Evolution of diapause in the African turquoise killifish by remodeling the ancient gene regulatory landscape.

Suspended animation states allow organisms to survive extreme environments. The African turquoise killifish has evolved diapause as a form of suspended development to survive a complete drought. However, the mechanisms underlying the evolution of extreme survival states are unknown. To understand diapause evolution, we performed integrative multi-omics (gene expression, chromatin accessibility, and lipidomics) in the embryos of multiple killifish species. We find that diapause evolved by a recent remodeling of regulatory elements at very ancient gene duplicates (paralogs) present in all vertebrates. CRISPR-Cas9-based perturbations identify the transcription factors REST/NRSF and FOXOs as critical for the diapause gene expression program, including genes involved in lipid metabolism. Indeed, diapause shows a distinct lipid profile, with an increase in triglycerides with very-long-chain fatty acids. Our work suggests a mechanism for the evolution of complex adaptations and offers strategies to promote long-term survival by activating suspended animation programs in other species.

Attenuated psychosis symptoms are related to working alliance between therapist and service user.

AIM: Many trials have demonstrated the efficacy of specific therapy modalities for individuals with attenuated psychosis symptoms (APS). Less is known regarding mechanisms behind positive outcomes, including the role of nonspecific therapeutic factors. This study explored working alliance (WA) in a clinic serving individuals with APS to see how WA changed across the course of treatment and its relation to APS. METHODS: Session level APS and WA data was available for 12 individuals of diverse racial and gender identity, (M = 48 sessions each). Multilevel models with random intercepts tested change in WA and APS over time, and cross-sectional and prospective relations. RESULTS: WA increased and APS decreased over time. Cross sectionally, WA and APS were inversely related. Prospective relations were non-significant. CONCLUSION: When symptoms increase, therapists for individuals with APS should be attentive to potential disruptions in WA, though strong WA may be a cross-sectional protective factor.

Chromatin Accessibility Profiling and Data Analysis Using ATAC-seq in Nothobranchius furzeri.

The state of genome-wide chromatin accessibility in cells, tissues, or organisms can be investigated with a technique called assay for transposase-accessible chromatin using sequencing (ATAC-seq). ATAC-seq is a powerful approach for profiling the epigenomic landscape of cells using very low input materials. Analysis of chromatin accessibility data allows for prediction of gene expression and identification of regulatory elements such as potential enhancers and specific transcription-factor binding sites. Here, we describe an optimized ATAC-seq protocol for the preparation of isolated nuclei and subsequent next-generation sequencing from whole embryos and tissues of the African turquoise killifish (Nothobranchius furzeri). Importantly, we provide an overview of a pipeline for processing and analyzing ATAC-seq data from killifish.

Collaborative Research Activities of the Arase and Van Allen Probes.

This paper presents the highlights of joint observations of the inner magnetosphere by the Arase spacecraft, the Van Allen Probes spacecraft, and ground-based experiments integrated into spacecraft programs. The concurrent operation of the two missions in 2017-2019 facilitated the separation of the spatial and temporal structures of dynamic phenomena occurring in the inner magnetosphere. Because the orbital inclination angle of Arase is larger than that of Van Allen Probes, Arase collected observations at higher L -shells up to L ∼ 10 . After March 2017, similar variations in plasma and waves were detected by Van Allen Probes and Arase. We describe plasma wave observations at longitudinally separated locations in space and geomagnetically-conjugate locations in space and on the ground. The results of instrument intercalibrations between the two missions are also presented. Arase continued its normal operation after the scientific operation of Van Allen Probes completed in October 2019. The combined Van Allen Probes (2012-2019) and Arase (2017-present) observations will cover a full solar cycle. This will be the first comprehensive long-term observation of the inner magnetosphere and radiation belts.

Contributions to Loss Across the Magnetopause During an Electron Dropout Event.

