bluuebunny/crossref_metadata_2025 huggingface dataset:
Raftlin Controls Lipopolysaccharide-Induced TLR4 Internalization and TICAM-1 Signaling in a Cell Type–Specific Manner
Authors: Tatematsu Megumi , Yoshida Ryuji , Morioka Yuka , Ishii Noriko , Funami Kenji , Watanabe Ayako , Saeki Kazuko , Seya Tsukasa , Matsumoto Misako
Published: March 2016

The clathrin-dependent endocytic pathway is crucial for endosomal TLR3- and TLR4-mediated Toll–IL-1R domain–containing adaptor molecule-1 (TICAM-1) signaling. TLR4 uses a different signaling platform, plasma membrane and endosomes, for activation of TIRAP-MyD88 and TICAM-2–TICAM-1, respectively. LPS-induced endocytosis of TLR4 is mandatory for TICAM-1–mediated signaling including IFN-β production. Several molecules/mechanisms such as CD14, clathrin, and phosphatidylinositol metabolism have been reported to act as inducers of TLR4 translocation. However, the molecular mechanism of spatiotemporal regulation of TLR4 signaling remains unresolved. We have previously shown that Raftlin is essential for clathrin-dependent endocytosis of TLR3 ligand in human epithelial cells and myeloid dendritic cells (DCs). In this article, we demonstrate that Raftlin also mediated LPS-induced TLR4 internalization and TICAM-1 signaling in human monocyte-derived DCs and macrophages (Mo-Mϕs). When Raftlin was knocked down, LPS-induced TLR4-mediated IFN-β promoter activation, but not NF-κB activation, was decreased in HEK293 cells overexpressing TLR4/MD-2 or TLR4/MD-2/CD14. LPS-induced IFN-β production by monocyte-derived DCs and Mo-Mϕs was significantly decreased by knockdown of Raftlin. Upon LPS stimulation, Raftlin moved from the cytoplasm to the plasma membrane in Mo-Mϕs, where it colocalized with TLR4. Raftlin associated with clathrin-associated adaptor protein–2 in resting cells and transiently bound to TLR4 and clathrin at the cell surface in response to LPS. Thus, Raftlin appears to modulate cargo selection as an accessary protein of clathrin-associated adaptor protein–2 in clathrin-mediated endocytosis of TLR3/4 ligands.
Cutting Edge: BAFF Promotes Autoantibody Production via TACI-Dependent Activation of Transitional B Cells
Authors: Jacobs Holly M. , Thouvenel Christopher D. , Leach Sarah , Arkatkar Tanvi , Metzler Genita , Scharping Nicole E. , Kolhatkar Nikita S. , Rawlings David J. , Jackson Shaun W.
Published: March 2016

Mice overexpressing B cell activating factor of the TNF family (BAFF) develop systemic autoimmunity characterized by class-switched anti-nuclear Abs. Transmembrane activator and CAML interactor (TACI) signals are critical for BAFF-mediated autoimmunity, but the B cell developmental subsets undergoing TACI-dependent activation in settings of excess BAFF remain unclear. We report that, although surface TACI expression is usually limited to mature B cells, excess BAFF promotes the expansion of TACI-expressing transitional B cells. TACI+ transitional cells from BAFF-transgenic mice are characterized by an activated, cycling phenotype, and the TACI+ cell subset is specifically enriched for autoreactivity, expresses activation-induced cytidine deaminase and T-bet, and exhibits evidence of somatic hypermutation. Consistent with a potential contribution to BAFF-mediated humoral autoimmunity, TACI+ transitional B cells from BAFF-transgenic mice spontaneously produce class-switched autoantibodies ex vivo. These combined findings highlight a novel mechanism through which BAFF promotes humoral autoimmunity via direct, TACI-dependent activation of transitional B cells.
Understanding relational conditions necessary for effective mentoring of black-owned small businesses: A South African perspective
Authors: Matabooe Makatleho J. , Venter Elmarie , Rootman Chantal
Published: March 2016

Orientation: To gain an understanding of the relational conditions required for effective mentoring of black-owned small businesses.Research purpose: To identify relational-based conditions for effective mentoring, which can be used to enhance business management skills of owner-managers of black-owned small businesses and eventually improve the survival of these businesses in South Africa.Motivation for the study: By identifying relational-based conditions needed for effective mentoring of black-owned small businesses, recommendations can be put forward that could help achieve harmonious mentoring relationships and ultimately ensure effective mentoring of these businesses.Research design, approach and method: An interpretivism paradigm was adopted and aqualitative research methodology was selected. Semistructured interviews were used to gauge the perceptions of participants about relational issues necessary for effective mentoring. Content and constant comparative analyses were used to analyse data.Main findings: The findings revealed that conditions surrounding the knowledge and expertise of the mentor, experience and age of the mentor, approachability of the mentor, mutual respect, open communication, mutual trust and honesty, passion and patience of the mentor, mentee’s willingness to learn, alignment of expectations, as well as culture sensitivity of the mentor are to be considered for effective mentor–mentee relationship.Practical/managerial implications: Although mentoring is important to develop management skills of owner–managers, it is equally important that the mentor–mentee relationship is nurtured to achieve the desired outcomes of the relationship.Contribution/value-add: The alarming failure rates of small businesses in general and blackowned small businesses in particular could be improved by providing effective mentoring programmes to owner–managers by ensuring harmonious mentor–mentee relationships.
Integrative Analysis of mRNA, microRNA, and Protein Correlates of Relative Cerebral Blood Volume Values in GBM Reveals the Role for Modulators of Angiogenesis and Tumor Proliferation
Authors: Rao Arvind , Manyam Ganiraju , Rao Ganesh , Jain Rajan
Published: March 2016

