bluuebunny/crossref_metadata_2025 huggingface dataset:
Software Development Integrating Methodology with Epistemology Promoting Knowledge Production
Authors: Ceja Jesús Manuel Olivares , Cervantes Emilio Buendía
Published: April 2014

Currently, many specialties should be mastered to produce software, consequently they fall in different levels of knowledge: project, system, program, or routine. This consideration was obtained through an epistemological approach in software development. Therefore, this article develops this consideration for students learning software production. The epistemological approach compliments the methodologies used during software generation. The main focus in this proposal is on applying learning principles, combining both the epistemological approach and methodologies to promote student knowledge production for software development. The implementation of the proposal provides students with a framework that prepares them to face software development problems with different levels of complexity. Evaluation is based on verifying which of the different epistemological categories the student masters.
An Increase in Tolerogenic Dendritic Cell and Natural Regulatory T Cell Numbers during Experimental Autoimmune Encephalomyelitis in Rras−/− Mice Results in Attenuated Disease
Authors: Ray Avijit , Basu Sreemanti , Miller Nichole M. , Chan Andrew M. , Dittel Bonnie N.
Published: April 2014

R-Ras is a member of the Ras superfamily of small GTPases, which are regulators of various cellular processes, including adhesion, survival, proliferation, trafficking, and cytokine production. R-Ras is expressed by immune cells and has been shown to modulate dendritic cell (DC) function in vitro and has been associated with liver autoimmunity. We used Rras-deficient mice to study the mechanism whereby R-Ras contributes to autoimmunity using experimental autoimmune encephalomyelitis (EAE), a mouse model of the CNS autoimmune disease multiple sclerosis. We found that a lack of R-Ras in peripheral immune cells resulted in attenuated EAE disease. Further investigation revealed that, during EAE, absence of R-Ras promoted the formation of MHC IIlow DC concomitant with a significant increase in proliferation of natural regulatory T cells, resulting in an increase in their cell numbers in the periphery. Our study suggests a novel role for R-Ras in promoting autoimmunity through negative regulation of natural regulatory T cell numbers by inhibiting the development of MHCIIlow DC with tolerogenic potential.
Citrullination Alters Immunomodulatory Function of LL-37 Essential for Prevention of Endotoxin-Induced Sepsis
Authors: Koziel Joanna , Bryzek Danuta , Sroka Aneta , Maresz Katarzyna , Glowczyk Izabela , Bielecka Ewa , Kantyka Tomasz , Pyrć Krzysztof , Svoboda Pavel , Pohl Jan , Potempa Jan
Published: April 2014

Cathelicidin LL-37 plays an essential role in innate immunity by killing invading microorganisms and regulating the inflammatory response. These activities depend on the cationic character of the peptide, which is conferred by arginine and lysine residues. At inflammatory foci in vivo, LL-37 is exposed to peptidyl arginine deiminase (PAD), an enzyme released by inflammatory cells. Therefore, we hypothesized that PAD-mediated citrullination of the arginine residues within LL-37 will abrogate its immunomodulatory functions. We found that, when citrullinated, LL-37 was at least 40 times less efficient at neutralizing the proinflammatory activity of LPS due to a marked decrease in its affinity for endotoxin. Also, the ability of citrullinated LL-37 to quench macrophage responses to lipoteichoic acid and poly(I:C) signaling via TLR2 and TLR3, respectively, was significantly reduced. Furthermore, in stark contrast to native LL-37, the modified peptide completely lost the ability to prevent morbidity and mortality in a mouse model of d-galactosamine–sensitized endotoxin shock. In fact, administration of citrullinated LL-37 plus endotoxin actually exacerbated sepsis due to the inability of LL-37 to neutralize LPS and the subsequent enhancement of systemic inflammation due to increased serum levels of IL-6. Importantly, serum from septic mice showed increased PAD activity, which strongly correlated with the level of citrullination, indicating that PAD-driven protein modification occurs in vivo. Because LL-37 is a potential treatment for sepsis, its administration should be preceded by a careful analysis to ensure that the citrullinated peptide is not generated in treated patients.
Overlapping and Asymmetric Functions of TCR Signaling during Thymic Selection of CD4 and CD8 Lineages
Authors: Sinclair Charles , Seddon Benedict
Published: April 2014

TCR signaling plays a central role in directing developmental fates of thymocytes. Current models suggest TCR signal duration directs CD4 versus CD8 lineage development. To investigate the role of TCR signaling during positive selection directly, we switched signaling off in a cohort of selecting thymocytes and followed, in time, their subsequent fate. We did this using an inducible Zap70 transgenic mouse model that allowed Zap70-dependent signaling to be turned on and then off again. Surprisingly, loss of TCR signaling in CD4+CD8lo thymocytes did not prevent their development into committed CD4 single positives (SPs), nor their continued maturation to HSAlo SPs. However, numbers of CD4 SPs underwent a substantial decline following loss of Zap70 expression, suggesting an essential survival role for the kinase. Termination of TCR signaling is considered an essential step in CD8 lineage development. Loss of Zap70 expression, however, resulted in the rapid death of CD8 lineage precursor thymocytes and a failure to generate CD8 SPs. Significantly, extending the window of Zap70 expression was sufficient for generation and export of both CD4 and CD8 T cells. These data reveal a parallel requirement for TCR-mediated survival signaling, but an asymmetric requirement for TCR-mediated maturation signals.
NADPH Oxidase–Independent Formation of Extracellular DNA Traps by Basophils
Authors: Morshed Mahbubul , Hlushchuk Ruslan , Simon Dagmar , Walls Andrew F. , Obata-Ninomiya Kazushige , Karasuyama Hajime , Djonov Valentin , Eggel Alexander , Kaufmann Thomas , Simon Hans-Uwe , Yousefi Shida
Published: April 2014

