bluuebunny/crossref_metadata_2025 huggingface dataset:
Recovery of African horse sickness virus from synthetic RNA
Authors: Kaname Yuuki , Celma Cristina C. P. , Kanai Yuta , Roy Polly
Published: July 2013

African horse sickness virus (AHSV) is an insect-vectored emerging pathogen of equine species. AHSV (nine serotypes) is a member of the genus Orbivirus, with a morphology and coding strategy similar to that of the type member, bluetongue virus. However, these viruses are distinct at the genetic level, in the proteins they encode and in their pathobiology. AHSV infection of horses is highly virulent with a mortality rate of up to 90 %. AHSV is transmitted by Culicoides, a common European insect, and has the potential to emerge in Europe from endemic countries of Africa. As a result, a safe and effective vaccine is sought urgently. As part of a programme to generate a designed highly attenuated vaccine, we report here the recovery of AHSV from a complete set of RNA transcripts synthesized in vitro from cDNA clones. We have demonstrated the generation of mutant and reassortant AHSV genomes, their recovery, stable passage, and characterization. Our findings provide a new approach to investigate AHSV replication, to design AHSV vaccines and to aid diagnosis.
Sucrose responsiveness, learning success, and task specialization in ants
Authors: Perez Margot , Rolland Uther , Giurfa Martin , d’Ettorre Patrizia
Published: July 2013

Social insects possess remarkable learning capabilities, which are crucial for their ecological success. They also exhibit interindividual differences in responsiveness to environmental stimuli, which underlie task specialization and division of labor. Here we investigated for the first time the relationships between sucrose responsiveness, behavioral specialization, and appetitive olfactory learning in ants, including reproductive castes. We show that castes of the ant Camponotus aethiops differ in their responsiveness to sucrose and in their learning success in olfactory conditioning experiments in which sucrose is used as reward. Olfactory learning was better in foragers than in nurses, in agreement with their higher sucrose responsiveness. Interindividual variation in stimulus responsiveness and in learning may be, therefore, a crucial factor for division of labor in social insects.
Advances inin situpowder diffraction of battery materials: a case study of the new beamline P02.1 at DESY, Hamburg
Authors: Herklotz Markus , Scheiba Frieder , Hinterstein Manuel , Nikolowski Kristian , Knapp Michael , Dippel Ann-Christin , Giebeler Lars , Eckert Jürgen , Ehrenberg Helmut
Published: July 2013

A brief review ofin situpowder diffraction methods for battery materials is given. Furthermore, it is demonstrated that the new beamline P02.1 at the synchrotron source PETRA III (DESY, Hamburg), equipped with a new electrochemical test cell design and a fast two-dimensional area detector, enables outstanding conditions forin situdiffraction studies on battery materials with complex crystal structures. For instance, the time necessary to measure a pattern can be reduced to the region of milliseconds accompanied by an excellent pattern quality. It is shown that even at medium detector distances the instrumental resolution is suitable for crystallite size refinements. Additional crucial issues like contributions to the background and availableqrange are determined.
Application of immune and genetic algorithms to the identification of a polymer based on its X-ray diffraction curve
Authors: Rabiej Małgorzata
Published: July 2013

This paper describes how a combination of two methods of artificial intelligence, an immune algorithm and a genetic algorithm, can be used to recognize a polymer by the shape of its X-ray diffraction curve. To this end, the hybrid algorithm uses a database which contains theoretical functions describing wide-angle X-ray diffraction curves of different polymers. These curves are compared by the algorithm with the experimental diffraction curve and the most similar are chosen. Such theoretical curves are kept in the immunological memory, and their parameters can be set as the starting ones in the optimization methods used for decomposition of the experimental curve into crystalline peaks and amorphous component. Using this algorithm, the preparation of the starting parameters is much easier and faster. Decomposition is the most important step in polymer crystallinity determination.
A prototype direct-detection CCD for protein crystallography
Authors: Green Katherine S. , Szebenyi Doletha M. E. , Boggs Kasey , Bredthauer Richard , Tate Mark W. , Gruner Sol M.
Published: July 2013

The fabrication and testing of a prototype deep-depletion direct-conversion X-ray CCD detector are described. The device is fabricated on 600 µm-thick high-resistivity silicon, with 24 × 24 µm pixels in a 4k × 4k pixel format. Calibration measurements and the results of initial protein crystallography experiments at the Cornell High Energy Synchrotron Source (CHESS) F1 beamline are described, as well as suggested improvements for future versions of the detector.
Combined X-ray diffraction and solid-state19F magic angle spinning NMR analysis of lattice defects in nanocrystalline CaF2
Authors: Abdellatief Mahmoud , Abele Matthias , Leoni Matteo , Scardi Paolo
Published: July 2013

