Semantic cognition: a re-examination of the recurrent network "hub" model

This paper explores a model of “semantic cognition” first described in Rogers et al. (2004). This model was shown to reproduce the behaviour of neurological patients who perform poorly on a variety of tests of semantic knowledge; thus purporting to provide a comprehensive explanation for semantic deficits as found in patients with semantic dementia and, as extended in Lambon Ralph, Lowe, and Rogers (2007), individuals with herpes simplex virus encephalitis. Therefore, not only does the model emulate these semantic impairments, it also underpins a theoretical account of such memory disturbances. We report preliminary results arising from an attempted reimplementation of the Rogers et al. model. Specifically, while we were able to successfully reimplement the fully-functioning model and recreate “normal” behaviour, our attempts to replicate the behaviour of semantically impaired patients by lesioning the model were mixed. Our results suggest that while semantic impairments reminiscent of patients may arise when the Rogers et al. model is lesioned, such impairments are not a necessary consequence of the model. We discuss the implications of these apparently negative results for the Rogers et al. account of semantic cognition

Towards Decolonising Computational Sciences

This article sets out our perspective on how to begin the journey of decolonising computational fi elds, such as data and cognitive sciences. We see this struggle as requiring two basic steps: a) realisation that the present-day system has inherited, and still enacts, hostile, conservative, and oppressive behaviours and principles towards women of colour; and b) rejection of the idea that centring individual people is a solution to system-level problems. The longer we ignore these two steps, the more “our” academic system maintains its toxic structure, excludes, and harms Black women and other minoritised groups. This also keeps the door open to discredited pseudoscience, like eugenics and physiognomy. We propose that grappling with our fi elds’ histories and heritage holds the key to avoiding mistakes of the past. In contrast to, for example, initiatives such as “diversity boards”, which can be harmful because they superfi cially appear reformatory but nonetheless center whiteness and maintain the status quo. Building on the work of many women of colour, we hope to advance the dialogue required to build both a grass-roots and a top-down re-imagining of computational sciences — including but not limited to psychology, neuroscience, cognitive science, computer science, data science, statistics, machine learning, and artifi cial intelligence. We aspire to progress away fromthese fi elds’ stagnant, sexist, and racist shared past into an ecosystem that welcomes and nurturesdemographically diverse researchers and ideas that critically challenge the status quo

Towards decolonising computational sciences

This article sets out our perspective on how to begin the journey of decolonising computational fields, such as data and cognitive sciences. We see this struggle as requiring two basic steps: a) realisation that the present-day system has inherited, and still enacts, hostile, conservative, and oppressive behaviours and principles towards women of colour (WoC); and b) rejection of the idea that centering individual people is a solution to system-level problems. The longer we ignore these two steps, the more "our" academic system maintains its toxic structure, excludes, and harms Black women and other minoritised groups. This also keeps the door open to discredited pseudoscience, like eugenics and physiognomy. We propose that grappling with our fields' histories and heritage holds the key to avoiding mistakes of the past. For example, initiatives such as "diversity boards" can still be harmful because they superficially appear reformatory but nonetheless center whiteness and maintain the status quo. Building on the shoulders of many WoC's work, who have been paving the way, we hope to advance the dialogue required to build both a grass-roots and a top-down re-imagining of computational sciences -- including but not limited to psychology, neuroscience, cognitive science, computer science, data science, statistics, machine learning, and artificial intelligence. We aspire for these fields to progress away from their stagnant, sexist, and racist shared past into carving and maintaining an ecosystem where both a diverse demographics of researchers and scientific ideas that critically challenge the status quo are welcomed.Comment: A version of this work will appear in the Danish Journal of Women, Gender and Research (https://koensforskning.soc.ku.dk/english/kkof/) in December 202

Sensing the Shape of Canine Responses to Cancer

We conducted a short study investigating the pressure patterns produced by cancer detection dogs via a canine-centered interface while searching samples of amyl acetate. We advance previous work by providing further insights into the potential of the approach for supporting and partly automating the practice of cancer detection with dogs

Biobehavioral effects of Tai Chi Qigong in men with prostate cancer: Study design of a three-arm randomized clinical trial.

