bluuebunny/crossref_metadata_2025_split huggingface dataset:
A multiyear estimate of methane fluxes in Alaska from CARVE atmospheric observations
Authors: Miller Scot M. , Miller Charles E. , Commane Roisin , Chang Rachel Y.‐W. , Dinardo Steven J. , Henderson John M. , Karion Anna , Lindaas Jakob , Melton Joe R. , Miller John B. , Sweeney Colm , Wofsy Steven C. , Michalak Anna M. 
Published: September 2016

AbstractMethane (CH4) fluxes from Alaska and other arctic regions may be sensitive to thawing permafrost and future climate change, but estimates of both current and future fluxes from the region are uncertain. This study estimates CH4 fluxes across Alaska for 2012–2014 using aircraft observations from the Carbon in Arctic Reservoirs Vulnerability Experiment (CARVE) and a geostatistical inverse model (GIM). We find that a simple flux model based on a daily soil temperature map and a static map of wetland extent reproduces the atmospheric CH4 observations at the statewide, multiyear scale more effectively than global‐scale process‐based models. This result points to a simple and effective way of representing CH4 fluxes across Alaska. It further suggests that process‐based models can improve their representation of key processes and that more complex processes included in these models cannot be evaluated given the information content of available atmospheric CH4 observations. In addition, we find that CH4 emissions from the North Slope of Alaska account for 24% of the total statewide flux of 1.74 ± 0.26 Tg CH4 (for May–October). Global‐scale process models only attribute an average of 3% of the total flux to this region. This mismatch occurs for two reasons: process models likely underestimate wetland extent in regions without visible surface water, and these models prematurely shut down CH4 fluxes at soil temperatures near 0°C. Lastly, we find that the seasonality of CH4 fluxes varied during 2012–2014 but that total emissions did not differ significantly among years, despite substantial differences in soil temperature and precipitation.
Observational evidence of the nonlinear wave growth theory of plasmaspheric hiss
Authors: Nakamura Satoko , Omura Yoshiharu , Summers Danny , Kletzing Craig A. 
Published: September 2016

AbstractWe test the recently developed nonlinear wave growth theory of plasmaspheric hiss against discrete rising tone elements of hiss emissions observed by the Van Allen Probes. From the phase variation of the waveforms processed by bandpass filters, we calculate the instantaneous frequencies and wave amplitudes. We obtain the theoretical relation between the wave amplitude and frequency sweep rates at the observation point by applying the convective growth rates and dispersion factors to the known relation at the equator. By plotting the theoretical relation over scatterplots of the wave amplitudes and the frequency sweep rates for rising tone elements, we find good agreement between the hiss observations and the nonlinear theory. We also find that the duration periods of the hiss elements are in good agreement with the nonlinear transition time necessary for the formation of a resonant current through coherent nonlinear wave‐particle interactions.
A new paradigm for large earthquakes in stable continental plate interiors
Authors: Calais E. , Camelbeeck T. , Stein S. , Liu M. , Craig T. J. 
Published: September 2016

AbstractLarge earthquakes within stable continental regions (SCR) show that significant amounts of elastic strain can be released on geological structures far from plate boundary faults, where the vast majority of the Earth's seismic activity takes place. SCR earthquakes show spatial and temporal patterns that differ from those at plate boundaries and occur in regions where tectonic loading rates are negligible. However, in the absence of a more appropriate model, they are traditionally viewed as analogous to their plate boundary counterparts, occurring when the accrual of tectonic stress localized at long‐lived active faults reaches failure threshold. Here we argue that SCR earthquakes are better explained by transient perturbations of local stress or fault strength that release elastic energy from a prestressed lithosphere. As a result, SCR earthquakes can occur in regions with no previous seismicity and no surface evidence for strain accumulation. They need not repeat, since the tectonic loading rate is close to zero. Therefore, concepts of recurrence time or fault slip rate do not apply. As a consequence, seismic hazard in SCRs is likely more spatially distributed than indicated by paleoearthquakes, current seismicity, or geodetic strain rates.
Off‐great‐circle paths in transequatorial propagation: 2. Nonmagnetic‐field‐aligned reflections
Authors: Tsunoda Roland T. , Maruyama Takashi , Tsugawa Takuya , Yokoyama Tatsuhiro , Ishii Mamoru , Nguyen Trang T. , Ogawa Tadahiko , Nishioka Michi 
Published: September 2016

