bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of hyperthyroidism on expression of vascular endothelial growth factor (VEGF) and apoptosis in fetal adrenal glands
Authors: Karaca T. , Hulya Uz Y. , Karabacak R. , Karaboga I. , Demirtas S. , Cagatay Cicek A.
Published: December 2015

This study investigated the expression of vascular endothelial growth factor (VEGF), vascular density, and apoptosis in fetal rat adrenal glands with hyperthyroidism in late gestation. Twelve mature female Wistar albino rats with the same biological and physiological features were used for this study. Rats were divided into two groups: control and hyperthyroidism. Hyperthyroidism was induced by daily subcutaneous injections of L-thyroxine (250 Î¼g/kg) before pregnancy for 21 days and during pregnancy. Rats in the control and hyperthyroidism groups were caged according to the number of male rats. Zero day of pregnancy (Day 0) was indicated when the animals were observed to have microscopic sperm in vaginal smears. Pregnant rats were sacrificed on the 20th day of pregnancy; blood from each animal was collected to determine the concentrations of maternal adrenocorticotropic hormone and thyroxine. Rat fetuses were then quickly removed from the uterus, and the adrenal glands of the fetuses were dissected. VEGF expression, vascular density, and apoptosis were analyzed in fetal rat adrenal glands. Maternal serum levels of the adrenocorticotropic hormone and free thyroxine were significantly higher in the hyperthyroidism group than in the control group. Immunohistochemistry revealed that the number of VEGF positive cells and vessel density significantly increased in the hyperthyroidism rat fetal adrenal group compared with the control group. Hyperthyroidism did not change the fetal and placental weights and the number of fetuses. This study demonstrates that hyperthyroidism may have an effect on the development of rat adrenal glands mediated by VEGF expression, angiogenesis, and apoptosis.Â
New light in flavin autofluorescence
Authors: Croce A.C. , Bottiroli G.
Published: December 2015

Our attention was captured by the interesting debate on the identification of lipofuscins, lipofuscin-like lipopigments, or flavins as the responsible for intracellular autofluorescence (AF) detected in epithelial cancer stem cells when exciting at 480-490 nm. Evidence was provided leading to ascribe AF emission to flavins accumulating in cytoplasmic structures, bounded to membranes and bearing ATP-dependent ABCG2 transporters. Flavins were then proposed as an intrinsic AF biomarker of cancer stem cells, with advantageous implications on cell invasiveness and chemoresistance investigations. It is however worth recalling the huge amount of literature on flavins and NAD(P)H as AF biomarkers of cell energetic metabolism and redox state, an aspect that should not be overlooked in the renewed course to extend the potential of flavins as AF biomarkers, entailing also a recent proposal of Flavin-based fluorescent proteins as substitutes of Green fluorescent proteins.
Dirhinus giffardii (Hymenoptera: Chalcididae), parasitoid affecting Black Soldier Fly production systems in West Africa
Authors: Devic Emilie , Maquart Pierre-Olivier
Published: December 2015

Interest for insect farming is currently growing globally. Conditions in West Africa appear suitable for developing such farming systems that can benefit communities by improving livelihoods, food and feed security or sanitation. In Ghana and Mali, the Black Soldier Fly (Hermetia illucens Linnaeus, 1758) is being produced for waste recycling and animal feed. In a two stages process (egg and larvae production), egg production was hampered by a pupal parasitoid, Dirhinus giffardii Silvestri, 1913 (Hymenoptera: Chalcididae), which reduced future broodstock by almost 72%. This is the first time D. giffardii is reported as a parasitoid of H. illucens pupae and one of the first reports of parasitism in this commercially important fly species. The introduction of precautionary measures is highly recommended for the success of H. illucens production systems in West Africa.
Gallbladder mucocoele: A review
Authors: Smalle Tesh M. , Cahalane Alane K. , Köster Liza S.
Published: December 2015

Gallbladder mucocoele (GBM) is an abnormal, intraluminal accumulation of inspissated bile and/or mucous within the gallbladder. Older, small- to medium-breed dogs seem to be predisposed, but no sex predilection has been identified. Clinical signs are often non-specific and include vomiting, lethargy, anorexia, abdominal pain, icterus and polyuria–polydipsia. Results of a complete blood count may be unremarkable, but serum biochemistry usually reveals increased liver enzymes. The ultrasonographic appearance is diagnostic and well described in the literature. Surgical intervention for the treatment of GBM remains the therapeutic gold standard, with short- and long-term survival for biliary surgery being 66%. The worst outcome is seen in those dogs requiring cholecystoenterostomy. With GBM becoming an apparently increasingly common cause of extrahepatic biliary disease in canines, it is essential that clinicians become familiar with the current literature pertaining to this condition. Numerous predisposing factors are highlighted in this review article and the role of certain endocrinopathies (e.g. hyperadrenocorticism and hypothyroidism) in the development of GBM is touched upon. Furthermore, the aetiopathogenesis of this disease is discussed with reference to the latest literature. Cholecystectomy remains the treatment of choice, but other options are considered based on a current literature review.
Intestinal helminth infections amongst HIV-infected adults in Mthatha General Hospital, South Africa
Authors: Adeleke Olukayode A. , Yogeswaran Parimalaranie , Wright Graham
Published: December 2015

