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Background Extracellular vesicles (EVs), containing microRNAs (miRNAs) and other molecules, play a central role in intercellular communication, especially in viral infections caused by SARS-CoV-2. This study explores the miRNA profiles in plasma-derived EVs from patients with severe COVID-19 vs controls, identifying potential mortality predictors. Methods This prospective study included 36 patients with severe COVID-19 and 33 controls without COVID-19. EV-derived miRNAs were sequenced, and bioinformatics and differential expression analysis between groups were performed. The plasma miRNA profile of an additional cohort of patients with severe COVID-19 (n = 32) and controls (n = 12) was used to compare with our data. Survival analysis identified potential mortality predictors among the significantly differentially expressed (SDE) miRNAs in EVs. Results Patients with severe COVID-19 showed 50 SDE miRNAs in plasma-derived EVs. These miRNAs were associated with pathways related to inflammation and cell adhesion. Fifteen of these plasma-derived EV miRNAs were SDE in the plasma of severe cases vs controls. Two miRNAs, hsa-miR-1469 and hsa-miR-6124, were identified as strong mortality predictors with an area under the receiver operating characteristic curve of 0.938. Conclusions This research provides insights into the role of miRNAs within EVs in severe COVID-19 and their potential as clinical biomarkers for mortality. [ABSTRACT FROM AUTHOR]

Aims There is lack of agreement on late gadolinium enhancement cardiac magnetic resonance (LGE-CMR) imaging processing for guiding ventricular tachycardia (VT) ablation. We aim at developing and validating a systematic processing approach on LGE-CMR images to identify VT corridors that contain critical VT isthmus sites. Methods and results This is a translational study including 18 pigs with established myocardial infarction and inducible VT undergoing in vivo characterization of the anatomical and functional myocardial substrate associated with VT maintenance. Clinical validation was conducted in a multicentre series of 33 patients with ischaemic cardiomyopathy undergoing VT ablation. Three-dimensional LGE-CMR images were processed using systematic scanning of 15 signal intensity (SI) cut-off ranges to obtain surface visualization of all potential VT corridors. Analysis and comparisons of imaging and electrophysiological data were performed in individuals with full electrophysiological characterization of the isthmus sites of at least one VT morphology. In both the experimental pig model and patients undergoing VT ablation, all the electrophysiologically defined isthmus sites (n = 11 and n = 19, respectively) showed overlapping regions with CMR-based potential VT corridors. Such imaging-based VT corridors were less specific than electrophysiologically guided ablation lesions at critical isthmus sites. However, an optimized strategy using the 7 most relevant SI cut-off ranges among patients showed an increase in specificity compared to using 15 SI cut-off ranges (70 vs. 62%, respectively), without diminishing the capability to detect VT isthmus sites (sensitivity 100%). Conclusion Systematic imaging processing of LGE-CMR sequences using several SI cut-off ranges may improve and standardize procedure planning to identify VT isthmus sites. [ABSTRACT FROM AUTHOR]

This study investigates the clustering and bias of Luminous Red Galaxies (LRG) in the BOSS-LOWZ, -CMASS, -COMB, and eBOSS samples, using two types of simulated lightcones: (i) high-fidelity lightcones from Uchuu N -body simulation, employing SHAM technique to assign LRG to (sub)haloes, and (ii) 16 000 covariance lightcones from GLAM-Uchuu N -body simulations, including LRG using HOD data from Uchuu. Our results indicate that Uchuu and glam lightcones closely replicate BOSS/eBOSS data, reproducing correlation function and power spectrum across scales from redshifts 0.2 to 1.0, from 2 to |$150 \,h^{-1}\,\mathrm{Mpc}$| in configuration space, from 0.005 to |$0.7\, h\,\mathrm{Mpc}^{-1}$| in Fourier space, and across different LRG stellar masses. Furthermore, comparing with existing MD-Patchy and EZmock BOSS/eBOSS lightcones based on approximate methods, our GLAM-Uchuu lightcones provide more precise clustering estimates. We identify significant deviations from observations within |$20 \,h^{-1}\,\mathrm{Mpc}$| scales in MD-Patchy and EZmock , with our covariance matrices indicating that these methods underestimate errors by between 10 per cent and 60 per cent. Lastly, we explore the impact of cosmology on galaxy clustering. Our findings suggest that, given the current level of uncertainties in BOSS/eBOSS data, distinguishing models with and without massive neutrino effects on large-scale structure (LSS) is challenging. This paper highlights the Uchuu and GLAM-Uchuu simulations' robustness in verifying the accuracy of Planck cosmological parameters, providing a strong foundation for enhancing lightcone construction in future LSS surveys. We also demonstrate that generating thousands of galaxy lightcones is feasible using N -body simulations with adequate mass and force resolution. [ABSTRACT FROM AUTHOR]

