Analysis of the Stability of Openings Excavated in Anisotropic Rocks

Openings excavated in rocks with anisotropic strength are often affected by serious instability, related to slip along the weakness planes. The Jaeger criterion, which is a discontinuous approach, is widely used in the mining and oil and gas industry, because is based on well-known rock strength parameters. However, this model cannot capture features related to the stability of openings drilled in some anisotropic rocks with the combined effect of the in situ state of stress. The Hoek & Brown criterion, adapted to anisotropic rocks, is a continuous criterion that can describe the complex behavior of different types of anisotropy exhibited by rock material. Here we interpreted the results of triaxial tests carried out on a shale and we defined the parameters of the Jaeger criterion and the modified Hoek & Brown criterion. We investigated the stability of boreholes drilled in this shale by varying the in situ state of stress and we compared the results of the two criteria. We found that the Hoek & Brown criterion can appropriately describe the behavior of this shale and can predict more accurately the width of the instability of openings excavated in different conditions

Plasma peptidome profiling of acute hepatitis E patients by MALDI-TOF/TOF

Background Hepatitis E is endemic to resource-poor regions, where it manifests as sporadic cases and large waterborne outbreaks. The disease severity ranges from acute self-limited hepatitis with low mortality to fulminant hepatic failure with high mortality. It is believed that the host response plays an important role in determining the progression and outcome of this disease. We profiled the plasma peptidome from hepatitis E patients to discover suitable biomarkers and understand disease pathogenesis. Results The peptidome (< 10 kDa) fraction of plasma was enriched and analyzed by mass spectrometry. A comparative analysis of the peptide pattern of hepatitis E patients versus healthy controls was performed using ClinPro Tools. We generated a peptide profile that could be used for selective identification of hepatitis E cases. We have identified five potential biomarker peaks with m/z values of 9288.6, 7763.6, 4961.5, 1060.572 and 2365.139 that can be used to reliably differentiate between hepatitis E patients and controls with areas under the receiver operating characteristic curve (AUROC) values of 1.00, 0.954, 0.989, 0.960 and 0.829 respectively. A number of proteins involved in innate immunity were identified to be differentially present in the plasma of patients compared to healthy controls. Conclusions Besides the utility of this approach for biomarker discovery, identification of changes in endogenous peptides in hepatitis E patient plasma has increased our understanding of disease pathogenesis. We have identified peptides in plasma that can reliably distinguish hepatitis E patients from healthy controls. Results from this and an earlier proteomics study are discussed

Evaluation of the generalized gamma as a tool for treatment planning optimization

Purpose: The aim of that work is to study the theoretical behavior and merits of the Generalized Gamma (generalized dose response gradient) as well as to investigate the usefulness of this concept in practical radiobiological treatment planning.Methods: In this study, the treatment planning system RayStation 1.9 (Raysearch Laboratories AB, Stockholm, Sweden) was used. Furthermore, radiobiological models that provide the tumor control probability (TCP), normal tissue complication probability (NTCP), complication-free tumor control probability (P+) and the Generalized Gamma were employed. The Generalized Gammas of TCP and NTCP, respectively were calculated for given heterogeneous dose distributions to different organs in order to verify the TCP and NTCP computations of the treatment planning system. In this process, a treatment plan was created, where the target and the organs at risk were included in the same ROI in order to check the validity of the system regarding the objective function P+ and the Generalized Gamma. Subsequently, six additional treatment plans were created with the target organ and the organs at risk placed in the same or different ROIs. In these plans, the mean dose was increased in order to investigate the behavior of dose change on tissue response and on Generalized Gamma before and after the change in dose. By theoretically calculating these quantities, the agreement of different theoretical expressions compared to the values that the treatment planning system provides could be evaluated. Finally, the relative error between the real and approximate response values using the Poisson and the Probit models, for the case of having a target organ consisting of two compartments in a parallel architecture and with the same number of clonogens could be investigated and quantified. Results: The computations of the RayStation regarding the values of the Generalized Gamma and the objective function (P+) were verified by using an independent software. Furthermore, it was proved that after a small change in dose, the organ that is being affected most is the organ with the highest Generalized Gamma. Apart from that, the validity of the theoretical expressions that describe the change in response and the associated Generalized Gamma was verified but only for the case of small change in dose. Especially for the case of 50% TCP and NTCP, the theoretical values (ΔPapprox.) and those calculated by the RayStation show close agreement, which proves the high importance of the D50 parameter in specifying clinical response levels. Finally, the presented findings show that the behavior of ΔPapprox. looks sensible because, for both of the models that were used (Poisson and Probit), it significantly approaches the real ΔP around the region of 37% and 50% response. The present study managed to evaluate the mathematical expression of Generalized Gamma for the case of non-uniform dose delivery and the accuracy of the RayStation to calculate its values for different organs. Conclusion: A very important finding of this work is the establishment of the usefulness and clinical relevance of Generalized Gamma. That is because it gives the planner the opportunity to precisely determine which organ will be affected most after a small increase in dose and as a result an optimal treatment plan regarding tumor control and normal tissue complications can be found

