bluuebunny/crossref_metadata_2025_split huggingface dataset:
Methane Mitigation: Methods to Reduce Emissions, on the Path to the Paris Agreement
Authors: Nisbet E. G. , Fisher R. E. , Lowry D. , France J. L. , Allen G. , Bakkaloglu S. , Broderick T. J. , Cain M. , Coleman M. , Fernandez J. , Forster G. , Griffiths P. T. , Iverach C. P. , Kelly B. F. J. , Manning M. R. , Nisbet‐Jones P. B. R. , Pyle J. A. , Townsend‐Small A. , al‐Shalaan A. , Warwick N. , Zazzeri G. 
Published: January 2020

AbstractThe atmospheric methane burden is increasing rapidly, contrary to pathways compatible with the goals of the 2015 United Nations Framework Convention on Climate Change Paris Agreement. Urgent action is required to bring methane back to a pathway more in line with the Paris goals. Emission reduction from “tractable” (easier to mitigate) anthropogenic sources such as the fossil fuel industries and landfills is being much facilitated by technical advances in the past decade, which have radically improved our ability to locate, identify, quantify, and reduce emissions. Measures to reduce emissions from “intractable” (harder to mitigate) anthropogenic sources such as agriculture and biomass burning have received less attention and are also becoming more feasible, including removal from elevated‐methane ambient air near to sources. The wider effort to use microbiological and dietary intervention to reduce emissions from cattle (and humans) is not addressed in detail in this essentially geophysical review. Though they cannot replace the need to reach “net‐zero” emissions of CO2, significant reductions in the methane burden will ease the timescales needed to reach required CO2reduction targets for any particular future temperature limit. There is no single magic bullet, but implementation of a wide array of mitigation and emission reduction strategies could substantially cut the global methane burden, at a cost that is relatively low compared to the parallel and necessary measures to reduce CO2, and thereby reduce the atmospheric methane burden back toward pathways consistent with the goals of the Paris Agreement.
Biphasic exocytosis of herpesvirus from hippocampal neurons and mechanistic implication to membrane fusion
Authors: Liu Yun-Tao , Shivakoti Sakar , Jia Fan , Tao Chang-Lu , Zhang Bin , Xu Fuqiang , Lau Pakming , Bi Guo-Qiang , Zhou Z. Hong 
Published: January 2020

AbstractExocytosis is a crucial cellular process involved in the release of neural transmitters or signaling hormones, and disposal of waste or toxic materials. The relationship between structural transition and temporal progression of this process is poorly understood, partly due to lack of adequate tools to resolve such dynamic structures at sufficient resolution in 3D. Exocytosis can be hijacked by some viruses, exemplified by the widely used model α-herpesvirus pseudorabies virus (PRV), which relies on exocytosis for trans-synaptic spread across neurons. Here, we have used cryo electron tomography (cryoET) to capture 199 events of PRV exocytosis from cultured hippocampal neurons. We established cumulative frequency analysis to estimate the relative duration of an exocytosis stage based on the frequency of observed viral particles at that stage. This analysis revealed that PRV exocytosis is biphasic, including a fast, “release phase” driven by fusion proteins and fused membranes, and a slow, “recovery phase” driven by flattening of curved membranes. The biphasic property of exocytosis discovered here appears to be conserved for membrane fusion during viral entry, and our approach of cumulative frequency analysis should have general utility for characterizing other membrane fusion events.
The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models
Authors: Salvy Pierre , Hatzimanikatis Vassily 
Published: January 2020

AbstractSystems biology has long been interested in models capturing both metabolism and expression in a cell. We propose here an implementation of the metabolism and expression model formalism (ME-models), which we call ETFL, for Expression and Thermodynamics Flux models. ETFL is a hierarchical model formulation, from metabolism to RNA synthesis, that allows simulating thermodynamics-compliant intracellular fluxes as well as enzyme and mRNA concentration levels. ETFL formulates a mixed-integer linear problem (MILP) that enables both relative and absolute metabolite, protein, and mRNA concentration integration. ETFL is compatible with standard MILP solvers and does not require a non-linear solver, unlike the previous state of the art. It also accounts for growth-dependent parameters, such as relative protein or mRNA content. We present ETFL along with its validation using results obtained from a well-characterized E. coli model. We show that ETFL is able to reproduce proteome-limited growth. We also subject it to several analyses, including the prediction of feasible mRNA and enzyme concentrations and gene essentiality.
Dorsal root ganglion macrophages contribute to both the initiation and persistence of neuropathic pain
Authors: Yu Xiaobing , Liu Hongju , Hamel Katherine A. , Morvan Maelig G. , Yu Stephen , Leff Jacqueline , Guan Zhonghui , Braz Joao M. , Basbaum Allan I. 
Published: January 2020

