Exploring machine learning in chemistry through the classification of spectra: an undergraduate project

Applications of machine learning in chemistry are many and varied, from prediction of structure–property relationships, to modeling of potential energy surfaces for large scale atomistic simulations. We describe a generalized approach for the application of machine learning to the classification of spectra which can be used as the basis for a wide variety of undergraduate projects. While our examples use FTIR and mass spectra, the approach could equally well be used with UV–visible, Raman, NMR, or indeed any other type of spectra. We summarize a number of different unsupervised and supervised machine learning algorithms that can be used to classify spectra into groups, and illustrate their application using data from three different projects carried out by fourth year chemistry undergraduates. The three projects investigated the ability of the various machine learning approaches to correctly classify spectra of a variety of fruits, whiskies, and teas, respectively. In all cases the algorithms were able to differentiate between the various samples used in each study, and the trained machine learning models could then be used to classify unknown samples with a high degree of accuracy (>98% in many cases). Depending on the extent to which students are expected to write their own code to perform the data analysis, the general model adopted in this work can be adapted for a variety of purposes, from short (one to two day) practical exercises and workshops, to much longer independent student projects

Development and validation of Australian aphasia rehabilitation best practice statements using the RAND/UCLA appropriateness method

Objectives: To develop and validate a national set of best practice statements for use in post-stroke aphasia rehabilitation. Design: Literature review and statement validation using the RAND/UCLA Appropriateness Method (RAM). Participants: A national Community of Practice of over 250 speech pathologists, researchers, consumers and policymakers developed a framework consisting of eight areas of care in aphasia rehabilitation. This framework provided the structure for the development of a care pathway containing aphasia rehabilitation best practice statements. Nine speech pathologists with expertise in aphasia rehabilitation participated in two rounds of RAND/UCLA appropriateness ratings of the statements. Panellists consisted of researchers, service managers, clinicians and policymakers. Main outcomes measures: Statements that achieved a high level of agreement and an overall median score of 7–9 on a nine-point scale were rated as ‘appropriate’. Results: 74 best practice statements were extracted from the literature and rated across eight areas of care (eg, receiving the right referrals, providing intervention). At the end of Round 1, 71 of the 74 statements were rated as appropriate, no statements were rated as inappropriate, and three statements were rated as uncertain. All 74 statements were then rated again in the face-to-face second round. 16 statements were added through splitting existing items or adding new statements. Seven statements were deleted leaving 83 statements. Agreement was reached for 82 of the final 83 statements. Conclusions: This national set of 82 best practice statements across eight care areas for the rehabilitation of people with aphasia is the first to be validated by an expert panel. These statements form a crucial component of the Australian Aphasia Rehabilitation Pathway (AARP) (http://www.aphasiapathway.com.au) and provide the basis for more consistent implementation of evidence-based practice in stroke rehabilitation

Anticipating and Managing Future Trade-offs and Complementarities between Ecosystem Services