Basophils are primarily associated with a proinflammatory and immunoregulatory role in allergic diseases and parasitic infections. Recent studies have shown that basophils can also bind various bacteria both in the presence and the absence of opsonizing Abs. In this report, we show that both human and mouse basophils are able to produce mitochondrial reactive oxygen species and to form extracellular DNA traps upon IL-3 priming and subsequent activation of the complement factor 5 a receptor or FcεRI. Such basophil extracellular traps (BETs) contain mitochondrial, but not nuclear DNA, as well as the granule proteins basogranulin and mouse mast cell protease 8. BET formation occurs despite the absence of any functional NADPH oxidase in basophils. BETs can be found in both human and mouse inflamed tissues, suggesting that they also play a role under in vivo inflammatory conditions. Taken together, these findings suggest that basophils exert direct innate immune effector functions in the extracellular space.
TLR Costimulation Causes Oxidative Stress with Unbalance of Proinflammatory and Anti-Inflammatory Cytokine Production
Authors: Lavieri Rosa , Piccioli Patrizia , Carta Sonia , Delfino Laura , Castellani Patrizia , Rubartelli Anna
Published: April 2014

IL-1β acts in concert with anti-inflammatory cytokines, in particular, IL-1R antagonist (IL-1Ra), to ensure the correct development and outcome of the inflammation: imbalance in the IL-1β/IL-1Ra ratio is implicated in many human diseases and may lead to dramatic consequences. In this article, we show that single TLR engagement induces IL-1β and, with a little delay, IL-1Ra. Differently, costimulation of TLR2, TLR4, and TLR7/8 enhances IL-1β secretion but severely inhibits IL-1Ra production. The IL-1β/IL-1Ra unbalance after activation of multiple TLRs depends on the insurgence of oxidative stress, because of enhanced production of reactive oxygen species and failure of the antioxidant systems. Increased reactive oxygen species levels increase ATP externalization by monocytes, resulting in enhanced inflammasome activation and IL-1β secretion. Oxidative stress then induces cell responses to stress, including inhibition of protein synthesis, which, in turn, is responsible for the impaired production of IL-1Ra. IL-1Ra secretion is restored by exogenous antioxidants that oppose oxidative stress. Similar effects are evident also on other cytokines: TNF-α is induced, whereas IL-6 is inhibited by costimulation. Our findings provide a molecular basis to the imbalance between proinflammatory and regulatory cytokine circuits that occur in various pathologic conditions, and suggest new strategies for controlling inflammation.
Human Lymphoid Development in the Absence of Common γ-Chain Receptor Signaling
Authors: Kohn Lisa A. , Seet Christopher S. , Scholes Jessica , Codrea Felicia , Chan Rebecca , Zaidi-Merchant Sania , Zhu Yuhua , De Oliveira Satiro , Kapoor Neena , Shah Ami , Abdel-Azim Hisham , Kohn Donald B. , Crooks Gay M.
Published: April 2014

Despite the power of model systems to reveal basic immunologic mechanisms, critical differences exist between species that necessitate the direct study of human cells. Illustrating this point is the difference in phenotype between patients with SCID caused by mutations affecting the common γ-chain (γc) cytokine signaling pathway and mice with similar mutations. Although in both species, null mutations in either IL-2RG (which encodes γc), or its direct downstream signaling partner JAK3, result in T and NK cell deficiency, an associated B cell deficiency is seen in mice but not in humans with these genetic defects. In this study, we applied recent data that have revised our understanding of the earliest stages of lymphoid commitment in human bone marrow (BM) to determine the requirement for signaling through IL-2RG and JAK3 in normal development of human lymphoid progenitors. BM samples from SCID patients with IL-2RG (n = 3) or JAK3 deficiency (n = 2), which produce similar “T-NK-B+” clinical phenotypes, were compared with normal BM and umbilical cord blood as well as BM from children on enzyme treatment for adenosine deaminase–deficient SCID (n = 2). In both IL-2RG– and JAK3-SCID patients, the early stages of lymphoid commitment from hematopoietic stem cells were present with development of lymphoid-primed multipotent progenitors, common lymphoid progenitors and B cell progenitors, normal expression patterns of IL-7RA and TLSPR, and the DNA recombination genes DNTT and RAG1. Thus, in humans, signaling through the γc pathway is not required for prethymic lymphoid commitment or for DNA rearrangement.
Myeloid PTEN Deficiency Protects Livers from Ischemia Reperfusion Injury by Facilitating M2 Macrophage Differentiation
Authors: Yue Shi , Rao Jianhua , Zhu Jianjun , Busuttil Ronald W. , Kupiec-Weglinski Jerzy W. , Lu Ling , Wang Xuehao , Zhai Yuan
Published: April 2014