Nanocrystalline CaF2powder specimens were produced both by co-precipitation of CaCl2and NH4F and by ball milling of a coarse powder. The specimen homogeneity and a detailed picture of the lattice defects can be assessed by the simultaneous analysis of the powder diffraction pattern and of the solid-state19F magic angle spinning NMRT1relaxometry data. While diffraction line profiles provide information on domain size distribution and the content of dislocations,T1relaxometry is more sensitive to inhomogeneity of the powder (large defect-free grainsversusdefective small ones). After extensive milling it is possible to obtain fluorite domains of comparable size to the chemically synthesized CaF2(circa10–12 nm), but with a marked difference in the lattice defect types and content. It is then proved that surface defects (related to domain size), line defects (dislocations) and point (Frenkel) defects have a quite different effect on the powder pattern as well as on theT1spin-lattice relaxation time.
DOES ECONOMIC ADVERSITY BREED CRIMINAL COOPERATION? CONSIDERING THE MOTIVATION BEHIND GROUP CRIME
Authors: NGUYEN HOLLY , McGLOIN JEAN MARIE
Published: July 2013

The fact that most offenders have accomplices at some point in their criminal career is curious, given the risks associated with criminal cooperation. McCarthy, Hagan, and Cohen () offered the first formal theory of the decision to co‐offend, which addressed explicitly the uncertainties attached to the decision to engage in group crime. They posited that when offenders experience adversity, they become more risk seeking and oriented toward the chance for potential gain, which essentially outweighs the uncertainties attached to criminal cooperation. McCarthy, Hagan, and Cohen's analysis of street youth offered some empirical support for their premise but left open many important questions. The current study uses data from two different samples of incarcerated felons in Nebraska (N = 321 offenders) and Colorado (N = approximately 1,120 observations nested within approximately 640 offenders) that provide information on different forms of economic adversity. Logistic regression models provide some evidence for the association between adversity and co‐offending, but they are inconsistent. In contrast, a preference for excitement is a consistent and powerful predictor of offending.
A New Somphospondylan Sauropod (Dinosauria, Titanosauriformes) from the Late Cretaceous of Ganzhou, Jiangxi Province of Southern China
Authors: Junchang LÜ , Laiping YI , Hui ZHONG , Xuefang WEI
Published: July 2013

A new somphospondylan sauropod (Dinosauria, Titanosauriformes): Gannansaurus sinensis gen. et sp. nov. from the Late Cretaceous Nanxiong Formation of Ganzhou Basin, Jiangxi Province of southern China is erected based on one nearly complete dorsal vertebra and a mid‐caudal vertebra. It is characterized by two centroprezygapophyseal lamina fossae; large, square‐shaped concavity formed by centroprezygapophyseal lamina and dorsal margin of the centrum; large infraparapophyseal fossa; three openings present within the large lateral concavity, which occupy 65% length of the centrum; the posterior centroparapophyseal lamina (PCPL) and the anterior centroparapophyseal lamina (ACPL) weakly developed; the posterior centrodiapophyseal lamina (PCDL) separated by an infradiapophyseal fossa into two branches dorsally; parapophyseal and diapophyseal laminae cross to form “K” configuration. It shares some characters with the Early Cretaceous form‐Euhelopus, indicating that it is more closely related to Euhelopus rather than to other titanosauriform sauropods. This means Gannansaurus may have a close phylogenetic relationship with Euhelopus.
A New Material of Lindera (Lauraceae) of the Late Pliocene from Tengchong, Yunnan and the Genus' Biogeography Significance
Authors: Kequn DAO , Junlin CHEN , Peihong JIN , Chong DONG , Yi YANG , Xiaohui XU , Jingyu WU , Sanping XIE , Zhicheng LIN , Bainian SUN
Published: July 2013

Lindera is a large genus of graceful, pleasantly scented and common native trees and shrubs of southern China and neighboring regions of SE Asia. There is a well‐documented Cenozoic fossil record not only in these regions but also from elsewhere. A new fossil leaf record has been found in diatomite beds from the Upper Pliocene Mangbang Formation of Tuantian, Tengchong County, Yunnan. The leaves are identified and assigned to Lindera acuminatissima K. Q. Dao et B. N. Sun sp. nov., by comparing their leaf architecture and epidermal characteristics with those of 51 extant Lauraceae species and with 15 known fossil Lindera taxa. The specimens have well‐preserved cuticles, with typical leaf architecture and epidermal characteristics of the Lauraceae, including entire leaf margin, intramarginal veins, basal ternate acrodromous primary veins, one‐cell trichome base, paracytic stomatal apparatus, sunken guard cells, subsidiary hardly staining cells and presence of oil cells. These characteristics are consistent with Lindera sect. Daphnidium but are different from reported fossil and extant species of Lindera. The cuticles of Lindera are fragile and delicate with only three Lindera fossils reported based on this tissue. In terms of paleobiogeography, the fossil record indicates that Lindera is distributed in high‐ to mid‐latitude regions of the Late Cretaceous to Paleocene northern hemisphere. Coincidentally, the records of Lindera located on both sides of the Bering Land Bridge possibly support the hypothesis that ancient plants extended via transcontinental exchanges through the Bering Corridor. In the Eocene, ancient Lindera spread to Europe through the Northern Degeer Route and the Southern Thulian Route. At the same time, ancient Lindera spread into Central Asia. Climatic changes and tectonization since the Neogene prevented the propagation of Lindera throughout Asia, North America and Europe, and hence the distribution areas have just regressed to the low‐latitude regions in Asia and North America. From the Paleogene to the Neogene, Lindera has changed its distribution by surviving extreme climate changes. Quaternary glaciations ultimately led to Lindera becoming extinct in Europe. The new record from Tengchong, Yunnan, with its lower latitude located in tropical and subtropical regions, indicates that Lindera has lived in those regions since the late Pliocene.
Formation of the Moping Dome in the Xuefengshan Orocline, Central China and its Tectonic Significance
Authors: Wei SHI , Shuwen DONG , Jianhua LI , Mi TIAN , Guoli WU
Published: July 2013

