bluuebunny/crossref_metadata_2025 huggingface dataset:
Exploring the variability of aerosol particle composition in the Arctic: a study from the springtime ACCACIA campaign
Authors: Young G. , Jones H. M. , Darbyshire E. , Baustian K. J. , McQuaid J. B. , Bower K. N. , Connolly P. J. , Gallagher M. W. , Choularton T. W.
Published: October 2015

Abstract. Single-particle compositional analysis of filter samples collected on-board the FAAM BAe-146 aircraft is presented for six flights during the springtime Aerosol-Cloud Coupling and Climate Interactions in the Arctic (ACCACIA) campaign (March–April 2013). Scanning electron microscopy was utilised to derive size distributions and size-segregated particle compositions. These data were compared to corresponding data from wing-mounted optical particle counters and reasonable agreement between the calculated number size distributions was found. Significant variability in composition was observed, with differing external and internal mixing identified, between air mass trajectory cases based on HYSPLIT analyses. Dominant particle classes were silicate-based dusts and sea salts, with particles notably rich in K and Ca detected in one case. Source regions varied from the Arctic Ocean and Greenland through to northern Russia and the European continent. Good agreement between the back trajectories was mirrored by comparable compositional trends between samples. Silicate dusts were identified in all cases, and the elemental composition of the dust was consistent for all samples except one. It is hypothesised that long-range, high-altitude transport was primarily responsible for this dust, with likely sources including the Asian arid regions.
Particle water and pH in the Eastern Mediterranean: sources variability and implications for nutrients availability
Authors: Nikolaou P. , Bougiatioti A. , Stavroulas I. , Kouvarakis G. , Nenes A. , Weber R. , Kanakidou M. , Mihalopoulos N.
Published: October 2015

Abstract. Particle water (LWC) and aerosol pH drive the aerosol phase, heterogeneous chemistry and bioavailability of nutrients that profoundly impact cloud formation, atmospheric composition and atmospheric fluxes of nutrients to ecosystems. Few measurements of in-situ LWC and pH however exist in the published literature. Using concurrent measurements of aerosol chemical composition, cloud condensation nuclei activity and tandem light scattering coefficients, the particle water mass concentrations associated with the aerosol inorganic (Winorg) and organic (Worg) components are determined for measurements conducted at the Finokalia atmospheric observation station in the eastern Mediterranean between August and November 2012. These data are interpreted using the ISORROPIA-II thermodynamic model to predict pH of aerosols originating from the various sources that influence air quality in the region. On average, closure between predicted aerosol water and that determined by comparison of ambient with dry light scattering coefficients was achieved to within 8 % (slope = 0.92, R2 = 0.8, n = 5201 points). Based on the scattering measurements a parameterization is also derived, capable of reproducing the hygroscopic growth factor (f(RH)) within 15 % of the measured values. The highest aerosol water concentrations are observed during nighttime, when relative humidity is highest and the collapse of the boundary layer increases the aerosol concentration. A significant diurnal variability is found for Worg with morning and afternoon average mass concentrations being 10–15 times lower than nighttime concentrations, thus rendering Winorg the main form of particle water during daytime. The average value of total aerosol water was 2.19 ± 1.75 μg m−3, contributing on average up to 33 % of the total submicron mass concentration. Average aerosol water associated with organics, Worg, was equal to 0.56 ± 0.37 μg m−3, thus organics contributed about 27.5 % to the total aerosol water, mostly during early morning, late evening and nighttime hours. The aerosol was found to be highly acidic with calculated aerosol pH varying from 0.5 to 2.8 throughout the study period. Biomass burning aerosol presented the highest values of pH in the submicron fraction and the lowest values in total water mass concentration. The low pH values observed in the submicron mode and independently of air masses origin could increase nutrient availability and especially P solubility, which is the nutrient limiting sea water productivity of the eastern Mediterranean.
Global stratospheric measurements of the isotopologues of methane from the Atmospheric Chemistry Experiment Fourier Transform Spectrometer
Authors: Buzan E. M. , Beale C. A. , Boone C. D. , Bernath P. F.
Published: October 2015

Abstract. This paper presents an analysis of observations of methane and its two major isotopologues, CH3D and 13CH4 from the Atmospheric Chemistry Experiment (ACE) satellite between 2004 and 2013. Additionally, atmospheric methane chemistry is modeled using the Whole Atmospheric Community Climate Model (WACCM). ACE retrievals of methane extend from 6 km for all isotopologues to 75 km for 12CH4, 35 km for CH3D, and 50 km for 13CH4. While total methane concentrations retrieved from ACE agree well with the model, values of δD–CH4 and δ13C–CH4 show a bias toward higher δ compared to the model and balloon-based measurements. Calibrating δD and δ13C from ACE using WACCM in the troposphere gives improved agreement in δD in the stratosphere with the balloon measurements, but values of δ13C still disagree. A model analysis of methane's atmospheric sinks is also performed.
A spatial Bayesian network model to assess the benefits of early warning for urban flood risk to people
Authors: Balbi S. , Villa F. , Mojtahed V. , Hegetschweiler K. T. , Giupponi C.
Published: October 2015