Fatigue is often one of the most commonly reported symptoms in prostate cancer survivors, but it is also one of the least understood cancer-related symptoms. Fatigue is associated with psychological distress, disruptions in sleep quality, and impairments in health-related quality of life. Moreover, inflammatory processes and changes related to the hypothalamic-pituitary-adrenal (HPA) axis and/or autonomic nervous system may also play a role in cancer-related fatigue. Thus, effective treatments for fatigue in prostate cancer survivors represent a current unmet need. Prior research has shown that Tai Chi Qigong, a mind-body exercise intervention, can improve physical and emotional health. Herein, we describe the protocol of the ongoing 3-arm randomized controlled Health Empowerment & Recovery Outcomes (HERO) clincal trial. One hundred sixty-six prostate cancer survivors with fatigue are randomized to a modified Tai Chi Qigong intervention (TCQ), intensity-matched body training intervention (BT), or usual care (UC) condition. Guided by biopsychosocial and psychoneuroimmunology models, we propose that TCQ, as compared to BT or UC will: i) reduce fatigue (primary outcome) in prostate cancer survivors; ii) reduce inflammation; and iii) regulate the expression of genes from two major functional clusters: a) inflammation, vasodilation and metabolite sensing and b) energy and adrenergic activation. Assessments are conducted at baseline, the 6-week midpoint of the intervention, and 1 week, 3 months, and 12 months post-intervention. If our findings show that TCQ promotes recovery from prostate cancer and its treatment, this type of intervention can be integrated into survivorship care plans as the standard of care. The study's findings will also provide novel information about underlying biobehavioral mechanisms of cancer-related fatigue. Trial registration number:NCT03326713; clinicaltrials.gov

Sustainable computational science: the ReScience initiative

Computer science o ers a large set of tools for prototyping, writing, running, testing, validating, sharing and reproducing results, however computational science lags behind. In the best case, authors may provide their source code as a compressed archive and they may feel con dent their research is reproducible. But this is not exactly true. Jonathan Buckheit and David Donoho proposed more than two decades ago that an article about computational results is advertising, not scholarship. e actual scholarship is the full so ware environment, code, and data that produced the result. is implies new work ows, in particular in peer-reviews. Existing journals have been slow to adapt: source codes are rarely requested, hardly ever actually executed to check that they produce the results advertised in the article. ReScience is a peer-reviewed journal that targets computational research and encourages the explicit replication of already published research, promoting new and open-source implementations in order to ensure that the original research can be replicated from its description. To achieve this goal, the whole publishing chain is radically di erent from other traditional scienti c journals. ReScience resides on GitHub where each new implementation of a computational study is made available together with comments, explanations, and so ware tests

Membrane protein extraction and purification using partially-esterified SMA polymers

Styrene maleic acid (SMA) polymers have proven to be very successful for the extraction of membrane proteins, forming SMA lipid particles (SMALPs), which maintain a lipid bilayer around the membrane protein. SMALP-encapsulated membrane proteins can be used for functional and structural studies. The SMALP approach allows retention of important protein-annular lipid interactions, exerts lateral pressure, and offers greater stability than traditional detergent solubilisation. However, SMA polymer does have some limitations, including a sensitivity to divalent cations and low pH, an absorbance spectrum that overlaps with many proteins, and possible restrictions on protein conformational change. Various modified polymers have been developed to try to overcome these challenges, but no clear solution has been found. A series of partially-esterified variants of SMA (SMA 2625, SMA 1440 and SMA 17352) has previously been shown to be highly effective for solubilisation of plant and cyanobacterial thylakoid membranes. It was hypothesised that the partial esterification of maleic acid groups would increase tolerance to divalent cations. Therefore, these partially-esterified polymers were tested for the solubilisation of lipids and membrane proteins, and their tolerance to magnesium ions. It was found that all partially esterified polymers were capable of solubilising and purifying a range of membrane proteins, but the yield of protein was lower with SMA 1440, and the degree of purity was lower for both SMA1440 and SMA17352. SMA2625 performed comparably to SMA 2000. SMA 1440 also showed an increased sensitivity to divalent cations. Thus, it appears the interactions between SMA and divalent cations are more complex than proposed and require further investigation