Many equiaxial dome‐like structures developed in the north segment of the Xuefengshan orocline, Central China are obviously inconcordant with the NE‐trending linear structures in this area, which contain important records for understanding the structural framework and evolution of this belt. In this paper, taking one of the typical dome‐like structures in the Xuefengshan orcline (e.g. Moping dome‐like structure) as an example, based on its structural framework interpratatoin, superposed deformation analysis and paleo‐stress fields reconstruction, we propose the Moping dome‐like structure is composed of two populations of different‐striking thrust‐fold structures, ∼E‐trending and NE‐striking structures, indicative of two‐stages shortening, ∼N‐ and NW‐striking, respectively. Together with the geochronological analysis, we suggest the first stage of shortening occurred in Late Triassic to Early Jurassic, due to the Indosinian intercollisional orogeny of the Yangtze Block and the North China Block The second occurred during Late Jurassic–Early Cretaceous owing to Yanshanian intracontinental orogeny, leading to the intensive superposition of the NE‐trending structures onto the ∼E‐trending structures, and the final ocurrence of the Moping dome. Thus, our study indicates the Xuefengshan arc‐shape belt also experienced two‐phase deformation, and resulted from the superposition of NE–SW structures onto ∼E–W structures in Late Jurassic–Early Cretaceous, which could provide new structural evidence for probing the Mesozoic tectonic framework and evolution of the Xuefengshan orocline.
Authigenic Gypsum in Gas‐Hydrate Associated Sediments from the East Coast of India (Bay of Bengal)
Authors: KOCHERLA M.
Published: July 2013

Authigenic gypsum crystals, along with pyrite and carbonate mineralization, predominantly calcites were noticed in distinct intervals in a 32 m long piston core, collected in the gas hydrate‐bearing sediments in the northern portion of the Krishna‐Godavari basin, eastern continental margin of India at a water depth of 1691 m. X‐ray diffraction and energy dispersive spectrum studies confirm presence of pyrite, gypsum, calcite, and other mineral aggregates. The occurrence of gypsum in such deep sea environment is intriguing, because gypsum is a classical evaporite mineral and is under saturated with respect to sea water. Sedimentological, geochemical evidences point to diagenetic formation of the gypsum due to oxidation of sulphide minerals (i.e. pyrite). Euhedral, transparent gypsum crystals, with pyrite inclusions are cemented with authigenic carbonates, possibly indicating that they were formed authigenically in situ in the gas hydrate‐influenced environment due to late burial diagenesis involving sulphate reduction and anaerobic oxidation of methane (AOM). Therefore, the authigenic gypsums found in sediments of the Krishna‐Godavari and Mahanadi offshore regions could be seen as one of the parameters to imply the presence of high methane flux possibly from gas hydrate at depth.
Gas Sources of Natural Gas Hydrates in the Shenhu Drilling Area, South China Sea: Geochemical Evidence and Geological Analysis
Authors: Youhai ZHU , Xia HUANG , Shaoying FU , Pibo SU
Published: July 2013

The Shenhu gas hydrate drilling area is located in the central Baiyun sag, Zhu II depression, Pearl River Mouth basin, northern South China Sea. The gas compositions contained in the hydrate‐bearing zones is dominated by methane with content up to 99.89% and 99.91%. The carbon isotope of the methane (δ13C1) are −56.7‰ and −60.9‰, and its hydrogen isotope (δD) are −199‰ and −180‰, respectively, indicating the methane from the microbial reduction of CO2. Based on the data of measured seafloor temperature and geothermal gradient, the gas formed hydrate reservoirs are from depths 24–1699 m below the seafloor, and main gas‐generation zone is present at the depth interval of 416–1165 m. Gas‐bearing zones include the Hanjiang Formation, Yuehai Formation, Wanshan Formation and Quaternary sediments. We infer that the microbial gas migrated laterally or vertically along faults (especially interlayer faults), slump structures, small‐scale diapiric structures, regional sand beds and sedimentary boundaries to the hydrate stability zone, and formed natural gas hydrates in the upper Yuehai Formation and lower Wanshan Formation, probably with contribution of a little thermogenic gas from the deep sedments during this process.
Origin, Flow of Formation Water and Hydrocarbon Accumulation in the Zhenwu Area of the North Jiangsu Basin, China
Authors: Mei LI , Zhanghua LOU , Aimin JIN , Rong ZHU , Changjian SHANG , Ying YE , Zhenhong ZHU
Published: July 2013

