bluuebunny/crossref_metadata_2025 huggingface dataset:
Efficiently detecting polymorphisms during the fragment
assembly process
Authors: Fasulo Daniel , Halpern Aaron , Dew Ian , Mobarry Clark
Published: May 2011

Motivation: Current genomic sequence assemblers assume that the input data is derived from a single, homogeneous source. However, recent whole-genome shotgun sequencing projects have violated this assumption, resulting in input fragments covering the same region of the genome whose sequences differ due to polymorphic variation in the population. While single-nucleotide polymorphisms (SNPs) do not pose a significant problem to state-of-the-art assembly methods, these methods do not handle insertion/deletion (indel) polymorphisms of more than a few bases.

Results: This paper describes an efficient method for detecting sequence discrepencies due to polymorphism that avoids resorting to global use of more costly, less stringent affine sequence alignments. Instead, the algorithm uses graph-based methods to determine the small set of fragments involved in each polymorphism and performs more sophisticated alignments only among fragments in that set. Results from the incorporation of this method into the Celera Assembler are reported for the D. melanogaster, H. sapiens, and M. musculus genomes.

Availability: The method described herein does not constitute a stand-alone software application, but is laid out in sufficient detail to be implemented as a component of any genomic sequence assembler.

Contact: daniel.fasulo@celera.com

Keywords: whole-genome assembly; shotgun sequencing; polymorphism.
Prediction of contact maps by GIOHMMs and recurrent
neural networks using lateral propagation from all four cardinal
corners
Authors: Pollastri G. , Baldi P.
Published: May 2011

Motivation: Accurate prediction of protein contact maps is an important step in computational structural proteomics. Because contact maps provide a translation and rotation invariant topological representation of a protein, they can be used as a fundamental intermediary step in protein structure prediction.

Results: We develop a new set of flexible machine learning architectures for the prediction of contact maps, as well as other information processing and pattern recognition tasks. The architectures can be viewed as recurrent neural network implemantations of a class of Bayesian networks we call generalized input-output HMMs (GIOHMMs). For the specific case of contact maps, contextual information is propagated laterally through four hidden planes, one for each cardinal corner. We show that these architectures can be trained from examples and yield contact map predictors that outperform previously reported methods. While several extensions and improvements are in progress, the current version can accurately predict 60.5% of contacts at a distance cutoff of 8 Å and 45% of distant contacts at 10 Å, for proteins of length up to 300.

Availability: The contact map predictor will be made available through http://promoter.ics.uci.edu/BRNN-PRED/ as part of an existing suite of proteomics predictors.

Contact: gpollast@ics.uci.edupfbaldi@ics.uci.edu

Keywords: protein structure prediction; protein contacts, contact map; graphical models; recurrent neural networks.

*To whom correspondence should be addressed.
Rate4Site: an algorithmic tool for the identification of functional regions
in proteins by surface mapping of evolutionary determinants within their
homologues
Authors: Pupko Tal , Bell Rachel E. , Mayrose Itay , Glaser Fabian , Ben-Tal Nir
Published: May 2011

Motivation: A number of proteins of known three-dimensional (3D) structure exist, with yet unknown function. In light of the recent progress in structure determination methodology, this number is likely to increase rapidly. A novel method is presented here: ‘Rate4Site’, which maps the rate of evolution among homologous proteins onto the molecular surface of one of the homologues whose 3D-structure is known. Functionally important regions often correspond to surface patches of slowly evolving residues.

Results: Rate4Site estimates the rate of evolution of amino acid sites using the maximum likelihood (ML) principle. The ML estimate of the rates considers the topology and branch lengths of the phylogenetic tree, as well as the underlying stochastic process. To demonstrate its potency, we study the Src SH2 domain. Like previously established methods, Rate4Site detected the SH2 peptide-binding groove. Interestingly, it also detected inter-domain interactions between the SH2 domain and the rest of the Src protein that other methods failed to detect.

Availability: Rate4Site can be downloaded at: http://ashtoret.tau.ac.il/ It is implemented as a web server at: bioinfo.tau.ac.il/ConSurf

Contact: tal@ism.ac.jprebell@ashtoret.tau.ac.ilfabian@ashtoret.tau.ac.ilbental@ashtoret.tau.ac.il

Supplementary Information: Multiple sequence alignment of homologous SH2 domains, the corresponding phylogenetic tree and additional examples are available at http://ashtoret.tau.ac.il/~rebell

Keywords: rate variation among sites; evolutionary conservation; protein evolution; maximum likelihood; SH2 domains.

*To whom correspondence should be addressed.

†These authors contributed equally.
A similarity-based method for genome-wide prediction of
disease-relevant human genes
Authors: Freudenberg J. , Propping P.
Published: May 2011

Motivation: A method for prediction of disease relevant human genes from the phenotypic appearance of a query disease is presented. Diseases of known genetic origin are clustered according to their phenotypic similarity. Each cluster entry consists of a disease and its underlying disease gene. Potential disease genes from the human genome are scored by their functional similarity to known disease genes in these clusters, which are phenotypically similar to the query disease.

