bluuebunny/crossref_metadata_2025_split huggingface dataset:
Environmental isotopes and noble gases in the deep aquifer system of Kazan Trona Ore Field, Ankara, central Turkey and links to paleoclimate
Authors: Arslan Sebnem , Yazicigil Hasan , Stute Martin , Schlosser Peter 
Published: January 2013

AbstractEnvironmental isotopes and noble gases in groundwater samples from the Kazan Trona Ore Field are studied to establish the temperature change between the Holocene and the late Pleistocene. Noble gas temperatures (NGTs) presented in this study add an important facet to the global paleotemperature map in the region between Europe and North Africa. The groundwater system under investigation consists of three different aquifers named shallow, middle and deep in which δ18O and δ2H vary from − 8.10‰ to − 12.80‰ and from − 60.89‰ to − 92.60‰ VSMOW, respectively. The average isotopic depletion between unconfined and confined parts of the system is − 2.5‰ in δ18O and − 20‰ in δ2H. It is not possible to explain this depletion solely with the elevation effect. Recharge temperatures derived from dissolved atmospheric noble gases reflect the current average yearly ground temperatures (13°C) for samples collected near the recharge area but are 3 to 8°C lower than today's temperatures in the deep aquifer system. Low 14C activities and high He excesses in the confined parts of the aquifer system suggest that the water in the deep aquifer was recharged during the last Pleistocene under considerably cooler climatic conditions.
Closed subgroups generated by generic measure automorphisms
Authors: SOLECKI SŁAWOMIR 
Published: January 2013

AbstractWe prove that for a generic measure-preserving transformation $T$, the closed group generated by $T$ is a continuous homomorphic image of a closed linear subspace of $L_0(\lambda , {\mathbb R})$, where $\lambda $ is the Lebesgue measure, and that the closed group generated by $T$contains an increasing sequence of finite-dimensional tori whose union is dense.
EFFICIENT TILLAGE AND NUTRIENT MANAGEMENT PRACTICES FOR SUSTAINABLE YIELDS, PROFITABILITY AND ENERGY USE EFFICIENCY FOR RICE-BASED CROPPING SYSTEM IN DIFFERENT SOILS AND AGRO-CLIMATIC CONDITIONS
Authors: SANKAR G. R. MARUTHI , SHARMA K. L. , REDDY K. SRINIVAS , PRATIBHA G. , SHINDE RESHMA , SINGH S. R. , NEMA A. K. , SINGH R. P. , RATH B. S. , MISHRA A. , BEHERA B. D. , SUBUDHI C. R. , SINGH BHAGWAN , SINGH H. C. , SINGH ASHOK KUMAR , RUSIA D. K. , YADAVA M. S. , THYAGARAJ C. R. , MISHRA P. K. , CHANDRIKA M. SUMA , VENKATESWARLU B. 
Published: January 2013

SUMMARYLong-term tillage and fertilizer experiments were conducted in rice in kharif followed by lentil in dry subhumid Inceptisols at Varanasi and Faizabad; horse gram at Phulbani and linseed at Ranchi in moist subhumid Alfisols in rabi during 2001 to 2010. The study was conducted to assess the effect of conventional tillage (CT), low tillage + interculture (LT1) and low tillage + herbicide (LT2) together with 100% N (organic) (F1), 50% N (organic) + 50% N (inorganic) (F2) and 100% N (inorganic) (F3) on productivity, profitability, rainwater and energy use efficiencies. The results at Varanasi revealed that CT was superior with mean yield of 2389 kg ha−1, while F1 was superior with 2378 kg ha−1 in rice. At Faizabad, CT was superior with mean rice yield of 1851 kg ha−1 and lentil yield of 977 kg ha−1, while F1 was superior with 1704 and 993 kg ha−1 of rice and lentil, respectively. At Phulbani, F2 was superior with rice yield of 1170 kg ha−1. At Ranchi, F2 with rice yield of 986 kg ha−1 and F3 with linseed yield of 224 kg ha−1 were superior. The regression model of crop seasonal rainfall and yield deviations indicated an increasing trend in rice yield over mean (positive deviation) with increase in rainfall at all locations; while a decreasing trend (negative deviation) was found for lentil at Faizabad, horse gram at Phulbani and linseed at Ranchi. Based on economic analysis, CTF1 at Varanasi and Faizabad, CTF2 at Phulbani and LT2F2 at Ranchi were superior.
Liquidity Risk, Return Predictability, and Hedge Funds’ Performance: An Empirical Study
Authors: Brandon Rajna Gibson , Wang Songtao 
Published: January 2013