Self-activated photoblinking of nitrogen vacancy centers in nanodiamonds (sandSTORM): A method for rapid single molecule localization microscopy with unlimited observation time

Stochastic optical reconstruction microscopy (STORM) is one of the most commonly used super-resolution microscopy techniques. Popular implementations of STORM utilize aromatic fluorophores and consist of a number of intrinsic limitations such the finite photostability of the dyes, the reliance upon non-physiological redox buffers and speed which is ultimately limited by the off-rates of the photoblinking. Self-activated nanodiamond-based STORM (sandSTORM) has been developed as an accelerated STORM protocol which harvests the rapid, high quantum-yield and sustained photoblinking of nanodiamonds (ND). Photoluminescence emanating from the stochastic charge-state interconversion of Nitrogen Vacancy (NV) centers between NV0 and NV- is localized using conventional STORM-optimized hardware and image processing protocols over an unlimited duration of imaging. This produces super-resolution images of matching resolution at ~ 3-times the speed and ~ 100 times less light exposure to the sample compared to traditional STORM. The enabling NDs have been used to map arrays of ryanodine receptor in skeletal muscle tissues via immunolabelling and directly visualize the internal spaces of living neurons via endocytosis of NDs. This paper details the physical basis of sandSTORM, factors which optimize its performance, and key characteristics which make it a powerful STORM protocol suitable for imaging nanoscale sub-cellular structures

Radiofrequency ablation for Barrett's oesophagus related neoplasia with the 360 Express catheter: initial experience from the United Kingdom and Ireland—preliminary results

BACKGROUND: Radio-frequency ablation (RFA) for Barrett's oesophagus (BE)-related neoplasia is currently used after endoscopic resection of visible neoplasia. The HALO 360 balloon has been used to ablate long segment BE. The Barrx™ 360 Express RFA self-sizing catheter ('RFA Express') may potentially allow quicker ablation times and improved treatment outcomes. The aim of this paper is to present real world data on the use of the 360 Express Device. METHODS: Centres in the UK and Ireland submitted cases where the RFA Express was used. The primary outcome was regression of BE at 3 months. Secondary outcomes were the rate of symptomatic stricture formation and resolution of intestinal metaplasia (CR-IM) and dysplasia (CR-D) at End of Treatment (EoT). RESULTS: 11 centres submitted 123 consecutive patients. 112 had a follow up endoscopy. The median age was 67 years (IQR 62-75). 3 dosimetries were used. The mean reduction in Circumferential (C) length was 78% ± 36 and mean reduction in Maximal length (M) was 55% ± 36. 17 patients (15%) developed strictures requiring dilation. There was a higher rate of stricture formation when the 12 J energy was used (p < 0.05). 47 patients had EoT biopsies, 40 (85%) had CR-D and 34(76%) had CR-IM. CONCLUSIONS: The RFA 360 Express catheter shows reduction in length of baseline BE at 3 months after index treatment, and eradication of intestinal metaplasia and dysplasia at 12 months similar to other studies with earlier devices. It appears that the symptomatic stricture rate is slightly higher than previous series with the HALO 360 catheter. This study was performed as part of the HALO registry and has been approved by the Research Ethics Committee - MREC Number 08/H0714/27 Local project reference 08/0104 Project ID 15,033 IRAS Number 54678 EudraCT 2009-015980-1. Registered on ISRCTN as below: ISRCTN93069556. https://doi.org/10.1186/ISRCTN93069556

