bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-pressure crystal structures and superconductivity of Stannane (SnH
4
)
Authors: Gao Guoying , Oganov Artem R. , Li Peifang , Li Zhenwei , Wang Hui , Cui Tian , Ma Yanming , Bergara Aitor , Lyakhov Andriy O. , Iitaka Toshiaki , Zou Guangtian 
Published: January 2010

There is great interest in the exploration of hydrogen-rich compounds upon strong compression where they can become superconductors. Stannane (SnH
4
) has been proposed to be a potential high-temperature superconductor under pressure, but its high-pressure crystal structures, fundamental for the understanding of superconductivity, remain unsolved. Using an ab initio evolutionary algorithm for crystal structure prediction, we propose the existence of two unique high-pressure metallic phases having space groups
Ama
2 and
P
6
3
/
mmc
, which both contain hexagonal layers of Sn atoms and semimolecular (perhydride) H
2
units. Enthalpy calculations reveal that the
Ama
2 and
P
6
3
/
mmc
structures are stable at 96–180 GPa and above 180 GPa, respectively, while below 96 GPa SnH
4
is unstable with respect to elemental decomposition. The application of the Allen-Dynes modified McMillan equation reveals high superconducting temperatures of 15–22 K for the
Ama
2 phase at 120 GPa and 52–62 K for the
P
6
3
/
mmc
phase at 200 GPa.
Percolative theories of strongly disordered ceramic high-temperature superconductors
Authors: Phillips J. C. 
Published: January 2010

Optimally doped ceramic superconductors (cuprates, pnictides, etc.) exhibit transition temperaturesTcmuch larger than strongly coupled metallic superconductors like Pb (Tc = 7.2 K,Eg/kTc = 4.5) and exhibit many universal features that appear to contradict the Bardeen, Cooper, and Schrieffer theory of superconductivity based on attractive electron-phonon pairing interactions. These complex materials are strongly disordered and contain several competing nanophases that cannot be described effectively by parameterized Hamiltonian models, yet their phase diagrams also exhibit many universal features in both the normal and superconductive states. Here we review the rapidly growing body of experimental results that suggest that these anomalously universal features are the result of marginal stabilities of the ceramic electronic and lattice structures. These dual marginal stabilities favor both electronic percolation of a dopant network and rigidity percolation of the deformed lattice network. This “double percolation” model has previously explained many features of the normal-state transport properties of these materials and is the only theory that has successfully predicted strict lowest upper bounds forTcin the cuprate and pnictide families. Here it is extended to include Coulomb correlations and percolative band narrowing, as well as an angular energy gap equation, which rationalizes angularly averaged gap/Tcratios, and shows that these are similar to those of conventional strongly coupled superconductors.
Disambiguating the species of biomedical named entities using natural language parsers
Authors: Wang Xinglong , Tsujii Jun'ichi , Ananiadou Sophia 
Published: January 2010

Abstract
Motivation: Text mining technologies have been shown to reduce the laborious work involved in organizing the vast amount of information hidden in the literature. One challenge in text mining is linking ambiguous word forms to unambiguous biological concepts. This article reports on a comprehensive study on resolving the ambiguity in mentions of biomedical named entities with respect to model organisms and presents an array of approaches, with focus on methods utilizing natural language parsers.
Results: We build a corpus for organism disambiguation where every occurrence of protein/gene entity is manually tagged with a species ID, and evaluate a number of methods on it. Promising results are obtained by training a machine learning model on syntactic parse trees, which is then used to decide whether an entity belongs to the model organism denoted by a neighbouring species-indicating word (e.g. yeast). The parser-based approaches are also compared with a supervised classification method and results indicate that the former are a more favorable choice when domain portability is of concern. The best overall performance is obtained by combining the strengths of syntactic features and supervised classification.
Availability: The corpus and demo are available at http://www.nactem.ac.uk/deca_details/start.cgi, and the software is freely available as U-Compare components (Kano et al., 2009): NaCTeM Species Word Detector and NaCTeM Species Disambiguator. U-Compare is available at http://-compare.org/
Contact: xinglong.wang@manchester.ac.uk
The good(ish), the bad, and the ugly: a tripartite classification of ecosystem trends
Authors: Bundy Alida , Shannon Lynne J. , Rochet Marie-Joëlle , Neira Sergio , Shin Yunne-Jai , Hill Louize , Aydin Kerim 
Published: January 2010

