lists of words each of which was first presented and recalled individually. We observe a hierarchy of grouping organizations of FFR, most notably many participants sequentially recalled relatively long chunks of words from each list before recalling words from another list. Moreover, participants who exhibited strongest organization during FFR achieved highest levels of performance. Based on these results, we develop a hierarchical model of memory recall that is broadly compatible with our findings. Our study shows how highly controlled memory experiments with random and meaningless material, when combined with simple models, can be used to quantitatively probe the way meaningful information can efficiently be organized and processed in the brain.