bluuebunny/crossref_metadata_2025 huggingface dataset:
Toward a comprehensive global electric circuit model: Atmospheric conductivity and its variability in CESM1(WACCM) model simulations
Authors: G. Baumgaertner A. J. , Thayer J. P. , Neely R. R. , Lucas G.
Published: August 2013

As an important step in further modeling and understanding the global electric circuit, the Community Earth System Model (CESM1) has been extended to provide a calculation of conductivity in the troposphere and stratosphere. Conductivity depends on ion mobility and ion concentration, the latter being controlled by a number of ion production and loss processes. This leads to a complex dependency of conductivity on most importantly galactic cosmic ray flux, radon emissions from the Earth's surface, aerosol number concentrations, clouds, and temperature. To cover this variety in parameters for calculating and evaluating conductivity, an Earth system model is extremely useful. Here the extension of CESM1 to calculate conductivity is described, and the results are discussed with a focus on their spatial and temporal variabilities. The results are also compared to balloon and aircraft measurements, and good agreement is found for undisturbed conditions and during a solar proton event. The conductivity model implementation is a significant improvement to previous studies because of the high‐quality, high‐resolution model data input. Notably, the aerosol representation provided by off‐line calculations of tropospheric and stratospheric aerosol using the Community Aerosol and Radiation Model for Atmospheres as part of CESM1(WACCM) (Whole Atmosphere Community Climate Model) provides a realistic computation of the impact of the background aerosol distribution for the first time. In addition to the novel high‐resolution information on conductivity, it is found that an intra‐annual cycle exists in the total global resistance, varying between 220 and 245 Ω. The model shows that this cycle is driven equally by seasonal aerosol and cloud variations.
Identification and uncertainty estimation of vertical reflectivity profiles using a Lagrangian approach to support quantitative precipitation measurements by weather radar
Authors: Hazenberg P. , Torfs P. J. J. F. , Leijnse H. , Delrieu G. , Uijlenhoet R.
Published: August 2013

This paper presents a novel approach to estimate the vertical profile of reflectivity (VPR) from volumetric weather radar data using both a traditional Eulerian as well as a newly proposed Lagrangian implementation. For this latter implementation, the recently developed Rotational Carpenter Square Cluster Algorithm (RoCaSCA) is used to delineate precipitation regions at different reflectivity levels. A piecewise linear VPR is estimated for either stratiform or neither stratiform/convective precipitation. As a second aspect of this paper, a novel approach is presented which is able to account for the impact of VPR uncertainty on the estimated radar rainfall variability. Results show that implementation of the VPR identification and correction procedure has a positive impact on quantitative precipitation estimates from radar. Unfortunately, visibility problems severely limit the impact of the Lagrangian implementation beyond distances of 100 km. However, by combining this procedure with the global Eulerian VPR estimation procedure for a given rainfall type (stratiform and neither stratiform/convective), the quality of the quantitative precipitation estimates increases up to a distance of 150 km. Analyses of the impact of VPR uncertainty shows that this aspect accounts for a large fraction of the differences between weather radar rainfall estimates and rain gauge measurements.
Collagen scaffold meniscus implant integration in a canine model: A histological analysis
Authors: Hansen Robert , Bryk Eli , Vigorita Vincent
Published: August 2013

In the situation of an irreparable meniscus tear, an implant comparable to a normal meniscus is an attractive option. Using a canine model, we assessed the early and late histologic response to a tissue engineered meniscal collagen scaffold (CS). All animals received bilateral arthrotomies, and all joints receiving the CS had an 80% resection of the meniscus. Animals were sacrificed at 3 and 6 weeks, and 12, 13, and 17 months. The CS/tissue complex and host meniscal rim were sectioned for histologic examination with specific focus on the extracellular matrix, angiogenesis, cellular resorption of the scaffold, scaffold appearance, and CS/Host integration. Early histologic samples (3–6 weeks) revealed active angiogenesis and fibrin clots evolving into cellular granulation type tissue. At 12 months, a mature fibrochondrocytic matrix was depositing with gradations of dissolution and integration of the CS implant. Maturing CS/host integration was observed at 18 months. Active cellular resorption of the implant decreased over time. Four cases showed a mild non‐specific chronic inflammation and one additional case showed inflammatory engulfment of the scaffold with giant cells at 3 weeks. No evidence of infection either clinically or histologically was observed at any time point. Overall, this histologic analysis demonstrated the active integration of a meniscal like cartilage into a tissue engineered biological scaffold in a canine model. © 2013 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 31:1914–1919, 2013
Analysis of microRNAs expressions in chondrosarcoma
Authors: Yoshitaka Teruhito , Kawai Akira , Miyaki Shigeru , Numoto Kunihiko , Kikuta Kazutaka , Ozaki Toshifumi , Lotz Martin , Asahara Hiroshi
Published: August 2013