Dynamic susceptibility contrast-enhanced magnetic resonance imaging is routinely used to provide hemodynamic assessment of brain tumors as a diagnostic as well as a prognostic tool. Recently, it was shown that the relative cerebral blood volume (rCBV), obtained from the contrast-enhancing as well as -nonenhancing portion of glioblastoma (GBM), is strongly associated with overall survival. In this study, we aim to characterize the genomic correlates (microRNA, messenger RNA, and protein) of this vascular parameter. This study aims to provide a comprehensive radiogenomic and radioproteomic characterization of the hemodynamic phenotype of GBM using publicly available imaging and genomic data from the Cancer Genome Atlas GBM cohort. Based on this analysis, we identified pathways associated with angiogenesis and tumor proliferation underlying this hemodynamic parameter in GBM.
Hormone Receptors in Serous Ovarian Carcinoma: Prognosis, Pathogenesis, and Treatment Considerations
Authors: Voutsadakis Ioannis A.
Published: March 2016

A few breakthroughs have been accomplished for the treatment of ovarian cancer, the most deadly gynecologic carcinoma, in the current era of targeted oncologic treatment. The estrogen receptor was the first target of such treatments with the introduction of tamoxifen four decades ago in breast cancer therapeutics. Attempts to duplicate the success of hormonal therapies in ovarian cancer met with mixed results, which may be due to an inferior degree of hormone dependency in this cancer. Alternatively, this may be due to the failure to clearly identify the subsets of ovarian cancer with hormone sensitivity. This article reviews the expression of hormone receptors by ovarian cancer cells, the prognostic value of these expressions, and their predictive capacity for response to hormonal agents. The possible ways ahead are briefly discussed.
Human Infections by Multiple Spotted Fever Group Rickettsiae in Tennessee
Authors: Delisle Josie , Mendell Nicole L. , Stull-Lane Annica , Bloch Karen C. , Bouyer Donald H. , Moncayo Abelardo C.
Published: March 2016

Rocky Mountain spotted fever is the most common tick-borne disease in Tennessee. However, Rickettsia rickettsii has rarely been isolated from endemic ticks, suggesting rickettsioses may be caused by other species. A total of 56 human serum samples that were serologically positive for exposure to Rickettsia were obtained from commercial laboratories in 2010 and 2011. In addition, 20 paired sera from patients with encephalitis and positive Rickettsia serology were obtained from the Tennessee Unexplained Encephalitis Surveillance (TUES) study. Using an immunofluorescence assay, reactivity of the sera to R. rickettsii, Rickettsia montanensis, Rickettsia parkeri, and Rickettsia amblyommii was tested, and a comparison of endpoint titers was used to determine the probable antigen that stimulated the antibody response. Cross-absorption was conducted for 94.8% (N = 91) of the samples due to serologic cross-reactivity. Of the commercial laboratory samples, 55.4% (N = 31) had specific reactivity to R. amblyommii and 44.6% (N = 25) were indeterminate. Of the paired TUES samples, 20% (N = 4) had specific reactivity to R. amblyommii, 5% (N = 1) to R. montanensis, and 5% (N = 1) to R. parkeri. Patients with specific reactivity to R. amblyommii experienced fever (75%), headache (68%) and myalgia (58%). Rash (36%) and thrombocytopenia (40%) were less common. To our knowledge, this is the first time R. amblyommii has been reported as a possible causative agent of rickettsioses in Tennessee.
Assessing Perceived Challenges to Laboratory Testing at a Malawian Referral Hospital
Authors: Petrose Lia G. , Fisher Arielle M. , Douglas Gerald P. , Terry Martha A. , Muula Adamson , Chawani Marlen S. , Limula Henry , Driessen Julia
Published: March 2016

Adequate laboratory infrastructure in sub-Saharan Africa is vital for tackling the burden of infectious diseases such as human immunodeficiency virus and acquired immune deficiency syndrome, malaria, and tuberculosis, yet laboratories are ill-integrated into the diagnostic and care delivery process in low-resource settings. Although much of the literature focuses on disease-specific challenges around laboratory testing, we sought to identify horizontal challenges to the laboratory testing process through interviews with clinicians involved in the diagnostic process. Based on 22 interviews with physicians, nurses, clinical officers, medical students, and laboratory technicians, technologists and supervisors, we identified 12 distinct challenges in the areas of staff, materials, workflow, and the blood bank. These challenges underscore the informational challenges that compound more visible resource shortages in the laboratory testing process, which lend themselves to horizontal strengthening efforts around the diagnostic process.
Venom and Purified Toxins of the Spectacled Cobra (Naja naja) from Pakistan: Insights into Toxicity and Antivenom Neutralization
Authors: Wong Kin Ying , Tan Choo Hock , Tan Nget Hong
Published: March 2016