Dropout events are dramatic decreases in radiation belt electron populations that can occur in as little as 30 minutes. Loss to magnetopause due to a combination of magnetopause shadowing and outward radial transport plays a significant role in these events. We examine the dropout of relativistic electron populations during the October 2012 geomagnetic storm using simulated electron phase space density, evaluating the contribution of different processes to losses across the magnetopause. We compare loss contribution from outward transport calculated using a standard empirical radial diffusion model that assumes a dipolar geomagnetic field to an event-specific radial diffusion model evaluated with a non-dipolar geomagnetic field. We additionally evaluate the contribution of Shabansky type 1 particles, which bounce along magnetic field lines with local equatorial maxima, to the loss calculated during this event. We find that the empirical radial diffusion model with a dipolar background field underestimates the contribution of radial diffusion to this dropout event by up to 10% when compared to the event-specific, non-dipolar radial diffusion model. We additionally find that including Shabansky type 1 particles in the initial electron phase space density, that is, allowing some magnetic field lines distorted from the typical single-minima configuration in drift shell construction, increases the calculated loss by an average of 0.75%. This shows that the treatment of the geomagnetic field significantly impacts the calculation of electron losses to the magnetopause during dropout events, with the non-dipolar treatment of radial diffusion being essential to accurately quantify the loss of outer radiation belt populations.

The Magnetic Electron Ion Spectrometer: A Review of On-Orbit Sensor Performance, Data, Operations, and Science.

Measurements from NASA's Van Allen Probes have transformed our understanding of the dynamics of Earth's geomagnetically-trapped, charged particle radiation. The Van Allen Probes were equipped with the Magnetic Electron Ion Spectrometers (MagEIS) that measured energetic and relativistic electrons, along with energetic ions, in the radiation belts. Accurate and routine measurement of these particles was of fundamental importance towards achieving the scientific goals of the mission. We provide a comprehensive review of the MagEIS suite's on-orbit performance, operation, and data products, along with a summary of scientific results. The purpose of this review is to serve as a complement to the MagEIS instrument paper, which was largely completed before flight and thus focused on pre-flight design and performance characteristics. As is the case with all space-borne instrumentation, the anticipated sensor performance was found to be different once on orbit. Our intention is to provide sufficient detail on the MagEIS instruments so that future generations of researchers can understand the subtleties of the sensors, profit from these unique measurements, and continue to unlock the mysteries of the near-Earth space radiation environment. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11214-021-00855-2.

Ethnicity and the surgical management of early invasive breast cancer in over 164 000 women.

BACKGROUND: Limited information is available about patterns of surgical management of early breast cancer by ethnicity of women in England, and any potential inequalities in the treatment received for breast cancer. METHODS: National Cancer Registration and Analysis Service data for women diagnosed with early invasive breast cancer (ICD-10 C50) during 2012-2017 were analysed. Multivariable logistic regression was used to estimate odds ratios (ORs) and 95 per cent confidence intervals for the risk of mastectomy versus breast-conserving surgery by ethnicity (black African, black Caribbean, Indian, Pakistani and white), adjusting for age, region, deprivation, year of diagnosis, co-morbidity and stage at diagnosis. RESULTS: Data from 164 143 women were included in the analysis. The proportion of women undergoing mastectomy fell by approximately 5 per cent between 2012 and 2017 across all the ethnic groups examined. In unadjusted analyses, each ethnic minority group had a significantly higher odds of mastectomy than white women; however, in the fully adjusted model, there were no significantly increased odds of having mastectomy for women of any ethnic minority group examined. For example, compared with white women, the unadjusted and fully adjusted ORs for mastectomy were 1·14 (95 per cent c.i. 1·05 to 1·20) and 1·04 (0·96 to 1·14) respectively for Indian women, and 1·45 (1·30 to 1·62) and 1·00 (0·89 to 1·13) for black African women. This attenuation in OR by ethnicity was largely due to adjustment for age and stage. CONCLUSION: Allowing for different patterns of age and stage at presentation, the surgical management of early breast cancer is similar in all women, regardless of ethnicity.

Approximating posteriors with high-dimensional nuisance parameters via integrated rotated Gaussian approximation.

Posterior computation for high-dimensional data with many parameters can be challenging. This article focuses on a new method for approximating posterior distributions of a low- to moderate-dimensional parameter in the presence of a high-dimensional or otherwise computationally challenging nuisance parameter. The focus is on regression models and the key idea is to separate the likelihood into two components through a rotation. One component involves only the nuisance parameters, which can then be integrated out using a novel type of Gaussian approximation. We provide theory on approximation accuracy that holds for a broad class of forms of the nuisance component and priors. Applying our method to simulated and real data sets shows that it can outperform state-of-the-art posterior approximation approaches.

