Molecular Modeling Approaches for Determining Gene Function: application to a Putative Poly-A Binding Protein from Leishmania amazonensis (LaPABP)

The great expansion in the number of genome sequencing projects has revealed the importance of computational methods to speed up the characterization of unknown genes. These studies have been improved by the use of three dimensional information from the predicted proteins generated by molecular modeling techniques. In this work, we disclose the structure-function relationship of a gene product from Leishmania amazonensis by applying molecular modeling and bioinformatics techniques. The analyzed sequence encodes a 159 aminoacids polypeptide (estimated 18 kDa) and was denoted LaPABP for its high homology with poly-A binding proteins from trypanosomatids. The domain structure, clustering analysis and a three dimensional model of LaPABP, basically obtained by homology modeling on the structure of the human poly-A binding protein, are described. Based on the analysis of the electrostatic potential mapped on the model's surface and conservation of intramolecular contacts responsible for folding stabilization we hypothesize that this protein may have less avidity to RNA than it's L. major counterpart but still account for a significant functional activity in the parasite. The model obtained will help in the design of mutagenesis experiments aimed to elucidate the mechanism of gene expression in trypanosomatids and serve as a starting point for its exploration as a potential source of targets for a rational chemotherapy.

MAMOT: hidden Markov modeling tool.

Hidden Markov models (HMMs) are probabilistic models that are well adapted to many tasks in bioinformatics, for example, for predicting the occurrence of specific motifs in biological sequences. MAMOT is a command-line program for Unix-like operating systems, including MacOS X, that we developed to allow scientists to apply HMMs more easily in their research. One can define the architecture and initial parameters of the model in a text file and then use MAMOT for parameter optimization on example data, decoding (like predicting motif occurrence in sequences) and the production of stochastic sequences generated according to the probabilistic model. Two examples for which models are provided are coiled-coil domains in protein sequences and protein binding sites in DNA. A wealth of useful features include the use of pseudocounts, state tying and fixing of selected parameters in learning, and the inclusion of prior probabilities in decoding. AVAILABILITY: MAMOT is implemented in C++, and is distributed under the GNU General Public Licence (GPL). The software, documentation, and example model files can be found at http://bcf.isb-sib.ch/mamot

Modelación de la distribución de especies y ecosistemas en el tiempo y en el espacio: una revisión de las nuevas herramientas y enfoques disponibles

This article aims to present the conceptual and methodological framework in which models techniques for species and ecosystems distribution are developed. An historical review of concepts behind these techniques is made as well as the presentation of the major methodological steps involved in these tests. A discussion on how these approaches are useful for the development of new questions in the field of biogeography and biological conservation is generated. Finally, an application of distribution modeling techniques, using the specie Beilschmiedia miersii (belloto Del Norte) as a study case, is presented. This conceptual and methodological review as well as the example applied, seeks to clarify the usefulness and potential of distribution models techniques, with the objective to go forward in biogeography research and thus, farther progress in understanding spatial and temporal patterns of organism's distribution

A Framework for Quality in Long-Term Residential Care for Older People in Ireland

The National Council on Ageing and Older People has long been concerned about the quality of long-term residential care for older people in Ireland. In 1986, its predecessor, the National Council for the Aged published “It’s Our Home”. The Quality of Life in Private and Voluntary Nursing Homes. In 1999 the Council commissioned a postal survey of all long-term residential care facilities in the country to determine whether facilities had quality initiatives in operation; providers’ views and aspirations for future provision of long-term care; providers’ views on the introduction of a national quality monitoring policy Download the Report here

Towards a Standardised Framework for Inter-Country Adoption - Report of the Implementation Group

The report contains Background to the commissioning of the Report â?~â?~Towards a Standardised Framework for Intercountry Adoption Assessment Proceduresâ?Tâ?T; the Government decision arising; and the principal findings and recommendations of the Report (Chapter 1); Detailed information on progress made in relation to the recommendations contained in the Report (Chapters 2-5); Statistical data in relation to intercountry adoption services at June, 2000 (Chapter 6); A summary of key findings of the Implementation Group (Chapter 7); and The Implementation Groupâ?Ts recommendations regarding the future of intercountry adoption services (Chapter 8). Download the Report here

Towards a Standardised Framework for Inter-Country Adoption - Assessment Procedures

In the first part the background on inter-country adoption and assessment of prospective adopters are considered in general terms in Chapters Two and Three respectively. The second chapter places the objectives of the research into context. Due to the declining numbers of children being put forward for domestic adoption, there is increasing recourse to inter-country adoption. An overview of the situation is outlined. The legislation section outlines both Irish legislation and the pivotal international agreement relevant to inter-country adoption, namely the Hague Convention. The implications for inter-country adoption processes are described Download the Report here

Analyzing complex rock slope deformation at Stampa, western Norway, by integrating geomorphology, kinematics and numerical modeling

