MADIBA: A web server toolkit for biological interpretation of Plasmodium and plant gene clusters

<p>Abstract</p> <p>Background</p> <p>Microarray technology makes it possible to identify changes in gene expression of an organism, under various conditions. Data mining is thus essential for deducing significant biological information such as the identification of new biological mechanisms or putative drug targets. While many algorithms and software have been developed for analysing gene expression, the extraction of relevant information from experimental data is still a substantial challenge, requiring significant time and skill.</p> <p>Description</p> <p>MADIBA (MicroArray Data Interface for Biological Annotation) facilitates the assignment of biological meaning to gene expression clusters by automating the post-processing stage. A relational database has been designed to store the data from gene to pathway for <it>Plasmodium</it>, rice and <it>Arabidopsis</it>. Tools within the web interface allow rapid analyses for the identification of the Gene Ontology terms relevant to each cluster; visualising the metabolic pathways where the genes are implicated, their genomic localisations, putative common transcriptional regulatory elements in the upstream sequences, and an analysis specific to the organism being studied.</p> <p>Conclusion</p> <p>MADIBA is an integrated, online tool that will assist researchers in interpreting their results and understand the meaning of the co-expression of a cluster of genes. Functionality of MADIBA was validated by analysing a number of gene clusters from several published experiments – expression profiling of the <it>Plasmodium </it>life cycle, and salt stress treatments of <it>Arabidopsis </it>and rice. In most of the cases, the same conclusions found by the authors were quickly and easily obtained after analysing the gene clusters with MADIBA. </p

Feasibility of intensity-modulated and image-guided radiotherapy for functional organ preservation in locally advanced laryngeal cancer

Purpose: The study aims to assess the feasibility of intensity-modulated and image-guided radiotherapy (IMRT, and IGRT, respectively) for functional preservation in locally advanced laryngeal cancer. A retrospective review of 27 patients undergoing concurrent chemoradiation for locally advanced laryngeal cancers (8 IMRT, 19 IGRT) was undertaken. In addition to regular clinical examinations, all patients had PET imaging at 4 months and 10 months after radiotherapy, then yearly. Loco-regional control, speech quality and feeding-tube dependency were assessed during follow-up visits. Results: At a median follow-up of 20 months (range 6-57 months), four out of 27 patients (14.8%) developed local recurrence and underwent salvage total laryngectomy. One patient developed distant metastases following salvage surgery. Among the 23 patients who conserved their larynx with no sign of recurrence at last follow-up, 22 (95%) reported normal or near normal voice quality, allowing them to communicate adequately. Four patients (14.8%) had long-term tube feeding-dependency because of severe dysphagia (2 patients) and chronic aspiration (2 patients, with ensuing death from aspiration pneumonia in one patient). Conclusions and Clinical Relevance: Functional laryngeal preservation is feasible with IMRT and IGRT for locally advanced laryngeal cancer. However, dysphagia and aspiration remain serious complications, due most likely to high radiation dose delivery to the pharyngeal musculatures. © 2012 Nguyen et al

The coaching schematic: validation through expert coach consensus.

Current research in coaching development infers that coaching is predominantly a decision-making process. The same and other research is not, however, informing the coaching development process due to a lack of a big picture approach. Consequently, there is a need for a model of coaching. In this paper, we offer such a model in the form of a schematic that reflects the coaching process from both a content and information-processing stance. To assess the validity of the schematic, 16 expert coaches were interviewed to elicit a complete description of their coaching process. The coaches were then shown a copy of the schematic and asked to comment on its design and content with respect to its accuracy in reflecting their coaching process. Following analysis of the interview, six general categories emerged: Roles, Goals, Typical Actions, Required Knowledge, Support for the Schematic, and Factors Influencing Development. The first four categories clearly displayed an implicit support for the schematic. Furthermore, all coaches offered explicit support for the schematic. Such strong support confirmed that the schematic was valid and could form the basis of focused interventions in coaching developmen

La Participación Ciudadana desde un Acercamiento Sociopolítico. Una Perspectiva del Docente Universitario

La participación ciudadana ha sido por mucho un tema de constante estudio, donde se han generado diversos modelos y acercamientos según los tipos de democracias acorde tiempo y espacio del entorno social. En este artículo se hace una revisión sobre los modelos de participación ciudadana y la perspectiva que tiene el docente universitario desde el ámbito comunitario, pues se busca identificar que perciben los trasmisores del conocimiento acerca de la participación, desde lo personal hasta sus experiencias vividas como habitantes dentro de una comunidad; en lo que corresponde a la metodología del estudio es de corte cualitativo, ya que se aplicaron entrevistas semiestructuradas. Los objetivos del presente estudio consisten en indagar cuáles son las perspectiva de los docentes universitarios con relación a la participación ciudadana en espacios comunitarios, de igual forma, conocer las causas o factores que, en opinión de los docentes universitarios influyen o no en las y los ciudadanos para participar en sectores comunitarios, así como comprobar la existencia de acciones sociales impulsadas por instituciones universitarias que motivan al alumnado a participar en actividades cívicas.Community participation has been a subject of constant study, where diverse models and approaches have been generated according to the types of democracy in line with time and space of the social environment. In this article a review is made about the models of citizen participation, and the perspective that the university professor has from the community level, since it seeks to identify what the transmitters of knowledge about participation perceive, from personal to their lived experiences as an inhabitant within a community; in what corresponds to the methodology of the study is qualitative, since semi-structured interviews were applied. The objectives of this study are to investigate which are the perspectives of the university professors regarding citizen participation in community spaces, likewise, to know the causes or factors that, with the opinion of university professors, influence or not in the citizens to participate in community spaces, and to verify the existence of social actions promoted by university institutions that motivate students to participate in community activities