Results:For assessment of the approach, a leave-one-out cross-validation of 878 diseases from the OMIM database, using 10672 candidate genes from the human genome, is performed. Depending on the applied parameters, in roughly one-third of cases the true solution is contained within the top scoring 3% of predictions and in two-third of cases the true solution is contained within the top scoring 15% of predictions.

The prediction results can either be used to identify target genes, when searching for a mutation in monogenic diseases or for selection of loci in genotyping experiments in genetically complex diseases.

Contact: jan.freudenberg@uni-bonn.de
Breakpoint medians and breakpoint phylogenies: A
fixed-parameter approach
Authors: Gramm Jens , Niedermeier Rolf
Published: May 2011

With breakpoint distance, the genome rearrangement field delivered one of the currently most popular measures in phylogenetic studies for related species. Here, Breakpoint Median, which is NP-complete already for three given species (whose genomes are represented as signed orderings), is the core basic problem. For the important special case of three species, approximation (ratio 7/6) and exact heuristic algorithms were developed. Here, we provide an exact, fixed-parameter algorithm with provable performance bounds. For instance, a breakpoint median for three signed orderings over nelements that causes at most d breakpoints can be computed in time O((2.15)d·n). We show the algorithm's practical usefulness through experimental studies. In particular, we demonstrate that a simple implementation of our algorithm combined with a new tree construction heuristic allows for a new approach to breakpoint phylogeny, yielding evolutionary trees that are competitive in comparison with known results developed in a recent series of papers that use clever algorithm engineering methods.
Stochastic pairwise alignments
Authors: Mückstein U. , Hofacker I.L. , Stadler P.F.
Published: May 2011

Motivation: The level of sequence conservation between related nucleic acids or proteins often varies considerably along the sequence. Both regions with high variability (mutational hot-spots) and regions of almost perfect sequence identity may occur in the same pair of molecules. The reliability of an alignment therefore strongly depends on the level of local sequence similarity. Especially in regions of high variability, many alignments of almost equal quality exist, and the optimal alignment is highly arbitrary.

Results: We discuss two approaches which deal with the inherent ambiguity of the alignment problem based on the computation of the partition function over all canonical pairwise alignments. The ensemble of possible alignments can be described by the probabilities Pij of a match between position i in the first and position j in the second sequence. Alternatively, we introduce a probabilistic backtracking procedure that generates ensembles of suboptimal alignments with correct statistical weights.

A comparison between structure based alignments and large samples of stochastic alignments shows that the ensemble contains correct alignments with significant probabilities even though the optimal alignment deviates significantly from the structural alignment. Ensembles of suboptimal alignments obtained by stochastic backtracking can be used as input to any bioinformatics method based on pairwise alignment in order to gain reliability information not available from a single optimal alignment.

Availability: The software described in this contribution is available for downloading at http://www.tbi.univie.ac.at/~ulim/probA/

Contact: ivo@tbi.univie.ac.at
Selecting targets for therapeutic validation through
differential protein expression using chromatography-mass
spectrometry
Authors: Patterson Scott
Published: May 2011

The identification of potential targets for therapeutic intervention can be accomplished on a systematic basis by a variety of techniques that include quantitative analysis of gene-specific mRNA levels and expressed proteins in normal and diseased cells. Differences in the expression levels of nucleic acid and protein gene products could suggest protein drug targets that are directly causative of disease, or reveal biochemical pathways that could be modulated by therapeutic molecules. Any effort based on mRNA or protein expression level comparisons could be confounded by a number of factors:

level in steady-state may not be correlated with actual encoded protein levels;

differentially expressed protein levels might be a result of disease process, and not causative of the process, and therapeutic intervention based on such a difference will be unproductive and

the differential expression of mRNA or protein may be the result of biological variation unrelated to the disease process under study.

In order to address these possibly confounding factors, it is necessary to validate potential targets by establishing their firm association with disease, and their minimal distribution in non-diseased tissues of any type. This requirement suggests that emphasis on true and reproducible quantitation of protein expression levels in a variety of samples will be an effective and highly efficient method of generating drug targets with a high degree of utility. To achieve this aim, we have established an industrial-scale proteomics-based discovery platform consisting of cell biology, protein chemistry, and mass spectrometry technical groups together with bioinformatics groups. The analytical method used for quantitation employs isotope labeling for differential analysis (ICATTM, Applied Biosystems, Inc.). With this technique, tryptic peptides are generated from labeled proteins that have been specifically captured from various subcellular locations or protein families. The resulting peptides are identified and quantified by mass spectrometry. To evaluate this approach on a large-scale, we have applied it to a study of continuous cell lines derived from human pancreatic adenocarcinomas. We have been able to establish processes for target discovery for small molecule drug targets as well as therapeutic antibody target identification for cell surface proteins. In addition, we have developed a process for identification of serum markers of this disease based upon standardized fractionation procedures. The results of these analyses will be presented together with the some of the issues from both the wet and dry (computational) lab that need to be addressed in such an undertaking.
An approximate matching algorithm for finding (sub-)optimal
sequences in S-attributed grammars
Authors: Waldispühl J. , Behzadi B. , Steyaert J.-M.
Published: May 2011

Motivation: S-attributed grammars (a generalization of classical Context-Free grammars) provide a versatile formalism for sequence analysis which allows to express long range constraints: the RNA folding problem is a typical example of application. Efficient algorithms have been developed to solve problems expressed with these tools, which generally compute the optimal attribute of the sequence w.r.t. the grammar. However, it is often more meaningful and/or interesting from the biological point of view to consider almost optimal attributes as well as approximate sequences; we thus need more flexible and powerful algorithms able to perform these generalized analyses.

