Time-resolved fluorescence of 2-aminopurine as a probe of base flipping in M.HhaI–DNA complexes

DNA base flipping is an important mechanism in molecular enzymology, but its study is limited by the lack of an accessible and reliable diagnostic technique. A series of crystalline complexes of a DNA methyltransferase, M.HhaI, and its cognate DNA, in which a fluorescent nucleobase analogue, 2-aminopurine (AP), occupies defined positions with respect the target flipped base, have been prepared and their structures determined at higher than 2 Å resolution. From time-resolved fluorescence measurements of these single crystals, we have established that the fluorescence decay function of AP shows a pronounced, characteristic response to base flipping: the loss of the very short (∼100 ps) decay component and the large increase in the amplitude of the long (∼10 ns) component. When AP is positioned at sites other than the target site, this response is not seen. Most significantly, we have shown that the same clear response is apparent when M.HhaI complexes with DNA in solution, giving an unambiguous signal of base flipping. Analysis of the AP fluorescence decay function reveals conformational heterogeneity in the DNA–enzyme complexes that cannot be discerned from the present X-ray structures

Evaluating implicit feedback models using searcher simulations

In this article we describe an evaluation of relevance feedback (RF) algorithms using searcher simulations. Since these algorithms select additional terms for query modification based on inferences made from searcher interaction, not on relevance information searchers explicitly provide (as in traditional RF), we refer to them as implicit feedback models. We introduce six different models that base their decisions on the interactions of searchers and use different approaches to rank query modification terms. The aim of this article is to determine which of these models should be used to assist searchers in the systems we develop. To evaluate these models we used searcher simulations that afforded us more control over the experimental conditions than experiments with human subjects and allowed complex interaction to be modeled without the need for costly human experimentation. The simulation-based evaluation methodology measures how well the models learn the distribution of terms across relevant documents (i.e., learn what information is relevant) and how well they improve search effectiveness (i.e., create effective search queries). Our findings show that an implicit feedback model based on Jeffrey's rule of conditioning outperformed other models under investigation

Characterisation of breast fine-needle aspiration biopsies by centrosome aberrations and genomic instability

Recent studies have suggested that aneuploidy in malignant tumours could be a consequence of centrosome aberrations. Using immunofluorescence analysis with an antibody against γ-tubulin and DNA image cytometry, we measured centrosome aberrations and DNA ploidy patterns in fine-needle aspiration biopsies (FNABs) of 58 breast lesions. Benign lesions did not show any centrosome aberrations. DNA diploid carcinomas showed a mean percentage of cells with centrosomal defects of 2.1%. The aneuploid invasive carcinomas could be divided into two subgroups by their significantly (P=0.0003) different percentage of cells with centrosome aberrations (2.0 and 10.3%, respectively) and their significantly (P=0.0003) different percentage of cells with nonmodal DNA content values determined by the Stemline Scatter Index (SSI), a measure of genomic instability. The percentage of cells with centrosome aberrations demonstrated a positive, linear correlation with the corresponding SSI (r=0.82, P<0.0001) and loss of tissue differentiation (r=0.78, P<0.0001). Our results indicate the percentage of cells with centrosome aberrations as being sufficient to divide the investigated tumours into three significantly different groups: benign lesions with no centrosomal aberrations, and two malignant tumour types with mean values of 2.1 and 9.6% of centrosomal defects, respectively. Together, these results demonstrate that centrosome aberrations correlate with genomic instability and loss of tissue differentiation. Furthermore, this study shows the feasibility of centrosomal analysis in FNAB of the breast and suggests centrosomal aberrations as possessing diagnostic and prognostic value

Bacteria-instructed synthesis of polymers for self-selective microbial binding and labelling

The detection and inactivation of pathogenic strains of bacteria continues to be an important therapeutic goal. Hence, there is a need for materials that can bind selectively to specific microorganisms, for diagnostic or anti-infective applications, but which can be formed from simple and inexpensive building blocks. Here, we exploit bacterial redox systems to induce a copper-mediated radical polymerisation of synthetic monomers at cell surfaces, generating polymers in situ that bind strongly to the microorganisms which produced them. This ‘bacteria-instructed synthesis’ can be carried out with a variety of microbial strains, and we show that the polymers produced are self-selective binding agents for the ‘instructing’ cell types. We further expand on the bacterial redox chemistries to ‘click’ fluorescent reporters onto polymers directly at the surfaces of a range of clinical isolate strains, allowing rapid, facile and simultaneous binding and visualisation of pathogens

Taking Two-Photon Excitation to Exceptional Path-Lengths in Photonic Crystal Fiber

