• Parallel evaluation of Doxorubicin inducing Genetic damage in human lymphocytes and sperm using the Comet assay and spectral karyotyping

      Anderson, Diana; Baumgartner, Adolf; Cemeli, Eduardo; Schmid, Thomas E. (2004)
      In recent years, two techniques for detecting genetic damage in the whole genome have gained importance: the alkaline comet assay, to detect DNA damage such as strand breaks and alkali-labile sites, and a multicolour FISH method, spectral karyotyping (SKY), to identify chromosomal aberrations simultaneously in all metaphase chromosomes. In the present study, the induction of DNA damage in human sperm and lymphocytes in vitro has been studied employing an anticancer drug, doxorubicin (DX). An increase in DNA damage was observed with the comet assay as the median per cent head DNA of sperm significantly decreased from 82.07 and 85.14% in the untreated control groups to 63.48 and 72.52% at doses of 0.8 µM DX. At 1.6 µM the percentage declined to 60.96% (the corresponding tail moment increased from 4.42 to 12.19). In stimulated lymphocytes, a significant increase was observed in tail moment, from 0.72 and 0.53 in controls to 15.17 and 12.10 at 0.2 µM DX, continuing at the same level to a final concentration of 1.6 µM. Structural aberrations found in the parallel SKY study in stimulated lymphocytes at 0.2 µM DX consisted of 14% chromatid-type and 2% chromosome-type aberrations; none were found in controls. The SKY results correlate very well with the findings of the comet assay in lymphocytes where DNA damage was observed at similar doses. This study is the first reporting use of the comet assay and SKY analysis in parallel after chemical treatment. The potential of the two techniques together is evident, as they represent a set of assays feasible for evaluating damage in human somatic and germ cells after chemical treatment (i) by direct observation of two different end-points, detecting general DNA damage and chromosomal aberrations and (ii) by extrapolation from lymphocytes to sperm, which provides a `parallelogram¿ approach in human cells.
    • Parallel RNA interference screens identify EGFR activation as an escape mechanism in FGFR3-mutant cancer

      Herrera-Abreu, M.T.; Pearson, A.; Campbell, J.; Shnyder, Steven D.; Knowles, M.A.; Ashworth, A.; Turner, N.C. (2013)
      Activation of fibroblast growth factor receptors (FGFR) is a common oncogenic event. Little is known about the determinants of sensitivity to FGFR inhibition and how these may vary between different oncogenic FGFRs. Using parallel RNA interference (RNAi) genetic screens, we show that the EGF receptor (EGFR) limits sensitivity to FGFR inhibition in FGFR3-mutant and -translocated cell lines, but not in other FGFR-driven cell lines. We also identify two distinct mechanisms through which EGFR limits sensitivity. In partially FGFR3-dependent lines, inhibition of FGFR3 results in transient downregulation of mitogen-activated protein kinase signaling that is rescued by rapid upregulation of EGFR signaling. In cell lines that are intrinsically resistant to FGFR inhibition, EGFR dominates signaling via repression of FGFR3, with EGFR inhibition rescued by delayed upregulation of FGFR3 expression. Importantly, combinations of FGFR and EGFR inhibitors overcome these resistance mechanisms in vitro and in vivo. Our results illustrate the power of parallel RNAi screens in identifying common resistance mechanisms to targeted therapies. SIGNIFICANCE: Our data identify a novel therapeutic approach to the treatment of FGFR3-mutant cancer, emphasizing the potential of combination approaches targeting both FGFR3 and EGFR. Our data extend the role of EGFR in mediating resistance to inhibitors targeting a mutant oncogene, showing that EGFR signaling can repress mutant FGFR3 to induce intrinsic resistance to FGFR targeting.
    • Part-time versus full-time occlusion therapy for treatment of amblyopia: A meta-analysis