Background Lymphatic filariasis (LF) is a debilitating, poverty-promoting, neglected tropical disease (NTD) targeted for worldwide elimination as a public health problem (EPHP) by 2030. Evaluating progress towards this target for national programmes is challenging, due to differences in disease transmission and interventions at the subnational level. Mathematical models can help address these challenges by capturing spatial heterogeneities and evaluating progress towards LF elimination and how different interventions could be leveraged to achieve elimination by 2030. Methods Here we used a novel approach to combine historical geo-spatial disease prevalence maps of LF in Ethiopia with 3 contemporary disease transmission models to project trends in infection under different intervention scenarios at subnational level. Results Our findings show that local context, particularly the coverage of interventions, is an important determinant for the success of control and elimination programmes. Furthermore, although current strategies seem sufficient to achieve LF elimination by 2030, some areas may benefit from the implementation of alternative strategies, such as using enhanced coverage or increased frequency, to accelerate progress towards the 2030 targets. Conclusions The combination of geospatial disease prevalence maps of LF with transmission models and intervention histories enables the projection of trends in infection at the subnational level under different control scenarios in Ethiopia. This approach, which adapts transmission models to local settings, may be useful to inform the design of optimal interventions at the subnational level in other LF endemic regions. [ABSTRACT FROM AUTHOR]

Background Lymphatic filariasis (LF) is a neglected tropical disease targeted for elimination as a public health problem by 2030. Although mass treatments have led to huge reductions in LF prevalence, some countries or regions may find it difficult to achieve elimination by 2030 owing to various factors, including local differences in transmission. Subnational projections of intervention impact are a useful tool in understanding these dynamics, but correctly characterizing their uncertainty is challenging. Methods We developed a computationally feasible framework for providing subnational projections for LF across 44 sub-Saharan African countries using ensemble models, guided by historical control data, to allow assessment of the role of subnational heterogeneities in global goal achievement. Projected scenarios include ongoing annual treatment from 2018 to 2030, enhanced coverage, and biannual treatment. Results Our projections suggest that progress is likely to continue well. However, highly endemic locations currently deploying strategies with the lower World Health Organization recommended coverage (65%) and frequency (annual) are expected to have slow decreases in prevalence. Increasing intervention frequency or coverage can accelerate progress by up to 5 or 6 years, respectively. Conclusions While projections based on baseline data have limitations, our methodological advancements provide assessments of potential bottlenecks for the global goals for LF arising from subnational heterogeneities. In particular, areas with high baseline prevalence may face challenges in achieving the 2030 goals, extending the "tail" of interventions. Enhancing intervention frequency and/or coverage will accelerate progress. Our approach facilitates preimplementation assessments of the impact of local interventions and is applicable to other regions and neglected tropical diseases. [ABSTRACT FROM AUTHOR]

Background Holding times for raw materials are relevant since they enable us to understand the allowable time that a raw material can be kept under ideal storage conditions before the start of the manufacturing process without its quality attributes being affected. The quantification of water activity can be used as an indicator of the microbiological, physicochemical, and organoleptic stability of a specimen, since low water activity retards autohydrolysis and microbiological growth. Objective The main purpose of this investigation was to test the stability of powdered raw materials for a maximum holding time of 8 days through water activity measurements. Thus microbiological, physicochemical, and organoleptic measurements were carried out in parallel and simultaneously to experimentally establish a relationship between the status of the water activity of processed raw materials and the microbiological, physicochemical, and organoleptic results. Methods The raw materials were stored for a maximum holding time of 8 days, in accordance with United States Pharmacopeia monographs. For all the raw materials tested, water activity measurements were performed using the dew point chilled-mirror method on days 0, 3, and 8. On days 0 and 8, microbiological, physicochemical, and organoleptic assessments were performed. Results It was established that under these storage conditions, the processed raw materials exhibited water activity below 0.60 during the entire holding time. However, there were statistically significant differences in water activity levels between days 0, 3, and 8 (ANOVA P  < 0.05). Despite observing statistically significant differences between days, the microbiological, physicochemical, and organoleptic features were within specification at those water activity levels below 0.60. Conclusions Water activity below 0.60 does not allow the growth of microorganisms, and the organoleptic and physicochemical features remain unperturbed. The results indicate that water activity can be used as an indicator of the microbiological load and chemical stability of the raw materials tested. Highlights This research provides evidence that corroborates that water activity status may be used as a reliable indicator for the microbiological burden and physicochemical features of pharmaceutical material during stability studies. [ABSTRACT FROM AUTHOR]

