Single-qubit rotations in two-dimensional optical lattices with multiqubit addressing

Published versio

Species abundance information improves sequence taxonomy classification accuracy.

Popular naive Bayes taxonomic classifiers for amplicon sequences assume that all species in the reference database are equally likely to be observed. We demonstrate that classification accuracy degrades linearly with the degree to which that assumption is violated, and in practice it is always violated. By incorporating environment-specific taxonomic abundance information, we demonstrate a significant increase in the species-level classification accuracy across common sample types. At the species level, overall average error rates decline from 25% to 14%, which is favourably comparable to the error rates that existing classifiers achieve at the genus level (16%). Our findings indicate that for most practical purposes, the assumption that reference species are equally likely to be observed is untenable. q2-clawback provides a straightforward alternative for samples from common environments

redbiom: a Rapid Sample Discovery and Feature Characterization System.

Meta-analyses at the whole-community level have been important in microbiome studies, revealing profound features that structure Earth's microbial communities, such as the unique differentiation of microbes from the mammalian gut relative to free-living microbial communities, the separation of microbiomes in saline and nonsaline environments, and the role of pH in driving soil microbial compositions. However, our ability to identify the specific features of a microbiome that differentiate these community-level patterns have lagged behind, especially as ever-cheaper DNA sequencing has yielded increasingly large data sets. One critical gap is the ability to search for samples that contain specific features (for example, sub-operational taxonomic units [sOTUs] identified by high-resolution statistical methods for removing amplicon sequencing errors). Here we introduce redbiom, a microbiome caching layer, which allows users to rapidly query samples that contain a given feature, retrieve sample data and metadata, and search for samples that match specified metadata values or ranges (e.g., all samples with a pH of >7), implemented using an in-memory NoSQL database called Redis. By default, redbiom allows public anonymous sample access for over 100,000 publicly available samples in the Qiita database. At over 100,000 samples, the caching server requires only 35 GB of resident memory. We highlight how redbiom enables a new type of characterization of microbiome samples and provide tutorials for using redbiom with QIIME 2. redbiom is open source under the BSD license, hosted on GitHub, and can be deployed independently of Qiita to enable search of proprietary or clinically restricted microbiome databases.IMPORTANCE Although analyses that combine many microbiomes at the whole-community level have become routine, searching rapidly for microbiomes that contain a particular sequence has remained difficult. The software we present here, redbiom, dramatically accelerates this process, allowing samples that contain microbiome features to be rapidly identified. This is especially useful when taxonomic annotation is limited, allowing users to identify environments in which unannotated microbes of interest were previously observed. This approach also allows environmental or clinical factors that correlate with specific features, or vice versa, to be identified rapidly, even at a scale of billions of sequences in hundreds of thousands of samples. The software is integrated with existing analysis tools to enable fast, large-scale microbiome searches and discovery of new microbiome relationships

Classroom as complex adaptive system (CAS): Credible framing, useful metaphor or mis-designation?

This paper discusses the legitimacy of framing school classrooms as complex adaptive systems (CASs) with the aim of advancing discourse about the extent to which systems within education can be usefully designated as complex. Perspectives differ on criteria for applying a complexity framing to human systems, a consequence of the lack of any single definition of complexity theory, or agreement on the framing of CAS in human networks. However, the literature on complexity and education appears to both open (ajar) and close the door on descriptions and theoretical treatment of classrooms as CASs, and as a site for complexity-sensitive empirical research. The paper begins by presenting an overview of complexity discourse with respect to education, articulates conceptual framings for CAS and classrooms then moves on to advance the principal arguments in opposition to a conception of classrooms as CASs. Arguments from those in the field who are receptive, albeit tentatively, to applying a CAS lens to classroom systems are then explained. The paper concludes that whilst these arguments have merit, the legitimacy or otherwise of framing classrooms as CASs hinges to some extent on how both classrooms and CASs are framed. Finally, a primer is presented for an empirical complexity-sensitive classroom study undertaken in July 2020, findings from which will be published later this year