Although the role of phosphatase and tensin homolog deleted on chromosome 10 (PTEN) in regulating cell proliferation is well established, its function in immune responses remains to be fully appreciated. In the current study, we analyzed myeloid-specific PTEN function in regulating tissue inflammatory immune response in a murine liver partial warm ischemia model. Myeloid-specific PTEN knockout (KO) resulted in liver protection from ischemia reperfusion injury (IRI) by deviating the local innate immune response against ischemia reperfusion toward the regulatory type: expression of proinflammatory genes was selectively decreased and anti-inflammatory IL-10 was simultaneously increased in ischemia reperfusion livers of PTEN KO mice compared with those of wild-type (WT) mice. PI3K inhibitor and IL-10–neutralizing Abs, but not exogenous LPS, recreated liver IRI in these KO mice. At the cellular level, Kupffer cells and peritoneal macrophages isolated from KO mice expressed higher levels of M2 markers and produced lower TNF-α and higher IL-10 in response to TLR ligands than did their WT counterparts. They had enhanced Stat3- and Stat6-signaling pathway activation, but diminished Stat1-signaling pathway activation, in response to TLR4 stimulation. Inactivation of Kupffer cells by gadolinium chloride enhanced proinflammatory immune activation and increased IRI in livers of myeloid PTEN KO mice. Thus, myeloid PTEN deficiency protects livers from IRI by facilitating M2 macrophage differentiation.
Games on graphs
Authors: Allen Benjamin , Nowak Martin A.
Published: April 2014

Evolution occurs in populations of reproducing individuals. The trajectories and outcomes of evolutionary processes depend on the structure of the population. Evolutionary graph theory is a powerful approach to studying the consequences of spatial or social population structure. The vertices of the graph represent individuals. The edges determine who interacts with whom for game payoff and who competes with whom for reproduction. Interaction and competition can be governed by the same graph or by two different graphs. In this paper, we review the basic approach for evolutionary games on graphs and provide new proofs for key results. We formalize the method of identity by descent to derive conditions for strategy selection on finite, weighted graphs. We generalize our results to nonzero mutation rates, and to the case where the interaction and competition graphs do not coincide. We conclude with a perspective of open problems and future directions.
Atomic Decomposition for Morrey Spaces
Authors: Iida Takeshi , Sawano Yoshihiro , Tanaka Hitoshi
Published: April 2014

The Hardy space

H^p ({\mathbb R}^n)

substitutes for the Lebesgue space

L^p ({\mathbb R}^n)

. When

p>1

, then the Hardy space

H^p ({\mathbb R}^n)

coincides with the Lebesgue spaces

L^p ({\mathbb R}^n)

. This is shown by using the reflexivity of the function spaces. The atomic decomposition is readily available for

H^p ({\mathbb R}^n)

with

0<p<\infty

. This idea can be applied to many function spaces. As example of such an attempt, we now propose here a non-smooth decomposition of Morrey spaces. As applications, we consider the Olsen inequality. In the end of this article, we compare our results with existing ones and propose some possibility of extensions, which are left as future works.
Pointwise Limits of Sequences of Right-Continuous Functions and Measurability of Functions of Two Variables
Authors: Grande Zbigniew
Published: April 2014

In this article I prove that the pointwise limit

f\colon\mathbb R \to \mathbb R

of a sequence of right-continuous functions has some special property (G) and that bounded functions of two variables

g\colon\mathbb R^2 \to \mathbb R

whose vertical sections

g_x

,

x\in \mathbb R

, are derivatives and horizontal sections

g^y

,

y\in \mathbb R

, are pointwise limits of sequences of right-continuous functions, are measurable and sup-measurable in the sense of Lebesgue.
Asymptotics of Solutions of the Poisson Equation near Straight Edges
Authors: Rossmann Jürgen
Published: April 2014

The paper deals with the Dirichlet problem for the Poisson equation

\Delta u =f

in the domain

{\cal D}=K\times{\mathbb R}^{n-m}

, where

K

is a cone in

{\mathbb R}^m

. The author describes the singularities of the Green function near the edge of the domain. Using this result, he obtains the asymptotics of the solution of the boundary value problem for a right-hand side

f

belonging to a weighted

L_p

Sobolev space. Here, precise formulas for all coefficients in the asymptotics are given.
The effects of competition on the nature of cheating behavior
Authors: Rigdon Mary L. , D'Esterre Alexander P.
Published: April 2014

Competition among individuals comes in a variety of forms: for mates, for resources, and for prestige and recognition. Such competitive pressure can lead individuals to engage in unethical behavior in an effort to get ahead. There are several forms of cheating in which individuals may engage to improve their own outcome: they may lie about their own performance in a task and they may lie about others’ performance in a task. Our research is the first to examine how competition affects each of these two types of cheating behavior. We find that individuals are much more willing to cheat by lying about themselves than they are willing to sabotage another when under competitive pressure.
Environmental controls of anammox and denitrification in southern New England estuarine and shelf sediments
Authors: Brin Lindsay D. , Giblin Anne E. , Rich Jeremy J.
Published: April 2014

