bluuebunny/crossref_metadata_2025_split huggingface dataset:
Silicate bioweathering and biomineralization in lacustrine microbialites: ancient analogues from the Miocene Duero Basin, Spain
Authors: SANZ-MONTERO M. ESTHER , RODRÍGUEZ-ARANDA J. PABLO 
Published: February 2009

AbstractThe Miocene dolomite-chert microbialites studied here offer a complete record of the geochemical cycles of silicate weathering and the subsequent formation of secondary products. The microbialites were formed in lacustrine systems during the Miocene of the Duero Basin, central Spain. Mineralogical, chemical and petrographic results provide evidence of the mediation of microbes in early weathering and by-product formation processes. Irrespective of the composition, the surfaces of the grains were subject to microbial attachment and concomitant weathering. Palaeo-weathering textures range from surface etching and pitting to extensive physical disaggregation of the minerals. Extreme silicate weathering led to the complete destruction of the silicate grains, whose prior existence is inferred from pseudomorphs exhibiting colonial textures like those recognized in the embedding matrix. Detailed petrographic and microanalytical examinations of the weathering effects in K-feldspars show that various secondary products with diverse crystallinity and chemical composition can coexist in the interior of a mineral. The coexistence of by-products is indicative of different microenvironmental conditions, likely created by microbial reactions. Thus, the presence of varied secondary products can be used as a criterion of biogenicity. Intensive alteration of P-bearing feldspars suggests that mineral weathering may have been driven by the nutrient requirements of the microbial consortium involved in the precipitation of dolomite. The rock record provides useful information on mineral weathering mediated by microbes.
Predictors of 10-year outcome of first-episode psychosis
Authors: White C. , Stirling J. , Hopkins R. , Morris J. , Montague L. , Tantam D. , Lewis S. 
Published: February 2009

BackgroundPredictors of outcome for psychosis are poorly understood. Duration of untreated psychosis (DUP) appears to predict short-term outcome although its medium- to long-term role remains unclear. Neurodevelopmental indices such as pre-morbid function and/or neurological soft signs may predict longer-term outcome. We aimed to assess the impact of a range of clinical and demographic variables on long-term outcome of a geographically defined, epidemiological first-episode psychosis cohort.MethodA 10-year follow-up was undertaken of a consecutively presenting sample of 109 cases of first-episode psychosis aged 16–50 years. Baseline assessments included positive, negative and depression symptoms, DUP, neurological soft signs and pre-morbid functioning. Multi-dimensional outcomes were assessed blind to baseline data.ResultsAll participants were traced at a mean of 10.5 years post-index admission: 11 had died, 10 from non-natural causes. Of the surviving cases, 70% were comprehensively re-assessed by interview. Summary data on the remainder were collected from their family practitioner and chart review. Poor 10-year outcomes were predicted independently by poor pre-morbid functioning, baseline negative symptoms and longer DUP. The same measures, plus neurological soft signs, appeared to predict outcomes in a DSM-IV schizophrenia/schizo-affective subgroup.ConclusionsPoor pre-morbid functioning, baseline symptoms, DUP and neurological soft signs at onset independently predict poor long-term outcome in first-episode psychosis.
Entropy production at weak Gibbs measures and a generalized variational principle
Authors: YURI MICHIKO 
Published: February 2009

AbstractWe consider piecewise invertible systems exhibiting intermittency and establish a generalized variational principle adapted to a non-stationary process in the following sense; the supremum is attained by non-singular (not necessarily invariant) probability measures and if the system exhibits hyperbolicity, then it reduces to the usual variational principle for the pressure. Our method relies on Ruelle’s program in the study of non-equilibrium statistical mechanics to analyze dissipative phenomena. We show non-positivity of entropy production at weak Gibbs measures and clarify when it indeed vanishes. We also discuss a generalized variational principle in the context of σ-finite invariant measures.
Convergence of diagonal ergodic averages
Authors: TOWSNER HENRY 
Published: February 2009

