Application of next generation sequencing to CEPH cell lines to discover variants associated with FDA approved chemotherapeutics

After publication of this work [1], it has come to our attention that there is an error in the author list of the initial version of this manuscript; rather than Ernest J Lam, the second author of the manuscript should be listed as Ernest T Lam

Pre-existing invasive fungal infection is not a contraindication for allogeneic HSCT for patients with hematologic malignancies: a CIBMTR study.

Patients with prior invasive fungal infection (IFI) increasingly proceed to allogeneic hematopoietic cell transplantation (HSCT). However, little is known about the impact of prior IFI on survival. Patients with pre-transplant IFI (cases; n=825) were compared with controls (n=10247). A subset analysis assessed outcomes in leukemia patients pre- and post 2001. Cases were older with lower performance status (KPS), more advanced disease, higher likelihood of AML and having received cord blood, reduced intensity conditioning, mold-active fungal prophylaxis and more recently transplanted. Aspergillus spp. and Candida spp. were the most commonly identified pathogens. 68% of patients had primarily pulmonary involvement. Univariate and multivariable analysis demonstrated inferior PFS and overall survival (OS) for cases. At 2 years, cases had higher mortality and shorter PFS with significant increases in non-relapse mortality (NRM) but no difference in relapse. One year probability of post-HSCT IFI was 24% (cases) and 17% (control, P<0.001). The predominant cause of death was underlying malignancy; infectious death was higher in cases (13% vs 9%). In the subset analysis, patients transplanted before 2001 had increased NRM with inferior OS and PFS compared with later cases. Pre-transplant IFI is associated with lower PFS and OS after allogeneic HSCT but significant survivorship was observed. Consequently, pre-transplant IFI should not be a contraindication to allogeneic HSCT in otherwise suitable candidates. Documented pre-transplant IFI is associated with lower PFS and OS after allogeneic HSCT. However, mortality post transplant is more influenced by advanced disease status than previous IFI. Pre-transplant IFI does not appear to be a contraindication to allogeneic HSCT

Methods for the Study of Marine Biodiversity

Recognition of the threats to biodiversity and its importance to society has led to calls for globally coordinated sampling of trends in marine ecosystems. As a step to defining such efforts, we review current methods of collecting and managing marine biodiversity data. A fundamental component of marine biodiversity is knowing what, where, and when species are present. However, monitoring methods are invariably biased in what taxa, ecological guilds, and body sizes they collect. In addition, the data need to be placed, and/or mapped, into an environmental context. Thus a suite of methods will be needed to encompass representative components of biodiversity in an ecosystem. Some sampling methods can damage habitat and kill species, including unnecessary bycatch. Less destructive alternatives are preferable, especially in conservation areas, such as photography, hydrophones, tagging, acoustics, artificial substrata, light-traps, hook and line, and live-traps. Here we highlight examples of operational international sampling programmes and data management infrastructures, notably the Continuous Plankton Recorder, Reef Life Survey, and detection of Harmful Algal Blooms and MarineGEO. Data management infrastructures include the World Register of Marine Species for species nomenclature and attributes, the Ocean Biogeographic Information System for distribution data, Marine Regions for maps, and Global Marine Environmental Datasets for global environmental data. Existing national sampling programmes, such as fishery trawl surveys and intertidal surveys, may provide a global perspective if their data can be integrated to provide useful information. Less utilised and emerging sampling methods, such as artificial substrata, light-traps, microfossils and eDNA also hold promise for sampling the less studied components of biodiversity. All of these initiatives need to develop international standards and protocols, and long-term plans for their governance and support.published_or_final_versio

The challenges faced in the design, conduct and analysis of surgical randomised controlled trials

