Discovery and Preclinical Validation of Salivary Transcriptomic and Proteomic Biomarkers for the Non-Invasive Detection of Breast Cancer

A sensitive assay to identify biomarkers using non-invasively collected clinical specimens is ideal for breast cancer detection. While there are other studies showing disease biomarkers in saliva for breast cancer, our study tests the hypothesis that there are breast cancer discriminatory biomarkers in saliva using de novo discovery and validation approaches. This is the first study of this kind and no other study has engaged a de novo biomarker discovery approach in saliva for breast cancer detection. In this study, a case-control discovery and independent preclinical validations were conducted to evaluate the performance and translational utilities of salivary transcriptomic and proteomic biomarkers for breast cancer detection.Salivary transcriptomes and proteomes of 10 breast cancer patients and 10 matched controls were profiled using Affymetrix HG-U133-Plus-2.0 Array and two-dimensional difference gel electrophoresis (2D-DIGE), respectively. Preclinical validations were performed to evaluate the discovered biomarkers in an independent sample cohort of 30 breast cancer patients and 63 controls using RT-qPCR (transcriptomic biomarkers) and quantitative protein immunoblot (proteomic biomarkers). Transcriptomic and proteomic profiling revealed significant variations in salivary molecular biomarkers between breast cancer patients and matched controls. Eight mRNA biomarkers and one protein biomarker, which were not affected by the confounding factors, were pre-validated, yielding an accuracy of 92% (83% sensitive, 97% specific) on the preclinical validation sample set.Our findings support that transcriptomic and proteomic signatures in saliva can serve as biomarkers for the non-invasive detection of breast cancer. The salivary biomarkers possess discriminatory power for the detection of breast cancer, with high specificity and sensitivity, which paves the way for prediction model validation study followed by pivotal clinical validation

Rationale, study design, and analysis plan of the Alveolar Recruitment for ARDS Trial (ART): study protocol for a randomized controlled trial

BACKGROUND: Acute respiratory distress syndrome (ARDS) is associated with high in-hospital mortality. Alveolar recruitment followed by ventilation at optimal titrated PEEP may reduce ventilator-induced lung injury and improve oxygenation in patients with ARDS, but the effects on mortality and other clinical outcomes remain unknown. This article reports the rationale, study design, and analysis plan of the Alveolar Recruitment for ARDS Trial (ART). METHODS/DESIGN: ART is a pragmatic, multicenter, randomized (concealed), controlled trial, which aims to determine if maximum stepwise alveolar recruitment associated with PEEP titration is able to increase 28-day survival in patients with ARDS compared to conventional treatment (ARDSNet strategy). We will enroll adult patients with ARDS of less than 72 h duration. The intervention group will receive an alveolar recruitment maneuver, with stepwise increases of PEEP achieving 45 cmH2O and peak pressure of 60 cmH2O, followed by ventilation with optimal PEEP titrated according to the static compliance of the respiratory system. In the control group, mechanical ventilation will follow a conventional protocol (ARDSNet). In both groups, we will use controlled volume mode with low tidal volumes (4 to 6 mL/kg of predicted body weight) and targeting plateau pressure 6430 cmH2O. The primary outcome is 28-day survival, and the secondary outcomes are: length of ICU stay; length of hospital stay; pneumothorax requiring chest tube during first 7 days; barotrauma during first 7 days; mechanical ventilation-free days from days 1 to 28; ICU, in-hospital, and 6-month survival. ART is an event-guided trial planned to last until 520 events (deaths within 28 days) are observed. These events allow detection of a hazard ratio of 0.75, with 90% power and two-tailed type I error of 5%. All analysis will follow the intention-to-treat principle. DISCUSSION: If the ART strategy with maximum recruitment and PEEP titration improves 28-day survival, this will represent a notable advance to the care of ARDS patients. Conversely, if the ART strategy is similar or inferior to the current evidence-based strategy (ARDSNet), this should also change current practice as many institutions routinely employ recruitment maneuvers and set PEEP levels according to some titration metho

Prognostic markers in cancer: the evolution of evidence from single studies to meta-analysis, and beyond