AbstractTao has recently proved that ifT1,…,Tlare commuting, invertible, measure-preserving transformations on a dynamical system, then for anyL∞functionsf1,…,fl, the average (1/N)∑n=0N−1∏i≤lfi∘Tinconverges in theL2norm. Tao’s proof is unusual in that it translates the problem into a more complicated statement about the combinatorics of finite spaces by using the Furstenberg correspondence ‘backwards’. In this paper, we give an ergodic proof of this theorem, essentially a translation of Tao’s argument to the ergodic setting. In order to do this, we develop two new variations on the usual Furstenberg correspondence, both of which take recurrence-type statements in one dynamical system and give equivalent statements in a different dynamical system with desirable properties.
Periodic unique beta-expansions: the Sharkovskiĭ ordering
Authors: ALLOUCHE JEAN-PAUL , CLARKE MATTHEW , SIDOROV NIKITA 
Published: February 2009

AbstractLetβ∈(1,2). Eachx∈[0,1/(β−1)] can be represented in the formwhere εk∈{0,1} for allk(aβ-expansion ofx). If$\beta &gt;{(1+\sqrt 5)}/{2}$, then, as is well known, there always existx∈(0,1/(β−1)) which have a uniqueβ-expansion. We study (purely) periodic uniqueβ-expansions and show that for eachn≥2 there exists$\beta _n\in [{(1+\sqrt 5)}/{2},2)$such that there are no unique periodicβ-expansions of smallest periodnforβ≤βnand at least one such expansion forβ>βn. Furthermore, we prove thatβk<βmif and only ifkis less thanmin the sense of the Sharkovskiĭ ordering. We give two proofs of this result, one of which is independent, and the other one links it to the dynamics of a family of trapezoidal maps.
The Mañé–Conze–Guivarc’h lemma for intermittent maps of the circle
Authors: MORRIS IAN D. 
Published: February 2009

AbstractWe study the existence of solutions g to the functional inequality f≤g ∘T−g+β, where f is a prescribed continuous function, T is a weakly expanding transformation of the circle having an indifferent fixed point, and β is the maximum ergodic average of f. Using a method due to T. Bousch, we show that continuous solutions g always exist when the Hölder exponent of f is close to 1. In the converse direction, we construct explicit examples of continuous functions f with low Hölder exponent for which no continuous solution g exists. We give sharp estimates on the best possible Hölder regularity of a solution g given the Hölder regularity of f.
Transitivity of Euclidean-type extensions of hyperbolic systems
Authors: MELBOURNE I. , NIŢICĂ V. , TÖRÖK A. 
Published: February 2009

AbstractLetf:X→Xbe the restriction to a hyperbolic basic set of a smooth diffeomorphism. We show that in the class ofCr(r>0) cocycles with fiber the special Euclidean group SE(n), those that are transitive form a residual set (countable intersection of open dense sets). This result is new for odd values ofn≥3. More generally, we consider Euclidean-type groupsG⋉ℝnwhereGis a compact connected Lie group acting linearly on ℝn. When Fix G={0}, it is again the case that the transitive cocycles are residual. When Fix G≠{0}, the same result holds upon restriction to the subset of cocycles that avoid an obvious and explicit obstruction to transitivity.
Nuclear DNA replication and seed quality
Authors: Sliwinska Elwira 
Published: February 2009

AbstractThe quality of a seed (germination and vigour) is established during its development and maturation, but can be improved by post-harvest processing and pre-sowing treatments. During commercial seed production, maturity is usually estimated visually, relying on experience of the growers, but seed researchers are working to find molecular markers that can be applied easily to help in establishing optimal harvest time. One marker is cell cycle activity expressed as DNA replication in the seeds, analysed by flow cytometry. This fast and accurate method for the estimation of DNA content in plant nuclei allows detection of nuclei at different replication stages in different seed tissues and thus makes it possible to follow changes in the physiological state of a seed. DNA replication, as a late event during germination, can also be used to mark completion of germination and transition to early seedling growth. This information can be useful in the evaluation of seed quality and for following the advancement of priming. Flow cytometric analysis of ploidy can be also used as a basis for control of purity of some polyploid species seed lots.
THE USE OF WHITE PHOSPHORUS AND THE LAW OF WAR
Authors: MacLeod I.J. , Rogers A.P.V. 
Published: February 2009