AbstractBundy, A., Shannon, L. J., Rochet, M-J., Neira, S., Shin, Y-J., Hill, L., and Aydin, K. 2010. The good(ish), the bad, and the ugly: a tripartite classification of ecosystem trends. – ICES Journal of Marine Science, 67: 745–768. Marine ecosystems have been exploited for a long time, growing increasingly vulnerable to collapse and irreversible change. How do we know when an ecosystem may be in danger? A measure of the status of individual stocks is only a partial gauge of its status, and does not include changes at the broader ecosystem level, to non-commercial species or to its structure or functioning. Six ecosystem indicators measuring trends over time were collated for 19 ecosystems, corresponding to four ecological attributes: resource potential, ecosystem structure and functioning, conservation of functional biodiversity, and ecosystem stability and resistance to perturbations. We explored the use of a decision-tree approach, a definition of initial ecosystem state (impacted or non-impacted), and the trends in the ecosystem indicators to classify the ecosystems into improving, stationary, and deteriorating. Ecosystem experts classified all ecosystems as impacted at the time of their initial state. Of these, 15 were diagnosed as “ugly”, because they had deteriorated from an already impacted state. Several also exhibited specific combinations of trends indicating “fishing down the foodweb”, reduction in size structure, reduction in diversity and stability, and changed productivity. The classification provides an initial evaluation for scientists, resource managers, stakeholders, and the general public of the concerning status of ecosystems globally.
Chloroplastic Phosphoadenosine Phosphosulfate Metabolism Regulates Basal Levels of the Prohormone Jasmonic Acid in Arabidopsis Leaves
Authors: Rodríguez Víctor M. , Chételat Aurore , Majcherczyk Paul , Farmer Edward E. 
Published: January 2010

Abstract
Levels of the enzymes that produce wound response mediators have to be controlled tightly in unwounded tissues. The Arabidopsis (Arabidopsis thaliana) fatty acid oxygenation up-regulated8 (fou8) mutant catalyzes high rates of α -linolenic acid oxygenation and has higher than wild-type levels of the α -linolenic acid-derived wound response mediator jasmonic acid (JA) in undamaged leaves. fou8 produces a null allele in the gene SAL1 (also known as FIERY1 or FRY1). Overexpression of the wild-type gene product had the opposite effect of the null allele, suggesting a regulatory role of SAL1 acting in JA synthesis. The biochemical phenotypes in fou8 were complemented when the yeast (Saccharomyces cerevisiae) sulfur metabolism 3′(2′), 5′-bisphosphate nucleotidase MET22 was targeted to chloroplasts in fou8. The data are consistent with a role of SAL1 in the chloroplast-localized dephosphorylation of 3′-phospho-5′-adenosine phosphosulfate to 5′-adenosine phosphosulfate or in a closely related reaction (e.g. 3′,5′-bisphosphate dephosphorylation). Furthermore, the fou8 phenotype was genetically suppressed in a triple mutant (fou8 apk1 apk2) affecting chloroplastic 3′-phospho-5′-adenosine phosphosulfate synthesis. These results show that a nucleotide component of the sulfur futile cycle regulates early steps of JA production and basal JA levels.
Molecular immunology lessons from therapeutic T‐cell receptor gene transfer
Authors: Thomas Sharyn , Stauss Hans J. , Morris Emma C. 
Published: January 2010