Dynamic Properties of Particle Injections Inside Geosynchronous Orbit: A Multisatellite Case Study.

Four closely located satellites at and inside geosynchronous orbit (GEO) provided a great opportunity to study the dynamical evolution and spatial scale of premidnight energetic particle injections inside GEO during a moderate substorm on 23 December 2016. Just following the substorm onset, the four spacecraft, a LANL satellite at GEO, the two Van Allen Probes (also called "RBSP") at ~5.8 R E, and a THEMIS satellite at ~5.3 R E, observed substorm-related particle injections and local dipolarizations near the central meridian (~22 MLT) of a wedge-like current system. The large-scale evolution of the electron and ion (H, He, and O) injections was almost identical at the two RBSP spacecraft with ~0.5 R E apart. However, the initial short-timescale particle injections exhibited a striking difference between RBSP-A and -B: RBSP-B observed an energy dispersionless injection which occurred concurrently with a transient, strong dipolarization front (DF) with a peak-to-peak amplitude of ~25 nT over ~25 s; RBSP-A measured a dispersed/weaker injection with no corresponding DF. The spatiotemporally localized DF was accompanied by an impulsive, westward electric field (~20 mV m-1). The fast, impulsive E × B drift caused the radial transport of the electron and ion injection regions from GEO to ~5.8 R E. The penetrating DF fields significantly altered the rapid energy- and pitch angle-dependent flux changes of the electrons and the H and He ions inside GEO. Such flux distributions could reflect the transient DF-related particle acceleration and/or transport processes occurring inside GEO. In contrast, O ions were little affected by the DF fields.

Oxygen torus and its coincidence with EMIC wave in the deep inner magnetosphere: Van Allen Probe B and Arase observations.

We investigate the longitudinal structure of the oxygen torus in the inner magnetosphere for a specific event found on 12 September 2017, using simultaneous observations from the Van Allen Probe B and Arase satellites. It is found that Probe B observed a clear enhancement in the average plasma mass (M) up to 3-4 amu at L = 3.3-3.6 and magnetic local time (MLT) = 9.0 h. In the afternoon sector at MLT ~ 16.0 h, both Probe B and Arase found no clear enhancements in M. This result suggests that the oxygen torus does not extend over all MLT but is skewed toward the dawn. Since a similar result has been reported for another event of the oxygen torus in a previous study, a crescent-shaped torus or a pinched torus centered around dawn may be a general feature of the O+ density enhancement in the inner magnetosphere. We newly find that an electromagnetic ion cyclotron (EMIC) wave in the H+ band appeared coincidently with the oxygen torus. From the lower cutoff frequency of the EMIC wave, the ion composition of the oxygen torus is estimated to be 80.6% H+, 3.4% He+, and 16.0% O+. According to the linearized dispersion relation for EMIC waves, both He+ and O+ ions inhibit EMIC wave growth and the stabilizing effect is stronger for He+ than O+. Therefore, when the H+ fraction or M is constant, the denser O+ ions are naturally accompanied by the more tenuous He+ ions, resulting in a weaker stabilizing effect (i.e., larger growth rate). From the Probe B observations, we find that the growth rate becomes larger in the oxygen torus than in the adjacent regions in the plasma trough and the plasmasphere.

Vertebrate diapause preserves organisms long term through Polycomb complex members.

Diapause is a state of suspended development that helps organisms survive extreme environments. How diapause protects living organisms is largely unknown. Using the African turquoise killifish (Nothobranchius furzeri), we show that diapause preserves complex organisms for extremely long periods of time without trade-offs for subsequent adult growth, fertility, and life span. Transcriptome analyses indicate that diapause is an active state, with dynamic regulation of metabolism and organ development genes. The most up-regulated genes in diapause include Polycomb complex members. The chromatin mark regulated by Polycomb, H3K27me3, is maintained at key developmental genes in diapause, and the Polycomb member CBX7 mediates repression of metabolism and muscle genes in diapause. CBX7 is functionally required for muscle preservation and diapause maintenance. Thus, vertebrate diapause is a state of suspended life that is actively maintained by specific chromatin regulators, and this has implications for long-term organism preservation.

Transport and Loss of Ring Current Electrons Inside Geosynchronous Orbit During the 17 March 2013 Storm.