MicroRNAs (miRNAs) are small non‐coding RNAs capable of inhibiting gene expression post‐transcriptionally and expression profiling can provide therapeutic targets and tools for cancer diagnosis. Chondrosarcoma is a mesenchymal tumor with unknown cause and differentiation status. Here, we profiled miRNA expression of chondrosarcoma, namely clinical samples from human conventional chondrosarcoma tissue, established chondrosarcoma cell lines, and primary non‐tumorous adult articular chondrocytes, by miRNA array and quantitative real‐time PCR. A wide variety of miRNAs were differently downregulated in chondrosarcoma compared to non‐tumorous articular chondrocytes; 27 miRNAs: miR‐10b, 23b, 24‐1*, 27b, 100, 134, 136, 136*, 138, 181d, 186, 193b, 221*, 222, 335, 337‐5p, 376a, 376a*, 376b, 376c, 377, 454, 495, 497, 505, 574‐3p, and 660, were significantly downregulated in chondrosarcoma and only 2: miR‐96 and 183, were upregulated. We further validated the expression levels of miRNAs by quantitative real‐time PCR for miR‐181a, let‐7a, 100, 222, 136, 376a, and 335 in extended number of chondrosarcoma clinical samples. Among them, all except miR‐181a were found to be significantly downregulated in chondrosarcoma derived samples. The findings provide potential diagnostic value and new molecular understanding of chondrosarcoma. © 2013 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 31:1992–1998, 2013
Heavy metal accumulation in leaves affects physiological performance and litter quality of Quercus ilex L.
Authors: Maisto Giulia , Santorufo Lucia , Arena Carmen
Published: August 2013

This study aimed to investigate the relationships between leaf functional modifications and heavy metal concentrations of Quercus ilex L., a good bioindicator of air quality. In addition, as metal concentration in litter plays an important role in decomposition and, in turn, in biogeochemical cycles, samples of undecomposed and whole‐leaf litter were analyzed for heavy metals. Leaves and leaf litter of Q. ilex were collected at six sites (roadsides, motorway sites, and urban parks) in Naples (Southern Italy) and characterized for Cd, Cr, Cu, Ni, and Pb concentrations. The investigated functional leaf traits were: leaf area (LA), specific leaf area (SLA), leaf dry‐matter content (LDMC), water content (WC), leaf relative water content (RWC), maximal PSII photochemical efficiency (Fv/Fm, variable fluorescence / maximal fluorescence), and total chlorophyll concentration. The motorways were the most contaminated sites, and Pb was the main responsible source of contamination. The metal contamination caused slight variation of Fv/Fm, suggesting that metals did not significantly alter functionality of the photosynthetic apparatus. On the other hand, it can be supposed that higher leaf deposit can cause an increase of pigment biosynthesis in response to the shading increase caused by dust deposition.
Nutrient‐rich compost versus nutrient‐poor vermicompost as growth media for ornamental‐plant production
Authors: Belda Rosa M. , Mendoza‐Hernández Daicy , Fornes Fernando
Published: August 2013

A comparative study on the suitability of one compost and two vermicomposts, obtained from the same batch of tomato‐crop waste, as growth media for ornamental plant production was carried out. Each material was mixed with Sphagnum peat at 100 : 0, 75 : 25, 50 : 50, 25 : 75, and 0 : 100 (peat control) proportions by volume. Two ornamentals (Calendula officinalis, Viola cornuta) were sown and grown in the 13 substrates. Substrates were characterized physically and chemically. Seed germination, total leaf chlorophyll (SPAD units), plant growth, and plant nutrient concentrations were determined. The compost and the vermicomposts were markedly different from peat. Compost and the vermicomposts had greater bulk density and lower total porosity than peat. Compost had larger aeration and lower water‐holding capacity than vermicomposts and peat. Compost and vermicomposts were alkaline (pH = 8.8 on average) whilst peat was acidic (pH = 5.9). Electrical conductivity was low in peat (0.23 dS m–1) and vermicomposts (0.65 dS m–1), and high in compost (2.85 dS m–1) due to the high concentrations of K+ and SO$ _4^{2-} $. Mixing compost and vermicomposts with peat produced substrates with intermediate characteristics. Physical properties were within adequate range for all mixes except for the compost ones. pH was within adequate range only in pure peat, and salinity was extremely high in the compost mixes. Compost was phytotoxic, as shown by the strong reduction of seed germination, chlorophyll content, and plant growth of both ornamentals. Vermicomposts did not affect seed germination but reduced plant growth, though much less than compost. Mixing these materials with peat improved germination and growth. The diluted materials (compost at the 25 : 75 and vermicomposts at the 50 : 50 and 25 : 75 proportions) produced good‐quality plants.
Soil‐quality‐index model for assessing the impact of groundwater on soil in an intensively farmed coastal area of E China
Authors: Yao Rong‐Jiang , Yang Jing‐Song , Gao Peng , Zhang Jian‐Bin , Jin Wen‐Hui , Yu Shi‐Peng
Published: August 2013

Soil quality is important in measuring sustainable land‐use and soil‐management practices. It is usually assessed by evaluating important physical, chemical, and biological soil properties. For this study, a site‐specific 22 variables representing pertinent soil (0–10 cm) and groundwater properties were selected as potential soil‐quality indicators in a coastal salt‐affected farmland of E China. To investigate the role of groundwater in soil‐quality assessment, we designed two sets of minimum data sets (MDSs). Minimum data set 1 (MDS1) had inputs of the 19 soil chemical and physical properties whereas MDS2 was based on the 22 soil and groundwater properties. Using principal‐component analysis, discriminant analysis, and soil‐quality‐index (SQI) model, we demonstrated the procedures of MDS selection, indicator normalization, and integration of MDS into SQI value for soils used for the two cropping systems. Results indicated selection of SOCD, AK, and ρb as MDS1 indicators but MDS2 indicators included SOM, SOCD, Cl, Na, WTg, and ECg. These were found to be the most effective discriminators between the two cropping systems. Available K (AK) made greatest contribution to SQI using MDS1 indicators, however, WTg, ECg, and Cl were the greatest contributors to the SQI for MDS2. Contribution of SOCD to SQI was severely inhibited in cotton–barley rotation system while ECg and WTg contributions to SQI were inhibited in rice–rape rotation system. In general, cotton–barley rotation system had a better soil quality over rice–rape rotation system as the former had higher SQI values than the latter for both MDSs. Crop parameters did also exhibit significant relationship with the SQI values using MDS2 but it was not significant for MDS1. Our results suggest that in addition to soil chemical, physical, and biological indicators, groundwater properties particularly the WTg and ECg are also important for assessing soil quality in an intensively farmed coastal area.
Predicting apple (cv. Elshof) postharvest dry matter and soluble solids content with near infrared spectroscopy
Authors: Travers Sylvia , Bertelsen Marianne G , Kucheryavskiy Sergey V
Published: August 2013

