Minerva and minepy: a C engine for the MINE suite and its R, Python and MATLAB wrappers

We introduce a novel implementation in ANSI C of the MINE family of algorithms for computing maximal information-based measures of dependence between two variables in large datasets, with the aim of a low memory footprint and ease of integration within bioinformatics pipelines. We provide the libraries minerva (with the R interface) and minepy for Python, MATLAB, Octave and C++. The C solution reduces the large memory requirement of the original Java implementation, has good upscaling properties, and offers a native parallelization for the R interface. Low memory requirements are demonstrated on the MINE benchmarks as well as on large (n=1340) microarray and Illumina GAII RNA-seq transcriptomics datasets. Availability and Implementation: Source code and binaries are freely available for download under GPL3 licence at http://minepy.sourceforge.net for minepy and through the CRAN repository http://cran.r-project.org for the R package minerva. All software is multiplatform (MS Windows, Linux and OSX).Comment: Bioinformatics 2012, in pres

Multi-Word Expressions in spoken language: PoliSdict

The term multiword expressions (MWEs) is referred-to a group of words with a unitary meaning, not inferred from that of the words that compose it, both in current use and in technical-specialized languages. In this paper, we describe PoliSdict an Italian electronic dictionary composed of multi-word expressions (MWEs) automatically extracted from a multimodal corpus grounded on political speech language, currently being developed at the "Maurice Gross" Laboratory of the Department of Political Sciences, Social and Communication of the University of Salerno, thanks to a loan from the company Network Contacts. We introduce the methodology of creation and the first results of a systematic analysis which considered terminological labels, frequency labels, recurring syntactic patterns, further proposing an associated ontology.Con il termine polirematica si fa generalmente riferimento ad un gruppo di parole con significato unitario, non desumibile da quello delle parole che lo compongono, sia nell’uso corrente sia in linguaggi tecnico-specialistici. In questo contributo viene presentato PoliSdict un dizionario elettronico in lingua italiana composto da espressioni polirematiche occorrenti nel parlato spontaneo estratte a partire da un corpus multimodale di dominio politico in lingua italiana in corso di ampliamento presso il Laboratorio “Maurice Gross” del Dipartimento di Scienze Politiche, Sociali e della Comunicazione dell’Università degli Studi di Salerno, grazie a un finanziamento della società Network Contacts. Viene presentata la metodologia di creazione ed i primi risultati di un'analisi sistematica che ha considerato etichette terminologiche, marche d'uso e pattern ricorrenti, proponendo infine un’ontologia associata

A workflow to generate physical 3D models of cerebral aneurysms applying open source freeware for CAD modeling and 3D printing

Objectives: 3D anatomical models are becoming a new frontier in surgery for planning and simulation on an individualized patient specific basis. Since 1999, 3D cerebral aneurysms models for neurosurgery have been proposed. The possibility of reproducing in a realistic 3D fashion the malformation with the surrounding vascular structures, provides important preoperative information for the treatment strategy. The same models can be used for training and teaching.Unfortunately stereolitography is often burdened by high costs and long times of production. These factors limit the possibility to use 3D models to plan surgeries in an easy daily fashion. Patients and methods: Our study enrolled 5 patients harboring cerebral aneurysms. DICOM data of each aneurysm were elaborated by an open source freeware to obtain CAD molds. Afterwards, the 3D models were produced using a fused deposition or a stereolitography printer. Results: Models were evaluated by Neurosurgeons in terms of quality and usefulness for surgical planning. Costs and times of production were recorded. Conclusions: Models were reliable, economically affordable and quick to produce. Keywords: Stereolitography, Cerebral aneurysms, 3D printing, Surgical planning, Aneurysm model

Transcatheter aortic valve implantation with the novel-generation Navitor device. Procedural and early outcomes

Transcatheter aortic valve implantation (TAVI) has proved beneficial in patients with severe aortic stenosis, especially when second-generation devices are used. We aimed at reporting our experience with Navitor, a third-generation device characterized by intrannular, large cell, and cuffed design, as well as high deliverability and minimization of paravalvular leak. Between June and December 2021, a total of 39 patients underwent TAVI with Navitor, representing 20% of all TAVI cases. Mean age was 80.0 +/- 6.7 years, and 14 (36.8%) women were included. Severe aortic stenosis was the most common indication to TAVI (37 [97.4%] cases), whereas 2 (5.3%) individuals were at low surgical risk. Device and procedural success was obtained in all patients, with a total hospital stay of 6.6 +/- 4.5 days. One (2.9%) patient required permanent pacemaker implantation, but no other hospital events occurred. At 1-month follow-up, a cardiac death was adjudicated in an 87-year-old man who had been at high surgical risk. Echocardiographic follow-up showed no case of moderate or severe aortic regurgitation, with mild regurgitation in 18 (47%), and none or trace regurgitation in 20 (53%). The Navitor device, thanks to its unique features, is a very promising technology suitable to further expand indications and risk-benefit profile of TAVI

