bluuebunny/crossref_metadata_2025_split huggingface dataset:
IMF Control of Alfvénic Energy Transport and Deposition at High Latitudes
Authors: Hatch Spencer M. , LaBelle James , Lotko William , Chaston Christopher C. , Zhang Binzheng 
Published: November 2017

AbstractWe investigate the influence of the interplanetary magnetic field (IMF) clock angle ϕIMF on high‐latitude inertial Alfvén wave (IAW) activity in the magnetosphere‐ionosphere transition region using Fast Auroral SnapshoT (FAST) satellite observations. We find evidence that negative IMF Bz coincides with nightside IAW power generation and enhanced rates of IAW‐associated electron energy deposition, while positive IMF Bz coincides with enhanced dayside wave and electron energy deposition. Large (
nT) negative IMF By coincides with enhanced postnoon IAW power, while large positive IMF By coincides with enhanced but relatively weaker prenoon IAW power. For each ϕIMF orientation we compare IAW Poynting flux and IAW‐associated electron energy flux distributions with previously published distributions of Alfvénic Poynting flux over ∼2–22 mHz, as well as corresponding wave‐driven electron energy deposition derived from Lyon‐Fedder‐Mobarry global MHD simulations. We also compare IAW Poynting flux distributions with distributions of broad and diffuse electron number flux, categorized using an adaptation of the Newell et al. (2009) precipitation scheme for FAST. Under negative IMF Bz in the vicinity of the cusp (9.5–14.5 magnetic local time), regions of intense dayside IAW power correspond to enhanced diffuse electron number flux but relatively weaker broadband electron precipitation. Differences between cusp region IAW activity and broadband precipitation illustrate the need for additional information, such as fields or pitch angle measurements, to identify the physical mechanisms associated with electron precipitation in the vicinity of the cusp.
Magnetotelluric Imaging of Lower Crustal Melt and Lithospheric Hydration in the Rocky Mountain Front Transition Zone, Colorado, USA
Authors: Feucht D. W. , Sheehan A. F. , Bedrosian P. A. 
Published: November 2017

AbstractWe present an electrical resistivity model of the crust and upper mantle from two‐dimensional (2‐D) anisotropic inversion of magnetotelluric data collected along a 450 km transect of the Rio Grande rift, southern Rocky Mountains, and High Plains in Colorado, USA. Our model provides a window into the modern‐day lithosphere beneath the Rocky Mountain Front to depths in excess of 150 km. Two key features of the 2‐D resistivity model are (1) a broad zone (~200 km wide) of enhanced electrical conductivity (<20 Ωm) in the midcrust to lower crust that is centered beneath the highest elevations of the southern Rocky Mountains and (2) hydrated lithospheric mantle beneath the Great Plains with water content in excess of 100 ppm. We interpret the high conductivity region of the lower crust as a zone of partially molten basalt and associated deep‐crustal fluids that is the result of recent (less than 10 Ma) tectonic activity in the region. The recent supply of volatiles and/or heat to the base of the crust in the late Cenozoic implies that modern‐day tectonic activity in the western United States extends to at least the western margin of the Great Plains. The transition from conductive to resistive upper mantle is caused by a gradient in lithospheric modification, likely including hydration of nominally anhydrous minerals, with maximum hydration occurring beneath the Rocky Mountain Front. This lithospheric “hydration front” has implications for the tectonic evolution of the continental interior and the mechanisms by which water infiltrates the lithosphere.
Dioctahedral Phyllosilicates Versus Zeolites and Carbonates Versus Zeolites Competitions as Constraints to Understanding Early Mars Alteration Conditions
Authors: Viennet Jean‐Christophe , Bultel Benjamin , Riu Lucie , Werner Stephanie C. 
Published: November 2017