      Yazdani, N.; Sadeghi, R.; Momeni-Moghaddam, H.; Zarifmahmoudi, L.; Ehsaei, Asieh; Barrett, Brendan T. (2017)
      Purpose: To compare full-time occlusion (FTO) and part-time occlusion (PTO) therapy in the treatment of amblyopia, with the secondary aim of evaluating the minimum number of hours of part-time patching required for maximal effect from occlusion. Methods: A literature search was performed in PubMed, Scopus, Science Direct, Ovid, Web of Science and Cochrane library. Methodological quality of the literature was evaluated according to the Oxford Center for Evidence Based Medicine and modified Newcastle-Ottawa scale. Statistical analyses were performed using Comprehensive Meta-Analysis (version 2, Biostat Inc., USA). Results: The present meta-analysis included six studies (three randomized controlled trials [RCTs] and three non-RCTs). Pooled standardized difference in the mean changes in the visual acuity was 0.337 [lower and upper limits: 0.009, 0.683] higher in the FTO as compared to the PTO group; however, this difference was not statistically significant (P ¼ 0.056, Cochrane Q value ¼ 20.4 (P ¼ 0.001), I2 ¼ 75.49%). Egger's regression intercept was 5.46 (P ¼ 0.04). The pooled standardized difference in means of visual acuity changes was 1.097 [lower and upper limits: 0.68, 1.513] higher in the FTO arm (P < 0.001), and 0.7 [lower and upper limits: 0.315, 1.085] higher in the PTO arm (P < 0.001) compared to PTO less than two hours. Conclusions: This meta-analysis shows no statistically significant difference between PTO and FTO in treatment of amblyopia. However, our results suggest that the minimum effective PTO duration, to observe maximal improvement in visual acuity is six hours per day.
    • Particle formation by mixing with supercritical antisolvent at high Reynolds numbers.

      Shekunov, Boris Yu.; Baldyga, J.; York, Peter (2001)
      A precipitation process is considered in which completely miscible solution and supercritical antisolvent are passed through premixing and diluting zones of a turbulent flow. The influence of flow velocity on particle size and nuclei concentration is discussed in terms of mixing and precipitation time constants and their supersaturation dependencies. The proposed model allowed the major process parameters such as supersaturation profile, mixed fluid fraction and mean particle size to be calculated and compared with experimental data. For the crystallization system paracetamol/ethanol/CO2 studied, the supersaturation profile becomes established at Re104. The particle size and shape are defined, firstly, by increase of supersaturation and relative volume of mixed (on molecular scale) fluid with increase of flow velocity and, secondly, by decrease of residence time available for nucleation with increase of flow velocity. These competitive processes can result in minimum particle size at a defined flow rate.
    • Partition of neutral molecules and ions from water to o-nitrophenyl octyl ether and of neutral molecules from the gas phase to o-nitrophenyl octyl ether

      Abraham, M.H.; Acree Jr, W.E.; Liu, Xiangli (2018-02)
      We have set out an equation for partition of 87 neutral molecules from water to o-nitrophenyl octyl ether, NPOE, an equation for partition of the 87 neutral molecules and 21 ionic species from water to NPOE, and an equation for partition of 87 neutral molecules from the gas phase to NPOE. Comparison with equations for partition into other solvents shows that, as regards partition of neutral (nonelectrolyte) compounds, NPOE would be a good model for 1,2-dichloroethane and for nitrobenzene. In terms of partition of ions and ionic species, NPOE is quite similar to 1,2-dichloroethane and not far away from other aprotic solvents such as nitrobenzene.
    • Paternal smoking as a cause for transgenerational damage in the offspring

      Anderson, Diana; Schmid, Thomas E.; Baumgartner, Adolf (2015)
      In 2013, the World Health Organization referred to tobacco smoking as an epidemic and a great threat to human health. Despite the obvious exposures from first- and secondhand smoking contributing to illnesses, an increased cancer risk, and death, there is a hidden risk to the next generation(s) from transgenerational mutations. In human populations, paternal preconceptional germ cell damage leading to genomic instability in offspring has always been difficult to evaluate as preconceptional and gestational exposures usually cannot be analyzed independently. Clear indications have been found that the effect of pre- and periconceptional paternal smoking may have been transmitted to the offspring via the spermatozoal genome and epigenome. Hence, cigarette smoke has to be considered a human germ cell mutagen due to its potential of inducing transgenerational DNA alterations in the unexposed F1 offspring of smoking-exposed fathers. For cohort studies, the practice of almost exclusively employing mother–childbirth pairs for the evaluation of lifestyle factors, such as smoking, while excluding the fathers’ contribution has to be reconsidered. Evidence now strongly points to the necessity of including the fathers in order not to miss paternal transgenerational damage in the offspring. This applies for genetic, epigenetic, and other transmissible effects.
    • Pathobiology of chemotherapy-induced hair loss.