Background: In South Africa, studies on the prevalence of intestinal helminth co-infection amongst HIV-infected patients as well as possible interactions between these two infection sare limited.Aim: To investigate the prevalence of intestinal helminth infestation amongst adults living with HIV or AIDS at Mthatha General Hospital.Setting: Study participants were recruited at the outpatient department of Mthatha General Hospital, Mthatha, South Africa.Methods: This cross-sectional study was conducted between October and December 2013 amongst consecutive consenting HIV-positive adult patients. Socio-demographic and clinical information were obtained using data collection forms and structured interviews. Stool samples were collected to investigate the presence of helminths whilst blood samples were obtained for the measurement of CD4+ T-cell count and viral load.Results: Data were obtained on 231 participants, with a mean age of 34.9 years, a mean CD4 count of 348 cells/μL and a mean viral load of 4.8 log10 copies/mL. Intestinal helminth prevalence was 24.7%, with Ascaris Lumbricoides (42.1%) the most prevalent identified species. Statistically significant association was found between CD4 count of less than 200 cells/ μLand helminth infection (p = 0.05). No statistically significant association was found between intestinal helminth infection and the mean CD4 count (p = 0.79) or the mean viral load (p = 0.98).Conclusion: A high prevalence of intestinal helminth infections was observed amongst the study population. Therefore, screening and treatment of helminths should be considered as part of the management of HIV and AIDS in primary health care.
Trafficking and Functions of Bioactive Sphingolipids: Lessons from Cells and Model Membranes
Authors: Zhou Kecheng , Blom Tomas
Published: December 2015

Ceramide and sphingosine and their phosphorylated counterparts are recognized as “bioactive sphingolipids” and modulate membrane integrity, the activity of enzymes, or act as ligands of G protein-coupled receptors. The subcellular distribution of the bioactive sphingolipids is central to their function as the same lipid can mediate diametrically opposite effects depending on its location. To ensure that these lipids are present in the right amount and in the appropriate organelles, cells employ selective lipid transport and compartmentalize sphingolipid-metabolizing enzymes to characteristic subcellular sites. Our knowledge of key mechanisms involved in sphingolipid signaling and trafficking has increased substantially in the past decades–- thanks to advances in biochemical and cell biological methods. In this review, we focus on the bioactive sphingolipids and discuss how the combination of studies in cells and in model membranes have contributed to our understanding of how they behave and function in living organisms.
The Efficacy of Patients’ Wristband Bar-code on Prevention of Medical Errors
Authors: Khammarnia M. , Kassani A. , Eslahi M.
Published: December 2015

Background: Patient misidentification, as a major patient safety issue, occurs in any healthcare setting and leads to inappropriate medical procedures, diagnosis or treatment, with serious outcomes.

Objectives: The study aimed to investigate the effectiveness of wristband bar-code medication scanning to reduce medical errors (ME).

Methods: A meta-analysis study was conducted. The relevant studies were searched in PubMed, Embase, Cochrane Library, Web of Science and Scopus from 1990 to March 2015. Thereafter, the studies retrieved were screened based on predefined inclusion and exclusion criteria. Data were extracted, and the quality of the included studies was evaluated using the STROBE checklist.

Results: In total, 14 articles involving 483 cases were included. The meta-analysis indicated that the use of wristband bar-code medication scanning can reduce the ME around 57.5% (OR=0.425, 95% CI: 0.28-0.65, P<0.001). The study results showed a marked heterogeneity in the subgroup analysis (I-squared=98%). This was I2=70.35, P-value=0.018 for the type of samples and I2=99%, P-value<0.001 for years and countries.

Conclusion: Wristband bar-code medication scanning can decrease the ME in hospital setting. Since the patient’s safety is the main goal of the World Health Organization, it is recommended that a unique patient identification barcode should be used with name, medical record number, and bar-coded financial number.
Global temperature response to the major volcanic eruptions in multiple reanalysis data sets
Authors: Fujiwara M. , Hibino T. , Mehta S. K. , Gray L. , Mitchell D. , Anstey J.
Published: December 2015