AbstractThis article analyzes the effect of liquidity risk on the performance of equity hedge fund portfolios. Similarly to Avramov, Kosowski, Naik, and Teo (2007), (2011), we observe that, before accounting for the effect of liquidity risk, hedge fund portfolios that incorporate predictability in managerial skills generate superior performance. This outperformance disappears or weakens substantially for most emerging markets, event-driven, and long/short hedge fund portfolios once we account for liquidity risk. Moreover, we show that the equity market-neutral and long/short hedge fund portfolios’ “alphas” also entail rents for their service as liquidity providers. These results hold under various robustness tests.
Response ofEvernia prunastrito urban environmental conditions in Central Europe after the decrease of air pollution
Authors: LACKOVIČOVÁ Anna , GUTTOVÁ Anna , BAČKOR Martin , PIŠÚT Peter , PIŠÚT Ivan 
Published: January 2013

AbstractThe epiphytic lichenEvernia prunastriis sensitive to air pollution and reacted by total retreat to the worsening of air quality during the peak of SO2pollution in Central Europe (1950s–1990). Since 1990, after a significant decrease in air pollution, epiphytic lichens recolonized previously polluted areas, includingE. prunastri. We investigated the physiological status ofE. prunastri, transplanted for six months in 34 sites in the urban area of Bratislava (Slovakia) under current conditions. The content of chlorophylls, cortical and medullar secondary metabolites and soluble proteins were explored. We then examined the relationship of these parameters with the environmental quality status, reflected by the diversity of epiphytic lichens. The results showed that the physiological status ofE. prunastridid not change significantly after exposure. Positive correlations were found between lichen diversity in the sampling sites and physiological parameters (photosynthetic pigments and phaeophytinization quotient) in the transplants. Transplants from sampling sites with a greater proportion of nitrophilous lichens displayed a decrease in photosynthetic pigments. Sites whereE. prunastrinaturally occurred had a lower proportion of nitrophilous species in comparison to sites whereE. prunastriwas not present. This suggests that the indicator speciesE. prunastrimay also recolonize sites with low eutrophication in urban environments under decreased air pollution, and the information on its presence can help to assess the pressure caused by nitrogen excess.
Hydrogen sulphide inhibits PSII of lichen photobionts
Authors: BERTUZZI Stefano , TRETIACH Mauro 
Published: January 2013

AbstractThe effects of hydrogen sulphide (H2S) on five lichens with different photobionts, ecology, and tolerance to the pollutant were studied by means of samples exposed in closed chambers containing two known H2S solutions. The H2S concentration in the void volume at equilibrium with the liquid phase was measured by gas chromatography-mass spectrometry, combined with the use of solid phase micro extraction (GC/MS SPME). It was determined as 8 and 28 ppm H2S in the absence of lichen material, andc. 2 and 10 ppm H2S respectively with living lichen material inserted for 8 hours in the exposure chambers. Significant differences in the species-specific emission of chlorophyllafluorescence (ChlaF) were observed, with a pronounced depression ofFv/Fmalready detectable after 2 h exposure at 28 ppm H2S in all the species. The decreased intensity was positively correlated to sample surface and, to a lesser extent, to the species-specific pre-exposureFv/Fmvalue. Dark-exposed samples were less affected than light-exposed ones. All four chlorolichens could recover the pre-exposure ChlaF emission after two days in the absence of H2S, both in the light and in the dark, whereas the cyanolichen did not recover when kept in the dark. The results are thoroughly discussed on the basis of the known action mechanisms of H2S on the photosynthetic apparatus of vascular plants and cyanobacteria.
The feasibility of the north-eastern USA supporting the return of the cougar Puma concolor
Authors: Laundré John W. 
Published: January 2013

AbstractThe cougar Puma concolor was part of the pre-European fauna of the north-eastern USA. It was extirpated in the late 1800s and since the late 1900s there have been discussions concerning its reintroduction to the region. One site considered is Adirondack State Park in northern New York. In 1981 an assessment of the feasibility of returning cougars concluded that the Park had adequate prey and forest cover to support a small population of cougars but that conflicts with humans would cause the demise of this population within 10 years. Thus reintroduction at that time was not advised. Since then knowledge of cougar ecology and how cougars interact with humans has increased substantially. Based on information compiled since the 1980s I conducted a landscape-scale analysis to assess whether cougars could live in the Park. The results indicate that cougars could occupy 15,300–17,000 km2 (61–69%) of the Park, with minimal contact with human habitation. Based on reported cougar densities the Park could support a population of 150–350 cougars. These cougars would consume < 10% of the adult deer population annually and fawn production would be sufficient to replace these losses. Human and road densities in the Park are similar to those of the Black Hills, South Dakota and southern Florida, both of which have viable populations of cougars. I concluded that Adirondack State Park could support a population of cougars. What is now required is the will to bring them back.
ECONOMIC EVALUATIONS AND DIAGNOSTIC TESTING: AN ILLUSTRATIVE CASE STUDY APPROACH
Authors: Sanghera Sabina , Orlando Rosanna , Roberts Tracy 
Published: January 2013