Geographical variations of snake venoms can result in suboptimal effectiveness of Indian antivenoms that are currently used in most South Asian countries. This study investigated the toxicity and neutralization profile of the venom and toxins from Pakistani spectacled cobra, Naja naja, using VINS polyvalent antivenom (VPAV, India), Naja kaouthia monovalent antivenom (NKMAV, Thailand), and neuro bivalent antivenom (NBAV, Taiwan). Cation-exchange and reverse-phase high-performance liquid chromatography fractionations followed by toxin identification through liquid chromatography–mass spectrometry (MS)/MS indicated that the venom comprised mainly of postsynaptic neurotoxins (NTXs) (long neurotoxins [LNTXs], 28.3%; short neurotoxins [SNTXs], 8%), cytotoxins (CTXs) (31.2%), and acidic phospholipases A2 (12.3%). NKMAV is the most effective in neutralizing the lethal effect of the venom (potency = 1.1 mg venom/mL) and its LNTX (potency = 0.5 mg toxin/mL), consistent with the high content of LNTX in N. kaouthia venom. VPAV was effective in neutralizing the CTX (potency = 0.4 mg toxin/mL), in agreement with the higher CTX abundance in Indian cobra venom. All the three antivenoms were weak in neutralizing the SNTX (potency = 0.03–0.04 mg toxin/mL), including NBAV that was raised from the SNTX-rich Taiwanese cobra venom. In a challenge-rescue experiment, envenomed mice were prevented from death by a maximal dose of VPAV (intravenous 200 μL) but the recovery from paralysis was slow, indicating the need for higher or repeated doses of VPAV. Our results suggest that optimal neutralization for Pakistani N. naja venom may be achieved by improving the formulation of antivenom production to enhance antivenom immunoreactivity against long and SNTXs.
Environmental controls on pyrocumulus and pyrocumulonimbus initiation and development
Authors: Lareau Neil P. , Clements Craig B.
Published: March 2016

Abstract. In this paper we present the first direct observational evidence that the condensation level in pyrocumulus and pyrocumulonimbus clouds can be significantly higher than the ambient lifted condensation level. In addition, we show that the environmental thermodynamic profile, day-to-day variations in humidity, and ambient wind shear all exert significant influence over the onset and development of pyroconvective clouds. These findings are established using a scanning Doppler lidar and mobile radiosonde system during two large wildfires in northern California, the Bald Fire and the Rocky Fire. The lidar is used to distinguish liquid water from smoke backscatter during the plume rise, and thus provides a direct detection of plume condensations levels. Plume tops are subsequently determined from both the lidar and nearby radar observations. The radiosonde data, obtained adjacent to the fires, contextualize the lidar and radar observations, and enable estimates of the plume ascent, convective available potential energy, and equilibrium level. A noteworthy finding is that in these cases, the convective condensation level, not the lifted condensation level, provides the best estimate of the pyrocumulus initiation height.
Direct measurements of OH and other product yields from the HO2  + CH3C(O)O2 reaction
Authors: Winiberg Frank A. F. , Dillon Terry J. , Orr Stephanie C. , Groß Christoph B. M , Bejan Iustinian , Brumby Charlotte A. , Evans Matthew J. , Smith Shona C. , Heard Dwayne E. , Seakins Paul W.
Published: March 2016

Abstract. The reaction CH3C(O)O2 + HO2  →  CH3C(O)OOH + O2 (Reaction R5a), CH3C(O)OH + O3 (Reaction R5b), CH3 + CO2 + OH + O2 (Reaction R5c) was studied in a series of experiments conducted at 1000 mbar and (293 ± 2) K in the HIRAC simulation chamber. For the first time, products, (CH3C(O)OOH, CH3C(O)OH, O3 and OH) from all three branching pathways of the reaction have been detected directly and simultaneously. Measurements of radical precursors (CH3OH, CH3CHO), HO2 and some secondary products HCHO and HCOOH further constrained the system. Fitting a comprehensive model to the experimental data, obtained over a range of conditions, determined the branching ratios α(R5a)  =  0.37 ± 0.10, α(R5b) =  0.12 ± 0.04 and α(R5c) =  0.51 ± 0.12 (errors at 2σ level). Improved measurement/model agreement was achieved using k(R5)  =  (2.4 ± 0.4)  ×  10−11 cm3 molecule−1 s−1, which is within the large uncertainty of the current IUPAC and JPL recommended rate coefficients for the title reaction. The rate coefficient and branching ratios are in good agreement with a recent study performed by Groß et al. (2014b); taken together, these two studies show that the rate of OH regeneration through Reaction (R5) is more rapid than previously thought. GEOS-Chem has been used to assess the implications of the revised rate coefficients and branching ratios; the modelling shows an enhancement of up to 5 % in OH concentrations in tropical rainforest areas and increases of up to 10 % at altitudes of 6–8 km above the equator, compared to calculations based on the IUPAC recommended rate coefficient and yield. The enhanced rate of acetylperoxy consumption significantly reduces PAN in remote regions (up to 30 %) with commensurate reductions in background NOx.
Deriving Brown Carbon from Multi-Wavelength Absorption Measurements: Method and Application to AERONET and Surface Observations
Authors: Wang Xuan , Heald Colette L. , Sedlacek Arthur J. , de Sá Suzane S. , Martin Scot T. , Alexander M. Lizabeth , Watson Thomas B. , Aiken Allison C. , Springston Stephen R. , Artaxo Paulo
Published: March 2016