AbstractWidespread occurrence of Fe,Mg‐phyllosilicates has been observed on Noachian Martian terrains. Therefore, the study of Fe,Mg‐phyllosilicate formation, in order to characterize early Martian environmental conditions, is of particular interest to the Martian community. Previous studies have shown that the investigation of Fe,Mg‐smectite formation alone helps to describe early Mars environmental conditions, but there are still large uncertainties in terms of pH range, oxic/anoxic conditions, etc. Interestingly, carbonates and/or zeolites have also been observed on Noachian surfaces in association with the Fe,Mg‐phyllosilicates. Consequently, the present study focuses on the dioctahedral/trioctahedral phyllosilicate/carbonate/zeolite formation as a function of various CO2 contents (100% N2, 10% CO2/90% N2, and 100% CO2), from a combined approach including closed system laboratory experiments for 3 weeks at 120°C and geochemical simulations. The experimental results show that as the CO2 content decreases, the amount of dioctahedral clay minerals decreases in favor of trioctahedral minerals. Carbonates and dioctahedral clay minerals are formed during the experiments with CO2. When Ca‐zeolites are formed, no carbonates and dioctahedral minerals are observed. Geochemical simulation aided in establishing pH as a key parameter in determining mineral formation patterns. Indeed, under acidic conditions dioctahedral clay minerals and carbonate minerals are formed, while trioctahedral clay minerals are formed in basic conditions with a neutral pH value of 5.98 at 120°C. Zeolites are favored from pH ≳ 7.2. The results obtained shed new light on the importance of dioctahedral clay minerals versus zeolites and carbonates versus zeolites competitions to better define the aqueous alteration processes throughout early Mars history.
Temperature Dependence of Apparent Respiratory Quotients and Oxygen Penetration Depth in Contrasting Lake Sediments
Authors: Sobek Sebastian , Gudasz Cristian , Koehler Birgit , Tranvik Lars J. , Bastviken David , Morales‐Pineda María 
Published: November 2017

AbstractLake sediments constitute an important compartment in the carbon cycle of lakes, by burying carbon over geological timescales and by production and emission of greenhouse gases. The degradation of organic carbon (OC) in lake sediments is linked to both temperature and oxygen (O2), but the interactive nature of this regulation has not been studied in lake sediments in a quantitative way. We present the first systematic investigation of the effects of temperature on the apparent respiratory quotient (RQ, i.e., the molar ratio between carbon dioxide (CO2) production and O2consumption) in two contrasting lake sediments. Laboratory incubations of sediment cores of a humic lake and an eutrophic lake across a 1–21°C temperature gradient over 157 days revealed that both CO2production and O2consumption were positively, exponentially, and similarly dependent on temperature. The apparent RQ differed significantly between the lake sediments (0.63 ± 0.26 and 0.99 ± 0.28 in the humic and the eutrophic lake, respectively; mean ± SD) and was significantly and positively related to temperature. The O2penetration depth into the sediment varied by a factor of 2 over the 1–21°C temperature range and was significantly, negatively, and similarly related to temperature in both lake sediments. Accordingly, increasing temperature may influence the overall extent of OC degradation in lake sediments by limiting O2supply to aerobic microbial respiration to the topmost sediment layer, resulting in a concomitant shift to less effective anaerobic degradation pathways. This suggests that temperature may represent a key controlling factor of the OC burial efficiency in lake sediments.
Short‐Term Changes in Physical and Chemical Properties of Soil Charcoal Support Enhanced Landscape Mobility
Authors: Pyle Lacey A. , Magee Kate L. , Gallagher Morgan E. , Hockaday William C. , Masiello Caroline A. 
Published: November 2017

