A new method for indexing genomes using on-disk suffix trees

We propose a new method to build persistent suffix trees for indexing the genomic data. Our algorithm DiGeST (Disk-Based Genomic Suffix Tree) improves significantly over previous work in reducing the random access to the in-put string and performing only two passes over disk data. DiGeST is based on the two-phase multi-way merge sort paradigm using a concise binary representation of the DNA alphabet. Furthermore, our method scales to larger genomic data than managed before

Base-By-Base: Single nucleotide-level analysis of whole viral genome alignments

BACKGROUND: With ever increasing numbers of closely related virus genomes being sequenced, it has become desirable to be able to compare two genomes at a level more detailed than gene content because two strains of an organism may share the same set of predicted genes but still differ in their pathogenicity profiles. For example, detailed comparison of multiple isolates of the smallpox virus genome (each approximately 200 kb, with 200 genes) is not feasible without new bioinformatics tools. RESULTS: A software package, Base-By-Base, has been developed that provides visualization tools to enable researchers to 1) rapidly identify and correct alignment errors in large, multiple genome alignments; and 2) generate tabular and graphical output of differences between the genomes at the nucleotide level. Base-By-Base uses detailed annotation information about the aligned genomes and can list each predicted gene with nucleotide differences, display whether variations occur within promoter regions or coding regions and whether these changes result in amino acid substitutions. Base-By-Base can connect to our mySQL database (Virus Orthologous Clusters; VOCs) to retrieve detailed annotation information about the aligned genomes or use information from text files. CONCLUSION: Base-By-Base enables users to quickly and easily compare large viral genomes; it highlights small differences that may be responsible for important phenotypic differences such as virulence. It is available via the Internet using Java Web Start and runs on Macintosh, PC and Linux operating systems with the Java 1.4 virtual machine

Prediction of cardiovascular disease risk by cardiac biomarkers in 2 United Kingdom cohort studies: does utility depend on risk thresholds for treatment?

We tested the predictive ability of cardiac biomarkers N-terminal pro B-type natriuretic peptide (NT-proBNP), high-sensitivity troponin T, and midregional pro adrenomedullin for cardiovascular disease (CVD) events using the British Regional Heart Study (BRHS) of men aged 60 to 79 years, and the MIDSPAN Family Study (MFS) of men and women aged 30 to 59 years. They included 3757 and 2226 participants, respectively, and during median 13.0 and 17.3 years follow-up the primary CVD event rates were 16.6 and 5.3 per 1000 patient-years, respectively. In Cox models adjusted for basic classical risk factors, 1 SD increases in log-transformed NT-proBNP, high-sensitivity troponin T, and midregional pro adrenomedullin were generally associated with increased primary CVD risk in both the studies (P<0.006) except midregional pro adrenomedullin in MFS (P=0.10). In BRHS, QRISK2 risk factors yielded a C-index of 0.657, which was improved by 0.017 (P=0.005) by NT-proBNP, but not by other biomarkers. Using 28% 14-year risk as a proxy for 20% 10-year risk, NT-proBNP improved risk classification for primary CVD cases (case net reclassification index, 5.9%; 95% confidence interval, 2.8%–9.2%), but only improved classification of noncases at a 14% 14-year risk threshold (4.6%; 2.9%–6.3%). In MFS, ASSIGN risk factors yielded a C-index of 0.752 for primary CVD; none of the cardiac biomarkers improved the C-index. Improvements in risk classification were only seen using NT-proBNP and high-sensitivity troponin T among cases using the 28% 14-year risk threshold (4.7%; 1.0%–9.2% and 2.6%; 0.0%–5.8%, respectively). In conclusion, the improvement in treatment allocation gained by adding cardiac biomarkers to risk scores seems to depend on the risk threshold chosen for commencing preventative treatments

Which circulating antioxidant vitamins are confounded by socioeconomic deprivation? The MIDSPAN family study

<p><b>Background:</b> Antioxidant vitamins are often described as having “independent” associations with risk of cancer, cardiovascular disease (CVD) and mortality. We aimed to compare to what extent a range of antioxidant vitamins and carotenoids are associated with adulthood and childhood markers of socioeconomic deprivation and to adverse lifestyle factors.</p> <p><b>Methods and Findings:</b> Socioeconomic and lifestyle measures were available in 1040 men and 1298 women from the MIDSPAN Family Study (30–59 years at baseline) together with circulating levels of vitamins A, C, E, and carotenoids (α-carotene, β-carotene, lutein and lycopene). Markers of socioeconomic deprivation in adulthood were consistently as strongly associated with lower vitamin C and carotenoid levels as markers of adverse lifestyle; the inverse association with overcrowding was particularly consistent (vitamin C and carotenoids range from 19.1% [95% CI 30.3–6.0] to 38.8% [49.9–25.3] lower among those in overcrowded residencies). These associations were consistent after adjusting for month, classical CVD risk factors, body mass index, physical activity, vitamin supplements, dietary fat and fibre intake. Similar, but weaker, associations were seen for childhood markers of deprivation. The association of vitamin A or E were strikingly different; several adult adverse lifestyle factors associated with higher levels of vitamin A and E, including high alcohol intake for vitamin A (9.5% [5.7–13.5]) and waist hip ratio for vitamin E (9.5% [4.8–14.4]), with the latter associations partially explained by classical risk factors, particularly cholesterol levels.</p> <p><b>Conclusions:</b> Plasma vitamin C and carotenoids have strong inverse associations with adulthood markers of social deprivation, whereas vitamin A and E appear positively related to specific adverse lifestyle factors. These findings should help researchers better contextualize blood antioxidant vitamin levels by illustrating the potential limitations associated with making causal inferences without consideration of social deprivation.</p&gt