Abstract. The radiative impact of organic aerosols (OA) is a large source of uncertainty in estimating the global direct radiative effect (DRE) of aerosols. This radiative impact includes not only light scattering but also light absorption from a subclass of OA referred to as brown carbon (BrC). However the absorption properties of BrC are poorly understood leading to large uncertainties in modelling studies. To obtain observational constraints from measurements, a simple Absorption Ångström Exponent (AAE) method is often used to separate the contribution of BrC absorption from that of black carbon (BC). However, this attribution method is based on assumptions regarding the spectral dependence of BC that are often violated in the ambient atmosphere. Here we develop a new method that decreases the uncertainties associated with estimating BrC absorption. By applying this method to multi-wavelength absorption aerosol optical depth (AAOD) measurements at AERONET sites worldwide and surface aerosol absorption measurements at multiple ambient sites, we estimate that BrC globally contributes 6–40 % of the absorption at 440 nm. We find that the mass absorption coefficient of OA (OA-MAC) is positively correlated with BC / OA mass ratio. Based on the variability of BC properties and BC / OA emission ratio, we estimate a range of 0.05–1.2 m2/g for OA-MAC at 440 nm. Using the combination of AERONET and OMI UV absorption observations we estimate that the AAE388/440 nm for BrC is generally ~ 4 world-wide, with a smaller value in Europe (< 2). Our analyses of two surface sites (Cape Cod, to the southeast of Boston, and the GoAmazon2014/5 T3 site, to the west of Manaus, Brazil) reveal no significant relationship between BrC absorptivity and photochemical aging in typical urban-influenced conditions. However, the absorption of BrC measured during the biomass burning season near Manaus is found to decrease with photochemical aging with a lifetime of ~ 1 day. This lifetime is comparable to previous observations within a biomass burning plume but much slower than estimated from laboratory studies.
Growth of nucleation mode particles in the summertime Arctic: a case study
Authors: Willis Megan D. , Burkart Julia , Thomas Jennie L. , Köllner Franziska , Schneider Johannes , Bozem Heiko , Hoor Peter M. , Aliabadi Amir A. , Schulz Hannes , Herber Andreas B. , Leaitch W. Richard , Abbatt Jonathan P. D.
Published: March 2016

Abstract. The summertime Arctic lower troposphere is a relatively pristine, background aerosol environment dominated by nucleation and Aitken mode particles. Understanding the mechanisms that control the formation and growth of aerosol is crucial for our ability to predict cloud properties, and therefore radiative balance and climate. We present an analysis of an aerosol growth event observed in the Canadian Arctic Archipelago during summer as part of the NETCARE project. Under stable and clean atmospheric conditions, with low inversion heights, carbon monoxide less than 80 ppbv and black carbon less than 5 ng m−3, we observe growth of small particles, < 20 nm in diameter, into sizes above 50 nm. Aerosol growth was correlated with the presence of organic species, trimethylamine and methanesulfonic acid (MSA) in particles ~ 80 nm and larger, where the organics are similar to those previously observed in marine settings. MSA-to-sulfate ratios as high as 0.15 were observed during aerosol growth, suggesting an important marine influence. The organic-rich aerosol contributes significantly to particles active as cloud condensation nuclei (CCN, supersaturation = 0.6 %), which are elevated in concentration during aerosol growth above background levels of ~ 100 cm3 to ~ 220 cm
Vertical profiles of aerosol optical properties and the solar heating rate estimated by combining sky radiometer and lidar measurements
Authors: Kudo Rei , Nishizawa Tomoaki , Aoyagi Toshinori
Published: March 2016

Abstract. The SKYLIDAR algorithm was developed to estimate vertical profiles of aerosol optical properties from sky radiometer (SKYNET) and lidar (AD-Net) measurements. The solar heating rate was also estimated from the SKYLIDAR retrievals. The algorithm consists of two retrieval steps: (1) columnar properties are retrieved from the sky radiometer measurements and the vertically mean depolarization ratio obtained from the lidar measurements, and (2) vertical profiles are retrieved from the lidar measurements and the results of the first step. The derived parameters are the vertical profiles of the size distribution, refractive index (real and imaginary parts), extinction coefficient, single-scattering albedo, and asymmetry factor. Sensitivity tests were conducted by applying the SKYLIDAR algorithm to the simulated sky radiometer and lidar data for vertical profiles of three different aerosols, continental average, transported dust, and pollution aerosols. The vertical profiles of the size distribution, extinction coefficient, and asymmetry factor were well estimated in all cases. The vertical profiles of the refractive index and single-scattering albedo of transported dust were well estimated but not those of transported pollution aerosol. To demonstrate the performance and validity of the SKYLIDAR algorithm, we applied the SKYLIDAR algorithm to the actual measurements at Tsukuba, Japan. The detailed vertical structures of the aerosol optical properties and solar heating rate of transported dust and smoke were investigated. Examination of the relationship between the solar heating rate and the aerosol optical properties showed that the vertical profile of the asymmetry factor played an important role in creating vertical variation in the solar heating rate. We then compared the columnar optical properties between SKYLIDAR and SKYRAD.PACK retrievals, and the surface solar irradiance calculated from the SKYLIDAR retrievals was compared with pyranometer measurement. The results showed good agreements: The columnar values of the SKYLIDAR retrievals agreed with reliable SKYRAD.PACK retrievals, and the SKYLIDAR retrievals were sufficiently accurate to evaluate the surface solar irradiance.
Recommendations for processing atmospheric attenuated backscatter profiles from Vaisala CL31 Ceilometers
Authors: Kotthaus Simone , O'Connor Ewan , Münkel Christoph , Charlton-Perez Cristina , Gabey Andrew M. , Grimmond C. Sue B.
Published: March 2016