In order to understand the origin and flow of formation water and to evaluate the hydrocarbon accumulation and preservation conditions, the properties of formation water chemistry and dynamics of the Zhenwu area in the southern Gaoyou Sag, North Jiangsu Basin, China, have been investigated. The results show that Xuzhuang oilfield is infiltrated discontinuously by meteoric water under gravity, which consequently leads to the desalination of formation water. Formation water in the Zhenwu and Caozhuang oilfields is less influenced by meteoric water infiltration, and the origin is interpreted to be connate water. Hydrocarbon migration, accumulation and preservation are closely related to the hydrodynamic field of formation water. Formation water concentrates gradually during the process of centrifugal flow released by mudstone compaction and the centripetal flow of meteoric water infiltration, leading to the high salinity of the central part. The geological conditions of the southern fault–terrace belt are poor for hydrocarbon accumulation and preservation as meteoric water infiltration, leaching and oxidation, while the central part, i.e., northern Zhenwu and Caozhuang oilfields is beneficial for an abundance of hydrocarbon accumulation. Most of the large scale oil–gas fields locate herein.
Hydrothermal Alteration Mapping in Northern Khur, Iran, Using ASTER Image Processing: a New Insight to the Type of Copper Mineralization
Authors: SHAFAROUDI Azadeh Malekzadeh , KARIMPOUR Mohammad Hassan
Published: July 2013

Eastern Iran has great potential for the discovery of different types of mineralization. The study area encompasses Tertiary magmatism in the northern Lut block located in northern Khur, South Khorasan, eastern Iran and is mostly covered by volcanic rocks, which are intruded by porphyritic subvolcanic intrusions in some places. Application of the spectral angle mapper (SAM) technique to Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) images detected sericitic, argillic, and propylitic alterations, silicification, and secondary iron oxides. The alteration is linear and associated within vein‐type mineralization. Twelve prospective areas are selected for detailed exploration and based on our processing results, in addition to NW–SE faults, which are associated with Cu mineralization indications, NE–SW faults are also shown to be important. Based on the presence of subvolcanic rocks and numerous Cu ± Fb‐Zn vein‐type mineralizations, extensive alteration, high anomaly of Cu and Zn (up to 100 ppm), the age (43.6 to 31.4 Ma) and the initial 87Sr/86Sr ratio (0.7047 to 0.7065) of the igneous rocks, and the metallogenic epoch of the Lut block (middle Eocene–lower Oligocene) for the formation of porphyry Cu and epithermal deposits, the studied area shows great potential for porphyry copper deposits.
Geochemical‐geomorphological Evidence for the Provenance of Aeolian Sands and Sedimentary Environments in the Hunshandake Sandy Land, Eastern Inner Mongolia, China
Authors: Ziting LIU , Xiaoping YANG
Published: July 2013

Identifying the provenance of aeolian sediments in the Hunshandake Sandy Land is of great importance for understanding the formation of the dune fields in the mid‐latitudes and for deciphering information about desert's responses to global change. By determining the major and trace elements concentrations of aeolian sands in three grain size fractions from the central and western parts of the Hunshandake Sandy Land, we systematically study the provenance and the depositional history of aeolian sands in this desert environment Our results show that aeolian sands from the Hunshandake Sandy Land are enriched in SiO2 and are depleted in many other elements compared to those of the Upper Continent Crust (UCC). Variations of the immobile elements ratios like Zr/Hf, La/Yb, Th/Nb, La/Nb, LaN/YbN, GdN/YbN are relatively large in the coarse and medium fractions but minor in the fine fractions. Eu anomalies are quite different in the coarse fractions, but mostly positive in the medium fractions and all negative in the fine fractions. Decreasing tendency of Zr concentrations from the west to the east in the Hunshandake Sandy Land is evident in the coarse sands but rather weak in the fine grain size fractions. Our geochemical data indicate that the sources for the coarse and medium fractions of aeolian sands are diverse, influenced by local geology and geomorphology, while the fine sand fractions are more homogenous due to intensive mixture mainly by aeolian processes. Various ratios of immobile elements suggest that these sands should be sourced primarily from the surrounding mountains by fluvial/alluvial processes rather than from any remote territories. Aeolian sands with Ce negative anomalies are widely distributed in the Hunshandake Sandy Land, indicating that aquatic environments have occurred extensively prior to the occurrence of the dune field.
Financial Reporting Opacity and Expected Crash Risk: Evidence from Implied Volatility Smirks
Authors: Kim Jeong‐Bon , Zhang Liandong
Published: July 2013

The recent financial crisis has stimulated a renewed interest in understanding the determinants of stock price crash risk (i.e., left tail risk). Recent research shows that opaque financial reports enable managers to hide and accumulate bad news for extended periods. When the accumulated bad news reaches a certain tipping point, it will be suddenly released to the market at once, resulting in an abrupt decline in stock price (i.e., a crash). This study extends this line of research by examining the impact of financial reporting opacity on perceived or expected crash risk. Prominent economists, such as Olivier Blanchard, argue that removing the perception of tail risks (in addition to realized tail risks) is crucial in restoring investor confidence and stabilizing the stock market. Using the steepness of option implied volatility skew as a proxy for perceived crash risk, we find that accrual management, the presence of financial statement restatements, and auditor‐attested internal control weakness are all positively and significantly associated with the level of perceived crash risk. Our results suggest that improving financial reporting transparency is an important mechanism for firms and policymakers to reduce the perception of tail risks and stabilize the stock market.
The 12‐15‐lipoxygenase is a modulator of Alzheimer's‐related tau pathology in vivo
Authors: Giannopoulos Phillip F. , Joshi Yash B. , Chu Jin , Praticò Domenico
Published: July 2013