Efficacy of a gamified digital therapy for speech production in people with chronic aphasia (iTalkBetter): behavioural and imaging outcomes of a phase II item-randomised clinical trial

Background Aphasia is among the most debilitating of symptoms affecting stroke survivors. Speech and language therapy (SLT) is effective, but many hours of practice are required to make clinically meaningful gains. One solution to this ‘dosage’ problem is to automate therapeutic approaches via self-supporting apps so people with aphasia (PWA) can amass practice as it suits them. However, response to therapy is variable and no clinical trial has yet identified the key brain regions required to engage with word-retrieval therapy. Methods Between Sep 7, 2020 and Mar 1, 2022 at University College London in the UK, we carried out a phase II, item-randomised clinical trial in 27 PWA using a novel, self-led app, ‘iTalkBetter’, which utilises confrontation naming therapy. Unlike previously reported apps, it has a real-time utterance verification system that drives its adaptive therapy algorithm. Therapy items were individually randomised to provide balanced lists of ‘trained’ and ‘untrained’ items matched on key psycholinguistic variables and baseline performance. PWA practised with iTalkBetter over a 6-week therapy block. Structural and functional MRI data were collected to identify therapy-related changes in brain states. A repeated-measures design was employed. The trial was registered at ClinicalTrials.gov (NCT04566081). Findings iTalkBetter significantly improved naming ability by 13% for trained items compared with no change for untrained items, an average increase of 29 words (SD = 26) per person; beneficial effects persisted at three months. PWA’s propositional speech also significantly improved. iTalkBetter use was associated with brain volume increases in right auditory and left anterior prefrontal cortices. Task-based fMRI identified dose-related activity in the right temporoparietal junction. Interpretation Our findings suggested that iTalkBetter significantly improves PWAs’ naming ability on trained items. The effect size is similar to a previous RCT of computerised therapy, but this is the first study to show transfer to a naturalistic speaking task. iTalkBetter usage and dose caused observable changes in brain structure and function to key parts of the surviving language perception, production and control networks. iTalkBetter is being rolled-out as an app for all PWA and anomia: https://www.ucl.ac.uk/icn/research/research-groups/neurotherapeutics/projects/digital-interventions-neuro-rehabilitation-0 so that they can increase their dosage of practice-based SLT

Circulating 250HD, dietary vitamin D, PTH, and calcium associations with incident cardiovascular disease and mortality: The MIDSPAN Family Study

<p>Context: Observational studies relating circulating 25-hydroxyvitamin D (25OHD) and dietary vitamin D intake to cardiovascular disease (CVD) have reported conflicting results.</p> <p>Objective: Our objective was to investigate the association of 25OHD, dietary vitamin D, PTH, and adjusted calcium with CVD and mortality in a Scottish cohort.</p> <p>Design and Setting: TheMIDSPAN Family Study is a prospective study of 1040 men and 1298 women from the West of Scotland recruited in 1996 and followed up for a median 14.4 yr. Participants: Locally resident adult offspring of a general population cohort were recruited from 1972–1976.</p> <p>Main Outcome Measures: CVD events (n = 416) and all-cause mortality (n=100) were evaluated.</p> <p>Results: 25OHD was measured using liquid chromatography-tandem mass spectrometry in available plasma (n=2081). Median plasma 25OHD was 18.6 ng/ml, and median vitamin D intake was 3.2 µ g/d (128 IU/d). Vitamin D deficiency (25OHD<15 ng/ml) was present in 689 participants (33.1%). There was no evidence that dietary vitamin D intake, PTH, or adjusted calcium were associated with CVD events or with mortality. Vitamin D deficiency was not associated with CVD (fully adjusted hazard ratio=1.00; 95% confidence interval=0.77–1.31). Results were similar after excluding patients who reported an activity-limiting longstanding illness at baseline (18.8%) and those taking any vitamin supplements (21.7%). However, there was some evidence vitamin D deficiency was associated with all-cause mortality (fully adjusted hazard ratio=2.02; 95% confidence interval=1.17–3.51).</p> <p>Conclusion: Vitamin D deficiency was not associated with risk of CVD in this cohort with very low 25OHD. Future trials of vitamin D supplementation in middle-aged cohorts should be powered to detect differences inmortality outcomes as well as CVD.(J Clin EndocrinolMetab97: 0000 –0000, 2012)</p&gt