Abstract. The global temperature responses to the eruptions of Mount Agung in 1963, El Chichón in 1982, and Mount Pinatubo in 1991 are investigated using nine currently available reanalysis data sets (JRA-55, MERRA, ERA-Interim, NCEP-CFSR, JRA-25, ERA-40, NCEP-1, NCEP-2, and 20CR). Multiple linear regression is applied to the zonal and monthly mean time series of temperature for two periods, 1979–2009 (for eight reanalysis data sets) and 1958–2001 (for four reanalysis data sets), by considering explanatory factors of seasonal harmonics, linear trends, Quasi-Biennial Oscillation, solar cycle, and El Niño Southern Oscillation. The residuals are used to define the volcanic signals for the three eruptions separately, and common and different responses among the older and newer reanalysis data sets are highlighted for each eruption. In response to the Mount Pinatubo eruption, most reanalysis data sets show strong warming signals (up to 2–3 K for 1-year average) in the tropical lower stratosphere and weak cooling signals (down to −1 K) in the subtropical upper troposphere. For the El Chichón eruption, warming signals in the tropical lower stratosphere are somewhat smaller than those for the Mount Pinatubo eruption. The response to the Mount Agung eruption is asymmetric about the equator with strong warming in the Southern Hemisphere midlatitude upper troposphere to lower stratosphere. Comparison of the results from several different reanalysis data sets confirms the atmospheric temperature response to these major eruptions qualitatively, but also shows quantitative differences even among the most recent reanalysis data sets. The consistencies and differences among different reanalysis data sets provide a measure of the confidence and uncertainty in our current understanding of the volcanic response. The results of this intercomparison study may be useful for validation of climate model responses to volcanic forcing and for assessing proposed geoengineering by stratospheric aerosol injection, as well as to link studies using only a single reanalysis data set to other studies using a different reanalysis data set.
Reactive uptake of ammonia to secondary organic aerosols: kinetics of organonitrogen formation
Authors: Liu Y. , Liggio J. , Staebler R. , Li S.-M.
Published: December 2015

Abstract. As a class of brown carbon, organonitrogen compounds originating from the heterogeneous uptake of NH3 by secondary organic aerosol (SOA) have received significant attention recently. In the current work, particulate organonitrogen formation during the ozonolysis of α-pinene and the OH oxidation of m-xylene in the presence of ammonia (34–125 ppb) was studied in a smog chamber equipped with a high resolution time-of-flight aerosol mass spectrometer and a quantum cascade laser instrument. A large diversity of nitrogen-containing organic (NOC) fragments was observed which were consistent with the reactions between ammonia and carbonyl-containing SOA. Ammonia uptake coefficients onto SOA which led to organonitrogen compounds were reported for the first time, and were in the range of ∼ 10-3–10−2, decreasing significantly to < 10-5 after 6 h of reaction. At the end of experiments (~ 6 h) the NOC mass contributed 8.9 ± 1.7 and 31.5 ± 4.4 wt % to the total α-pinene- and m-xylene-derived SOA, respectively, and 4–15 wt % of the total nitrogen in the system. Uptake coefficients were also found to be positively correlated with particle acidity and negatively correlated with NH3 concentration, indicating that heterogeneous reactions were responsible for the observed NOC mass, possibly limited by liquid phase diffusion. Under these conditions, the data also indicate that the formation of NOC can compete kinetically with inorganic acid neutralization. The formation of NOC in this study suggests that a significant portion of the ambient particle associated N may be derived from NH3 heterogeneous reactions with SOA. NOC from such a mechanism may be an important and unaccounted for source of PM associated nitrogen. This mechanism may also contribute to the medium or long-range transport and wet/dry deposition of atmospheric nitrogen.
Viscosity controls humidity dependence of N2O5 uptake to citric acid aerosol
Authors: Gržinić G. , Bartels-Rausch T. , Berkemeier T. , Türler A. , Ammann M.
Published: December 2015

Abstract. The heterogeneous loss of dinitrogen pentoxide (N2O5) to aerosol particles has a significant impact on the night-time nitrogen oxide cycle and therefore the oxidative capacity in the troposphere. Using a 13N short-lived radioactive tracer method, we studied the uptake kinetics of N2O5 on citric acid aerosol particles as a function of relative humidity (RH). The results show that citric acid exhibits lower reactivity than similar dicarboxylic and polycarboxylic acids, with uptake coefficients between ∼ 3 × 10-4–∼ 3 × 10-3 depending on humidity (17–70 % RH). At RH above 50 %, the magnitude and the humidity dependence can be best explained by the viscosity of citric acid as compared to aqueous solutions of simpler organic and inorganic solutes and the variation of viscosity with RH and, hence, diffusivity in the organic matrix. Since the diffusion rates of N2O5 in highly concentrated citric acid solutions are not well established, we present four different parameterizations of N2O5 diffusivity based on the available literature data or estimates for viscosity and diffusivity of H2O. Above 50 % RH, uptake is consistent with the reacto-diffusive kinetic regime whereas below 50 % RH, the uptake coefficient is higher than expected from hydrolysis of N2O5 within the bulk of the particles, and the uptake kinetics is most likely limited by loss on the surface only. This study demonstrates the impact of viscosity in highly oxidized and highly functionalized secondary organic aerosol material on the heterogeneous chemistry of N2O5 and may explain some of the unexpectedly low loss rates to aerosol derived from field studies.
A wide field-of-view imaging DOAS instrument for two-dimensional trace gas mapping from aircraft
Authors: Schönhardt A. , Altube P. , Gerilowski K. , Krautwurst S. , Hartmann J. , Meier A. C. , Richter A. , Burrows J. P.
Published: December 2015