We measured denitrification and anammox potential rates in homogenized sediments over two annual cycles from two estuarine sites (Providence River estuary and Narragansett Bay) and two continental shelf sites (Block Island and Rhode Island sounds). Denitrification varied both spatially and seasonally, but anammox only varied spatially. Denitrification ranged from 2.5 to 112 nmol N h−1 mL−1 sediment, and anammox from 0 to 8.7 nmol N h−1 mL−1 sediment, with the contribution of anammox to N2 fluxes (ra) ranging from undetectable to 4% in estuarine sites and 8–42% on the shelf. Oxygen microprofiles were analyzed in intact cores and concentrations of nitrate, nitrite, and ammonium were measured in the sediment slice corresponding to the depth layer in which potential rates were measured. Denitrification rates correlated positively with diffusive O2 consumption and temperature and potential anammox rates correlated positively with pore‐water concentrations. Anammox was positively correlated with denitrification in shelf sediments where anammox was regularly detected, but not in estuarine sediments. ra was negatively correlated with diffusive O2 consumption and positively correlated with pore‐water nitrate. Both organic matter and nitrate were important factors regulating the contribution of anammox to N2 production. As a whole, our results demonstrate that incorporating processes that control these two factors into models of N cycling, rather than focusing on organic matter availability alone, may improve predictions of the relative importance of anammox to N2 production in marine sediments.
Seasonal dynamics and sedimentation patterns of Microcystis oligopeptide‐based chemotypes reveal subpopulations with different ecological traits
Authors: Agha Ramsy , Àngeles Lezcano Marià , del Mar Labrador Marià , Cirés Samuel. , Quesada Antonio
Published: April 2014

The patchy distribution of oligopeptide production abilities in cyanobacterial populations enables the classification of strains into different oligopeptide‐based chemotypes. In order to evaluate the ecological significance of chemotypes in natural systems, we tracked the seasonal dynamics and sedimentation losses of Microcystis chemotypes in the eutrophic Valmayor reservoir (Spain). Fifty‐three distinct chemotypes were identified throughout the season, six of them only present as benthic colonies. There was no correlation between chemotype affiliation and taxonomic morphospecies or colony size. The succession of chemotypes in the water column occurred synchronically in pelagic and littoral habitats and at different depths. Shifts in chemotype assemblages successfully explained temporal fluctuations in biomass‐standardized microcystin contents of the bloom. The dynamics of chemotypes were driven both by asynchronous proliferation in the water column and significantly different sedimentation rates among chemotypes. While differential settling was the most important loss process shaping chemotype succession, the existence of alternative processes selectively inflicting massive losses to individual chemotypes was observed. Together, the significant differences in sedimentation and pelagic net growth rates among chemotypes, their segregation among pelagic and benthic habitats, as well as the existence of chemotype‐selective loss processes, show that Microcystis oligopeptide chemotypes interact differently with their environment and represent commonly overlooked ecologically functional intraspecific linages.
The in situ light microenvironment of corals
Authors: Wangpraseurt Daniel , Polerecky Lubos , Larkum Anthony W.D. , Ralph Peter J. , Nielsen Daniel A. , Pernice Mathieu , Kühl Michael
Published: April 2014

We used a novel diver‐operated microsensor system to collect in situ spectrally resolved light fields on corals with a micrometer spatial resolution. The light microenvironment differed between polyp and coenosarc tissues with scalar irradiance (400–700 nm) over polyp tissue, attenuating between 5.1‐ and 7.8‐fold from top to base of small hemispherical coral colonies, whereas attenuation was at most 1.5‐fold for coenosarc tissue. Fluctuations in ambient solar irradiance induced changes in light and oxygen microenvironments, which were more pronounced and faster in coenosarc compared with polyp tissue. Backscattered light from the surrounding benthos contributed > 20% of total scalar irradiance at the coral tissue surface and enhanced symbiont photosynthesis and the local O2 concentration, indicating an important role of benthos optics for coral ecophysiology. Light fields on corals are species and tissue specific and exhibit pronounced variation on scales from micrometers to decimeters. Consequently, the distribution, genetic diversity, and physiology of coral symbionts must be coupled with the measurements of their actual light microenvironment to achieve a more comprehensive understanding of coral ecophysiology.
Famine and feast in a common freshwater calanoid: Effects of diet and temperature on fatty acid dynamics of Eudiaptomus gracilis
Authors: Koussoroplis Apostolos-Manuel , Nussbaumer Julia , Arts Michael T. , Guschina Irina A. , Kainz Martin J.
Published: April 2014

We investigated the effects of temperature (4°C, 8°C, and 12°C) on structural and storage dynamics, as measured by changes in fatty acids (FA) associated with cell membrane phospholipids (PL) and triacylglycerols (TAG), respectively, as well as on body weight and survival of a freshwater calanoid copepod (Eudiaptomus gracilis) during fasting (10 d) and refeeding (10 d) with two algae of differing nutritional quality (Cryptomonas ozolinii and Scenedesmus obliquus). Fasting led to 50% loss in body weight, a near total depletion of TAG, and a drastic decrease of the polyunsaturated FA (PUFA) in TAG and PL, indicating their preferential utilization and alterations in membrane function, respectively. Higher temperatures accelerated the decrease of body weight and of PUFA in PL and TAG, and decreased survival. After 10 d of refeeding, copepods partially recovered their initial lipid stores and cell membrane composition. The effects of food quality were temperature dependent: Cryptomonas promoted better recovery (i.e., return to or close to the levels at the beginning of the experiment) of both body weight and TAG at only the two higher temperatures (8°C and 12°C), whereas no recovery was observed at 4°C. Higher temperatures and refeeding on Cryptomonas also had a positive, but minor, influence on the recovery of membrane FA composition. Survival differed among treatments but was lowest at the intermediate temperature (8°C) for both diets. We conclude that temperature changes on the order of 4–8°C significantly influence TAG and PL during fasting periods and interact with food quality to determine the extent of recovery in copepod lipids.
Influence of cyanobacteria blooms on sediment biogeochemistry and nutrient fluxes
Authors: Gao Yonghui , Cornwell Jeffrey C. , Stoecker, Diane K. , Owens Michael S.
Published: April 2014