BACKGROUND

Fruit dry matter (DM) and soluble solids content (SSC) are primarily composed of carbohydrate and are standard parameters for assessing quality. Near infrared spectroscopy provides potential for non‐destructive fruit quality analysis but the collinearity between DM and SSC is an issue for prediction. Shorter wavelength spectra have been used for the prediction of fruit DM and SSC, but radiation between 1000 and 2500 nm may be suitable for distinguishing between the two forms of carbohydrate.

RESULTS

Spectra and DM and SSC samples were taken for a total of 450 ‘Elshof’ apples 30, 58 and 93 days after harvest. Regression models were built using the interval partial least squares method. Prediction models for DM and SSC for each day yielded R2 values between 0.63 and 0.86 and residual predictive deviations (RPDs) between 1.7 and 2.7 for DM, and R2 = 0.76–0.85 and RPDs = 2.2–2.6 for SSC.

CONCLUSION

Model RPD values were not high enough for general quantitative predictions, although they compare well to previous work. Certain factors affected model success, including changes in fruit physiology over time and the range of reference data. The complexity of absorbance spectra for DM and SSC plus their strong correlation suggests that prediction models cannot easily distinguish between soluble and non‐soluble forms of carbohydrate. © 2013 Society of Chemical Industry
Relationship between condensed tannin structures and their ability to precipitate feed proteins in the rumen
Authors: Lorenz Martin M , Alkhafadji Loy , Stringano Elisabetta , Nilsson Staffan , Mueller‐Harvey Irene , Udén Peter
Published: August 2013

BACKGROUND

Tannins can bind to and precipitate protein by forming insoluble complexes resistant to fermentation and with a positive effect on protein utilisation by ruminants. Three protein types, Rubisco, rapeseed protein and bovine serum albumin (a single high‐molecular weight protein), were used to test the effects of increasing concentrations of structurally different condensed tannins on protein solubility/precipitation.

RESULTS

Protein type (PT) influenced solubility after addition of condensed tannins (P < 0.001) in the order: Rubisco < rapeseed < BSA (P < 0.05). The type of condensed tannin (CT) affected protein solubility (P = 0.001) with a CT × PT interaction (P = 0.001). Mean degree of polymerisation, proportions of cis‐ versus trans‐flavanol subunits or prodelphinidins versus procyanidins among CTs could not explain precipitation capacities. Increasing tannin concentration decreased protein solubility (P < 0.001) with a PT × CT concentration interaction. The proportion of low‐molecular weight rapeseed proteins remaining in solution increased with CT concentration but not with Rubisco.

CONCLUSIONS

Results of this study suggest that PT and CT type are both of importance for protein precipitation but that the CT structures investigated did not allow identification of parameters that contribute most to precipitation. It is possible that the three‐dimensional structures of tannins and proteins may be more important factors in tannin–protein interactions. © 2013 Society of Chemical Industry
Role of whey proteins in combating geriatric disorders
Authors: V Sreeja , Jana Atanu , Aparnathi Kishore , Prajapati Jashbhai
Published: August 2013

Ageing in humans is usually accompanied by deterioration in physical fitness and increased susceptibility to disease, adding to the economic burden of the person concerned. Inadequate food intake, reduced desire to eat, decline in food digestion or absorption, compromise in nutritional metabolic pathways, poor dental hygiene or preponderance of chronic diseases, which are commonly found in the elderly, can lead to an increased risk of under‐nutrition. Adequate dietary nutrition has an undisputed role in healthy ageing. Among the various nutrients, proteins play an important role in geriatric health. This review emphasizes the nutritional aspects of milk‐based whey proteins and their role in tackling health problems in the geriatric population. Nutritionally rich whey protein constituents such as β‐lactoglobulin, α‐lactalbumin, bovine serum albumin, lactoferrin and proteose peptone have all been reported to have a plethora of functional roles in various biological processes and organ systems in geriatrics and thus help in the management of geriatric health problems through proper nutrition. © 2013 Society of Chemical Industry
Effect of two Spanish breeds and diet on beef quality including consumer preferences
Authors: Ripoll Guillermo , Blanco Mireia , Albertí Pere , Panea Begoña , Joy Margalida , Casasús Isabel
Published: August 2013

BACKGROUND

Farmers in dry mountain areas are changing their management strategies to improve livestock farming efficiency, by using different forages or different breeds. The effect of breed (Parda de Montaña vs. Pirenaica) and finishing diet (grazing on meadows vs. a total mixed ration (50% alfalfa, 40% maize grain, 10% straw)) on carcass characteristics and meat quality of steers was studied.

RESULTS

Parda de Montaña had a greater (P < 0.01) amount of intramuscular fat than Pirenaica. The finishing diet did not influence carcass fat color, but fatty acid composition was slightly affected. Finishing steers on a total mixed ration increased the percentage of fat of the 10th rib (P < 0.001). Supplementation with concentrates increased the diet energy concentration and also increased the dressing percentage.