AbstractParalleling the activation of dorsal horn microglia after peripheral nerve injury is a significant expansion and proliferation of macrophages around injured sensory neurons in dorsal root ganglia (DRG). Here we demonstrate a critical contribution of DRG macrophages, but not those at the nerve injury site, to both the initiation and maintenance of the mechanical hypersensitivity that characterizes the neuropathic pain phenotype. In contrast to the reported sexual dimorphism in the microglial contribution to neuropathic pain, depletion of DRG macrophages reduces nerve injury-induced mechanical hypersensitivity and expansion of DRG macrophages in both male and female mice. However, fewer macrophages are induced in the female mice and deletion of colony-stimulating factor 1 from sensory neurons, which prevents nerve injury-induced microglial activation and proliferation, only reduces macrophage expansion in male mice. Finally, we demonstrate molecular cross-talk between axotomized sensory neurons and macrophages, revealing potential peripheral DRG targets for neuropathic pain management.
Nanoscopic diffusion of water on a topological insulator
Authors: Tamtögl Anton , Sacchi Marco , Avidor Nadav , Calvo-Almazán Irene , Townsend Peter S. M. , Bremholm Martin , Hofmann Philip , Ellis John , Allison William 
Published: January 2020

AbstractThe microscopic motion of water is a central question, but gaining experimental information about the interfacial dynamics of water in fields such as catalysis, biophysics and nanotribology is challenging due to its ultrafast motion, and the complex interplay of inter-molecular and molecule-surface interactions. Here we present an experimental and computational study of the nanoscale-nanosecond motion of water at the surface of a topological insulator (TI), Bi$${}_{2}$$2Te$${}_{3}$$3. Understanding the chemistry and motion of molecules on TI surfaces, while considered a key to design and manufacturing for future applications, has hitherto been hardly addressed experimentally. By combining helium spin-echo spectroscopy and density functional theory calculations, we are able to obtain a general insight into the diffusion of water on Bi$${}_{2}$$2Te$${}_{3}$$3. Instead of Brownian motion, we find an activated jump diffusion mechanism. Signatures of correlated motion suggest unusual repulsive interactions between the water molecules. From the lineshape broadening we determine the diffusion coefficient, the diffusion energy and the pre-exponential factor.
Dynamic organelle distribution initiates actin-based spindle migration in mouse oocytes
Authors: Duan Xing , Li Yizeng , Yi Kexi , Guo Fengli , Wang HaiYang , Wu Pei-Hsun , Yang Jing , Mair Devin B. , Morales Edwin Angelo , Kalab Petr , Wirtz Denis , Sun Sean X. , Li Rong 
Published: January 2020

AbstractMigration of meiosis-I (MI) spindle from the cell center to a sub-cortical location is a critical step for mouse oocytes to undergo asymmetric meiotic cell division. In this study, we investigate the mechanism by which formin-2 (FMN2) orchestrates the initial movement of MI spindle. By defining protein domains responsible for targeting FMN2, we show that spindle-periphery localized FMN2 is required for spindle migration. The spindle-peripheral FMN2 nucleates short actin bundles from vesicles derived likely from the endoplasmic reticulum (ER) and concentrated in a layer outside the spindle. This layer is in turn surrounded by mitochondria. A model based on polymerizing actin filaments pushing against mitochondria, thus generating a counter force on the spindle, demonstrated an inherent ability of this system to break symmetry and evolve directional spindle motion. The model is further supported through experiments involving spatially biasing actin nucleation via optogenetics and disruption of mitochondrial distribution and dynamics.
Environmental DNA reveals seasonal shifts and potential interactions in a marine community
Authors: Djurhuus Anni , Closek Collin J. , Kelly Ryan P. , Pitz Kathleen J. , Michisaki Reiko P. , Starks Hilary A. , Walz Kristine R. , Andruszkiewicz Elizabeth A. , Olesin Emily , Hubbard Katherine , Montes Enrique , Otis Daniel , Muller-Karger Frank E. , Chavez Francisco P. , Boehm Alexandria B. , Breitbart Mya 
Published: January 2020

