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A data-driven, knowledge-based approach to biomarker discovery: application to circulating microRNA markers of colorectal cancer prognosis
Get PDF© The Author(s) 2018. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.Recent advances in high-throughput technologies have provided an unprecedented opportunity to identify molecular markers of disease processes. This plethora of complex-omics data has simultaneously complicated the problem of extracting meaningful molecular signatures and opened up new opportunities for more sophisticated integrative and holistic approaches. In this era, effective integration of data-driven and knowledge-based approaches for biomarker identification has been recognised as key to improving the identification of high-performance biomarkers, and necessary for translational applications. Here, we have evaluated the role of circulating microRNA as a means of predicting the prognosis of patients with colorectal cancer, which is the second leading cause of cancer-related death worldwide. We have developed a multi-objective optimisation method that effectively integrates a data-driven approach with the knowledge obtained from the microRNA-mediated regulatory network to identify robust plasma microRNA signatures which are reliable in terms of predictive power as well as functional relevance. The proposed multi-objective framework has the capacity to adjust for conflicting biomarker objectives and to incorporate heterogeneous information facilitating systems approaches to biomarker discovery. We have found a prognostic signature of colorectal cancer comprising 11 circulating microRNAs. The identified signature predicts the patients’ survival outcome and targets pathways underlying colorectal cancer progression. The altered expression of the identified microRNAs was confirmed in an independent public data set of plasma samples of patients in early stage vs advanced colorectal cancer. Furthermore, the generality of the proposed method was demonstrated across three publicly available miRNA data sets associated with biomarker studies in other diseases
Review of Biopolitics and Memory in Postcolonial Literature and Culture by Michael R. Griffiths
No full textReview of Biopolitics and Memory in Postcolonial Literature and Culture by Michael R. Griffith
Outcomes of Older Patients (≥ 70 Years) Treated With Targeted Therapy in Metastatic Chemorefractory Colorectal Cancer: Retrospective Analysis of NCIC CTG CO.17 and CO.20
Get PDF© 2018 Elsevier Inc. This manuscript version is made available under the CC-BY-NC-ND 4.0 license:
http://creativecommons.org/licenses/by-nc-nd/4.0/
This author accepted manuscript is made available following 12 month embargo from date of publication (November 2018) in accordance with the publisher’s archiving policyBackground
The safety and efficacy of targeted therapy in older patients (≥ 70 years) with metastatic colorectal cancer is not well evaluated.
Patients and Methods
Outcomes of older patients (including overall survival [OS], progression-free survival [PFS], toxicity, and quality of life [QoL]) were compared to young patients using data from 2 large previously reported clinical trials, CO.17 (cetuximab vs. best supportive care) and CO.20 (cetuximab plus placebo vs. cetuximab plus brivanib). Only patients with wild-type KRAS tumors were included.
Results
A total of 251 (26.3%) of 955 patients were ≥ 70 years old. No significant differences in OS, PFS, or grade 3/4 adverse events were observed between older and younger patients treated with cetuximab (or cetuximab with placebo) in either trial. Younger patients trended toward superior OS in both CO.17 (hazard ratio = 1.80; P = .16) and CO.20 (hazard ratio = 1.34; P = .07). QoL maintenance favored younger patients in CO.17 (3.6 vs. 5.7 months; P = .046) but no difference of QoL maintenance was observed in the larger CO.20 trial (1.7 vs. 1.8 months; P = .64). Combination therapy of cetuximab and brivanib was significantly more toxic in older adults (87% vs. 77%; P = .03).
Conclusion
OS, PFS, and toxicities were similar between older and younger patients with wild-type KRAS metastatic colorectal cancer when treated with cetuximab. Both age groups likely experience similar QoL maintenance with cetuximab. Dual targeted therapy was significantly more toxic in older patients
Late presentation for HIV care in Southwest Ethiopia in 2003–2015: prevalence, trend, outcomes and risk factors
Get PDF© The Author(s). 2018 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0
International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and
reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to
the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver
(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise statedBackground
Early presentation for HIV care is vital as an initial tread in the UNAIDS 90–90–90 targets. However, late presentation for HIV care (LP) challenges achieving the targets. This study assessed the prevalence, trends, outcomes and risk factorsfor LP.
Methods
A 12 year retrospective cohort study was conducted using electronic medical records extracted from an antiretroviral therapy (ART) clinic at Jimma University Teaching Hospital. LP for children refers to moderate or severe immune-suppression, or WHO clinical stage 3 or 4 at the time of first presentation to the ART clinics. LP for adults refers to CD4 lymphocyte count of < 200 cells/ μl and < 350 cells/μl irrespective of clinical staging, or WHO clinical stage 3 or 4 irrespective of CD4 count at the time of first presentation to the ART clinics. Binary logistic regression was used to identify factors that were associated with LP, and missing data were handled using multiple imputations.