Abstract. Ceilometer lidars are used for cloud base height detection, to probe aerosol layers in the atmosphere (e.g. detection of elevated layers of Saharan dust or volcanic ash) and to examine boundary layer dynamics. Sensor optics and acquisition algorithms can strongly influence the observed attenuated backscatter profiles; therefore, physical interpretation of the profiles can require corrections to be applied carefully. This study addresses the commonly deployed Vaisala CL31 ceilometers. Attenuated backscatter profiles are studied to evaluate the impact of both the generation of the hardware and version of the firmware. In response to this work and discussion within the CL31/TOPROF user community (TOPROF is a European COST Action aiming to harmonise remote sensing networks across Europe), Vaisala released new firmware (versions 1.72 & 2.03) for the CL31 sensors. These firmware versions are tested against previous versions showing that several artificial features introduced by the data processing have been removed. Hence, it is recommended to use this recent firmware if attenuated backscatter is to be analysed. To allow for consistent processing of historic data, correction procedures are developed that account for the range-dependent electronic background signal and other artefacts detected in data collected with older firmware. Recommendations are made for the processing of attenuated backscatter observed with Vaisala CL31 sensors, including the estimation of noise which is not provided in the standard CL31 output. Taking these aspects into account, attenuated backscatter profiles from Vaisala CL31 ceilometers are considered to provide valuable information for a range of applications including, for example, atmospheric boundary layer studies, detection of elevated aerosol layers, and model verification.
Application of the 15N gas-flux method for measuring in situ N2 and N2O fluxes due to denitrification in natural and semi-natural terrestrial ecosystems and comparison with the acetylene inhibition technique
Authors: Sgouridis Fotis , Stott Andrew , Ullah Sami
Published: March 2016

Abstract. Soil denitrification is considered the most un-constrained process in the global N cycle due to uncertain in situ N2 flux measurements, particularly in natural and semi-natural terrestrial ecosystems. 15N tracer approaches can provide in situ measurements of both N2 and N2O simultaneously, but their use has been limited to fertilized agro-ecosystems due to the need for large 15N additions in order to detect 15N2 production against the high atmospheric N2. For 15N–N2 analyses, we have used an “in-house” laboratory designed and manufactured N2 preparation instrument which can be interfaced to any commercial continuous flow isotope ratio mass spectrometer (CF-IRMS). The N2 prep unit has gas purification steps and a copper-based reduction furnace, and allows the analysis of small gas injection volumes (4 µL) for 15N–N2 analysis. For the analysis of N2O, an automated Tracegas Preconcentrator (Isoprime Ltd) coupled to an IRMS was used to measure the 15N–N2O (4 mL gas injection volume). Consequently, the coefficient of variation for the determination of isotope ratios for N2 in air and in standard N2O (0.5 ppm) was better than 0.5 %. The 15N gas-flux method was adapted for application in natural and semi-natural land use types (peatlands, forests, and grasslands) by lowering the 15N tracer application rate to 0.04–0.5 kg 15N ha−1. The minimum detectable flux rates were 4 µg N m−2 h−1 and 0.2 ng N m−2 h−1 for the N2 and N2O fluxes respectively. Total denitrification rates measured by the acetylene inhibition technique in the same land use types correlated (r =  0.58) with the denitrification rates measured under the 15N gas-flux method, but were underestimated by a factor of 4, and this was partially attributed to the incomplete inhibition of N2O reduction to N2, under a relatively high soil moisture content, and/or the catalytic NO decomposition in the presence of acetylene. Even though relatively robust for in situ denitrification measurements, methodological uncertainties still exist in the estimation of N2 and N2O fluxes with the 15N gas-flux method due to issues related to non-homogenous distribution of the added tracer and subsoil gas diffusion using open-bottom chambers, particularly during longer incubation duration. Despite these uncertainties, the 15N gas-flux method constitutes a more reliable field technique for large-scale quantification of N2 and N2O fluxes in natural terrestrial ecosystems, thus significantly improving our ability to constrain ecosystem N budgets.
A process-based model for ammonia emission from urine patches, GAG (Generation of Ammonia from Grazing): description and sensitivity analysis
Authors: Móring Andrea , Vieno Massimo , Doherty Ruth M. , Laubach Johannes , Taghizadeh-Toosi Arezoo , Sutton Mark A.
Published: March 2016

Abstract. In this paper a new process-based, weather-driven model for ammonia (NH3) emission from a urine patch has been developed and its sensitivity to various factors assessed. The GAG model (Generation of Ammonia from Grazing) is capable of simulating the TAN (total ammoniacal nitrogen) and the water content of the soil under a urine patch and also soil pH dynamics. The model tests suggest that ammonia volatilization from a urine patch can be affected by the possible restart of urea hydrolysis after a rain event as well as CO2 emission from the soil. The vital role of temperature in NH3 exchange is supported by our model results; however, the GAG model provides only a modest overall temperature dependence in total NH3 emission compared with the literature. This, according to our findings, can be explained by the higher sensitivity to temperature close to urine application than in the later stages and may depend on interactions with other nitrogen cycling processes. In addition, we found that wind speed and relative humidity are also significant influencing factors. Considering that all the input parameters can be obtained for larger scales, GAG is potentially suitable for field and regional scale application, serving as a tool for further investigation of the effects of climate change on ammonia emissions and deposition.
Using present-day observations to detect when anthropogenic change forces surface ocean carbonate chemistry outside pre-industrial bounds
Authors: Sutton Adrienne J. , Sabine Christopher  L. , Feely Richard A. , Cai Wei-Jun , Cronin Meghan F. , McPhaden Michael J. , Morell Julio M. , Newton Jan A. , Noh Jae-Hoon , Olafsdottir Sólveig R. , Salisbury Joseph E. , Send Uwe , Vandemark Douglas C. , Weller Robert A.
Published: March 2016