Objective:The aim of this study was to present a clear process of synthesizing test accuracy data when conducting economic evaluations of diagnostic tests for health technology assessment (HTA) assessors and health economists.Methods:We appraised the methods advocated for using diagnostic test accuracy data in economic evaluations. We used a case study of fetal anemia in which data from a screening test are used in combination with a confirmatory test.Results:We developed a step-by-step guide and consider two scenarios: when data on test accuracy from several studies are based on (i) thesametest threshold for positivity and (ii)differenttest thresholds.Conclusions:We conclude that each approach has its strengths and limitations. We show that the optimal operating point of the test should be identified to determine the true cost-effectiveness of the test. We advocate that these issues require a multidisciplinary team of health economists, decision modelers and statisticians.
Plant health challenges for a sustainable land use and rural economy.
Authors: Pautasso M. , Dehnen-Schmutz K. , Ilbery B. , Jeger M. J. , Jones G. , Little R. , MacLeod A. , Maye D. , Parker S. , Pietravalle S. , Mills P. 
Published: January 2013

Abstract
Plant health is a key condition for a sustainable land use and rural economy. Drawing on a Rural Economy and Land Use (RELU)-funded project on the growing risk of plant diseases in the UK, current and future challenges to plant health are discussed. It is well recognized that farmers have an important role in shaping plant health policies at a time of major structural changes in agricultural industries. However, the role of consumers has also much potential to improve sustainability of plant disease management options. The phytosanitary legislation is catching up with the many recent developments in plant health, but needs to be integrated with policies aimed at achieving animal and human health. Interdisciplinary approaches in research on plant health, as well as an increasing involvement of stakeholders in the management of plant epidemics, are to be welcomed. Plant diseases also influence (and are influenced by) land use and environmental regulations in general. Climate change is likely to increase the frequency and magnitude of new plant disease outbreaks, particularly when combined with globalization of trade, intensification of land use and structural evolution of the agricultural sector. To tackle the many challenges to plant health, it is mandatory to ensure long-term funding for interdisciplinary plant health research and management.
Recombinant vaccines and infectious bursal disease virus.
Authors: Lucero M. S. , Gómez E. , Carballeda J. M. , Gravisaco M. J. , Chimeno Zoth S. , Berinstein A. 
Published: January 2013

Abstract
Infectious bursal disease virus (IBDV) is the aetiological agent of infectious bursal disease (IBD), an immunosuppressive and highly contagious disease that affects young birds causing important economic losses in the poultry industry worldwide. Currently, vaccination programmes with inactivated and live-attenuated viruses have been used to prevent IBD. However, these vaccines present a number of disadvantages, mainly because of their viral nature. Consequently, in the last two decades, many studies have been conducted in order to replace conventional virus-based vaccines by new, rationally designed vaccines that are safer as well as effective. In this review, we will present a background on the disease and its causative agent, and focus on the development of new generation vaccines against this significant poultry disease.
NucleoFinder: a statistical approach for the detection of nucleosome positions
Authors: Becker Jeremie , Yau Christopher , Hancock John M. , Holmes Christopher C. 
Published: January 2013

Abstract
Motivation: The identification of nucleosomes along the chromatin is key to understanding their role in the regulation of gene expression and other DNA-related processes. However, current experimental methods (MNase-ChIP, MNase-Seq) sample nucleosome positions from a cell population and contain biases, making thus the precise identification of individual nucleosomes not straightforward. Recent works have only focused on the first point, where noise reduction approaches have been developed to identify nucleosome positions.
Results: In this article, we propose a new approach, termed NucleoFinder, that addresses both the positional heterogeneity across cells and experimental biases by seeking nucleosomes consistently positioned in a cell population and showing a significant enrichment relative to a control sample. Despite the absence of validated dataset, we show that our approach (i) detects fewer false positives than two other nucleosome calling methods and (ii) identifies two important features of the nucleosome organization (the nucleosome spacing downstream of active promoters and the enrichment/depletion of GC/AT dinucleotides at the centre of in vitro nucleosomes) with equal or greater ability than the other two methods.
Availability: The R code of NucleoFinder, an example datafile and instructions are available for download from https://sites.google.com/site/beckerjeremie/
Contact: cholmes@stats.ox.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Detecting and understanding genetic and structural features in HIV-1 B subtype V3 underlying HIV-1 co-receptor usage
Authors: Chen Mengjie , Svicher Valentina , Artese Anna , Costa Giosuè , Alteri Claudia , Ortuso Francesco , Parrotta Lucia , Liu Yang , Liu Chang , Perno Carlo Federico , Alcaro Stefano , Zhang Jing 
Published: January 2013