AbstractEnvironmental DNA (eDNA) analysis allows the simultaneous examination of organisms across multiple trophic levels and domains of life, providing critical information about the complex biotic interactions related to ecosystem change. Here we used multilocus amplicon sequencing of eDNA to survey biodiversity from an eighteen-month (2015–2016) time-series of seawater samples from Monterey Bay, California. The resulting dataset encompasses 663 taxonomic groups (at Family or higher taxonomic rank) ranging from microorganisms to mammals. We inferred changes in the composition of communities, revealing putative interactions among taxa and identifying correlations between these communities and environmental properties over time. Community network analysis provided evidence of expected predator-prey relationships, trophic linkages, and seasonal shifts across all domains of life. We conclude that eDNA-based analyses can provide detailed information about marine ecosystem dynamics and identify sensitive biological indicators that can suggest ecosystem changes and inform conservation strategies.
Digitally virtualized atoms for acoustic metamaterials
Authors: Cho Choonlae , Wen Xinhua , Park Namkyoo , Li Jensen 
Published: January 2020

AbstractBy designing tailor-made resonance modes with structured atoms, metamaterials allow us to obtain constitutive parameters outside their limited range from natural materials. Nonetheless, tuning the constitutive parameters depends on our ability to modify the physical structure or external circuits attached to the metamaterials, posing a fundamental challenge to the range of tunability in many real-time applications. Here, we propose the concept of virtualized metamaterials on their signal response function to escape the boundary inherent in the physical structure of metamaterials. By replacing the resonating physical structure with a designer mathematical convolution kernel with a fast digital signal processing circuit, we demonstrate a decoupled control of the effective bulk modulus and mass density of acoustic metamaterials on-demand through a software-defined frequency dispersion. Providing freely software-reconfigurable amplitude, center frequency, bandwidth of frequency dispersion, our approach adds an additional dimension to constructing non-reciprocal, non-Hermitian, and topological systems with time-varying capability as potential applications.
Market integration reduces kin density in women’s ego-networks in rural Poland
Authors: Colleran Heidi 
Published: January 2020

AbstractIt is widely assumed that as populations become more market integrated the ‘inner circles’ of people’s social networks become less densely connected and family-oriented. This ‘loosening’ of kin networks may fundamentally alter the social dynamics of reproduction, facilitating demographic transitions to low fertility. Few data exist to test this hypothesis. Previous research in urbanized populations has not explicitly measured kin density in ego-networks, nor assessed how market integration influences network structure at different levels of aggregation. Here I analyze the ego-networks of ~2000 women in 22 rural Polish communities transitioning from subsistence farming to market-dependence. I compare how ego-network size, density and kin density co-vary with household and community-level market integration. Market integration is associated with less kin-dense networks, but not necessarily less dense ones, and is unrelated to network size. Declining kin density during economic transitions may be a critical mechanism for the broader cultural transmission of low fertility values.
Extreme genetic signatures of local adaptation during Lotus japonicus colonization of Japan
Authors: Shah Niraj , Wakabayashi Tomomi , Kawamura Yasuko , Skovbjerg Cathrine Kiel , Wang Ming-Zhuo , Mustamin Yusdar , Isomura Yoshiko , Gupta Vikas , Jin Haojie , Mun Terry , Sandal Niels , Azuma Fuyuki , Fukai Eigo , Seren Ümit , Kusakabe Shohei , Kikuchi Yuki , Nitanda Shogo , Kumaki Takashi , Hashiguchi Masatsugu , Tanaka Hidenori , Hayashi Atsushi , Sønderkær Mads , Nielsen Kaare Lehmann , Schneeberger Korbinian , Vilhjalmsson Bjarni , Akashi Ryo , Stougaard Jens , Sato Shusei , Schierup Mikkel Heide , Andersen Stig Uggerhøj 
Published: January 2020

