A toolbox for representational similarity analysis.

Neuronal population codes are increasingly being investigated with multivariate pattern-information analyses. A key challenge is to use measured brain-activity patterns to test computational models of brain information processing. One approach to this problem is representational similarity analysis (RSA), which characterizes a representation in a brain or computational model by the distance matrix of the response patterns elicited by a set of stimuli. The representational distance matrix encapsulates what distinctions between stimuli are emphasized and what distinctions are de-emphasized in the representation. A model is tested by comparing the representational distance matrix it predicts to that of a measured brain region. RSA also enables us to compare representations between stages of processing within a given brain or model, between brain and behavioral data, and between individuals and species. Here, we introduce a Matlab toolbox for RSA. The toolbox supports an analysis approach that is simultaneously data- and hypothesis-driven. It is designed to help integrate a wide range of computational models into the analysis of multichannel brain-activity measurements as provided by modern functional imaging and neuronal recording techniques. Tools for visualization and inference enable the user to relate sets of models to sets of brain regions and to statistically test and compare the models using nonparametric inference methods. The toolbox supports searchlight-based RSA, to continuously map a measured brain volume in search of a neuronal population code with a specific geometry. Finally, we introduce the linear-discriminant t value as a measure of representational discriminability that bridges the gap between linear decoding analyses and RSA. In order to demonstrate the capabilities of the toolbox, we apply it to both simulated and real fMRI data. The key functions are equally applicable to other modalities of brain-activity measurement. The toolbox is freely available to the community under an open-source license agreement (http://www.mrc-cbu.cam.ac.uk/methods-and-resources/toolboxes/license/)

Neurobiological systems for lexical representation and analysis in English.

Current research suggests that language comprehension engages two joint but functionally distinguishable neurobiological processes: a distributed bilateral system, which supports general perceptual and interpretative processes underpinning speech comprehension, and a left hemisphere (LH) frontotemporal system, selectively tuned to the processing of combinatorial grammatical sequences, such as regularly inflected verbs in English [Marslen-Wilson, W. D., & Tyler, L. K. Morphology, language and the brain: The decompositional substrate for language comprehension. Philosophical Transactions of the Royal Society: Biological Sciences, 362, 823-836, 2007]. Here we investigated how English derivationally complex words engage these systems, asking whether they selectively activate the LH system in the same way as inflections or whether they primarily engage the bilateral system that support nondecompositional access. In an fMRI study, we saw no evidence for selective activation of the LH frontotemporal system, even for highly transparent forms like bravely. Instead, a combination of univariate and multivariate analyses revealed the engagement of a distributed bilateral system, modulated by factors of perceptual complexity and semantic transparency. We discuss the implications for theories of the processing and representation of English derivational morphology and highlight the importance of neurobiological constraints in understanding these processes

Comparison of two cash transfer strategies to prevent catastrophic costs for poor tuberculosis-affected households in low- and middle-income countries: An economic modelling study

BACKGROUND:Illness-related costs for patients with tuberculosis (TB) ≥20% of pre-illness annual household income predict adverse treatment outcomes and have been termed "catastrophic." Social protection initiatives, including cash transfers, are endorsed to help prevent catastrophic costs. With this aim, cash transfers may either be provided to defray TB-related costs of households with a confirmed TB diagnosis (termed a "TB-specific" approach); or to increase income of households with high TB risk to strengthen their economic resilience (termed a "TB-sensitive" approach). The impact of cash transfers provided with each of these approaches might vary. We undertook an economic modelling study from the patient perspective to compare the potential of these 2 cash transfer approaches to prevent catastrophic costs. METHODS AND FINDINGS:Model inputs for 7 low- and middle-income countries (Brazil, Colombia, Ecuador, Ghana, Mexico, Tanzania, and Yemen) were retrieved by literature review and included countries' mean patient TB-related costs, mean household income, mean cash transfers, and estimated TB-specific and TB-sensitive target populations. Analyses were completed for drug-susceptible (DS) TB-related costs in all 7 out of 7 countries, and additionally for drug-resistant (DR) TB-related costs in 1 of the 7 countries with available data. All cost data were reported in 2013 international dollars ($). The target population for TB-specific cash transfers was poor households with a confirmed TB diagnosis, and for TB-sensitive cash transfers was poor households already targeted by countries' established poverty-reduction cash transfer programme. Cash transfers offered in countries, unrelated to TB, ranged from$217 to $1,091/year/household. Before cash transfers, DS TB-related costs were catastrophic in 6 out of 7 countries. If cash transfers were provided with a TB-specific approach, alone they would be insufficient to prevent DS TB catastrophic costs in 4 out of 6 countries, and when increased enough to prevent DS TB catastrophic costs would require a budget between$3.8 million (95% CI: $3.8 million-$3.8 million) and $75 million (95$50 million-$100 million) per country. If instead cash transfers were provided with a TB-sensitive approach, alone they would be insufficient to prevent DS TB-related catastrophic costs in any of the 6 countries, and when increased enough to prevent DS TB catastrophic costs would require a budget between$298 million (95% CI: $219 million-$378 million) and $165,367 million (95$134,085 million-$196,425 million) per country. DR TB-related costs were catastrophic before and after TB-specific or TB-sensitive cash transfers in 1 out of 1 countries. Sensitivity analyses showed our findings to be robust to imputation of missing TB-related cost components, and use of 10% or 30% instead of 20% as the threshold for measuring catastrophic costs. Key limitations were using national average data and not considering other health and social benefits of cash transfers. CONCLUSIONS:A TB-sensitive cash transfer approach to increase all poor households' income may have broad benefits by reducing poverty, but is unlikely to be as effective or affordable for preventing TB catastrophic costs as a TB-specific cash transfer approach to defray TB-related costs only in poor households with a confirmed TB diagnosis. Preventing DR TB-related catastrophic costs will require considerable additional investment whether a TB-sensitive or a TB-specific cash transfer approach is used

