A novel clustering methodology based on modularity optimisation for detecting authorship affinities in Shakespearean era plays

© 2016 Naeni et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. In this study we propose a novel, unsupervised clustering methodology for analyzing large datasets. This new, efficient methodology converts the general clustering problem into the community detection problem in graph by using the Jensen-Shannon distance, a dissimilarity measure originating in Information Theory. Moreover, we use graph theoretic concepts for the generation and analysis of proximity graphs. Our methodology is based on a newly proposed memetic algorithm (iMA-Net) for discovering clusters of data elements by maximizing the modularity function in proximity graphs of literary works. To test the effectiveness of this general methodology, we apply it to a text corpus dataset, which contains frequencies of approximately 55,114 unique words across all 168 written in the Shakespearean era (16th and 17th centuries), to analyze and detect clusters of similar plays. Experimental results and comparison with state-of-the-art clustering methods demonstrate the remarkable performance of our new method for identifying high quality clusters which reflect the commonalities in the literary style of the plays

Unveiling Clusters of RNA Transcript Pairs Associated with Markers of Alzheimer's Disease Progression

Background: One primary goal of transcriptomic studies is identifying gene expression patterns correlating with disease progression. This is usually achieved by considering transcripts that independently pass an arbitrary threshold (e.g. p<0.05). In diseases involving severe perturbations of multiple molecular systems, such as Alzheimer's disease (AD), this univariate approach often results in a large list of seemingly unrelated transcripts. We utilised a powerful multivariate clustering approach to identify clusters of RNA biomarkers strongly associated with markers of AD progression. We discuss the value of considering pairs of transcripts which, in contrast to individual transcripts, helps avoid natural human transcriptome variation that can overshadow disease-related changes. Methodology/Principal Findings: We re-analysed a dataset of hippocampal transcript levels in nine controls and 22 patients with varying degrees of AD. A large-scale clustering approach determined groups of transcript probe sets that correlate strongly with measures of AD progression, including both clinical and neuropathological measures and quantifiers of the characteristic transcriptome shift from control to severe AD. This enabled identification of restricted groups of highly correlated probe sets from an initial list of 1,372 previously published by our group. We repeated this analysis on an expanded dataset that included all pair-wise combinations of the 1,372 probe sets. As clustering of this massive dataset is unfeasible using standard computational tools, we adapted and re-implemented a clustering algorithm that uses external memory algorithmic approach. This identified various pairs that strongly correlated with markers of AD progression and highlighted important biological pathways potentially involved in AD pathogenesis. Conclusions/Significance: Our analyses demonstrate that, although there exists a relatively large molecular signature of AD progression, only a small number of transcripts recurrently cluster with different markers of AD progression. Furthermore, considering the relationship between two transcripts can highlight important biological relationships that are missed when considering either transcript in isolation. © 2012 Arefin et al

Advance healthcare directives: moving towards a universally recognized right

Advance healthcare directives (AD) are still intensively animating debates in Europe and worldwide, leading to the enactment of different laws, according to the diverse legal, sociocultural, religious and philosophical traditions of each society1 . After a long complicated seemingly ever-lasting process, on the 14th of December 2017 the Italian Parliament finally approved the Law on “Informed consent and Advance healthcare directives” putting Italy on the same level as other European countries, which have previously regulated this complicated matter2 . The most controversial point of the law is represented by AD. Section 4 states that everyone able to make a proper judgment, regarding any possible future inability to self-determine, can, through AD, express their beliefs and preferences concerning health treatments, consent or refusal to any diagnostic or therapeutic choice, including artificial nutrition and hydration. One can also indicate a person of trust to represent him/her in the relationships with doctors and hospitals2 . Furthermore, the same provision specifies that the doctor is obliged to respect the AD, unless: a) the patient requests a treatment opposing the law or medical deontology, or b) the AD is clearly incongruous, or c) new and unpredictable therapies have come into force. Therefore, ADs are binding; conscientious objection is not foreseen. The reference of the law to medical deontology finds its rationale in section 38 of the Italian Code of Medical Ethics, updated in May 2014, where the requirements that AD must meet are stated3 . With this new law2 Italy conforms to the orientation of the other main European countries, obliging the respect of ADs, even if the limits are slightly different, France4 , Germany5 , Spain6 and England7 they are binding. We wish to draw the attention of the whole medical scientific community to this matter, advocating for an open dialogue to discuss the ethical and medical issues concerning AD, thereby facilitating the improvement and implementation of guidelines and policies to safeguard patients together with healthcare providers1 . There has been considerable progress in addressing all the ethical issues regarding AD and as a consequence of the constant innovation in medical science and an increase in life expectancy we can demand more research into this topic