Randomised evaluations of surgical interventions are rare; some interventions have been widely adopted without rigorous evaluation. Unlike other medical areas, the randomised controlled trial (RCT) design has not become the default study design for the evaluation of surgical interventions. Surgical trials are difficult to successfully undertake and pose particular practical and methodological challenges. However, RCTs have played a role in the assessment of surgical innovations and there is scope and need for greater use. This article will consider the design, conduct and analysis of an RCT of a surgical intervention. The issues will be reviewed under three headings: the timing of the evaluation, defining the research question and trial design issues. Recommendations on the conduct of future surgical RCTs are made. Collaboration between research and surgical communities is needed to address the distinct issues raised by the assessmentof surgical interventions and enable the conduct of appropriate and well-designed trials.The Health Services Research Unit is funded by the Scottish Government Health DirectoratesPeer reviewedPublisher PD

c-erbB-2 is not a major factor in the development of colorectal cancer

We have investigated c-erbB-2 protein expression in a large cohort of well-characterized colorectal tumours, and in a subset of lymph node metastases. We have also evaluated a Val655Ile single nucleotide polymorphism, which is associated with an increased risk of breast cancer, in a subset of the colorectal cancer patients and in healthy control subjects. Immunohistochemical studies revealed that while 81.8% of tumours expressed c-erbB-2, in the majority of cases equivalent levels of c-erb-B2 were seen in adjacent normal mucosa. Colon tumours were significantly more likely to express c-erbB-2 than rectal tumours (P=0.015). Only 52.4% of the metastases displayed staining patterns concordant with their primary tumour, indicating that determination of c-erbB-2 protein in colorectal tumours cannot predict the status of lymph node metastases. PCR–RFLP analysis of the Val655Ile single nucleotide polymorphism demonstrated that allele frequencies were identical between colorectal cancer patients and a control group of Caucasian subjects (Ile=0.80 and Val=0.20 in each case), indicating that it is not related to the risk of developing colorectal cancer in this population. Furthermore, there was no relationship between c-erbB-2 protein expression and gene polymorphism (P=0.58). In terms of prognosis, no association was seen between either c-erbB-2 protein expression or the presence of the Val allele and patient survival (P>0.05 in each case), suggesting that c-erbB-2 is not a prognostic marker in colorectal cancer

Substrate stabilisation and small structures in coral restoration: State of knowledge, and considerations for management and implementation.

Coral reef ecosystems are under increasing pressure from local and regional stressors and a changing climate. Current management focuses on reducing stressors to allow for natural recovery, but in many areas where coral reefs are damaged, natural recovery can be restricted, delayed or interrupted because of unstable, unconsolidated coral fragments, or rubble. Rubble fields are a natural component of coral reefs, but repeated or high-magnitude disturbances can prevent natural cementation and consolidation processes, so that coral recruits fail to survive. A suite of interventions have been used to target this issue globally, such as using mesh to stabilise rubble, removing the rubble to reveal hard substrate and deploying rocks or other hard substrates over the rubble to facilitate recruit survival. Small, modular structures can be used at multiple scales, with or without attached coral fragments, to create structural complexity and settlement surfaces. However, these can introduce foreign materials to the reef, and a limited understanding of natural recovery processes exists for the potential of this type of active intervention to successfully restore local coral reef structure. This review synthesises available knowledge about the ecological role of coral rubble, natural coral recolonisation and recovery rates and the potential benefits and risks associated with active interventions in this rapidly evolving field. Fundamental knowledge gaps include baseline levels of rubble, the structural complexity of reef habitats in space and time, natural rubble consolidation processes and the risks associated with each intervention method. Any restoration intervention needs to be underpinned by risk assessment, and the decision to repair rubble fields must arise from an understanding of when and where unconsolidated substrate and lack of structure impair natural reef recovery and ecological function. Monitoring is necessary to ascertain the success or failure of the intervention and impacts of potential risks, but there is a strong need to specify desired outcomes, the spatial and temporal context and indicators to be measured. With a focus on the Great Barrier Reef, we synthesise the techniques, successes and failures associated with rubble stabilisation and the use of small structures, review monitoring methods and indicators, and provide recommendations to ensure that we learn from past projects

Night-time measurements of HO<inf>x</inf> during the RONOCO project and analysis of the sources of HO<inf>2</inf>

