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Nematodes of the genus Auanema are interesting models for studying sex determination mechanisms because their populations consist of three sexual morphs (males, females, and hermaphrodites) and produce skewed sex ratios. Here, we introduce a new undescribed species of this genus, Auanema melissensis n. sp., together with its draft nuclear genome. This species is also trioecious and does not cross with the other described species A. rhodensis or A. freiburgensis. Similar to A. freiburgensis, A. melissensis’ maternal environment influences the hermaphrodite versus female sex determination of the offspring. The genome of A. melissensis is ~60 Mb, containing 11,040 protein-coding genes and 8.07% of repeat sequences. Using the estimated ancestral chromosomal gene content (Nigon elements), it was possible to identify putative X chromosome scaffolds.

Oil palm is regarded as one of the tree crops that utilize a high amount of soil nutrients for optimum growth and development. Farmers in the western region of Ghana have complained immensely of small fruit bunch of their oil palm, but in oil palm plantation, nutrient management is the key to higher fruit bunch of crops hence this study was carried out to evaluate the fertility status of selected oil palm plantations in the Mpohor district in the Western Region of Ghana. Two farming communities namely Odumase and Edum Banso were selected for soil sampling. Farmers in the Odumase community have been applying fertilizer and organic manure while farmers in Edum Banso hardly do. Soil samples from Odumase (A) and Edum Banso (B) showed mean pH values of 5.45 and 5.03, respectively. Odumase (A) recorded high nitrogen, phosphorus and Potassium content of 0.07%, 7.69 mg kg-1 and 0.4 cmol kg-1, respectively exceeding the critical nutrient (NPK) content for the oil palm tree. Soil samples from Edum Banso (B) recorded N, P and K contents below the critical nutrient (NPK) content for oil palm tree. The nutrient availability index indicated a low nutrient availability of TN, OM, P and Mg for soil samples from Edum Banso (B). Therefore proper nutrient management approaches such as the application of inorganic fertilizer should be adopted especially for nutrients that are deficient and low from Edum Banso (B).

A large proportion of rural households, particularly in the dry land areas, representative for more than 10% of the world's land surface and up to 80% in Morocco, depend for their livelihoods on livestock. They exploit livestock's capacity to live in very harsh environments using herd-mobility at multiple scale level. Understanding the multiple contributions of livestock to the household and national economy raises complex research issues and challenges linked with the multitude of goods and services derived from livestock, their interactions with other family activities, and the local and national context. The objective of our research was therefore to analyse the diversity and assess the resilience of livelihood strategies of farming households oriented to livestock using a set of data collected in the dry land areas (oases and mountainous zones) of Morocco and discuss the livelihood outcome indicators. To achieve this, we have realized a cross-sectional analysis of livelihoods and adaptive capacity, to select a set of pertinent indicators. These indicators have been developed using an adapted version of the Rural Household Multi-Indicator Survey (RHoMIS) toolkit for pastoral and agropastoral household systems. Our results highlight the critical importance of livelihood diversification (off-farm diversification, livestock diversification, and crop diversification) in building household resilience and the livelihood outcomes. While livelihood strategies undoubtedly contribute to livelihood outcomes, there is also a critical iterative process, i.e., livelihood outcomes also influence the livelihood strategies at the farming households. The present work proposes an aggregated indicator of livelihood outcomes allowing us to capture the heterogeneity of living conditions of agropastoral systems by considering the main drivers of this system, i.e., mobility, livestock species, and physiological stage composition of the herd. This approach could constitute a valuable contribution to help fill the knowledge gaps that do not allow policy makers in developing contextualized rural development policies and instruments in these very harsh environments.

Background: Comparisons of incidence and mortality rates are the metrics used most commonly to define cancer-related racial disparities. In the US, and particularly in South Carolina, these largely disfavor African Americans (AAs). Computed from readily available data sources, the mortality-to-incidence rate ratio (MIR) provides a population-based indicator of survival.Methods: South Carolina Central Cancer Registry incidence data and Vital Registry death data were used to construct MIRs. ArcGIS 9.2 mapping software was used to map cancer MIRs by sex and race for 8 Health Regions within South Carolina for all cancers combined and for breast, cervical, colorectal, lung, oral, and prostate cancers.Results: Racial differences in cancer MIRs were observed for both sexes for all cancers combined and for most individual sites. The largest racial differences were observed for female breast, prostate, and oral cancers, and AAs had MIRs nearly twice those of European Americans (EAs).Conclusions: Comparing and mapping race- and sex-specific cancer MIRs provides a powerful way to observe the scope of the cancer problem. By using these methods, in the current study, AAs had much higher cancer MIRs compared with EAs for most cancer sites in nearly all regions of South Carolina. Future work must be directed at explaining and addressing the underlying differences in cancer outcomes by region and race. MIR mapping allows for pinpointing areas where future research has the greatest likelihood of identifying the causes of large, persistent, cancer-related disparities. Other regions with access to high-quality data may find it useful to compare MIRs and conduct MIR mapping. [ABSTRACT FROM AUTHOR]