      Paus, R.; Haslam, I.S.; Sharov, A.A.; Botchkarev, Vladimir A. (2013)
      Hair loss can be a psychologically devastating adverse effect of chemotherapy, but satisfactory management strategies for chemotherapy-induced alopecia remain elusive. In this Review we focus on the complex pathobiology of this side-effect. We discuss the clinical features and current management approaches, then draw upon evidence from mouse models and human hair-follicle organ-culture studies to explore the main pathobiology principles and explain why chemotherapy-induced alopecia is so challenging to manage. P53-dependent apoptosis of hair-matrix keratinocytes and chemotherapy-induced hair-cycle abnormalities, driven by the dystrophic anagen or dystrophic catagen pathway, play important parts in the degree of hair-follicle damage, alopecia phenotype, and hair-regrowth pattern. Additionally, the degree of hair-follicle stem-cell damage determines whether chemotherapy-induced alopecia is reversible. We highlight the need for carefully designed preclinical research models to generate novel, clinically relevant pointers to how this condition may be overcome.
    • Pathogens

      Lazenby, J.; Chang, Chien-Yi (2014)
    • Pathway-dependent gold nanoparticle formation by biocatalytic self-assembly

      Sahoo, J.K.; Roy, S.; Javid, Nadeem; Duncan, K.; Aitken, L.; Ulijn, R.V. (2017-09)
      We report on the use of non-equillibrium biocatalytic self-assembly and gelation to guide the reductive synthesis of gold nanoparticles. We show that biocatalytic rates simultaneously dictate supramolecular order and presentation of reductive phenols which in turn results in size control of nanoparticles that are formed.
    • Patient and public involvement in designing and conducting doctoral research: the whys and the hows

      Tomlinson, Justine; Medlinskiene, Kristina; Cheong, V-Lin; Khan, Sarah; Fylan, Beth (2019-08)
      Public and patient involvement (PPI) has been shown to have a positive impact on health and social care research. However, adequate examples describing how to operationalise effective PPI, especially in doctoral studies, are lacking. Hence, doctoral researchers new to research, or those with limited experience, can be discouraged from facilitating PPI in their research. This paper aims to describe and discuss in detail the approaches used by four doctoral researchers to incorporate PPI at different stages of their research studies from study design to disseminating findings. We aim to inform other doctoral researchers about the challenges and limitations relating to PPI that we faced. Through these, we share pragmatic recommendations for facilitating PPI during doctoral studies. The description of four case studies demonstrated that PPI could be incorporated at various stages during doctoral research. This has had a beneficial impact on our research study progression, researcher self-esteem and lastly, helped alleviate researcher isolation during doctoral studies.
    • Patients' hands and healthcare-associated infection

      Kerr, Kevin G.; Banfield, Kathleen R.; Jones, K.A.; Snelling, Anna M. (2007)
      Not available
    • Patients' knowledge of new medicines after discharge from hospital: What are the effects of hospital-based discharge counseling and community-based medicines use reviews (MURs)?

      Elson, Rachel; Cook, Helen; Blenkinsopp, Alison (2017-05)
      Background Interventions to reduce medicines discontinuity at transitions during and reinforced after discharge are effective. However, few studies have linked hospital-based counseling with onward referral for community pharmacy-based follow-up to support patients' medicines use. Objective To determine the effects of targeted hospital pharmacist counseling on discharge or targeted community pharmacy medicines reviews post-discharge on patients' knowledge of newly started medication. Methods The study was a controlled trial of targeted medicines discharge counseling provided by hospital pharmacists or follow-up post-discharge medicines review provided by community pharmacists compared with usual care (nurse counseling). Outcomes measured using a structured telephone survey conducted at two and four weeks after patients were discharged from hospital. Results Patients who received hospital pharmacist counseling were significantly more likely to report being told the purpose of their new medicine and how to take it versus those receiving usual care. Fewer than half of the patients who were allocated to receive a community pharmacy medicines review received one. Conclusions Patient knowledge of medicines newly prescribed in the hospital was increased by targeted counseling of hospital pharmacists. The findings suggest the need to improve the consistency of the information covered when providing counseling, perhaps by the implementation of a counseling checklist for use by all disciplines of staff involved in patient counseling. The potential of community pharmacy follow-up medicines review is currently undermined by several barriers to uptake.
    • Patients’ experiences with home parental nutrition: A grounded theory study