We present the data release of the Uchuu–SDSS galaxies: a set of 32 high-fidelity galaxy light-cones constructed from the large Uchuu 2.1 trillion particles N -body simulation using Planck cosmology. We adopt subhalo abundance matching to populate the Uchuu-box halo catalogues with SDSS galaxy luminosities. These box catalogues generated at several redshifts are combined to create a set of light-cones with redshift-evolving galaxy properties. The Uchuu–SDSS galaxy light-cones are built to reproduce the footprint and statistical properties of the SDSS main galaxy survey, along with stellar masses and star formation rates. This facilitates a direct comparison of the observed SDSS and simulated Uchuu–SDSS data. Our light-cones reproduce a large number of observational results, such as the distribution of galaxy properties, galaxy clustering, stellar mass functions, and halo occupation distributions. Using simulated and real data, we select samples of bright red galaxies at z eff = 0.15 to explore redshift space distortions and baryon acoustic oscillations (BAO) by fitting the full two-point correlation function and the BAO peak. We create a set of 5100 galaxy light-cones using GLAM N -body simulations to compute covariance errors. We report a |$\sim 30~{{\ \rm per\ cent}}$| precision increase on f σ8 and the pre-reconstruction BAO scale, due to our better estimate of the covariance matrix. From our BAO-inferred α∥ and α⊥ parameters, we obtain the first SDSS measurements of the Hubble and angular diameter distances |$D_\mathrm{H}(z=0.15) / r_d = 27.9^{+3.1}_{-2.7}$|⁠ , |$D_\mathrm{M}(z=0.15) / r_d = 5.1^{+0.4}_{-0.4}$|⁠. Overall, we conclude that the Planck Λ CDM cosmology nicely explains the observed large-scale structure statistics of SDSS. All data sets are made publicly available. [ABSTRACT FROM AUTHOR]

We measure the two-point correlation function (CF) of 1357 galaxy clusters with a mass of log10 M 200 ≥ 13.6 h −1 M⊙ and at a redshift of z ≤ 0.125. This work differs from previous analyses in that it utilizes a spectroscopic cluster catalogue, |$\tt {SDSS-GalWCat}$|⁠ , to measure the CF and detect the baryon acoustic oscillation (BAO) signal. Unlike previous studies which use statistical techniques, we compute covariance errors directly by generating a set of 1086 galaxy cluster light-cones from the GLAM N -body simulation. Fitting the CF with a power-law model of the form ξ(s) = (s / s 0)−γ, we determine the best-fitting correlation length and power-law index at three mass thresholds. We find that the correlation length increases with increasing the mass threshold while the power-law index is almost constant. For log10 M 200 ≥ 13.6 h −1 M⊙, we find s 0 = 14.54 ± 0.87 h −1 Mpc and γ = 1.97 ± 0.11. We detect the BAO signal at s  = 100 h −1 Mpc with a significance of 1.60σ. Fitting the CF with a Lambda cold dark matter model, we find |$D_\mathrm{V}(z = 0.089)\mathit{r}^{\mathrm{ fid}}_\mathrm{ d}/\mathit{r}_\mathrm{ d} = 267.62 \pm 26$|   h −1 Mpc, consistent with Planck 2015 cosmology. We present a set of 108 high-fidelity simulated galaxy cluster light-cones from the high-resolution Uchuu N -body simulation, employed for methodological validation. We find D V(z  = 0.089)/ r d = 2.666 ± 0.129, indicating that our method does not introduce any bias in the parameter estimation for this small sample of galaxy clusters. [ABSTRACT FROM AUTHOR]

