scholarly journals Semalytics: a semantic analytics platform for the exploration of distributed and heterogeneous cancer data in translational research

Database ◽  
2019 ◽  
Vol 2019 ◽  
Author(s):  
Andrea Mignone ◽  
Alberto Grand ◽  
Alessandro Fiori ◽  
Enzo Medico ◽  
Andrea Bertotti
Keyword(s):  
Large Scale ◽  
Clinical Care ◽  
Predictive Biomarkers ◽  
Molecular Profile ◽  
Biological Traits ◽  
Semantic Web Technologies ◽  
Cancer Data ◽  
Molecular Features ◽  
Data Framework

Abstract Each cancer is a complex system with unique molecular features determining its dynamics, such as its prognosis and response to therapies. Understanding the role of these biological traits is fundamental in order to personalize cancer clinical care according to the characteristics of each patient’s disease. To achieve this, translational researchers propagate patients’ samples through in vivo and in vitro cultures to test different therapies on the same tumor and to compare their outcomes with the molecular profile of the disease. This in turn generates information that can be subsequently translated into the development of predictive biomarkers for clinical use. These large-scale experiments generate huge collections of hierarchical data (i.e. experimental trees) with relative annotations that are extremely difficult to analyze. To address such issues in data analyses, we came up with the Semalytics data framework, the core of an analytical platform that processes experimental information through Semantic Web technologies. Semalytics allows (i) the efficient exploration of experimental trees with irregular structures together with their annotations. Moreover, (ii) the platform links its data to a wider open knowledge base (i.e. Wikidata) to add an extended knowledge layer without the need to manage and curate those data locally. Altogether, Semalytics provides augmented perspectives on experimental data, allowing the generation of new hypotheses, which were not anticipated by the user a priori. In this work, we present the data core we created for Semalytics, focusing on its semantic nucleus and on how it exploits semantic reasoning and data integration to tackle issues of this kind of analyses. Finally, we describe a proof-of-concept study based on the examination of several dozen cases of metastatic colorectal cancer in order to illustrate how Semalytics can help researchers generate hypotheses about the role of genes alterations in causing resistance or sensitivity of cancer cells to specific drugs.

scholarly journals Cancer metabolic subtypes and their association with molecular and clinical features

2021 ◽  
Author(s):  
Enrico Moiso ◽  
Paolo Provero
Keyword(s):  
Clinical Data ◽  
Large Scale ◽  
Tumor Grade ◽  
Point Of View ◽  
General Point ◽  
Protein Abundance ◽  
Phenotypic Data ◽  
Cancer Subtypes ◽  
Molecular Features

Alteration of metabolic pathways in cancer has been investigated for many years, beginning way before the discovery of the role of oncogenes and tumor suppressors, and the last few years have witnessed a renewed interest in this topic. Large-scale molecular and clinical data on tens of thousands of samples allow us today to tackle the problem from a general point of view. Here we show that trancriptomic profiles of tumors can be exploited to define metabolic cancer subtypes, that can be systematically investigated for association with other molecular and clinical data. We find thousands of significant associations between metabolic subtypes and molecular features such as somatic mutations, structural variants, epigenetic modifications, protein abundance and activation; and with clinical/phenotypic data including survival probability, tumor grade, and histological types. Our work provides a methodological framework and a rich database of statistical associations, accessible from https://metaminer.unito.it, that will contribute to the understanding of the role of metabolic alterations in cancer and to the development of precision therapeutic strategies.

scholarly journals Environmental Factors Are Stronger Predictors of Primate Species’ Distributions Than Basic Biological Traits

2021 ◽  
Author(s):  
Katherine A. Williams ◽  
Helen D. Slater ◽  
Phillipa Gillingham ◽  
Amanda H. Korstjens
Keyword(s):  
Environmental Conditions ◽  
Environmental Variables ◽  
Large Scale ◽  
Species Distributions ◽  
Sub Saharan Africa ◽  
Primate Species ◽  
Biological Traits ◽  
Data Set ◽  
Environmental Processes