The purpose of this investigation was to examine social desirability and social approval as sources of error in three self-reported physical activity assessments using objective measures of physical activity as reference measures. In 1997, women (n = 81) living in Worcester, Massachusetts, completed doubly labeled water measurements and wore an activity monitor for 14 days. They also completed seven interviewer-administered 24-hour physical activity recalls (PARs) and two different self-administered 7-day PARs. Measures of the personality traits 'social desirability' and 'social approval' were regressed on 1) the difference between physical activity energy expenditure estimated from doubly labeled water and each physical activity assessment instrument and 2) the difference between monitor-derived physical activity duration and each instrument. Social desirability was associated with overreporting of activity, resulting in overestimation of physical activity energy expenditure by 0.65 kcal/kg/day on the second 7-day PAR (95% confidence interval: 0.06, 1.25) and overestimation of activity durations by 4.15-11.30 minutes/day (both 7-day PARs). Social approval was weakly associated with underestimation of physical activity on the 24-hour PAR (-0.15 kcal/kg/day, 95% confidence interval: -0.30, 0.005). Body size was not associated with reporting bias in this study. The authors conclude that social desirability and social approval may influence self-reported physical activity on some survey instruments. [ABSTRACT FROM AUTHOR]

Abstract Background Disease management programs, especially those based on the Chronic Care Model (CCM), are increasingly common in the Netherlands. While disease management programs have been well-researched quantitatively and economically, less qualitative research has been done. The overall aim of the study is to explore how disease management programs are implemented within primary care settings in the Netherlands; this paper focuses on the early development and implementation stages of five disease management programs in the primary care setting, based on interviews with project leadership teams. Methods Eleven semi-structured interviews were conducted at the five selected sites with sixteen professionals interviewed; all project directors and managers were interviewed. The interviews focused on each project’s chosen chronic illness (diabetes, eating disorders, COPD, multi-morbidity, CVRM) and project plan, barriers to development and implementation, the project leaders’ action and reactions, as well as their roles and responsibilities, and disease management strategies. Analysis was inductive and interpretive, based on the content of the interviews. After analysis, the results of this research on disease management programs and the Chronic Care Model are viewed from a traveling technology framework. Results This analysis uncovered four themes that can be mapped to disease management and the Chronic Care Model: (1) changing the health care system, (2) patient-centered care, (3) technological systems and barriers, and (4) integrating projects into the larger system. Project leaders discussed the paths, both direct and indirect, for transforming the health care system to one that addresses chronic illness. Patient-centered care was highlighted as needed and a paradigm shift for many. Challenges with technological systems were pervasive. Project leaders managed the expenses of a traveling technology, including the social, financial, and administration involved. Conclusions At the sites, project leaders served as travel guides, assisting and overseeing the programs as they traveled from the global plans to local actions. Project leaders, while hypothetically in control of the programs, in fact shared control of the traveling of the programs with patients, clinicians, and outside consultants. From this work, we can learn what roadblocks and expenses occur while a technology travels, from a project leader’s point of view.

Abstract The semantic architecture of CML consists of conventions, dictionaries and units. The conventions conform to a top-level specification and each convention can constrain compliant documents through machine-processing (validation). Dictionaries conform to a dictionary specification which also imposes machine validation on the dictionaries. Each dictionary can also be used to validate data in a CML document, and provide human-readable descriptions. An additional set of conventions and dictionaries are used to support scientific units. All conventions, dictionaries and dictionary elements are identifiable and addressable through unique URIs.

Abstract The Ami project was a six month Rapid Innovation project sponsored by JISC to explore the Virtual Research Environment space. The project brainstormed with chemists and decided to investigate ways to facilitate monitoring and collection of experimental data. A frequently encountered use-case was identified of how the chemist reaches the end of an experiment, but finds an unexpected result. The ability to replay events can significantly help make sense of how things progressed. The project therefore concentrated on collecting a variety of dimensions of ancillary data - data that would not normally be collected due to practicality constraints. There were three main areas of investigation: 1) Development of a monitoring tool using infrared and ultrasonic sensors; 2) Time-lapse motion video capture (for example, videoing 5 seconds in every 60); and 3) Activity-driven video monitoring of the fume cupboard environs. The Ami client application was developed to control these separate logging functions. The application builds up a timeline of the events in the experiment and around the fume cupboard. The videos and data logs can then be reviewed after the experiment in order to help the chemist determine the exact timings and conditions used. The project experimented with ways in which a Microsoft Kinect could be used in a laboratory setting. Investigations suggest that it would not be an ideal device for controlling a mouse, but it shows promise for usages such as manipulating virtual molecules.