CONCLUSIONS

Both breeds had similar carcass characteristics. Consumers preferred beef from the Pirenaica breed because of its greater tenderness. Consumers did not differentiate between beef from animals fed different finishing diets. However, consumers who like meat very much preferred meat aged in a cooler at 4 °C for 15 days rather than 8 days. © 2013 Society of Chemical Industry
Management of raccoon roundworm in free‐ranging raccoon populations via anthelmintic baiting
Authors: Smyser Timothy J. , Page L. Kristen , Johnson Scott A. , Hudson Cassie M. , Kellner Kenneth F. , Swihart Robert K. , Rhodes Olin E.
Published: August 2013

Raccoon roundworm (Baylisascaris procyonis), a common gastrointestinal parasite of the raccoon (Procyon lotor), has been implicated in population declines of Allegheny woodrats (Neotoma magister). Medicinal baiting is a viable tool in wildlife disease management although unique challenges exist for pathogenic systems in which the host can be immediately re‐infected following treatment. Our goals were to evaluate the efficacy of using monthly distribution of anthelmintic baits to reduce the prevalence of B. procyonis infection in raccoons and to quantify patterns and rates of bait acceptance among populations repeatedly exposed to medicinal baits. We distributed baits monthly at a density of 200/km2 throughout 300‐m buffer areas surrounding woodrat habitats in Indiana. We conducted raccoon latrine surveys annually to quantify the effect of treatment on roundworm prevalence and used remote cameras to identify the species contacting baits and determine the rate at which baits were removed. We observed declines in B. procyonis prevalence in response to treatment, but our ability to resolve statistical differences was limited by low pretreatment prevalence and high annual variability. Baits were removed rapidly from camera stations with 60% taken within 24 hours, 80% within 48 hours, and 90% within 72 hours. Virginia opossums (Didelphis virginiana) removed 51% of baits whereas raccoons removed 44%. Identification of opossums as the predominant consumer of baits emphasizes the limitations imposed by non‐target bait consumption for mitigation of B. procyonis and other wildlife diseases. The rapid removal of baits despite repeated bait exposure suggests that habituation did not result in bait aversion and fishmeal baits are a viable delivery system for mitigation of raccoon‐borne diseases requiring repeated treatments. Similar treatment measures may facilitate conservation of Allegheny woodrats in habitats with high rates of B. procyonis‐related mortality and could be used to reduce human exposure to this zoonotic parasite. © 2013 The Wildlife Society.
Soil and Water Assessment Tool Soil Loss Simulation at the Sub‐Basin Scale in the Alt Penedès–Anoia Vineyard Region (Ne Spain) in the 2000s
Authors: Martínez‐Casasnovas José A. , Ramos Maria C. , Benites Grace
Published: August 2013

This paper evaluates soil loss due to water erosion in an area of 32,362 ha with a predominant land use of vineyards (Alt Penedès–Anoia region, Catalonia, Spain). The Soil and Water Assessment Tool (SWAT) was used incorporating daily climatic data for the period 2000–2010 and also detailed soil and land use maps. Particular attention was given to the universal soil loss equation cover and management factor (C factor) of vineyards, with a minimum value of 0·15 being determined for this crop. The model was calibrated using daily flow data for the year 2010, which yielded satisfactory results. Even so, significant differences were obtained on days with high‐intensity rainfall events, when the model overestimated runoff and peak discharge. In these vineyards, the simulated average soil losses per sub‐basin ranged between 0·13 and 9·73 Mg ha−1 y−1, with maximum values of between 26·32 and 42·60 Mg ha−1 y−1 registered in fine‐loamy soils developed on unconsolidated Tertiary marls. Other findings were related to problems associated with SWAT calibration under Mediterranean conditions characterised by major climate variability and high‐intensity rainfall events. Copyright © 2013 John Wiley & Sons, Ltd.
Influence of Different Bryophyte Carpets on Vascular Plant Establishment Around Pools in Restored Peatlands
Authors: Laberge Virginie , Hugron Sandrine , Rochefort Line , Poulin Monique
Published: August 2013

Vascular plants associated to natural peatland pools do not spontaneously colonize edges of man‐made pools in restored peatlands and have proven to be recalcitrant to the usual restoration techniques. The goal of this study was to evaluate the effect of the species used as a seedbed (Cladopodiella fluitans, Sphagnum cuspidatum, or Sphagnum magellanicum) and its developmental stage (established carpet or newly reintroduced fragments) on establishment success in the field of the seeds of four vascular species: Carex limosa, Carex magellanica, Carex oligosperma, and Scheuchzeria palustris. The germination rate was measured after one season and growth after two seasons. Seedbed composition and developmental stage had no effect on Carex, whereas the germination of S. palustris was higher on S. cuspidatum. Growth of vascular plants was slightly improved on S. magellanicum carpets and was lower on seedbeds of C. fluitans. Our results lead us to recommend seeding at the same time as bryophyte fragments are spread and fostering introduction of Sphagnum mosses, preferably to C. fluitans, around artificial pool edges. Copyright © 2013 John Wiley & Sons, Ltd.
Serum concentrations of perfluorinated alkyl acids and their associations with diet and personal characteristics among Swedish adults
Authors: Bjermo Helena , Darnerud Per Ola , Pearson Monika , Barbieri Heléne Enghardt , Lindroos Anna Karin , Nälsén Cecilia , Lindh Christian H. , Jönsson Bo A. G. , Glynn Anders
Published: August 2013

Scope

In this study, food is suggested as a major source of human exposure to perfluorinated alkyl acids (PFAA). We investigated relations between serum levels of PFAA in adults and diet/lifestyle factors nationwide in Sweden.