Abstract. This article presents a novel methodology to assess flood risk to people by integrating people's vulnerability and ability to cushion hazards through coping and adapting. The proposed approach extends traditional risk assessments beyond material damages; complements quantitative and semi-quantitative data with subjective and local knowledge, improving the use of commonly available information; produces estimates of model uncertainty by providing probability distributions for all of its outputs. Flood risk to people is modeled using a spatially explicit Bayesian network model calibrated on expert opinion. Risk is assessed in terms of: (1) likelihood of non-fatal physical injury; (2) likelihood of post-traumatic stress disorder; (3) likelihood of death. The study area covers the lower part of the Sihl valley (Switzerland) including the city of Zurich. The model is used to estimate the benefits of improving an existing Early Warning System, taking into account the reliability, lead-time and scope (i.e. coverage of people reached by the warning). Model results indicate that the potential benefits of an improved early warning in terms of avoided human impacts are particularly relevant in case of a major flood event: about 75 % of fatalities, 25 % of injuries and 18 % of post-traumatic stress disorders could be avoided.
Estados Unidos y la guerra por el desarrollo: el control de la natalidad en Chile, 1960-1970
Authors: Castro Arcos Javier
Published: October 2015

Bajo el paradigma de modernización y desarrollo norteamericano -y en un contexto de Guerra Fría-, durante la década de 1960 se adecuaron a la realidad chilena programas de control de natalidad que no sólo buscaron disminuir las altas tasas de mortalidad materno infantil, sino que además respondieron al proyecto de seguridad hemisférica norteamericana de contención a posibles revoluciones populares en países del Tercer Mundo.
El Congreso por la Libertad de la Cultura y su apoyo a la disidencia intelectual durante el franquismo
Authors: Glondys Olga
Published: October 2015

El artículo reconstruye los principales aspectos de la labor del Congreso por la Libertad de la Cultura entre la oposición antifranquista del interior. Se describen las circunstancias políticas que motivaron la fundación del Comité Español (1959-1977), así como las principales características de esa célula intelectual antifranquista. El artículo indaga en los objetivos ideológicos y políticos de la actividad del Congreso por la Libertad de la Cultura entre las elites intelectuales y culturales disidentes durante el tardofranquismo. Nos concentramos especialmente en el capítulo que atañe a la ayuda directa dispensada por el Congreso por la Libertad de la Cultura a los intelectuales y artistas españoles mediante la concesión de becas de libros y bolsas de viaje a través del Comité d’Ecrivains et d’Editeurs pour une Entraide Européenne. Reconstruimos asimismo los nombres de los principales beneficiarios españoles de esas ayudas, así como la principal problemática vinculada al desarrollo del programa. El análisis histórico se apoya en documentos procedentes de diversos archivos nacionales e internacionales.
The Management of School Indiscipline in Elementary School Historical Review and Current Reality
Authors: Karaffillis Athanasios , Doulgeris Grigorios
Published: October 2015

This work is a summary of the postgraduate thesis carried out at the Department of Primary Education, Democritus University of Thrace, so as to explore the issue of school indiscipline from both theoretical and empirical terms. In previous years, inappropriate behaviors were dealt with severely painful means, but at present the above methods have been banned and replaced with other interventionist actions, each of which has a different degree of efficacy to the unruly child. Lately, however, greater emphasis is given on preventing incidents of disobedience, a project that depends on various factors. Finally, research was conducted on a sample of 192 primary school teachers in the prefecture of Serres, whose answers were correlated with the variable “gender”.
Use of Blended Learning for Effective Implementation of English-Medium Instruction in a Non-English Higher Education Context
Authors: Im Jin-Hyouk , Kim Jeongyeon
Published: October 2015

Although researchers agree with the strengths of an English-medium instruction (EMI) in addressing internationalization of a non-English higher education (HE) context, its implementation in classrooms has been widely criticized, mostly because of ineffective delivery of course content and a lack of evidence of English improvement. Grounded upon a critical review of the current state of internationalization of Korean HE and the subsequent examination of supplementary interview data from 15 college students who have taken EMI courses, this study proposes a model which integrates critical factors of EMI into one framework. This model aims at guiding the EMI policy from initiation to implementation. A major feature of this model is blended learning as a strategy to address the shortcomings of current EMI in this context and to facilitate the allocation of diverse online materials to scaffold EMI instruction. The benefits of the approach are presented from the perspectives both of policy-makers and of classroom participants.
Best Practices for Quality Improvement—Lessons from Top Ranked Engineering Institutions
Authors: Rao Potti Srinivasa , Viswanadhan K. G. , K. Raghunandana
Published: October 2015