SummaryThe T‐cell receptor (TCR) is critical for T‐cell lineage selection, antigen specificity, effector function and survival. Recently, TCR gene transfer has been developed as a reliable method to generate ex vivo large numbers of T cells of a given antigen‐specificity and functional avidity. Such approaches have major applications for the adoptive cellular therapy of viral infectious diseases, virus‐associated malignancies and cancer. TCR gene transfer utilizes retroviral or lentiviral constructs containing the gene sequences of the TCR‐α and TCR‐β chains, which have been cloned from a clonal T‐cell population of the desired antigen specificity. The TCR‐encoding vector is then used to infect (transduce) primary T cells in vitro. To generate a transduced T cell with the desired functional specificity, the introduced TCR‐α and TCR‐β chains must form a heterodimer and associate with the CD3 complex in order to be stably expressed at the T‐cell surface. In order to optimize the function of TCR‐transduced T cells, researchers in the field of TCR gene transfer have exploited many aspects of basic research in T‐cell immunology relating to TCR structure, TCR–CD3 assembly, cell‐surface TCR expression, TCR‐peptide/major histocompatibility complex (MHC) affinity and TCR signalling. However, improving the introduction of exogenous TCRs into naturally occurring T cells has provided further insights into basic T‐cell immunology. The aim of this review was to discuss the molecular immunology lessons learnt through therapeutic TCR transfer.
TEM investigation of ductile iron alloyed with vanadium
Authors: DYMEK S. , BLICHARSKI M. , MORGIEL J. , FRAŚ E. 
Published: January 2010

SummaryThis article presents results of the processing and microstructure evolution of ductile cast iron, modified by an addition of vanadium. The ductile iron was austenitized closed to the solidus (1095°C) for 100 h, cooled down to 640°C and held on at this temperature for 16 h. The heat treatment led to the dissolution of primary vanadium‐rich carbides and their subsequent re‐precipitation in a more dispersed form. The result of mechanical tests indicated that addition of vanadium and an appropriate heat treatment makes age hardening of ductile iron feasible. The precipitation processes as well as the effect of Si content on the alloy microstructure were examined by scanning and transmission electron microscopy. It was shown that adjacent to uniformly spread out vanadium‐rich carbides with an average size of 50 nm, a dispersoid composed of extremely small ∼1 nm precipitates was also revealed.
General quantitative genetic methods for comparative biology: phylogenies, taxonomies and multi-trait models for continuous and categorical characters
Authors: Hadfield J. D. , Nakagawa S. 
Published: January 2010

AbstractAlthough many of the statistical techniques used in comparative biology were originally developed in quantitative genetics, subsequent development of comparative techniques has progressed in relative isolation. Consequently, many of the new and planned developments in comparative analysis already have well-tested solutions in quantitative genetics. In this paper, we take three recent publications that develop phylogenetic meta-analysis, either implicitly or explicitly, and show how they can be considered as quantitative genetic models. We highlight some of the difficulties with the proposed solutions, and demonstrate that standard quantitative genetic theory and software offer solutions. We also show how results from Bayesian quantitative genetics can be used to create efficient Markov chain Monte Carlo algorithms for phylogenetic mixed models, thereby extending their generality to non-Gaussian data. Of particular utility is the development of multinomial models for analysing the evolution of discrete traits, and the development of multi-trait models in which traits can follow different distributions. Meta-analyses often include a nonrandom collection of species for which the full phylogenetic tree has only been partly resolved. Using missing data theory, we show how the presented models can be used to correct for nonrandom sampling and show how taxonomies and phylogenies can be combined to give a flexible framework with which to model dependence.
Chronic malaria infections increase family inequalities and reduce parental fitness: experimental evidence from a wild bird population
Authors: Knowles S. C. L. , Palinauskas V. , Sheldon B. C. 
Published: January 2010

Abstract
Avian malaria parasites (Plasmodium) occur commonly in wild birds and are an increasingly popular model system for understanding host–parasite co-evolution. However, whether these parasites have fitness consequences for hosts in endemic areas is much debated, particularly since wild-caught individuals almost always harbour chronic infections of very low parasite density. We used the anti-malarial drug MalaroneTM to test experimentally for fitness effects of chronic malaria infection in a wild population of breeding blue tits (Cyanistes caeruleus). Medication caused a pronounced reduction in Plasmodium infection intensity, usually resulting in complete clearance of these parasites from the blood, as revealed by quantitative PCR. Positive effects of medication on malaria-infected birds were found at multiple stages during breeding, with medicated females showing higher hatching success, provisioning rates and fledging success compared to controls. Most strikingly, we found that treatment of maternal malaria infections strongly altered within-family differences, with reduced inequality in hatching probability and fledging mass within broods reared by medicated females. These within-brood effects appear to explain higher fledging success among medicated females and are consistent with a model of parental optimism in which smaller (marginal) offspring can be successfully raised to independence if additional resources become available during the breeding attempt. Overall, these results demonstrate that chronic avian malaria infections, far from being benign, can have significant effects on host fitness and may thus constitute an important selection pressure in wild bird populations.
Morphology, cytology and taxonomic remarks of four species ofStigeoclonium(Chaetophorales, Chlorophyceae) from Argentina
Authors: Michetti Karina M. , Leonardi Patricia I. , Cáceres Eduardo J. 
Published: January 2010