Methods and results

In 2010–2011, adults (18–80 years, N = 270) recorded their diet for 4 days and answered a food frequency questionnaire. PFAA were measured in blood serum as well as v‐3 fatty acids in plasma phospholipids as a biomarker for fish consumption. Higher levels of PFAA were associated with male sex, increased age, and higher education. Women reporting full breastfeeding for ≥12 months had 32–44% lower levels of perfluorooctane sulfonate, perfluorooctanoic acid, and perfluorohexane sulfonate than women who never nursed their infants full‐time. Serum perfluorooctane sulfonate, perfluorononanoic acid, perfluorodecanoic acid, and perfluoroundecanoic acid were positively related to n‐3 fatty acids in plasma (partial r = 0.19–0.34, p ≤ 0.05).

Conclusion

The relatively strong correlations between biomarkers of fish consumption and certain PFAA suggest that PFAA exposure should be taken into account in health risk and benefit assessment of fish consumption. Breastfeeding appears to be a major source of elimination of certain PFAA among women, and consequently PFAA exposure of nursed infants could be significant.
Minimal clinically important difference in myasthenia gravis: Outcomes from a randomized trial
Authors: Katzberg Hans D. , Barnett Carolina , Merkies Ingemar S.J. , Bril Vera
Published: August 2013

Introduction: The minimal clinically important difference (MCID) is the smallest outcome change that has clinical significance. Its use has not been established in the study of myasthenia gravis (MG). Methods: Patients from a published intravenous immunoglobulin (IVIg) vs. placebo study were studied. One anchor‐based and 3 distribution‐based techniques were used to identify quantitative myasthenia gravis score (QMGS), repetitive nerve stimulation (RNS), and single‐fiber electromyography (SFEMG) MCID cut‐offs. Patients with a change‐score exceeding MCID cut‐offs were compared. Results: MCID cut‐offs were below a QMGS change of 3.0. Anchor‐based and 1 × SEM cut‐offs showed 58.3% vs. 30.7% responders (P = 0.017), ½ SD 54.2% vs. 19.2% responders (P = 0.018), and effect size 0.519 vs. 0.164 (P = 0.011) in IVIg vs. placebo. Anchor‐based (P = 0.73) and effect‐size (P = 0.41) MCID cut‐offs did not show a difference between IVIg and placebo. MCID methods did not produce meaningful RNS cut‐offs. Conclusions: QMGS MCID values provide clinically relevant information and are recommended in MG trials. MCID analysis shows that improvement in MG patients treated with IVIg reflects clinically meaningful changes. Muscle Nerve 49: 661–665, 2014
Mapping the consumption of government communication: a qualitative study in Germany
Authors: Heinze Jana , Schneider Helmut , Ferié Frederik
Published: August 2013

Successful communication between citizens and government is critical for the effective implementation of governance. Although government communication is highly relevant to society, few governments fully exploit the potential benefits of the direct communication instruments at their disposal. To establish foundations for encouraging various forms of government communication, this article starts by examining its reception among German focus groups and thus offering general implications for successful, citizen‐sensitive government communication. The results suggest the need for better articulation of interests in government communication, such that they appear more egalitarian, closer to the citizen, and online—that is, successful government communication demands considerable proximity to citizens, interactive feedback channels, and systematic participation by citizens in political processes. Copyright © 2013 John Wiley & Sons, Ltd.
Holocene shifts of the Subtropical Shelf Front off southeastern South America controlled by high and low latitude atmospheric forcings
Authors: Bender Vera B. , Hanebuth Till J. J. , Chiessi Cristiano M.
Published: August 2013

Over the Uruguayan shelf and uppermost slope, the coalescence of northward flowing Subantarctic Shelf Water and southward flowing Subtropical Shelf Water forms a distinct thermohaline front termed the Subtropical Shelf Front (STSF). Running in a SW direction diagonally across the shelf from the coastal waters at 32°S toward the shelf break at ca. 36°S, the STSF represents the shelfward extension of the Brazil‐Malvinas Confluence zone. This study reconstructs latitudinal STSF shifts during the Holocene based on benthic foraminifera δ18O and δ13C, total organic carbon, carbonate contents, Ti/Ca, and grain size distribution from a high‐accumulation sedimentary record located at an uppermost continental‐slope terrace. Our data provide direct evidence for: (1) a southern STSF position (to the South of the core site) at the beginning of the early Holocene (>9.4 cal ka BP) linked to a more southerly position of the Southern Westerly Winds in combination with restricted shelf circulation intensity due to lower sea level; (2) a gradual STSF northward migration (bypassing the core site toward the North) primarily forced by the northward migration of the Southern Westerly Winds from 9.4 cal ka BP onward; (3) a relatively stable position of the front in the interval between 7.2 and 4.0 cal ka BP; (4) millennial‐scale latitudinal oscillations close to 36°S of the STSF after 4.0 cal ka BP probably linked to the intensification in El Niño Southern Oscillation; and (5) a southward migration of the STSF during the last 200 years possibly linked to anthropogenic influences on the atmosphere.
Testing the impact of diagenesis on the δ18O and δ13C of benthic foraminiferal calcite from a sediment burial depth transect in the equatorial Pacific
Authors: Edgar Kirsty M. , Pälike Heiko , Wilson Paul A.
Published: August 2013