Maximum number of privately funded engineering institutions have been established in India in the last two decades to meet the growing needs of technical manpower required by the Engineering and IT companies as well as aspiring students after completion of the Pre-University Program. However, a large number of institutions have not been able to attract the talented students for their undergraduate programs. The private managements of those institutions have realized then, the need for maintaining high quality in imparting engineering education. In addition, the regulatory bodies like NBA insist on maintaining the quality in the educational programs before giving accreditation. Therefore, the young institutes need to know the best practices adopted by the high performing institutions and introduce those best practices in their programs. In this paper, an attempt has been made to identify the best practices of the reputed and ranking institutes, to classify and codify those practices so as to enable the young institutes to implement them. Quality indicators have been identified through literature review, by summarizing previous studies, by conducting discussion with experts in the field. A few top ranked engineering institutions are selected to identify and list the best practices, by referring to the finding of various magazines. Practices followed with respect to the quality indicators identified have been composed by conducting structured interviews and discussions with various core groups & stake holders of these institutions. The details of literature review, data collection & analysis, findings and policy implications of the research work are presented in this paper. The best practices enlisted through this study will act as guidelines to implement the quality initiatives for the young institutions.
Application of the method of spatial point pattern analysis to the horizontal spatial distribution of preferential flow paths
Authors: Lu Wenxing , Cheng Jinhua , Wang Wei , Zhang Hongjiang , Zhou Hongwen
Published: October 2015

Preferential flow significantly influences hydrological processes in forests. The occurrence and development of this flow is directly affected by its spatial distribution. To determine whether or not point pattern analysis method can be used to examine the horizontal spatial distribution of preferential flow paths, experiments were conducted with dye tracer permeation to observe flow processes. Results indicated that an increase in penetration water volume exerted only a specific effect on preferential flow paths of large class in the topmost soil. Moreover, such paths showed distinct clumped patterns at the 25-cm scale under both high permeation water volume and low permeation water volume treatments. Nonetheless, the distribution pattern became uniform as scale range increased. The significance of the correlation between the spatial distribution of preferential flow paths and plant roots decreased from the top soil layer to the bottom. These findings suggest that soil depth and water permeation volume are important to the horizontal spatial distribution of preferential flow paths. Moreover, point pattern analysis method is suitable for investigating the horizontal spatial distribution of preferential flow paths and determining the correlation between the spatial distribution of preferential flow paths and plant roots.
Modelling deadwood supply for biodiversity conservation: Considerations, challenges and recommendations
Authors: Venier L.A. , Hébert C. , De Grandpré L. , Arsenault A. , Walton R. , Morris D.M.
Published: October 2015

There are concerns that deadwood supply (both snags and downed wood) may become a limiting resource for biodiversity conservation as the bio-economy develops. Despite this concern, it remains difficult to monitor all elements of biodiversity to ensure that forest management activities are not reducing deadwood below minimum thresholds. As a dynamic resource, deadwood quantity and quality does change throughout forest succession. Simulation modelling represents one approach to integrating this variability and supporting the refinement of forest management guidelines. In this paper, we review important considerations for developing deadwood models that address biodiversity concerns. These include defining initial conditions, estimating deadwood inputs over time, identifying parameters necessary to represent biodiversity, identifying data available to parameterize, calibrate and validate models, and identifying requirements for model validation and documentation. In addition, we consider how deadwood characteristics such as form, size, state of decay, tree species, cause of mortality and position can be treated in models to represent the full range of biodiversity requirements. Lastly, we review examples of stand-alone and study-specific deadwood modelling approaches to provide a road map for development of a robust, temporally dynamic deadwood model that addresses biodiversity and sustainability issues related to biomass harvest for bioenergy.
Integrating Library Instruction into the Course Management System for a First-Year Engineering Class: An Evidence-Based Study Measuring the Effectiveness of Blended Learning on Students’ Information Literacy Levels
Authors: Zhang Qinqin , Goodman Maren , Xie Shiyi
Published: October 2015

This research examines students in a first-year engineering course who receive library instruction by using a newly developed online module and attending optional in-person tutorials. It aims to evaluate the outcomes of library information literacy instruction using this module combined with in-person help. Results show a significant improvement in information literacy skills from a pre-test to a post-test. Focus group and survey data indicate that most students preferred the self-paced learning style of the online module and that the content of the module helped them to conduct library research for the course. This study also considers best practices for online library instruction. A blended instruction approach provides students with the flexibility to learn from a variety of formats at their own pace and also reduces library staff workload, especially for a large course.
A Survey of Campus Coordinators of Undergraduate Research Programs
Authors: Hensley Merinda Kaye , Shreeves Sarah L. , Davis-Kahl Stephanie
Published: October 2015

Interest in supporting undergraduate research programs continues to grow within academic librarianship. This article presents how undergraduate research program coordinators perceive and value library support of their programs. Undergraduate research coordinators from a variety of institutions were surveyed on which elements of libraries and library services they valued, and where libraries could improve and develop services for undergraduate researchers and their faculty mentors. This article seeks to present a critical perspective on library support for undergraduate research programs from an important external constituent group of faculty and administrators. The data and recommendations can further conversations and aid collaboration between librarians and their campus colleagues.
Fluorine-19 Labeling of Stromal Vascular Fraction Cells for Clinical Imaging Applications
Authors: Rose Laura C. , Kadayakkara Deepak K. , Wang Guan , Bar-Shir Amnon , Helfer Brooke M. , O'Hanlon Charles F. , Kraitchman Dara L. , Rodriguez Ricardo L. , Bulte Jeff W.M.
Published: October 2015

