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Identifying differentially abundant microbes is a common goal of microbiome studies. Multiple methods are used interchangeably for this purpose in the literature. Yet, there are few large-scale studies systematically exploring the appropriateness of using these tools interchangeably, and the scale and significance of the differences between them. Here, we compare the performance of 14 differential abundance testing methods on 38 16S rRNA gene datasets with two sample groups. We test for differences in amplicon sequence variants and operational taxonomic units (ASVs) between these groups. Our findings confirm that these tools identified drastically different numbers and sets of significant ASVs, and that results depend on data pre-processing. For many tools the number of features identified correlate with aspects of the data, such as sample size, sequencing depth, and effect size of community differences. ALDEx2 and ANCOM-II produce the most consistent results across studies and agree best with the intersect of results from different approaches. Nevertheless, we recommend that researchers should use a consensus approach based on multiple differential abundance methods to help ensure robust biological interpretations. Many microbiome differential abundance methods are available, but it lacks systematic comparison among them. Here, the authors compare the performance of 14 differential abundance testing methods on 38 16S rRNA gene datasets with two sample groups, and show ALDEx2 and ANCOM-II produce the most consistent results.

Mental fatigue is a commonplace human experience which is the focus of a growing body of research. Whilst researchers in numerous disciplines have attempted to uncover the origins, nature, and effects of mental fatigue, the literature is marked by many contradictory findings. We identified two major methodological problems for mental fatigue research. First, researchers rarely use objective measures of mental fatigue. Instead, they rely heavily on subjective reports as evidence that mental fatigue has been induced in participants. We aimed to develop a task which led to not only a subjective increase in mental fatigue, but a corresponding performance decrement in the mentally fatiguing task as an objective measure. Secondly, current mental fatigue paradigms have low ecological validity – in most prior studies participants have been fatigued with a single repetitive task such as the n-back or Stroop. To move towards a more ecologically valid paradigm, our participants undertook a battery of diverse cognitive tasks designed to challenge different aspects of executive function. The AX-CPT, n-back, mental rotation, and visual search tasks were chosen to challenge response inhibition, working memory, spatial reasoning, and attention. We report results from 45 participants aged 19 to 63 years who completed a two-hour battery comprising four different cognitive tasks. Subjective fatigue ratings and task performance were measured at the beginning and end of the battery. Our novel method resulted in an increase in subjective ratings of fatigue ( p < 0.001) and a reduction in task performance ( p = 0.008). Future research into mental fatigue may benefit from using this task battery.

Dated, geo‐referenced museum specimens are a rich data source for reconstructing species' distribution and abundance patterns. However, museum records are potentially biased towards over‐representation of rare species, and it is unclear whether museum records can be used to estimate relative abundance in the field. We assembled 17 coupled field and museum datasets to quantitatively compare relative abundance estimates with the Dirichlet distribution. Collectively, these datasets comprise 73,039 museum records and 1,405,316 field observations of 2,240 species. Although museum records of rare species overestimated relative abundance by 1‐fold to over 100‐fold (median study = 9.0), the relative abundance of species estimated from museum occurrence records was strongly correlated with relative abundance estimated from standardized field surveys (r2 range of 0.10–0.91, median study = 0.43). These analyses provide a justification for estimating species relative abundance with carefully curated museum occurrence records, which may allow for the detection of temporal or spatial shifts in the rank ordering of common and rare species. Resumen Los especímenes de museo fechados y georreferenciados son una rica fuente de datos para reconstruir los patrones de distribución y abundancia de las especies. Sin embargo, los registros de los museos están potencialmente sesgados hacia la sobrerrepresentación de especies raras, y no está claro si estos registros pueden utilizarse para estimar la abundancia relativa en el campo. Se reunieron 17 conjuntos de datos acoplados de campo y de museo para comparar cuantitativamente las estimaciones de abundancia relativa con la distribución de Dirichlet. Colectivamente, estos conjuntos de datos comprenden 73.039 registros de museo y 1.405.316 observaciones de campo para 2.240 especies. Aunque los registros de museo de especies raras sobreestimaron la abundancia relativa desde 1 hasta más de 100 veces (mediana del estudio = 9,0), la abundancia relativa de las especies que se estimada a partir de los registros de ocurrencia de los museos mostró una fuerte correlación con la abundancia relativa estimada a partir de los estudios de campo estandarizados (rango r2 de 0,10 a 0,91, mediana del estudio = 0,43). Estos análisis justifican la estimación de la abundancia relativa de las especies a partir de los registros de ocurrencia de los museos, lo que permitiría la detección de cambios temporales o espaciales en el rango de ordenamiento de las especies comunes y raras.