Results: In this paper we present a basic algorithm which, given a grammar G and a sequence ω, computes the optimal attribute for all (approximate) strings ω′∈ L(G) such that d(ω, ω′)≤ M, and whose complexity is 𝒪(nr+1) in time and 𝒪(n2) in space (r is the maximal length of the right-hand side of any production of G). We will also give some extensions and possible improvements of this algorithm.

Keywords: S-Attribute Grammar, Approximate matching, Dynamic Algorithm.

Contact: waldispu@lix.polytechnique.fr
Detecting genomic features under weak selective pressure:
the example of codon usage in animals and plants
Authors: Duret Laurent
Published: May 2011

Large scale experiments of gene inactivation in yeast have shown that 50% of genes have no detectable impact on the phenotype, and similar observations have been made in other model organisms. This apparent paradox is probably due to the fact that many genes only have a marginal contribution to the fitness of organisms. Because of the size of populations and the number of generations that can be studied in laboratories, experimental approaches only permit to detect functional elements that have a strong phenotypic impact. Comparative sequence analysis can help to solve this problem: the analysis of sequences evolution permits to detect the action of selection, and hence to reveal functional features of genomes. This approach will be illustrated by the study of synonymous codon usage in animals and plants.
Dialysis in acute kidney injury
Authors: Levy Jeremy , Brown Edwina , Daley Christine , Lawrence Anastasia
Published: May 2011

This chapter discusses dialysis in acute kidney injury (AKI), including indications for acute dialysis, choice of modality, psychosocial effects of dialysis in AKI, dialysis adequacy in AKI, prescribing acute haemodialysis, continuous renal replacement therapy (CRRT) and other continuous renal replacement techniques, anticoagulation for CRRT, complications of CRRT, peritoneal dialysis in acute kidney injury, prescribing peritoneal dialysis in acute kidney injury, haemodialysis and haemoperfusion for poisoning, and drugs and toxins removed by haemodialysis and haemoperfusion.
Complications of ESKD: anaemia
Authors: Levy Jeremy , Brown Edwina , Daley Christine , Lawrence Anastasia
Published: May 2011

This chapter discusses anaemia as a complication of end-stage kidney disease (ESKD), including causes of anaemia, assessment of anaemia and haemolysis, management of anaemia, erythropoietin, iron metabolism, assessing iron status, iron supplements (oral and intravenous iron), high ferritin and low transferrin saturation index, and non-iron adjuvants to EPO treatment.
Complications of ESKD: cardiovascular disease
Authors: Levy Jeremy , Brown Edwina , Daley Christine , Lawrence Anastasia
Published: May 2011

This chapter discusses cardiovascular disease as a complication of end-stage kidney disease (ESKD), including cardiovascular risk factor intervention in dialysis patients, management of ischaemic heart disease, acute coronary syndrome, hypertension, BP control in patients on haemodialysis and peritoneal dialysis, cerebrovascular disease, and peripheral vascular disease.
Other complications of ESKD
Authors: Levy Jeremy , Brown Edwina , Daley Christine , Lawrence Anastasia
Published: May 2011

This chapter discusses complications of end-stage kidney disease (ESKD), including dialysis amyloid, renal cysts and retroperitoneal bleeding, renal cell carcinoma, neurological complications, depression, cognitive impairment, GI bleeding, acidosis, sexual dysfunction, aluminium toxicity, gadolinium, blood biochemistry in ESKD, tumour markers in ESKD, quality of life, compliance, and employment and rehabilitation.
Evidence-based psychiatry
Authors: Semple David , Smyth Roger
Published: May 2011

Abstracts and keywords to be supplied.
Depressive illness
Authors: Semple David , Smyth Roger
Published: May 2011

Abstracts and keywords to be supplied.
Substance misuse
Authors: Semple David , Smyth Roger
Published: May 2011

Abstracts and keywords to be supplied.
Fusarium Crown and Root Rot of Tarragon in California Caused by Fusarium solani
Authors: Koike S. T.
Published: May 2011