Web services at the European Bioinformatics Institute-2009

The European Bioinformatics Institute (EMBL-EBI) has been providing access to mainstream databases and tools in bioinformatics since 1997. In addition to the traditional web form based interfaces, APIs exist for core data resources such as EMBL-Bank, Ensembl, UniProt, InterPro, PDB and ArrayExpress. These APIs are based on Web Services (SOAP/REST) interfaces that allow users to systematically access databases and analytical tools. From the user's point of view, these Web Services provide the same functionality as the browser-based forms. However, using the APIs frees the user from web page constraints and are ideal for the analysis of large batches of data, performing text-mining tasks and the casual or systematic evaluation of mathematical models in regulatory networks. Furthermore, these services are widespread and easy to use; require no prior knowledge of the technology and no more than basic experience in programming. In the following we wish to inform of new and updated services as well as briefly describe planned developments to be made available during the course of 2009–2010

Improvement over time in outcomes for patients undergoing endoscopic therapy for Barrett's oesophagus-related neoplasia: 6-year experience from the first 500 patients treated in the UK patient registry.

BACKGROUND: Barrett's oesophagus (BE) is a pre-malignant condition leading to oesophageal adenocarcinoma (OAC). Treatment of neoplasia at an early stage is desirable. Combined endoscopic mucosal resection (EMR) followed by radiofrequency ablation (RFA) is an alternative to surgery for patients with BE-related neoplasia. METHODS: We examined prospective data from the UK registry of patients undergoing RFA/EMR for BE-related neoplasia from 2008 to 2013. Before RFA, visible lesions were removed by EMR. Thereafter, patients had RFA 3-monthly until all BE was ablated or cancer developed (endpoints). End of treatment biopsies were recommended at around 12 months from first RFA treatment or when endpoints were reached. Outcomes for clearance of dysplasia (CR-D) and BE (CR-IM) at end of treatment were assessed over two time periods (2008-2010 and 2011-2013). Durability of successful treatment and progression to OAC were also evaluated. RESULTS: 508 patients have completed treatment. CR-D and CR-IM improved significantly between the former and later time periods, from 77% and 56% to 92% and 83%, respectively (p<0.0001). EMR for visible lesions prior to RFA increased from 48% to 60% (p=0.013). Rescue EMR after RFA decreased from 13% to 2% (p<0.0001). Progression to OAC at 12 months is not significantly different (3.6% vs 2.1%, p=0.51). CONCLUSIONS: Clinical outcomes for BE neoplasia have improved significantly over the past 6 years with improved lesion recognition and aggressive resection of visible lesions before RFA. Despite advances in technique, the rate of cancer progression remains 2-4% at 1 year in these high-risk patients. TRIAL REGISTRATION NUMBER: ISRCTN93069556

Exploring the development of a cultural care framework for European caring science

The aim of this paper is to discuss the development of a cultural care framework that seeks to inform and embrace the philosophical ideals of caring science. Following a review of the literature that identified a lack of evidence of an explicit relationship between caring science and cultural care, a number of well-established transcultural care frameworks were reviewed. Our purpose was to select one that would resonate with underpinning philosophical values of caring science and that drew on criteria generated by the European Academy of Caring Science members. A modified framework based on the work of Giger and Davidhizar was developed as it embraced many of the values such as humanism that are core to caring science practice. The proposed caring science framework integrates determinants of cultural lifeworld-led care and seeks to provide clear directions for humanizing the care of individuals. The framework is offered to open up debate and act as a platform for further academic enquiry