AbstractThere is considerable evidence that plasma structure in nighttime equatorial F layer develops from large‐scale wave structure (LSWS) in bottomside F layer. However, crucial details of how this process proceeds, from LSWS to equatorial plasma bubbles (EPBs), remain to be sorted out. A major obstacle to success is the paucity of measurements that provide a space‐time description of the bottomside F layer over a broad geographical region. The transequatorial propagation (TEP) experiment is one of few methods that can do so. New findings using a TEP experiment, between Shepparton (SHP), Australia, and Oarai (ORI), Japan, are presented in two companion papers. In Paper 1 (P1), (1) off‐great‐circle (OGC) paths are described in terms of discrete and diffuse types, (2) descriptions of OGC paths are generalized from a single‐reflection to a multiple‐reflection process, and (3) discrete type is shown to be associated with an unstructured but distorted upwelling, whereas the diffuse type is shown to be associated with EPBs. In Paper 2 (P2), attention is placed on differences in east‐west (EW) asymmetry, found between OGC paths from the SHP‐ORI experiment and those from another near‐identical TEP experiment. Differences are reconciled by allowing three distinct sources for the EW asymmetries: (1) reflection properties within an upwelling (see P1), (2) OGC paths that depend on magnetic declination of geomagnetic field (B), and (3) OGC paths supported by non‐B‐aligned reflectors at latitudes where inclination of B is finite.
The effect of losing and gaining flow conditions on hyporheic exchange in heterogeneous streambeds
Authors: Fox A. , Laube G. , Schmidt C. , Fleckenstein J. H. , Arnon S. 
Published: September 2016

AbstractBed form‐induced hyporheic exchange flux (qH) is increasingly viewed as a key process controlling water fluxes and biogeochemical processes in river networks. Despite the fact that streambeds are inherently heterogeneous, the majority of bed form flume‐scale studies were done on homogeneous systems. We conducted salt and dye tracer experiments to study the effects of losing and gaining flow conditions on qH using a laboratory recirculating flume system packed with a heterogeneous streambed, and equipped with a drainage system that enabled us to apply losing or gaining fluxes. We found that when either losing or gaining fluxes increased (regardless of whether the flux was upward or downward), qH followed an exponential decline, the volume of the hyporheic flow cell drastically reduced, and the mean residence times declined moderately. A numerical flow model for the heterogeneous streambed was set up and fitted against the experimental data in order to test whether an equivalent homogeneous case exists. The measured qH were accurately predicted with the heterogeneous model, while it was underestimated using a homogeneous model characterized by the geometric mean of the hydraulic conductivity. It was also shown that in order to produce the results of the heterogeneous model with an equivalent hydraulic conductivity, the latter had to be increased as the losing or gaining fluxes increase. The results strongly suggest that it is critical to adequately account for the heterogeneous streambed structure in order to accurately predict the effect of vertical exchange fluxes between the stream and groundwater on hyporheic exchange.
Transposons: Prokaryotic
Authors: Chandler Michael 
Published: September 2016

AbstractTransposons are DNA (deoxyribonucleic acid) segments found ubiquitously in the genomes of living organisms and capable of moving from place to place within a genome. They are frequently associated with the sequestration and transmission of accessory genes in bacteria and archaea. They carry genes such as resistance to anti‐bacterials, virulence and symbiotic factors and catabolism of xenobiotics. They have a large impact on public health by facilitating the spread of these phenotypic characters. Transposons generate a variety of DNA rearrangements that have profound consequences for cell survival and evolution. These rearrangements are associated with transposition events (catalysed by transposon‐specific enzymes, transposases) but repeated transposon copies can act as portable regions of homology and undergo homologous recombination using the host recombination system. Transposons are diverse in structure, highly regulated by a multitude of mechanisms but only specify a limited number of catalytic chemistries. Transposons can represent a large proportion of prokaryotic genomes.Key ConceptsTransposable elements are ubiquitous and show a high degree of diversity.Transposable elements use a limited number of different chemical mechanisms for their transposition.Transposons are key elements in the short‐term evolution of prokaryotic genomes.Trasposons are central to driving the spread of antibiotic resistance.
Hydrophobic Interaction Chromatography
Authors: Jennissen Herbert P 
Published: September 2016