Abstract. Measurements of the radical species OH and HO2 were made using the fluorescence assay by gas expansion (FAGE) technique during a series of night-time and daytime flights over the UK in summer 2010 and winter 2011. OH was not detected above the instrument's 1σ limit of detection during any of the night-time flights or during the winter daytime flights, placing upper limits on [OH] of 1.8 × 106 molecule cm−3 and 6.4 × 105 molecule cm−3 for the summer and winter flights, respectively. HO2 reached a maximum concentration of 3.2 × 108 molecule cm−3 (13.6 pptv) during a night-time flight on 20 July 2010, when the highest concentrations of NO3 and O3 were also recorded. An analysis of the rates of reaction of OH, O3, and the NO3 radical with measured alkenes indicates that the summer night-time troposphere can be as important for the processing of volatile organic compounds (VOCs) as the winter daytime troposphere. An analysis of the instantaneous rate of production of HO2 from the reactions of O3 and NO3 with alkenes has shown that, on average, reactions of NO3 dominated the night-time production of HO2 during summer and reactions of O3 dominated the night-time HO2 production during winter. This work was funded by the UK Natural Environment Research Council (NE/F004664/1). The authors would like to thank ground staff, engineers, scientists, and pilots involved in RONOCO for making this project a success. Airborne data were obtained using the BAe 146-301 Atmospheric Research Aircraft (ARA) flown by Directflight Ltd. and managed by the Facility for Airborne Atmospheric Measurements (FAAM), which is a joint entity of the Natural Environment Research Council (NERC) and the Met Office.This is the final version of the article. It first appeared from Copernicus Publications via http://dx.doi.org/10.5194/acp-15-8179-201

Night-time measurements of HOx during the RONOCO project and analysis of the sources of HO2

Measurements of the radical species OH and HO2 were made using the fluorescence assay by gas expansion (FAGE) technique during a series of night-time and daytime flights over the UK in summer 2010 and winter 2011. OH was not detected above the instrument's 1σ limit of detection during any of the night-time flights or during the winter daytime flights, placing upper limits on [OH] of 1.8 × 106 molecule cm−3 and 6.4 × 105 molecule cm−3 for the summer and winter flights, respectively. HO2 reached a maximum concentration of 3.2 × 108 molecule cm−3 (13.6 pptv) during a night-time flight on 20 July 2010, when the highest concentrations of NO3 and O3 were also recorded. An analysis of the rates of reaction of OH, O3, and the NO3 radical with measured alkenes indicates that the summer night-time troposphere can be as important for the processing of volatile organic compounds (VOCs) as the winter daytime troposphere. An analysis of the instantaneous rate of production of HO2 from the reactions of O3 and NO3 with alkenes has shown that, on average, reactions of NO3 dominated the night-time production of HO2 during summer and reactions of O3 dominated the night-time HO2 production during winter

A numerical modelling and simulation of core-scale sandstone acidizing process: a study on the effect of temperature

A wide and comprehensive understanding of the chemical reactions and mechanisms of HBF4 is crucial as it significantly influences its performance in stimulating a sandstone formation. In general, it is well-known that HBF4 is able to provide a deeper penetration into the sandstone matrix before being spent due to its uniquely slow hydrolysis ability to produce HF. In the present study, a 3D numerical modelling and simulation were conducted to examine the capability of HBF4 in enhancing the porosity and permeability of the sandstone matrix. The model is built in COMSOL® Multiphysics commercial software of computational fluid dynamics (CFD) to simulate the acid core flooding process on sandstone core. The model had been validated against the experimental data in the literature. The results matched with the measured plot data very well. The effect of temperature on the performance HBF4 sandstone acidizing is evaluated in this study. The simulation results indicated that at low temperature of 25 °C, HBF4 is not very effective, as justified in its poor porosity and permeability increments of only 1.07 and 1.23, respectively. However, at elevated temperatures, the porosity and permeability enhancement also become increasingly more significant, which showed 1.26 and 2.06, respectively, at 65 °C; and 1.67 and 7.06, respectively, at 105 °C. Therefore, one can conclude that HBF4 acid treatment performed better at elevated temperatures due to increased hydrolysis rate, which is a governing function in HBF4 sandstone acidizing. Overall, this model had provided a reliable alternative to optimize various other parameters of HBF4 acid treatment