Results
Three hundred ninety-nine children and 4900 adults were enrolled in ART care between 2003 and 15. The prevalence of LP was 57% in children and 66.7% in adults with an overall prevalence of 65.5%, and the 10-year analysis of LP showed upward trends. 57% of dead children, 32% of discontinued children, and 97% of children with immunological failure were late presenters for HIV care. Similarly, 65% of dead adults, 65% of discontinued adults, and 79% of adults with immunological failure presented late for the care. Age between 25- < 50 years (AOR = 0.4,95% CI:0.3–0.6) and 50+ years (AOR = 0.4,95% CI:0.2–0.6), being female (AOR = 1.2, 95% CI: 1.03–1.5), having Tb/HIV co-infection (AOR = 1.6, 95% CI: 1.09–2.1), having no previous history of HIV testing (AOR = 1.2, 95% CI: 1.1–1.4), and HIV care enrollment period in 2012 and after (AOR = 0.8, 95% CI: 0.7–0.9) were the factors associated with LP for Adults. For children, none of the factors were associated with LP.
Conclusions
The prevalence of LP was high in both adults and children. The majority of both children and adults who presented late for HIV care had died and developed immunological failure. Effective programs should be designed and implemented to tackle the gap in timely HIV care engagement.
Protective Effects of Hydroxychloroquine against Accelerated Atherosclerosis in Systemic Lupus Erythematosus
Get PDFThis is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Cardiovascular (CV) morbidity and mortality are a challenge in management of patients with systemic lupus erythematosus (SLE). Higher risk of CV disease in SLE patients is mostly related to accelerated atherosclerosis. Nevertheless, high prevalence of traditional cardiovascular risk factors in SLE patients does not fully explain the increased CV risk. Despite the pathological bases of accelerated atherosclerosis are not fully understood, it is thought that this process is driven by the complex interplay between SLE and atherosclerosis pathogenesis. Hydroxychloroquine (HCQ) is a cornerstone in treatment of SLE patients and has been thought to exert a broad spectrum of beneficial effects on disease activity, prevention of damage accrual, and mortality. Furthermore, HCQ is thought to protect against accelerated atherosclerosis targeting toll-like receptor signaling, cytokine production, T-cell and monocyte activation, oxidative stress, and endothelial dysfunction. HCQ was also described to have beneficial effects on traditional CV risk factors, such as dyslipidemia and diabetes. In conclusion, despite lacking randomized controlled trials unambiguously proving the protection of HCQ against accelerated atherosclerosis and incidence of CV events in SLE patients, evidence analyzed in this review is in favor of its beneficial effect
Continental-scale animal tracking reveals functional movement classes across marine taxa
Get PDFOpen Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.Acoustic telemetry is a principle tool for observing aquatic animals, but coverage over large spatial scales remains a challenge. To resolve this, Australia has implemented the Integrated Marine Observing System’s Animal Tracking Facility which comprises a continental-scale hydrophone array and coordinated data repository. This national acoustic network connects localized projects, enabling simultaneous monitoring of multiple species over scales ranging from 100 s of meters to 1000 s of kilometers. There is a need to evaluate the utility of this national network in monitoring animal movement ecology, and to identify the spatial scales that the network effectively operates over. Cluster analyses assessed movements and residency of 2181 individuals from 92 species, and identified four functional movement classes apparent only through aggregating data across the entire national network. These functional movement classes described movement metrics of individuals rather than species, and highlighted the plasticity of movement patterns across and within populations and species. Network analyses assessed the utility and redundancy of each component of the national network, revealing multiple spatial scales of connectivity influenced by the geographic positioning of acoustic receivers. We demonstrate the significance of this nationally coordinated network of receivers to better reveal intra-specific differences in movement profiles and discuss implications for effective management
Novel pressure-impedance parameters for evaluating esophageal function in pediatric achalasia
Get PDFObjective: In achalasia, absent peristalsis and reduced esophagogastric junction (EGJ) relaxation and compliance underlie dysphagia symptoms. Novel high-resolution impedance manometry variables, that is, bolus presence time (BPT) and trans-EGJ-bolus flow time (BFT) have been developed to estimate the duration of EGJ opening and trans-EGJ bolus flow. The aim of this study was to evaluate esophageal motor function and bolus flow in children diagnosed with achalasia using these variables.
Methods: High-resolution impedance manometry recordings from 20 children who fulfilled the Chicago Classification (V3) criteria for achalasia were compared with recordings of 15 children with normal esophageal high-resolution manometry findings and no other evidence suggestive of achalasia. Matlab-based analysis software was used to calculate BPT and BFT.
Results: Both BPT and BFT were significantly reduced in achalasia patients compared with children with normal esophageal motility (BPT 3.3 s vs 5.1 s P < 0.01; BFT 1.4 s vs 4.3 s P < 0.001). BFT was significantly lower than BPT (achalasia difference 1.9 s ± 1.3 s, P = 0.001 and normal difference 0.9 ± 0.3 s, P = 0.001). Overall, there was a significant correlation between BPT and BFT (r = 0.825, P < 0.001). We observed a 2-way differentiation of achalasia patients; those in whom the BPT and BFT were proportional, but significantly lower than in patients with normal peristalsis, and those in whom BFT was disproportionately lower than BPT.
Conclusions: Calculation of BPT and BFT may help determine whether esophageal bolus transport to the EGJ and/or esophageal emptying through the EGJ are aberrant. For achalasia, this may detect flow resistance at the EGJ, potentially improving both diagnosis and objective assessment of therapeutic effects