Abstract. The Airborne imaging differential optical absorption spectroscopy (DOAS) instrument for Measurements of Atmospheric Pollution (AirMAP) has been developed for the purpose of trace gas measurements and pollution mapping. The instrument has been characterized and successfully operated from aircraft. Nitrogen dioxide (NO2) columns were retrieved from the AirMAP observations. A major benefit of the push-broom imaging instrument is the spatially continuous, gap-free measurement sequence independent of flight altitude, a valuable characteristic for mapping purposes. This is made possible by the use of a charge coupled device (CCD) frame-transfer detector. A broad field of view across track of around 48° is achieved with wide-angle entrance optics. This leads to a swath width of about the same size as the flight altitude. The use of fibre coupled light intake optics with sorted light fibres allows flexible instrument positioning within the aircraft and retains the very good imaging capabilities. The measurements yield ground spatial resolutions below 100 m depending on flight altitude. The number of viewing directions is chosen from a maximum of 35 individual viewing directions (lines of sight, LOS) represented by 35 individual fibres. The selection is adapted to each situation by averaging according to signal-to-noise or spatial resolution requirements. Observations at 30 m spatial resolution are obtained when flying at 1000 m altitude and making use of all 35 viewing directions. This makes the instrument a suitable tool for mapping trace gas point sources and small-scale variability. The position and aircraft attitude are taken into account for accurate spatial mapping using the Attitude and Heading Reference System of the aircraft. A first demonstration mission using AirMAP was undertaken in June 2011. AirMAP was operated on the AWI Polar-5 aircraft in the framework of the AIRMETH-2011 campaign. During a flight above a medium-sized coal-fired power plant in north-west Germany, AirMAP clearly detected the emission plume downwind from the exhaust stack, with NO2 vertical columns around 2 × 1016 molecules cm−2 in the plume centre. NOx emissions estimated from the AirMAP observations are consistent with reports in the European Pollutant Release and Transfer Register. Strong spatial gradients and variability in NO2 amounts across and along flight direction are observed, and small-scale enhancements of NO2 above a motorway are detected.
Microphysical particle properties derived from inversion algorithms developed in the framework of EARLINET
Authors: Müller D. , Böckmann C. , Kolgotin A. , Schneidenbach L. , Chemyakin E. , Rosemann J. , Znak P. , Romanov A.
Published: December 2015

Abstract. We present a summary on the current status of two inversion algorithms that are used in EARLINET for the inversion of data collected with EARLINET multiwavelength Raman lidars. These instruments measure backscatter coefficients at 355, 532, and 1064 nm, and extinction coefficients at 355 and 532 nm. Development of these two algorithms started in 2000 when EARLINET was founded. The algorithms are based on manually controlled inversion of optical data which allows for detailed sensitivity studies and thus provides us with comparably high quality of the derived data products. The algorithms allow us to derive particle effective radius, and volume and surface-area concentration with comparably high confidence. The retrieval of the real and imaginary parts of the complex refractive index still is a challenge in view of the accuracy required for these parameters in climate change studies in which light-absorption needs to be known with high accuracy. Single-scattering albedo can be computed from the retrieved microphysical parameters and allows us to categorize aerosols into high and low absorbing aerosols. We discuss the current status of these manually operated algorithms, the potentially achievable accuracy of data products, and the goals for future work on the basis of a few exemplary simulations with synthetic optical data. The optical data used in our study cover a range of Ångström exponents and extinction-to-backscatter (lidar) ratios that are found from lidar measurements of various aerosol types. We also tested aerosol scenarios that are considered highly unlikely, e.g., the lidar ratios fall outside the commonly accepted range of values measured with Raman lidar, even though the underlying microphysical particle properties are not uncommon. The goal of this part of the study is to test robustness of the algorithms toward their ability to identify aerosol types that have not been measured so far, but cannot be ruled out based on our current knowledge of aerosol physics. We computed the optical data from monomodal logarithmic particle size distributions, i.e., we explicitly excluded the more complicated case of bimodal particle size distributions which is a topic of ongoing research work. Another constraint is that we only considered particles of spherical shape in our simulations. We considered particle radii as large as 7–10 μm in our simulations. That particle size does not only cover the size range of particles in the fine-mode fraction of naturally occurring particle size distributions but also covers a considerable part of the coarse-mode fraction of particle size distributions. We considered optical-data errors of 15 % in the simulation studies. We target 50 % uncertainty as a reasonable threshold for our data products, though we attempt to obtain data products with less uncertainty in future work.
Profiling the PM2.5 mass concentration vertical distribution in the boundary layer
Authors: Tao Z. , Wang Z. , Yang S. , Shan H. , Ma X. , Zhang H. , Zhao S. , Liu D. , Xie C. , Wang Y.
Published: December 2015