Tarragon, also known as estragon or dragon's-wort (Artemisia dracunculus), is a perennial plant in the Asteraceae. Tarragon is grown for use in cooking as a fresh and dried herb. In May 2010, commercial tarragon grown in a field on California's central coast was affected by a previously undescribed disease. Initial symptoms consisted of chlorosis of leaves and wilting of shoot tips. As the disease progressed, entire shoots and branches turned brown and died. The plant crown epidermis and cortex and the upper cortex of the main roots turned brown with occasional black streaking. Diseased plants died several weeks after the onset of wilting. A Fusarium species was consistently isolated from symptomatic crown and root tissues. On carnation leaf agar (CLA) incubated under lights, the isolates produced stout, slightly curved macroconidia having blunt apical cells. One- and two-celled oval to cylindrical microconidia were abundant and born in false heads on extremely long monophialides. Chlamydospores were present in 1-month-old cultures. On potato dextrose agar incubated under lights, the isolates produced abundant white aerial mycelium with bluish coloration of the culture surface. The isolates were identified as Fusarium solani (2). Pathogenicity tests were conducted using six isolates, with inoculum produced on CLA. For each isolate, 250 ml of a spore suspension (1 × 106 conidia/ml) were poured onto the roots of 10-cm potted tarragon plants. Ten plants were inoculated for each of the six isolates. A control set of tarragon was treated with 250 ml of water. All plants were maintained in a greenhouse set at 24 to 25°C. After 8 weeks, plants inoculated with the spore suspensions began to show wilting and browning of leaves. Crown epidermis and cortex and root cortex tissues were brown; Fusarium solani was reisolated from the crowns and roots. The experiment was repeated and the results were the same. To my knowledge, this is the first report of F. solani causing a crown and root rot disease of tarragon. The disease caused significant damage with approximately 50% of the commercial field affected. The other Fusarium species previously reported on tarragon is an uncharacterized F. oxysporum isolated from roots of plants grown in California (1).

References: (1) D. F. Farr and A. Y. Rossman. Fungal Databases. Systematic Mycology and Microbiology Laboratory, ARS, USDA. Retrieved from http://nt.ars-grin.gov/fungaldatabases/ , March 8, 2011, (2) P. E. Nelson et al. Fusarium Species: An Illustrated Manual for Identification. Pennsylvania State University Press, University Park, PA, 1983.
Nurses attitudes towards the importance of families in psychiatric care following an educational and training intervention program
Authors: SVEINBJARNARDOTTIR E. K. , SVAVARSDOTTIR E. K. , SAVEMAN B.‐I.
Published: May 2011

Accessible summary

The attitude that psychiatric nurses have towards the importance of involving families in their care is fundamental to the quality of the intervention family members are offered. Research evidence supports the view that psychiatric nurses' positive attitudes towards families, in psychiatric care, encourage them to engage more frequently in therapeutic conversations with families.

The main focus of the family nursing education and intervention program (ETI‐PROGRAM) was to educate psychiatric nurses in family systems nursing. One of the beliefs in family nursing is that illness is a family affair and therefore it is important to involve families in the care of the patients to be able to soften the suffering of the psychiatric patients and their family members.

The main results of this study emphasize that after the psychiatric nurses had received the education and training program (ETI‐PROGRAM) on family system nursing, they viewed families as less burdensome in their psychiatric care.

This study measures the attitudes of the psychiatric nurses, after having received an education and training intervention program (ETI‐PROGRAM) in family systems nursing, towards the importance of the families in their care. Nurses' knowledge of the impact that family nursing intervention can have on family members may increase positive attitudes towards families. However, little is known about the impact that education and training intervention can have on nurses' attitudes, towards families in clinical practice. Quasi‐experimental design was used to assess the change in nurses' attitudes towards families in psychiatric care after the intervention, which included a one‐day seminar on the Calgary family nursing conceptual frameworks and skills training with clinical vignettes of families from psychiatry. The Families Importance in Nursing Care – Nurses' Attitude questionnaire was used to evaluate nurses' attitudes. A total of 81 nurses (65%) working in psychiatric care responded to the questionnaire. Nurses with more than 15 years of work experience were significantly more supportive of families in their care compared with less experienced nurses. Out of the 81 nurses, 52 (64%) answered the questionnaire again 14 months later. Furthermore, psychiatric nurses saw families significantly less burdensome after having participated in the ETI‐PROGRAM.
Commentary: the importance of education and vaccination in reducing the risk of hepatitis infection among nursing students
Authors: Cutter Jayne
Published: May 2011

CUTTER J. (2011) Commentary: the importance of education and vaccination in reducing the risk of hepatitis infection among nursing students. International Nursing Review58, 186–187

Background:  Healthcare workers are at risk of contracting blood‐borne viral infection during contact with blood and body fluids. Nursing students may be at particular risk because of their inexperience. Adoption of suitable precautions, hepatitis B vaccination and appropriate post‐exposure prophylaxis will significantly reduce the risk of infection.

Aim:  This commentary puts into context the findings of a study by Yamazhan et al. who explored nursing students' knowledge on hepatitis together with their immunization status.

Evaluation:  Knowledge of hepatitis, its mode of transmission and the risks of infection following adverse exposure to blood and body fluids are essential to ensure safe practice. This paper identifies that nursing students' knowledge of hepatitis is moderate only and varies between universities. However, the uptake of hepatitis B vaccination among the sample was high, suggesting a high commitment to reducing the risk of this infection by the universities and clinical placements.