AbstractHydrophobic interaction chromatography (HIC) – today a key method in the purification of monoclonal antibodies – involves the separation of protein molecules in their native and biologically active state owing to a differential interaction of these molecules with hydrophobic sites on the surface of a solid support. Therefore, an understanding of the principles involved in this method is crucial. In the separation process, hydrophobic patches on the protein surface interact with hydrophobic molecules (e.g. alkyl residues) immobilised on the hydrophilic solid‐phase surface (e.g. agarose). In the article, a historical overview is followed by a consideration of the biochemical and biophysical mechanisms involved in HIC and a discussion of the critical hydrophobicity method and other approaches to hydrophobic interaction chromatographic methods. A detailed protocol for the individual synthesis and screening of gel libraries for specific needs has been published elsewhere. The treatise is concluded with a discussion on the predictability of chromatographic results, new developments and an outlook into the future.Key ConceptsHydrophobic interaction chromatography is a biological recognition process corresponding to a two‐dimensional lock‐and‐key model, that is, the dynamic pairing of a 2D key (protein) with its complementary 2D ‘lock’ (alkyl lattice).Proteins are adsorbed to hydrophobic agaroses as metastable states of adsorption–desorption hysteresis, indicating energetically that a local energy minimum exists (i.e. nonequilibrium state) in distinction to the global energy minimum, that is, true equilibrium.Critical hydrophobicity is the threshold hydrophobicity under low salt concentrations (e.g. 50 mM Tris, 150 mM NaCl and pH 7.0) and characterises a gel for reversible HIC binding properties.A homologous gel library consists of gels carrying covalently immobilised hydrocarbons (e.g. alkyl residues) comprising a homologous series.A quantised hydrophobicity gradient is a hydrophobicity gradient separated into a library of distinct gels of varying hydrophobicity for determining the critical hydrophobicity.The lattice‐site binding function is a protein adsorption isotherm (often showing positive cooperativity) as a function of the surface concentration of immobilised hydrocarbons (e.g. alkyl residues).The bulk ligand‐binding function is a protein adsorption isotherm on immobilised hydrocarbons (often showing negative cooperativity) as a function of the bulk protein concentration.Predicting chromatographic behaviour from sorption isotherms and protein structure are the ultimate aim in understanding and utilising HIC.The critical hydrophobic patch area hypothesis is a method of predicting the chromatographic behaviour of proteins in HIC from protein structure, utilising the area of hydrophobic patches on the surface of proteins.
Foraging
Authors: Roitberg Bernard D , Roitberg Gabi 
Published: September 2016

Abstract

Foraging theory can be used to explain two important phenomena, how and why organisms choose particular foodstuffs (Optimal Diet Theory) and how long individuals will remain in resource patches before seeking others (marginal value theorem). The theories are analytical and produce explicit, quantitative predictions. In order to test predictions from foraging theory, one must tweak the theory to account for details of an organism's natural history. In general, experimental tests of the theory support its predictions but most often in a qualitative, not quantitative manner. Foraging theory can be applied to a wide range of resources beyond the classic food examples including mates and hosts for parasitoids. The conditions under which a game theoretical approach is best used to explain foraging decisions are, for example when the performance of a focal individual depends on the number and behaviour of other competitors in any given patch.

Key Concepts

Resources (e.g. food) can vary in quality as well as in distribution (e.g. aggregated).

Optimal foraging theory was developed to explain how and why foods of particular quality are chosen by resource‐seeking individuals.

Further, because resources are often patchily distributed, foragers must decide when to give up and seek other patches. Such decisions can be understood by employing the marginal value theorem, a theorem that falls under the foraging theory umbrella.