To explore the influence of cyanobacteria blooms on internal nutrient loading and sediment biogeochemistry, we conducted a 3 yr (2008–2010) field investigation in the upper Sassafras River, a shallow tidal freshwater tributary of Chesapeake Bay, Maryland. During 2010 a dense diazotrophic cyanobacteria bloom was accompanied by abnormally high pH (9.0–10.5) and supersaturated oxygen throughout the summer. With the persistence of high pH in the water column and organic matter inputs from sedimented phytoplankton detritus, flux rates of NH+4 and soluble reactive phosphate were significantly higher during the summer of the bloom year than the same period in nonbloom years. Although low summer N2‐N flux rates generally coincided with reduced water‐column NO−3 concentrations, the efficiency of nitrification was constrained by elevated pH that converted NH+4 to more toxic NH3. Denitrification was subsequently limited by nitrate supply, elevated pH, and the deepening of the oxic layer in the sediment. During blooms, we observed increases in bioavailable nutrient release from the sediment, coupled with decreases in inorganic N : P flux ratios and inhibition of N2 loss from the ecosystem. These changes in sediment nutrient recycling created positive feedbacks that may have fueled the prolonged blooms and selectively fostered growth of diazotrophic cyanobacteria.
Stratigraphic controls on fluid and solute fluxes across the sediment—water interface of an estuary
Authors: Sawyer Audrey H. , Lazareva Olesya , Kroeger Kevin D. , Crespo Kyle , Chan Clara S. , Stieglitz Thomas , Michael Holly A.
Published: April 2014

Shallow stratigraphic features, such as infilled paleovalleys, modify fresh groundwater discharge to coastal waters and fluxes of saltwater and nutrients across the sediment—water interface. We quantify the spatial distribution of shallow surface water—groundwater exchange and nitrogen fluxes near a paleovalley in Indian River Bay, Delaware, using a hand resistivity probe, conventional seepage meters, and pore‐water samples. In the interfluve (region outside the paleovalley) most nitrate‐rich fresh groundwater discharges rapidly near the coast with little mixing of saline pore water, and nitrogen transport is largely conservative. In the peat‐filled paleovalley, fresh groundwater discharge is negligible, and saltwater exchange is deep (∼1 m). Long pore‐water residence times and abundant sulfate and organic matter promote sulfate reduction and ammonium production in shallow sediment. Reducing, iron‐rich fresh groundwater beneath paleovalley peat discharges diffusely around paleovalley margins offshore. In this zone of diffuse fresh groundwater discharge, saltwater exchange and dispersion are enhanced, ammonium is produced in shallow sediments, and fluxes of ammonium to surface water are large. By modifying patterns of groundwater discharge and the nature of saltwater exchange in shallow sediments, paleovalleys and other stratigraphic features influence the geochemistry of discharging groundwater. Redox reactions near the sediment—water interface affect rates and patterns of geochemical fluxes to coastal surface waters. For example, at this site, more than 99% of the groundwater‐borne nitrate flux to the Delaware Inland Bays occurs within the interfluve portion of the coastline, and more than 50% of the ammonium flux occurs at the paleovalley margin.
Effect of climatic changes on stratification and deep‐water renewal in Lake Constance assessed by sensitivity studies with a 3D hydrodynamic model
Authors: Wahl Bernd , Peeters Frank
Published: April 2014

The implications of climatic change on Lake Constance are studied by long‐term hydrodynamic model simulations. In contrast to earlier studies that mostly have applied one‐dimensional models, this investigation utilizes a three‐dimensional hydrodynamic model and thus profits from the advantages of a spatial representation of lake bathymetry and hydrophysical processes. Model adaptation and validation are based on half a century of vertically resolved temperature recordings (1961 to 2011). Three different horizontal grid layouts are used to test the sensitivity of the thermal stratification and effective vertical turbulent diffusivities (DVeff) determined with the heat‐budget method to grid resolution. DVeff calculated from observations and from simulations with different grid resolutions agree rather well. However, in the deep water simulated DVeff are overestimated if the basin is resolved only by few grid cells. The investigation of the effect of climatic changes on Lake Constance is focused on the effects of altered air temperatures and wind velocities on deep‐water renewal. Numerical tracers are used as indicators of the winter vertical transport and mixing. Effects on stratification and mixing strongly depend on the seasonal course of the climatic changes. Warmer winter temperatures result in reduced deep‐water exchange and more frequent years with incomplete mixing. Increased air temperatures in summer have almost no effect on deep‐water renewal in winter but increase water‐column stability during summer and autumn. Increased wind speeds influence vertical mixing and surface heat fluxes and cause higher deep‐water temperatures if wind speeds are higher during the summer.
Pro-shareholder income distribution, debt accumulation, and cyclical fluctuations in a post-Keynesian model with labor supply constraints*
Authors: Sasaki Hiroaki , Fujita Shinya
Published: April 2014

In modern capitalist economies, income distribution has a tendency to be in favor of shareholders. This paper interprets pro-shareholder distribution as a decrease in the retention ratio of firms and an increase in the profit share. We introduce labor supply constraints into a post-Keynesian growth model with debt accumulation and investigate the effects of changes in the natural rate of growth, retention ratio, profit share, and interest rate on the rate of capacity utilization and the financial structure of firms. We further analyse the stability of the steady-state equilibrium and the transitional dynamics toward the equilibrium and show that, depending on conditions, there could be cyclical fluctuations such that the financial structure changes periodically between speculative finance and Ponzi finance.
A theory of aggregate consumption*
Authors: Kim Yun K. , Setterfield Mark , Mei Yuan
Published: April 2014