In oncology, prognostic markers are clinical measures used to help elicit an individual patient's risk of a future outcome, such as recurrence of disease after primary treatment. They thus facilitate individual treatment choice and aid in patient counselling. Evidence-based results regarding prognostic markers are therefore very important to both clinicians and their patients. However, there is increasing awareness that prognostic marker studies have been neglected in the drive to improve medical research. Large protocol-driven, prospective studies are the ideal, with appropriate statistical analysis and clear, unbiased reporting of the methods used and the results obtained. Unfortunately, published prognostic studies rarely meet such standards, and systematic reviews and meta-analyses are often only able to draw attention to the paucity of good-quality evidence. We discuss how better-quality prognostic marker evidence can evolve over time from initial exploratory studies, to large protocol-driven primary studies, and then to meta-analysis or even beyond, to large prospectively planned pooled analyses and to the initiation of tumour banks. We highlight articles that facilitate each stage of this process, and that promote current guidelines aimed at improving the design, analysis, and reporting of prognostic marker research. We also outline why collaborative, multi-centre, and multi-disciplinary teams should be an essential part of future studies

Data-independent proteomic screen identifies novel tamoxifen agonist that mediates drug resistance

A label-free quantitative variation of the recently developed data-independent shotgun proteomic method Precursor Acquisition Independent From Ion Count (PAcIFIC) was used to identify novel proteins implicated in cancer progression and resistance. Specifically, this screen identified the pro-metastatic protein anterior gradient 2 (AGR2) as significantly up-regulated in tamoxifen treated cells. Highlighting the need for direct proteome profiling methods like PAcIFIC, neither data-dependent gas-phase fractionation nor a transcriptomic screen detected AGR2 protein/transcript at significantly up-regulated levels. Further cell-based experiments using human cancer cell lines and in vivo xenografts confirmed the PAcIFIC hypothesis that AGR2 is up-regulated in MCF-7 cells post tamoxifen treatment, and that it is implicated in drug resistance mediation

Rationale, study design, and analysis plan of the Alveolar Recruitment for ARDS Trial (ART): Study protocol for a randomized controlled trial

Background: Acute respiratory distress syndrome (ARDS) is associated with high in-hospital mortality. Alveolar recruitment followed by ventilation at optimal titrated PEEP may reduce ventilator-induced lung injury and improve oxygenation in patients with ARDS, but the effects on mortality and other clinical outcomes remain unknown. This article reports the rationale, study design, and analysis plan of the Alveolar Recruitment for ARDS Trial (ART). Methods/Design: ART is a pragmatic, multicenter, randomized (concealed), controlled trial, which aims to determine if maximum stepwise alveolar recruitment associated with PEEP titration is able to increase 28-day survival in patients with ARDS compared to conventional treatment (ARDSNet strategy). We will enroll adult patients with ARDS of less than 72 h duration. The intervention group will receive an alveolar recruitment maneuver, with stepwise increases of PEEP achieving 45 cmH(2)O and peak pressure of 60 cmH2O, followed by ventilation with optimal PEEP titrated according to the static compliance of the respiratory system. In the control group, mechanical ventilation will follow a conventional protocol (ARDSNet). In both groups, we will use controlled volume mode with low tidal volumes (4 to 6 mL/kg of predicted body weight) and targeting plateau pressure <= 30 cmH2O. The primary outcome is 28-day survival, and the secondary outcomes are: length of ICU stay; length of hospital stay; pneumothorax requiring chest tube during first 7 days; barotrauma during first 7 days; mechanical ventilation-free days from days 1 to 28; ICU, in-hospital, and 6-month survival. ART is an event-guided trial planned to last until 520 events (deaths within 28 days) are observed. These events allow detection of a hazard ratio of 0.75, with 90% power and two-tailed type I error of 5%. All analysis will follow the intention-to-treat principle. Discussion: If the ART strategy with maximum recruitment and PEEP titration improves 28-day survival, this will represent a notable advance to the care of ARDS patients. Conversely, if the ART strategy is similar or inferior to the current evidence-based strategy (ARDSNet), this should also change current practice as many institutions routinely employ recruitment maneuvers and set PEEP levels according to some titration method.Hospital do Coracao (HCor) as part of the Program 'Hospitais de Excelencia a Servico do SUS (PROADI-SUS)'Brazilian Ministry of Healt

Propionibacterium acnes as a Cause of Prosthetic Valve Aortic Root Abscess

Propionibacterium acnes isolates usually have relatively low virulence and are often classified as contaminants when isolated from blood and tissue cultures. We report a patient with Propionibacterium acnes bacteremia and late prosthetic valve endocarditis, complicated by an aortic root abscess

Consideraciones metodológicas para el análisis de ciclo de vida de la mampostería de arcilla