AbstractMotivation: To define V3 genetic elements and structural features underlying different HIV-1 co-receptor usage in vivo.Results: By probabilistically modeling mutations in the viruses isolated from HIV-1 B subtype patients, we present a unique statistical procedure that would first identify V3 determinants associated with the usage of different co-receptors cooperatively or independently, and then delineate the complicated interactions among mutations functioning cooperatively. We built a model based on dual usage of CXCR4 and CCR5 co-receptors. The molecular basis of our statistical predictions is further confirmed by phenotypic and molecular modeling analyses. Our results provide new insights on molecular basis of different HIV-1 co-receptor usage. This is critical to optimize the use of genotypic tropism testing in clinical practice and to obtain molecular-implication for design of vaccine and new entry-inhibitors.Contact: jing.zhang.jz349@yale.edu or cf.perno@uniroma2.itSupplementary information: Supplementary data are available at Bioinformatics online.
First Report of Pod and Stem Blight of Lima Bean Caused by Diaporthe phaseolorum var. sojae in Malaysia
Authors: Mahmodi F. , Kadir J. B. , Puteh A. , Wong M. Y. , Nasehi A. 
Published: January 2013

In July 2011, a severe outbreak of pod and stem blight was observed on lima bean (Phaseolus lunatus L.) plants grown in the Cameron Highlands, located in Pahang State, Malaysia. Disease incidence varied from 33 to 75% in different fields. Pods and stems exhibited withered, light brown to reddish brown necrotic areas. Sub-circular and brown lesions were produced on the leaves. These lesions varied in size, often reaching a diameter of 1 to 2 cm. After tissue death, numerous pycnidia were observed on the surface of the pod or stem. The pycnidia diameter varied from 155 to 495 μm, averaging 265.45 μm, and on the surface of the pod or stem, pycnidia were often arranged concentrically or linearly, respectively. Pycnidiospores were hyaline, 1-celled, usually straight, and rarely, slightly curved. The α-spores varied from 5.5 to 9.0 × 2.5 to 4.0 μm; averaging 7.3 × 3.5 μm. The β-spores found either alone or with pycnidiospores in pycnidia were slender, hyaline, nonseptate, and straight or curved. Size varied from 15.8 to 38.0 × 1.3 to 2.1 μm; averaging 25.86 × 1.8 μm. The colony characteristics were recorded from pure cultures grown on potato dextrose agar plates, and incubated in darkness for 7 days at 25 °C, then exposed to 16/8 h light and dark periods at 25°C for a further 14 to 21 days. Morphological characteristics of the colonies and spores on PDA matched those described for P. phaseolorum var. sojae (2). Colonies were white, compact, with wavy mycelium and stromata with pycnidia that contained abundant β-spores. Sequence analysis of the ribosomal DNA internal transcribed spacer obtained from the Malaysian isolate FM1 (GenBank Accession No. JQ514150) using primers ITS5 and ITS4 (1) aligned with deposited sequences from GenBank confirmed identity and revealed 99% to 100% DNA similarity with P. phaseolorum strains (AY577815, AF001020, HM012819, JQ936148). The isolate FM1 was used for pathogenicity testing. Five non-infected detached leaves and pods of 4-week-old lima bean were surface sterilized and inoculated by placing 10 μl of conidial suspension (106 conidia ml–1) on the surface of leaves and pods using either the wound/drop or non-wound/drop method and distilled water used as control (3). The inoculated leaves and pods were incubated at 25 °C and 98% RH, and the experiment was performed twice. Disease reactions and symptoms were evaluated after inoculation. After one week, typical symptoms of pod and stem blight appeared with formation of pycnidia on the surface of the tissues, but not on non-inoculated controls. P. phaseolorum var. sojae was consistently reisolated from symptoms. To our knowledge, this is the first report of P. phaseolorum var. sojae causing pod and stem blight of lima bean in Malaysia. References: (1) R. Ford et al. Aust. Plant Pathol. 33:559, 2004. (2) G. L. Hartman et al. Compendium of Soybean Diseases. 4th ed. American Phytopathological Society, St. Paul, MN, 1999. (3) P. P. Than et al. Plant Pathol. 57:562, 2008.
β-Galactosyl Yariv Reagent Binds to the β-1,3-Galactan of Arabinogalactan Proteins
Authors: Kitazawa Kiminari , Tryfona Theodora , Yoshimi Yoshihisa , Hayashi Yoshihiro , Kawauchi Susumu , Antonov Liudmil , Tanaka Hiroshi , Takahashi Takashi , Kaneko Satoshi , Dupree Paul , Tsumuraya Yoichi , Kotake Toshihisa 
Published: January 2013