AbstractCharcoal is a major component of the stable soil organic carbon reservoir, and the physical and chemical properties of charcoal can sometimes significantly alter bulk soil properties (e.g., by increasing soil water holding capacity). However, our understanding of the residence time of soil charcoal remains uncertain, with old measured soil charcoal ages in apparent conflict with relatively short modeled and measured residence times. These discrepancies may exist because the fate of charcoal on the landscape is a function not just of its resistance to biological decomposition but also its physical mobility. Mobility may be important in controlling charcoal landscape residence time and may artificially inflate estimates of its degradability, but few studies have examined charcoal vulnerability to physical redistribution. Charcoal landscape redistribution is likely higher than other organic carbon fractions owing to charcoal's low bulk density, typically less than 1.0 g/cm3. Here we examine both the physical and chemical properties of soil and charcoal over a period of two years following a 2011 wildfire in Texas. We find little change in properties with time; however, we find evidence of enhanced mobility of charcoal relative to other forms of soil organic matter. These data add to a growing body of evidence that charcoal is preferentially eroded, offering another explanation for variations observed in its environmental residence times.
Simulation of the Unexpected Photosynthetic Seasonality in Amazonian Evergreen Forests by Using an Improved Diffuse Fraction‐Based Light Use Efficiency Model
Authors: Yan Hao , Wang Shao‐Qiang , da Rocha Humberto R. , Rap Alexandru , Bonal Damien , Butt Nathalie , Coupe Natalia Restrepo , Shugart Herman H. 
Published: November 2017

AbstractUnderstanding the mechanism of photosynthetic seasonality in Amazonian evergreen forests is critical for its formulation in global climate and carbon cycle models. However, the control of the unexpected photosynthetic seasonality is highly uncertain. Here we use eddy‐covariance data across a network of Amazonian research sites and a novel evapotranspiration (E) and two‐leaf‐photosynthesis‐coupled model to investigate links between photosynthetic seasonality and climate factors on monthly scales. It reproduces the GPP seasonality (R2 = 0.45–0.69) with a root‐mean‐square error (RMSE) of 0.67–1.25 g C m−2 d−1 and a Bias of −0.03–1.04 g C m−2 d−1 for four evergreen forest sites. We find that the proportion of diffuse and direct sunlight governs the photosynthetic seasonality via their interaction with sunlit and shaded leaves, supported by a proof that canopy light use efficiency (LUE) has a strong linear relationship with the fraction of diffuse sunlight for Amazonian evergreen forests. In the transition from dry season to rainy season, incident total radiation (Q) decreased while LUE and diffuse fraction increased, which produced the large seasonal increase (~34%) in GPP of evergreen forests. We conclude that diffuse radiation is an important environmental driver of the photosynthetic seasonality in tropical Amazon forests yet depending on light utilization by sunlit and shaded leaves. Besides, the GPP model simulates the precipitation‐dominated GPP seasonality (R2 = 0.40–0.69) at pasture and savanna sites. These findings present an improved physiological method to relate light components with GPP in tropical Amazon.
Greenhouse Gas Emissions Under Different Drainage and Flooding Regimes of Cultivated Peatlands
Authors: Hu Jing , VanZomeren Christine M. , Inglett Kanika S. , Wright Alan L. , Clark Mark W. , Reddy K. R. 
Published: November 2017

AbstractGlobally, approximately 10–20% of peatlands have been drained for agricultural purposes. A strategy to protect peatlands and mitigate carbon dioxide (CO2) emissions, while continuing agricultural production, is the use of intermittent flooding and drainage. A potential drawback of this strategy could be increases in methane (CH4) and nitrous oxide (N2O) emissions. The objective of this study was to compare greenhouse gas (GHG) emissions from peatlands under various flooding–drainage cycles. A laboratory study was performed using intact soil cores subjected to different durations of flooding and drainage for 6 months. Average daily emissions of CO2 and N2O were significantly higher (P < 0.001) under drained (667 ± 37 mg CO2–C m−2 d−1 and 135 ± 19 μg N2O–N m−2 d−1) than flooded conditions (86 ± 6 mg CO2–C m−2 d−1 and 48 ± 2 μg N2O–N m−2 d−1). Methane emissions were not influenced by drained/flooded conditions, with an average rate of 116 ± 11 μg CH4–C m−2 d−1. Peaks of CH4 and N2O emissions were observed after flooding events and lasted less than 24 h. The peak emissions were approximately 8 and 19 times higher than the mean CH4 and N2O emissions, respectively. Carbon dioxide was the dominant component of GHGs, irrespective of hydrologic regime, accounting for more than 92% of overall global warming potential. Global warming potential was inversely proportional to the flooding period, indicating that prolonging the flooding period of peatlands would help mitigate soil oxidation and GHG emissions and enhance sustainability of these agricultural peatlands.
Kinship and Inbreeding
Authors: Fernando Rohan L , Habier David 
Published: November 2017