12/15‐lipoxygenase (12‐15LO) is a lipid‐peroxidizing enzyme widely expressed in the central nervous system where it has been involved in the neurobiology of Alzheimer's disease (AD) because it modulates amyloid beta (Aβ) and APP processing. However, its biological effect on tau protein is unknown. We investigated the effect of 12‐15LO on tau levels and metabolism in vivo and in vitro and the mechanism involved by using genetic and pharmacologic approaches. While no significant differences were observed in the levels of total tau for both groups, compared with controls, Tg2576 mice overexpressing 12‐15LO had elevated levels of phosphorylated tau at two specific epitopes, Ser 202/Thr 205 and Ser 396. In vitro and in vivo studies show that 12‐15LO modulates tau metabolism specifically via the cdk5 kinase pathway. Associated with these changes were biochemical markers of synaptic pathology. Finally, 12‐15LO‐dependent alteration of tau metabolism was independent from an effect on Aβ. Our findings reveal a novel pathway by which 12‐15LO modulates endogenous tau metabolism making this protein an appealing pharmacologic target for treatment of AD and related tauopathies.
Modeling Clinical Endpoints as a Function of Time of Switch to Second‐Line ART with Incomplete Data on Switching Times
Authors: Johnson Brent A. , Ribaudo Heather , Gulick Roy M. , Eron Joseph J.
Published: July 2013

Modeling clinical endpoints as a function of change in antiretroviral therapy (ART) attempts to answer one simple but very challenging question: was the change in ART beneficial or not? We conceive a similar scientific question of interest in the current manuscript except that we are interested in modeling the time of ART regimen change rather than a comparison of two or more ART regimens. The answer to this scientific riddle is unknown and has been difficult to address clinically. Naturally, ART regimen change is left to a participant and his or her provider and so the date of change depends on participant characteristics. There exists a vast literature on how to address potential confounding and those techniques are vital to the success of the method here. A more substantial challenge is devising a systematic modeling strategy to overcome the missing time of regimen change for those participants who do not switch to second‐line ART within the study period even after failing the initial ART. In this article, we adopt and apply a statistical method that was originally proposed for modeling infusion trial data, where infusion length may be informatively censored, and argue that the same strategy may be employed here. Our application of this method to therapeutic HIV/AIDS studies is new and interesting. Using data from the AIDS Clinical Trials Group (ACTG) Study A5095, we model immunological endpoints as a polynomial function of a participant's switching time to second‐line ART for 182 participants who already failed the initial ART. In our analysis, we find that participants who switch early have somewhat better sustained suppression of HIV‐1 RNA after virological failure than those who switch later. However, we also found that participants who switched very late, possibly censored due to the end of the study, had good HIV‐1 RNA suppression, on average. We believe our scientific conclusions contribute to the relevant HIV literature and hope that the basic modeling strategy outlined here would be useful to others contemplating similar analyses with partially missing treatment length data.
New diagnostic criteria for common variable immune deficiency (CVID), which may assist with decisions to treat with intravenous or subcutaneous immunoglobulin
Authors: Ameratunga R , Woon S-T , Gillis D , Koopmans W , Steele R
Published: July 2013

Common variable immune deficiency (CVID) is the most frequent symptomatic primary immune deficiency in adults. The standard of care is intravenous immunoglobulin (IVIG) or subcutaneous immunoglobulin (scIG) therapy. The cause of CVID is currently unknown, and there is no universally accepted definition of CVID. This creates problems in determining which patients will benefit from IVIG/scIG treatment. In this paper, we review the difficulties with the commonly used European Society of Immune Deficiencies (ESID) and the Pan American Group for Immune Deficiency (PAGID) definition of CVID. We propose new criteria for the diagnosis of CVID, which are based on recent scientific discoveries. Improved diagnostic precision will assist with treatment decisions including IVIG/scIG replacement. We suggest that asymptomatic patients with mild hypogammaglobulinaemia are termed hypogammaglobulinaemia of uncertain significance (HGUS). These patients require long-term follow-up, as some will evolve into CVID.
Karyotyping of diffuse large B‐cell lymphomas: loss of 17p is associated with poor patient outcome
Authors: Fiskvik Idun , Aamot Hege V. , Delabie Jan , Smeland Erlend B. , Stokke Trond , Heim Sverre , Holte Harald
Published: July 2013

Background

Cytogenetic studies of patients with diffuse large B‐cell lymphoma (DLBCL) have revealed a large spectrum of chromosomal abnormalities, some of which may be clinically relevant. We wanted to evaluate possible associations between commonly acquired chromosome aberrations and prognosis in a large cohort of patients.

Methods

All patients with DLBCL treated at our center during 1999–2010 with an abnormal G‐banding karyotype determined on cells short‐term cultured from diagnostic biopsies were included. Detailed information on staging, treatment, and outcome was available for all patients.

Results

Of the 110 patients available for analysis, there were 48 deaths and 27 relapses after a median follow‐up of 4.5 yr. Eleven different chromosomal abnormalities were detected in more than ten percent of patients. Of those, only loss of 17p, including the TP53 tumor suppressor gene, was significantly associated with inferior long‐term prognosis. Five year overall and progression‐free survival frequencies were 32% and 27% for patients with loss of 17p and 67% and 59% in patients without this abnormality.