AbstractYariv phenylglycosides [1,3,5-tri(p-glycosyloxyphenylazo)-2,4,6-trihydroxybenzene] are a group of chemical compounds that selectively bind to arabinogalactan proteins (AGPs), a type of plant proteoglycan. Yariv phenylglycosides are widely used as cytochemical reagents to perturb the molecular functions of AGPs as well as for the detection, quantification, purification, and staining of AGPs. However, the target structure in AGPs to which Yariv phenylglycosides bind has not been determined. Here, we identify the structural element of AGPs required for the interaction with Yariv phenylglycosides by stepwise trimming of the arabinogalactan moieties using combinations of specific glycoside hydrolases. Whereas the precipitation with Yariv phenylglycosides (Yariv reactivity) of radish (Raphanus sativus) root AGP was not reduced after enzyme treatment to remove α-l-arabinofuranosyl and β-glucuronosyl residues and β-1,6-galactan side chains, it was completely lost after degradation of the β-1,3-galactan main chains. In addition, Yariv reactivity of gum arabic, a commercial product of acacia (Acacia senegal) AGPs, increased rather than decreased during the repeated degradation of β-1,6-galactan side chains by Smith degradation. Among various oligosaccharides corresponding to partial structures of AGPs, β-1,3-galactooligosaccharides longer than β-1,3-galactoheptaose exhibited significant precipitation with Yariv in a radial diffusion assay on agar. A pull-down assay using oligosaccharides cross linked to hydrazine beads detected an interaction of β-1,3-galactooligosaccharides longer than β-1,3-galactopentaose with Yariv phenylglycoside. To the contrary, no interaction with Yariv was detected for β-1,6-galactooligosaccharides of any length. Therefore, we conclude that Yariv phenylglycosides should be considered specific binding reagents for β-1,3-galactan chains longer than five residues, and seven residues are sufficient for cross linking, leading to precipitation of the Yariv phenylglycosides.
Iron Is Involved in the Maintenance of Circadian Period Length in Arabidopsis
Authors: Chen Yong-Yi , Wang Ying , Shin Lung-Jiun , Wu Jing-Fen , Shanmugam Varanavasiappan , Tsednee Munkhtsetseg , Lo Jing-Chi , Chen Chyi-Chuann , Wu Shu-Hsing , Yeh Kuo-Chen 
Published: January 2013

Abstract
The homeostasis of iron (Fe) in plants is strictly regulated to maintain an optimal level for plant growth and development but not cause oxidative stress. About 30% of arable land is considered Fe deficient because of calcareous soil that renders Fe unavailable to plants. Under Fe-deficient conditions, Arabidopsis (Arabidopsis thaliana) shows retarded growth, disordered chloroplast development, and delayed flowering time. In this study, we explored the possible connection between Fe availability and the circadian clock in growth and development. Circadian period length in Arabidopsis was longer under Fe-deficient conditions, but the lengthened period was not regulated by the canonical Fe-deficiency signaling pathway involving nitric oxide. However, plants with impaired chloroplast function showed long circadian periods. Fe deficiency and impaired chloroplast function combined did not show additive effects on the circadian period, which suggests that plastid-to-nucleus retrograde signaling is involved in the lengthening of circadian period under Fe deficiency. Expression pattern analyses of the central oscillator genes in mutants defective in CIRCADIAN CLOCK ASSOCIATED1/LATE ELONGATED HYPOCOTYL or GIGANTEA demonstrated their requirement for Fe deficiency-induced long circadian period. In conclusion, Fe is involved in maintaining the period length of circadian rhythm, possibly by acting on specific central oscillators through a retrograde signaling pathway.