We develop a Keynesian model of aggregate consumption. Our theory emphasizes the importance of the relative income hypothesis and debt finance for understanding household consumption behavior. It is shown that particular importance attaches to how net debtor households service their debts, and that the treatment of debt-servicing commitments as a substitute for savings by these households creates the potential for ‘sudden stops’ in consumption spending (and hence aggregate demand).
Simultaneous aerosol measurements of unusual aerosol enhancement in the troposphere over Syowa Station, Antarctica
Authors: Hara K. , Hayashi M. , Yabuki M. , Shiobara M. , Nishita-Hara C.
Published: April 2014

Abstract. Unusual aerosol enhancement is often observed at Syowa Station, Antarctica, during winter and spring. Simultaneous aerosol measurements near the surface and in the upper atmosphere were conducted twice using a ground-based optical particle counter, a balloon-borne optical particle counter, and micropulse lidar (MPL) in August and September 2012. During 13–15 August, aerosol enhancement occurred immediately after a storm condition. A high backscatter ratio and high aerosol concentrations were observed from the surface to ca. 2.5 km over Syowa Station. Clouds appeared occasionally at the top of the aerosol-enhanced layer during the episode. Aerosol enhancement was terminated on 15 August by strong winds from a cyclone's approach. In the second case, on 5–7 September, aerosol number concentrations in Dp > 0.3 μm near the surface reached > 104 L−1 at about 15:00 UT (Universal Time) on 5 September despite calm wind conditions, whereas MPL measurement exhibited aerosols were enhanced at about 04:00 UT at 1000–1500 m above Syowa Station. The aerosol enhancement occurred near the surface to ca. 4 km. In both cases, air masses with high aerosol enhancement below 2.5–3 km were transported mostly from the boundary layer over the sea-ice area. In addition, air masses at 3–4 km in the second case came from the boundary layer over the open-sea area. This air mass history strongly suggests that dispersion of sea-salt particles from the sea-ice surface contributes considerably to aerosol enhancement in the lower free troposphere (about 3 km) and that the release of sea-salt particles from the ocean surface engenders high aerosol concentrations in the free troposphere (3–4 km). Continuous MPL measurements indicate that high aerosol enhancement occurred mostly in surface–lower free troposphere (3 km) during the period July–September.
Net ecosystem CO2 exchange measurements by the closed chamber method and the eddy covariance technique and their dependence on atmospheric conditions
Authors: Riederer M. , Serafimovich A. , Foken T.
Published: April 2014

Abstract. Carbon dioxide flux measurements in ecosystem sciences are mostly conducted by eddy covariance technique or the closed chamber method. But there is a lack of detailed comparisons that assess present differences and uncertainties. To determine underlying processes, a 10-day, side-by-side measurement of the net ecosystem exchange with both techniques was evaluated with regard to various atmospheric conditions during the diurnal cycle. It was found that, depending on the particular atmospheric condition, the chamber carbon dioxide flux was either (i) equal to the carbon dioxide flux measured by the reference method eddy covariance, by day with well-developed atmospheric turbulence; (ii) higher, in the afternoon in times of oasis effect; (iii) lower, predominantly at night while large coherent structure fluxes or high wind velocities prevailed; or (iv) showed less variation in the flux pattern, at night while stable stratification was present. At night – when respiration forms the net ecosystem exchange – lower chamber carbon dioxide fluxes were found. In the afternoon – when the ecosystem is still a net carbon sink – the carbon dioxide fluxes measured by the chamber prevailed. These two complementary aspects resulted in an overestimation of the ecosystem sink capacity by the chamber of 40% in this study.
Quantitative infrared absorption cross-sections of isoprene for atmospheric measurements
Authors: Brauer C. S. , Blake T. A. , Guenther A. B. , Sams R. L. , Johnson T. J.
Published: April 2014

Abstract. Isoprene (C5H8, 2-methyl-1,3-butadiene) is a volatile organic compound (VOC) that is one of the primary contributors to annual global VOC emissions. Produced by vegetation as well as anthropogenic sources, the OH- and O3-initiated oxidations of isoprene are a major source of atmospheric oxygenated organics. Few quantitative infrared studies have been reported for isoprene, however, limiting the ability to quantify isoprene emissions via stand-off infrared or in situ detection. We thus report absorption coefficients and integrated band intensities for isoprene in the 600–6500 cm−1 region. The pressure-broadened (1 atmosphere N2) spectra were recorded at 278, 298 and 323 K in a 19.94 cm path length cell at 0.112 cm−1 resolution, using a Bruker 66v FTIR. Composite spectra are derived from a minimum of seven isoprene sample pressures at each temperature and the number densities are normalized to 296 K and 1 atmosphere.
Re-construction of global solar radiation time series from 1933 to 2013 at the Izaña Atmospheric Observatory
Authors: García R. D. , Cuevas E. , García O. E. , Cachorro V. E. , Pallé P. , Bustos J. J. , Romero-Campos P. M. , de Frutos A. M.
Published: April 2014