SUMMARYFour species ofStigeocloniumfrom Argentina were studied by means of transmission electron microscopy and light microscopy. For species identification, we collected data related to the prostrate system and zoospore germination. We also determined the chromosome number for each species.Stigeoclonium aestivaleshowed a more developed erect system than the prostrate one, zoospore germination was predominantly of erect type and the chromosome number was 8.Stigeoclonium tenuepresented well developed, erect and prostrate systems, zoospore germination was initially of the prostrate type and the chromosome number was 5. InStigeoclonium variabilethe prostrate system predominated over the erect one, zoospore germination was strictly of the prostrate type and the chromosome number was 3.Stigeoclonium farctumpresented a more developed prostrate system than the erect one, zoospore germination was strictly of the prostrate type and the chromosome number was 8. The ontogeny of the zoospore germination was related to the final relative development of the prostrate and erect portions of adult thalli.
Genetic diversity of Gambierdiscus spp. (Gonyaulacales, Dinophyceae) in Japanese coastal areas
Authors: Kuno Sotaro , Kamikawa Ryoma , Yoshimatsu Sadaaki , Sagara Takefumi , Nishio Sachio , Sako Yoshihiko 
Published: January 2010

SUMMARYThe genetic diversity of the ciguatera fish poisoning‐related dinoflagellate distributed in Japanese coastal areas was investigated. The entire sequence of the 5.8S rRNA gene and two internal transcribed (ITS) regions were determined, which included putative pseudogenes, from 19 strains of dinoflagellates assigned to the genus Gambierdiscus Adachi et Fukuyo collected from Japanese subtropical and temperate coastal areas. The sequences obtained from the 19 strains were divided into two types based on sequence similarity. Here we designate the two types as type 1 and type 2. For the relationship between the genotypes and origins of the strains used, the strains collected from subtropical areas possessed the type 1 sequence; whereas those from temperate areas possessed the type 2. This observation led us to question former reputations that Gambierdiscus cells observed in Japanese temperate areas are immigrants from Japanese subtropical areas. Subsequently, we sequenced a part of the 18S rRNA gene from two strains from subtropical areas and two from temperate areas. Unfortunately, phylogenetic analysis including the sequences obtained from various gonyaulacales dinoflagellates failed to determine the species phylogenetically closely related to and possible origin(s) of the Gambierdiscus sp. from the Japanese coastal areas.
Phylogenetic position of a rare loricated green alga, Cephalomonas granulata N. L. Higinb. (Volvocales, Chlorophyceae)
Authors: Nakada Takashi , Soga Tomoyoshi , Tomita Masaru 
Published: January 2010

SUMMARY Cephalomonas (Cp.) granulata N. L. Higinb. (Volvocales, Chlorophyceae), a rare volvocalean phytoflagellate, has recently been isolated from a paddy field in Japan and examined by light and fluorescence microscopy. The vegetative cells of Cp. granulata have granulate loricae and a characteristic mushroom‐like shape with a hemispherical to spherical anterior part and narrower posterior part. Cp. granulata has been classified among the Phacotaceae along with other loricated genera. However, its phylogenetic position has not been investigated using molecular phylogeny. To evaluate the phylogenetic position of Cephalomonas, the 18S rRNA gene sequence of the Japanese strain was determined. The phylogenetic analyses revealed that Cp. granulata was not closely related to other loricated taxa with known phylogenetic affinities, such as Phacotaceae sensu stricto (Phacotus, Pteromonas, and Wislouchiella) and Dysmorphococcus globosus. This indicates at least three independent origins of loricae within the Volvocales.
Recovering from recurrent mental health problems: Giving up and fighting to get better
Authors: Kartalova‐O'Doherty Yulia , Tedstone Doherty Donna 
Published: January 2010

