Buchananclemons3234

Deficits in attention underpin many of the cognitive and neuropsychiatric features of Lewy body dementia. These attention-related symptoms remain difficult to treat and there are many gaps in our understanding of their neurobiology. An improved understanding of attention-related impairments can be achieved via mathematical modelling approaches, which identify cognitive parameters to provide an intermediate level between observed behavioural data and its underlying neural correlate. Here, we apply this approach to identify the role of impaired sensory evidence accumulation in the attention deficits that characterize Lewy body dementia. In 31 people with Lewy body dementia (including 13 Parkinson's disease dementia and 18 dementia with Lewy bodies cases), 16 people with Alzheimer's disease, and 23 healthy controls, we administered an attention task whilst they underwent functional 3 T MRI. Using hierarchical Bayesian estimation of a drift-diffusion model, we decomposed task performance into drift rate and decisd to activity in the dorsal attention network across all three groups, whereas the Lewy body dementia group showed a divergent relationship relative to the Alzheimer's disease and control groups for the default network, consistent with altered default network modulation being associated with impaired evidence accumulation. Together, our findings reveal impaired sensory evidence accumulation as a specific marker of attention problems in Lewy body dementia, which may relate to large-scale network abnormalities. By identifying impairments in a specific sub-process of attention, these findings will inform future exploratory and intervention studies that aim to understand and treat attention-related symptoms that are a key feature of Lewy body dementia.Phylogenetics is nowadays at the center of numerous studies in many fields, ranging from comparative genomics to molecular epidemiology. However, phylogenetic analysis workflows are usually complex and difficult to implement, as they are often composed of many small, reccuring, but important data manipulations steps. Among these, we can find file reformatting, sequence renaming, tree re-rooting, tree comparison, bootstrap support computation, etc. Eeyarestatin 1 in vitro These are often performed by custom scripts or by several heterogeneous tools, which may be error prone, uneasy to maintain and produce results that are challenging to reproduce. For all these reasons, the development and reuse of phylogenetic workflows is often a complex task. We identified many operations that are part of most phylogenetic analyses, and implemented them in a toolkit called Gotree/Goalign. The Gotree/Goalign toolkit implements more than 120 user-friendly commands and an API dedicated to multiple sequence alignment and phylogenetic tree manipulations. It is developed in Go, which makes executables easily installable, integrable in workflow environments, and parallelizable when possible. Moreover, Go is a compiled language, which accelerates computations compared to interpreted languages. This toolkit is freely available on most platforms (Linux, MacOS and Windows) and most architectures (amd64, i386) on GitHub at https//github.com/evolbioinfo/gotree, Bioconda and DockerHub.Estimating the co-expression of cell identity factors in single-cell is crucial. Due to the low efficiency of scRNA-seq methodologies, sensitive computational approaches are critical to accurately infer transcription profiles in a cell population. We introduce COTAN, a statistical and computational method, to analyze the co-expression of gene pairs at single cell level, providing the foundation for single-cell gene interactome analysis. The basic idea is studying the zero UMI counts' distribution instead of focusing on positive counts; this is done with a generalized contingency tables framework. COTAN can assess the correlated or anti-correlated expression of gene pairs, providing a new correlation index with an approximate p-value for the associated test of independence. COTAN can evaluate whether single genes are differentially expressed, scoring them with a newly defined global differentiation index. Similarly to correlation network analysis, it provides ways to plot and cluster genes according to their co-expression pattern with other genes, effectively helping the study of gene interactions, becoming a new tool to identify cell-identity markers. We assayed COTAN on two neural development datasets with very promising results. COTAN is an R package that complements the traditional single cell RNA-seq analysis and it is available at https//github.com/seriph78/COTAN.Current evolutionary scenarios posit the emergence of Mycobacterium tuberculosis from an environmental saprophyte through a cumulative process of genome adaptation. Mycobacterium riyadhense, a related bacillus, is being increasingly isolated from human clinical cases with tuberculosis-like symptoms in various parts of the world. To elucidate the evolutionary relationship between M. riyadhense and other mycobacterial species, including members of the M. tuberculosis complex (MTBC), eight clinical isolates of M. riyadhense were sequenced and analyzed. We show, among other features, that M. riyadhense shares a large number of conserved orthologs with M. tuberculosis and shows the expansion of toxin/antitoxin pairs, PE/PPE family proteins compared with other non-tuberculous mycobacteria. We observed M. riyadhense lacks wecE gene which may result in the absence of lipooligosaccharides (LOS) IV. Comparative transcriptomic analysis of infected macrophages reveals genes encoding inducers of Type I IFN responses, such as cytosolic DNA sensors, were