Charting Coordination Needs in Large-Scale Agile Organisations with Boundary Objects and Methodological Islands

Large-scale system development companies are increasingly adopting agile methods. While this adoption may improve lead-times, such companies need to balance two trade-offs: (i) the need to have a uniform, consistent development method on system level with the need for specialised methods for teams in different disciplines (e.g., hardware, software, mechanics, sales, support); (ii) the need for comprehensive documentation on system level with the need to have lightweight documentation enabling iterative and agile work. With specialised methods for teams, isolated teams work within larger ecosystems of plan-driven culture, i.e., teams become agile “islands”. At the boundaries, these teams share knowledge which needs to be managed well for a correct system to be developed. While it is useful to support diverse and specialised methods, it is important to understand which islands are repeatedly encountered, the reasons or factors triggering their existence, and how best to handle coordination between them. Based on a multiple case study, this work presents a catalogue of islands and the boundary objects between them. We believe this work will be beneficial to practitioners aiming to understand their ecosystems and researchers addressing communication and coordination challenges in large-scale development

Take a walk on the wild side: Exploring, identifying, and developing consultancy expertise with elite performance team leaders

Objectives: Stemming from sport psychology’s recent shift to examine the effective management of elite sports team organizations, the extensive, significant, and complex challenges faced by those with responsibility for team performance have been emphasized. Recognizing that most work in this budding area has been theoretical in nature, our contribution to this special issue consequently identifies and critically evaluates some implications for excellence in practitioners who support leaders of elite sport performance teams. Method: Narrative review and commentary. Results and Conclusions: To survive and succeed, leaders of elite teams must: (a) negotiate complex and contested socio-political dynamics both within and outside their performance department; (b) make impactful and consistent real-time decisions; and (c) continually reinforce and protect their programme. To provide an optimally impactful and valued service, sport psychologists must therefore be able to advise on a broad and politically-astute leadership style and, most critically for consultancy excellence: (a) work within a professional judgment and decision making model; (b) facilitate the leader’s adaptive expertise and nested decision making; and (c) operate a proactive, forthright, and straight approach to ethical considerations. Based on these implications, we conclude by providing suggestions for the training and development of applied consultants

The illusion of competency versus the desirability of expertise: Seeking a common standard for support professions in sport

In this paper we examine and challenge the competency-based models which currently dominate accreditation and development systems in sport support disciplines, largely the sciences and coaching. Through consideration of exemplar shortcomings, the limitations of competency-based systems are presented as failing to cater for the complexity of decision making and the need for proactive experimentation essential to effective practice. To provide a better fit with the challenges of the various disciplines in their work with performers, an alternative approach is presented which focuses on the promotion, evaluation and elaboration of expertise. Such an approach resonates with important characteristics of professions, whilst also providing for the essential ‘shades of grey’ inherent in work with human participants. Key differences between the approaches are considered through exemplars of evaluation processes. The expertise-focused method, although inherently more complex, is seen as offering a less ambiguous and more positive route, both through more accurate representation of essential professional competence and through facilitation of future growth in proficiency and evolution of expertise in practice. Examples from the literature are also presented, offering further support for the practicalities of this approach

Feasibility of Tomotherapy-Based Image-Guided Radiotherapy for Locally Advanced Oropharyngeal Cancer

PURPOSE: The study aims to assess the feasibility of tomotherapy-based image-guided (IGRT) radiotherapy for locally advanced oropharyngeal cancer. A retrospective review of 33 patients undergoing concurrent chemoradiation for locally advanced oropharyngeal cancers was conducted. Radiotherapy planning, treatment toxicity and loco-regional control were assessed. RESULTS: At a median follow-up of 32 months (6-47 months), no patient developed loco-regional recurrence. Two patients (6%) developed distant metastases. Grade 3-4 acute toxicity was respectively 72% and 25% for mucositis and gastrointestinal toxicity. Two patients (6%) had long-term dependence on tube feedings. Dose-volume histogram demonstrated excellent target volume coverage and low radiation dose to the organs at risk for complications. CONCLUSIONS AND CLINICAL RELEVANCE: IGRT provides excellent loco-regional control but acute toxicity remains significant and needs to be addressed in future prospective trials. The feasibility of Tomotherapy to decrease radiation dose to the normal tissues merits further investigations

Feasibility of image-guided radiotherapy based on helical tomotherapy to reduce contralateral parotid dose in head and neck cancer

Background To evaluate the feasibility of image-guided radiotherapy based on helical Tomotherapy to spare the contralateral parotid gland in head and neck cancer patients with unilateral or no neck node metastases. Methods A retrospective review of 52 patients undergoing radiotherapy for head and neck cancers with image guidance based on daily megavoltage CT imaging with helical tomotherapy was performed. Results Mean contralateral parotid dose and the volume of the contralateral parotid receiving 40 Gy or more were compared between radiotherapy plans with significant constraint (SC) of less than 20 Gy on parotid dose (23 patients) and the conventional constraint (CC) of 26 Gy (29 patients). All patients had PTV coverage of at least 95% to the contralateral elective neck nodes. Mean contralateral parotid dose was, respectively, 14.1 Gy and 24.7 Gy for the SC and CC plans (p < 0.0001). The volume of contralateral parotid receiving 40 Gy or more was respectively 5.3% and 18.2% (p < 0.0001) Conclusion Tomotherapy for head and neck cancer minimized radiotherapy dose to the contralateral parotid gland in patients undergoing elective node irradiation without sacrificing target coverage