Ring current electrons (1-100 keV) have received significant attention in recent decades, but many questions regarding their major transport and loss mechanisms remain open. In this study, we use the four-dimensional Versatile Electron Radiation Belt code to model the enhancement of phase space density that occurred during the 17 March 2013 storm. Our model includes global convection, radial diffusion, and scattering into the Earth's atmosphere driven by whistler-mode hiss and chorus waves. We study the sensitivity of the model to the boundary conditions, global electric field, the electric field associated with subauroral polarization streams, electron loss rates, and radial diffusion coefficients. The results of the code are almost insensitive to the model parameters above 4.5 R E R E, which indicates that the general dynamics of the electrons between 4.5 R E and the geostationary orbit can be explained by global convection. We found that the major discrepancies between the model and data can stem from the inaccurate electric field model and uncertainties in lifetimes. We show that additional mechanisms that are responsible for radial transport are required to explain the dynamics of ≥40-keV electrons, and the inclusion of the radial diffusion rates that are typically assumed in radiation belt studies leads to a better agreement with the data. The overall effect of subauroral polarization streams on the electron phase space density profiles seems to be smaller than the uncertainties in other input parameters. This study is an initial step toward understanding the dynamics of these particles inside the geostationary orbit.

A Revised Look at Relativistic Electrons in the Earth's Inner Radiation Zone and Slot Region.

We describe a new, more accurate procedure for estimating and removing inner zone background contamination from Van Allen Probes Magnetic Electron Ion Spectrometer (MagEIS) radiation belt measurements. This new procedure is based on the underlying assumption that the primary source of background contamination in the electron measurements at L shells less than three, energetic inner belt protons, is relatively stable. Since a magnetic spectrometer can readily distinguish between foreground electrons and background signals, we are able to exploit the proton stability to construct a model of the background contamination in each MagEIS detector by only considering times when the measurements are known to be background dominated. We demonstrate, for relativistic electron measurements in the inner zone, that the new technique is a significant improvement upon the routine background corrections that are used in the standard MagEIS data processing, which can "overcorrect" and therefore remove real (but small) electron fluxes. As an example, we show that the previously reported 1-MeV injection into the inner zone that occurred in June of 2015 was distributed more broadly in L and persisted in the inner zone longer than suggested by previous estimates. Such differences can have important implications for both scientific studies and spacecraft engineering applications that make use of MagEIS electron data in the inner zone at relativistic energies. We compare these new results with prior work and present more recent observations that also show a 1-MeV electron injection into the inner zone following the September 2017 interplanetary shock passage.

RBSP-ECT Combined Spin-Averaged Electron Flux Data Product.

We describe a new data product combining the spin-averaged electron flux measurements from the Radiation Belt Storm Probes (RBSP) Energetic Particle Composition and Thermal Plasma (ECT) suite on the National Aeronautics and Space Administration's Van Allen Probes. We describe the methodology used to combine each of the data sets and produce a consistent set of spectra for September 2013 to the present. Three-minute-averaged flux spectra are provided spanning energies from 15 eV up to 20 MeV. This new data product provides additional utility to the ECT data and offers a consistent cross calibrated data set for researchers interested in examining the dynamics of the inner magnetosphere across a wide range of energies.

Energization of the Ring Current by Substorms.

The substorm process releases large amounts of energy into the magnetospheric system, although where the energy is transferred to and how it is partitioned remains an open question. In this study, we address whether the substorm process contributes a significant amount of energy to the ring current. The ring current is a highly variable region, and understanding the energization processes provides valuable insight into how substorm-ring current coupling may contribute to the generation of storm conditions and provide a source of energy for wave driving. In order to quantify the energy input into the ring current during the substorm process, we analyze Radiation Belt Storm Probes Ion Composition Experiment and Helium Oxygen Proton Electron ion flux measurements for H+, O+, and He+. The energy content of the ring current is estimated and binned spatially for L and magnetic local time. The results are combined with an independently derived substorm event list to perform a statistical analysis of variations in the ring current energy content with substorm phase. We show that the ring current energy is significantly higher in the expansion phase compared to the growth phase, with the energy enhancement persisting into the substorm recovery phase. The characteristics of the energy enhancement suggest the injection of energized ions from the tail plasma sheet following substorm onset. The local time variations indicate a loss of energetic H+ ions in the afternoon sector, likely due to wave-particle interactions. Overall, we find that the average energy input into the ring current is ∼9% of the previously reported energy released during substorms.