Abstract. Fine particle (PM2.5) affects human life and activities directly; the detection of PM2.5 mass concentration profile is very essential due to its practical and scientific meanings (such as, quantifying of air quality and its variability, and improving air quality forecast and assessment). But so far, it is difficult to detect PM2.5 mass concentration profile. The proposed methodology to study the relationship between aerosol extinction coefficient and PM2.5 mass concentration is described, which indicates that the PM2.5 mass concentration profile could be retrieved by combining a charge-coupled device (CCD) side-scatter lidar and a PM2.5 sampling detector. When the relative humidity is less than 70 %, PM2.5 mass concentration is proportional to aerosol extinction coefficient, and then the specific coefficient can be calculated. Using this specific coefficient, aerosol extinction profile is converted to PM2.5 mass concentration profile. Three cases of clean night (on 21 September 2014), pollutant night (on 17 March 2014), and heavy pollutant night (on 13 February 2015) are studied. The characteristic of PM2.5 mass concentration profile in near-ground during these three nights' cases in the western suburb of Hefei city was discussed. The PM2.5 air pollutant concentration is comparatively large in close surface varying with time and altitude. The experiment results show that the CCD side-scatter lidar combined with a PM2.5 detector is an effective and new method to explore pollutant mass concentration profile in near-ground.
Particle-size distribution of polybrominated diphenyl ethers (PBDEs) and its implications for health
Authors: Lyu Y. , Xu T. , Li X. , Cheng T. , Yang X. , Sun X. , Chen J.
Published: December 2015

Abstract. In order better to understand the particle-size distribution of particulate PBDEs and their deposition pattern in human respiratory tract, we made an one year campaign 2012–2013 for the measurement of size-resolved aerosol particles at Shanghai urban site. The results showed that particulate PBDEs exhibited a bimodal distribution with a mode peak in the accumulation particle size range and the second mode peak in the coarse particle size ranges. As the number of bromine atoms in the molecule increased, accumulation mode peak intensity increased while coarse mode peak intensity decreased. This change was the consistent with the variation of PBDEs' sub-cooled vapor pressure. Absorption and adsorption process dominated the distribution of PBDEs among the different size particles. Evaluated deposition flux of Σ13PBDE was 26.8 pg h−1, in which coarse particles contributed most PBDEs in head and tracheobronchial regions, while fine mode particles contributed major PBDEs in the alveoli region. In associated with the fact that fine particles can penetrate deeper into the respiratory system, fine particle-bound highly brominated PBDEs can be inhaled more deeply into human lungs and cause a greater risk to human health.
Ocean dynamic processes causing spatially heterogeneous distribution of sedimentary caesium-137 massively released from the Fukushima Daiichi Nuclear Power Plant
Authors: Higashi H. , Morino Y. , Furuichi N. , Ohara T.
Published: December 2015

Abstract. Massive amounts of anthropogenic radiocaesium 137Cs that were released into the environment by the Fukushima Daiichi Nuclear Power Plant accident in March 2011 are widely known to have extensively migrated to Pacific Ocean sediment off of eastern Japan. Several recent reports have stated that the sedimentary 137Cs is now stable with a remarkably heterogeneous distribution. The present study elucidates ocean dynamic processes causing this heterogeneous sedimentary 137Cs distribution in and around the shelf off Fukushima and adjacent prefectures. We performed a numerical simulation of oceanic 137Cs behaviour for about 10 months after the accident, using a comprehensive dynamic model involving advection–diffusion transport in seawater, adsorption and desorption to and from particulate matter, sedimentation and suspension on and from the bottom, and vertical diffusion transport in the sediment. A notable simulated result was that the sedimentary 137Cs significantly accumulated in a swath just offshore of the shelf break (along the 50–100 m isobath) as in recent observations, although the seabed in the entire simulation domain was assumed to have ideal properties such as identical bulk density, uniform porosity, and aggregation of particles with a single grain diameter. This result indicated that the heterogeneous sedimentary 137Cs distribution was not necessarily a result of the spatial distribution of 137Cs sediment adsorptivity. The present simulation suggests that the shape of the swath is mainly associated with spatiotemporal variation between bottom shear stress in the shallow shelf (< 50 m depths) and that offshore of the shelf break. In a large part of the shallow shelf, the simulation indicated that strong bottom friction suspending particulate matter from the seabed frequently occurred via a periodic spring tide about every 2 weeks and via occasional strong wind. The sedimentary 137Cs thereby could hardly stay on the surface of the seabed with the result that the simulated sediment-surface 137Cs activity tended to decrease steadily for a long term after the initial 137Cs migration. By contrast, in the offshore region, neither the spring tide nor the strong wind caused bottom disturbance. Hence, the particulate matter incorporated with 137Cs, which was horizontally transported from the adjacent shallow shelf, readily settled and remained on the surface of the sediment just offshore of the shelf break.
Reviews and syntheses: Effects of permafrost thaw on Arctic aquatic ecosystems
Authors: Vonk J. E. , Tank S. E. , Bowden W. B. , Laurion I. , Vincent W. F. , Alekseychik P. , Amyot M. , Billet M. F. , Canário J. , Cory R. M. , Deshpande B. N. , Helbig M. , Jammet M. , Karlsson J. , Larouche J. , MacMillan G. , Rautio M. , Walter Anthony K. M. , Wickland K. P.
Published: December 2015