AbstractThe controversy surrounding recent uses of white phosphorus (WP) to ‘flush-out’ suspected insurgents or in attacks against military targets in open ground has led to a renewed media interest in the legal status of WP-based munitions. An inherent public dislike for weapons that cause death or injury by fire is very natural, so one is entitled to ask whether humanity should not prevail when it comes to anti-personnel uses of such weapons. In the absence of a specific treaty dealing with the use of WP, this article, written jointly by a retired military lawyer and a scientist interested in the law, examines the use of such weapons in practice as well as the relevant legal and scientific background before attempting to reach conclusions about their legality. This involves a consideration of the reasons for the development of WP-based munitions, of their usual military uses and of some unconventional uses of such weapons. There follows an examination of the basic principles of customary international law as well as the treaty provisions dealing with incendiary weapons. Furthermore, because of the various harmful physiological interactions of WP, it was necessary to look closely at the legal provisions on poison, gas and chemical weapons. That demanded an interpretation of multiple aspects of the Chemical Weapons Convention before the legal status of WP could be fully determined. The convention is constructed in such a way that what at first sight appears to be a chemical weapon may not be as a matter of law unless it is consciously applied in a prohibited manner.
UPDATE ON UNITED STATES MILITARY COMMISSIONS
Authors: Finnin Sarah 
Published: February 2009

AbstractThis article provides a detailed update on the progress of the United States military commissions under the regime established by the Military Commissions Act of 2006 for the trial of detainees captured during the War on Terror for so-called war crimes. In particular, the author examines the plea and sentencing of Australian detainee David Hicks, the pre-trial developments in the case of Canadian detainee Omar Khadr, and the early litigation involving the detainees who have been dubbed the ‘September 11 co-conspirators’. The author also touches on the Supreme Court decision inHamdanv.Rumsfeld, some of the significant features of the Military Commission Act, the recent federal court litigation in the case ofBoumedienev.Bush, and the construction of the new military commission building at Guantanamo Bay Naval Base.
AN APPRAISAL OF US PRACTICE RELATING TO ‘ENEMY COMBATANTS’
Authors: Rona Gabor 
Published: February 2009

Following the terrorist attacks of 9/11, the United States sought to establish a framework for detaining, interrogating and possibly prosecuting persons suspected of various degrees of connection to international terrorism. There were several factors militating against reliance on a tried and true law enforcement paradigm of arrest and prosecution in federal courts. Perhaps the most significant one, as described by then Attorney General Ashcroft and other senior officials in the Department of Justice, was the felt need for a fundamental shift in approach when dealing with terrorist suspects, from prosecution to prevention of future attacks.It was presumed that these two interests were at odds: on the one hand, preparing and trying criminal cases, and on the other hand, obtaining actionable intelligence about terrorist groups and their plans; in other words, that the application of criminal justice procedures would hamper the intelligence gathering effort. After all, ‘you have a right to remain silent and a right to an attorney’ (the so-calledMirandawarnings) was not the message that the administration wanted to convey.
RECALLING THE SUBLIME: THE LOGIC OF CREATION IN HAYDN’S CREATION
Authors: KRAMER LAWRENCE 
Published: February 2009

ABSTRACTIn its opening representation of chaos and subsequent depiction of the creation of light, Joseph Haydn’s oratorio The Creation famously begins with two forays into the musical sublime. But the work thereafter devotes itself to recalling the sublime, in the double sense of rescinding the sublime and of making it a matter of memory rather than of practice. This process is already under way in the depiction of light; its progressive advance may be measured in such ensuing episodes as the depictions of the first sun- and moonrise and Adam and Eve’s climactic hymn of praise, ‘Von deiner Güt’’. The withdrawal of the sublime gradually becomes coextensive with the creation itself and the place of humanity in the order of creation, reflecting (and refashioning) a historically specific understanding not only of the sublime but also, and more weightily, of the conditions of possibility for knowing the world and defining the human. Despite its forceful articulation in The Creation, however, this was an understanding already well on its way to becoming obsolete by the end of the eighteenth century.
Evaluating integrated healthcare for refugees and hosts in an African context
Authors: TUEPKER ANAIS , CHI CHUNHUEI 
Published: February 2009