Invasive everywhere? Phylogeographic analysis of the globally distributed tree pathogen Lasiodiplodia theobromae

Fungi in the Botryosphaeriaceae are important plant pathogens that persist endophytically in infected plant hosts. Lasiodiplodia theobromae is a prominent species in this family that infects numerous plants in tropical and subtropical areas. We characterized a collection of 255 isolates of L. theobromae from 52 plants and from many parts of the world to determine the global genetic structure and a possible origin of the fungus using sequence data from four nuclear loci. One to two dominant haplotypes emerged across all loci, none of which could be associated with geography or host; and no other population structure or subdivision was observed. The data also did not reveal a clear region of origin of the fungus. This global collection of L. theobromae thus appears to constitute a highly connected population. The most likely explanation for this is the human-mediated movement of plant material infected by this fungus over a long period of time. These data, together with related studies on other Botryosphaeriaceae, highlight the inability of quarantine systems to reduce the spread of pathogens with a prolonged latent phase.Supplementary material. Figure S1: Maximum likelihood tree of the tef1a sequence dataset for the initial identification of isolates for inclusion in this study. Included were type and paratype strains of other Lasiodiplodia species, Figure S2: STRUCTURE output from pairwise comparisons of populations. Each plot includes the DeltaK analysis from STRUCTURE HARVESTER (top) and the corresponding barplot for the highest value of K. Pairwise comparisons as follows: (a) north America and south America, (b) north America and Africa, (c) north America and Eurasia, (d) north America and Australasia, (e) south America and Africa, (f) south America and Eurasia, (g) south America and Australasia, (h) Africa and Eurasia, (i) Africa and Australasia and (j) Eurasia and Australasia, Table S1: Polymorphic sites for the respective haplotypes for the ITS, tef1a and tub2 datasets, Table S2: Haplotype assignments for every isolate used in this study, based on the sequence datasets, Table S3: Summary of haplotypes obtained and unique haplotypes (listed in brackets) found for each locus, Table S4: Posterior probabilities (with 95% confidence intervals in parentheses) of pairwise comparisons for three scenarios to test for possible ancestry between populations done in DIYABC. In scenario 1, population 1 is ancestral to both. In scenario 2, population 2 is ancestral to both. In scenario 3, both populations diverged from an unknown source population.The Department of Science and Technology (DST)-National Research Foundation (NRF) Centre of Excellence in Tree Health Biotechnology (CTHB) and members of the Tree Protection Co-operative Programme (TPCP), South Africa.http://www.mdpi.com/journal/forestsam2017Forestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant PathologyPlant Production and Soil Scienc

Botryosphaeriaceae associated with die-back of Schizolobium parahyba trees in South Africa and Ecuador