Implications:  This paper highlights the need for a standardized education package to be developed and delivered by all universities in Turkey to ensure that nursing students have a sound knowledge of hepatitis and other blood‐borne infections. Vaccination programmes must continue to ensure that nursing students are protected from hepatitis B.
Adopting external currencies for trade growth in the Pacific
Authors: Freitag Stephan
Published: May 2011

This article reviews the currency and trade experiences of the six Pacific states that issue their own currencies: Fiji, Papua New Guinea (PNG), Samoa, Solomon Islands, Tonga, and Vanuatu. At independence, these states were advised to adopt their own currencies by the colonial powers, the International Monetary Fund, and other international organisations. The former imperial countries dominated Pacific trade, but empirical data indicate that a large and increasing proportion of trade, now with emerging Asia, denominates its trade in US dollars. This article shows that the six Pacific states manage their currencies in relation to the US dollar. Optimal currency area theory suggests that independent Pacific states would gain substantially by adopting the US dollar in the place of their own currencies. Gravity‐model estimations for all Pacific islands were used to test this hypothesis. The results suggest that replacing their own currencies with an external currency, such as the US dollar, would substantially stimulate the independent Pacific states' trade.
Finance and long‐term development issues in Southeast Asia
Authors: Huff Gregg
Published: May 2011

This article analyses Southeast Asian finance over more than a century in light of three issues: the realisation of finance‐leading development; indigenous entrepreneurship; and effective credit provision in rural areas. Colonial currency board systems and non‐interventionist government characterised finance in pre‐World War II Southeast Asia. There was decisive change after independence to a variety of state‐directed, or indeed socialist, attempts to overcome unfavourable pre‐war development legacies. Despite these departures, the article finds that throughout Southeast Asian history, finance rarely, if ever, led development. Today, indigenous entrepreneurship, explored for Malaysia, is generally either bolstered by political patrons or even entirely substituted for by state finance. More positively, market‐aware state initiatives in microfinance may offer a realistic institutional alternative to rural Southeast Asia's historic reliance on informal finance.
The next paradigm shift in China and India?
Authors: Chibba Michael
Published: May 2011

China and India were relatively unscathed by the global financial and economic crisis: after a brief downturn, stellar economic growth is back on track. New global and regional economic and political orders are also emerging in the post‐crisis period with both nations playing a prominent role. There is heightened attention being given to the nature of their development paradigm and related matters such as governance. This paper begins with a brief introduction to the subject. Second, China and India's paradigms for development progress are outlined. Third, the key current and emerging risks and challenges facing these nations are discussed. Fourth, their respective fault lines are exposed. Fifth, some final thoughts are offered on the possible shape of the next development paradigm shift. I conclude by suggesting that the next paradigm shift in China and India will likely successfully tackle some of the unresolved developmental problems that these nations face.
Regional trade liberalisation: a theoretical review of dynamic time‐path and stability issues
Authors: Wei Zhang
Published: May 2011

In recent years, the use of regional trade liberalisation arrangements (RTAs) has proliferated, while multilateral negotiations under the WTO have proceeded slowly, resulting in a debate over the roles of regional and multilateral liberalisation. This paper reviews the key theoretical contributions in the debate over RTAs, especially the recently developed themes addressing dynamic time‐path and stability issues. However, due to the variety of motivations for RTA member countries to expand trading blocs and for non‐members to seek entry, research has found few general conditions under which the formation of RTAs can become the ‘stepping stone’ or ‘stumbling block’ towards global free trade.
A review of corporate governance in China
Authors: Yang Jingjing , Chi Jing , Young Martin
Published: May 2011

The paper reviews the literature on internal and external corporate governance mechanisms in China. Chinese regulatory bodies have made considerable efforts to improve the corporate governance of listed firms. However, research has shown that most of the governance instruments that are effective in developed nations are less effective in China. We attribute the ineffectiveness to the large stake of the state in listed firms, strong political connections between listed firms and the government, and the lack of a truly independent judicial system. Some suggestions for making corporate governance more effective in China are provided.
Chinese macroeconomic management through the crisis and beyond
Authors: McKissack Adam , Xu Jessica Y.
Published: May 2011

As in all the other major economies, China's macroeconomic policy framework was put to the test during the global financial crisis. China applied one of the world's largest stimulus packages. The package provided a very rapid boost to activity in the Chinese economy, with empirical evidence suggesting the package added around 2–3 per cent to the level of GDP in both 2009 and 2010. The stimulus package was clearly a success for China, but there are challenges in unwinding the effects of the stimulus and addressing structural imbalances. Pressures to rebalance Chinese growth and integrate China further into global capital markets will necessitate changes in China's macroeconomic policy framework.
GRIEF: A NARRATIVE ACCOUNT
Authors: Goldie Peter
Published: May 2011

Grief is not a kind of feeling, or a kind of judgement, or a kind of perception, or any kind of mental state or event the identity of which can be adequately captured at a moment in time. Instead, grief is a kind of process; more specifically, it is a complex pattern of activity and passivity, inner and outer, which unfolds over time, and the unfolding pattern over time is explanatorily prior to what is the case at any particular time. The pattern of a particular grieving is best understood and explained through a narrative account, and not merely through a causal account, for narrative accounts in such cases have powerful explanatory, revelatory, and expressive powers which causal accounts lack. Although I will not argue for it here, I believe that this view of grief can be generalised to other kinds of emotion. If this is so, then many philosophical accounts of emotion are at fault in identifying emotion with a kind of mental state or event.
ENFRANCHISING INCOMPETENTS: SURETYSHIP AND THE JOINT AUTHORSHIP OF LAWS
Authors: Goodin Robert E. , Lau Joanne C.
Published: May 2011