Low-energy electronic interactions in ferrimagnetic Sr2CrReO6 thin films

We reveal in this study the fundamental low-energy landscape in the ferrimagnetic Sr2CrReO6 double perovskite and describe the underlying mechanisms responsible for the three low-energy excitations below 1.4 eV. Based on resonant inelastic x-ray scattering and magnetic dynamics calculations, and experiments collected from both Sr2CrReO6 powders and epitaxially strained thin films, we reveal a strong competition between spin-orbit coupling, Hund's coupling, and the strain-induced tetragonal crystal field. We also demonstrate that a spin-flip process is at the origin of the lowest excitation at 200 meV, and we bring insights into the predicted presence of orbital ordering in this material. We study the nature of the magnons through a combination of ab initio and spin-wave theory calculations, and show that two nondegenerate magnon bands exist and are dominated either by rhenium or chromium spins. The rhenium band is found to be flat at about 200 meV ($\pm$25 meV) through X-L-W-U high-symmetry points and is dispersive toward $\Gamma$Comment: 6 figure

Deploying and Optimizing Embodied Simulations of Large-Scale Spiking Neural Networks on HPC Infrastructure

Simulating the brain-body-environment trinity in closed loop is an attractive proposal to investigate how perception, motor activity and interactions with the environment shape brain activity, and vice versa. The relevance of this embodied approach, however, hinges entirely on the modeled complexity of the various simulated phenomena. In this article, we introduce a software framework that is capable of simulating large-scale, biologically realistic networks of spiking neurons embodied in a biomechanically accurate musculoskeletal system that interacts with a physically realistic virtual environment. We deploy this framework on the high performance computing resources of the EBRAINS research infrastructure and we investigate the scaling performance by distributing computation across an increasing number of interconnected compute nodes. Our architecture is based on requested compute nodes as well as persistent virtual machines; this provides a high-performance simulation environment that is accessible to multi-domain users without expert knowledge, with a view to enable users to instantiate and control simulations at custom scale via a web-based graphical user interface. Our simulation environment, entirely open source, is based on the Neurorobotics Platform developed in the context of the Human Brain Project, and the NEST simulator. We characterize the capabilities of our parallelized architecture for large-scale embodied brain simulations through two benchmark experiments, by investigating the effects of scaling compute resources on performance defined in terms of experiment runtime, brain instantiation and simulation time. The first benchmark is based on a large-scale balanced network, while the second one is a multi-region embodied brain simulation consisting of more than a million neurons and a billion synapses. Both benchmarks clearly show how scaling compute resources improves the aforementioned performance metrics in a near-linear fashion. The second benchmark in particular is indicative of both the potential and limitations of a highly distributed simulation in terms of a trade-off between computation speed and resource cost. Our simulation architecture is being prepared to be accessible for everyone as an EBRAINS service, thereby offering a community-wide tool with a unique workflow that should provide momentum to the investigation of closed-loop embodiment within the computational neuroscience community.journal articl

Beyond species counts for assessing, valuing, and conserving biodiversity:response to Wallach et al. 2019

Article impact statement: Combining native and non‐native species to evaluate biodiversity is overly simplistic and may undermine the conservation of ecosystems

Deconstructing compassionate conservation

Compassionate conservation focuses on 4 tenets: first, do no harm; individuals matter; inclusivity of individual animals; and peaceful coexistence between humans and animals. Recently, compassionate conservation has been promoted as an alternative to conventional conservation philosophy. We believe examples presented by compassionate conservationists are deliberately or arbitrarily chosen to focus on mammals; inherently not compassionate; and offer ineffective conservation solutions. Compassionate conservation arbitrarily focuses on charismatic species, notably large predators and megaherbivores. The philosophy is not compassionate when it leaves invasive predators in the environment to cause harm to vastly more individuals of native species or uses the fear of harm by apex predators to terrorize mesopredators. Hindering the control of exotic species (megafauna, predators) in situ will not improve the conservation condition of the majority of biodiversity. The positions taken by so-called compassionate conservationists on particular species and on conservation actions could be extended to hinder other forms of conservation, including translocations, conservation fencing, and fertility control. Animal welfare is incredibly important to conservation, but ironically compassionate conservation does not offer the best welfare outcomes to animals and is often ineffective in achieving conservation goals. Consequently, compassionate conservation may threaten public and governmental support for conservation because of the limited understanding of conservation problems by the general public