Data Mining Approaches to Diffuse Large B–Cell Lymphoma Gene Expression Data Interpretation

This paper presents a comprehensive study of gene expression patterns originating from a diffuse large B–cell lymphoma (DLBCL) database. It focuses on the implementation of feature selection and classification techniques. Thus, it firstly tackles the identification of relevant genes for the prediction of DLBCL types. It also allows the determination of key biomarkers to differentiate two subtypes of DLBCL samples: Activated B–Like and Germinal Centre B–Like DLBCL. Decision trees provide knowledge–based models to predict types and subtypes of DLBCL. This research suggests that the data may be insufficient to accurately predict DLBCL types or even detect functionally relevant genes. However, these methods represent reliable and understandable tools to start thinking about possible interesting non–linear interdependencies

Analysis of correlation-based biomolecular networks from different omics data by fitting stochastic block models

Background: Biological entities such as genes, promoters, mRNA, metabolites or proteins do not act alone, but in concert in their network context. Modules, i.e., groups of nodes with similar topological properties in these networks characterize important biological functions of the underlying biomolecular system. Edges in such molecular networks represent regulatory and physical interactions, and comparing them between conditions provides valuable information on differential molecular mechanisms. However, biological data is inherently noisy and network reduction techniques can propagate errors particularly to the level of edges. We aim to improve the analysis of networks of biological molecules by deriving modules together with edge relevance estimations that are based on global network characteristics. Methods: The key challenge we address here is investigating the capability of stochastic block models (SBMs) for representing and analyzing different types of biomolecular networks. Fitting them to SBMs both delivers modules of the networks and enables the derivation of edge confidence scores, and it has not yet been investigated for analyzing biomolecular networks. We apply SBM-based analysis independently to three correlation-based networks of breast cancer data originating from high-throughput measurements of different molecular layers: either transcriptomics, proteomics, or metabolomics. The networks were reduced by thresholding for correlation significance or by requirements on scale-freeness. Results and discussion: We find that the networks are best represented by the hierarchical version of the SBM, and many of the predicted blocks have a biologically and phenotypically relevant functional annotation. The edge confidence scores are overall in concordance with the biological evidence given by the measurements. We conclude that biomolecular networks can be appropriately represented and analyzed by fitting SBMs. As the SBM-derived edge confidence scores are based on global network connectivity characteristics and potential hierarchies within the biomolecular networks are considered, they could be used as additional, integrated features in network-based data comparisons

An effective non-parametric method for globally clustering genes from expression profiles

Clustering is widely used in bioinformatics to find gene correlation patterns. Although many algorithms have been proposed, these are usually confronted with difficulties in meeting the requirements of both automation and high quality. In this paper, we propose a novel algorithm for clustering genes from their expression profiles. The unique features of the proposed algorithm are twofold: it takes into consideration global, rather than local, gene correlation information in clustering processes; and it incorporates clustering quality measurement into the clustering processes to implement non-parametric, automatic and global optimal gene clustering. The evaluation on simulated and real gene data sets demonstrates the effectiveness of the algorithm. <br /

Integrated Ugi-Based Assembly of Functionally, Skeletally, and Stereochemically Diverse 1,4-Benzodiazepin-2-ones

A practical, integrated and versatile U-4CR-based assembly of 1,4-benzodiazepin-2-ones exhibiting functionally, skeletally, and stereochemically diverse substitution patterns is described. By virtue of its convergence, atom economy, and bond-forming efficiency, the methodology documented herein exemplifies the reconciliation of structural complexity and experimental simplicity in the context of medicinal chemistry projects.This work was financially supported by the Galician Government (Spain), Projects: 09CSA016234PR and GPC-2014-PG037. J.A. thanks FUNDAYACUCHO (Venezuela) for a predoctoral grant and Deputación da Coruña (Spain) for a postdoctoral research grant. A.N.-V. thanks the Spanish government for a Ramón y Cajal research contract

NEON terrestrial field observations: designing continental-scale, standardized sampling.