Abstract. One of the major challenges to assessing the impact of ocean acidification on marine life is the need to better understand the magnitude of long-term change in the context of natural variability. This study addresses this need through a global synthesis of monthly pH and aragonite saturation state (Ωarag) climatologies for 12 open ocean, coastal, and coral reef locations using 3-hourly moored observations of surface seawater partial pressure of CO2 and pH collected together since as early as 2010. Mooring observations suggest open ocean subtropical and subarctic sites experience present-day surface pH and Ωarag conditions outside the bounds of pre-industrial variability throughout most, if not all, of the year. In general, coastal mooring sites experience more natural variability and thus, more overlap with pre-industrial conditions; however, present day Ωarag conditions surpass biologically relevant thresholds associated with ocean acidification impacts on Mytilus californianus (Ωarag < 1.8) and Crassostrea gigas (Ωarag < 2.0) larvae in the California Current Ecosystem (CCE) and Mya arenaria larvae in the Gulf of Maine (Ωarag < 1.6). At the most variable mooring locations in coastal systems of the CCE, subseasonal conditions approached Ωarag = 1. Global and regional models and data syntheses of ship-based observations tended to underestimate seasonal variability compared to mooring observations. Efforts such as this to characterize all modes of pH and Ωarag variability and change at key locations are fundamental to assessing present-day biological impacts of ocean acidification, further improving experimental design to interrogate organism response under real-world conditions, and improving predictive models and vulnerability assessments seeking to quantify the broader impacts of ocean acidification.
Integrated soil fertility management drives the effect of cover crops on GHG emissions in an irrigated field
Authors: Guardia Guillermo , Abalos Diego , García-Marco Sonia , Quemada Miguel , Alonso-Ayuso María , Cárdenas Laura M. , Dixon Elizabeth R. , Vallejo Antonio
Published: March 2016

Abstract. Agronomical and environmental benefits are associated with replacing winter fallow by cover crops (CC). Yet, the effect of this practice on nitrous oxide (N2O) emissions remains poorly understood. In this context, a field experiment was carried out under Mediterranean conditions to evaluate the effect of replacing the traditional winter fallow (F) by vetch (Vicia sativa L.; V) or barley (Hordeum vulgare L.; B) on greenhouse gas (GHG) emissions during the intercrop and the maize (Zea mays L.) cropping period. The maize was fertilized following Integrated Soil Fertility management (ISFM) criteria. Maize nitrogen (N) uptake, soil mineral N concentrations, soil temperature and moisture, dissolved organic carbon (DOC) and GHG fluxes were measured during the experiment. The ISFM resulted in low cumulative N2O emissions (0.57 to 0.75 kg N2O-N ha−1), yield-scaled N2O emissions (3–6 g N2O-N kg aboveground N uptake−1) and N surplus (31 to 56 kg N ha−1) for all treatments. Although CCs increased N2O emissions during the intercrop period compared to F (1.6 and 2.6 times in B and V, respectively), the ISFM resulted in similar cumulative emissions for the CCs and F at the end of the maize cropping period. The higher C:N ratio of the B residue led to a greater proportion of N2O losses from the synthetic fertilizer in these plots, when compared to V. No significant differences were observed in CH4 and CO2 fluxes at the end of the experiment. This study shows that the use of both legume and non-legume CCs combined with ISFM could provide, in addition to the advantages reported in previous studies, an opportunity to maximize agronomic efficiency (lowering synthetic N requirements for the subsequent cash crop) without increasing cumulative or yield-scaled N2O losses.
A coupled wave-3D hydrodynamics model of the Taranto Sea (Italy): a multiple-nesting approach
Authors: Gaeta Maria Gabriella , Samaras Achilleas G. , Federico Ivan , Archetti Renata
Published: March 2016

Abstract. The present work describes an operational strategy for the development of a multiscale modelling system, based on a multiple–nesting approach and open–source numerical models. The strategy was applied and validated for the Gulf of Taranto in South Italy, scaling large–scale oceanographic model results to high–resolution coupled wave – 3D hydrodynamics simulations for the area of Mar Grande in Taranto Sea. The spatial and temporal high – resolution simulations were performed using the open–source TELEMAC suite, forced by wind data from the COSMO–ME database, boundary wave spectra from the RON Buoy at Crotone, and results from the Southern Adriatic Northern Ionian coastal Forecasting System (SANIFS) regarding sea levels and current fields. Model validation was carried out using data collected in the Mar Grande basin from a fixed monitoring station and during an oceanographic campaign in October 2014. The overall agreement between measurements and model results in terms of waves, sea levels, surface currents, circulation patterns and vertical velocity profiles is deemed to be satisfactory, and the methodology followed in the process can constitute a useful tool for both research and operational applications on the same field and and as support of decisions for management and design of infrastructures.
sUAS and their application in observing geomorphological processes
Authors: Gallik Jozef , Bolešová Lenka
Published: March 2016

Abstract. Methodologies and procedures in processing gained data vary based on possibilities and needs of scientific projects. Technology moves ahead very fast. Application of different patents and remote control mechanisms has higher usage not only in military sector, but also in civil sector. These papers should help to get general overview in the choice of "small unmanned aircraft systems" (sUAS or commonly known as drones) for scientific purposes, for example remote sensing. Geomorphologic processes and the development of high mountain area are difficult for mapping and research with respect to accessibility of explored surface, slope of terrain, and mainly weather conditions that are rapidly changing. All high mountain areas in European countries are legislatively protected, and so various permissions and observation of strict procedures are needed, in order not to contaminate or not to have a negative influence on the environment. Nowadays several types of UAS and operating systems exist that could effectively help us in such protection, as well as in fully-fledged utilization when answering scientific questions.
On the path to the digital rock physics of gas hydrate bearing sediments – processing of in-situ synchrotron-tomography data
Authors: Sell Kathleen , Saenger Erik-H. , Falenty Andrzej , Chaouachi Marwen , Haberthür David , Enzmann Frieder , Kuhs Werner F. , Kersten Michael
Published: March 2016