TOLOSAT project: Gravimetry and communication

The use of Constellations for weather science, security and disaster monitoring is a major challenge for space application services. Satellite to satellite communication using existing constellations has not been extensively explored yet. It can improve the communication times for small-satellite missions which have limited access to ground stations. Thus, a mission to demonstrate the feasibility of this link is required. Another element of interest in space application is Earth Observation, especially in the context of Climate Change. Gravimetry allows an understanding of mass transport in the Earth System through the remote sensing of the time variation of the Earth gravity field. CubeSats are low-cost small-scale and hence lower risk solutions to Earth Observation missions. University CubeSats have shown their success in demonstration and scientific missions, and have a great potential in providing students with practice and application on real space systems. In this context, the student associations ASTRE and SUPAERO CubeSat Club have joined in a CubeSat program called TOLOSAT, with the hope of demonstrating such technologies. Gathering 70 students from Toulouse, the team was split into subsystems in accordance with the concurrent engineering principles. The work performed followed recommendations from experts from the French National Centre for Space Studies (CNES) and the industry. The TOLOSAT payloads have to test and demonstrate new means of measuring gravity and addressing communication issues. Firstly, for the gravimetry mission, our approach relies solely on GNSS to compute the gravity field, avoiding expensive gravimeters. For the communication mission: the Iridium constellation will be used as an intermediate between the CubeSat and the ground station. Off-the-shelf components such as patch antennas are planned to prove their efficiency in orbit. This would improve the coverage and the communication window. The preliminary design was completed. TOLOSAT was designed as a 3-unit nanosatellite, on a 97.4° inclined, 500km high orbit. Margins were also ensured to allow a third payload to be defined in the future, that will be used for finance and partnerships. Detailed designs are still required, but the educational purposes have been fulfilled, in terms of discovery of the development of space missions as well as in the teamwork culture. The team is now moving on to a new phase, dedicated to a more detailed conception with an on-going focus on the introduction to students to technical - but not only - fields of knowledge applied to space system

Equine Assisted Therapy and Changes in Gait for a Young Adult Female with Down Syndrome

The purpose of this study was to examine the effects of equine assisted therapy on selected gait parameters in a person with Down syndrome. One female participant with Down syndrome completed two therapeutic horseback riding programs, each consisting of six riding sessions. Specific gait characteristics were analyzed with a trend analysis of the data by examining the means of the different variables. The trend analysis revealed a difference in stride length as well as hip and knee angle. These results indicate that over the course of the two therapeutic horseback riding programs, changes in gait occurred. Therefore, therapeutic horseback riding may have the potential to benefit gait characteristics and stability in young adult females with Down syndrome; however, further research is warranted

Dietary Prebiotics and Bioactive Milk Fractions Improve NREM Sleep, Enhance REM Sleep Rebound and Attenuate the Stress-Induced Decrease in Diurnal Temperature and Gut Microbial Alpha Diversity.

Severe, repeated or chronic stress produces negative health outcomes including disruptions of the sleep/wake cycle and gut microbial dysbiosis. Diets rich in prebiotics and glycoproteins impact the gut microbiota and may increase gut microbial species that reduce the impact of stress. This experiment tested the hypothesis that consumption of dietary prebiotics, lactoferrin (Lf) and milk fat globule membrane (MFGM) will reduce the negative physiological impacts of stress. Male F344 rats, postnatal day (PND) 24, received a diet with prebiotics, Lf and MFGM (test) or a calorically matched control diet. Fecal samples were collected on PND 35/70/91 for 16S rRNA sequencing to examine microbial composition and, in a subset of rats; Lactobacillus rhamnosus was measured using selective culture. On PND 59, biotelemetry devices were implanted to record sleep/wake electroencephalographic (EEG). Rats were exposed to an acute stressor (100, 1.5 mA, tail shocks) on PND 87 and recordings continued until PND 94. Test diet, compared to control diet, increased fecal Lactobacillus rhamnosus colony forming units (CFU), facilitated non-rapid eye movement (NREM) sleep consolidation (PND 71/72) and enhanced rapid eye movement (REM) sleep rebound after stressor exposure (PND 87). Rats fed control diet had stress-induced reductions in alpha diversity and diurnal amplitude of temperature, which were attenuated by the test diet (PND 91). Stepwise multiple regression analysis revealed a significant linear relationship between early-life Deferribacteres (PND 35) and longer NREM sleep episodes (PND 71/72). A diet containing prebiotics, Lf and MFGM enhanced sleep quality, which was related to changes in gut bacteria and modulated the impact of stress on sleep, diurnal rhythms and the gut microbiota