Proposals to lower the age of voting, to 15 for example, are regularly met with worries that people that age are not sufficiently ‘competent’. Notice however that we allow people that age to sign binding legal contracts, provided that those contracts are co‐signed by their parents. Notice, further, that in a democracy voters are collectively ‘joint authors’ of the laws that they enact. Enfranchising some less competent voters is no worry, the Condorcet Jury Theorem assures us, so long as the electorate's competence averaging across all voters remains better‐than‐random.
ABNORMALITY AND GETTIER SITUATIONS: AN EXPLANATORY PROPOSAL
Authors: Hetherington Stephen
Published: May 2011

Analytic epistemologists reach regularly for favoured ‘intuitions’. And the anti‐luck intuition (as Duncan Pritchard calls it) is possibly one of the best‐entrenched epistemological intuitions at present, seemingly guiding standard reactions to Gettier situations. But why is that intuition true (if it is)? This paper argues that the anti‐luck intuition (like the ability intuition) rests upon something even more deeply explanatory – the normality intuition. And to recognise this is to understand better what most epistemologists want from a concept of knowledge. (It also helps to explain recent epistemological reactions to lottery cases.)1
DARWIN AND THE HINDU TRADITION: “DOES WHAT GOES AROUND COME AROUND?”
Authors: Gosling David L.
Published: May 2011

Abstract.  The introduction of English as the medium of instruction for higher education in India in 1835 created a ferment in society and in the religious beliefs of educated Indians—Hindus, Muslims, and, later, Christians. There was a Hindu renaissance characterized by the emergence of reform movements led by charismatic figures who fastened upon aspects of Western thought, especially science, now available in English. The publication of Darwin's On the Origin of Species in 1859 was readily assimilated by educated Hindus, and several reformers, notably Vivekananda and Aurobindo, incorporated evolution into their philosophies. Hindu scientists such as Jagadish Chandra Bose were also influenced by Darwinian evolution, as were a number of modern Hindu thinkers. The results of an investigation into the religious beliefs of young Indian scientists at four centers were also summarized. The view that “what goes around comes around” appears increasingly to be open to doubt. Many educated Indians, not only Hindus, are raising more probing questions that call for deeper dialogues between science and religion, especially about what each believes it means to be truly human.
THE AMBIGUITY OF INTERDISCIPLINARITY
Authors: Hollingsworth Andrea
Published: May 2011

Abstract.  What kind of consciousness is best prepared to undertake effective interdisciplinary explorations in religion and science in our twenty‐first century context? This paper draws on the thought of theologian David Tracy and psychologist and philosopher of religion James W. Jones to suggest that negation and ecstasy are mutually conditioning factors that go into the shaping of just such a consciousness. Healthy, constructive modes of relating to the disciplinary other imply the emergence of a transformed way of knowing and being wherein the scholar countenances the loss of controlling and autonomous ways of relating (negation), and precisely in that loss, enters into shared spaces of mutually illuminative and transformative understanding (ecstasy).
ZIONISM AND THE EROS OF SCIENCE AND TECHNOLOGY
Authors: Efron Noah
Published: May 2011

Abstract.  From the earliest nineteenth‐century manifestos through the big, technology‐rich development projects of Israel's recent history, science and technology have loomed large in Zionist ideologies. There were several reasons for this. From the start, science and technology fit snuggly with many aims, ideals, and ideologies of Zionism. Science and technology offered means to establish Jewish title to the land. They made plain that Jewish settlement of Palestine was a Western project imbued with Western ideals. Science and technology (and scientific industry) made plain the progressive nature of the Zionist undertaking. They informed arguments that Jewish settlement would even benefit those locals displaced by the Zionists, bringing them culture of universal value, and providing a bridge between these “backward” societies and the “advanced” West. More importantly, science and technology helped meet growing practical needs of Jews building a national infrastructure in Palestine. The imprint of these considerations has remained large and influential in Israeli society until today.
MEASURING THE TRADE SECTOR IN THE NATIONAL ACCOUNTS OF INDIA
Authors: KOLLI RAMESH
Published: May 2011

Trade accounts for a significant number of enterprises and contributes a large part to total employment and gross domestic product (GDP) in most developing countries. In India, trade now accounts for 38 percent of all enterprises and contributes about 14 percent to GDP. In real terms, gross value added in trade has been growing at around 8 percent per annum since 1999–2000, indicating that the trade industry is one of the key drivers of GDP growth in India. Since the retail trade industry in India is predominantly run by unincorporated enterprises, measuring the output of this industry and its contribution to the GDP is difficult. The problem is compounded by the fact that at present the periodic enterprises sample surveys carried out in India on the “unorganized” sector do not cover trade. This paper explains how India has approached the problem of measuring the gross value added of the retail trade sector by an indirect method involving what is here described as a “labor input method” and a benchmark‐indicator approach using a special trade index. The paper also briefly reviews country practices in measuring the output of retail trade and presents the advantages and disadvantages of India's approach, particularly in the context of achieving GDP exhaustiveness.
Evaluation of modified Wright‐staining of dried urinary sediment as a method for accurate detection of bacteriuria in cats
Authors: Swenson Cheryl L. , Boisvert Agatha M. , Gibbons‐Burgener Suzanne N. , Kruger John M.
Published: May 2011

Background:Urinary sediment examination and quantitative urinary culture results are frequently discordant.