Abstract. To date, very little is known about the distribution of gas hydrates in sedimentary matrices and the resulting matrix-pore network affecting the seismic properties at low hydrate concentration. Digital rock physics offers a unique solution to this issue yet requires good quality, high resolution 3D representations for the accurate modelling of petrophysical and transport properties. Although such models are readily available via in-situ synchrotron radiation X-ray tomography the analysis of such data asks for complex workflows and high computational power to maintain valuable results. Here, we present a best-practise procedure complementing data from Chaouachi et al. (Geochemistry, Geophysics, Geosystems 2015, 16 (6), 1711–1722) with data post-processing, including image enhancement and segmentation as well as numerical simulations in 3D using the derived results as a direct model input. The method presented opens a path to a model-free deduction of the properties of gas hydrate bearing sediments when aiming for in-situ experiments linked to synchrotron-based tomography and 3D modelling.
Delineating small karst watersheds based on digital elevation model and eco-hydrogeological principles
Authors: Luo Guang Jie , Wang Shi Jie , Bai Xiao Yong , Liu Xiu  Ming , Cheng An Yun
Published: March 2016

Abstract. Dominated by specific eco-hydrogeological backgrounds, a small watershed delineated by using the traditional method is always inauthentic in karst regions because it cannot accurately reflect the eco-hydrological process of the dual structure of the surface and subsurface. This study proposes a new method for the delineation of small watersheds based on digital elevation models (DEMs) and eco-hydrogeological principles in karst regions. This method is applied to one section of the tributary area (Sancha River) of the Yangtze River in China. By comparing the quantity, shape, superimposition, and characteristics of the internal hydrological process of a small watershed extracted by using the digital elevation model with that extracted by using the proposed method of this study, we conclude that the small karst watersheds extracted by the new method accurately reflect the hydrological process of the river basin. Furthermore, we propose that the minimum unit of the river basin in karst regions should be the watershed, whose exit is the corrosion and corrasion baselevel and a further division of watershed may cause a significant inconsistency with the true eco-hydrological process.
Challenges of NGO-to-state Referral in the Delivery of HIV Prevention Programs in Ukraine Supported by the Global Fund
Authors: McGill Svetlana
Published: March 2016

Background: Ukraine has one of the world’s fastest growing HIV rates and was one of the largest recipients of funding from the Global Fund to Fight AIDS, Tuberculosis and Malaria (GF). The objective of this study was to close the gaps in the literature on the delivery of HIV prevention services by NGOs and the perceptions of NGO delivered services, using as an example HIV prevention programs in Ukraine funded by the GF.Methods: The aim of this qualitative study was to determine how NGO-based services were implemented in the context of a state-owned healthcare system of Ukraine. An ethnographic study, which included 50 participant interviews, was conducted in three oblasts in Ukraine and in the capital, Kyiv, between 2011 and 2013. This article presents some of the findings that emerged from the analysis.Results: Participants reported that NGOs were focused more on reporting numbers of rapid tests, and less on motivating clients to continue onto treatment. The role division between NGOs and the state in HIV services was largely perceived by participants as unclear and challenging. Overall,  lack of clarity on the role of government healthcare providers and NGOs in providing HIV services compromised the process of finding, referring, and retaining HIV patients in care.Conclusions: Gaps in linking HIV patients to the HIV care continuum have been identified as a potentially problematic issue in delivery of HIV prevention services by GF funded NGOs. With an anticipated GF exit from Ukraine, the lack of clearly defined NGO-to-state referrals of HIV patients complicates the transition of NGO run services into state funding. Further steps to improve referral systems are necessary to ensure a smooth transition and enable Ukraine to fight its HIV epidemic effectively.
A Longitudinal View of Look at the Effectiveness of Elicited Imitation with Computer Assisted Pronunciation Training (CAPT)
Authors: Hsu Liwei
Published: March 2016

It is the aim for most EFL learners to have a clear pronunciation in English; however, pronunciation training has always been a challenge for EFL teachers and learners alike. The advent of Computer Assisted Pronunciation Training (CAPT) seems to be the solution to this problem. This longitudinal study adopted a latent growth curve to describe 30 EFL learner’s (N = 30) development of imitated pronunciation in English as well as their satisfaction regarding CAPT. These 30 participants were randomly assigned to the experimental group (N = 18) and control group (N = 12). There were no significant differences among the participants in their pronunciation of English or attitudes toward CAPT at the beginning of this study. After 16 months of training, the growth curve analysis showed that participants in the CAPT group made significantly greater development in English pronunciation, and they were more satisfied with the CAPT. The large effect size indicated that the grouping was the major effect that led to a significant difference in satisfaction. Moreover, the qualitative data derived from focus-group interviews confirmed the benefits of CAPT in participant’s pronunciation training. These findings suggest that EFL learner’s opportunities to conduct elicited imitation with the help of ASR-CAPT will be helpful for their development of imitated pronunciation in English and increase their satisfaction of it, which is a key aspect in the effectiveness of pronunciation training. 
Periprosthetic Pathology in ‘At Risk’ Ceramic-on-Polyethylene Total HIP Arthroplasty: A Clinical Study Using MARS-MRI in 50 Patients
Authors: Das Dirk H. , van der Weegen Walter , Wullems Jorgen A. , Brakel Koen , Sijbesma Thea , Nelissen Rob G.
Published: March 2016

Purpose

Recent studies of metal-on-metal (MoM) total hip arthroplasty (THA) using metal-artefact-reducing-sequence software for magnetic resonance Imaging (MARS-MRI) have revealed remarkable soft tissue pathology around the hip, usually referred to as pseudotumours. Case reports describe identical pathology in non-MoM THA, but descriptive overviews of MRI abnormalities in patients with non-MoM prosthesis are scarce.