Abstract. This paper presents the re-construction of the 80 year time series of daily global shortwave downward radiation (SDR) at the subtropical high-mountain Izaña Atmospheric Observatory (IZO, Spain). For this purpose, we combine SDR estimates from sunshine duration (SD) data using the Ångström–Prescott method over the 1933/1991 period, and SDR observations directly performed by pyranometers between 1992 and 2013. Since SDR measurements have been used as a reference, a strict quality control has been applied, when it was not possible data have been re-calibrated by using the LibRadtran model. By comparing to high quality SDR measurements, the precision and consistency over time of SDR estimations from SD data have successfully been documented. We obtain a overall root mean square error (RMSE) of 9.2% and an agreement between the variances of SDR estimations and SDR measurements within 92% (correlation coefficient of 0.96). Nonetheless, this agreement significantly increases when the SDR estimation is done considering different daily fractions of clear sky (FCS). In that case, RMSE is reduced by half, up to about 4.5%, when considering percentages of FCS > 40% (90% of days in the testing period). Furthermore, we prove that the SDR estimations can monitor the SDR anomalies in consistency with SDR measurements and, then, can be suitable for re-constructing solar radiation time series. The re-constructed IZO global SDR time series between 1933 and 2013 confirms discontinuities and periods of increases/decreases of solar radiation at Earth's surface observed at a global scale, such as the early brightening, dimming and brightening. This fact supports the consistency of the IZO SDR time series presented in this work, which may be a reference for solar radiation studies in the subtropical North Atlantic region.
Excitation of planetary electromagnetic waves in the inhomogeneous ionosphere
Authors: Rapoport Yu. , Selivanov Yu. , Ivchenko V. , Grimalsky V. , Tkachenko E. , Rozhnoi A. , Fedun V.
Published: April 2014

Abstract. In this paper we develop a new method for the analysis of excitation and propagation of planetary electromagnetic waves (PEMW) in the ionosphere of the Earth. The nonlinear system of equations for PEMW, valid for any height, from D to F regions, including intermediate altitudes between D and E and between E and F regions, is derived. In particular, we have found the system of nonlinear one-fluid MHD equations in the β-plane approximation valid for the ionospheric F region (Aburjania et al., 2003a, 2005). The series expansion in a "small" (relative to the local geomagnetic field) non-stationary magnetic field has been applied only at the last step of the derivation of the equations. The small mechanical vertical displacement of the media is taken into account. We have shown that obtained equations can be reduced to the well-known system with Larichev–Reznik vortex solution in the equatorial region (see e.g. Aburjania et al., 2002). The excitation of planetary electromagnetic waves by different initial perturbations has been investigated numerically. Some means for the PEMW detection and data processing are discussed.
Changes in soil organic carbon storage predicted by Earth system models during the 21st century
Authors: Todd-Brown K. E. O. , Randerson J. T. , Hopkins F. , Arora V. , Hajima T. , Jones C. , Shevliakova E. , Tjiputra J. , Volodin E. , Wu T. , Zhang Q. , Allison S. D.
Published: April 2014

Abstract. Soil is currently thought to be a sink for carbon; however, the response of this sink to increasing levels of atmospheric carbon dioxide and climate change is uncertain. In this study, we analyzed soil organic carbon (SOC) changes from 11 Earth system models (ESMs) contributing simulations to the Coupled Model Intercomparison Project Phase 5 (CMIP5). We used a reduced complexity model based on temperature and moisture sensitivities to analyze the drivers of SOC change for the historical and high radiative forcing (RCP 8.5) scenarios between 1850 and 2100. ESM estimates of SOC changed over the 21st century (2090–2099 minus 1997–2006) ranging from a loss of 72 Pg C to a gain of 253 Pg C with a multi-model mean gain of 65 Pg C. Many ESMs simulated large changes in high-latitude SOC that ranged from losses of 37 Pg C to gains of 146 Pg C with a multi-model mean gain of 39 Pg C across tundra and boreal biomes. All ESMs showed cumulative increases in global NPP (11 to 59%) and decreases in SOC turnover times (15 to 28%) over the 21st century. Most of the model-to-model variation in SOC change was explained by initial SOC stocks combined with the relative changes in soil inputs and decomposition rates (R2 = 0.89, p < 0.01). Between models, increases in decomposition rate were well explained by a combination of initial decomposition rate, ESM-specific Q10-factors, and changes in soil temperature (R2 = 0.80, p < 0.01). All SOC changes depended on sustained increases in NPP with global change (primarily driven by increasing CO2). Many ESMs simulated large accumulations of SOC in high-latitude biomes that are not consistent with empirical studies. Most ESMs poorly represented permafrost dynamics and omitted potential constraints on SOC storage, such as priming effects, nutrient availability, mineral surface stabilization, and aggregate formation. Future models that represent these constraints are likely to estimate smaller increases in SOC storage over the 21st century.
Constraint of soil moisture on CO2 efflux from tundra lichen, moss, and tussock in Council, Alaska using a hierarchical Bayesian model
Authors: Kim Y. , Nishina K. , Chae N. , Park S. , Yoon Y. , Lee B.
Published: April 2014