Foraging theory models are quantitative and explicit. For example, they predict diet breadth (i.e. which resources should be included in the diet of a foraging individual) under a specific set of environmental conditions.

Foraging theory predictions can be tested using wild or domesticated organisms in the laboratory or in nature.

Tests of foraging theory predictions generally support the theory in a qualitative sense (e.g. the diet will expand as highest‐quality resources become rare) but often not quantitatively (e.g. the exact resource value at which diet expansion will occur).

Classic foraging theory ignores the physiological state of foraging organisms (e.g. energy reserves) but the theory can easily be modified to take into account such parameters.
Factor
V
L
eiden
Authors: Dahlbäck Björn 
Published: September 2016

Abstract

Factor V (FV) circulates in plasma as a procofactor with little procoagulant activity. It is activated by thrombin to FVa, which is a highly efficient cofactor to factor Xa in the activation of prothrombin. FVa is regulated by activated protein C (APC) together with its cofactor protein S. A single point mutation in the FV gene (
F5
), FV Leiden, is a common genetic risk factor for venous thrombosis. It results in the replacement of arginine506 with a glutamine. Arginine506 constitutes one of the three APC‐cleavage sites in FVa. The resulting APC resistance causes an imbalance between pro‐ and anticoagulant forces and a lifelong hypercoagulable state that increases the risk of venous thrombosis approximately three‐ to sevenfold. The FV Leiden mutation is the result of a single mutation event that is estimated to have occurred around 20–25 000 years ago in a Caucasian ancestor, which explains why the mutation is highly prevalent (up to 15%) in Caucasian and rare in other ethnic groups.

Key Concepts

Factor V is an important blood coagulation protein, which after its activation by thrombin functions as cofactor to factor Xa in the activation of prothrombin to thrombin.

Blood coagulation is controlled by several anticoagulant pathways.

Protein C, protein S, TFPI (tissue factor pathway inhibitor) and antithrombin are the main anticoagulant proteins in plasma.

Activated protein C (APC) together with its cofactor protein S regulates coagulation by cleaving and inactivating factor Va and factor VIIIa.

Venous thrombosis is a multifactorial disease.

Multiple genetic and circumstantial risk factors contribute to the risk of venous thrombosis.

The APC resistance phenotype is the most common inherited risk factor for venous thrombosis. It is caused by a single factor V gene (
F5
) mutation (Factor V Leiden) that results in the loss of one of the APC cleavage sites as Arg506 is replaced with a Gln.

Factor V Leiden is the result of a single mutation event that took place around 20–25 000 years ago.

Factor V Leiden is mainly present in Caucasians.

Heterozygous carriers of the FV Leiden mutation have a lifelong three‐ to sevenfold increased risk of thrombosis.
Genetics and Genomics Education of Primary Care Health Professionals in
B
ritain
Authors: Kirk Maggie , Tonkin Emma 
Published: September 2016

Abstract

There is long‐standing acknowledgement that primary care has a pivotal role in ensuring patients benefit from the rapid advances in genetic science and technologies and subsequent emergence of genomic medicine as an integral part of mainstream healthcare. However, significant deficits in knowledge and skills in genetics and genomics have been found in primary care professionals, exacerbated by a lack of education guidelines and limited accessible resources. That picture is changing with new strategic initiatives such as England's Genomics Education Programme, built on a strong policy foundation and driving development of curriculum guidelines and learning resources. Although significant challenges remain, there is evidence of an evolution from justification of the incorporation of genetics and genomics into mainstream healthcare and education, to an exploration of the effectiveness of different educational approaches and their impact on practice. More recently, global leaders have been driving a growing interest in strategic, collaborative effort across healthcare.

Key Concepts

The scope and pace of developments in genomics have implications across all areas of healthcare, including primary care.

Governments such as in the United Kingdom and the United States are promoting policies and initiatives to optimise the benefits that genomics can bring to healthcare.

There are significant challenges to address in engaging healthcare staff in genomics, including those in primary care, and in providing relevant, accessible education and training.