Abstract

The kinship coefficient quantifies the genetic similarity between two individuals by the probability that randomly sampled homologous genes from the two individuals are identical by descent (IBD) given their pedigree‐based relationship. Inbreeding is the probability that the two genes at a locus are IBD. These probabilities played a key role in modelling genetic covariances between relatives, which provided the theoretical foundation for the quantitative genetic analyses of polygenic traits. At present, genotypes are becoming available at the trait loci or at the loci closely linked to them. Given such genotypic information, analyses that are based on genetic covariances between relatives conditional on pedigree are becoming obsolete together with pedigree‐based coefficients of kinship and inbreeding.

Key Concepts

Before the availability of genotype information, covariance between relatives conditional on pedigree information provided the theoretical foundation for the quantitative analyses of polygenic traits.

Kinship and inbreeding coefficients played a key role in modelling genetic covariances between relatives.

Analyses that are conditional on genotypes are more informative than those conditional on pedigrees.

Pedigree‐based analyses are being replaced by genotype‐based analyses.
Modelling Plant Cell Growth
Authors: Liu Junli , Moore Simon , Lindsey Keith 
Published: November 2017

Abstract

Plants are sessile organisms and they must adapt their growth to a changing environment. Understanding plant growth requires to study the interplay of turgor, cellular hydrodynamics, mechanical properties of cell walls and addition of materials to cell walls, as well as the actions of phytohormones. Mathematical modelling is a useful tool for tackling the complexity in plant growth. The scope of this article is to discuss the fundamental aspects of modelling plant cell growth. In order for a plant cell to grow, the cell wall must expand, water must enter the cell and turgor pressure must be able to provide mechanical support. During cell growth, the relative change in the water volume and the relative change in cell wall chamber volume are approximately equal. Mathematical equations for modelling plant cell growth are described to establish how cell volume and turgor can be calculated. Mathematical equations for ion transport are introduced to establish how osmotic pressure can be calculated. Combination of those equations formulates a method for modelling plant cell growth. Modelling of auxin dynamics, which play a key role in controlling cell expansion, is also described. One of the future challenges is to model the interplay between plant growth and auxin dynamics.

Key Concepts

The plant cell is surrounded by the cell wall.

In order for a plant cell to grow, the cell wall must expand, water must enter the cell and turgor pressure must be able to provide mechanical support.

Turgor and cell volume are calculated using the mathematical equations, which describe that the relative change in the water volume and the relative change in cell wall chamber volume are approximately equal during the cell growth.

Cellular ion concentrations and osmotic pressure are calculated using the equations that describe reversal potentials and voltage gating.

The phytohormone auxin plays an essential role in many aspects of plant growth and development.

Auxin concentration in the cells is a function of multiple factors including biosynthesis, degradation and conjugation, and transport.

Modelling auxin dynamics needs to appropriately formulate the equations including auxin biosynthesis, degradation and transport.

To model the role of auxin in plant cell growth, it is necessary to establish how auxin is related to the key factors for plant cell growth including turgor, cellular hydrodynamics, mechanical properties of cell wall materials and addition of materials to the cell wall.
Molecular Genetics of
U
sher Syndrome: Current State of Understanding
Authors: Slijkerman Ralph WN , Kremer Hannie , van Wijk Erwin 
Published: November 2017

Abstract

Usher syndrome affects hearing, vision and balance. The syndrome is genetically heterogeneous and mutations in ten genes have been identified to be disease causing. Proteins encoded by these genes cofunction with each other and with other proteins, composing an Usher interactome with diverse functions including structural support, transport and potentially signalling at different subcellular locations in hair cells of the inner ear and in photoreceptors of the retina. In hair cells, Usher proteins mainly contribute to the formation of fibrous links, including the tip link, that connect stereocilia and stereocilia to the kinocilium. In addition, Usher proteins are found in the synaptic region where they might contribute to signal transduction by regulating the cell surface levels of Ca
v
1.3 Ca
2+
channels and exocytosis. In photoreceptor cells, the Usher proteins are seen in the region of the connecting cilium including the periciliary region, the basal body, accessory centriole and calyceal processes. Also here, Usher proteins are present in the synaptic region. Although the function of Usher proteins in photoreceptors and hair cells is not yet fully understood, promising therapeutic developments are ongoing to alleviate the phenotypic burden resulting from mutations in any of the Usher genes.

