Semantic integration of gene expression analysis tools and data sources using software connectors

Abstract Background The study and analysis of gene expression measurements is the primary focus of functional genomics. Once expression data is available, biologists are faced with the task of extracting (new) knowledge associated to the underlying biological phenomenon. Most often, in order to perform this task, biologists execute a number of analysis activities on the available gene expression dataset rather than a single analysis activity. The integration of heteregeneous tools and data sources to create an integrated analysis environment represents a challenging and error-prone task. Semantic integration enables the assignment of unambiguous meanings to data shared among different applications in an integrated environment, allowing the exchange of data in a semantically consistent and meaningful way. This work aims at developing an ontology-based methodology for the semantic integration of gene expression analysis tools and data sources. The proposed methodology relies on software connectors to support not only the access to heterogeneous data sources but also the definition of transformation rules on exchanged data. Results We have studied the different challenges involved in the integration of computer systems and the role software connectors play in this task. We have also studied a number of gene expression technologies, analysis tools and related ontologies in order to devise basic integration scenarios and propose a reference ontology for the gene expression domain. Then, we have defined a number of activities and associated guidelines to prescribe how the development of connectors should be carried out. Finally, we have applied the proposed methodology in the construction of three different integration scenarios involving the use of different tools for the analysis of different types of gene expression data. Conclusions The proposed methodology facilitates the development of connectors capable of semantically integrating different gene expression analysis tools and data sources. The methodology can be used in the development of connectors supporting both simple and nontrivial processing requirements, thus assuring accurate data exchange and information interpretation from exchanged data.

World Federation of Societies of Biological Psychiatry (WFSBP) Guidelines for Biological Treatment of Schizophrenia, Part 1: Update 2012 on the acute treatment of schizophrenia and the management of treatment resistance

These updated guidelines are based on a first edition of the World Federation of Societies of Biological Psychiatry Guidelines for Biological Treatment of Schizophrenia published in 2005. For this 2012 revision, all available publications pertaining to the biological treatment of schizophrenia were reviewed systematically to allow for an evidence-based update. These guidelines provide evidence-based practice recommendations that are clinically and scientifically meaningful and these guidelines are intended to be used by all physicians diagnosing and treating people suffering from schizophrenia. Based on the first version of these guidelines, a systematic review of the MEDLINE/PUBMED database and the Cochrane Library, in addition to data extraction from national treatment guidelines, has been performed for this update. The identified literature was evaluated with respect to the strength of evidence for its efficacy and then categorised into six levels of evidence (A-F; Bandelow et al. 2008b, World J Biol Psychiatry 9: 242). This first part of the updated guidelines covers the general descriptions of antipsychotics and their side effects, the biological treatment of acute schizophrenia and the management of treatment-resistant schizophrenia.

Prenatal detection and postnatal management of an intranasal glioma

Nasal gliomas are rare benign congenital midline tumors composed of heterotopic neuroglial tissue. They have potential for intracranial extension through a bony defect in the skull base. Neuroimaging is essential for identifying nasal lesions and for determining their exact location and any possible intracranial extension. Computed tomography is often the initial imaging study obtained because it provides good visualization of the bony landmarks of the skull base; it is not, however, well suited for soft tissue imaging. Magnetic resonance imaging has better soft tissue resolution and may be the best initial study in patients seen early in life because the anterior skull base consists of an unossified cartilage and may falsely appear as if there is a bony dehiscence on computed tomography. A frontal craniotomy approach is recommended if intracranial extension is identified, followed by a transnasal endoscopic approach for intranasal glioma. A case is presented of a huge fetal facial mass that was shown by ultrasound that protruded through the left nostril at 33 weeks of gestation. Computed tomography of the neonate suggested a transethmoidal encephalocele. Magnetic resonance imaging showed a huge mass occupying the nasopharynx and the nasal cavity and protruding externally to the face but ruled out bony discontinuity in the skull base and, therefore, any intracranial connection. The infant underwent an endoscopic resection of the mass via oral and nasal routes and pathologic examination revealed intranasal glioma. (C) 2012 Elsevier Inc. All rights reserved.

Periodontal Manifestations and Ambulatorial Management in a Patient With Sturge Weber Syndrome

Sturge-Weber syndrome is a nonhereditary congenital condition characterized by leptomeningeal and facial skin angiomatous malformation following the trigeminal nerve path. The intraoral angiomatosis are presented in 40% of cases and results in an important periodontal alteration, increasing the risk of bleeding during dental procedures. A 43-year-old male patient presented with port wine stain on the right side of the face, the entire hard and soft palates, the alveolar ridge, and buccal mucosa, and had an excessive accumulation of calcified masses in both supragingival and subgingival sites, with swelling and generalized inflammation throughout the gingiva and alveolar mucosa. He reported not having sanitized the area for years for fear of bleeding. Periodontal management, to remove calculus and to control gingivitis initiated in the supragingival region and gradually reaching the subgingival region to control oral microbiota, was performed with mild bleeding. The redness of the staining greatly diminished with time and the extreme halitosis of the patient also improved sharply leading to a dramatic improvement in quality of life. Ambulatory care is a feasible alternative for periodontal management that within safety limits for bleeding risks reduces the operational cost.