ABSTRACTThe purpose of this paper is to present selected findings of a grounded theory study that aims to explore individual processes and desired outcomes of recovery from recurrent health problems in order to build up a theoretical framework of recovery in an Irish context. Volunteers included mental health service users or participants of peer support groups who have experienced recurrent mental health problems for two or more years, consider themselves in improvement, and are willing to participate in individual interviews. The current paper is based on the analysis of 15 audiorecorded and transcribed interviews. We identified two open codes of ‘giving up’ and ‘fighting to get better’. Giving up was associated with accepting a passive identity of a patient with a chronic mental illness and a lack of intrinsic motivation to get better. Fighting had both positive (fighting for) and negative (fighting against) dimensions, as well as internal and external ones. The fight for recovery entailed substantial and sometimes risky effort. Starting such a fight required strong, self‐sustained motivation. Service providers might need to discuss internal and external motivators of fighting for recovery with service users, with a view to including such motivators in the care plans.
Confusion of recovery: One solution
Authors: Collier Elizabeth 
Published: January 2010

ABSTRACTThis paper questions the current mental health discourse that offers new definitions of the concept of ‘recovery’ and offers a different perspective that aims to clarify its meaning. Confusion is caused when medical language continues to be used in discussions that aim to challenge traditional medical understanding of the term ‘recovery’ (meaning cure). Medical and non‐medical concepts of recovery are referred to interchangeably in many narratives and the common references to and acceptance of the Harding et al. papers and similar that report on how people can ‘get better’ from schizophrenia perpetuates this confusion. In this paper, it is suggested that ‘recovery’ should not be viewed as having new meaning, but that two different concepts have been confused, with the same word having been used to describe two completely different things altogether. This means that what is referred to in this paper as ‘medical’ recovery (traditional definitions of recovery that aims for cure), becomes subordinate to ‘life’ recovery (personal development and change) in which psychiatric classification might have no part in a person's understanding of their experience and where improving ‘symptoms’ could be irrelevant in the personal process of growth and discovery.
Systemic atherosclerosis in patients with perforating artery territorial infarction
Authors: Choi H.‐Y. , Yang J. H. , Cho H. J. , Kim Y. D. , Nam H. S. , Heo J. H. 
Published: January 2010

Background:  Perforating artery territorial infarction (PAI) is usually a small artery disease (SAD). However, it may also result from branch artery occlusion or arterial embolism from the proximal atherosclerotic lesions. We hypothesized that patients with PAI caused by a SAD may have a distinct pattern of systemic artery involvement from those with PAI caused by large artery diseases.Methods:  We investigated retrospectively 329 consecutive patients with PAI who had angiographic studies. Patients were grouped according to the presence or absence of atherosclerosis in the parent artery or relevant artery: no arterial lesion (NAL), relevant artery atherosclerosis (RAA) and parent artery atherosclerosis (PAA). The relevant artery was defined as any artery which can cause index stroke. The parent artery was defined as an original artery that branches out and forms small artery which was responsible for index PAI. Systemic evidence of atherosclerosis and risk factors were compared.Results:  Of the 329 patients with PAI, 109 had RAA, 45 had PAA and 175 had neither RAA nor PAA. There were no differences amongst the groups in the classic risk factors for atherosclerosis. Evidence of atherosclerosis in arterial beds other than the relevant artery to the infarction (other cerebral arteries, coronary arteries, descending aorta and peripheral arteries) was significantly lower in the NAL group (49.7%) than in either the PAA group (88.9%) or RAA group (93.6%).Conclusions:  Perforating artery territorial infarction with RAA or PAA when compared to PAI without atherosclerosis showed different involvement patterns of systemic atherosclerosis, suggesting potentially different aetiological mechanisms.