Die-back of Schizolobium parahyba var. amazonicum is a serious problem in plantations of these trees in Ecuador. Similar symptoms have also been observed on trees of this species in various parts of South Africa. The most common fungi isolated from disease symptoms on S. parahyba var. amazonicum in both locations were species of the Botryosphaeriaceae. The aim of this study was to identify these fungi from both Ecuador and South Africa, and to test their pathogenicity in greenhouse and field trials. Isolates obtained were grouped based on culture morphology and identified using comparisons of DNA sequence data for the internal transcribed spacer (ITS) and translation elongation factor 1[alpha] (TEF-1[alpha]) gene regions. The β-tubulin-2 (BT2) locus was also sequenced for some isolates where identification was difficult. Three greenhouse trials were conducted in South Africa along with a field trial in Ecuador. Neofusicoccum parvum was obtained from trees in both areas and was the dominant taxon in South Africa. Lasiodiplodia theobromae was the dominant taxon in Ecuador, probably due to the subtropical climate in the area. Isolates of Neofusicoccum vitifusiforme (from South Africa only), Neofusicoccum umdonicola and Lasiodiplodia pseudotheobromae (from Ecuador only) were also obtained. All isolates used in the pathogenicity trials produced lesions on inoculated plants, suggesting that the Botryosphaeriaceae contribute to the die-back of S. parahyba trees. While the disease is clearly not caused by a single species of the Botryosphaeriaceae in either region, N. parvum has been introduced into at least one of the regions. This species has a broad host range and could have been introduced on other hosts.The Department of Science and Technology (DST)/National Research Foundation (NRF) Centre of Excellence in Tree Health Biotechnology (CTHB) and members of the Tree Protection Co-operative Programme (TPCP), South Africa.http://onlinelibrary.wiley.comjournal/10.1111/(ISSN)1439-03292015-10-30hj201

Die-back of kiaat (Pterocarpus angolensis) in southern Africa : a cause for concern?

Pterocarpus angolensis (kiaat) is a well-known southern African tree species of commercial importance that occurs in several vegetation types in the Zambezian regional centre of endemism. The most prominent of these vegetation types are the Zambezian miombo woodland and undifferentiated woodland. A diverse range of ecosystems within these vegetation types necessitate adaptation by tree species to survive extremes of drought, temperature, altitude, soil nutrition and tolerate fire in order to compete with other plant species. There are several reports of a die-back disease of P. angolensis in Zambia, Zimbabwe and South Africa, but very little is known regarding the cause or significance of this problem. In this review, we provide details regarding the history of the disease and consider its possible causal agents. A pathology study conducted at three locations in South Africa on diseased and dying trees resulted in the collection of 199 fungal isolates; comprising saprophytic species such as Candida, Penicillium and Humicola, and potentially pathogenic species such as Lasiodiplodia theobromae, Cytospora spp. and Fusarium spp. Drought, during several years preceding disease, along with a lack of fire management may have contributed to both the present and past reports of tree die-back and death. Finally, an analysis is made of the importance of the problem and actions that might be taken to alleviate it.DST/NRF Centre of Excellence in Tree Health Biotechnology (CTHB)http://www.tandfonline.com/loi/tsfs20nf201

The Campbells: lordship, literature and liminality

The Campbells have the potential to offer much to the theme of literature and borders, given that the kindred’s astonishing political success in the late medieval and early modern period depended heavily upon the ability to negotiate multiple frontiers: between Highlands and Lowlands; between Gaelic Scotland and Ireland, and, especially after the Reformation, with England and the matter of Britain. This paper will explore the literary dimension to Campbell expansionism, from the Book of the Dean of Lismore in the earlier sixteenth century, to poetry addressed to dukes of Argyll in the earlier eighteenth century. Particular attention will be paid to the literary proclivities of the household of the Campbells of Glenorchy on either side of what appears to be a major watershed in 1550; and to the agenda of the Campbell protégé John Carswell, first post-Reformation bishop of the Isles, and author of the first printed book in Gaelic in either Scotland or Ireland, Foirm na n-Urrnuidheadh (‘The Form of Prayers’), published at Edinburgh in 1567

Diversity of symptom phenotypes in SARS-CoV-2 community infections observed in multiple large datasets

Variability in case severity and in the range of symptoms experienced has been apparent from the earliest months of the COVID-19 pandemic. From a clinical perspective, symptom variability might indicate various routes/mechanisms by which infection leads to disease, with different routes requiring potentially different treatment approaches. For public health and control of transmission, symptoms in community cases were the prompt on which action such as PCR testing and isolation was taken. However, interpreting symptoms presents challenges, for instance in balancing sensitivity and specificity of individual symptoms with the need to maximise case finding, whilst managing demand for limited resources such as testing. For both clinical and transmission control reasons, we require an approach that allows for the possibility of distinct symptom phenotypes, rather than assuming variability along a single dimension. Here we address this problem by bringing together four large and diverse datasets deriving from routine testing, a population-representative household survey and participatory smartphone surveillance in the United Kingdom. Through use of cutting-edge unsupervised classification techniques from statistics and machine learning, we characterise symptom phenotypes among symptomatic SARS-CoV-2 PCR-positive community cases, making comparisons across datasets and by age bands. While we observe separation due to the total number of symptoms experienced by cases, we also see a separation of symptoms into gastrointestinal, respiratory and other types, and different symptom co-occurrence patterns at the extremes of age. In this way, we are able to demonstrate the deep structure of symptoms of COVID-19 without usual biases due to study design.Comment: 52 pages; 25 figure

Convocation

Program listing performers and works performe