Stromal vascular fraction (SVF) cells are used clinically for various therapeutic targets. The location and persistence of engrafted SVF cells are important parameters for determining treatment failure versus success. We used the GID SVF-1 platform and a clinical protocol to harvest and label SVF cells with the fluorinated (19F) agent CS-1000 as part of a first-in-human phase I trial (clinicaltrials.gov identifier NCT02035085) to track SVF cells with magnetic resonance imaging during treatment of radiation-induced fibrosis in breast cancer patients. Flow cytometry revealed that SVF cells consisted of 25.0% ± 15.8% CD45+, 24.6% ± 12.5% CD34+, and 7.5% ± 3.3% CD31+ cells, with 2.1 ± 0.7 × 105 cells per cubic centimeter of adipose tissue obtained. Fluorescent CS-1000 (CS-ATM DM Green) labeled 87.0% ± 13.5% of CD34+ progenitor cells compared with 47.8% ± 18.5% of hematopoietic CD45+ cells, with an average of 2.8 ± 2.0 × 1012 19F atoms per cell, determined using nuclear magnetic resonance spectroscopy. The vast majority (92.7% ± 5.0%) of CD31+ cells were also labeled, although most coexpressed CD34. Only 16% ± 22.3% of CD45−/CD31−/CD34− (triple-negative) cells were labeled with CS-ATM DM Green. After induction of cell death by either apoptosis or necrosis, >95% of 19F was released from the cells, indicating that fluorine retention can be used as a surrogate marker for cell survival. Labeled-SVF cells engrafted in a silicone breast phantom could be visualized with a clinical 3-Tesla magnetic resonance imaging scanner at a sensitivity of approximately 2 × 106 cells at a depth of 5 mm. The current protocol can be used to image transplanted SVF cells at clinically relevant cell concentrations in patients.

Significance

Stromal vascular fraction (SVF) cells harvested from adipose tissue offer great promise in regenerative medicine, but methods to track such cell therapies are needed to ensure correct administration and monitor survival. A clinical protocol was developed to harvest and label SVF cells with the fluorinated (19F) agent CS-1000, allowing cells to be tracked with 19F magnetic resonance imaging (MRI). Flow cytometry evaluation revealed heterogeneous 19F uptake in SVF cells, confirming the need for careful characterization. The proposed protocol resulted in sufficient 19F uptake to allow imaging using a clinical MRI scanner with point-of-care processing.
Caracterização parcial de tripsina extraída de vísceras digestivas de Lutjanus Synagris: sensibilidade a íons metálicos
Authors: Oliveira Vagne De Melo , Roberto Nathalia Albuquerque , Assis Caio Rodrigo Dias , Bezerra Ranilson De Souza
Published: October 2015

O Lutjanus synagris distribui-se ao longo da costa nordestina, apresentando grande importância comercial e artesanal. Este trabalho objetivou extrair e avaliar sensibilidade da tripsina de Lutjanus synagris através da exposição a diferentes íons metálicos: MnCl2, KCl, ZnCl2, FeCl3, CuCl2, CaCl2, BaCl2 e AlCl3, em cinco concentrações (0,001, 0,01, 0,1, 1 e 10 mM). Para tanto, foram utilizados 500g de vísceras intestinais de espécimes capturadas no litoral alagoano. A etapa de extração enzimática foi realizada através de processo de maceração e homogeneização. A etapa de sensibilidade foi realizada de acordo com protocolo padrão cientifico internacional. Os resultados indicaram diferentes graus de inibição para os íons: KCl, ZnCl2, FeCl3 e CuCl2. Os dados obtidos pelo CaCl2 variaram de acordo com as concentrações testadas (0,001, 0,01 e 0,1 provocaram inibição, enquanto que 1 e 10 mM provocaram aumento de atividade, levando em consideração o grupo controle 100%). Todas as concentrações do MnCl2 acarretaram em aumento da atividade, enquanto todos de CuCl2 acarretaram em redução. Os íons BaCl2 e AlCl3 também acarretaram redução de atividade, embora sem haver diferença significativa. Os resultados obtidos sugerem diferentes graus de relação em diferentes concentrações de exposição, transformando a tripsina em um marcador bioquímico de possíveis alterações para elementos metálicos.
pp32 and APRIL are host cell-derived regulators of influenza virus RNA synthesis from cRNA
Authors: Sugiyama Kenji , Kawaguchi Atsushi , Okuwaki Mitsuru , Nagata Kyosuke
Published: October 2015

Replication of influenza viral genomic RNA (vRNA) is catalyzed by viral RNA-dependent RNA polymerase (vRdRP). Complementary RNA (cRNA) is first copied from vRNA, and progeny vRNAs are then amplified from the cRNA. Although vRdRP and viral RNA are minimal requirements, efficient cell-free replication could not be reproduced using only these viral factors. Using a biochemical complementation assay system, we found a novel activity in the nuclear extracts of uninfected cells, designated IREF-2, that allows robust unprimed vRNA synthesis from a cRNA template. IREF-2 was shown to consist of host-derived proteins, pp32 and APRIL. IREF-2 interacts with a free form of vRdRP and preferentially upregulates vRNA synthesis rather than cRNA synthesis. Knockdown experiments indicated that IREF-2 is involved in in vivo viral replication. On the basis of these results and those of previous studies, a plausible role(s) for IREF-2 during the initiation processes of vRNA replication is discussed.
Fucosylation and protein glycosylation create functional receptors for cholera toxin
Authors: Wands Amberlyn M , Fujita Akiko , McCombs Janet E , Cervin Jakob , Dedic Benjamin , Rodriguez Andrea C , Nischan Nicole , Bond Michelle R , Mettlen Marcel , Trudgian David C , Lemoff Andrew , Quiding-Järbrink Marianne , Gustavsson Bengt , Steentoft Catharina , Clausen Henrik , Mirzaei Hamid , Teneberg Susann , Yrlid Ulf , Kohler Jennifer J
Published: October 2015