Stable oxygen and carbon isotope (δ18O and δ13C) values measured in foraminiferal calcite are one of the primary tools used in paleoceanography. Diagenetic recrystallization of foraminiferal calcite can act to reset primary isotopic values, but its effects are typically poorly quantified. Here we test the impact of early stage diagenesis on stable isotope records generated from a suite of drill sites in the equatorial Pacific Ocean recovered during Ocean Drilling Program Leg 199 and Integrated Ocean Drilling Program Expedition 320. Our selected sites form paleowater and burial depth transects, with excellent stratigraphic control allowing us to confidently correlate our records. We observe large intersite differences in the preservation state of benthic foraminiferal calcite, implying very different recrystallization histories, but negligible intersite offsets in benthic δ18O and δ13C values. We infer that diagenetic alteration of benthic foraminiferal calcite (in sedimentary oozes) must predominantly occur at shallow burial depths (<100 m) where offsets in both the temperature and isotopic composition of waters in which the foraminifera calcified and pore waters in which diagenesis occurs are small. Our results suggest that even extensive recrystallization of benthic foraminiferal calcite results in minimal shifts from primary δ18O and δ13C values. This finding supports the long‐held suspicion that diagenetic alteration of foraminiferal calcite is less problematic in benthic than in planktic foraminifera and that in deep‐sea sediments routinely employed for paleoceanographic studies benthic foraminifera are robust recorders of stable isotope values in the fossil record.
Clinical characteristics and treatment outcome of childhood acute lymphoblastic leukemia in Saudi Arabia: A multi‐institutional retrospective national collaborative study
Authors: Al‐Sudairy Reem , Al‐Nasser Abdullah , Alsultan Abdulrahman , Ahmari Ali Al , Abosoudah Ibraheem , Al‐Hayek Reema , Al‐Harbi Talal , Al‐Manjomi Fahad , Al‐Harbi Musa , Al‐Ghamdi Hasna , Al‐Shahrani Mohammed , Belgaumi Asim F.
Published: August 2013

Background

Treatment of childhood acute lymphoblastic leukemia (ALL) has been available in Saudi Arabia (SA) for over 30 years; however, only limited data have been published from there. This study was conducted to establish processes for collaborative data collection and provide clinical characteristics and outcome of children with ALL in SA.

Procedure

Clinical data for patients diagnosed from 2004 to 2008 were retrospectively collected at eight institutions and entered remotely into a custom‐built database. Statistics regarding clinical and genetic characteristics and treatment outcome were calculated.

Results

The 594 evaluable patients had a median age of 4.37 years and 56.4% were boys. Majority of patients had B‐precursor ALL while 10.7% had T‐ALL. CNS leukemia was present in 5.2% of patients. The distribution of common genetic abnormalities was similar to that reported from western populations, with 24.6% hyperdiploidy, 21% RUNX1‐ETV6 positivity, 4.2% BCR‐ABL1 positivity, and 2.5% with MLL gene rearrangement. Patients received risk‐adapted therapy according to various protocols, although treatment strategies for the majority were similar. Five‐year OS, RFS and EFS were 86.9%, 79.1%, and 73.3%, respectively. The OS for patients with pre‐B ALL was significantly higher than for T‐ALL (88.0% vs. 71.8%; P = 0.019, Log‐Rank test). Patients with pre‐B ALL categorized as low‐risk by NCI/Rome criteria and those with hyperdiploidy had OS of 93.4% and 95.8%, respectively.

Conclusions

The characteristics of childhood ALL in SA are similar to those observed in developed countries. Future prospective studies utilizing unified national protocols are needed to further improve the outcome of our patients. Pediatr Blood Cancer 2014;61:74–80. © 2013 Wiley Periodicals, Inc.
Intensive induction chemotherapy followed by myeloablative chemotherapy with autologous hematopoietic progenitor cell rescue for young children newly‐diagnosed with central nervous system atypical teratoid/rhabdoid tumors: The head start III experience
Authors: Zaky Wafik , Dhall Girish , Ji Lingyun , Haley Kelley , Allen Jeffrey , Atlas Mark , Bertolone Salvatore , Cornelius Albert , Gardner Sharon , Patel Ramesh , Pradhan Kamnesh , Shen Violet , Thompson Stephen , Torkildson Joseph , Sposto Richard , Finlay Jonathan L.
Published: August 2013

Background

Atypical teratoid/rhabdoid tumor (AT/RT) of the central nervous system (CNS) is a rare embryonal neoplasm of early childhood with dismal outcome and no current uniformly accepted treatment. Given its highly aggressive nature and predilection for dissemination at diagnosis, intensive multimodal therapy is required.

Materials and Methods

Nineteen children with newly diagnosed CNS AT/RT were treated on the head start (HS) III protocol. Treatment consisted of surgical resection, 5 cycles of induction chemotherapy, followed by consolidation with myeloablative chemotherapy and autologous hematopoietic progenitor cell rescue (AuHCR). Irradiation was given following recovery from consolidation based on patient age, disease extent at diagnosis, and treatment response to induction.

Results

Nineteen children (median age of 14 months) were treated on HS III between 2003 and 2009. Only four finished induction and three proceeded to consolidation. There are presently four survivors at 40, 42, 46, and 79 months from study enrollment. Eleven patients experienced tumor progression at a median time to progression of 4.1 months of whom 10 died with a median time from progression to death of 2.6 months. Five toxic deaths occurred, three of them while on the study. The 3‐year event‐free survival (EFS) and overall survival (OS) for the whole group was 21 ± 9% and 26 ± 10%, respectively. Five patients received irradiation at progression with only one long‐term survivor.