Conclusion

In a relatively large cohort of patients with DLBCL analyzed by chromosome banding, loss of 17p was the only chromosomal abnormality associated with inferior survival in uni‐ and multivariate analysis.
Measuring reactive metal in soil: a comparison of multi‐element isotopic dilution and chemical extraction
Authors: Marzouk E. R. , Chenery S. R. , Young S. D.
Published: July 2013

The isotopically exchangeable metal pool (E‐value) of zinc (Zn), cadmium (Cd) and lead (Pb) were simultaneously measured, using stable isotope dilution, in soils contaminated by Pb/Zn mining activities and varying in properties likely to affect metal reactivity, including pH, organic matter content, metal concentration and land use. E‐values were compared with single and sequential extraction schemes. Results showed a wide range of metal reactivity (approximately 1–100% of total) depending on the extent of contamination and on the prevailing soil conditions. Across the range of soils, the E‐values showed no consistent correspondence to any single chemical extraction procedure (EDTA, DTPA and HNO3) although there was reasonable agreement with the extractants 0.05 m EDTA and 0.43 m HNO3 in acidic organic soils. Extraction with 0.005 m DTPA substantially under‐estimated the isotopically exchangeable metal content. E‐values corresponded reasonably well with the exchangeable metal (fraction 1 (F1) of the sequential extraction procedure) in calcareous soils but relatively poorly and inconsistently with F1–F2, F1–F3 or F1–F4 in acidic‐neutral soils. Operational aspects associated with determination of multi‐element E‐values are discussed.
Microbial selenium transformations in seleniferous soils
Authors: Fellowes J. W. , Pattrick R. A. D. , Boothman C. , Al Lawati W. M. M. , van Dongen B. E. , Charnock J. M. , Lloyd J. R. , Pearce C. I.
Published: July 2013

Selenium (Se) is an essential trace element for animals and displays a narrow range between dietary deficiency and toxicity. The toxicity of Se depends on its bioavailability, which is directly related to its oxidation states, of which four occur in the environment (SeVI, SeIV, Se0 and SeII−). Microbial communities drive the cycling of Se between these oxidation states. In order to investigate the effect of microbial activity on Se cycling in the environment, a field site in County Meath, Ireland, was identified with anomalously large concentrations of Se as a result of weathering of black shales within the Lucan formation, leading to cases of Se toxicity in farm animals. Soil cores were extracted from the site for Se speciation and microbial community analysis prior to microcosm experiments to assess Se stability and microbial Se transformations. Selenium was present as a recalcitrant, reduced organic phase that was strongly coordinated with carbon, concordant with suggested hypotheses of Se phyto‐concentration within a clay‐lined, postglacial marshland. Selenium was not mobilized in microcosm experiments, and supplementation with SeVI resulted in rapid reduction and removal from solution as Se0. Additional electron donors did not affect Se stability or removal from solution, although nitrate did hinder SeVI reduction. Terminal restriction fragment length polymorphism analysis indicated a significant shift in microbial community after amendment with SeVI. This work extends the current knowledge of Se cycling in the environment, and provides information on the bioavailability of Se in the soil, which determines Se content of foodstuffs.
Characterizing scale‐ and location‐specific variation in non‐linear soil systems using the wavelet transform
Authors: Biswas A. , Cresswell H. P. , Viscarra Rossel R. A. , Si B. C.
Published: July 2013

The combined action of physical, chemical and biological soil processes, which occur at different intensities and scales, causes complex spatial variation in soil that is difficult to characterize. The presence of non‐stationarity and non‐linearity increases this complexity. Wavelet transforms have been used to analyse non‐stationary soil spatial variation. In this study we used the wavelet transform to characterize the spatial variation of non‐linear soil systems. In the wavelet transform, a mathematical function (mother wavelet) is used to examine the frequency behaviour of a spatial series by translating or dilating the function. The effective resolution in identifying the frequency is dependent on the translation‐dilation parameter, which is further dependent on the central frequency of the mother wavelet. The central frequency of the commonly used mother wavelet (Morlet) has been modified in this study to capture up to 95% of the uncertainty in identifying frequency components present in spatial series. Increased central frequency resulted in more oscillations within a localized window and thus provided enhanced frequency resolution, which helped to identify the instantaneous (≡ localized) frequency (IF). Identification of the IF can reduce the local unpredictability and enable characterization of non‐linear systems. We have demonstrated the method with a case study using soil water storage and clay content data. The wavelet spectra and the wavelet IF spectra provided improved spatial resolution in identifying the dominant frequency (scale) of variation in the spatial series. Information on dominant scales can be used for scale‐specific prediction of soil properties and multiscale soil mapping and modelling.
Identifying critical unrecognized sugar–protein interactions in GH10 xylanases from Geobacillus stearothermophilus using STD NMR
Authors: Balazs Yael S. , Lisitsin Elina , Carmiel Oshrat , Shoham Gil , Shoham Yuval , Schmidt Asher
Published: July 2013