Key Concepts

Usher syndrome is clinically and genetically heterogeneous.

Usher syndrome type I (USH1) and type II (USH2) proteins interact and form highly dynamic protein networks.

Usher protein networks fulfil a role in providing structural support, play a role in intracellular transport mechanisms and are suggested to be involved in cellular signalling cascades.

A range of cellular and animal models are used to unravel the molecular pathogenesis of Usher syndrome and to evaluate promising therapeutic strategies.

Promising progress in the development of (pre)clinical genetic (i.e. gene augmentation, splice modulation, translational read‐through and gene editing) and nongenetic (i.e. small compounds, neurotrophic factors and cell replacement) therapeutic strategies have been published for Usher syndrome.
Protein Conformational Disease: Visit the Facts at a Glance
Authors: Peng Yunhui , Alexov Emil 
Published: November 2017

Abstract

Proteins perform their function for adopting a particular 3D structure, referred as native structure, and failure to fold into the native structure has profound deleterious effects, frequently causing diseases. Such diseases, termed as protein conformational diseases, are a large group of disorders that arise from protein adopting abnormal conformational states. In the past two decades, it has been shown that conformational diseases affect large fraction of human population and present significant challenges to human health. Many protein conformational diseases are multifactorial diseases and result from very complicated molecular mechanisms. The most prominent disease‐associated phenomena of protein conformational diseases are toxic gain of function, loss of function, improper degradation and improper localisation. Furthermore, recent promising therapeutic approaches are developed for treating conformational disease.

Key Concepts

A remarkable relationship exists between the protein's functionality and specific three‐dimensional structure.

The energy landscape in protein folding resembles a rough funnel and proteins could be trapped in the intermediate states, resulting in misfolded proteins.

Protein conformational disease refers to the pathology that a protein adopts abnormal conformational states, disturbing the normal role of a protein in the cell.

Multiple phenomena including loss of function, toxic gain of function, improper degradation and localisation are associated with protein conformational diseases.

Protein conformational disease affects large human populations and developing therapeutic approach is a priority task for better public health.
Neurobiology of Circadian and Interval Timing
Authors: Agostino Patricia V , Acosta Julieta , Meck Warren H 
Published: November 2017

Abstract

Temporal processing in the brain is fundamental to environmental adaptation in humans and other animals. Biological timing ranges from the microsecond scale (e.g. sound localisation) to seasonal frequencies (such as reproductive cycles). Two of the main scales of biological timing ubiquitous in most organisms are interval timing (seconds‐to‐minutes range) and circadian timing (24 h range). Interval timing is crucial to learning, memory, decision‐making and other cognitive tasks, whereas circadian timing is essential for the regulation of several physiological and behavioural functions. Several brain areas, circuits and neuromodulators that are critical to temporal processing have now been identified. However, with the exception of the circadian system, the genetic and molecular machinery that regulates biological clocks has not been systematically examined. As a consequence, the molecular basis of these two temporal mechanisms is currently the subject of intense research, as well as their possible relationship.

Key Concepts

Biological timing (from microseconds to seasonal cycles) is fundamental for survival and optimal goal reaching in humans and other animals.

Circadian timing (24 h) and interval timing (hundreds of milliseconds to minutes) are ubiquitous in nature and are required for normal physiology and behaviour.

Dopamine metabolism in the striatum is critical for interval timing, and it is also the subject of circadian control.

Circadian and interval timing may share some common pathways, including dopamine metabolism.

Circadian and interval timing are seriously disrupted in human pathologies with dopamine dysfunction.