Abstract. The Arctic is a water-rich region, with freshwater systems covering about 16 % of the northern permafrost landscape. Permafrost thaw creates new freshwater ecosystems, while at the same time modifying the existing lakes, streams, and rivers that are impacted by thaw. Here, we describe the current state of knowledge regarding how permafrost thaw affects lentic (still) and lotic (moving) systems, exploring the effects of both thermokarst (thawing and collapse of ice-rich permafrost) and deepening of the active layer (the surface soil layer that thaws and refreezes each year). Within thermokarst, we further differentiate between the effects of thermokarst in lowland areas vs. that on hillslopes. For almost all of the processes that we explore, the effects of thaw vary regionally, and between lake and stream systems. Much of this regional variation is caused by differences in ground ice content, topography, soil type, and permafrost coverage. Together, these modifying factors determine (i) the degree to which permafrost thaw manifests as thermokarst, (ii) whether thermokarst leads to slumping or the formation of thermokarst lakes, and (iii) the manner in which constituent delivery to freshwater systems is altered by thaw. Differences in thaw-enabled constituent delivery can be considerable, with these modifying factors determining, for example, the balance between delivery of particulate vs. dissolved constituents, and inorganic vs. organic materials. Changes in the composition of thaw-impacted waters, coupled with changes in lake morphology, can strongly affect the physical and optical properties of thermokarst lakes. The ecology of thaw-impacted lakes and streams is also likely to change; these systems have unique microbiological communities, and show differences in respiration, primary production, and food web structure that are largely driven by differences in sediment, dissolved organic matter, and nutrient delivery. The degree to which thaw enables the delivery of dissolved vs. particulate organic matter, coupled with the composition of that organic matter and the morphology and stratification characteristics of recipient systems will play an important role in determining the balance between the release of organic matter as greenhouse gases (CO2 and CH4), its burial in sediments, and its loss downstream. The magnitude of thaw impacts on northern aquatic ecosystems is increasing, as is the prevalence of thaw-impacted lakes and streams. There is therefore an urgent need to quantify how permafrost thaw is affecting aquatic ecosystems across diverse Arctic landscapes, and the implications of this change for further climate warming.
High-resolution ocean pH dynamics in four subtropical Atlantic benthic habitats
Authors: Hernández C. A. , Clemente S. , Sangil C. , Hernández J. C.
Published: December 2015

Abstract. Oscillations of ocean pH are largely unknown in coastal environments and ocean acidification studies often do not account for natural variability yet most of what is known about marine species and populations is found out via studies conducted in near shore environments. Most experiments designed to make predictions about future climate change scenarios are carried out in coastal environments with no research that takes into account the natural pH variability. In order to fill this knowledge gap and to provide reliable measures of pH oscillation, seawater pH was measured over time using moored pH sensors in four contrasting phytocenoses typical of the north Atlantic subtropical region. Each phytocenosis was characterized by its predominant engineer species: (1) Cystoseira abies-marina, (2) a mix of gelidiales and geniculate corallines, (3) Lobophora variegata, and (4) encrusting corallines. The autonomous pH measuring systems consisted of a pH sensor; a data logger and a battery encased in a waterproof container and allowed the acquisition of high-resolution continuous pH data at each of the study sites. The pH variation observed ranged by between 0.09 and 0.24 pHNBS units. A clear daily variation in seawater pH was detected at all the studied sites (0.04–0.12 pHNBS units). Significant differences in daily pH oscillations were also observed between phytocenoses, which shows that macroalgal communities influence the seawater pH in benthic habitats. Natural oscillations in pH must be taken into account in future ocean acidification studies to put findings in perspective and for any ecological recommendations to be realistic.
The South American Monsoon Variability over the Last Millennium in CMIP5/PMIP3 simulations
Authors: Rojas M. , Arias P. A. , Flores-Aqueveque V. , Seth A. , Vuille M.
Published: December 2015

Abstract. In this paper we assess South American Monsoon System (SAMS) variability throughout the Last Millennium as depicted by the Coupled Modelling Intercomparison Project version 5/Paleo Modelling Intercomparison Project version 3 (CMIP5/PMIP3) simulations. High-resolution proxy records for the South American monsoon over this period show a coherent regional picture of a weak monsoon during the Medieval Climate Anomaly period and a stronger monsoon during the Little Ice Age (LIA). Due to the small forcing during the past 1000 years, CMIP5/PMIP3 model simulations do not show very strong temperature anomalies over these two specific periods, which in turn do not translate into clear precipitation anomalies, as suggested by rainfall reconstructions in South America. However, with an ad-hoc definition of these two periods for each model simulation, several coherent large-scale atmospheric circulation anomalies were identified. The models feature a stronger Monsoon during the LIA associated with: (i) an enhancement of the rising motion in the SAMS domain in austral summer, (ii) a stronger monsoon-related upper-troposphere anticyclone, (iii) activation of the South American dipole, which results to a certain extent in a poleward shift in the South Atlantic Convergence Zone and (iv) a weaker upper-level sub tropical jet over South America, this providing important insights into the mechanisms of these climate anomalies over South America during the past millennium.
Implementation of an optimal stomatal conductance scheme in the Australian Community Climate Earth Systems Simulator (ACCESS1.3b)
Authors: Kala J. , De Kauwe M. G. , Pitman A. J. , Lorenz R. , Medlyn B. E. , Wang Y.-P , Lin Y.-S , Abramowitz G.
Published: December 2015