Abstract The World-Wide Molecular Matrix (WWMM) is a ten year project to create a peer-to-peer (P2P) system for the publication and collection of chemical objects, including over 250, 000 molecules. It has now been instantiated in a number of repositories which include data encoded in Chemical Markup Language (CML) and linked by URIs and RDF. The technical specification and implementation is now complete. We discuss the types of architecture required to implement nodes in the WWMM and consider the social issues involved in adoption.

Abstract Computational Quantum Chemistry has developed into a powerful, efficient, reliable and increasingly routine tool for exploring the structure and properties of small to medium sized molecules. Many thousands of calculations are performed every day, some offering results which approach experimental accuracy. However, in contrast to other disciplines, such as crystallography, or bioinformatics, where standard formats and well-known, unified databases exist, this QC data is generally destined to remain locally held in files which are not designed to be machine-readable. Only a very small subset of these results will become accessible to the wider community through publication. In this paper we describe how the Quixote Project is developing the infrastructure required to convert output from a number of different molecular quantum chemistry packages to a common semantically rich, machine-readable format and to build respositories of QC results. Such an infrastructure offers benefits at many levels. The standardised representation of the results will facilitate software interoperability, for example making it easier for analysis tools to take data from different QC packages, and will also help with archival and deposition of results. The repository infrastructure, which is lightweight and built using Open software components, can be implemented at individual researcher, project, organisation or community level, offering the exciting possibility that in future many of these QC results can be made publically available, to be searched and interpreted just as crystallography and bioinformatics results are today. Although we believe that quantum chemists will appreciate the contribution the Quixote infrastructure can make to the organisation and and exchange of their results, we anticipate that greater rewards will come from enabling their results to be consumed by a wider community. As the respositories grow they will become a valuable source of chemical data for use by other disciplines in both research and education. The Quixote project is unconventional in that the infrastructure is being implemented in advance of a full definition of the data model which will eventually underpin it. We believe that a working system which offers real value to researchers based on tools and shared, searchable repositories will encourage early participation from a broader community, including both producers and consumers of data. In the early stages, searching and indexing can be performed on the chemical subject of the calculations, and well defined calculation meta-data. The process of defining more specific quantum chemical definitions, adding them to dictionaries and extracting them consistently from the results of the various software packages can then proceed in an incremental manner, adding additional value at each stage. Not only will these results help to change the data management model in the field of Quantum Chemistry, but the methodology can be applied to other pressing problems related to data in computational and experimental science.

Abstract The Open-Source Chemistry Analysis Routines (OSCAR) software, a toolkit for the recognition of named entities and data in chemistry publications, has been developed since 2002. Recent work has resulted in the separation of the core OSCAR functionality and its release as the OSCAR4 library. This library features a modular API (based on reduction of surface coupling) that permits client programmers to easily incorporate it into external applications. OSCAR4 offers a domain-independent architecture upon which chemistry specific text-mining tools can be built, and its development and usage are discussed.

Abstract Linked Open Data presents an opportunity to vastly improve the quality of science in all fields by increasing the availability and usability of the data upon which it is based. In the chemical field, there is a huge amount of information available in the published literature, the vast majority of which is not available in machine-understandable formats. PatentEye, a prototype system for the extraction and semantification of chemical reactions from the patent literature has been implemented and is discussed. A total of 4444 reactions were extracted from 667 patent documents that comprised 10 weeks' worth of publications from the European Patent Office (EPO), with a precision of 78% and recall of 64% with regards to determining the identity and amount of reactants employed and an accuracy of 92% with regards to product identification. NMR spectra reported as product characterisation data are additionally captured.

Abstract Background The Blue Obelisk movement was established in 2005 as a response to the lack of Open Data, Open Standards and Open Source (ODOSOS) in chemistry. It aims to make it easier to carry out chemistry research by promoting interoperability between chemistry software, encouraging cooperation between Open Source developers, and developing community resources and Open Standards. Results This contribution looks back on the work carried out by the Blue Obelisk in the past 5 years and surveys progress and remaining challenges in the areas of Open Data, Open Standards, and Open Source in chemistry. Conclusions We show that the Blue Obelisk has been very successful in bringing together researchers and developers with common interests in ODOSOS, leading to development of many useful resources freely available to the chemistry community.