The well-known, defining feature of two-photon excitation (TPE) is the tight, three-dimensional confinement of excitation at the intense focus of a laser beam. The extremely small excitation volume, on the order of 1 μm3 (1 femtoliter), is the basis of far-reaching applications of TPE in fluorescence imaging, photodynamic therapy, nanofabrication, and three-dimensional optical memory. Paradoxically, the difficulty of detecting photochemical events in such a small volume is a barrier to the development of the two-photon-activated molecular systems that are essential to the realization of such applications. We show, using two-photon-excited fluorescence to directly visualize the excitation path, that confinement of both laser beam and sample solution within the 20 μm hollow core of a photonic crystal fiber permits TPE to be sustained over an extraordinary path-length of more than 10 cm, presenting a new experimental paradigm for ultrasensitive studies of two-photon-induced processes in solution. (Figure Presented).We are grateful to the Koerber Foundation (Germany) and the EPSRC (UK) for financial support. G.O.S.W. is a recipient of an EPSRC Prize Postdoctoral Fellowshi

Considerations on Genre and Gender Conventions in Translating from Old English

The Old English poem The Wife's Lament is an extremely conventional and, at the same time, original text. It portrays a female character suffering for the absence of her loved one, through the framework of the so-called 'elegiac' style and a mainly heroic vocabulary. The traditional exile theme is, thus, interwoven with the uncommon motif of love sickness. While this appraisal of the poem is the most widely accepted one, disagreement still remains about the translation of some keywords, strictly related to the exile theme, such as sīþ or wræcsīþ. The aim of this paper is to examine diverging readings and glosses of the above mentioned 'exilic/elegiac' keywords, and to show that an accurate translation should not neglect a thorough appraisal of the text in its complexity and the association with related literary patterns and imagery in other poetic and prose texts

A multicentre, randomised controlled trial to compare the clinical and cost-effectiveness of Lee Silverman Voice Treatment versus standard NHS Speech and Language Therapy versus control in Parkinson’s disease: a study protocol for a randomised controlled trial

Abstract: Background: Parkinson’s disease (PD) affects approximately 145,519 people in the UK. Speech impairments are common with a reported prevalence of 68%, which increase physical and mental demands during conversation, reliance on family and/or carers, and the likelihood of social withdrawal reducing quality of life. In the UK, two approaches to Speech and Language Therapy (SLT) intervention are commonly available: National Health Service (NHS) SLT or Lee Silverman Voice Treatment (LSVT LOUD®). NHS SLT is tailored to the individuals’ needs per local practice typically consisting of six to eight weekly sessions; LSVT LOUD® comprises 16 sessions of individual treatment with home-based practice over 4 weeks. The evidence-base for their effectiveness is inconclusive. Methods/design: PD COMM is a phase III, multicentre, three-arm, unblinded, randomised controlled trial. Five hundred and forty-six people with idiopathic PD, reporting speech or voice problems will be enrolled. We will exclude those with a diagnosis of dementia, laryngeal pathology or those who have received SLT for speech problems in the previous 2 years. Following informed consent and completion of baseline assessments, participants will be randomised in a 1:1:1 ratio to no-intervention control, NHS SLT or LSVT LOUD® via a central computer-generated programme, using a minimisation procedure with a random element, to ensure allocation concealment. Participants randomised to the intervention groups will start treatment within 4 (NHS SLT) or 7 (LSVT LOUD®) weeks of randomisation. Primary outcome: Voice Handicap Index (VHI) total score at 3 months. Secondary outcomes include: VHI subscales, Parkinson’s Disease Questionnaire-39; Questionnaire on Acquired Speech Disorders; EuroQol-5D-5 L; ICECAP-O; resource utilisation; adverse events and carer quality of life. Mixed-methods process and health economic evaluations will take place alongside the trial. Assessments will be completed before randomisation and at 3, 6 and 12 months after randomisation. The trial started in December 2015 and will run for 77 months. Recruitment will take place in approximately 42 sites around the UK. Discussion: The trial will test the hypothesis that SLT is effective for the treatment of speech or voice problems in people with PD compared to no SLT. It will further test whether NHS SLT or LSVT LOUD® provide greater benefit and determine the cost-effectiveness of both interventions. Trial registration: International Standard Randomised Controlled Trials Number (ISRCTN) Registry, ID: 12421382. Registered on 18 April 2016

A multicentre, randomised controlled trial to compare the clinical and cost-effectiveness of Lee Silverman Voice Treatment versus standard NHS Speech and Language Therapy versus control in Parkinson’s disease: a study protocol for a randomised controlled trial