      Wong, C.; Lucas, Beverley J.; Wood, Diana (2018-04)
      Background & aims Parenteral nutrition (PN) provides nourishment and hydration as an intravenous infusion to patients with intestinal failure (IF). The aim of the study is to generate theory that explains the experiences of adult patients living with home parenteral nutrition (HPN) and complex medication regimens. Methods A grounded theory methodology was used to explore the experiences of twelve patients receiving HPN. A semi-structured interview was conducted and recorded in each participant's home setting. Each interview was transcribed verbatim. The simultaneous process of data collection and analysis was followed reflecting the principles of the constant comparative approach. Results A total of 15 patients gave written consent, with 12 of them agreeing to be interviewed. All the participants had previously undergone surgery as a result of chronic ill health or sudden illness. Analysis revealed two core categories: stoma and HPN, and these were supported by the subcategories: maintaining stoma output, access to toilets, managing dietary changes, maintaining the HPN infusion routine, access to technical help to set up an HPN infusion, mobility with HPN equipment and general health changes. The strategy of living with loss was demonstrated by all the participants, and this was supported by the action strategies of maintaining daily activities and social interactions. Conclusions This study generates new understanding and insight into the views and experiences of patients receiving HPN in the UK. The findings from these participants have been shown to resonate with the Kubler-Ross Model [1] of the five stages of grief. The theory of living with loss was generated by the use of a grounded theory methodology. This small scale exploratory study reveals opportunities for improvements in practice to be considered by the nutrition support team (NST) and other healthcare professionals involved in the patient's hospital stay prior to discharge on HPN.
    • Patients’ experiences with home parenteral nutrition: a literature review

      Wong, C.; Lucas, Beverley J.; Wood, Diana (2015)
      Aim The aim of this review is to summarise the literature relating to patients’ experiences with home parenteral nutrition (HPN). Method This literature review is based on searches of CINAHL, PubMed, Web of Knowledge and Web of Science for articles published between 1970 and 2013. Additional studies were included from Department of Health publications, NICE clinical guidance, UK patient support group with interests in HPN or intestinal failure (IF). Results Patients with severe IF have been successfully treated with HPN since the 1970s. Early published studies evaluated clinical outcomes such as catheter-related infections, metabolic complications, thrombosis of the catheterised vein and liver impairment. Since the 1980s questionnaire studies were used to evaluate the quality of life (QoL) of patients treated with HPN. These early studies used QoL assessment tools which were not validated for patients treated with HPN. Internationally, there were published qualitative research studies which explored the experiences of patients treated with HPN. Conclusions The long-term outcome of patients treated with HPN continues to attract research interest. The review of the literature did not identify any published qualitative studies on the experiences of patients treated with HPN in the UK, suggesting a gap in the research. The UK National Health Service advocates a patient-centred approach for service design and delivery in primary and secondary care. This literature review has highlighted opportunities for qualitative research into the experiences of patients living with HPN to achieve better understanding and awareness of the rehabilitation of these patients
    • Patients’ valuation of the prescribing nurse in primary care: a discrete choice experiment

