Support vector machines for drug discovery

Support vector machines (SVMs) have displayed good predictive accuracy on a wide range of classification tasks and are inherently adaptable to complex problem domains. Structure-property correlation (SPC) analysis is a vital part of the contemporary drug discovery process, in which several components of the search for novel molecular compounds with therapeutic potential may be performed by computer (in silicd). Inferred relationships between molecular structure and biological properties of interest are used to eliminate compounds unsuitable for further development. In order to improve process efficiency without rejecting useful compounds, predictive accuracy of such relationships must remain high despite a paucity of data from which to infer them. This thesis describes the application of SVMs to SPC analysis and investigates methods with which to enhance performance and facilitate integration of the technique into present practice. Overviews of contemporary drug discovery and the role of machine learning place the investigation into context. Computational discrimination between compounds according to their structures and properties of interest is described in detail, as is the SVM algorithm. A framework for the assessment of supervised machine learning performance on SPC data is proposed and employed to assess SVM performance alongside state-of-the-art techniques for in silico SPC analysis on data provided by GlaxoSmithKline. SVM performance is competitive and the comparison prompts adaptations of both data treatment and algorithmic application to explore the effects of data paucity, class imbalance and outlying data. Subsequent work weights the SVM kernel matrix to recognise heavily populated regions of training data and suggests the incorporation of domain-specific clustering methods to assist the standard SVM algorithm. The notion that SVM kernel functions may incorporate existing domain-specific methods leads to kernel functions that employ existing pharmaceutical similarity measures to treat an abstract, binary representation of molecular structure that is not used widely for SPC analysis

The total synthesis of (-)-cyanthiwigin F by means of double catalytic enantioselective alkylation

Double catalytic enantioselective transformations are powerful synthetic methods that can facilitate the construction of stereochemically complex molecules in a single operation. In addition to generating two or more stereocentres in a single reaction, multiple asymmetric reactions also impart increased enantiomeric excess to the final product in comparison with the analogous single transformation. Furthermore, multiple asymmetric operations have the potential to independently construct several stereocentres at remote points within the same molecular scaffold, rather than relying on pre-existing chiral centres that are proximal to the reactive site. Despite the inherent benefits of multiple catalytic enantioselective reactions, their application to natural product total synthesis remains largely underutilized. Here we report the use of a double stereoablative enantioselective alkylation reaction in a concise synthesis of the marine diterpenoid (-)-cyanthiwigin F (ref. 8). By employing a technique for independent, selective formation of two stereocentres in a single stereoconvergent operation, we demonstrate that a complicated mixture of racemic and meso diastereomers may be smoothly converted to a synthetically useful intermediate with exceptional enantiomeric excess. The stereochemical information generated by means of this catalytic transformation facilitates the easy and rapid completion of the total synthesis of this marine natural product

Developing a community based psychosocial intervention with older people and third sector workers for anxiety and depression: a qualitative study

Background: One-in-five people in the UK experience anxiety and/or depression in later life. However, anxiety and depression remain poorly detected in older people, particularly in those with chronic physical ill health. In the UK, a stepped care approach, to manage common mental health problems, is advocated which includes service provision from non-statutory organisations (including third/voluntary sector). However, evidence to support such provision, including the most effective interventions, is limited. The qualitative study reported here constitutes the first phase of a feasibility study which aims to assess whether third sector workers can deliver a psychosocial intervention to older people with anxiety and/or depression. The aim of this qualitative study is to explore the views of older people and third sector workers about anxiety and depression among older people in order to refine an intervention to be delivered by third sector workers. Methods: Semi-structured interviews with participants recruited through purposive sampling from third sector groups in North Staffordshire. Interviews were digitally recorded with consent, transcribed and analysed using principles of constant comparison. Results: Nineteen older people and 9 third sector workers were interviewed. Key themes included: multiple forms of loss, mental health as a personal burden to bear, having courage and providing/receiving encouragement, self- worth and the value of group activities, and tensions in existing service provision, including barriers and gaps. Conclusions: The experience of loss was seen as central to feelings of anxiety and depression among community- dwelling older people. This study contributes to the evidence pointing to the scale and severity of mental health needs for some older people which can arise from multiple forms of loss, and which present a significant challenge to health, social care and third sector services. The findings informed development of a psychosocial intervention and training for third sector workers to deliver the intervention

Real-time observation of multiexcitonic states in ultrafast singlet fission using coherent 2D electronic spectroscopy.

Singlet fission is the spin-allowed conversion of a spin-singlet exciton into a pair of spin-triplet excitons residing on neighbouring molecules. To rationalize this phenomenon, a multiexcitonic spin-zero triplet-pair state has been hypothesized as an intermediate in singlet fission. However, the nature of the intermediate states and the underlying mechanism of ultrafast fission have not been elucidated experimentally. Here, we study a series of pentacene derivatives using ultrafast two-dimensional electronic spectroscopy and unravel the origin of the states involved in fission. Our data reveal the crucial role of vibrational degrees of freedom coupled to electronic excitations that facilitate the mixing of multiexcitonic states with singlet excitons. The resulting manifold of vibronic states drives sub-100 fs fission with unity efficiency. Our results provide a framework for understanding singlet fission and show how the formation of vibronic manifolds with a high density of states facilitates fast and efficient electronic processes in molecular systems.This is the author accepted manuscript. The final version is available from NPG via http://dx.doi.org/10.1038/nchem.237

Singlet exciton fission in solution.