This paper shows how, with the aid of computer models developed in close collaboration with decision makers and other stakeholders, it is possible to quantify and map how policy decisions are likely to affect multiple ecosystem services in future. In this way, potential trade-offs and complementarities between different ecosystem services can be identified, so that policies can be designed to avoid the worst trade-offs, and where possible, enhance multiple services. The paper brings together evidence from across the Rural Economy and Land Use Programme’s Sustainable Uplands project for the first time, with previously unpublished model outputs relating to runoff, agricultural suitability, biomass, heather cover, age, and utility for Red Grouse (Lagopus scotica), grass cover, and accompanying scenario narratives and video. Two contrasting scenarios, based on policies to extensify or intensify land management up to 2030, were developed through a combination of interviews and discussions during site visits with stakeholders, literature review, conceptual modeling, and process-based computer models, using the Dark Peak of the Peak District National Park in the UK as a case study. Where extensification leads to a significant reduction in managed burning and grazing or land abandonment, changes in vegetation type and structure could compromise a range of species that are important for conservation, while compromising provisioning services, amenity value, and increasing wildfire risk. However, where extensification leads to the restoration of peatlands damaged by former intensive management, there would be an increase in carbon sequestration and storage, with a number of cobenefits, which could counter the loss of habitats and species elsewhere in the landscape. In the second scenario, land use and management was significantly intensified to boost UK self-sufficiency in food. This would benefit certain provisioning services but would have negative consequences for carbon storage and water quality and would lead to a reduction in the abundance of certain species of conservation concern. The paper emphasizes the need for spatially explicit models that can track how ecosystem services might change over time, in response to policy or environmental drivers, and in response to the changing demands and preferences of society, which are far harder to anticipate. By developing such models in close collaboration with decision makers and other stakeholders, it is possible to depict scenarios of real concern to those who need to use the research findings. By engaging these collaborators with the research findings through film, it was possible to discuss adaptive options to minimize trade-offs and enhance the provision of multiple ecosystem services under the very different future conditions depicted by each scenario. By preparing for as wide a range of futures as possible in this way, it may be possible for decision makers to act rapidly and effectively to protect and enhance the provision of ecosystem services in the face of unpredictable future change.Additional co-authors: Nanlin Jin, Brian J Irvine, Mike J Kirkby, William E Kunin, Christina Prell, Claire H Quinn, Bill Slee, Sigrid Stagl, Mette Termansen, Simon Thorp, and Fred Worral

A consensus statement on perinatal mental health during the COVID-19 pandemic and recommendations for post-pandemic recovery and re-build

Introduction: The COVID-19 pandemic posed a significant lifecourse rupture, not least to those who had specific physical vulnerabilities to the virus, but also to those who were suffering with mental ill health. Women and birthing people who were pregnant, experienced a perinatal bereavement, or were in the first post-partum year (i.e., perinatal) were exposed to a number of risk factors for mental ill health, including alterations to the way in which their perinatal care was delivered. Methods: A consensus statement was derived from a cross-disciplinary collaboration of experts, whereby evidence from collaborative work on perinatal mental health during the COVID-19 pandemic was synthesised, and priorities were established as recommendations for research, healthcare practice, and policy. Results: The synthesis of research focused on the effect of the COVID-19 pandemic on perinatal health outcomes and care practices led to three immediate recommendations: what to retain, what to reinstate, and what to remove from perinatal mental healthcare provision. Longer-term recommendations for action were also made, categorised as follows: Equity and Relational Healthcare; Parity of Esteem in Mental and Physical Healthcare with an Emphasis on Specialist Perinatal Services; and Horizon Scanning for Perinatal Mental Health Research, Policy, & Practice. Discussion: The evidence base on the effect of the pandemic on perinatal mental health is growing. This consensus statement synthesises said evidence and makes recommendations for a post-pandemic recovery and re-build of perinatal mental health services and care provision

Structural Basis of Cytotoxicity Mediated by the Type III Secretion Toxin ExoU from Pseudomonas aeruginosa

The type III secretion system (T3SS) is a complex macromolecular machinery employed by a number of Gram-negative pathogens to inject effectors directly into the cytoplasm of eukaryotic cells. ExoU from the opportunistic pathogen Pseudomonas aeruginosa is one of the most aggressive toxins injected by a T3SS, leading to rapid cell necrosis. Here we report the crystal structure of ExoU in complex with its chaperone, SpcU. ExoU folds into membrane-binding, bridging, and phospholipase domains. SpcU maintains the N-terminus of ExoU in an unfolded state, required for secretion. The phospholipase domain carries an embedded catalytic site whose position within ExoU does not permit direct interaction with the bilayer, which suggests that ExoU must undergo a conformational rearrangement in order to access lipids within the target membrane. The bridging domain connects catalytic domain and membrane-binding domains, the latter of which displays specificity to PI(4,5)P2. Both transfection experiments and infection of eukaryotic cells with ExoU-secreting bacteria show that ExoU ubiquitination results in its co-localization with endosomal markers. This could reflect an attempt of the infected cell to target ExoU for degradation in order to protect itself from its aggressive cytotoxic action

