Investigating bias in semantic similarity measures for analysis of protein interactions

Protein interactions are fundamental blocks of almost all cellular processes, so the study of the set of protein interactions in a single organism (also referred to as Protein Interaction Networks - PIN) is an important step in the comprehension of mechanism at molecular level. Recently, the possibility to annotate such data using Gene Ontology and the consequent use of ontology-based analysis has been exploited, e.g. the use of semantic similarity (SS) measures. Whereas, SS measures present many challenges and different issues that have to be faced. In particular SS measures are affected from three main biases: i) annotation length, ii) evidence codes, and iii) shallow annotation. The common cause of such biases are the structure of GO and the corpora of annotations (GOA). Consequently, the impact of this variability has to be considered when developing novel algorithms for protein interactions analysis. Although the criticality of these aspects, there is a lack in the systematic analysis of the bias. Few works dealt with the three sources of bias most affecting SS measures. This paper demonstrates the existence of the bias that affect main SS on a set of well-known yeast complexes. It also provides some evidences about the variability of the bias effects over the proteome

Progress in CTEQ-TEA PDF analysis

Recent developments in the CTEQ-TEA global QCD analysis are presented. The parton distribution functions CT10-NNLO are described, constructed by comparing data from many experiments to NNLO approximations of QCD.Comment: 4 pages, 3 figures; contribution to the Proceedings of the XX Workshop on Deep Inelastic Scattering and Related Subjects, Bonn, Germany, 26-30 March, 201

CTEQ-TEA parton distribution functions with intrinsic charm

The possibility of a (sizable) nonperturbative contribution to the charm parton distribution function (PDF) in a nucleon is investigated together with theoretical issues arising in its interpretation. Results from the global PDF analysis are presented. The separation of the universal component of the nonperturbative charm from the rest of the radiative contributions is discussed and the potential impact of a nonperturbative charm PDF on LHC scattering processes is illustrated. An estimate of nonperturbative charm magnitude in the CT14 and CT14HERA2 global QCD analyses at the next-to-next-to leading order (NNLO) in the QCD coupling strength is given by including the latest experimental data from HERA and the Large Hadron Collider (LHC). A comparison between different models of intrinsic charm is shown and prospects for standard candle observables at the LHC are illustrated.Comment: 7 pages, 2 figures. Conference Proceedings of CIPANP2018, 13th Conference on the Intersections of Particle and Nuclear Physics, May 29 - June 3, 2018 Palm Springs, CA. Based on arXiv: 1707.00657, published in JHEP 1802 (2018) 05

CTEQ-TEA parton distribution functions and HERA Run I and II combined data

We analyze the impact of the recent HERA run I+II combination of inclusive deep inelastic scattering cross-section data on the CT14 global analysis of PDFs. New PDFs at NLO and NNLO, called CT14$_{\textrm{HERA2}}$, are obtained by a refit of the CT14 data ensembles, in which the HERA run I combined measurements are replaced by the new HERA run I+II combination. The CT14 functional parametrization of PDFs is flexible enough to allow good descriptions of different flavor combinations, so we use the same parametrization for CT14$_{\textrm{HERA2}}$ but with an additional shape parameter for describing the strange quark PDF. We find that the HERA I+II data can be fit reasonably well, and both CT14 and CT14$_{\textrm{HERA2}}$ PDFs can describe equally well the non-HERA data included in our global analysis. Because the CT14 and CT14$_{\textrm{HERA2}}$ PDFs agree well within the PDF errors, we continue to recommend CT14 PDFs for the analysis of LHC Run 2 experiments.Comment: 19 pages, 6 figures and 3 table

Molecular mechanisms of the acute kidney injury to chronic kidney disease transition: An updated view

Increasing evidence has demonstrated the bidirectional link between acute kidney injury (AKI) and chronic kidney disease (CKD) such that, in the clinical setting, the new concept of a unified syndrome has been proposed. The pathophysiological reasons, along with the cellular and molecular mechanisms, behind the ability of a single, acute, apparently self-limiting event to drive chronic kidney disease progression are yet to be explained. This acute injury could promote progression to chronic disease through different pathways involving the endothelium, the inflammatory response and the development of fibrosis. The interplay among endothelial cells, macrophages and other immune cells, pericytes and fibroblasts often converge in the tubular epithelial cells that play a central role. Recent evidence has strengthened this concept by demonstrating that injured tubules respond to acute tubular necrosis through two main mechanisms: The polyploidization of tubular cells and the proliferation of a small population of self-renewing renal progenitors. This alternative pathophysiological interpretation could better characterize functional recovery after AKI