Polarization and Extent of Maser Emission from Late-Type Stars: Support for a Plasma Turbulence Model of Maser Production

The integrated spectrum of OH emission from late-type stars is often circularly polarized, by as much as 50% in some cases. While the spectra are partially polarized, the individual maser components revealed by VLBI are much more so. Using VLBI observations of late-type stars from the literature, we show that the difference in circular polarization between main lines correlates with a difference in angular extent for a given object. This is a natural result if turbulent magnetic fields are causing the masers to be polarized via the Cook mechanism, and might serve as a good diagnostic for determining which objects should be investigated in the search for magnetic fields around evolved stars.Comment: 5 pages, 2 figs ApJL, accepte

Sketching space

In this paper, we present a sketch modelling system which we call Stilton. The program resembles a desktop VRML browser, allowing a user to navigate a three-dimensional model in a perspective projection, or panoramic photographs, which the program maps onto the scene as a `floor' and `walls'. We place an imaginary two-dimensional drawing plane in front of the user, and any geometric information that user sketches onto this plane may be reconstructed to form solid objects through an optimization process. We show how the system can be used to reconstruct geometry from panoramic images, or to add new objects to an existing model. While panoramic imaging can greatly assist with some aspects of site familiarization and qualitative assessment of a site, without the addition of some foreground geometry they offer only limited utility in a design context. Therefore, we suggest that the system may be of use in `just-in-time' CAD recovery of complex environments, such as shop floors, or construction sites, by recovering objects through sketched overlays, where other methods such as automatic line-retrieval may be impossible. The result of using the system in this manner is the `sketching of space' - sketching out a volume around the user - and once the geometry has been recovered, the designer is free to quickly sketch design ideas into the newly constructed context, or analyze the space around them. Although end-user trials have not, as yet, been undertaken we believe that this implementation may afford a user-interface that is both accessible and robust, and that the rapid growth of pen-computing devices will further stimulate activity in this area

Continued analysis of OSO-8 and Kitt Peak data on solar faculae

An improved semi-empirical model of phosphoric faculae is presented in tabular form. The limitations of the model as well as other possible improvements are discussed

A review of journal policies for sharing research data

*Background:* Sharing data is a tenet of science, yet commonplace in only a few subdisciplines. Recognizing that a data sharing culture is unlikely to be achieved without policy guidance, some funders and journals have begun to request and require that investigators share their primary datasets with other researchers. The purpose of this study is to understand the current state of data sharing policies within journals, the features of journals which are associated with the strength of their data sharing policies, and whether the strength of data sharing policies impact the observed prevalence of data sharing. 

*Methods:* We investigated these relationships with respect to gene expression microarray data in the journals that most often publish studies about this type of data. We measured data sharing prevalence as the proportion of papers with submission links from NCBI's Gene Expression Omnibus (GEO) database. We conducted univariate and linear multivariate regressions to understand the relationship between the strength of data sharing policy and journal impact factor, journal subdiscipline, journal publisher (academic societies vs. commercial), and publishing model (open vs. closed access).

*Results:* Of the 70 journal policies, 18 (26%) made no mention of sharing publication-related data within their Instruction to Author statements. Of the 42 (60%) policies with a data sharing policy applicable to microarrays, we classified 18 (26% of 70) as moderately strong and 24 (34% of 70) as strong.
Existence of a data sharing policy was associated with the type of journal publisher: half of all commercial publishers had a policy compared to 82% of journals published by academic society. All four of the open-access journals had a data sharing policy. Policy strength was associated with impact factor: the journals with no data sharing policy, a weak policy, and a strong policy had respective median impact factors of 3.6, 4.5, and 6.0. Policy strength was positively associated with measured data sharing submission into the GEO database: the journals with no data sharing policy, a weak policy, and a strong policy had median data sharing prevalence of 11%, 19%, and 29% respectively.

*Conclusion:* This review and analysis begins to quantify the relationship between journal policies and data sharing outcomes and thereby contributes to assessing the incentives and initiatives designed to facilitate widespread, responsible, effective data sharing. 

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Prevalence and Patterns of Microarray Data Sharing

Sharing research data is a cornerstone of science. Although many tools and policies exist to encourage data sharing, the prevalence with which datasets are shared is not well understood. We report our preliminary results on patterns of sharing microarray data in public databases.

The most comprehensive method for measuring occurrences of public data sharing is manual curation of research reports, since data sharing plans are usually communicated in free text within the body of an article. Our early findings from manual curation of 100 papers suggest that 30% of investigators publicly share their full microarray datasets. Of these, 70% of the datasets are deposited at NCBI's Gene Expression Omnibus (GEO) database, 20% at EBI's ArrayExpress, and 10% in smaller databases or lab or publisher websites.