Abstract:This paper argues on ethical and practical grounds for more widespread use of an integrated approach to refugee healthcare, and proposes a basic model of assessment for integrated systems. A defining element of an integrated approach is an equal ability by refugee and host nationals to access the same healthcare resources from the same providers. This differs fundamentally from parallel care, currently the predominant practice in Africa. The authors put forward a general model for evaluation of integrated healthcare with four criteria: (1) improved health outcomes for both hosts and refugees, (2) increased social integration, (3) increased equitable use of healthcare resources, and (4) no undermining of protection. Historical examples of integrated care in Ethiopia and Uganda are examined in light of these criteria to illustrate how this evaluative model would generate evidence currently lacking in debates on the merit of integrated healthcare.
Access as a policy-relevant concept in low- and middle-income countries
Authors: MCINTYRE DI , THIEDE MICHAEL , BIRCH STEPHEN 
Published: February 2009

Abstract:Although access to health care is frequently identified as a goal for health care policy, the precise meaning of access to health care often remains unclear. We present a conceptual framework that defines access to health care as theempowermentof an individual to use health care and as a multidimensional concept based on the interaction (or degree of fit) between health care systems and individuals, households, and communities. Three dimensions of access are identified: availability, affordability, and acceptability, through which access can be evaluated directly instead of focusing on utilisation of care as a proxy for access. We present the case for the comprehensive evaluation of health care systems as well as the dimensions of access, and the factors underlying each dimension. Such systemic analyses can inform policy-makers about the ‘fit’ between needs for health care and receipt of care, and provide the basis for developing policies that promote improvements in the empowerment to use care.
SciMiner: web-based literature mining tool for target identification and functional enrichment analysis
Authors: Hur Junguk , Schuyler Adam D. , States David J. , Feldman Eva L. 
Published: February 2009

Abstract
Summary:SciMiner is a web-based literature mining and functional analysis tool that identifies genes and proteins using a context specific analysis of MEDLINE abstracts and full texts. SciMiner accepts a free text query (PubMed Entrez search) or a list of PubMed identifiers as input. SciMiner uses both regular expression patterns and dictionaries of gene symbols and names compiled from multiple sources. Ambiguous acronyms are resolved by a scoring scheme based on the co-occurrence of acronyms and corresponding description terms, which incorporates optional user-defined filters. Functional enrichment analyses are used to identify highly relevant targets (genes and proteins), GO (Gene Ontology) terms, MeSH (Medical Subject Headings) terms, pathways and protein–protein interaction networks by comparing identified targets from one search result with those from other searches or to the full HGNC [HUGO (Human Genome Organization) Gene Nomenclature Committee] gene set. The performance of gene/protein name identification was evaluated using the BioCreAtIvE (Critical Assessment of Information Extraction systems in Biology) version 2 (Year 2006) Gene Normalization Task as a gold standard. SciMiner achieved 87.1% recall, 71.3% precision and 75.8% F-measure. SciMiner's literature mining performance coupled with functional enrichment analyses provides an efficient platform for retrieval and summary of rich biological information from corpora of users' interests.
Availability: http://jdrf.neurology.med.umich.edu/SciMiner/. A server version of the SciMiner is also available for download and enables users to utilize their institution's journal subscriptions.
Contact: juhur@umich.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Benchmarking regulatory network reconstruction with GRENDEL
Authors: Haynes Brian C. , Brent Michael R. 
Published: February 2009