A review of gas-surface interaction models for orbital aerodynamics applications

Renewed interest in Very Low Earth Orbits (VLEO) - i.e. altitudes below 450 km - has led to an increased demand for accurate environment characterisation and aerodynamic force prediction. While the former requires knowledge of the mechanisms that drive density variations in the thermosphere, the latter also depends on the interactions between the gas-particles in the residual atmosphere and the surfaces exposed to the flow. The determination of the aerodynamic coefficients is hindered by the numerous uncertainties that characterise the physical processes occurring at the exposed surfaces. Several models have been produced over the last 60 years with the intent of combining accuracy with relatively simple implementations. In this paper the most popular models have been selected and reviewed using as discriminating factors relevance with regards to orbital aerodynamics applications and theoretical agreement with gas-beam experimental data. More sophisticated models were neglected, since their increased accuracy is generally accompanied by a substantial increase in computation times which is likely to be unsuitable for most space engineering applications. For the sake of clarity, a distinction was introduced between physical and scattering kernel theory based gas-surface interaction models. The physical model category comprises the Hard Cube model, the Soft Cube model and the Washboard model, while the scattering kernel family consists of the Maxwell model, the Nocilla-Hurlbut-Sherman model and the Cercignani-Lampis-Lord model. Limits and assets of each model have been discussed with regards to the context of this paper. Wherever possible, comments have been provided to help the reader to identify possible future challenges for gas-surface interaction science with regards to orbital aerodynamic applications

Economic evaluation protocol of a short, all-oral bedaquiline-containing regimen for the treatment of rifampicin-resistant tuberculosis from the STREAM trial

Introduction: A December 2019 WHO rapid communication recommended the use of 9-month all-oral regimens for treating multidrug-resistant tuberculosis (MDR-TB). Besides the clinical benefits, they are thought to be less costly than the injectable-containing regimens, for both the patient and the health system. STREAM is the first randomised controlled trial with an economical evaluation to compare all-oral and injectable-containing 9–11-month MDR-TB treatment regimens. Methods and analysis: Health system costs of delivering a 9-month injectable-containing regimen and a 9-month all-oral bedaquiline-containing regimen will be collected in Ethiopia, India, Moldova and Uganda, using ‘bottom-up’ and ‘top-down’ costing approaches. Patient costs will be collected using questionnaires that have been developed based on the STOP-TB questionnaire. The primary objective of the study is to estimate the cost utility of the two regimens, from a health system perspective. Secondary objectives include estimating the cost utility from a societal perspective as well as evaluating the cost-effectiveness of the regimens, using both health system and societal perspectives. The effect measure for the cost–utility analysis will be the quality-adjusted life years (QALY), while the effect measure for the cost-effectiveness analysis will be the efficacy outcome from the clinical trial. Ethics and dissemination: The study has been evaluated and approved by the Ethics Advisory Group of the International Union Against Tuberculosis and Lung Disease and also approved by ethics committees in all participating countries. All participants have provided written informed consent. The results of the economic evaluation will be published in a peer-reviewed journal. Trial registration number: ISRCTN18148631

Key role of NO3 radicals in the production of isoprene nitrates and nitrooxyorganosulfates in Beijing

The formation of isoprene nitrates (IsN) can lead to significant secondary organic aerosol (SOA) production and they can act as reservoirs of atmospheric nitrogen oxides. In this work, we estimate the rate of production of IsN from the reactions of isoprene with OH and NO3 radicals during the summertime in Beijing. While OH dominates the loss of isoprene during the day, NO3 plays an increasingly important role in the production of IsN from the early afternoon onwards. Unusually low NO concentrations during the afternoon resulted in NO3 mixing ratios of ca. 2 pptv at approximately 15:00, which we estimate to account for around a third of the total IsN production in the gas phase. Heterogeneous uptake of IsN produces nitrooxyorganosulfates (NOS). Two mono-nitrated NOS were correlated with particulate sulfate concentrations and appear to be formed from sequential NO3 and OH oxidation. Di- and tri-nitrated isoprene-related NOS, formed from multiple NO3 oxidation steps, peaked during the night. This work highlights that NO3 chemistry can play a key role in driving biogenic–anthropogenic interactive chemistry in Beijing with respect to the formation of IsN during both the day and night