Rapid changes in climate and land use and the resulting shifts in species distributions and ecosystem functions have motivated the development of the National Ecological Observatory Network (NEON). Integrating across spatial scales from ground sampling to remote sensing, NEON will provide data for users to address ecological responses to changes in climate, land use, and species invasion across the United States for at least 30 years. Although NEON remote sensing and tower sensor elements are relatively well known, the biological measurements are not. This manuscript describes NEON terrestrial sampling, which targets organisms across a range of generation and turnover times, and a hierarchy of measurable biological states. Measurements encompass species diversity, abundance, phenology, demography, infectious disease, ecohydrology, and biogeochemistry. The continental-scale sampling requires collection of comparable and calibrated data using transparent methods. Data will be publicly available in a variety of formats and suitable for integration with other long-term efforts. NEON will provide users with the data necessary to address large-scale questions, challenge current ecological paradigms, and forecast ecological change

Stab Injury to the Preauricular Region With Laceration of the External Carotid Artery Without Involvement of the Facial Nerve: a Case Report

BACKGROUND: Open injuries to the face involving the external carotid artery are uncommon. These injuries are normally associated with laceration of the facial nerve because this nerve is more superficial than the external carotid artery. Hence, external carotid artery lesions are usually associated with facial nerve dysfunction. We present an unusual case report in which the patient had an injury to this artery with no facial nerve compromise. CASE PRESENTATION: A 25-year-old Portuguese man sustained a stab wound injury to his right preauricular region with a broken glass. Immediate profuse bleeding ensued. Provisory tamponade of the wound was achieved at the place of aggression by two off-duty doctors. He was initially transferred to a district hospital, where a large arterial bleeding was observed and a temporary compressive dressing was applied. Subsequently, the patient was transferred to a tertiary hospital. At admission in the emergency room, he presented a pulsating lesion in the right preauricular region and slight weakness in the territory of the inferior buccal branch of the facial nerve. The physical examination suggested an arterial lesion superficial to the facial nerve. However, in the operating theater, a section of the posterior and lateral flanks of the external carotid artery inside the parotid gland was identified. No lesion of the facial nerve was observed, and the external carotid artery was repaired. To better understand the anatomical rationale of this uncommon clinical case, we dissected the preauricular region of six cadavers previously injected with colored latex solutions in the vascular system. A small triangular space between the two main branches of division of the facial nerve in which the external carotid artery was not covered by the facial nerve was observed bilaterally in all cases. CONCLUSIONS: This clinical case illustrates that, in a preauricular wound, the external carotid artery can be injured without facial nerve damage. However, no similar description was found in the reviewed literature, which suggests that this must be a very rare occurrence. According to the dissection study performed, this is due to the existence of a triangular space between the cervicofacial and temporofacial nerve trunks in which the external carotid artery is not covered by the facial nerve or its branches.info:eu-repo/semantics/publishedVersio

User relationship classification of facebook messenger mobile data using WEKA

© Springer Nature Switzerland AG 2018. Mobile devices are a wealth of information about its user and their digital and physical activities (e.g. online browsing and physical location). Therefore, in any crime investigation artifacts obtained from a mobile device can be extremely crucial. However, the variety of mobile platforms, applications (apps) and the significant size of data compound existing challenges in forensic investigations. In this paper, we explore the potential of machine learning in mobile forensics, and specifically in the context of Facebook messenger artifact acquisition and analysis. Using Quick and Choo (2017)’s Digital Forensic Intelligence Analysis Cycle (DFIAC) as the guiding framework, we demonstrate how one can acquire Facebook messenger app artifacts from an Android device and an iOS device (the latter is, using existing forensic tools. Based on the acquired evidence, we create 199 data-instances to train WEKA classifiers (i.e. ZeroR, J48 and Random tree) with the aim of classifying the device owner’s contacts and determine their mutual relationship strength