Bleeding risk evaluation in cerebral cavernous malformation, the role of medications, and hemorrhagic factors: a case-control study

Objective: Cerebral cavernous malformations (CCMs) are vascular lesions with an overall risk of rupture from 2% to 6% per year, which is associated with significant morbidity and mortality. The diagnostic incidence is increasing, so it is of paramount importance to stratify patients based on their risk of rupture. Data in the literature seem to suggest that specific medications, particularly antithrombotic and cardiovascular agents, are associated with a reduced risk of bleeding. However, the effect of the patient coagulative status on the cumulative bleeding risk remains unclear. The aim of this study was to assess the impact of different radiological, clinical, and pharmacological factors on the bleeding risk of CCMs and to assess the predictive power of an already validated scale for general bleeding risk, the HAS-BLED (hypertension, abnormal renal/liver function, stroke, bleeding history or predisposition, labile international normalized ratio, elderly, drugs/alcohol concomitantly). Method: This was a multicenter retrospective observational study. The authors collected imaging, clinical status, and therapy data on patients with bleeding and nonbleeding CCMs. Univariate analysis and subsequent multivariate logistic regression were performed between the considered variables and bleeding or nonbleeding status to identify potential independent predictors of bleeding. Results: The authors collected data on 257 patients (46.7% male, 25.3% with bleeding CCMs). Compared with patients with nonbleeding lesions, those with bleeding CCMs were younger, less frequently had hypertension, and less frequently required antiplatelet drugs and beta-blockers (all p < 0.05). Bleeding lesions, however, had significantly higher median volumes (1050 mm3 vs 523 mm3 , p < 0.001). On multivariate analyses, after adjusting for age, history of hypertension and diabetes, and use of antiplatelet drugs or beta-blockers, lesion volume ≥ 300 mm3 was the only significant predictor of bleeding (adjusted OR 3.11, 95% CI 1.09-8.86). When the diagnostic accuracy of different volume thresholds was explored, volume ≥ 300 mm3 showed a limited sensitivity (36.7%, 95% CI 24.6%-50.0%), but a high specificity 78.2% (95% CI 71.3%-84.2%), with an area under the curve of 0.57 (95% CI 0.51-0.64). Conclusions: This study supports previous findings that the CCM volume is the only factor influencing the bleeding risk. Antithrombotic agents and propranolol seem to have a protective role against the bleeding events. A high HAS-BLED score was not associated with an increased bleeding risk. Further studies are needed to confirm these results

Symmetries and exponential error reduction in Yang-Mills theories on the lattice

The partition function of a quantum field theory with an exact symmetry can be decomposed into a sum of functional integrals each giving the contribution from states with definite symmetry properties. The composition rules of the corresponding transfer matrix elements can be exploited to devise a multi-level Monte Carlo integration scheme for computing correlation functions whose numerical cost, at a fixed precision and at asymptotically large times, increases power-like with the time extent of the lattice. As a result the numerical effort is exponentially reduced with respect to the standard Monte Carlo procedure. We test this strategy in the SU(3) Yang--Mills theory by evaluating the relative contribution to the partition function of the parity odd states.Comment: 18 pages, 4 figures. Few typos corrected, data sets added, Appendix A added. To appear on Comput. Phys. Commu

Long-term outcome of subthalamic nucleus DBS in Parkinson's disease: from the advanced phase towards the late stage of the disease?

Deep Brain Stimulation of the Subthalamic Nucleus (STN-DBS) is an effective treatment for Parkinson's disease (PD), but only few studies investigated its long-term efficacy. Furthermore, little is known about the role of PD-subtype on STN-DBS long-term outcome

HQET at order 1/m1/m: II. Spectroscopy in the quenched approximation

Using Heavy Quark Effective Theory with non-perturbatively determined parameters in a quenched lattice calculation, we evaluate the splittings between the ground state and the first two radially excited states of the $B_s$ system at static order. We also determine the splitting between first excited and ground state, and between the $B_s^*$ and $B_s$ ground states to order $1/m_b$. The Generalized Eigenvalue Problem and the use of all-to-all propagators are important ingredients of our approach.Comment: (1+18) pages, 3 figures (4 pdf files); pdflatex; v2: corrections to table 1, results unaffecte