Mother, Monster, Mrs, I:A critical evaluation of gendered naming strategies in English sentencing remarks of women who kill

In this article, we take a novel approach to analysing English sentencing remarks in cases of women who kill. We apply computational, quantitative, and qualitative methods from corpus linguistics to analyse recurrent patterns in a collection of English Crown Court sentencing remarks from 2012 to 2015, where a female defendant was convicted of a homicide offence. We detail the ways in which women who kill are referred to by judges in the sentencing remarks, providing frequency information on pronominal, nominative, and categorising naming strategies. In discussion of the various patterns of preference both across and within these categories (e.g. pronoun vs. nomination, title + surname vs. forename + surname), we remark upon the identities constructed through the references provided. In so doing, we: (1) quantify the extent to which members of the judiciary invoke patriarchal values and gender stereotypes within their sentencing remarks to construct female defendants, and (2) identify particular identities and narratives that emerge within sentencing remarks for women who kill. We find that judges refer to women who kill in a number of ways that systematically create dichotomous narratives of degraded victims or dehumanised monsters. We also identify marked absences in naming strategies, notably: physical identification normally associated with narrativization of women’s experiences; and the first person pronoun, reflecting omissions of women’s own voices and narratives of their lived experiences in the courtroom

Economic evaluation of shortened, bedaquiline-containing treatment regimens for rifampicin-resistant tuberculosis (STREAM stage 2) : a within-trial analysis of a randomised controlled trial

Background: The STREAM stage 2 trial assessed two bedaquiline-containing regimens for rifampicin-resistant tuberculosis: a 9-month all-oral regimen and a 6-month regimen containing an injectable drug for the first 2 months. We did a within-trial economic evaluation of these regimens. Methods: STREAM stage 2 was an international, phase 3, non-inferiority randomised trial in which participants with rifampicin-resistant tuberculosis were randomly assigned (1:2:2:2) to the 2011 WHO regimen (terminated early), a 9-month injectable-containing regimen (control regimen), a 9-month all-oral regimen with bedaquiline (oral regimen), or a 6-month regimen with bedaquiline and an injectable for the first 2 months (6-month regimen). We prospectively collected direct and indirect costs and health-related quality of life data from trial participants until week 76 of follow-up. Cost-effectiveness of the oral and 6-month regimens versus control was estimated in four countries (oral regimen) and two countries (6-month regimen), using health-related quality of life for cost-utility analysis and trial efficacy for cost-effectiveness analysis. This trial is registered with ISRCTN, ISRCTN18148631. Findings: 300 participants were included in the economic analyses (Ethiopia, 61; India, 142; Moldova, 51; Uganda, 46). In the cost-utility analysis, the oral regimen was not cost-effective in Ethiopia, India, Moldova, and Uganda from either a provider or societal perspective. In Moldova, the oral regimen was dominant from a societal perspective. In the cost-effectiveness analysis, the oral regimen was likely to be cost-effective from a provider perspective at willingness-to-pay thresholds per additional favourable outcome of more than US$4500 in Ethiopia,$1900 in India, $3950 in Moldova, and$7900 in Uganda, and from a societal perspective at thresholds of more than $15 900 in Ethiopia,$3150 in India, and $4350 in Uganda, while in Moldova the oral regimen was dominant. In Ethiopia and India, the 6-month regimen would cost tuberculosis programmes and participants less than the control regimen and was highly likely to be cost-effective in both cost-utility analysis and cost-effectiveness analysis. Reducing the bedaquiline price from$1·81 to $1·00 per tablet made the oral regimen cost-effective in the provider-perspective cost-utility analysis in India and Moldova and dominate over the control regimen in the provider-perspective cost-effectiveness analysis in India. Interpretation: At current costs, the oral bedaquiline-containing regimen for rifampicin-resistant tuberculosis is unlikely to be cost-effective in many low-income and middle-income countries. The 6-month regimen represents a cost-effective alternative if injectable use for 2 months is acceptable. Funding: USAID and Janssen Research & Development