Cholera toxin (CT) enters and intoxicates host cells after binding cell surface receptors using its B subunit (CTB). The ganglioside (glycolipid) GM1 is thought to be the sole CT receptor; however, the mechanism by which CTB binding to GM1 mediates internalization of CT remains enigmatic. Here we report that CTB binds cell surface glycoproteins. Relative contributions of gangliosides and glycoproteins to CTB binding depend on cell type, and CTB binds primarily to glycoproteins in colonic epithelial cell lines. Using a metabolically incorporated photocrosslinking sugar, we identified one CTB-binding glycoprotein and demonstrated that the glycan portion of the molecule, not the protein, provides the CTB interaction motif. We further show that fucosylated structures promote CTB entry into a colonic epithelial cell line and subsequent host cell intoxication. CTB-binding fucosylated glycoproteins are present in normal human intestinal epithelia and could play a role in cholera.
Evaluating the generation efficiency of hydrogen peroxide in water by pulsed discharge over water surface and underwater bubbling pulsed discharge
Authors: Shang Kefeng , Li Jie , Wang Xiaojing , Yao Dan , Lu Na , Jiang Nan , Wu Yan
Published: October 2015

Pulsed electric discharge over water surface/in water has been used to generate reactive species for decomposing the organic compounds in water, and hydrogen peroxide (H2O2) is one of the strong reactive species which can be decomposed into another stronger oxidative species, hydroxyl radical. The production efficacy of H2O2 by a gas phase pulsed discharge over water surface and an underwater bubbling pulsed discharge was evaluated through diagnosis of H2O2 by a chemical probe method. The experimental results show that the yield and the production rate of H2O2 increased with the input energy regardless of the electric discharge patterns, and the underwater bubbling pulsed discharge was more advantageous for H2O2 production considering both the yield and the production rate of H2O2. Results also indicate that the electric discharge patterns also influenced the water solution properties including the conductivity, the pH value and the water temperature.
Excitation area dependence of lasing modes in thin hexagonal GaN microdisks
Authors: Kouno Tetsuya , Sakai Masaru , Kishino Katsumi , Hara Kazuhiko
Published: October 2015

Thin, hexagonal GaN microdisks act as optical microcavities based on the whispering gallery mode (WGM) and the quasi-WGM that can cause lasing action. We investigated the relationship between the excitation area in regular and asymmetric thin, hexagonal GaN microdisks as well as the characteristics of these lasing modes using a room temperature photoluminescence mapping technique under high-excitation conditions. The lasing modes that are preferentially exhibited in a thin asymmetric hexagonal GaN microdisk were found to depend on the most strongly excited area in the microdisk. This behavior is potentially useful for optical micro switches and similar applications.
Development of plasma-on-chip: Plasma treatment for individual cells cultured in media
Authors: Kumagai Shinya , Chang Chun-Yao , Jeong Jonghyeon , Kobayashi Mime , Shimizu Tetsuji , Sasaki Minoru
Published: October 2015

A device consisting of Si microwells and microplasma sources has been fabricated for plasma treatment of individual cells cultured in media. We named the device plasma-on-chip. The microwells have through-holes at the bottom where gas–liquid interfaces form when they are filled with media containing biological samples. The microplasma sources, which supply reactive species, are located on the back of each microwell. Through the gas–liquid interface, the reactive species are supplied to the cells. Chlorella cells were used to demonstrate the feasibility of the device and after three minutes of plasma treatment, the fluorescence intensity of Chlorella cells appeared to be decreased. Optical emission spectroscopy identified O and OH radicals in the plasma, which can affect the cells. In the analysis of biological samples such as human cells or tissues, this device raises the possibility of revealing the mechanisms of plasma medicine in more detail.
Influence of voltage pulse width on the discharge characteristics in an atmospheric dielectric-barrier-discharge plasma jet
Authors: Uchida Giichiro , Takenaka Kosuke , Setsuhara Yuichi
Published: October 2015

We present here the analysis of the discharge characteristics of a He dielectric-barrier-discharge (DBD) plasma jet operated in the voltage duty ratio of 20 to 80% under the condition of driving voltage frequency 5 kHz. Discharge strength is sensitive to the voltage pulse width, and the pulse width of 70 µs, which corresponds to the duty ratio of 35%, leads to high O optical emission intensity. We also performed time-resolved optical emission measurements in a transient pulse discharge driven by various voltage duty ratios. Two distinct pulse discharges are observed in the rising and falling periods of the positive rectangular voltage, and the first and second discharges have a peak intensity of optical emission at different duty ratio. The observations indicate that an adequate voltage pulse width could ignite a strong discharge both in the rising and falling period of applied voltage, which could produce a large amount of reactive excited O atoms.
Effects of the acanthocephalanPolymorphus minutusand the microsporidianDictyocoela duebenumon energy reserves and stress response of cadmium exposedGammarus fossarum
Authors: Chen Hui-Yu , Grabner Daniel S. , Nachev Milen , Shih Hsiu-Hui , Sures Bernd
Published: October 2015