Determination of trace elements in bovine semen samples by inductively coupled plasma mass spectrometry and data mining techniques for identification of bovine class

The reproductive performance of cattle may be influenced by several factors, but mineral imbalances are crucial in terms of direct effects on reproduction. Several studies have shown that elements such as calcium, copper, iron, magnesium, selenium, and zinc are essential for reproduction and can prevent oxidative stress. However, toxic elements such as lead, nickel, and arsenic can have adverse effects on reproduction. In this paper, we applied a simple and fast method of multi-element analysis to bovine semen samples from Zebu and European classes used in reproduction programs and artificial insemination. Samples were analyzed by inductively coupled plasma spectrometry (ICP-MS) using aqueous medium calibration and the samples were diluted in a proportion of 1:50 in a solution containing 0.01% (vol/vol) Triton X-100 and 0.5% (vol/vol) nitric acid. Rhodium, iridium, and yttrium were used as the internal standards for ICP-MS analysis. To develop a reliable method of tracing the class of bovine semen, we used data mining techniques that make it possible to classify unknown samples after checking the differentiation of known-class samples. Based on the determination of 15 elements in 41 samples of bovine semen, 3 machine-learning tools for classification were applied to determine cattle class. Our results demonstrate the potential of support vector machine (SVM), multilayer perceptron (MLP), and random forest (RF) chemometric tools to identify cattle class. Moreover, the selection tools made it possible to reduce the number of chemical elements needed from 15 to just 8.

Diaphragmatic pacing stimulation in spinal cord injury: anesthetic and perioperative management

OBJECTIVE: The standard therapy for patients with high-level spinal cord injury is long-term mechanical ventilation through a tracheostomy. However, in some cases, this approach results in death or disability. The aim of this study is to highlight the anesthetics and perioperative aspects of patients undergoing insertion of a diaphragmatic pacemaker. METHODS: Five patients with quadriplegia following high cervical traumatic spinal cord injury and ventilator-dependent chronic respiratory failure were implanted with a laparoscopic diaphragmatic pacemaker after preoperative assessments of their phrenic nerve function and diaphragm contractility through transcutaneous nerve stimulation. ClinicalTrials.gov:NCT01385384. RESULTS: The diaphragmatic pacemaker placement was successful in all of the patients. Two patients presented with capnothorax during the perioperative period, which resolved without consequences. After six months, three patients achieved continuous use of the diaphragm pacing system, and one patient could be removed from mechanical ventilation for more than 4 hours per day. CONCLUSIONS: The implantation of a diaphragmatic phrenic system is a new and safe technique with potential to improve the quality of life of patients who are dependent on mechanical ventilation because of spinal cord injuries. Appropriate indication and adequate perioperative care are fundamental to achieving better results.

Analysis of the interplay between knowledge and performance management in industrial clusters

The concept of industrial clustering has been studied in-depth by policy makers and researchers from many fields, mainly due to the competitive advantages it may bring to regional economies. Companies often take part in collaborative initiatives with local partners while also taking advantage of knowledge spillovers to benefit from locating in a cluster. Thus, Knowledge Management (KM) and Performance Management (PM) have become relevant topics for policy makers and cluster associations when undertaking collaborative initiatives. Taking this into account, this paper aims to explore the interplay between both topics using a case study conducted in a collaborative network formed within a cluster. The results show that KM should be acknowledged as a formal area of cluster management so that PM practices can support knowledge-oriented initiatives and therefore make better use of the new knowledge created. Furthermore, tacit and explicit knowledge resulting from PM practices needs to be stored and disseminated throughout the cluster as a way of improving managerial practices and regional strategic direction. Knowledge Management Research & Practice (2012) 10, 368-379. doi:10.1057/kmrp.2012.23

Sublingual ketorolac and sublingual piroxicam are equally effective for postoperative pain, trismus, and swelling management in lower third molar removal

