Using complex networks concepts to assess approaches for citations in scientific papers

The number of citations received by authors in scientific journals has become a major parameter to assess individual researchers and the journals themselves through the impact factor. A fair assessment therefore requires that the criteria for selecting references in a given manuscript should be unbiased with regard to the authors or journals cited. In this paper, we assess approaches for citations considering two recommendations for authors to follow while preparing a manuscript: (i) consider similarity of contents with the topics investigated, lest related work should be reproduced or ignored; (ii) perform a systematic search over the network of citations including seminal or very related papers. We use formalisms of complex networks for two datasets of papers from the arXiv and the Web of Science repositories to show that neither of these two criteria is fulfilled in practice. By representing the texts as complex networks we estimated a similarity index between pieces of texts and found that the list of references did not contain the most similar papers in the dataset. This was quantified by calculating a consistency index, whose maximum value is one if the references in a given paper are the most similar in the dataset. For the areas of "complex networks" and "graphenes", the consistency index was only 0.11-0.23 and 0.10-0.25, respectively. To simulate a systematic search in the citation network, we employed a traditional random walk search (i.e. diffusion) and a random walk whose probabilities of transition are proportional to the number of the ingoing edges of the neighbours. The frequency of visits to the nodes (papers) in the network had a very small correlation with either the actual list of references in the papers or with the number of downloads from the arXiv repository. Therefore, apparently the authors and users of the repository did not follow the criterion related to a systematic search over the network of citations. Based on these results, we propose an approach that we believe is fairer for evaluating and complementing citations of a given author, effectively leading to a virtual scientometry.

Satisfaction with the treatment, confidence and 'naturalness' in engaging in sexual activity in men with psychogenic erectile dysfunction: preliminary results of a randomized controlled trial of three therapeutic approaches

OBJECTIVE To assess the efficacy of group psychotherapy (GTP) and/or sildenafil for psychogenic erectile dysfunction (ED). PATIENTS AND METHODS A randomized controlled single-blind trial was performed at the Institute of Psychiatry of the Medical School of at Universidade de Sao Paulo, Sao Paulo, Brazil. In all, 30 men with mild and moderate psychogenic ED were randomized to receive for 6 months: GPT plus 50 mg sildenafil on-demand, or 50 mg sildenafil on-demand exclusively, or GPT exclusively. Changes in score from baseline for three questions of the Erectile Dysfunction Inventory of Treatment Satisfaction (EDITS) were evaluated at endpoint and after 3-months follow-up. RESULTS Satisfaction with the treatment, confidence and 'naturalness' increased in the GPT plus sildenafil and GPT exclusively groups (P = 0.001) from baseline to endpoint. The treatment-by-time comparison was not significant at endpoint vs the 3-month follow-up, in the three groups. There was no difference in the sildenafil group in the three study periods (P > 0.05) CONCLUSION Men with mild and moderate psychogenic ED had higher treatment satisfaction, confidence and naturalness in engaging in sexual activity when receiving GPT plus sildenafil or GP exclusively, when compared with sildenafil exclusively, as assessed by these three EDITS questions after 6-months treatment.

An anatomical analysis of the mini-modified orbitozygomatic and supra-orbital approaches

Seven sides of cadaver heads were used to compare the surgical exposures provided by the mini-modified orbitozygomatic (MOz) and supra-orbital (SO) approaches. The Optotrak 3020 computerized tracking system (Northern Digital, Waterloo, ON, Canada) was utilized to evaluate the area of anatomical exposure defined by six points: (1) ipsilateral sphenoid ridge; (2) most distal point of the ipsilateral middle cerebral artery (MCA); (3) most distal point of the ipsilateral posterior cerebral artery (PCA); (4) most distal point of the contralateral PCA; (5) most distal point of the contralateral MCA; and (6) contralateral sphenoid ridge. Additionally, angles of approach for the ipsilateral MCA bifurcation, ipsilateral ICA bifurcation, basilar artery tip, contralateral MCA and ICA bifurcation and anterior communicating artery (AcomA) were evaluated, first for SO and then for MOz. An image guidance system was used to evaluate the limits of surgical exposure. No differences in the area of surgical exposure were noted (p > 0.05). Vertical angles were significantly wider for the ipsilateral and contralateral ICA bifurcation, AcomA, contralateral MCA and basilar tip (p < 0.05) for MOz. No differences in horizontal angles were observed between the approaches for the six targets (p > 0.05). There were no differences in the limits of exposure. MOz affords no additional surgical working space. However, our results demonstrate systematically that vertical exposure is improved. The MOz should be performed while planning an approach to these regions and a wider exposure in the vertical axis is needed. (C) 2012 Elsevier Ltd. All rights reserved.