Abstract. We implement a new stomatal conductance scheme, based on the optimality approach, within the Community Atmosphere Biosphere Land Exchange (CABLEv2.0.1) land surface model. Coupled land–atmosphere simulations are then performed using CABLEv2.0.1 within the Australian Community Climate and Earth Systems Simulator (ACCESSv1.3b) with prescribed sea surface temperatures. As in most land surface models, the default stomatal conductance scheme only accounts for differences in model parameters in relation to the photosynthetic pathway but not in relation to plant functional types. The new scheme allows model parameters to vary by plant functional type, based on a global synthesis of observations of stomatal conductance under different climate regimes over a wide range of species. We show that the new scheme reduces the latent heat flux from the land surface over the boreal forests during the Northern Hemisphere summer by 0.5–1.0 mm day−1. This leads to warmer daily maximum and minimum temperatures by up to 1.0 °C and warmer extreme maximum temperatures by up to 1.5 °C. These changes generally improve the climate model's climatology of warm extremes and improve existing biases by 10–20 %. The bias in minimum temperatures is however degraded but, overall, this is outweighed by the improvement in maximum temperatures as there is a net improvement in the diurnal temperature range in this region. In other regions such as parts of South and North America where ACCESSv1.3b has known large positive biases in both maximum and minimum temperatures (~ 5 to 10 °C), the new scheme degrades this bias by up to 1 °C. We conclude that, although several large biases remain in ACCESSv1.3b for temperature extremes, the improvements in the global climate model over large parts of the boreal forests during the Northern Hemisphere summer which result from the new stomatal scheme, constrained by a global synthesis of experimental data, provide a valuable advance in the long-term development of the ACCESS modelling system.
Adaptive wavelet simulation of global ocean dynamics using a new Brinkman volume penalization
Authors: Kevlahan N. K.-R. , Dubos T. , Aechtner M.
Published: December 2015

Abstract. In order to easily enforce solid-wall boundary conditions in the presence of complex coastlines, we propose a new mass and energy conserving Brinkman penalization for the rotating shallow water equations. This penalization does not lead to higher wave speeds in the solid region. The error estimates for the penalization are derived analytically and verified numerically for linearized one-dimensional equations. The penalization is implemented in a conservative dynamically adaptive wavelet method for the rotating shallow water equations on the sphere with bathymetry and coastline data from NOAA's ETOPO1 database. This code could form the dynamical core for a future global ocean model. The potential of the dynamically adaptive ocean model is illustrated by using it to simulate the 2004 Indonesian tsunami and wind-driven gyres.
Geohydrological hazards and urban development in the Mediterranean area: an example from Genoa (Liguria, Italy)
Authors: Faccini F. , Luino F. , Sacchini A. , Turconi L. , De Graff J. V.
Published: December 2015

Abstract. The metropolitan area and the city of Genoa has become a national and international case study for geohydrological risk, mainly due to the frequency of floods. In 2014, there were landslides again, as well as flash floods that have particularly caused casualties and economic damage. The weather features of the Gulf of Genoa and the geomorphological–environmental setting of the Ligurian coastal land are the predisposing factors that determine heavy rains and their resulting effects on the ground. This study analysed the characteristics of the main meteorological disasters that have hit Genoa since the start of the 20th century; changes in the rainfall regime are evaluated and the main stages of urbanization of the area are detailed, with the resulting changes to the drainage network, in order to identify the main causes of this high geohydrological risk. To this end, scientists have used climate data recorded at the station of Genoa University, in operation since 1833, and at Ponte Carrega station, located in the middle reach of the Bisagno stream, a well-known watercourse because of its frequent floods. Urban sprawl was evaluated through a multi-temporal mapping comparison, using maps available from the beginning of the 19th century up to the current regional technical maps. The average air temperature in Genoa shows a statistically significant increase, while the number of rainy days displays an equally clear decrease over time. The total annual rain value does not seem to indicate rather noticeable changes. The intensity of rain in Genoa expressed as rainfall rate, i.e.~the ratio of annual rainfall and number of rainy days, shows statistically significant growth. The geohydrological vulnerability in Genoa has increased over time due to urban development which has established modifications in land use, from agricultural to urban, especially in the valley floor. Waterways have been confined and reduced to artificial channels, often covered in their final stretch; in some cases they have even been totally removed. These actions should be at least partially reversed in order to reduce the presently high hydrological risk.
Seasonal variability of the Ekman transport and pumping in the upwelling system off central-northern Chile (~ 30° S) based on a high-resolution atmospheric regional model (WRF)
Authors: Bravo L. , Ramos M. , Astudillo O. , Dewitte B. , Goubanova K.
Published: December 2015