AbstractUnderstanding the neutral, biological, and environmental processes driving species distributions is valuable in informing conservation efforts because it will help us predict how species will respond to changes in environmental conditions. Environmental processes affect species differently according to their biological traits, which determine how they interact with their environment. Therefore, functional, trait-based modeling approaches are considered important for predicting distributions and species responses to change but even for data-rich primate communities our understanding of the relationships between traits and environmental conditions is limited. Here we use a large-scale, high-resolution data set of African diurnal primate distributions, biological traits, and environmental conditions to investigate the role of biological traits and environmental trait filtering in primate distributions. We collected data from published sources for 354 sites and 14 genera with 57 species across sub-Saharan Africa. We then combined a three-table ordination method, RLQ, with the fourth-corner approach to test relationships between environmental variables and biological traits and used a mapping approach to visually assess patterning in primate genus and species’ distributions. We found no significant relationships between any groups of environmental variables and biological traits, despite a clear role of environmental filtering in driving genus and species’ distributions. The most important environmental driver of species distributions was temperature seasonality, followed by rainfall. We conclude that the relative flexibility of many primate genera means that not any one particular set of traits drives their species–environment associations, despite the clear role of such associations in their distribution patterns.

The Role of Sense of Direction and Other Factors During Navigation in a Large-Scale, Unconstrained Environment

2013 ◽  
Author(s):  
Elisabeth J. Ploran ◽  
Ericka Rovira ◽  
James C. Thompson ◽  
Raja Parasuraman
Keyword(s):  
Large Scale ◽  
Sense Of Direction

Magnetic Properties of xCeO2•(50 − x) PbO•50B2O3 Glasses and Glass Ceramics

2017 ◽  
Vol 13 (1) ◽  
pp. 4486-4494 ◽  
Author(s):  
G.El Damrawi ◽  
F. Gharghar
Keyword(s):  
Magnetic Properties ◽  
Large Scale ◽  
Glass Ceramics ◽  
Magnetic Behavior ◽  
Crystal Formation ◽  
Dual Roles ◽  
Effective Agent ◽  
Ordered Structures ◽  
Essential Change

Cerium oxide in borate glasses of composition xCeO2·(50 − x)PbO·50B2O3 plays an important role in changing both microstructure and magnetic behaviors of the system. The structural role of CeO2 as an effective agent for cluster and crystal formation in borate network is clearly evidenced by XRD technique. Both structure and size of well-formed cerium separated clusters have an effective influence on the structural properties. The cluster aggregations are documented to be found in different range ordered structures, intermediate and long range orders are the most structures in which cerium phases are involved. The nano-sized crystallized cerium species in lead borate phase are evidenced to have magnetic behavior.  The criteria of building new specific borate phase enriched with cerium as ferrimagnetism has been found to keep the magnetization in large scale even at extremely high temperature. Treating the glass thermally or exposing it to an effective dose of ionized radiation is evidenced to have an essential change in magnetic properties. Thermal heat treatment for some of investigated materials is observed to play dual roles in the glass matrix. It can not only enhance alignment processes of the magnetic moment but also increases the capacity of the crystallite species in the magnetic phases. On the other hand, reverse processes are remarked under the effect of irradiation. The magnetization was found to be lowered, since several types of the trap centers which are regarded as defective states can be produced by effect of ionized radiation. 

The Impact of Quantitative Easing on Emerging Markets – Literature Review

e-Finanse ◽  
2018 ◽  
Vol 14 (4) ◽  
pp. 67-76
Author(s):  
Piotr Bartkiewicz
Keyword(s):  
Emerging Markets ◽  
Large Scale ◽  
Empirical Literature ◽  
Quantitative Easing ◽  
Methodological Choices ◽  
The Subject ◽  
Methodological Approaches ◽  
The Impact ◽  
Sufficient Precision

AbstractThe article presents the results of the review of the empirical literature regarding the impact of quantitative easing (QE) on emerging markets (EMs). The subject is of interest to policymakers and researchers due to the increasingly larger role of EMs in the world economy and the large-scale capital flows occurring after 2009. The review is conducted in a systematic manner and takes into consideration different methodological choices, samples and measurement issues. The paper puts the summarized results in the context of transmission channels identified in the literature. There are few distinct methodological approaches present in the literature. While there is a consensus regarding the direction of the impact of QE on EMs, its size and durability have not yet been assessed with sufficient precision. In addition, there are clear gaps in the empirical findings, not least related to relative underrepresentation of the CEE region (in particular, Poland).