Abstract
Motivation: Over the past decade, the prospect of inferring networks of gene regulation from high-throughput experimental data has received a great deal of attention. In contrast to the massive effort that has gone into automated deconvolution of biological networks, relatively little effort has been invested in benchmarking the proposed algorithms. The rate at which new network inference methods are being proposed far outpaces our ability to objectively evaluate and compare them. This is largely due to a lack of fully understood biological networks to use as gold standards.
Results: We have developed the most realistic system to date that generates synthetic regulatory networks for benchmarking reconstruction algorithms. The improved biological realism of our benchmark leads to conclusions about the relative accuracies of reconstruction algorithms that are significantly different from those obtained with A-BIOCHEM, an established in silico benchmark.
Availability: The synthetic benchmark utility and the specific benchmark networks that were used in our analyses are available at http://mblab.wustl.edu/software/grendel/
Contact: brent@cse.wustl.edu
Development of a Rapid Method Using Oxalic Acid to Assess Resistance Among Hosta Cultivars to Petiole Rot Caused by Sclerotium rolfsii var. delphinii
Authors: Xu Zhihan , Gleason Mark L. , Mueller Daren S. 
Published: February 2009

A rapid assay was developed to assess hosta cultivars for resistance to petiole rot caused by Sclerotium rolfsii var. delphinii. Leaves of greenhouse-grown hosta (Hosta kikutii and Hosta spp. cultivars Munchkin, Lemon Lime, Tardiflora, Pearl Lake, Zounds, Gold Drop, Halcyon, and Honeybells) were treated with 20 ml of oxalic acid (50 mM) on a cotton swab, then incubated at 100% relative humidity and 27°C. After 4 days, incidence of leaves with lesions was evaluated. Cultivars Munchkin, Lemon Lime, and Tardiflora had a relatively high incidence of leaves with lesions, whereas Gold Drop and Halcyon had much lower incidence. These results were generally consistent with those of field and greenhouse cultivar screening tests in which whole plants were inoculated with the pathogen and rated for disease incidence. Additional screening methods, including spray application of either oxalic acid or mycelial fragments of S. rolfsii var. delphinii, were not as repeatable or simple to conduct as the cotton swab assay. The cotton swab method showed potential to accelerate identification of highly resistant hosta cultivars, and thereby aid efforts to breed resistance to petiole rot. Accepted for publication 1 December 2008. Published 28 January 2009.
Propagule Densities of Macrophomina phaseolina in Soybean Tissue and Soil as Affected by Tillage, Cover Crop, and Herbicide
Authors: Mengistu Alemu , Reddy Krishna N. , Zablotowicz Robert M. , Wrather Allen J. 
Published: February 2009

All current commercial soybean cultivars are susceptible to charcoal rot, a disease caused by Macrophomina phaseolina. Efforts to manage this disease through non-genetic means have not been effective. However, the combined effects of tillage, cover crop and herbicide use, and their roles in the population dynamics of this fungus have not been fully investigated. A field experiment was conducted in 2002 through 2004 at Stoneville, MS, to determine the population dynamics of Macrophomina phaseolina (Tassi) in soybean stem and root tissues at harvest and in soil at planting and harvest as affected by tillage, cover crop, and herbicide. The tillage treatments were conventional tillage (CT) and no-tillage (NT); the cover crops were hairy vetch, rye, and no cover crop; and the herbicide treatments were glyphosate- and non-glyphosate-based applications. Analysis of variance indicated that there was an effect due to tillage, cover crop, and tillage by year interaction on colony forming units (CFU) of M. phaseolina recovered from soybean tissue. Colony forming units in soybean tissue were greater under the CT than NT and were greater for hairy vetch and no cover crop than rye. Regardless of the cover crop system used, CFU in tissue was greater for CT in 2002 than in 2003 and 2004. Application of glyphosate did not affect the CFU in stem and root tissues or in the soil. The CFU from soil at harvest was significantly higher than at planting. The CFU in soil at planting and harvest was only affected by tillage and not by cover crop system. The CFU from stem and root tissues was greater than in soil suggesting that quantification of CFU in tissue may provide a better estimate of treatment effects at harvest. These results also suggest that charcoal rot may be better managed in the NT rather than in the CT system. Accepted for publication 11 December 2008. Published 30 January 2009.