Amphipods are commonly parasitized by acanthocephalans and microsporidians and co-infections are found frequently. Both groups of parasites are known to have severe effects on their host. For example, microsporidians can modify host sex ratio and acanthocephalans can manipulate the behavior of the amphipod to promote transmission to the final host. These effects influence host metabolism in general and will also affect the ability of amphipods to cope with additional stressors such as environmental pollution, e.g., by toxic metals. Here we tested the effects of sub-lethal concentrations of cadmium on glycogen and lipid levels, as well as on the 70kDa heat shock protein (hsp70) response of field collectedGammarus fossarum, which were naturally infected with microsporidians and the acanthocephalanPolymorphus minutus. Infected and uninfectedG. fossarumwere exposed to a nominal Cd concentration of 4 µg/L, which resembled measured aqueous Cd concentration of 2.9 µg/L in reconstituted water for 7 d at 15 °C in parallel to an unexposed control. After exposure gammarids were snap frozen, weighed, sexed and tested for microsporidian infection by PCR. Only individuals containing the microsporidianDictyocoela duebenumwere used for the further biochemical and metal analyses.P. minutusinfected amphipods were significantly smaller than their uninfected conspecifics. Mortality was insignificantly increased due to cadmium exposure, but not due to parasite infection. Microsporidian infection in combination with cadmium exposure led to increased glycogen levels in female gammarids. An increase of glycogen was also found due to interaction of acanthocephalan and microsporidian infection. Elevated lipid levels were observed in all groups infected with microsporidians, while acanthocephalans had the opposite effect. A positive correlation of lipid and glycogen levels was observed. The general stress response measured in form of hsp70 was significantly increased in microsporidian infected gammarids exposed to cadmium.P. minutusdid not affect the stress response of its host. Lipid levels were correlated negatively with hsp70 response, and indicated a possible increased stress susceptibility of individuals with depleted energy reserves. The results of our study clearly demonstrate the importance of parasitic infections, especially of microsporidians, for ecotoxicological research.
Getting the most out of RNA-seq data analysis
Authors: Khang Tsung Fei , Lau Ching Yee
Published: October 2015

Background.A common research goal in transcriptome projects is to find genes that are differentially expressed in different phenotype classes. Biologists might wish to validate such gene candidates experimentally, or use them for downstream systems biology analysis. Producing a coherent differential gene expression analysis from RNA-seq count data requires an understanding of how numerous sources of variation such as the replicate size, the hypothesized biological effect size, and the specific method for making differential expression calls interact. We believe an explicit demonstration of such interactions in real RNA-seq data sets is of practical interest to biologists.

Results.Using two large public RNA-seq data sets—one representing strong, and another mild, biological effect size—we simulated different replicate size scenarios, and tested the performance of several commonly-used methods for calling differentially expressed genes in each of them. We found that, when biological effect size was mild, RNA-seq experiments should focus on experimental validation of differentially expressed gene candidates. Importantly, at least triplicates must be used, and the differentially expressed genes should be called using methods with high positive predictive value (PPV), such as NOISeq or GFOLD. In contrast, when biological effect size was strong, differentially expressed genes mined from unreplicated experiments using NOISeq, ASC and GFOLD had between 30 to 50% mean PPV, an increase of more than 30-fold compared to the cases of mild biological effect size. Among methods with good PPV performance, having triplicates or more substantially improved mean PPV to over 90% for GFOLD, 60% for DESeq2, 50% for NOISeq, and 30% for edgeR. At a replicate size of six, we found DESeq2 and edgeR to be reasonable methods for calling differentially expressed genes at systems level analysis, as their PPV and sensitivity trade-off were superior to the other methods’.

Conclusion.When biological effect size is weak, systems level investigation is not possible using RNAseq data, and no meaningful result can be obtained in unreplicated experiments. Nonetheless, NOISeq or GFOLD may yield limited numbers of gene candidates with good validation potential, when triplicates or more are available. When biological effect size is strong, NOISeq and GFOLD are effective tools for detecting differentially expressed genes in unreplicated RNA-seq experiments for qPCR validation. When triplicates or more are available, GFOLD is a sharp tool for identifying high confidence differentially expressed genes for targeted qPCR validation; for downstream systems level analysis, combined results from DESeq2 and edgeR are useful.
Fimbristylis karthikeyanii, a new name for Fimbristylis breviculma Govind. (Cyperaceae)
Authors: Kottaimuthu Ramalingan , Gnanasekaran Gunadayalan
Published: October 2015

Fimbristylis karthikeyanii (Cyperaceae) is a new name for an Indian endemic species, Fimbristylis breviculma Govind. as that name is a homonym.
Tracing terrestrial DOC in the Baltic Sea—A 3‐D model study
Authors: Fransner Filippa , Nycander Jonas , Mörth Carl‐Magnus , Humborg Christoph , Markus Meier H. E. , Hordoir Robinson , Gustafsson Erik , Deutsch Barbara
Published: October 2015