Methods

A clinical study in a cohort of 50 ceramic-on-polyethylene (CoP) THA selected for high risk of peri-prosthetic pathology including 2 subgroups: (i) 40 patients with a high polyethylene (PE) wear rate (>0.2 mm per year) and 5-12 years follow-up; (ii) 10 patients with a 2 to 5 years follow-up and a documented history of persistent complaints. All patients were clinically evaluated, MARS-MRIs were completed and chrome and cobalt serum samples were taken.

Results

17 scans were normal (34%). Periprosthetic fluid collections were seen as a bursae iliopsoas (n = 12, 24%), in the trochanter bursae (n = 4, 8%) and in the surgical tract (n = 9, 18%). 1 case demonstrated a cyst on MARS-MRI resembling a pseudotumour as seen with MoM THA (2%). Intraosseous acetabular cysts were seen in 12 cases (24%), intraosseous trochanteric cysts in 10 cases (20%).

Conclusions

Soft tissue abnormalities after non-MoM THA are common in selected patients and can be clearly visualised with MARS-MRI. Pseudotumours as seen on MARS-MRI do occur in non-MoM hip arthroplasty but with low prevalence.
E1 Detection as Prognosticator in Human Papillomavirus-Positive Head and Neck Cancers
Authors: Vivenza Daniela , Lo Nigro Cristiana , Denaro Nerina , Fortunato Mirella , Monteverde Martino , Tonissi Federica , Lattanzio Laura , Astesana Valentina , Gloghini Annunziata , Volpi Chiara C. , Russi Elvio , Merlano Marco C.
Published: March 2016

Purpose

HPV-related locally advanced head and neck cancers (LA-HNCs) show a good prognosis. This study aimed to investigate the HPV prevalence in LA-HNCs and compare the prognostic value of E1, E6 and L1 genomic viral fragments and p16, individually and in combination, in order to find the best prognosticator in terms of overall survival (OS) and progression-free survival (PFS).

Patients and Methods

HPV16 was searched in 255 LA-HNC formalin-fixed paraffin-embedded tumor tissues, 89 oropharyngeal cancers (OPCs), and 166 non-OPCs by DNA-PCR with 3 primer pairs. p16 was analyzed by immunohistochemistry in 235 patients.

Results

The prevalence of positive samples decreased constantly from E6 to L1 and E1 in both OPCs and non-OPCs. Each LA-HNC patient highlighted variable positivity for each fragment. OPCs showed a higher prevalence of positive samples compared to non-OPCs. Positive coexistence of all the fragments was more common in OPCs (31.5%) than non-OPCs (4.2%), and E1 detection was always associated with E6 and L1. E1-positive OPCs showed improved OS (p = 0.012) and PFS (p = 0.036), while L1- or E6-positive ones did not. p16-positive patients were more prevalent in the OPC (29.8%) than the non-OPC group (7.3%) (p<0.0001) and its prognostic value was not superior to that of E1. However, the multivariate Cox analysis which included E1, L1, E6 status and p16 expression did not show a significant p value.

Conclusions

Though HPV16 positivity measured by DNA-PCR was higher for L1 and E6, they performed weakly as prognosticators; E1 might become a strong prognostic marker for OS and PFS in OPCs.
Assessment of Micro-Mechanical Variations in Experimental Arteriovenous Fistulae using Atomic Force Microscopy
Authors: Laurito Tyler , Sueiras Vivian , Fernandez Natasha , Escobar Luis A. , Martinez Laisel , Andreopoulos Fotios , Salman Loay H. , Vazquez-Padron Roberto I. , Ziebarth Noël M.
Published: March 2016

Purpose

This study presents a method to quantify micro-stiffness variations in experimental arteriovenous fistulae (AVF).

Methods

AVF created by anastomosing the superficial epigastric vein to the femoral artery in Sprague-Dawley rats were allowed to remodel for 21 days before being harvested and preserved in culture medium. A custom atomic force microscope was used to measure microvascular stiffness (Young's modulus) in three areas of the AVF: the inflow artery, the juxta-anastomotic area, and the outflow vein. Morphometric measurements and collagen and elastin contents were also determined.

Results

Atomic force microscopy indentation revealed an increased stiffness in the juxta-anastomotic area of the AVF compared to the outflow vein and inflow artery. The juxta-anastomotic area was also significantly stiffer than the contralateral vein. The lack of elasticity (higher Young's modulus) of the juxta-anastomotic region was associated with a thicker vascular wall that was rich in collagen but poor in elastin.

Conclusions

This study demonstrates for the first time the feasibility of using atomic force microscopy to measure local stiffness variations in experimental AVF. This technique could be instrumental in advancing our understanding of how micro-spatial organization of the AVF wall determines the overall biomechanical performance of this type of vascular access.