OH rotational temperatures are widely used to derive mesopause temperatures and their variations. Since most data sets are only based on a fixed set of lines of a single band, it is important to know possible systematic uncertainties related to the choice of lines. Therefore, a comprehensive study of as many OH bands as possible is desirable. For this purpose, astronomical echelle spectrographs at large telescopes are the most suitable instruments. They offer a wide wavelength coverage, relatively high spectral resolution, and high sensitivity. Moreover, since each ground-based astronomical observation has an imprint of the Earth's atmosphere, the data archives of large astronomical facilities are a treasure for atmospheric studies. For our project, we used archival data of the medium-resolution X-shooter echelle spectrograph operated by the European Southern Observatory at Cerro Paranal in Chile. The instrument can simultaneously observe all OH bands that are accessible from ground. We reduced and analysed a set of 343 high-quality spectra taken between 2009 and 2013 to measure OH line intensities and to derive rotational and vibrational temperatures of 25 bands between 0.58 and 2.24 μm. We studied the influence of the selected line set, OH band, upper vibrational level v′, and the molecular data on the derived level populations and temperatures. The rotational temperature results indicate differences by several degrees depending on the selection. The temperatures for bands of even and odd v′ show deviations which increase with v′. A study of the temporal variations revealed that the nocturnal variability pattern changes for v′ from 2 to 9. In particular, the spread of temperatures tends to increase during the night, and the time of the minimum temperature depends on v′. The vibrational temperatures depend on the range of v′ used for their determination, since the higher vibrational levels from 7 to 9 seem to be overpopulated compared to the lower levels. The vibrational temperature tends to increase during the night, while the intensity decreases. Our results support the assumption that the OH emission altitude depends on v′. Moreover, the emission layer appears to rise in the course of the night, which makes the OH thermalisation less efficient. The derived rotational temperatures and their change with v′ seem to be significantly affected by non-equilibrium populations.

Background Crohn’s disease (CD) has an unclear etiology, but there is growing evidence of a direct link with a dysbiotic microbiome. Many gut microbes have previously been associated with CD, but these have mainly been confounded with patients’ ongoing treatments. Additionally, most analyses of CD patients’ microbiomes have focused on microbes in stool samples, which yield different insights than profiling biopsy samples. Results We sequenced the 16S rRNA gene (16S) and carried out shotgun metagenomics (MGS) from the intestinal biopsies of 20 treatment-naïve CD and 20 control pediatric patients. We identified the abundances of microbial taxa and inferred functional categories within each dataset. We also identified known human genetic variants from the MGS data. We then used a machine learning approach to determine the classification accuracy when these datasets, collapsed to different hierarchical groupings, were used independently to classify patients by disease state and by CD patients’ response to treatment. We found that 16S-identified microbes could classify patients with higher accuracy in both cases. Based on follow-ups with these patients, we identified which microbes and functions were best for predicting disease state and response to treatment, including several previously identified markers. By combining the top features from all significant models into a single model, we could compare the relative importance of these predictive features. We found that 16S-identified microbes are the best predictors of CD state whereas MGS-identified markers perform best for classifying treatment response. Conclusions We demonstrate for the first time that useful predictors of CD treatment response can be produced from shotgun MGS sequencing of biopsy samples despite the complications related to large proportions of host DNA. The top predictive features that we identified in this study could be useful for building an improved classifier for CD and treatment response based on sufferers’ microbiome in the future. The BISCUIT project is funded by a Clinical Academic Fellowship from the Chief Scientist Office (Scotland)—CAF/08/01.

Travelling light The quantum description of light as photons leads to predictions that have no classical counterpart. Coalescence is a striking example: when two identical photons arrive simultaneously at the two sides of a partially reflecting mirror, they always leave the mirror together. Beugnon et al . demonstrate this effect by producing quantum interference between two single photons emitted by two independently trapped atoms. This is a step towards synchronized, independent sources emitting indistinguishable photons. Such sources would be a useful resource for quantum data processing. A collection of synchronized, independent sources emitting indistinguishable photons represents a highly useful resource for quantum data processing. Demonstration of quantum interference between two single photons emitted by two independently trapped single atoms is an important step towards this goal. When two indistinguishable single photons are fed into the two input ports of a beam splitter, the photons will coalesce and leave together from the same output port. This is a quantum interference effect, which occurs because two possible paths—in which the photons leave by different output ports—interfere destructively. This effect was first observed in parametric downconversion 1 (in which a nonlinear crystal splits a single photon into two photons of lower energy), then from two separate downconversion crystals 2 , as well as with single photons produced one after the other by the same quantum emitter 3 , 4 , 5 , 6 . With the recent developments in quantum information research, much attention has been devoted to this interference effect as a resource for quantum data processing using linear optics techniques 2 , 7 , 8 , 9 , 10 , 11 . To ensure the scalability of schemes based on these ideas, it is crucial that indistinguishable photons are emitted by a collection of synchronized, but otherwise independent sources. Here we demonstrate the quantum interference of two single photons emitted by two independently trapped single atoms, bridging the gap towards the simultaneous emission of many indistinguishable single photons by different emitters. Our data analysis shows that the observed coalescence is mainly limited by wavefront matching of the light emitted by the two atoms, and to a lesser extent by the motion of each atom in its own trap.