Education strategies are shifting in focus from defining content to effective approaches in teaching and learning.

Responses to these challenges have been robust, with international efforts in mobilising resources to support education of primary care health professionals and others.
Chromothripsis and Human Genetic Disease
Authors: Nazaryan‐Petersen Lusine , Tommerup Niels 
Published: September 2016

Abstract

Chromothripsis (CTH) is a newly discovered mutational mechanism, which in a single catastrophic event results in localised complex structural rearrangements confined to one or a few chromosomes. After an initial shattering or clustered fragmentation of a chromosomal region, the fragments join together in random order and orientation. During this process some of the generated fragments may be lost. It is not entirely clear which factors trigger the localised fragmentation; however, several mechanisms have been proposed, such as ionising radiation, aborted apoptosis, isolation of chromosome(s) in micronuclei, LINE1‐endonucleases, etc. CTH may disrupt multiple genes and/or regulatory regions. When it is incompatible with cell survival, the result should be apoptosis. However, if a cell escapes apoptosis, the extensive genomic rearrangements may have different phenotypic outcomes: cancer (somatic), congenital and developmental disorders (germline), neutral or even beneficial effects.

Key Concepts

Chromothripsis is a phenomenon where multiple localised double‐stranded DNA breaks result in complex genomic rearrangements.

Chromothripsis occurs within a single cell cycle.

Ionising radiation, aborted apoptosis, isolation of chromosome(s) in micronuclei and LINE1‐endonucleases are proposed to have a role in chromothripsis.

Chromothripsis in somatic cells may trigger cancer development.

Chromothripsis in the germline may result in congenital and developmental disorders.
Recovery of Gold from Incinerated Sewage Sludge
Authors: Sugawara Katsuyasu 
Published: September 2016

AbstractIn order to develop an efficient and selective recovery process for gold, which eliminates the need for water, the release behavior of gold from an incinerated sewage sludge ash heated to between 100 and 1000 °C under a chlorine gas stream was investigated. A release of gold was observed above 600 °C, with all gold being transferred to the gas phase at 1000 °C. The addition of solid carbon to the incinerated ash reduced this initial release temperature to 400 °C, with all gold being released into both the gas phase and on to the solid carbon at 700 °C. Subsequent optimization of the reaction conditions to maximize the amount of gold reporting to the solid carbon determined that the mixture of incinerated ash and carbon should first be heated to a terminal temperature of 800 °C under a nitrogen gas stream. Upon reaching this temperature, the gas stream should be switched from nitrogen to chlorine, and the mixture held at 800 °C for 1 h. Scanning electron microscopy and X‐ray diffraction measurements confirm that this produces a distribution of fine metallic gold over the carbon surface.
Life Cycle Sustainability Assessments
Authors: Halog Anthony , Manik Yosef 
Published: September 2016

Abstract
Assessing the sustainability of products (e.g., chemicals) and their process technologies is a challenging task, and hence key indicators and tools have to be developed continually to manage the impacts of social and economic threats while operating within ecological limits. The conventional life cycle assessment (LCA) method is one of such systems‐based tools, and standardized for environmental impact evaluation of product systems. However, LCA is pertinent to assessing mainly the “environmental dimension” of systems' sustainability; it was not historically developed to evaluate the other sustainability dimensions: economic and social. Hence, recent challenges in LCA have led to its broadening to encompass these other dimensions, which has resulted in what we call now the life cycle sustainability assessment (LCSA). LCSA needs to be a systemwide, integrated, and interdisciplinary analysis over space and time whereby an integrated modeling tool is needed to simulate and analyze the inter‐relationships among/between social, ecological, and economic systems. This article explains the basics of LCSA, LCA, life cycle costing, and social life cycle assessment and includes an initial LCSA application to palm oil‐based products. We introduced a framework here to provide a systematic basis for LCSA operationalization and identified a set of key economic, environmental, and social indicators at each stage of the palm oil biodiesel life cycle. The LCSA application thus helps to understand the complexity of a palm oil biodiesel life cycle through an integrated sustainability assessment and modeling.