AbstractColonization of new habitats is expected to require genetic adaptations to overcome environmental challenges. Here, we use full genome re-sequencing and extensive common garden experiments to investigate demographic and selective processes associated with colonization of Japan by Lotus japonicus over the past ~20,000 years. Based on patterns of genomic variation, we infer the details of the colonization process where L. japonicus gradually spread from subtropical conditions to much colder climates in northern Japan. We identify genomic regions with extreme genetic differentiation between northern and southern subpopulations and perform population structure-corrected association mapping of phenotypic traits measured in a common garden. Comparing the results of these analyses, we find that signatures of extreme subpopulation differentiation overlap strongly with phenotype association signals for overwintering and flowering time traits. Our results provide evidence that these traits were direct targets of selection during colonization and point to associated candidate genes.
Waves on Louisiana Continental Shelf Influenced by Atmospheric Fronts
Authors: Guo Biyun , Subrahmanyam M. V. , Li C. 
Published: January 2020

AbstractOcean-atmospheric dynamical processes influence the wave characteristics, and sea surface temperature (SST). The processes that affect SST in the ocean area included surface heat fluxes, wind, and precipitation. In this study, we analyzed the wave data in response to the cold front passages over Louisiana continental shelf. The data examined in this research is mainly from WAVCIS (Wave-Current-surge Information System), Coastal Ocean Estuarine Dynamics Lab at Louisiana State University and Global Precipitation Climatology Project (GPCP). With respect to the wave response to the atmospheric forcing, here we consider: (1) the connection between wave variability and atmospheric frontal passages, and (2) the influence on the SST variations during the processes. The occurrences of wind wave, precipitation, and weather processes have distinct regularities. Atmospheric cold fronts have an important influence on wave formation and associated processes over Louisiana continental shelf.
Investigating a Plasmodium falciparum erythrocyte invasion phenotype switch at the whole transcriptome level
Authors: Nyarko Prince B. , Tarr Sarah J. , Aniweh Yaw , Stewart Lindsay B. , Conway David J. , Awandare Gordon A. 
Published: January 2020

AbstractThe central role that erythrocyte invasion plays in Plasmodium falciparum survival and reproduction makes this process an attractive target for therapeutic or vaccine development. However, multiple invasion-related genes with complementary and overlapping functions afford the parasite the plasticity to vary ligands used for invasion, leading to phenotypic variation and immune evasion. Overcoming the challenge posed by redundant ligands requires a deeper understanding of conditions that select for variant phenotypes and the molecular mediators. While host factors including receptor heterogeneity and acquired immune responses may drive parasite phenotypic variation, we have previously shown that host-independent changes in invasion phenotype can be achieved by continuous culturing of the W2mef and Dd2 P. falciparum strains in moving suspension as opposed to static conditions. Here, we have used a highly biologically replicated whole transcriptome sequencing approach to identify the molecular signatures of variation associated with the phenotype switch. The data show increased expression of particular invasion-related genes in switched parasites, as well as a large number of genes encoding proteins that are either exported or form part of the export machinery. The genes with most markedly increased expression included members of the erythrocyte binding antigens (EBA), reticulocyte binding homologues (RH), surface associated interspersed proteins (SURFIN), exported protein family 1 (EPF1) and Plasmodium Helical Interspersed Sub-Telomeric (PHIST) gene families. The data indicate changes in expression of a repertoire of genes not previously associated with erythrocyte invasion phenotypes, suggesting the possibility that moving suspension culture may also select for other traits.
Complex marine bioturbation ecosystem engineering behaviors persisted in the wake of the end-Permian mass extinction
Authors: Cribb Alison T. , Bottjer David J. 
Published: January 2020

AbstractThe end-Permian mass extinction was the most severe mass extinction event of the Phanerozoic and was followed by a several million-year delay in benthic ecosystem recovery. While much work has been done to understand biotic recovery in both the body and trace fossil records of the Early Triassic, almost no focus has previously been given to analyzing patterns in ecosystem engineering complexity as a result of the extinction drivers. Bioturbation is a key ecosystem engineering behavior in marine environments, as it results in changes to resource flows and the physical environment. Thus, the trace fossil record can be used to examine the effect of the end-Permian mass extinction on bioturbating ecosystem engineers. We present a dataset compiled from previously published literature to analyze burrowing ecosystem engineering behaviors through the Permian-Triassic boundary. We report two key observations: first, that there is no loss in bioturbation ecosystem engineering behaviors after the mass extinction, and second, that these persisting behaviors include deep tier, high-impact, complex ecosystem engineering. These findings suggest that while environmental conditions may have limited deeper burrowing, complex ecosystem engineering behaviors were able to persist in the Early Triassic. Furthermore, the persistence of deep tier bioirrigated three-dimensional network burrows implies that benthic biogeochemical cycling could have been maintained at pre-extinction states in some local environments, stimulating ecosystem productivity and promoting biotic recovery in the Early Triassic.
Thermal sensitivity links to cellular cardiac decline in three spiny lobsters
Authors: Oellermann Michael , Hickey Anthony J. R. , Fitzgibbon Quinn P. , Smith Greg 
Published: January 2020