Objectives:The aims of this study were to compare accuracy of light microscopic examination of wet‐mounted unstained (wet‐unstained) and air‐dried modified Wright‐stained (dry‐stained) sedimented preparations of urine with results of quantitative aerobic bacterial culture for detection and characterization of bacteriuria in cats. In addition, the presence of pyuria detected by urinalysis and potential risk factors were assessed.

Methods:A blinded prospective study was conducted on 472 urinary samples collected from 410 cats by cystocentesis. The age and sex of each cat were recorded. Complete urinalyses were performed and included quantification of WBCs. Quantity and morphology of bacteria in each specimen were determined by light microscopic examination of wet‐unstained (performed by certified medical technologists) and dry‐stained (performed by a veterinary clinical pathologist) sedimented preparations of urine and compared with results of quantitative bacterial cultures.

Results:Of 472 urinary specimens, 29 were positive for bacteriuria by culture and considered true positives and 443 were considered true negatives. Compared with these results, examination of wet‐unstained and dry‐stained urines had sensitivities of 75.9% and 82.8%, specificities of 56.7% and 98.7%, and test efficiencies of 57.8% and 97.7%, respectively. Positive likelihood ratios were 1.8 and 63.7 and negative likelihood ratios were 0.42 and 0.17 for wet‐unstained and dry‐stained examinations, respectively. Compared with 29 culture‐positive samples, the wet‐unstained method had morphologic concordance and misclassification rates of 37.9% and 62.1%, respectively, whereas the dry‐stained method had morphologic concordance and misclassification rates of 65.5% and 34.5%, respectively. Only 34% of samples with bacteriuria had pyuria. Frequency of bacteriuria was not significantly different based on age and sex of the cats, but there was a tendency for increased frequency in female cats and in cats >10 years old.

Conclusions:Staining dried urinary sediment with a modified Wright‐stain significantly improved sensitivity, specificity, and test efficiency of microscopic detection and classification of bacteriuria compared with the wet‐unstained method. Pyuria should not be a criterion for determining the presence or absence of bacteriuria.
Teaching and Learning Democracy: Collaborative Development of Courses on Citizenship
Authors: Kahane David , von Lieres Bettina
Published: May 2011

How can educators work together to enhance work on democracy and citizenship? This paper analyses the trajectory and dynamics of the Teaching and Learning (T&L) group, an initiative that brought together educators from seven countries to address the challenges of developing and delivering courses on citizenship and democratising teaching and learning environments. Part of the Citizenship DRC, a wider research consortium that examined the dynamics of citizen participation in diverse contexts, the T&L group centred on peer‐to‐peer reflection, learning and support. Its innovative ways of working and success in developing a wide range of courses and trainings challenge expert‐driven models of pedagogical development. They also point to the importance of transnational collaborations in enhancing curricula, courses and teaching methods that effectively support both learning about democracy and citizenship, and democratic teaching capacities.
Ratcheting Assessment of a Fixed Tube Sheet Heat Exchanger Subject to In Phase Pressure and Temperature Cycles
Authors: Behseta Khosrow , Mackenzie Donald , Hamilton Robert
Published: May 2011

An investigation of the cyclic elastic-plastic response of an Olefin plant heat exchanger subject to cyclic thermal and pressure loading is presented. Design by analysis procedures for assessment of shakedown and ratcheting are considered, based on elastic and inelastic analysis methods. The heat exchanger tube sheet thickness is nonstandard as it is considerably less than that required by conventional design by formula rules. Ratcheting assessment performed using elastic stress analysis and stress linearization indicates that shakedown occurs under the specified loading when the nonlinear component of the through thickness stress is categorized as peak stress. In practice, the presence of the peak stress will cause local reverse plasticity or plastic shakedown in the component. In nonlinear analysis with an elastic–perfectly plastic material model the vessel exhibits incremental plastic strain accumulation for 10 full load cycles, with no indication that the configuration will adapt to steady state elastic or plastic action, i.e., elastic shakedown or plastic shakedown. However, the strain increments are small and would not lead to the development of a global plastic collapse or gross plastic deformation during the specified life of the vessel. Cyclic analysis based on a strain hardening material model indicates that the vessel will adapt to plastic shakedown after 6 load cycles. This indicates that the stress categorization and linearization assumptions made in the elastic analysis are valid for this configuration.
NEW EXPLICIT EXACT SOLUTIONS OF THE mKdV-sinh-GORDON EQUATION
Authors: SU KALIN , XIE YUANXI
Published: May 2011