1H solution NMR spectroscopy is used synergistically with 3D crystallographic structures to map experimentally significant hydrophobic interactions upon substrate binding in solution under thermodynamic equilibrium. Using saturation transfer difference spectroscopy (STD NMR), a comparison is made between wild‐type xylanase XT6 and its acid/base catalytic mutant E159Q – a non‐active, single‐heteroatom alteration that has been previously utilized to measure binding thermodynamics across a series of xylooligosaccharide–xylanase complexes [Zolotnitsky et al. (2004) Proc Natl Acad Sci USA 101, 11275–11280). In this study, performing STD NMR of one substrate screens binding interactions to two proteins, avoiding many disadvantages inherent to the technique and clearly revealing subtle changes in binding induced upon mutation of the catalytic Glu. To visualize and compare the binding epitopes of xylobiose–xylanase complexes, a ‘SASSY’ plot (saturation difference transfer spectroscopy) is used. Two extraordinarily strong, but previously unrecognized, non‐covalent interactions with H2–5 of xylobiose were observed in the wild‐type enzyme but not in the E159Q mutant. Based on the crystal structure, these interactions were assigned to tryptophan residues at the −1 subsite. The mutant selectively binds only the β–xylobiose anomer. The 1H solution NMR spectrum of a xylotriose–E159Q complex displays non‐uniform broadening of the NMR signals. Differential broadening provides a unique subsite assignment tool based on structural knowledge of face‐to‐face stacking with a conserved tyrosine residue at the +1 subsite. The results obtained herein by substrate‐observed NMR spectroscopy are discussed further in terms of methodological contributions and mechanistic understanding of substrate‐binding adjustments upon a charge change in the E159Q construct.
A nonlinear, low data requirement model for producing spatially explicit fishery forecasts
Authors: Glaser Sarah M. , Ye Hao , Sugihara George
Published: July 2013

Spatial variability can confound accurate estimates of catch per unit effort (CPUE), especially in highly migratory species. The incorporation of spatial structure into fishery stock assessment models should ultimately improve forecasts of stock biomass. Here, we describe a nonlinear time series model for producing spatially explicit forecasts of CPUE that does not require ancillary environmental or demographic data, or specification of a model functional form. We demonstrate this method using spatially resolved (1° × 1° cells) CPUE time series of North Pacific albacore in the California Current System. The spatial model is highly significant (P < 0.00001) and outperforms two spatial null models. We then create a spatial forecast map for years beyond the range of data. Such approaches can guide spatial management of resources and provide a complement to more data‐intensive, highly parameterized population dynamics and ecosystem models currently in use.
Projecting future grassland productivity to assess the sustainability of potential biofuel feedstock areas in the Greater Platte River Basin
Authors: Gu Yingxin , Wylie Bruce K. , Boyte Stephen P. , Phuyal Khem P.
Published: July 2013

This study projects future (e.g., 2050 and 2099) grassland productivities in the Greater Platte River Basin (GPRB) using ecosystem performance (EP, a surrogate for measuring ecosystem productivity) models and future climate projections. The EP models developed from a previous study were based on the satellite vegetation index, site geophysical and biophysical features, and weather and climate drivers. The future climate data used in this study were derived from the National Center for Atmospheric Research Community Climate System Model 3.0 ‘SRES A1B’ (a ‘middle’ emissions path). The main objective of this study is to assess the future sustainability of the potential biofuel feedstock areas identified in a previous study. Results show that the potential biofuel feedstock areas (the more mesic eastern part of the GPRB) will remain productive (i.e., aboveground grassland biomass productivity >2750 kg ha−1 year−1) with a slight increasing trend in the future. The spatially averaged EPs for these areas are 3519, 3432, 3557, 3605, 3752, and 3583 kg ha−1 year−1 for current site potential (2000–2008 average), 2020, 2030, 2040, 2050, and 2099, respectively. Therefore, the identified potential biofuel feedstock areas will likely continue to be sustainable for future biofuel development. On the other hand, grasslands identified as having no biofuel potential in the drier western part of the GPRB would be expected to stay unproductive in the future (spatially averaged EPs are 1822, 1691, 1896, 2306, 1994, and 2169 kg ha−1 year−1 for site potential, 2020, 2030, 2040, 2050, and 2099). These areas should continue to be unsuitable for biofuel feedstock development in the future. These future grassland productivity estimation maps can help land managers to understand and adapt to the expected changes in future EP in the GPRB and to assess the future sustainability and feasibility of potential biofuel feedstock areas.
HOUSE PRICES, SALES, AND TIME ON THE MARKET: A SEARCH‐THEORETIC FRAMEWORK
Authors: DÍAZ ANTONIA , JEREZ BELÉN
Published: July 2013

We assess the ability of a standard search and matching framework to account for the cyclical properties of key macroeconomic time series of the housing market. We calibrate a model with aggregate demand and supply shocks to match selected business cycle properties of vacancies and sales in the United States. Our model reproduces the cyclical time series properties of house prices and the positive and negative comovement of prices with sales and time on the market, respectively. Search and matching frictions produce trading delays that augment the volatility of prices and propagate the effect of aggregate shocks to future periods.
CENTRAL BANK INDEPENDENCE AND THE MONETARY INSTRUMENT PROBLEM
Authors: NIEMANN STEFAN , PICHLER PAUL , SORGER GERHARD
Published: July 2013

