From data to analysis: linking NWChem and Avogadro with the syntax and semantics of Chemical Markup Language

Background: Multidisciplinary integrated research requires the ability to couple the diverse sets of data obtained from a range of complex experiments and computer simulations. Integrating data requires semantically rich information. In this paper an end-to-end use of semantically rich data in computational chemistry is demonstrated utilizing the Chemical Markup Language (CML) framework. Semantically rich data is generated by the NWChem computational chemistry software with the FoX library and utilized by the Avogadro molecular editor for analysis and visualization. Results: The NWChem computational chemistry software has been modified and coupled to the FoX library to write CML compliant XML data files. The FoX library was expanded to represent the lexical input files and molecular orbitals used by the computational chemistry software. Draft dictionary entries and a format for molecular orbitals within CML CompChem were developed. The Avogadro application was extended to read in CML data, and display molecular geometry and electronic structure in the GUI allowing for an end-to-end solution where Avogadro can create input structures, generate input files, NWChem can run the calculation and Avogadro can then read in and analyse the CML output produced. The developments outlined in this paper will be made available in future releases of NWChem, FoX, and Avogadro. Conclusions: The production of CML compliant XML files for computational chemistry software such as NWChem can be accomplished relatively easily using the FoX library. The CML data can be read in by a newly developed reader in Avogadro and analysed or visualized in various ways. A community-based effort is needed to further develop the CML CompChem convention and dictionary. This will enable the long-term goal of allowing a researcher to run simple "Google-style" searches of chemistry and physics and have the results of computational calculations returned in a comprehensible form alongside articles from the published literature

Exploring Multiple‐discreteness in Freight Transport. A Multiple Discrete Extreme Value Model Application for Grain Consolidators in Argentina

There are some examples where freight choices may be of a multiple discrete nature, especially the ones at more tactical levels of planning. Nevertheless, this has not been investigated in the literature, although several discrete-continuous models for mode/vehicle type and shipment size choice have been developed in freight transport. In this work, we propose that the decision of port and mode of the grain consolidators in Argentina is of a discrete-continuous nature, where they can choose more than one alternative and how much of their production to send by each mode. The Multiple Discrete Extreme Value Model (MDCEV) framework was applied to a stated preference data set with a response variable that allowed this multiple-discreteness. To our knowledge, this is the only application of the MDCEV in regional freight context. Free alongside ship price, freight transport cost, lead-time and travel time were included in the utility function and observed and random heterogeneity was captured by the interaction with the consolidator’s characteristics and random coefficients. In addition, different discrete choice models were used to compare the forecasting performance, willingness to pay measures and structure of the utility function against

Attitudes toward integrative paediatrics: a national survey among youth health are physicians in the Netherlands

<p>Abstract</p> <p>Background</p> <p>Integrative Medicine (IM) is an emerging field in paediatrics, especially in the USA. The purpose of the present study was to assess the attitudes and beliefs of Youth Health Care (YHC) physicians in the Netherlands toward IM in paediatrics.</p> <p>Methods</p> <p>In October 2010, a link to an anonymous, self-reporting, 30-item web-based questionnaire was mailed to all members of the Dutch Organisation of YHC physicians. The questionnaire included questions on familiarity with IM, attitudes towards Integrative Paediatrics (IP), use and knowledge of Complementary and Alternative Medicine (CAM), demographic and practice characteristics.</p> <p>Results</p> <p>A total of 276 YHC physicians (response rate of 27%) responded to the survey. Of the respondents, 52% was familiar with IM and 56% had used some kind of CAM therapy during the past 2 years, of which self-medicated herbal and/or homeopathic remedies (61%) and supplements (50%) were most frequently mentioned. Most of the YHC physicians (62%) seldom asked parents of clients about CAM use. One third of the YHC physicians recommended CAM to their clients. In general, about 50% or more of the respondents had little knowledge of CAM therapies. Predictors for a positive attitude towards IP were familiarity with IM, own CAM use, asking their clients about CAM use and practising one or more forms of CAM therapy. Logistic regression analysis showed that the following factors were associated with a higher recommendation to CAM therapies: own CAM use (odds ratio (OR) = 3.8; 95% confidence interval (CI) = 2.1-6.9, <it>p </it>= 0.001) and practising CAM (OR 4.4; 95% CI = 1.6-11.7, <it>p </it>= 0.003).</p> <p>Conclusions</p> <p>In general Dutch YHC physicians have a relative positive attitude towards IP; more than half of the respondents used one or more forms of CAM and one third recommended CAM therapies. However, the majority of YHC physicians did not ask their clients about CAM use and seemed to have a lack of knowledge regarding CAM.</p

6-thioguanine treatment in inflammatory bowel disease: A critical appraisal by a European 6-TG working party

Recently, the suggestion to use 6-thioguanine (6-TG) as an alternative thiopurine in patients with inflammatory bowel disease (IBD) has been discarded due to reports about possible (hepato) toxicity. During meetings arranged in Vienna and Prague in 2004, European experts applying 6-TG further on in IBD patients presented data on safety and efficacy of 6-TG. After thorough evaluation of its risk-benefit ratio, the group consented that 6-TG may still be considered as a rescue drug in stringently defined indications in IBD, albeit restricted to a clinical research setting. As a potential indication for administering 6-TG, we delineated the requirement for maintenance therapy as well as intolerance and/or resistance to aminosalicylates, azathioprine, 6-mercaptopurine, methotrexate and infliximab. Furthermore, indications are preferred in which surgery is thought to be inappropriate. The standard 6-TG dosage should not exceed 25 mg daily. Routine laboratory controls are mandatory in short intervals. Liver biopsies should be performed after 6-12 months, three years and then three-yearly accompanied by gastroduodenoscopy, to monitor for potential hepatotoxicity, including nodular regenerative hyperplasia (NRH) and veno-occlusive disease (VOD). Treatment with 6-TG must be discontinued in case of overt or histologically proven hepatotoxicity. Copyright (c) 2006 S. Karger AG, Basel

Commentary on the WHO classification of tumors of lymphoid tissues (2008): aggressive B-cell lymphomas

In the novel WHO classification 2008, the classification of aggressive B-cell lymphoma has been revised for several categories with the aim to define “clean” entities. Within large B-cell lymphoma, a few distinct clinico-pathological entities have been recognized with more clinically defined entities than pathologically defined ones. The majority of known morphological variations were not considered to merit more than classification as a variant of DLBCL, not otherwise specified. Specifically, a biological subgrouping of DLBCL on the basis of molecular (activated B-cell versus germinal center B-cell) or immunophenotypic (CD5+) features was felt to be too immature to include at this stage. The role of EBV in aggressive B-cell lymphoma has been explored in more depth with the recognition of several novel and re-defined clinico-pathological entities. Also, in these diseases, clinical definitions play a very dominant role in the WHO classification 2008