The unstable rock slope, Stampa, above the village of Flåm, Norway, shows signs of both active and postglacial gravitational deformation over an area of 11 km2. Detailed structural field mapping, annual differential Global Navigation Satellite System (GNSS) surveys, as well as geomorphic analysis of high-resolution digital elevation models based on airborne and terrestrial laser scanning indicate that slope deformation is complex and spatially variable. Numerical modeling was used to investigate the influence of former rockslide activity and to better understand the failure mechanism. Field observations, kinematic analysis and numerical modeling indicate a strong structural control of the unstable area. Based on the integration of the above analyses, we propose that the failure mechanism is dominated by (1) a toppling component, (2) subsiding bilinear wedge failure and (3) planar sliding along the foliation at the toe of the unstable slope. Using differential GNSS, 18 points were measured annually over a period of up to 6 years. Two of these points have an average yearly movement of around 10 mm/year. They are located at the frontal cliff on almost completely detached blocks with volumes smaller than 300,000 m3. Large fractures indicate deep-seated gravitational deformation of volumes reaching several 100 million m3, but the movement rates in these areas are below 2 mm/year. Two different lobes of prehistoric rock slope failures were dated with terrestrial cosmogenic nuclides. While the northern lobe gave an average age of 4,300 years BP, the southern one resulted in two different ages (2,400 and 12,000 years BP), which represent most likely multiple rockfall events. This reflects the currently observable deformation style with unstable blocks in the northern part in between Joasete and Furekamben and no distinct blocks but a high rockfall activity around Ramnanosi in the south. With a relative susceptibility analysis it is concluded that small collapses of blocks along the frontal cliff will be more frequent. Larger collapses of free-standing blocks along the cliff with volumes > 100,000 m3, thus large enough to reach the fjord, cannot be ruled out. A larger collapse involving several million m3 is presently considered of very low likelihood.

Wellposedness of a nonlinear, logarithmic Schrödinger equation of Doebner-Goldin type modeling quantum dissipation

This paper is concerned with the modeling and analysis of quantum dissipation phenomena in the Schrödinger picture. More precisely, we do investigate in detail a dissipative, nonlinear Schrödinger equation somehow accounting for quantum Fokker–Planck effects, and how it is drastically reduced to a simpler logarithmic equation via a nonlinear gauge transformation in such a way that the physics underlying both problems keeps unaltered. From a mathematical viewpoint, this allows for a more achievable analysis regarding the local wellposedness of the initial–boundary value problem. This simplification requires the performance of the polar (modulus–argument) decomposition of the wavefunction, which is rigorously attained (for the first time to the best of our knowledge) under quite reasonable assumptions.

A Framework for Major Emergency Management

Major emergency management is a key challenge and a priority issue for Government. Clearly, the world in which we live is constantly changing and we need to develop our major emergency management architecture to enable us to deal effectively with the possibility of new risks and threats. In the last few years most European Countries have engaged in review and development of their major emergency or civil protection arrangements. This new Framework for Major Emergency Management moves in line with international trends in this field. Read the document (PDF, 1.9mb) Read the Appendices document (PDF, 1.3mb) A series of additional Framework Guidance Documents designed to support specific areas of major emergency management are currently under development. These documents will initially be posted here as Working Drafts for comment by practitioners involved in the implementation process. The first two guides: A Guide to Risk Assessment in Major Emergency Management and A Guide to Preparing a Major Emergency Plan are now available and further guides will emerge at intervals during the development programme. A Guide to Risk Assessment in Major Emergency Management (PDF, 387kb) A Guide to Preparing a Major Emergency Plan (PDF, 158kb)

Framework for Corporate and Financial Governance for Regulatory Bodies under the aegis of the Department of Health and Children

The document should be read as supplementary to existing requirements as set out both in statute â?" particularly legislation specific to your organisation, the Health Acts 1947-2004, Ombudsman Act, 1980, Data Protection Acts 1988 & 2003, Freedom of Information Acts 1997-2003, Ethics in Public Office Acts 1995 & 2001, Ombudsman for Children Act, 2002 and the Comptroller and Auditor General (Amendment) Act, 1993 – and in Government approved guidelines, including the Code of Practice for the Governance of State Bodies (2001), Public Financial Procedures, The Role and Responsibilities of Accounting Officers (2003) and Risk Management Guidance for Government Departments and Offices (2004). Read the report (PDF, 1.4mb)  

Framework for Corporate and Financial Governance for Agencies funded by the Department of Health and Children

Corporate governance is the system by which organisations direct and control their functions and relate to their stakeholders in order to manage their business, achieve their mission and objectives and meet the necessary standards of accountability, integrity and propriety. It is a key element in improving efficiency and accountability as well as enhancing openness and transparency. A significant element of the Governmentâ?Ts programme for health service reform is the strengthening of governance and accountability arrangements across the health system. Read the Report (PDF, 1mb)

Tackling Chronic Disease - A Policy Framework for the Management of Chronic Diseases

Tackling Chronic Disease – A Policy Framework for the Management of Chronic Diseases Chronic diseases are recognised as a major health challenge. In the healthcare system, they represent the major component of service activity and expenditure, as well as the major contributor to mortality and ill-health in this country. Given the population projections which predict a doubling of the elderly population over the next 30 years, this will give rise to a significant increase in chronic diseases with the consequent burden on society, the healthcare system and individuals. Click here to download PDF 1.8mb

A Review Of Practice Development In Nursing And Midwifery In The Republic Of Ireland And The Development Of A Strategic Framework

A Review Of Practice Development In Nursing And Midwifery In The Republic Of Ireland And The Development Of A Strategic Framework Click here to download PDF 1.52MB