Age Advantages of Emotional Experience during the COVID-19 Pandemic are Robust, but Diminished Compared to Pre-pandemic Conditions

2020 ◽  
Author(s):  
Rui Sun ◽  
Disa Sauter
Keyword(s):  
Older Adults ◽  
Large Scale ◽  
Negative Emotion ◽  
Emotional Experience ◽  
Negative Emotions ◽  
Older Individuals ◽  
Selection Strategies ◽  
Scale Test ◽  
Prolonged Stress

Getting old is generally seen as unappealing, yet aging confers considerable advantages in several psychological domains (North & Fiske, 2015). In particular, older adults are better off emotionally than younger adults, with aging associated with the so-called “age advantages,” that is, more positive and less negative emotional experiences (Carstensen et al., 2011). Although the age advantages are well established, it is less clear whether they occur under conditions of prolonged stress. In a recent study, Carstensen et al (2020) demonstrated that the age advantages persist during the COVID-19 pandemic, suggesting that older adults are able to utilise cognitive and behavioural strategies to ameliorate even sustained stress. Here, we build on Carstensen and colleagues’ work with two studies. In Study 1, we provide a large-scale test of the robustness of Carstensen and colleagues’ finding that older individuals experience more positive and less negative emotions during the COVID-19 pandemic. We measured positive and negative emotions along with age information in 23,629 participants in 63 countries in April-May 2020. In Study 2, we provide a comparison of the age advantages using representative samples collected before and during the COVID-19 pandemic. We demonstrate that older people experience less negative emotion than younger people during the prolonged stress of the COVID-19 pandemic. However, the advantage of older adults was diminished during the pandemic, pointing to a likely role of older adults use of situation selection strategies (Charles, 2010).

The changing role of GP clinicians working in community hospitals.

2018 ◽  
Vol 68 (suppl 1) ◽  
pp. bjgp18X696713
Author(s):  
David Seamark ◽  
Deborah Davidson ◽  
Helen Tucker ◽  
Angela Ellis-Paine ◽  
Jon Glasby
Keyword(s):  
Medical Care ◽  
Local Community ◽  
Community Hospital ◽  
Clinical Care ◽  
Hospital Setting ◽  
Community Hospitals ◽  
Recruitment Challenges ◽  
Acute Hospitals ◽  
Changing Role

BackgroundIn 2000 20% of UK GPs had admitting rights to community hospitals. In subsequent years the number of GPs engaged in community hospital clinical care has decreased.AimWhat models of medical care exist in English community hospitals today and what factors are driving changes?MethodInterviews with community hospital clinical staff conducted as part of a multimethod study of the community value of community hospitals.ResultsSeventeen interviews were conducted and two different models of medical care observed: GP led and Trust employed doctors. Factors driving changes were GP workload and recruitment challenges; increased medical acuity of patients admitted; fewer local patients being admitted; frustration over the move from ‘step-up’ care from the local community to ‘step-down’ care from acute hospitals; increased burden of GP medical support; inadequate remuneration; and GP admission rights removed due to bed closures or GP practices withdrawing from community hospital work.ConclusionMultiple factors have driven changes in the role of GP community hospital clinicians with a consequent loss of GP generalist skills in the community hospital setting. The NHS needs to develop a focused strategy if GPs are to remain engaged with community hospital care.

STEROID RECEPTOR PHENOTYPE, EXPRESSION OF HER-2/NEU, PD-1, PD-L1 AND LYMPHOCYTIC-MACROPHAGAL INFILTRATION OF ENDOMETRIAL CARCINOMAS: COMPARISON OF MODERN MOLECULAR BIOLOGICAL TYPES OF THE DISEASE (THE ROLE OF BODY MASS INDEX)

2020 ◽  
Vol 66 (1) ◽  
pp. 71-78
Author(s):  
Lev Bershteyn ◽  
Aleksandr Ivantsov ◽  
Aglaya Ievleva ◽  
A. Venina ◽  
I. Berlev
Keyword(s):  
Body Mass Index ◽  
Body Mass ◽  
Tumor Tissue ◽  
Immunohistochemical Analysis ◽  
The Body ◽  
Molecular Profile ◽  
Total N ◽  
Number Of Patients ◽  
Her 2