Different approaches, one target: understanding cellular mechanisms of Parkinson's and Alzheimer's diseases

Neurodegenerative disorders are undoubtedly an increasing problem in the health sciences, given the increase of life expectancy and occasional vicious life style. Despite the fact that the mechanisms of such diseases are far from being completely understood, a large number of studies; that derive from both the basic science and clinical approaches have contributed substantial data in that direction. In this review, it is discussed several frontiers of basic research on Parkinson's and Alzheimer's diseases, in which research groups from three departments of the Institute of Biomedical Sciences of the University of Sao Paulo have been involved in a multidisciplinary effort. The main focus of the review involves the animal models that have been developed to study cellular and molecular aspects of those neurodegenerative diseases, including oxidative stress, insulin signaling and proteomic analyses, among others. We anticipate that this review will help the group determine future directions of joint research in the field and, more importantly, set the level of cooperation we plan to develop in collaboration with colleagues of the Nucleus for Applied Neuroscience Research that are mostly involved with clinical research in the same field.

Proteomic Approaches Identify Members of Cofilin Pathway Involved in Oral Tumorigenesis

The prediction of tumor behavior for patients with oral carcinomas remains a challenge for clinicians. The presence of lymph node metastasis is the most important prognostic factor but it is limited in predicting local relapse or survival. This highlights the need for identifying biomarkers that may effectively contribute to prediction of recurrence and tumor spread. In this study, we used one-and two-dimensional gel electrophoresis, mass spectrometry and immunodetection methods to analyze protein expression in oral squamous cell carcinomas. Using a refinement for classifying oral carcinomas in regard to prognosis, we analyzed small but lymph node metastasis-positive versus large, lymph node metastasis-negative tumors in order to contribute to the molecular characterization of subgroups with risk of dissemination. Specific protein patterns favoring metastasis were observed in the "more-aggressive'' group defined by the present study. This group displayed upregulation of proteins involved in migration, adhesion, angiogenesis, cell cycle regulation, anti-apoptosis and epithelial to mesenchymal transition, whereas the "less-aggressive'' group was engaged in keratinocyte differentiation, epidermis development, inflammation and immune response. Besides the identification of several proteins not yet described as deregulated in oral carcinomas, the present study demonstrated for the first time the role of cofilin-1 in modulating cell invasion in oral carcinomas.

Different approaches for dealing with rare variants in family-based genetic studies: application of a Genetic Analysis Workshop 17 problem

Rare variants are becoming the new candidates in the search for genetic variants that predispose individuals to a phenotype of interest. Their low prevalence in a population requires the development of dedicated detection and analytical methods. A family-based approach could greatly enhance their detection and interpretation because rare variants are nearly family specific. In this report, we test several distinct approaches for analyzing the information provided by rare and common variants and how they can be effectively used to pinpoint putative candidate genes for follow-up studies. The analyses were performed on the mini-exome data set provided by Genetic Analysis Workshop 17. Eight approaches were tested, four using the trait’s heritability estimates and four using QTDT models. These methods had their sensitivity, specificity, and positive and negative predictive values compared in light of the simulation parameters. Our results highlight important limitations of current methods to deal with rare and common variants, all methods presented a reduced specificity and, consequently, prone to false positive associations. Methods analyzing common variants information showed an enhanced sensibility when compared to rare variants methods. Furthermore, our limited knowledge of the use of biological databases for gene annotations, possibly for use as covariates in regression models, imposes a barrier to further research.