Abstract Background Time-dependent chemotherapeutic agents can selectively target tumor cells in susceptible phases of the cell cycle however a fraction of tumor cells in non-vulnerable cell cycle phases remain drug-resistant. Immunotherapy represents a promising approach to overcome the limitation of phase-specific drugs and improve their clinical efficacy. Here, we investigated the potential use of anticancer chemotherapeutic drugs in combination with IL-18, a cytokine with strong immunostimulatory properties. Methods Four chemotherapeutic drugs commonly used in ovarian cancer were first tested for the ability to increase the immunogenicity and killing of the murine ovarian cancer cell line ID8 in vitro. Chemotherapeutric agents with measured time-dependent immune-enhancing effects were then tested for antitumor effectiveness in vivo in combination with IL-18 immunotherapy using the ID8-Vegf ovarian cancer model. Results Paclitaxel or topotecan exposure alone mediated incomplete, time-dependent killing against the murine ovarian cancer cell line ID8 in vitro, whereas carboplatin or gemcitabine mediated comprehensive, dose-dependent killing. In the plateau phase of the time-dependent killing by topotecan or paclitaxel, drug-resistant ID8 cells were more immunogenic with elevated expression of MHC-I and Fas, and increased sensitivity to CTL and Fas agonistic antibody in vitro. Moreover, the antitumor effectiveness of time-dependent agents in vivo was significantly improved with the addition of IL-18 through a T cell-dependent mechanism, while the effectiveness of drugs without significant phase specificity were not. Conclusions Tumor immunotherapy with IL-18 can significantly augment the killing fraction of phase-specific chemotherapeutic drugs and provide survival benefit. The safety profile of IL-18 and its positive interactions with select anticancer chemotherapeutic agents strongly supports the clinical investigation of this combinatorial approach.

Abstract Background Sindbis virus (SV) is the prototype of alphaviruses which are a group of widely distributed human and animal pathogens. Heterogeneous nuclear ribonucleoprotein (hnRNP) A1 is an RNA-binding protein that shuttles between the nucleus and the cytoplasm. Our recent studies found that hnRNP A1 relocates from nucleus to cytoplasm in Sindbis virus (SV)-infected cells. hnRNP A1 binds to the 5' UTR of SV RNA and facilitates the viral RNA replication and translation. Methods Making use of standard molecular techniques, virology methods and an in vitro system developed by our lab to assess the role of hnRNP A1 in SV positive strand RNA synthesis. Results hnRNP A1 interacted with the genomic (G) and subgenomic (SG) RNA promoters. Knockdown of hnRNP A1 resulted in markedly decrease in the synthesis of G and SG RNA both in infected cells and in vitro. Conclusions Our study provides the first direct evidence that hnRNP A1 actively participates in viral RNA replication and is required for the synthesis of G and SG RNA.

Abstract Background Predicting metabolic sites is important in the drug discovery process to aid in rapid compound optimisation. No interactive tool exists and most of the useful tools are quite expensive. Results Here a fast and reliable method to analyse ligands and visualise potential metabolic sites is presented which is based on annotated metabolic data, described by circular fingerprints. The method is available via the graphical workbench Bioclipse, which is equipped with advanced features in cheminformatics. Conclusions Due to the speed of predictions (less than 50 ms per molecule), scientists can get real time decision support when editing chemical structures. Bioclipse is a rich client, which means that all calculations are performed on the local computer and do not require network connection. Bioclipse and MetaPrint2D are free for all users, released under open source licenses, and available from http://www.bioclipse.net.

Abstract Background Liposomal doxorubicin (Doxil) is a cytotoxic chemotherapy drug with a favorable hematologic toxicity profile. Its active drug, doxorubicin, has interesting immunomodulatory properties. Here, the effects of Doxil on surviving tumor cell immunophenotype were investigated. Methods Using ID8 murine ovarian cancer cells, the immunomodulatory effects of Doxil were studied by measuring its impact on ovarian cancer cell expression of MHC class-I and Fas, and susceptibility to immune attack in vitro. To evaluate the ability of Doxil to cooperate with cancer immunotherapy, the interaction between Doxil and Interleukin 18 (IL-18), a pleiotropic immunostimulatory cytokine, was investigated in vivo in mice bearing ID8-Vegf tumors. Results While Doxil killed ID8 tumor cells in a dose-dependent manner, tumor cells escaping Doxil-induced apoptosis upregulated surface expression of MHC-I and Fas, and were sensitized to CTL killing and Fas-mediated death in vitro. We therefore tested the hypothesis that the combination of immunotherapy with Doxil provides positive interactions. Combination IL-18 and Doxil significantly suppressed tumor growth compared with either monotherapy in vivo and uniquely resulted in complete tumor regression and long term antitumor protection in a significant proportion of mice. Conclusion These data demonstrate that Doxil favorably changes the immunophenotype of a large fraction of the tumor that escapes direct killing thus creating an opportunity to expand tumor killing by immunotherapy, which can be capitalized through addition of IL-18 in vivo.