An extended variable separated ODE method is presented for exploring the explicit exact solutions of the mKdV-sinh-Gordon equation by introducing a more general auxiliary ODE, and by employing its rich types of solutions, we can not only recover the previously known exact solutions, but also derive some new formal solutions for the mKdV-sinh-Gordon equation.
STRUCTURAL PROPERTIES OF NANOCRYSTALLINE Ni–Al SPINEL FERRITES
Authors: RAGHAVENDER A. T.
Published: May 2011

Ultra fine NiAl x Fe 2-x O 4(0 ≤ x ≤ 1) nanopowders were synthesized by sol-gel method and their structural properties were investigated using X-ray diffractometer (XRD) and fourier transform infrared (FTIR) spectrometer. The particle size D, lattice constant a, density dx decreased with increasing non-magnetic Al content x. The combustion reaction mechanisms were explained with the help of FTIR analysis.
SYNTHESIS AND OPTICAL PROPERTIES OF THE MULTILAYER STARLIKE ZnO NANOSTRUCTURES
Authors: WANG PYINGHUA , WANG XINGCHANG , WANG AIHUA , ZHANG BINGLIN , TIAN YONGTIAO , YAO NING
Published: May 2011

A novel multilayer starlike ZnO nanostructure has been successfully synthesized on a Si (111) substrate at 600°C by chemical vapor deposition using Zn and zinc acetate dihydrate as the source materials. The morphology, structure, and optical properties are investigated by field emission scanning electron microscopy, X-ray diffraction, Raman and photoluminescence (PL) spectrum, respectively. The results show that the multilayer starlike ZnO nanostructures have hexagonal wurtzite structure. The room-temperature PL spectrum shows the dominant green band peak and the weak UV peak. The possible growth mechanism of the multilayer starlike ZnO nanostructures is also discussed.
STOCHASTIC CAR-FOLLOWING MODEL FOR EXPLAINING NONLINEAR TRAFFIC PHENOMENA
Authors: MENG JIANPING , SONG TAO , DONG LIYUN , DAI SHIQIANG
Published: May 2011

There is a common time parameter for representing the sensitivity or the lag (response) time of drivers in many car-following models. In the viewpoint of traffic psychology, this parameter could be considered as the perception–response time (PRT). Generally, this parameter is set to be a constant in previous models. However, PRT is actually not a constant but a random variable described by the lognormal distribution. Thus the probability can be naturally introduced into car-following models by recovering the probability of PRT. For demonstrating this idea, a specific stochastic model is constructed based on the optimal velocity model. By conducting simulations under periodic boundary conditions, it is found that some important traffic phenomena, such as the hysteresis and phantom traffic jams phenomena, can be reproduced more realistically. Especially, an interesting experimental feature of traffic jams, i.e., two moving jams propagating in parallel with constant speed stably and sustainably, is successfully captured by the present model.
MAGNETODYNAMICS OF A SUSPENSION OF HIGH-COERCIVITY FERROPARTICLES IN A SUBCRITICAL AC FIELD
Authors: KASHEVSKY B. E. , KASHEVSKY S. B. , PROKHOROV I. V.
Published: May 2011

Consideration is given to magnetodynamics of high-coercivity submicron particles suspended in a liquid and exposed to an AC magnetic field with subcritical (smaller than article coercivity) amplitude. In experiments, use is made of chromium dioxide particles, different-viscosity liquids, and magnetic fields with frequency of 430 Hz and amplitude of up to 230 Oe. The registered dynamic magnetization curves are analyzed within the framework of models of orientational dynamics of single-domain particles and magnetic clusters. The possibility of applying high-coercivity particles for magnetodynamic probing viscosity of liquids is discussed.
A MODEL FOR CRACK PROPAGATION BASED ON VISCOUS APPROXIMATION
Authors: LAZZARONI GIULIANO , TOADER RODICA
Published: May 2011

In the setting of antiplane linearized elasticity, we show the existence of quasistatic evolutions of cracks in brittle materials by using a vanishing viscosity approach, thus taking into account local minimization. The main feature of our model is that the path followed by the crack need not be prescribed a priori: indeed, it is found as the limit (in the sense of Hausdorff convergence) of curves obtained by an incremental procedure. The result is based on a continuity property for the energy release rate in a suitable class of admissible cracks.
DETECTING AN OBSTACLE IMMERSED IN A FLUID BY SHAPE OPTIMIZATION METHODS
Authors: BADRA MEHDI , CAUBET FABIEN , DAMBRINE MARC
Published: May 2011

The paper presents a theoretical study of an identification problem by shape optimization methods. The question is to detect an object immersed in a fluid. Here, the problem is modeled by the Stokes equations and treated as a nonlinear least-squares problem. We consider both the Dirichlet and Neumann boundary conditions. Firstly, we prove an identifiability result. Secondly, we prove the existence of the first-order shape derivatives of the state, we characterize them and deduce the gradient of the least-squares functional. Moreover, we study the stability of this setting. We prove the existence of the second-order shape derivatives and we give the expression of the shape Hessian. Finally, the compactness of the Riesz operator corresponding to this shape Hessian is shown and the ill-posedness of the identification problem follows. This explains the need of regularization to numerically solve this problem.