Abstract: Background: Parkinson’s disease (PD) affects approximately 145,519 people in the UK. Speech impairments are common with a reported prevalence of 68%, which increase physical and mental demands during conversation, reliance on family and/or carers, and the likelihood of social withdrawal reducing quality of life. In the UK, two approaches to Speech and Language Therapy (SLT) intervention are commonly available: National Health Service (NHS) SLT or Lee Silverman Voice Treatment (LSVT LOUD®). NHS SLT is tailored to the individuals’ needs per local practice typically consisting of six to eight weekly sessions; LSVT LOUD® comprises 16 sessions of individual treatment with home-based practice over 4 weeks. The evidence-base for their effectiveness is inconclusive. Methods/design: PD COMM is a phase III, multicentre, three-arm, unblinded, randomised controlled trial. Five hundred and forty-six people with idiopathic PD, reporting speech or voice problems will be enrolled. We will exclude those with a diagnosis of dementia, laryngeal pathology or those who have received SLT for speech problems in the previous 2 years. Following informed consent and completion of baseline assessments, participants will be randomised in a 1:1:1 ratio to no-intervention control, NHS SLT or LSVT LOUD® via a central computer-generated programme, using a minimisation procedure with a random element, to ensure allocation concealment. Participants randomised to the intervention groups will start treatment within 4 (NHS SLT) or 7 (LSVT LOUD®) weeks of randomisation. Primary outcome: Voice Handicap Index (VHI) total score at 3 months. Secondary outcomes include: VHI subscales, Parkinson’s Disease Questionnaire-39; Questionnaire on Acquired Speech Disorders; EuroQol-5D-5 L; ICECAP-O; resource utilisation; adverse events and carer quality of life. Mixed-methods process and health economic evaluations will take place alongside the trial. Assessments will be completed before randomisation and at 3, 6 and 12 months after randomisation. The trial started in December 2015 and will run for 77 months. Recruitment will take place in approximately 42 sites around the UK. Discussion: The trial will test the hypothesis that SLT is effective for the treatment of speech or voice problems in people with PD compared to no SLT. It will further test whether NHS SLT or LSVT LOUD® provide greater benefit and determine the cost-effectiveness of both interventions. Trial registration: International Standard Randomised Controlled Trials Number (ISRCTN) Registry, ID: 12421382. Registered on 18 April 2016

SPARC 2022 book of abstracts

Welcome to the Book of Abstracts for the 2022 SPARC conference. Our conference is called “Moving Forwards” reflecting our re-emergence from the pandemic and our desire to reconnect our PGR community, in celebration of their research. PGRs have continued with their research endeavours despite many challenges, and their ongoing successes are underpinned by the support and guidance of dedicated supervisors and the Doctoral School Team. To recognise supervision excellence we will be awarding our annual Supervisor of the Year prizes, based on the wonderful nominations received from their PGR students.Once again, we have received a tremendous contribution from our postgraduate research community; with over 60 presenters, 12 Three-Minute Thesis finalists, and 20 poster presentations, the conference showcases our extraordinarily vibrant, inclusive, and resilient PGR community at Salford. This year there will be prizes to be won for ‘best in conference’ presentations, in addition to the winners from each parallel session. Audience members too could be in for a treat, with judges handing out spot prizes for the best questions asked, so don’t miss the opportunity to put your hand up. These abstracts provide a taster of the diverse and impactful research in progress and provide delegates with a reference point for networking and initiating critical debate. Take advantage of the hybrid format: in online sessions by posting a comment or by messaging an author to say “Hello”, or by initiating break time discussions about the amazing research you’ve seen if you are with us in person. Who knows what might result from your conversation? With such wide-ranging topics being showcased, we encourage you to take up this great opportunity to engage with researchers working in different subject areas from your own. As recent events have shown, researchers need to collaborate to meet global challenges. Interdisciplinary and international working is increasingly recognised and rewarded by all major research funders. We do hope, therefore, that you will take this opportunity to initiate interdisciplinary conversations with other researchers. A question or comment from a different perspective can shed new light on a project and could lead to exciting collaborations, and that is what SPARC is all about. SPARC is part of a programme of personal and professional development opportunities offered to all postgraduate researchers at Salford. More information about this programme is available on our website: Doctoral School | University of Salford. Registered Salford students can access full details on the Doctoral School hub: Doctoral School Hub - Home (sharepoint.com) You can follow us on Twitter @SalfordPGRs and please use the #SPARC2022 to share your conference experience.We particularly welcome taught students from our undergraduate and master’s programmes as audience members. We hope you enjoy the presentations on offer and that they inspire you to pursue your own research career. If you would like more information about studying for a PhD here at the University of Salford, your lecturers can advise, or you can contact the relevant PGR Support Officer; their details can be found at Doctoral School | University of Salford. We wish you a rich and rewarding conference experience