The aim of this study was to evaluate steroid receptors’ status of tumor tissue in different molecular biological types of endometrial cancer (EC), subdivided according to the current classification, and their colonization by lymphocytic and macrophage cells, taking into account body mass index of the patients. Materials and methods: Material from treatment-naive patients with EC (total n = 229) was included; the number of sick persons varied depending on the method used. The average age of patients was close to 60 years, and about 90% of them were postmenopausal. It was possible to divide the results of the work into two main subgroups: a) depending on the molecular biological type of the tumor (determined on the basis of genetic and immunohistochemical analysis), and b) depending on the value of the body mass index (BMI). The latter approach was used in patients with EC type demonstrating a defective mismatch repair of the incorrectly paired nucleotides (MMR-D) and with a type without characteristic molecular profile signs (WCMP), but was not applied (due to the smaller number of patients) in EC types with a POLE gene mutation or with expression of the oncoprotein p53. According to the data obtained, when comparing various types of EC, the lowest values of Allred ER and PR scores were revealed for POLE-mutant and p53 types, while the “triple-negative” variant of the tumor (ER-, PR-, HER2/neu-) was most common in POLE-mutant (45.5% of cases) and WCMP (19.4%) types of EC. The p53+ type of EC is characterized by inclination to the higher expression of the macrophage marker CD68 and lymphocytic Foxp3, as well as mRNA of PD-1 and SALL4. In addition to the said above, for WCMP type of EC is peculiar, on the contrary, a decrease in the expression of lymphocytic markers CD8 (protein) and PD-L1 (mRNA). When assessing the role of BMI, its value of >30.0 (characteristic for obesity) was combined with an inclination to the increase of HER-2/neu expression in the case of MMR-D EC type and to the decrease of HER-2 /neu, FOXp3 and ER expression in WCMP type. Conclusions: The accumulated information (mainly describing here hormonal sensitivity of the tumor tissue and its lymphocytic-macrophage infiltration) additionally confirms our earlier expressed opinion that the differences between women with EC are determined by both the affiliation of the neoplasm to one or another molecular biological type (subdivided according to the contemporary classification), as well as by body mass value and (very likely) the associated hormonal and metabolic attributes.

Legislative tools in the Czech watershed management policy

1996 ◽  
Vol 33 (4-5) ◽  
pp. 39-44
Author(s):  
J. Holas ◽  
M. Konvicková
Keyword(s):  
Watershed Management ◽  
Large Scale ◽  
Agricultural Practices ◽  
Farming System ◽  
Management Policy ◽  
Running Water ◽  
The Czech Republic ◽  
Law System ◽  
Water Quality Regulations

Potential environmental impacts as a result of large-scale farming system in the Czech Republic have created a great deal of concern in recent years. This concern has led to several studies to identify the role of new regulations, directives and other legislative issues in the field of water pollution control. The set of legislative tools related to watershed management policy to promote better agricultural practices is shortly reviewed. The paper emphasises the running water law system amendment with respect to European community water quality regulations.

Inflammatory Biomarkers in Atrial Fibrillation

2019 ◽  
Vol 26 (5) ◽  
pp. 837-854 ◽  
Author(s):  
Effimia Zacharia ◽  
Nikolaos Papageorgiou ◽  
Adam Ioannou ◽  
Gerasimos Siasos ◽  
Spyridon Papaioannou ◽  
...  
Keyword(s):  
Atrial Fibrillation ◽  
Plasma Levels ◽  
Large Scale ◽  
Inflammatory Biomarkers ◽  
Inflammatory Pathways ◽  
Inflammatory State ◽  
Anti Inflammatory ◽  
Underlying Mechanisms

During the last few years, a significant number of studies have attempted to clarify the underlying mechanisms that lead to the presentation of atrial fibrillation (AF). Inflammation is a key component of the pathophysiological processes that lead to the development of AF; the amplification of inflammatory pathways triggers AF, and, in tandem, AF increases the inflammatory state. Indeed, the plasma levels of several inflammatory biomarkers are elevated in patients with AF. In addition, the levels of specific inflammatory biomarkers may provide information regarding to the AF duration. Several small studies have assessed the role of anti-inflammatory treatment in atrial fibrillation but the results have been contradictory. Large-scale studies are needed to evaluate the role of inflammation in AF and whether anti-inflammatory medications should be routinely administered to patients with AF.

Sign in / Sign up

Export Citation Format

Share Document