Modeling storm water control operated by green roofs at the urban catchment scale

The urban catchment of Colle Ometti, in the town of Genoa, Italy, where storm water runoff is monitored for both quantity and quality, was selected as a test site for the hydrologic modelling of greening scenarios. Although no green roof installations are now present in the area, this study modelled \u2013 using extensive green roof details \u2013 the hydrologic effects of three hypothetical roof greenin scenarios at the catchment scale (conversion of 10%, 20%, and 100% impervious to green roofs). The modelling of green roof performances was undertaken using the EPA SWMM and was calibrated and validated on a small size green roof system completed in September 2007 in the laboratory of the Department of Civil, Environmental and Architectural Engineering (DICAT \u2013 University of Genoa). Precipitation scenarios were developed based on eighteen years of high resolution (one minute) rain gauge data in Genoa (1990-2007).Hydrologic modelling demonstrated that widespread green roof implementation can significantly reduce peak runoff rates and the lag time (7min and 15 min) runoff volume (detention effect) while after introducing the drying process operated by evapo-traspiration during the inter-event period the runoff volume reduction at the event scale (retention effect) can also be appreciated

Multimodal approach of advanced gastric cancer: Based therapeutic algorithm

Gastric cancer (GC) is the third leading cause of cancer death in both sexes worldwide, with the highest estimated mortality rates in Eastern Asia and the lowest in Northern America. However, the availability of modern treatment has improved the survival and the prognosis is often poor due to biological characteristics of the disease. In oncology, we are living in the "Era" of target treatment and, to know biological aspects, prognostic factors and predictive response informations to therapy in GC is mandatory to apply the best strategy of treatment. The purpose of this review, according to the recently published English literature, is to summarize existing data on prognostic aspects and predictive factors to response to therapy in GC and to analyze also others therapeutic approaches (surgery and radiotherapy) in locally, locally advanced and advanced GC. Moreover, the multidisciplinary approach (chemotherapy, surgery and radiotherapy) can improve the prognosis of GC

Pharmacology and toxicology of xylazine: quid novum?

The current opioid overdose crisis is characterized by the presence of unknown psychoactive adulterants. Xylazine is an alpha-2 receptor agonist that is not approved for human use but is commonly used in veterinary medicine due to its sedative and muscle-relaxant properties. Cases of human intoxication due to accidental or voluntary use have been reported since the 1980s. However, reports of adulteration of illicit opioids (heroin and illicit fentanyl) with xylazine have been increasing all over Western countries. In humans, xylazine causes respiratory depression, bradycardia, and hypotension-posing individuals, using xylazine-adulterated opioids. We present a narrative review of the latest intoxication cases related to xylazine, to bring awareness to readers and also to help pathologists to detect and deal with xylazine cases

The role of integrative and complementary medicine in the management of breast cancer patients on behalf of the Integrative Medicine Research Group (IMRG)

The aim of this conference was to explain the role of integrative and complementary medicine in breast cancer patients. The topics covered are numerous and their peculiarities are the multidisciplinary characteristics of the researchers involved. The Integrative Medicine Research Group (IMRG) believes in the complementary and integrative approach in cancer patients to improve the quality of life in this particular setting

Prion protein conversion at two distinct cellular sites precedes fibrillisation

The self-templating nature of prions plays a central role in prion pathogenesis and is associated with infectivity and transmissibility. Since propagation of proteopathic seeds has now been acknowledged a principal pathogenic process in many types of dementia, more insight into the molecular mechanism of prion replication is vital to delineate specific and common disease pathways. By employing highly discriminatory anti-PrP antibodies and conversion-tolerant PrP chimera, we here report that de novo PrP conversion and formation of fibril-like PrP aggregates are distinct in mechanistic and kinetic terms. De novo PrP conversion occurs within minutes after infection at two subcellular locations, while fibril-like PrP aggregates are formed exclusively at the plasma membrane, hours after infection. Phenotypically distinct pools of abnormal PrP at perinuclear sites and the plasma membrane show differences in N-terminal processing, aggregation state and fibril formation and are linked by exocytic transport via synaptic and large-dense core vesicles