Singlet exciton fission, the spin-conserving process that produces two triplet excited states from one photoexcited singlet state, is a means to circumvent the Shockley-Queisser limit in single-junction solar cells. Although the process through which singlet fission occurs is not well characterized, some local order is thought to be necessary for intermolecular coupling. Here, we report a triplet yield of 200% and triplet formation rates approaching the diffusion limit in solutions of bis(triisopropylsilylethynyl (TIPS)) pentacene. We observe a transient bound excimer intermediate, formed by the collision of one photoexcited and one ground-state TIPS-pentacene molecule. The intermediate breaks up when the two triplets separate to each TIPS-pentacene molecule. This efficient system is a model for future singlet-fission materials and for disordered device components that produce cascades of excited states from sunlight.B.J.W. was supported by a Herchel Smith Research Fellowship. A.J.M. received funding from a Marie Curie Scholarship. D.B. is a FNRS Research Director. Both A.J.M and D.B. acknowledge support from the European Community’s Initial Training Network SUPERIOR (PITN-GA-2009-238177). Further funding for this project came from the Engineering and Physical Sciences Research Council (EPSRC) and a pump-prime grant from the Winton Programme for the Physics of Sustainability.This is the accepted version of an article originally published in Nature Chemistry 5, 1019–1024 and available online at http://www.nature.com/nchem/journal/v5/n12/full/nchem.1801.html. Nature Publishing Group's conditions for reuse are detailed at http://www.nature.com/authors/policies/license.html

The need of dermatologists, psychiatrists and psychologists joint care in psychodermatology

The mind-skin connection has been studied since the nineteenth century. The last 40 years have set the development of new research areas which allowed the clarifying of how these two dimensions interact. The diseases that involve skin and mind constitute the field of psychodermatology and require that specialists in dermatology, psychiatry and psychology together and integrated take part in it, since skin, nervous system and mind are simultaneously affected. This paper aims to expose how psychodermatoses are currently conceptualized and the need of integration of these three specialties for conveniently treating the patients

A feasibility study for NOn-Traditional providers to support the management of Elderly People with Anxiety and Depression: the NOTEPAD study Protocol

BACKGROUND: Anxiety and depression are common among older people, with up to 20% reporting such symptoms, and the prevalence increases with co-morbid chronic physical health problems. Access to treatment for anxiety and depression in this population is poor due to a combination of factors at the level of patient, practitioner and healthcare system. There is evidence to suggest that older people with anxiety and/or depression may benefit both from one-to-one interventions and group social or educational activities, which reduce loneliness, are participatory and offer some activity. Non-traditional providers (support workers) working within third-sector (voluntary) organisations are a valuable source of expertise within the community but are under-utilised by primary care practitioners. Such a resource could increase access to care, and be less stigmatising and more acceptable for older people. METHODS: The study is in three phases and this paper describes the protocol for phase III, which will evaluate the feasibility of recruiting general practices and patients into the study, and determine whether support workers can deliver the intervention to older people with sufficient fidelity and whether this approach is acceptable to patients, general practitioners and the third-sector providers. Phase III of the NOTEPAD study is a randomised controlled trial (RCT) that is individually randomised. It recruited participants from approximately six general practices in the UK. In total, 100 participants aged 65 years and over who score 10 or more on PHQ9 or GAD7 for anxiety or depression will be recruited and randomised to the intervention or usual general practice care. A mixed methods approach will be used and follow-up will be conducted 12 weeks post-randomisation. DISCUSSION: This study will inform the design and methods of a future full-scale RCT. TRIAL REGISTRATION: ISRCTN, ID: ISRCTN16318986 . Registered 10 November 2016. The ISRCTN registration is in line with the World Health Organization Trial Registration Data Set. The present paper represents the original version of the protocol. Any changes to the protocol will be communicated to ISRCTN

A two-step target binding and selectivity support vector machines approach for virtual screening of dopamine receptor subtype-selective ligands

10.1371/journal.pone.0039076PLoS ONE76

The association between internet addiction and psychiatric co-morbidity: A meta-analysis

Background: This study evaluates the association between Internal Addiction (IA) and psychiatric co-morbidity in the literature.Methods: Meta-analyses were conducted on cross-sectional, case-control and cohort studies which examined the relationship between IA and psychiatric co-morbidity. Selected studies were extracted from major online databases. The inclusion criteria are as follows: 1) studies conducted on human subjects; 2) IA and psychiatric co-morbidity were assessed by standardised questionnaires; and 3) availability of adequate information to calculate the effect size. Random-effects models were used to calculate the aggregate prevalence and the pooled odds ratios (OR).Results: Eight studies comprising 1641 patients suffering from IA and 11210 controls were included. Our analyses demonstrated a significant and positive association between IA and alcohol abuse (OR = 3.05, 95% CI = 2.14-4.37, z = 6.12, P < 0.001), attention deficit and hyperactivity (OR = 2.85, 95% CI = 2.15-3.77, z = 7.27, P < 0.001), depression (OR = 2.77, 95% CI = 2.04-3.75, z = 6.55, P < 0.001) and anxiety (OR = 2.70, 95% CI = 1.46-4.97, z = 3.18, P = 0.001).Conclusions: IA is significantly associated with alcohol abuse, attention deficit and hyperactivity, depression and anxiety. © 2014 Ho et al.; licensee BioMed Central Ltd