The fate of terrestrial organic matter brought to the coastal seas by rivers and its role in the global carbon cycle are still not very well known. Here the degradation rate of terrestrial dissolved organic carbon (DOCter) is studied in the Baltic Sea, a subarctic semienclosed sea, by releasing it as a tracer in a 3‐D circulation model and applying linear decay constants. A good agreement with available observational data is obtained by parameterizing the degradation in two rather different ways: one by applying a decay time on the order of 10 years to the whole pool of DOCter and one by dividing the DOCter into one refractory pool and one pool subject to a decay time on the order of 1 year. The choice of parameterization has a significant effect on where in the Baltic Sea the removal takes place, which can be of importance when modeling the full carbon cycle and the CO2 exchange with the atmosphere. In both cases the biogeochemical decay operates on time scales less than the water residence time. Therefore, only a minor fraction of the DOCter reaches the North Sea, whereas approximately 80% is removed by internal sinks within the Baltic Sea. This further implies that DOCter mineralization is an important link in land‐sea‐atmosphere cycling of carbon in coastal and shelf seas that are heavily influenced by riverine DOC.
The observed impacts of South Asian summer monsoon on the local atmosphere and the near‐surface turbulent heat exchange over the Southeast Tibet
Authors: Zhou Libo , Zou Han , Ma Shupo , Li Fei , Zhu Jinhuan , Li Peng , Zhang Yu
Published: October 2015

The Southeast Tibet is an important region of the Tibetan Plateau bearing the interaction between the Tibetan and the neighbor atmospheric systems. The South Asian summer monsoon (SASM) as a basic climate system in Asia could impact the local atmosphere and the near‐surface heat exchange process in the Southeast Tibet. An observational campaign, Observation on the Surface‐to‐air Exchange Processes in Southeast Tibet (OSEP2013), was carried out in this region during SASM in 2013. The atmospheric parameters and turbulent heat fluxes were observed and averaged over three different land surfaces of the inhomogeneous landscape during the observation campaign. Results show clear SASM impacts on the local atmosphere and near‐surface heat exchange in the Southeast Tibet. The South Asian summer monsoon was onset on 1 June 2013 and experienced a south phase and north phase during OSEP2013. The convection and humidity were increased in the Southeast Tibet by SASM, especially during the north phase. The observation domain received low radiation energy due to the convective clouds brought by SASM, and the soil and air temperatures were lowered as consequence. In addition, the air humidity was increased over this region by the wet air transportation of SASM circulation. The sensible and latent heat transfers were decreased by the low land‐air temperature difference and high air humidity during SASM. The latent heat transfer dominated the total heat transfer in the Southeast Tibet due to the low sensible heat transfer in the SASM situation, and the domination was increased as the sensible heat transfer was further decreased during the SASM north phase.
Ionosonde observations of ionospheric disturbances due to the 15 February 2013 Chelyabinsk meteor explosion
Authors: Pradipta Rezy , Valladares Cesar E. , Doherty Patricia H.
Published: October 2015

We report the results of our investigations on the potential ionospheric effects caused by the 15 February 2013 Chelyabinsk meteor explosion. We used the data from a number of digisonde stations located in Europe and Russia to detect the traveling ionospheric disturbances (TIDs) likely to have been caused by the meteor explosion. We found that certain characteristic signatures of the TIDs can be identified in individual ionogram records, mostly in the form of Y‐forking/splitting of the ionogram traces. Based on the arrival times of the disturbances, we have inferred the overall propagation speed of the TIDs from Chelyabinsk to be 171 ± 14 m/s.
Resolving daily wave 4 nonmigrating tidal winds at equatorial and midlatitudes with WINDII: DE3 and SE2
Authors: Cho Young‐Min , Shepherd Gordon
Published: October 2015

The Wind Imaging Interferometer observed nonmigrating tidal winds from 90 to 260 km during daytime and at 99 and 250 km during the night and found that the amplitudes and phases of the daytime and nighttime extracted wave 4 for a given day were different, indicating the presence of more than one component. The objective of this study is to resolve those components. Local time versus longitude propagation plots over individual seasons revealed the diurnal eastward propagating wave number 3 (DE3), the semidiurnal eastward propagating wave number 2 (SE2) and the stationary planetary wave number 4 (SPW4). Using a fitting procedure for individual days it was then found possible to determine the amplitudes and phases of DE3 and SE2 and the amplitude of SPW4 for each day, using a constant phase for the SPW4 obtained from the propagation plot. These DE3 and SE2 values were compared with data‐constrained model results yielding good agreement at 99 km but with mixed agreement at 250 km. Time series analysis of 164 days duration showed considerable variability in the amplitudes of the zonal wind for DE3 with the SPW4 tending to follow; DE3 power spectral peaks occurred near 12, 16, and 32 days. The SE2 showed less variability, also displaying spectral peaks but shifted from the DE3 peaks. Monthly averages of the DE3 and SE2 show that the DE3 is predominant at the equatorial mesosphere/lower thermosphere region. On the other hand, the SE2 is uniformly present at lower and midlatitudes and all altitudes.
Determining the magnetic attempt time τ0, its temperature dependence, and the grain size distribution from magnetic viscosity measurements
Authors: Berndt Thomas , Muxworthy Adrian R. , Paterson Greig A.
Published: October 2015