relatively less expressed by macrophages infected with M. riyadhense or M. kansasii, compared to BCG or M. tuberculosis. Overall, our work sheds new light on the evolution of M. riyadhense, its relationship to the MTBC, and its potential as a system for the study of mycobacterial virulence and pathogenesis.Hemiparetic walking after stroke is typically slow, asymmetric, and inefficient, significantly impacting activities of daily living. Extensive research shows that functional, intensive, and task-specific gait training is instrumental for effective gait rehabilitation, characteristics that our group aims to encourage with soft robotic exosuits. However, standard clinical assessments may lack the precision and frequency to detect subtle changes in intervention efficacy during both conventional and exosuit-assisted gait training, potentially impeding targeted therapy regimes. In this paper, we use exosuit-integrated inertial sensors to reconstruct three clinically meaningful gait metrics related to circumduction, foot clearance, and stride length. Our method corrects sensor drift using instantaneous information from both sides of the body. This approach makes our method robust to irregular walking conditions poststroke as well as usable in real-time applications, such as real-time movement monitoring, exosuit assistance control, and biofeedback. We validate our algorithm in eight people poststroke in comparison to lab-based optical motion capture. Mean errors were below 0.2 cm (9.9%) for circumduction, -0.6 cm (-3.5%) for foot clearance, and 3.8 cm (3.6%) for stride length. A single-participant case study shows our technique's promise in daily-living environments by detecting exosuit-induced changes in gait while walking in a busy outdoor plaza.Despite advances in deep learning methods for song recommendation, most existing methods do not take advantage of the sequential nature of song content. In addition, there is a lack of methods that can explain their predictions using the content of recommended songs and only a few approaches can handle the item cold start problem. In this work, we propose a hybrid deep learning model that uses collaborative filtering (CF) and deep learning sequence models on the Musical Instrument Digital Interface (MIDI) content of songs to provide accurate recommendations, while also being able to generate a relevant, personalized explanation for each recommended song. Compared to state-of-the-art methods, our validation experiments showed that in addition to generating explainable recommendations, our model stood out among the top performers in terms of recommendation accuracy and the ability to handle the item cold start problem. Moreover, validation shows that our personalized explanations capture properties that are in accordance with the user's preferences.Functional near-infrared spectroscopy (fNIRS) is a neuroimaging technique used for mapping the functioning human cortex. fNIRS can be widely used in population studies due to the technology's economic, non-invasive, and portable nature. fNIRS can be used for task classification, a crucial part of functioning with Brain-Computer Interfaces (BCIs). fNIRS data are multidimensional and complex, making them ideal for deep learning algorithms for classification. Deep Learning classifiers typically need a large amount of data to be appropriately trained without over-fitting. Generative networks can be used in such cases where a substantial amount of data is required. Still, the collection is complex due to various constraints. Conditional Generative Adversarial Networks (CGAN) can generate artificial samples of a specific category to improve the accuracy of the deep learning classifier when the sample size is insufficient. The proposed system uses a CGAN with a CNN classifier to enhance the accuracy through data augmentation. The system can determine whether the subject's task is a Left Finger Tap, Right Finger Tap, or Foot Tap based on the fNIRS data patterns. The authors obtained a task classification accuracy of 96.67% for the CGAN-CNN combination.Smart home technologies with the ability to learn over time promise to adjust their actions to inhabitants' unique preferences and circumstances. For example, by learning to anticipate their routines. However, these promises show frictions with the reality of everyday life, which is characterized by its complexity and unpredictability. These systems and their design can thus benefit from meaningful ways of eliciting reflections on potential challenges for integrating learning systems into everyday domestic contexts, both for the inhabitants of the home as for the technologies and their designers. For example, is there a risk that inhabitants' everyday lives will reshape to accommodate the learning system's preference for predictability and measurability? To this end, in this paper we build a designer's interpretation on the Social Practice Imaginaries method as developed by Strengers et al. to create a set of diverse, plausible imaginaries for the year 2030. As a basis for these imaginaries, we have selected three social practices in a domestic context waking up, doing groceries, and heating/cooling the home. For each practice, we create one imaginary in which the inhabitants' routine is flawlessly supported by the learning system and one that features everyday crises of that routine. The resulting social practice imaginaries are then viewed through the perspective of the inhabitant, the learning system, and the designer. In doing so, we aim to enable designers and design researchers to uncover a diverse and dynamic set of implications the integration of these systems in everyday life pose.