Objective. Lower third molar removal provides a clinical model for studying analgesic drugs. The present study's aim was to compare the clinical efficacy of sublingual ketorolac and sublingual piroxicam in managing pain, trismus and swelling after lower third molar extraction in adult volunteers. Study Design. In this double-blinded, randomized, crossover investigation, 47 volunteers received for 4 days ketorolac sublingually (10 mg 4 times daily) and piroxicam sublingually (20 mg once daily) during 2 separate appointments after lower third molar extraction of symmetrically positioned lower third molars. A surgeon evaluated objective parameters (surgery duration, mouth opening, rescue analgesic medication, and facial swelling) and volunteers documented subjective parameters (postoperative pain and global evaluation), comparing postoperative results for a total of 7 days after surgery. The means of the objective and subjective parameters were compared for statistical significance (P < .05). Results. Volunteers reported low pain scores during the postoperative period when treated with either sublingual ketorolac or piroxicam. Also, volunteers ingested similar amounts of analgesic rescue medication (paracetamol) when they received either drug sublingually (P > .05). Additionally, values for mouth openings measured just before surgery and immediately after suture removal 7 days later were similar among volunteers (P > .05), and the type of nonsteroidal antiinflammatory drug (NSAID) used in this study showed no significant differences between swellings on the second or seventh days after surgery (P > .05). Conclusions. Pain, trismus, and swelling after lower third molar extraction, independent of surgical difficulty, were successfully controlled by sublingual ketorolac (10 mg 4 times daily) or sublingual piroxicam (20 mg once daily), and no significant differences were observed between the NSAIDs evaluated. (Oral Surg Oral Med Oral Pathol Oral Radiol 2012;114:27-34)

Prevalence and correlates of dizziness in community-dwelling older people: a cross sectional population based study

Abstract Background Dizziness is a common complaint among older adults and has been linked to a wide range of health conditions, psychological and social characteristics in this population. However a profile of dizziness is still uncertain which hampers clinical decision-making. We therefore sought to explore the relationship between dizziness and a comprehensive range of demographic data, diseases, health and geriatric conditions, and geriatric syndromes in a representative sample of community-dwelling older people. Methods This is a cross-sectional, population-based study derived from FIBRA (Network for the Study of Frailty in Brazilian Elderly Adults), with 391 elderly adults, both men and women, aged 65 years and older. Elderly participants living at home in an urban area were enrolled through a process of random cluster sampling of census regions. The outcome variable was the self-report of dizziness in the last year. Several feelings of dizziness were investigated including vertigo, spinning, light or heavy headedness, floating, fuzziness, giddiness and instability. A multivariate logistic regression analysis was conducted to estimate the adjusted odds ratios and build the probability model for dizziness. Results The complaint of dizziness was reported by 45% of elderly adults, from which 71.6% were women (p=0.004). The multivariate regression analysis revealed that dizziness is associated with depressive symptoms (OR = 2.08; 95% CI 1.29���3.35), perceived fatigue (OR = 1.93; 95% CI 1.21-3.10), recurring falls (OR = 2.01; 95% CI 1.11-3.62) and excessive drowsiness (OR = 1.91; 95% CI 1.11���3.29). The discrimination of the final model was AUC = 0.673 (95% CI 0.619-0.727) (p< 0.001). Conclusions The prevalence of dizziness in community-dwelling elderly adults is substantial. It is associated with other common geriatric conditions usually neglected in elderly adults, such as fatigue and drowsiness, supporting its possible multifactorial manifestation. Our findings demonstrate the need to expand the design in future studies, aiming to estimate risk and identify possible causal relations.

A resource management scenario for traditional and scientific management of pink shrimp (Farfantepenaeus paulensis) in the Patos Lagoon estuary (RS), Brazil

Abstract Background This article aims to discuss the incorporation of traditional time in the construction of a management scenario for pink shrimp in the Patos Lagoon estuary (RS), Brazil. To meet this objective, two procedures have been adopted; one at a conceptual level and another at a methodological level. At the conceptual level, the concept of traditional time as a form of traditional ecological knowledge (TEK) was adopted. Method At the methodological level, we conduct a wide literature review of the scientific knowledge (SK) that guides recommendations for pink shrimp management by restricting the fishing season in the Patos Lagoon estuary; in addition, we review the ethno-scientific literature which describes traditional calendars as a management base for artisanal fishers in the Patos Lagoon estuary. Results Results demonstrate that TEK and SK describe similar estuarine biological processes, but are incommensurable at a resource management level. On the other hand, the construction of a ���management scenario��� for pink shrimp is possible through the development of ���criteria for hierarchies of validity��� which arise from a productive dialog between SK and TEK. Conclusions The commensurable and the incommensurable levels reveal different basis of time-space perceptions between traditional ecological knowledge and scientific knowledge. Despite incommensurability at the management level, it is possible to establish guidelines for the construction of ���management scenarios��� and to support a co-management process.