This paper presents the progress of an investigation developed in 2016, whose general objective was to set a methodology for the life cycle assessment of clay masonry in Cundinamarca State, based on the evaluation of energy resources consumption. Recently, progress in the study of energy efficiency in the production of the brick industry in Cundinamarca State have been developed, taking into account the equipment of combustion and / or fuel injection, as well as the combustion process and its proper functioning. On the other hand, regardless of the development of eco-labels methodologies type I, the LCA in this industry does not constitute an element that leads to an eco-label type III regulated by ISO 14040: 2006. This data could be an input for national and local sustainable construction policies, energy efficiency, low-carbon growth, environmental product declaration, and also, makes it as easy to deploy of standards under the Colombian Environmental Seal of the Ministry of Environment, and whose main goal is to minimize greenhouse gas emissions and improve energy efficiency from the construction industry and the brick industry.Postprint (published version

Relative sea level response to mixed carbonate-siliciclastic sediment loading along the Great Barrier Reef margin

The continental shelf along northeastern Australia is the world’s largest mixed carbonate-siliciclastic passive margin and the location of the Great Barrier Reef (GBR). Following sea-level transgression during the last deglaciation, extensive sediment was deposited along the GBR due to neritic carbonate deposition (including shelf edge reefs, Holocene reefs and Halimeda bioherms) and fluvial discharge of terrigenous siliciclastic sediments. Such sediment loading can alter local relative sea level (RSL) by several metres through the sediment isostatic adjustment (SIA) process, a signal that is poorly constrained at the GBR. In this study, we used a glacial isostatic adjustment (GIA) model to develop an ensemble-based sediment loading history for the GBR since Marine Isotope Stage 2 (MIS 2). A Bayesian style framework is adopted to calibrate the sediment history ensemble and GIA model parameters using a sea-level database. According to our results, 1853.7 Gt (1613.1-2078.7 Gt, 95% confidence interval) of sediment have been deposited across the GBR since MIS 2 (28 ka BP), causing spatially variable relative sea-level change with the highest magnitude (0.9-1.1 m) found in the outer shelf of the southern central GBR (18.4-21.6◦ S). Because the SIA-induced RSL rise is unrelated to ice mass loss, failing to correct for this signal will lead to systematic overestimation of grounded ice volume by up to ∼4.3 × 105 km3 during the Last Glacial Maximum. Additionally, we found that spatial variation in sediment loading and coastal environment may explain the different RSL history documented by published fossil coral reef records from Noggin Pass and Hydrographer’s Passage. These results highlight the importance of considering SIA for any postglacial sea-level studies adjacent to large sediment systems. Lastly, by quantifying both the GIA and SIA signals, we provide a spatially and temporally complete RSL reconstruction that is well-suited to be used as a boundary condition to study the evolution of the GBR shelf and slope sedimentary system

Swelling Behavior and Nanomechanical Properties of (Peptide-Modified) Poly(2-hydroxyethyl methacrylate) and Poly(poly(ethylene glycol) methacrylate) Brushes

Poly(2-hydroxyethyl methacrylate) (PHEMA) and poly(poly(ethylene glycol) methacrylate) (PPEGMA) brushes represent a class of thin, surface-tethered polymer films that have been extensively used e.g. to generate non-biofouling surfaces or as model systems to study fundamental biointerfacial questions related to cell–surface interactions. As the properties of PHEMA and PPEGMA brushes depend on the hydration and swelling of these thin films, it is important to understand the influence of basic structural parameters such as the composition of the polymer brush, the film thickness, or grafting density on these phenomena. This article reports results of a series of experiments that were performed to investigate the swelling behavior and mechanical properties of a diverse library of PHEMA and PPEGMA brushes covering a range of film thicknesses and grafting densities. The swelling ratios of the PHEMA and PPEGMA brushes were determined by ellipsometry and neutron reflectivity experiments and ranged from ∼1.5 to ∼5.0. Decreasing the grafting density and decreasing the film thickness generally results in an increase in the swelling ratio. Modification of the PHEMA and PPEGMA brushes with the cell adhesive RGD peptide ligand was found to result in a decrease in the swelling ratio. The neutron reflectivity experiments further revealed that solvated PHEMA and PPEGMA brushes are best described by a two-layer model, consisting of a polymer-rich layer close to the substrate and a second layer that is swollen to a much higher degree at the brush–water interface