We study the monetary instrument problem in a dynamic noncooperative game between separate, discretionary, fiscal and monetary policy makers. We show that monetary instruments are equivalent only if the policy makers' objectives are perfectly aligned; otherwise an instrument problem exists. When the central bank is benevolent while the fiscal authority is short‐sighted relative to the private sector, excessive public spending and debt emerge under a money growth policy but not under an interest rate policy. Despite this property, the interest rate is not necessarily the optimal instrument.
Composition of eggplant cultivars of the Occidental type and implications for the improvement of nutritional and functional quality
Authors: San José Raquel , Sánchez María C. , Cámara María M. , Prohens Jaime
Published: July 2013

We have investigated the diversity for composition in seven eggplant (Solanum melongena) cultivars of the Occidental type. The results show that, with the exception of moisture content and pH, there is a wide diversity for all the analysed traits. Protein content was variable, but generally low. The content in available carbohydrates ranged between 2.99 and 4.19 mg 100 g−1, and the main soluble sugars were glucose and fructose. The fibre content was the most variable trait. In all cases, the dehydroascorbic acid content was higher than the ascorbic acid content. Total phenolics content was on average thirty‐nine‐fold higher than vitamin C content. Multivariate analysis showed that accessions from the black and striped groups presented a similar composition profile, while the white and pickling fruits were very distinct. The pickling eggplant H11 is identified as the best source for improving the nutritional and functional properties of Occidental eggplants.
Investigating the in vitro bioaccessibility of polyphenols in fresh and sun‐dried figs (Ficus carica L.)
Authors: Kamiloglu Senem , Capanoglu Esra
Published: July 2013

In this study, in order to evaluate the in vitro bioaccessibility of fresh and sun‐dried figs, total antioxidant capacity (TAC), total proanthocyanidin content (TPA) and the major phenolic compounds were determined at different phases of simulated gastrointestinal (GI) tract digestion for Sarilop and Bursa siyahi fig varieties. Four major phenolic compounds (chlorogenic acid, rutin, cyanidin‐3‐glucoside (C3G) and cyanidin‐3‐rutinoside (C3R)) were investigated for GI tract digestion. The results of in vitro GI tract digestion revealed that the dialysed fraction (IN) represented 9–26% and 1–22% of the initial TAC of the whole‐fresh yellow and purple figs, respectively. Moreover, in case of 2,2‐azinobis(3‐ethylbenzothiazoline)‐6‐sulphonic acid (ABTS), TPA and chlorogenic acid contents, drying caused an increase in the IN fraction of yellow figs (38, 140, 50%, respectively). The bioaccessibility of C3G and C3R were quite low for fresh figs (0–5% of the initial values), whereas for dried figs, anthocyanins were not detected at all in the IN fraction.
Transition to a smoke‐free culture within mental health and drug and alcohol services: A survey of key stakeholders
Authors: Glover Marewa , Fraser Trish , Bullen Chris , Wallace‐Bell Mark , McRobbie Hayden , Hadwen Georgy
Published: July 2013

Tobacco smoking is common among people with mental illnesses, and they carry a higher burden of smoking‐related illnesses. Despite this, smoke‐free policies and systems for supporting cessation have proved difficult to introduce in mental health and drug and alcohol services (MHDAS). This paper examines the barriers to becoming smoke free within New Zealand services. Key informants, including staff, smoke‐free coordinators, and cessation specialists were interviewed. Of the 142 invited informants 61 agreed (42%) to participate in a telephone interview, and 56 provided useable data. Organizations had a permissive or transitioning smoking culture, or were smoke free, defined by smoke‐free environments, smoke‐free‐promoting attitudes and behaviours of management and staff, and cessation support. Most organizations were on a continuum between permissive and transitional cultures. Only eight services had a fully smoke‐free culture. MHDAS face many challenges in the transition to a smoke‐free culture. They are not helped by exemptions in smoke‐free policies for mental health services, staff smoking, negative staff attitudes to becoming smoke free, poor knowledge of nicotine dependence, smoking‐related harm and comorbidities, and poor knowledge and skills regarding cessation‐support options. Health inequalities will continue across both service and socioeconomic divides without a concerted effort to address smoking.
Animal and cellular models of Friedreich ataxia
Authors: Perdomini Morgane , Hick Aurore , Puccio Hélène , Pook Mark A.
Published: July 2013

The development and use of animal and cellular models of Friedreich ataxia (FRDA) are essential requirements for the understanding of FRDA disease mechanisms and the investigation of potential FRDA therapeutic strategies. Although animal and cellular models of lower organisms have provided valuable information on certain aspects of FRDA disease and therapy, it is intuitive that the most useful models are those of mammals and mammalian cells, which are the closest in physiological terms to FRDA patients. To date, there have been considerable efforts put into the development of several different FRDA mouse models and relevant FRDA mouse and human cell line systems. We summarize the principal mammalian FRDA models, discuss the pros and cons of each system, and describe the ways in which such models have been used to address two of the fundamental, as yet unanswered, questions regarding FRDA. Namely, what is the exact pathophysiology of FRDA and what is the detailed genetic and epigenetic basis of FRDA?