Disability and participation in breast and bowel cancer screening in England: a large prospective study.

BACKGROUND: There is limited information about participation in organised population-wide screening programmes by people with disabilities. METHODS: Data from the National Health Service routine screening programmes in England were linked to information on disability reported by the Million Women Study cohort participants. RESULTS: Of the 473 185 women offered routine breast or bowel cancer screening, 23% reported some disability. Women with disabilities were less likely than other women to participate in breast cancer screening (RR=0.64, 95% CI: 0.62-0.65) and in bowel cancer screening (RR=0.75, 0.73-0.76). Difficulties with self-care or vision were associated with the greatest reduction in screening participation. CONCLUSION: Participation in routine cancer screening programmes in England is reduced in people with disabilities and participation varies by type of disability.

Optimizing the stimulus presentation paradigm design for the P300-based brain-computer interface using performance prediction.

OBJECTIVE: The role of a brain-computer interface (BCI) is to discern a user's intended message or action by extracting and decoding relevant information from brain signals. Stimulus-driven BCIs, such as the P300 speller, rely on detecting event-related potentials (ERPs) in response to a user attending to relevant or target stimulus events. However, this process is error-prone because the ERPs are embedded in noisy electroencephalography (EEG) data, representing a fundamental problem in communication of the uncertainty in the information that is received during noisy transmission. A BCI can be modeled as a noisy communication system and an information-theoretic approach can be exploited to design a stimulus presentation paradigm to maximize the information content that is presented to the user. However, previous methods that focused on designing error-correcting codes failed to provide significant performance improvements due to underestimating the effects of psycho-physiological factors on the P300 ERP elicitation process and a limited ability to predict online performance with their proposed methods. Maximizing the information rate favors the selection of stimulus presentation patterns with increased target presentation frequency, which exacerbates refractory effects and negatively impacts performance within the context of an oddball paradigm. An information-theoretic approach that seeks to understand the fundamental trade-off between information rate and reliability is desirable. APPROACH: We developed a performance-based paradigm (PBP) by tuning specific parameters of the stimulus presentation paradigm to maximize performance while minimizing refractory effects. We used a probabilistic-based performance prediction method as an evaluation criterion to select a final configuration of the PBP. MAIN RESULTS: With our PBP, we demonstrate statistically significant improvements in online performance, both in accuracy and spelling rate, compared to the conventional row-column paradigm. SIGNIFICANCE: By accounting for refractory effects, an information-theoretic approach can be exploited to significantly improve BCI performance across a wide range of performance levels.

Cancer risk among 21st century blood transfusion recipients.

Background: Some carcinogenic viruses are known to be transmissible by blood transfusion. Intensive viral screening of transfused blood now exists in most countries. In the UK, high-sensitivity nucleic acid amplification tests for hepatitis C virus were introduced in 1999 and it was thought that this would reduce, and possibly eliminate, transfusion-related liver cancer. We aimed to investigate cancer risk in recipients of blood transfusion in 2000 or after. Methods: A total of 1.3 million UK women recruited in 1998 on average were followed for hospital records of blood transfusion and for cancer registrations. After excluding women with cancer or precancerous conditions before or at the time of transfusion, Cox regression yielded adjusted relative risks of 11 site-specific cancers for women with compared to without prior blood transfusion. Results: During follow up, 11 274 (0.9%) women had a first recorded transfusion in 2000 or after, and 1648 (14.6%) of them were subsequently diagnosed with cancer, a mean 6.8 years after the transfusion. In the first 5 years after transfusion there were significant excesses for most site-specific cancers examined, presumably because some had preclinical cancer. However, 5 or more years (mean 8 years) after blood transfusion, there were significant excess risks only for liver cancer (adjusted relative risk = 2.63, 95%CI 1.45-4.78) and for non-Hodgkin lymphoma (adjusted relative risk = 1.74, 1.21-2.51). When analyses were restricted to those undergoing hip or knee replacement surgery, the commonest procedure associated with transfusion, these relative risks were not materially altered. Conclusions: In a large cohort of UK women, transfusions in the 21st century were associated with long-term increased risks of liver cancer and non-Hodgkin lymphoma. Some of these malignancies may have been caused by carcinogenic agents that are not currently screened for in transfused blood.