Programmed cell death (PCD) is an integral part of plant development and of responses to abiotic stress or pathogens. Although the morphology of plant PCD is, in some cases, well characterised and molecular mechanisms controlling plant PCD are beginning to emerge, there is still confusion about the classification of PCD in plants. Here we suggest a classification based on morphological criteria. According to this classification, the use of the term ‘apoptosis’ is not justified in plants, but at least two classes of PCD can be distinguished: vacuolar cell death and necrosis. During vacuolar cell death, the cell contents are removed by a combination of autophagy-like process and release of hydrolases from collapsed lytic vacuoles. Necrosis is characterised by early rupture of the plasma membrane, shrinkage of the protoplast and absence of vacuolar cell death features. Vacuolar cell death is common during tissue and organ formation and elimination, whereas necrosis is typically found under abiotic stress. Some examples of plant PCD cannot be ascribed to either major class and are therefore classified as separate modalities. These are PCD associated with the hypersensitive response to biotrophic pathogens, which can express features of both necrosis and vacuolar cell death, PCD in starchy cereal endosperm and during self-incompatibility. The present classification is not static, but will be subject to further revision, especially when specific biochemical pathways are better defined.

Ultrarunning is gaining in popularity but no information is available on the physiological and psychological responses during backyard ultrarunning events. The aim of this study was to determine changes in cognitive function, markers of physiological resilience, and running performance during a backyard‐running event. Twelve male ultrarunners (38 ± 8 years old, BMI: 23.5 ± 1.6 kg/m2, and VO2max: 60.8 ± 4.7 mL/min/kg) were monitored before, during, and after the event. Cognitive performance was determined using a cognitive test battery before, during, and after the event. During the event, the rating of perceived exertion (RPE), blood lactate concentration, and heart rate (HR) were assessed. Physical performance was investigated using the total number of completed laps and running speed per lap. Athletes completed 34 ± 17 laps equaling 227.8 ± 113.9 km with average speeds starting at 9.0 km/h and slowing down to 7.5 km/h at the end of the event. Physiological resilience (estimated using HR/speed) varied between athletes, with significantly lower values in the more proficient backyard runners at the end of the event (p < 0.05). HR and lactate levels remained constant, whereas a progressive increase in RPE was noticed (p ≤ 0.001). A significantly worsened reaction time was observed for several cognitive tasks after the event compared to baseline measures (p ≤ 0.05). These observations show that physiological resilience differs depending on the level of endurance performance of the athletes. Furthermore, the backyard ultrarunning event negatively impacted psychomotor speed. Therefore, the results suggest that implementing strategies that enhance physiological resilience and/or psychomotor speed could potentially have a positive effect on performance in ultraendurance activities. Highlights Backyard running events showcase varying physiological resilience, emphasizing its role in differentiating top‐performing athletes. Pacing dynamics and cognitive decline during ultraendurance events highlight the complex interplay between physical and mental fatigues. Exploring resilience and cognitive functioning during ultraendurance events is important for optimizing training and other interventions in extreme endurance challenges.

Salinity tolerances of reef corals have been experimentally investigated since the early twentieth century. Yet, nearly 100 years later, we are no closer to having a threshold that can be applied in studies of the impacts of freshwater runoff on coral communities. We present an empirically derived salinity threshold for sensitive Acropora species from the Keppel Islands in the southern inshore Great Barrier Reef (GBR), based on in situ salinity exposure and coral responses during a major flood event in 2010–2011. This threshold is presented as a dose-time response for a salinity-sensitive range of 22–28 PSU and an exposure time of 3–16 days at the lowest and highest salinities, respectively. The robustness of the salinity threshold was confirmed by comparison with responses of corals to low salinity ~600 km north in the central GBR, which were exposed to substantially different turbidity and chlorophyll levels during the period of hypo-salinity.