Conclusion

A minority of children with CNS AT/RT treated on HS III may be long‐term survivors without irradiation. More effective therapies are desperately needed. Pediatr Blood Cancer 2014;61:95–101. © 2013 Wiley Periodicals, Inc.
Estimating the excess of inappropriate prescriptions of anti‐dopaminergic anti‐emetics during acute gastroenteritis epidemics in France
Authors: Roussel Victoire , Tritz Thomas , Souty Cécile , Turbelin Clément , Arena Christophe , Lambert Bruno , Lillo‐LeLouët Agnès , Kernéis Solen , Blanchon Thierry , Hanslik Thomas
Published: August 2013

Purpose

Anti‐dopaminergic anti‐emetics (ADA) use for the treatment of nausea associated with gastroenteritis (GE) can be considered inappropriate, as their effects are not supported by evidence of clinical efficacy and can potentially induce serious adverse events.

Objective

This study quantifies the suboptimal consumption of ADA attributable to seasonal GE epidemics in France and its cost.

Methods

GE epidemiological data were collected and transmitted by the general practitioners (GPs) of Sentinelles network. Epidemic periods were identified by periodic regression. Drug sales data were obtained from pharmacies, and costs data were obtained from the French National Social Security. The ADA use and costs incurred by seasonal GE epidemics were calculated.

Results

During the epidemic periods considered in this study, the median age of patients seen by GPs for GE was 24 years old. During each epidemic, a sale increase by 14% for domperidone, by 15% for metoclopramide and 30% for metopimazine was observed. The average cost attributable to seasonal GE epidemic was 5 030 000 Euros, of which 2 160 000 Euros were incurred by the French National Social Security.

Conclusion

Linking epidemiological databases helped to identify and quantify inappropriate ADA prescriptions. GE treatment guidelines should be disseminated more widely. Copyright © 2013 John Wiley & Sons, Ltd.
Automatic detection of adverse events to predict drug label changes using text and data mining techniques
Authors: Gurulingappa Harsha , Toldo Luca , Rajput Abdul Mateen , Kors Jan A. , Taweel Adel , Tayrouz Yorki
Published: August 2013

Purpose

The aim of this study was to assess the impact of automatically detected adverse event signals from text and open‐source data on the prediction of drug label changes.

Methods

Open‐source adverse effect data were collected from FAERS, Yellow Cards and SIDER databases. A shallow linguistic relation extraction system (JSRE) was applied for extraction of adverse effects from MEDLINE case reports. Statistical approach was applied on the extracted datasets for signal detection and subsequent prediction of label changes issued for 29 drugs by the UK Regulatory Authority in 2009.

Results

76% of drug label changes were automatically predicted. Out of these, 6% of drug label changes were detected only by text mining. JSRE enabled precise identification of four adverse drug events from MEDLINE that were undetectable otherwise.

Conclusions

Changes in drug labels can be predicted automatically using data and text mining techniques. Text mining technology is mature and well‐placed to support the pharmacovigilance tasks. Copyright © 2013 John Wiley & Sons, Ltd.
Exhaustive comparison and classification of ligand‐binding surfaces in proteins
Authors: Murakami Yoichi , Kinoshita Kengo , Kinjo Akira R. , Nakamura Haruki
Published: August 2013

Many proteins function by interacting with other small molecules (ligands). Identification of ligand‐binding sites (LBS) in proteins can therefore help to infer their molecular functions. A comprehensive comparison among local structures of LBSs was previously performed, in order to understand their relationships and to classify their structural motifs. However, similar exhaustive comparison among local surfaces of LBSs (patches) has never been performed, due to computational complexity. To enhance our understanding of LBSs, it is worth performing such comparisons among patches and classifying them based on similarities of their surface configurations and electrostatic potentials. In this study, we first developed a rapid method to compare two patches. We then clustered patches corresponding to the same PDB chemical component identifier for a ligand, and selected a representative patch from each cluster. We subsequently exhaustively as compared the representative patches and clustered them using similarity score, PatSim. Finally, the resultant PatSim scores were compared with similarities of atomic structures of the LBSs and those of the ligand‐binding protein sequences and functions. Consequently, we classified the patches into ∼2000 well‐characterized clusters. We found that about 63% of these clusters are used in identical protein folds, although about 25% of the clusters are conserved in distantly related proteins and even in proteins with cross‐fold similarity. Furthermore, we showed that patches with higher PatSim score have potential to be involved in similar biological processes.
An automated approach to network features of protein structure ensembles
Authors: Bhattacharyya Moitrayee , Bhat Chanda R. , Vishveshwara Saraswathi
Published: August 2013