      Gerard, K.; Tinelli, M.; Latter, S.; Smith, A.; Blenkinsopp, Alison (2015-11-27)
      Background Recently, primary care in the United Kingdom has undergone substantial changes in skill mix. Non-medical prescribing was introduced to improve patient access to medicines, make better use of different health practitioners’ skills and increase patient choice. There is little evidence about value-based patient preferences for ‘prescribing nurse’ in a general practice setting. Objective To quantify value-based patient preferences for the profession of prescriber and other factors that influence choice of consultation for managing a minor illness. Design Discrete choice experiment patient survey. Setting and participants Five general practices in England with non-medical prescribing services, questionnaires completed by 451 patients. Main outcome measure Stated choice of consultation. Main results There was a strong general preference for consulting ‘own doctor’ for minor illness. However, a consultation with a nurse prescriber with positive patient-focused attributes can be more acceptable to patients than a consultation provided by a doctor. Attributes ‘professional’s attention to patients’ views’ and extent of ‘help offered’ were pivotal. Past experience influenced preference. Discussion and conclusion Respondents demonstrated valid preferences. Preferences for consulting a doctor remained strong, but many were happy to consult with a nurse if other aspects of the consultation were improved. Findings show who to consult is not the only valued factor in choice of consultation for minor illness. The ‘prescribing nurse’ role has potential to offer consultation styles that patients value. Within the study’s limitations, these findings can inform delivery of primary care to enhance patient experience and substitute appropriate nurse prescribing consultations for medical prescribing consultations.
    • Pattern searches for the identification of putative lipoprotein genes in Gram positive bacterial genomes

      Harrington, Dean J.; Sutcliffe, I.C. (2002)
      N-terminal lipidation is a major mechanism by which bacteria can tether proteins to membranes and one which is of particular importance to Gram-positive bacteria due to the absence of a retentive outer membrane. Lipidation is directed by the presence of a cysteine-containing `lipobox' within the lipoprotein signal peptide sequence and this feature has greatly facilitated the identification of putative lipoproteins by gene sequence analysis. The properties of lipoprotein signal peptides have been described previously by the Prosite pattern PS00013. Here, a dataset of 33 experimentally verified Gram-positive bacterial lipoproteins (excluding those from Mollicutes) has been identified by an extensive literature review. The signal peptide features of these lipoproteins have been analysed to create a refined pattern, G+LPP, which is more specific for the identification of Gram-positive bacterial lipoproteins. The ability of this pattern to identify probable lipoprotein sequences is demonstrated by a search of the genome of Streptococcus pyogenes, in comparison with sequences identified using PS00013. Greater discrimination against likely false-positives was evident from the use of G+LPP compared with PS00013. These data confirm the likely abundance of lipoproteins in Gram-positive bacterial genomes, with at least 25 probable lipoproteins identified in S. pyogenes
    • Patterns of cancer cell sphere formation in primary cultures of human oral tongue squamous cell carcinoma and neck nodes

      Saleem, Saira; Jamshed, A.; Faisal, S.; Hussain, R.; Tahseen, M.; Loya, A.; Sutton, Chris W. (2014-12-21)
      Recently a sub-population of cells with stem cell characteristics, reported to be associated with initiation, growth, spread and recurrence, has been identified in several solid tumors including oral tongue squamous cell carcinoma (OTSCC). The aim of our pilot study was to isolate CD44+ cancer stem cells from primary cultures of OTSCC and neck node Level I (node-I) biopsies, grow cell spheres and observe their characteristics in primary cultures. Parallel cultures of hyperplastic lesions of tongue (non-cancer) were set up as a control. Immunohistochemistry was used to detect CD44/CD24 expression and magnetic activated cell sorting to isolate CD44+ cell populations followed by primary cell culturing. Both OTSCC and node-I biopsies produced floating spheres in suspension, however those grown in hyperplastic and node-I primary cultures did not exhibit self-renewal properties. Lymph node metastatic OTSCC, express higher CD44/CD24 levels, produce cancer cell spheres in larger number and rapidly (24 hours) compared to node negative OTSCC (1 week) and non-cancer specimens (3 weeks). In addition, metastatic OTSCC have the capacity for proliferation for up to three generations in primary culture. This in vitro system will be used to study cancer stem cell behavior, therapeutic drug screening and optimization of radiation dose for elimination of resistant cancer cells.
    • Peer-to-peer learning processes ¿ an Ecoversity case study

      Hopkinson, Peter G.; Miles, S.; Hughes, P.; Comerford Boyes, Louise (2009)
    • penalized: A MATLAB toolbox for fitting generalized linear models with penalties

      McIlhagga, William H. (2016-08-28)
      penalized is a exible, extensible, and e cient MATLAB toolbox for penalized maximum likelihood. penalized allows you to t a generalized linear model (gaussian, logistic, poisson, or multinomial) using any of ten provided penalties, or none. The toolbox can be extended by creating new maximum likelihood models or new penalties. The toolbox also includes routines for cross-validation and plotting.