AbstractUnderstanding mechanisms of thermal sensitivity is key to predict responses of marine organisms to changing temperatures. Sustaining heart function is critical for complex organisms to oxygenate tissues, particularly under temperature stress. Yet, specific mechanisms that define thermal sensitivity of cardiac function remain unclear. Here we investigated whole animal metabolism, cardiac performance and mitochondrial function in response to elevated temperatures for temperate, subtropical and tropical spiny lobster species. While oxygen demands increased with rising temperatures, heart function became limited or declined in all three species of lobsters. The decline in cardiac performance coincided with decreases in mitochondrial efficiency through increasing mitochondrial proton leakage, which predicts impaired compensation of ATP production. Species differences were marked by shifts in mitochondrial function, with the least thermal scope apparent for tropical lobsters. We conclude that acute temperature stress of spiny lobsters, irrespective of their climatic origin, is marked by declining cellular energetic function of the heart, contributing to an increasing loss of whole animal performance. Better understanding of physiological thermal stress cascades will help to improve forecasts of how changing environmental temperatures affect the fitness of these ecologically and commercially important species.
Vitamin D Supplementation in Overweight/obese Asian Indian Women with Prediabetes Reduces Glycemic Measures and Truncal Subcutaneous Fat: A 78 Weeks Randomized Placebo-Controlled Trial (PREVENT-WIN Trial)
Authors: Bhatt Surya Prakash , Misra Anoop , Pandey Ravindra Mohan , Upadhyay Ashish Datt , Gulati Seema , Singh Namrata 
Published: January 2020

AbstractVitamin D deficiency may contribute to etiology of type 2 diabetes in Asian Indians. The objectives of this study was to evaluate effect of vitamin D supplementation on glycemic profile and body composition in prediabetic and vitamin D deficient overweight/obese Asian Indian women. In this open-label randomized placebo-controlled trial (78 weeks duration), 121 females (aged 20–60 years) with prediabetes and vitamin D deficiency were randomly allocated in intervention (n, 61) and placebo (n, 60) groups. The primary outcome variables were fasting blood glucose (FBG), 2-h blood glucose post OGTT (2-h BG), hemoglobin A1c (HbA1C), and reversal to normoglycemia. In Intention-to-treat analysis, at the end of intervention, we observed significant decrease in FBG [−5.0 (−12.6–2.4), p = 0.04], 2-h blood glucose post OGTT [−11(−49.3–26.9), p = 0.02], hemoglobin A1c [−0.41 (5.89, 6.55), p = 0.05] and increase in 25(OH) D [7.5 (−6.0–20.9), p = 0.002] levels in intervention as compared to the placebo group. Changes in glycemic category based on FBG were as follows; intervention group: normal FBG, 58.6%; impaired fasting glucose (IFG), 39%; and type 2 diabetes mellitus (T2DM), 2.4%; placebo group: normal FBG, 48.8%; IFG, 46.3%; and T2DM, 4.9%. Changes in category of 2-hour glucose post OGTT after intervention were as follows; intervention group: normal glucose tolerance (NGT) 51.2% and prediabetes, 48.8%; placebo group: NGT, 43.9%; prediabetes, 53.7% and T2DM, 2.4%. After intervention, subscapular skinfold (visit Ist compared to visit IIIrd) and suprailiac skinfold (visit IInd compared to visit IIIrd) were significantly lower in intervention group vs. control group. In conclusion, we observed significant reduction in FBG, 2-hour glucose post OGTT, HbA1c, and truncal subcutaneous fat and reversal to normoglycemia in overweight/obese prediabetic vitamin D deficient Asian Indian women after 78 weeks of vitamin D supplementation.