Network theory applied to protein structures provides insights into numerous problems of biological relevance. The explosion in structural data available from PDB and simulations establishes a need to introduce a standalone‐efficient program that assembles network concepts/parameters under one hood in an automated manner. Herein, we discuss the development/application of an exhaustive, user‐friendly, standalone program package named PSN‐Ensemble, which can handle structural ensembles generated through molecular dynamics (MD) simulation/NMR studies or from multiple X‐ray structures. The novelty in network construction lies in the explicit consideration of side‐chain interactions among amino acids. The program evaluates network parameters dealing with topological organization and long‐range allosteric communication. The introduction of a flexible weighing scheme in terms of residue pairwise cross‐correlation/interaction energy in PSN‐Ensemble brings in dynamical/chemical knowledge into the network representation. Also, the results are mapped on a graphical display of the structure, allowing an easy access of network analysis to a general biological community. The potential of PSN‐Ensemble toward examining structural ensemble is exemplified using MD trajectories of an ubiquitin‐conjugating enzyme (UbcH5b). Furthermore, insights derived from network parameters evaluated using PSN‐Ensemble for single‐static structures of active/inactive states of β2‐adrenergic receptor and the ternary tRNA complexes of tyrosyl tRNA synthetases (from organisms across kingdoms) are discussed. PSN‐Ensemble is freely available from http://vishgraph.mbu.iisc.ernet.in/PSN‐Ensemble/psn_index.html.
Sparsely populated residue conformations in protein structures: Revisiting “experimental” Ramachandran maps
Authors: Kalmankar Neha V. , Ramakrishnan C. , Balaram P.
Published: August 2013

The Ramachandran map clearly delineates the regions of accessible conformational (φ–ψ) space for amino acid residues in proteins. Experimental distributions of φ, ψ values in high‐resolution protein structures, reveal sparsely populated zones within fully allowed regions and distinct clusters in apparently disallowed regions. Conformational space has been divided into 14 distinct bins. Residues adopting these relatively rare conformations are presented and amino acid propensities for these regions are estimated. Inspection of specific examples in a completely “arid”, fully allowed region in the top left quadrant establishes that side‐chain and backbone interactions may provide the energetic compensation necessary for populating this region of φ–ψ space. Asn, Asp, and His residues showed the highest propensities in this region. The two distinct clusters in the bottom right quadrant which are formally disallowed on strict steric considerations correspond to the gamma turn (C7 axial) conformation (Bin 12) and the i + 1 position of Type II′ β turns (Bin 13). Of the 516 non‐Gly residues in Bin 13, 384 occupied the i + 1 position of Type II′ β turns. Further examination of these turn segments revealed a high propensity to occur at the N‐terminus of helices and as a tight turn in β hairpins. The β strand–helix motif with the Type II′ β turn as a connecting element was also found in as many as 57 examples. Proteins 2014; 82:1101–1112. © 2013 Wiley Periodicals, Inc.
Leonidas Zervas award lecture: Abiotic ligands for new quaternary architectures of peptides and proteins
Authors: Jensen Knud J.
Published: August 2013

This review is the result of a kind invitation to provide a report on the basis of the Leonidas Zervas award lecture at the 32nd European Peptide Society in Athens, Greece, September 2012. The lecture covered several topics including contributions toward new methods for the assembly of peptides and chemical modification of proteins. The present review will focus on another topic from the Zervas lecture, namely, our recent efforts at creating new, artificial architectures for the organization of the quaternary structure of proteins. Crucially, this is achieved with abiotic ligands and not protein surface engineering. This concept was demonstrated for the important biopharmaceutical peptide insulin, by using both abiotic metal ion binding ligands and perfluoroalkyl chains. Copyright © 2013 European Peptide Society and John Wiley & Sons, Ltd.
Self‐trapping of the d‐d charge transfer exciton in rock‐salt structured Zn1–xNixO evidenced by soft X‐ray excited luminescence
Authors: Sokolov V. I. , Pustovarov V. A. , Churmanov V. N. , Ivanov V. Yu. , Gruzdev N. B. , Sokolov P. S. , Baranov A. N. , Moskvin A. S.
Published: August 2013

Luminescence spectra of NiO and solid solutions Zn1–xNixO have been investigated under vacuum ultra‐violet (VUV) and soft X‐ray (XUV) excitation (DESY, Hamburg). Photoluminescence (PL) spectra show broad emission violet and green bands centered at about 3.2 and 2.6 eV, respectively. The PL excitation (PLE) spec‐tral evolution and lifetime measurements reveal that the two mechanisms with short and long decay times, at‐tributed to the d(eg)‐d(eg) and p(π)‐d charge transfer (CT) transitions in the range 4–6 eV, respectively, are responsible for the observed emissions. The XUV excitation makes it possible to avoid the predominant role of the surface effects in luminescence and reveal a bulk violet luminescence with puzzling well isolated doublet of very narrow lines. These lines with close energies near 3.3 eV are attributed to recombination transitions in the self‐trapped d‐d CT excitons formed by the coupled Jahn‐Teller Ni+ and Ni3+ centers. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A framework for dynamic link prediction in heterogeneous networks
Authors: Aggarwal Charu C. , Xie Yan , Yu Philip S.
Published: August 2013

Network and linked data have become quite prevalent in recent years because of the ubiquity of the web and social media applications, which are inherently network oriented. Such networks are massive, dynamic, contain a lot of content, and may evolve over time. In this paper, we will study the problem of efficient dynamic link inference in temporal and heterogeneous information networks. The problem of efficiently performing dynamic link inference is extremely challenging in massive and heterogeneous information network because of the challenges associated with the dynamic nature of the network, and the different types of nodes and attributes in it. Both the topology and type information need to be used effectively for the link inference process. We propose an effective two‐level scheme which makes efficient macro‐ and micro‐decisions for combining structure and content in a dynamic and time‐sensitive way. The time‐sensitive nature of the links is leveraged in order to perform effective link prediction. We will also study how to apply the method to the problem of community prediction. We illustrate the effectiveness of our technique over a number of real data sets. Statistical Analysis and Data Mining 2013 DOI: 10.1002/sam.11198