Abstract. Two physical mechanisms can contribute to coastal upwelling, offshore Ekman transport and Ekman pumping due to the cyclonic wind stress curl, mainly caused by the abrupt decrease in wind stress (drop-off) in a cross-shore band of 100 km. This wind drop-off is thought to be an ubiquitous feature in coastal upwelling systems and to regulate the relative contribution of both mechanisms. It has been poorly studied along the central-northern Chile region because of the lack in wind measurements along the shoreline and of the relatively low-resolution of the available atmospheric Reanalysis. Here, the seasonal variability in Ekman transport, Ekman pumping and their relative contribution to total upwelling along the central-northern Chile region (~ 30° S) is evaluated from a high-resolution atmospheric model simulation. As a first step, the simulation is validated from satellite observations, which indicates a proper representation of the spatial and temporal variability of the wind along the coast by the model. The model outputs are then used to document the fine scale structures in the wind stress and wind curl in relation with the topographic features along the coast (headlands and embayments). Both wind stress and wind curl had a clear seasonal variability with a marked semiannual component. Alongshore wind stress maximum peak occurred in spring, second increase was in fall and minimum in winter. When a threshold of −3 x 10−5 s−1 for the across-shore wind curl was considered to define the region from which the winds decrease on-shoreward, the wind drop-off length scale varied between 8 and 45 km. The relative contribution of Ekman transport and Ekman pumping to the vertical transport along the coast, considering the estimated wind drop-off length, indicated meridional alternation between both mechanisms, modulated by orography and the intricate coastline. Roughly, coastal divergence predominated in areas with low orography and headlands. Ekman pumping was higher in regions with high orography and the presence of embayments along the coast. In the study region, the vertical transport induced by coastal divergence and Ekman pumping represented 60 and 40 % of the total upwelling transport, respectively. The potential role of Ekman pumping on the spatial structure of sea surface temperature is also discussed.
Soil indicators to assess the effectiveness of restoration strategies in dryland ecosystems
Authors: Costantini E. A. C. , Branquinho C. , Nunes A. , Schwilch G. , Stavi I. , Valdecantos A. , Zucca C.
Published: December 2015

Abstract. Soil indicators may be used for assessing both land suitability for restoration and the effectiveness of restoration strategies in restoring ecosystem functioning and services. In this review paper, several soil indicators, which can be used to assess the effectiveness of restoration strategies in dryland ecosystems at different spatial and temporal scales, are discussed. The selected indicators represent the different viewpoints of pedology, ecology, hydrology, and land management. The recovery of soil capacity to provide ecosystem services is primarily obtained by increasing soil rooting depth and volume, and augmenting water accessibility for vegetation. Soil characteristics can be used either as indicators of suitability, that is, inherently slow-changing soil qualities, or as indicators for modifications, namely dynamic, thus "manageable" soil qualities. Soil organic matter forms, as well as biochemistry, micro- and meso-biology, are among the most utilized dynamic indicators. On broader territorial scales, the Landscape Function Analysis uses a functional approach, where the effectiveness of restoration strategies is assessed by combining the analysis of spatial pattern of vegetation with qualitative soil indicators. For more holistic and comprehensive projects, effective strategies to combat desertification should integrate soil indicators with biophysical and socio-economic evaluation and include participatory approaches. The integrated assessment protocol of Sustainable Land Management developed by the World Overview of Conservation Approaches and Technologies network is thoroughly discussed. Two overall outcomes stem from the review: (i) the success of restoration projects relies on a proper understanding of their ecology, namely the relationships between soil, plants, hydrology, climate, and land management at different scales, which is particularly complex due to the heterogeneous pattern of ecosystems functioning in drylands, and (ii) the selection of the most suitable soil indicators follows a clear identification of the different and sometimes competing ecosystem services that the project is aimed at restoring.
Studying local earthquakes in the northern Fennoscandian Shield using the data of the POLENET/LAPNET temporary array
Authors: Usoltseva O. A. , Kozlovskaya E. G.
Published: December 2015

Abstract. Earthquakes within areas inside continental plates are still not completely understood and the progress in understanding intraplate seismicity is slow due to short history of instrumental seismology and sparse regional seismic networks in seismically non-active areas. However, knowledge about position and depth of seismogenic structures in such areas is necessary, in order to estimate seismic hazard for such critical facilities as nuclear power plants and nuclear waste deposits. In the present paper we address the problem of seismicity in the intraplate area of northern Fennoscandia using the information on local events recorded by the POLENET/LAPNET temporary seismic array during the International Polar Year 2007–2009. We relocate the seismic events by the program HYPOELLIPS and grid search method. We use the first arrivals of P-waves of local events in order to calculate a 3-D tomographic P-wave velocity model of the uppermost crust (down to 20 km) for selected region inside the study area and show that the velocity heterogeneities in the upper crust correlate well with known tectonic units. We compare position of the velocity heterogeneities with the seismogenic structures delineated by epicentres of relocated events and demonstrate that these structures generally do not correlate with the crustal units formed as a result of crustal evolution in Archean and Paleoproterozoic. On the contrary, they correlate well with the post-glacial faults located in the area of the Baltic–Bothnia Megashear (BBMS). Hypocentres of local events have depths down to 30 km. We also obtain focal mechanisms of two selected events with good data quality. Both focal mechanisms are of strike-slip type in which shift prevails over uplift. Our results demonstrate that Baltic–Bothnia Megashear is an important large-scale, reactivated tectonic structure that has to be taken into account in estimating seismic hazard in northern Fennoscandia.