New approaches and potential treatments for dry age-related macular degeneration

Emerging treatments for dry age-related macular degeneration (AMD) and geographi c atrophy focus on two strategies that target components involved in physiopathological pathways: prevention of photoreceptors and retinal pigment epithelium loss (neuroprotection induction, oxidative damage prevention, and visual cycle modification) and suppression of inflammation. Neuroprotective drugs, such as ciliary neurotrophic factor, brimonidine tartrate, tandospirone, and anti-amyloid β antibodies, aim to prevent apoptosis of retinal cells. Oxidative stress and depletion of essential micronutrients are targeted by the Age-Related Eye Disease Study (AREDS) formulation. Visual cycle modulators reduce the activity of the photoreceptors and retinal accumulation of toxic fluorophores and lipofuscin. Eyes with dry age-related macular degeneration present chronic inflammation and potential treatments include corticosteroid and complement inhibition. We review the current concepts and rationale of dry age-related macular degeneration treatment that will most likely include a combination of drugs targeting different pathways involved in the development and progression of age-related macular degeneration.

Therapeutic approaches for spinal cord injury

This study reviews the literature concerning possible therapeutic approaches for spinal cord injury. Spinal cord injury is a disabling and irreversible condition that has high economic and social costs. There are both primary and secondary mechanisms of damage to the spinal cord. The primary lesion is the mechanical injury itself. The secondary lesion results from one or more biochemical and cellular processes that are triggered by the primary lesion. The frustration of health professionals in treating a severe spinal cord injury was described in 1700 BC in an Egyptian surgical papyrus that was translated by Edwin Smith; the papyrus reported spinal fractures as a ''disease that should not be treated.'' Over the last biological or pharmacological treatment method. Science is unraveling the mechanisms of cell protection and neuroregeneration, but clinically, we only provide supportive care for patients with spinal cord injuries. By combining these treatments, researchers attempt to enhance the functional recovery of patients with spinal cord injuries. Advances in the last decade have allowed us to encourage the development of experimental studies in the field of spinal cord regeneration. The combination of several therapeutic strategies should, at minimum, allow for partial functional recoveries for these patients, which could improve their quality of life.

The Social City : Middle-way approaches to housing and sub-urban golvernmentality in southern Stockholm, 1900-1945

This dissertation deals with the period bridging the era of extreme housing shortages in Stockholm on the eve of industrialisation and the much admired programmes of housing provision that followed after the second world war, when Stockholm district Vällingby became an example for underground railway-serviced ”new towns”. It is argued that important changes were made in the housing and town planning policy in Stockholm in this period that paved the way for the successful ensuing period. Foremost among these changes was the uniquely developed practice of municipal leaseholding with the help of site leasehold rights (Erbbaurecht). The study is informed by recent developments in Foucauldian social research, which go under the heading ’governmentality’. Developments within urban planning are understood as different solutions to the problem of urban order. To a large extent, urban and housing policies changed during the period from direct interventions into the lives of inhabitants connected to a liberal understanding of housing provision, to the building of a disciplinary city, and the conduct of ’governmental’ power, building on increased activity on behalf of the local state to provide housing and the integration and co-operation of large collectives. Municipal leaseholding was a fundamental means for the implementation of this policy. When the new policies were introduced, they were limited to the outer parts of the city and administered by special administrative bodies. This administrative and spatial separation was largely upheld throughout the period, and represented as the parallel building of a ’social’ outer city, while things in the inner ’mercantile’ city proceeded more or less as before. This separation was founded in a radical difference in land holding policy: while sites in the inner city were privatised and sold at market values, land in the outer city was mostly leasehold land, distributed according to administrative – and thus politically decided – priorities. These differences were also understood and acknowledged by the inhabitants. Thorough studies of the local press and the organisational life of the southern parts of the outer city reveals that the local identity was tightly connected with the representations connected to the different land holding systems. Inhabitants in the south-western parts of the city, which in this period was still largely built on private sites, displayed a spatial understanding built on the contradictions between centre and periphery. The inhabitants living on leaseholding sites, however, showed a clear understanding of their position as members of model communities, tightly connected to the policy of the municipal administration. The organisations on leaseholding sites also displayed a deep co-operation with the administration. As the analyses of election results show, the inhabitants also seemed to have felt a greater degree of integration with the society at large, than people living in other parts of the city. The leaseholding system in Stockholm has persisted until today and has been one of the strongest in the world, although the local neo-liberal politicians are currently disposing it off.