Abstract. The tundra ecosystem is quite vulnerable to drastic climate change in the Arctic, and the quantification of carbon dynamics is of significant importance in response to thawing permafrost, changes in the snow-covered period and snow and shrub community extent, and the decline of sea ice in the Arctic. Here, CO2 efflux measurements using a manual chamber system within a 40 m × 40 m (5 m interval; 81 total points) plot were conducted in dominant tundra vegetation on the Seward Peninsula of Alaska, during the growing seasons of 2011 and 2012, for the assessment of the driving parameters of CO2 efflux. We applied a hierarchical Bayesian (HB) model – which is a function of soil temperature, soil moisture, vegetation type and thaw depth – to quantify the effect of environmental parameters on CO2 efflux, and to estimate growing season CO2 emission. Our results showed that average CO2 efflux in 2011 is 1.4-fold higher than in 2012, resulting from the distinct difference in soil moisture between the two years. Tussock-dominated CO2 efflux is 1.4 to 2.3 times higher than those measured in lichen and moss communities, reflecting tussock as a significant CO2 source in the Arctic, with wide area distribution on a circumpolar scale. CO2 efflux followed soil temperature nearly exponentially from both the observed data and the posterior medians of the HB model. This reveals soil temperature as the most important parameter in regulating CO2 efflux, rather than soil moisture and thaw depth. Obvious changes in soil moisture during the growing seasons of 2011 and 2012 resulted in an explicit difference in CO2 efflux – 742 and 539 g CO2 m−2 period−1 in 2011 and 2012, respectively, suggesting that the 2012 CO2 emission rate was constrained by 27% (95% credible interval: 17–36%) compared to 2011, due to higher soil moisture from severe rain. Estimated growing season CO2 emission rate ranged from 0.86 Mg CO2 period−1 in 2012 to 1.2 Mg CO2 period−1 in 2011 within a 40 m × 40 m plot, corresponding to 86% and 80% of the annual CO2 emission rates within the Alaska western tundra ecosystem. Therefore, the HB model can be readily applied to observed CO2 efflux, as it demands only four environmental parameters and can also be effective for quantitatively assessing the driving parameters of CO2 efflux.
A probabilistic model of chronological errors in layer-counted climate proxies: applications to annually banded coral archives
Authors: Comboul M. , Emile-Geay J. , Evans M. N. , Mirnateghi N. , Cobb K. M. , Thompson D. M.
Published: April 2014

Abstract. The ability to precisely date climate proxies is central to the reconstruction of past climate variations. To a degree, all climate proxies are affected by age uncertainties, which are seldom quantified. This article proposes a probabilistic age model for proxies based on layer-counted chronologies, and explores its use for annually banded coral archives. The model considers both missing and doubly counted growth increments (represented as independent processes), accommodates various assumptions about error rates, and allows one to quantify the impact of chronological uncertainties on different diagnostics of variability. In the case of a single coral record, we find that time uncertainties primarily affect high-frequency signals but also significantly bias the estimate of decadal signals. We further explore tuning to an independent, tree-ring-based chronology as a way to identify an optimal age model. A synthetic pseudocoral network is used as testing ground to quantify uncertainties in the estimation of spatiotemporal patterns of variability. Even for small error rates, the amplitude of multidecadal variability is systematically overestimated at the expense of interannual variability (El Niño–Southern Oscillation, or ENSO, in this case), artificially flattening its spectrum at periods longer than 10 years. An optimization approach to correct chronological errors in coherent multivariate records is presented and validated in idealized cases, though it is found difficult to apply in practice due to the large number of solutions. We close with a discussion of possible extensions of this model and connections to existing strategies for modeling age uncertainties.
Modeling the elastic transmission of tidal stresses to great distances inland in channelized ice streams
Authors: Thompson J. , Simons M. , Tsai V. C.
Published: April 2014

Abstract. Geodetic surveys suggest that ocean tides can modulate the motion of Antarctic ice streams. Data from Whillans Ice Plain, Rutford Ice Stream, and other Antarctic ice streams show periodicity in flow velocity at periods similar to those of ocean tides at geodetic stations many tens of kilometers inland from the grounding line. These data suggest that ocean tidal stresses can perturb ice stream motion at distances about an order of magnitude farther inland than tidal flexure of the ice stream alone. Recent models exploring the role of tidal perturbations in basal shear stress are primarily two-dimensional, with the impact of the ice stream margins either ignored or parameterized. Here, we use two- and three-dimensional finite element modeling to investigate transmission of tidal stresses in ice streams and the impact of considering more realistic, three-dimensional ice stream geometries. Using Rutford Ice Stream as a real-world comparison, we demonstrate that the assumption that elastic tidal stresses in ice streams propagate large distances inland fails for channelized glaciers due to an intrinsic, exponential decay in the stress due to resistance at the ice stream margins. This behavior is independent of basal conditions beneath the ice stream and cannot be fit to observations using either elastic or nonlinear viscoelastic rheologies without nearly complete decoupling of the ice stream from its lateral margins. Our results suggest that a mechanism external to the ice stream is necessary to explain the tidal modulation of stresses far upstream of the grounding line for narrow ice streams. We propose a hydrologic model based on time-dependent variability in till strength to explain transmission of tidal stresses inland of the grounding line. This conceptual model reproduces observations from Rutford Ice Stream.
Introduction
Authors: Fifth Forbes
Published: April 2014

Introduction
Cover Art: Sticky Pixels
Authors: Betts Julia
Published: April 2014

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Beehive
Authors: Lopez Ignacio
Published: April 2014

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Deep Blue Sea
Authors: Mooney Katherine
Published: April 2014

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A Sycamore Sings
Authors: Keleher Kate
Published: April 2014

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References
Authors: Fifth Forbes
Published: April 2014

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