Using Clinical Signs and Symptoms for Medical Management of Radiation Casualties - 2015 NATO Exercise.

The utility of early-phase (≤5 days) radiation-induced clinical signs and symptoms (e.g., vomiting, diarrhea, erythema and changes in blood cell counts) was examined for the prediction of later occurring acute radiation syndrome (ARS) severity and the development of medical management strategies. Medical treatment protocols for radiation accident victims (METREPOL) was used to grade ARS severities, which were assigned response categories (RCs). Data on individuals (n = 191) with mild (RC1, n = 45), moderate (RC2, n = 19), severe (RC3, n = 20) and fatal (RC4, n = 18) ARS, as well as nonexposed individuals (RC0, n = 89) were generated using either METREPOL (n = 167) or the system for evaluation and archiving of radiation accidents based on case histories (SEARCH) database (n = 24), the latter comprised of real-case descriptions. These data were converted into tables reflecting clinical signs and symptoms, and submitted to eight teams representing five participating countries. The teams were comprised of medical doctors, biologists and pharmacists with subject matter expertise. The tables comprised cumulated clinical data from day 1-3 and day 1-5 postirradiation. While it would have reflected a more realistic scenario to provide the data to the teams over the course of a 3- or 5-day period, the logistics of doing so proved too challenging. In addition, the team members participating in this exercise chose to receive the cumulated reports of day 1-3 and 1-5. The teams were tasked with predicting ARS incidence, ARS severity and the requirement for hospitalization for multiple cases, as well as providing the certainty of their diagnosis. Five of the teams also performed dose estimates. The teams did not employ harmonized methodologies, and the expertise among the members varied, as did the tools used and the means of analyzing the clinical data. The earliest report time was 3 h after the tables were sent to the team members. The majority of cases developing ARS (89.6% ± 3.3 SD) and requiring hospitalization (88.8% ± 4.6 SD) were correctly identified by all teams. Determination of ARS severity was particularly challenging for RC2-3, which was systematically overestimated. However, RC4 was correctly predicted at 94-100% by all teams. RC0 and RC1 ARS severities were more difficult to discriminate. When reported RCs (0-1 and 3-4) were merged, on average 89.6% (±3.3 SD) of all cases could be correctly classified. Comparisons on frequency distributions revealed no statistically significant differences among the following: 1. reported ARS from different teams (P > 0.2); 2. cases generated based on METREPOL or SEARCH (P > 0.5); or 3. results reported at day 3 and 5 postirradiation (P > 0.1). Dose estimates of all teams increased significantly along with ARS severity (P < 0.0001) as well as with dose estimates generated from dicentric chromosomal-aberration measurements available for SEARCH cases (P < 0.0001). In summary, early-phase radiation-induced clinical signs and symptoms proved to be useful for rapid and accurate assessment, with minor limitations, toward predicting life-threatening ARS severity and developing treatment management strategies.

Highly relativistic radiation belt electron acceleration, transport, and loss: Large solar storm events of March and June 2015.

Two of the largest geomagnetic storms of the last decade were witnessed in 2015. On 17 March 2015, a coronal mass ejection-driven event occurred with a Dst (storm time ring current index) value reaching -223 nT. On 22 June 2015 another strong storm (Dst reaching -204 nT) was recorded. These two storms each produced almost total loss of radiation belt high-energy (E ≳ 1 MeV) electron fluxes. Following the dropouts of radiation belt fluxes there were complex and rather remarkable recoveries of the electrons extending up to nearly 10 MeV in kinetic energy. The energized outer zone electrons showed a rich variety of pitch angle features including strong "butterfly" distributions with deep minima in flux at α = 90°. However, despite strong driving of outer zone earthward radial diffusion in these storms, the previously reported "impenetrable barrier" at L ≈ 2.8 was pushed inward, but not significantly breached, and no E ≳ 2.0 MeV electrons were seen to pass through the radiation belt slot region to reach the inner Van Allen zone. Overall, these intense storms show a wealth of novel features of acceleration, transport, and loss that are demonstrated in the present detailed analysis.