A new method to determine the atomic attempt time τ0 of magnetic relaxation of fine particles, which is central to rock and soil magnetism and paleomagnetic recording theory, is presented, including the determination of its temperature dependence, and simultaneously the grain size distribution of a sample. It is based on measuring a series of zero‐field magnetic viscous decay curves for saturation isothermal remanent magnetization at various different temperatures that are later joined together on a single grain size scale from which the grain size distribution and attempt time are determined. The attempt time was determined for three samples containing noninteracting, single‐domain titanomagnetites of different grain sizes for temperatures between 27 K and 374 K. No clear temperature‐dependent trend was found; however, values varied significantly from one sample to the other: from 10−11 to 10−8s; in particular, the sample containing multiple magnetic phases had an effective attempt time significantly lower than the more homogeneous samples, thereby questioning the applicability of the simple Néel‐Arhennius equation for magnetic relaxation for composite materials.
Role of regional thermal contrast over West Asia in interannual variation in atmospheric moisture transportation over the Indian Ocean and neighboring areas at summer monsoon onset
Authors: Watanabe Takeshi
Published: October 2015

The low‐level temperature contrast over West Asia influences the interannual variation in water vapor transportation over the northern and equatorial Indian Ocean and neighboring monsoon area. A composite analysis that takes into account the thermal contrast over West Asia during the monsoon seasonal transition is performed based on the reanalysis and merged observational precipitation data sets. The positive (negative) low‐level thermal contrast anomaly over the Iranian Plateau (IP) strengthens (weakens) the thermal contrast over the Arabian Sea. The low‐level westerly anomaly develops earlier in the positive IP thermal contrast years than in the negative years. As a result, water vapor transport varies. This variation in water vapor transport in turn has an influence on the abrupt increase in precipitation over South Asia and the Arabian Sea and the decrease over equatorial East Africa. The variation in low‐level temperature over the IP precedes the variation of precipitation over these regions by a few pentads. A numerical experiment using the Lagrangian particle dispersion model agrees with the results of the composite analysis. Particles are emitted from the western tropical Indian Ocean region from the preonset to onset period. Results of numerical experiments concerning positive IP thermal contrast years show that particles can be transported into South Asia and the Arabian Sea before the climatological Asian summer monsoon onset pentad. However, small amounts of particles arrive in South Asia and the Arabian Sea at the onset period in negative IP years. The transport into equatorial East Africa becomes weak earlier in positive IP years.
Global observations and modeling of nonmigrating diurnal tides generated by tide‐planetary wave interactions
Authors: Lieberman R. S. , Riggin D. M. , Ortland D. A. , Oberheide J. , Siskind D. E.
Published: October 2015

Advective processes that couple planetary waves with tides have long been proposed as sources of nonmigrating diurnal tides. This paper reports observations of short‐term variability in global observations of nonmigrating tides predicted to arise from the interaction of the migrating diurnal tide (DW1) with a quasi‐stationary planetary wave number one (PW1). PW1 and tidal definitions are extracted from satellite temperatures and high‐altitude meteorological analyses. During winter months, the evolution of westward traveling diurnal tides with zonal wave number 2 (DW2) generally tracks that of strong‐amplitude stratospheric PW1. DW1 and PW1 spectra are used to compute nonlinear tidal forcing terms arising from advection. We then examine the response of a primitive equation model to the observation‐based nonlinear forcing. The model experiments indicate that meridional advection of PW1 zonal momentum by DW1 is a significant source of lower thermospheric DW2. Modeled DW2 amplitudes are very consistent with observed DW2 amplitudes when stratospheric PW1 penetrates to equatorial latitudes. The model experiments also indicate that the interaction can imprint short‐term variability associated with wintertime PW1 upon DW2 in the summer hemisphere and the lower thermosphere.
Large methane emissions from a subarctic lake during spring thaw: Mechanisms and landscape significance
Authors: Jammet Mathilde , Crill Patrick , Dengel Sigrid , Friborg Thomas
Published: October 2015

The ice‐cover season and subsequent spring thaw are thought to be of particular importance for the biogeochemical cycle of northern lakes and wetlands. Yet the magnitude of their methane emissions during an entire cold season is uncertain due to scarce measurements. While wetlands are known to be the highest natural emitters of methane, emissions from northern lakes are an uncertain component of terrestrial carbon budgets. To evaluate the importance of methane emissions from a subarctic lake during winter and spring, surface methane fluxes were recorded with the eddy covariance method in a subarctic fen‐type wetland and in an adjacent shallow lake, from freezeup to complete ice out. The fen was a steady emitter of methane throughout winter. While no detectable flux was observed from the ice‐covered lake surface during winter, it was the largest methane source of the landscape in spring, with a cumulative release 1.7‐fold higher than at the fen, accounting for 53% of annual lake emissions. The high temporal resolution of the measurements allowed making a direct link between breakdown of the temperature stratification after ice breakup and the highest release of methane from the lake surface. A sediment upwelling at the end of the thaw season likely contributed to these emissions. We suggest that, unlike wetlands, shallow seasonally ice‐covered lakes can have their highest methane emission potential in the cold season, likely dominating the spring methane release of subarctic landscapes with high lake coverage.