Next, we supplemented this manual process with a rough automated estimate of data sharing prevalence. Using PubMed, we identified research articles with MeSH terms for both "Gene Expression Profiling" and "Oligonucleotide Array Sequence Analysis" and published in 2006. We then searched GEO and ArrayExpress for links to these PubMed IDs to determine which of the articles had been credited as an originating data source.

Of the 2503 articles, 440 (18%) articles had links from either GEO or ArrayExpress. Of these 440 articles, 70% had links from GEO and 30% from ArrayExpress, with an overlapping 12% from both GEO and ArrayExpress.

Interestingly, studies with free full text at PubMed were twice (Odds Ratio=2.1; 95% confidence interval: [1.7 to 2.5]) as likely to be linked as a data source within GEO or ArrayExpress than those without free full text. Studies with human data were less likely to have a link (OR=0.8 [0.6 to 0.9]) than studies with only non-human data. The proportion of articles with a link within these two databases has increased over time: the odds of a data-source link for studies was 2.5 [2.0 to 3.1] times greater for studies published in 2006 than 2002.

As might be expected, studies with the fewest funding sources had the fewest data-sharing links: only 28 (6%) of the 433 studies with no funding source were listed within GEO or ArrayExpress. In contrast, studies funded by the NIH, the US government, or a non-US government source had data-sharing links in 282 of 1556 cases (18%), while studies funded by two or more of these mechanisms were listed in the databases in 130 out of 514 cases (25%).

In summary, our initial manual approach for identifying studies which shared their data was comprehensive but time-consuming; natural language processing techniques could be helpful. Our subsequent automated approach yielded conservative estimates for total data sharing prevalence, nonetheless revealing several promising hypotheses for data sharing behavior

We hope these preliminary results will inspire additional investigations into data sharing behavior, and in turn the development of effective policies and tools to facilitate this important aspect of scientific research

Using open access literature to guide full-text query formulation

*Background* 
Much scientific knowledge is contained in the details of the full-text biomedical literature. Most research in automated retrieval presupposes that the target literature can be downloaded and preprocessed prior to query. Unfortunately, this is not a practical or maintainable option for most users due to licensing restrictions, website terms of use, and sheer volume. Scientific article full-text is increasingly queriable through portals such as PubMed Central, Highwire Press, Scirus, and Google Scholar. However, because these portals only support very basic Boolean queries and full text is so expressive, formulating an effective query is a difficult task for users. We propose improving the formulation of full-text queries by using the open access literature as a proxy for the literature to be searched. We evaluated the feasibility of this approach by building a high-precision query for identifying studies that perform gene expression microarray experiments.
 
*Methodology and Results* 
We built decision rules from unigram and bigram features of the open access literature. Minor syntax modifications were needed to translate the decision rules into the query languages of PubMed Central, Highwire Press, and Google Scholar. We mapped all retrieval results to PubMed identifiers and considered our query results as the union of retrieved articles across all portals. Compared to our reference standard, the derived full-text query found 56% (95% confidence interval, 52% to 61%) of intended studies, and 90% (86% to 93%) of studies identified by the full-text search met the reference standard criteria. Due to this relatively high precision, the derived query was better suited to the intended application than alternative baseline MeSH queries.
 
*Significance* 
Using open access literature to develop queries for full-text portals is an open, flexible, and effective method for retrieval of biomedical literature articles based on article full-text. We hope our approach will raise awareness of the constraints and opportunities in mainstream full-text information retrieval and provide a useful tool for today’s researchers.
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On the scaling behaviour of cross-tie domain wall structures in patterned NiFe elements

The cross-tie domain wall structure in micrometre and sub-micrometre wide patterned elements of NiFe, and a thickness range of 30 to 70nm, has been studied by Lorentz microscopy. Whilst the basic geometry of the cross-tie repeat units remains unchanged, their density increases when the cross-tie length is constrained to be smaller than the value associated with a continuous film. This occurs when element widths are sufficiently narrow or when the wall is forced to move close to an edge under the action of an applied field. To a very good approximation the cross-tie density scales with the inverse of the distance between the main wall and the element edge. The experiments show that in confined structures, the wall constantly modifies its form and that the need to generate, and subsequently annihilate, extra vortex/anti-vortex pairs constitutes an additional source of hysteresis.Comment: 4 pages, 5 figures, accepted for publication in Europhysics Letters (EPL