Photometric time series gathered by space telescopes such as CoRoT and Kepler allow to detect solar-like oscillations in red giant stars and to measure their global seismic constraints, which can be used to infer global stellar properties (e.g. masses, radii, and evolutionary states). Combining such precise constraints with photospheric abundances provides a means of testing mixing processes that occur inside red-giant stars. In this work, we conduct a detailed spectroscopic and seismic analysis of nine nearby (d < 200 pc) red giant stars observed by Kepler. Both seismic constraints and grid-based modelling approaches are used to determine precise fundamental parameters for those evolved stars. We compare distances and radii derived from Gaia Data Release 3 parallaxes with those inferred by a combination of seismic, spectroscopic, and photometric constraints. We find no deviations within errors bars, however the small sample size and the associated uncertainties are a limiting factor for such comparison. We use the period spacing of mixed modes to distinguish between ascending red-giants and red clump stars. Based on the evolutionary status, we apply corrections to the values of Δν for some stars, resulting in a slight improvement to the agreement between seismic and photometric distances. Finally, we couple constraints on detailed chemical abundances with the inferred masses, radii, and evolutionary states. Our results corroborate previous studies that show that observed abundances of lithium and carbon isotopic ratio are in contrast with predictions from standard models, giving robust evidence for the occurrence of additional mixing during the red-giant phase. [ABSTRACT FROM AUTHOR]

Crocodylus acutus is the most widely distributed crocodile in the Neotropics, playing a key role in the ecosystems it inhabits. However, unsustainable use and habitat degradation have depleted its populations across its range. In Colombia, it is classified as Endangered by local authorities, and a legislative framework for its protection has been created, implementing hunting bans and breeding programmes. Successful implementation of these programmes depends on the existence of baseline genetic information, which is currently insufficient for the species. We assess the genetic diversity, phylogeography, and demographic patterns of the American crocodile in Colombia based on three mitochondrial markers (cox1 , cytb , and trnP/trnF/D-Loop) and propose actions for its management and conservation. We processed 33 American crocodile samples from both wild and captive populations and performed genetic variability, phylogenetic, phylogeographical, and neutrality tests, including previously reported sequences. We found evidence of high genetic variability in Colombia, the existence of clearly differentiated mitochondrial phylogenetic clades, and possible human-influenced or stochastic demographic variation events. We propose guidelines for the translocation of American crocodiles based on our findings and present evidence of possible dispersal events in the Caribbean and Magdalena regions. Finally, we suggest the implementation of management units and identify research priorities for future work. [ABSTRACT FROM AUTHOR]

Objective: The present investigation studies the efficacy of an automated growth-based system for a quantitative determination of Candida albicans and Aspergillus brasiliensis in several personal care products. The main purpose of this validation study was to prove that the alternative method's entire performance is not inferior to the conventional pour-plate method for a quantitative determination of yeasts and molds. Thus, a performance equivalence was established in accordance with the United Stated Pharmacopeia (USP-NF) Validation of Alternative Microbiological Methods <1223>. Methods: C. albicans and A. brasiliensis were pooled to use as inoculum (equivalent to 1.0 x 108 CFU/mL) in the suitability of the method test. PCP's preservatives were chemically neutralized leading to the yeast and mold recovery by means of the alternative microbiological method (AMM) and the pour-plate method. A correlation curve was generated for each PCP by plotting DTs relative to the corresponding log CFU values. Results: Thirty PCPs have been tested for quantification of yeasts and molds using an AMM. An equivalence of results was made through the construction of correlation curves that allowed the establishment of numerically equivalent results between the enumeration data from the reference method (CFU) and the alternative method (Detection times, DTs). Thus, following the guidelines of USP Ch.1223, essential validation parameters were tested, such as equivalence of results (Correlation coeficient, CC >0.95), linearity (R2 >0.9025), accuracy (% recovery >70%), operating range, precision (CV <35%), ruggedness (one-way ANOVA, P>0.05), specificity, LOD, and LOQ. Conclusion: It was shown that all the test results obtained from the alternative method were in statistical agreement with the standard plate-count method (PCM). Thus, this new technology was found to meet all the validation criteria needed to be considered for an alternative method for yeast and mold quantification in the PCPs tested. Highlights: In accordance with the United Stated Pharmacopeia (USP-NF) Validation of Alternative Microbiological Methods <1223>, the implementation of alternative methods can offer benefits in execution and automation while improving accuracy, sensitivity, and precision and reduce the microbiological process time compared to the traditional ones. [ABSTRACT FROM AUTHOR]

Background Genetic causes are increasingly recognized in patients with focal segmental glomerulosclerosis (FSGS), but it remains unclear which patients should undergo genetic study. Our objective was to determine the frequency and distribution of genetic variants in steroid-resistant nephrotic syndrome FSGS (SRNS-FSGS) and in FSGS of undetermined cause (FSGS-UC). Methods We performed targeted exome sequencing of 84 genes associated with glomerulopathy in patients with adult-onset SRNS-FSGS or FSGS-UC after ruling out secondary causes. Results Seventy-six patients met the study criteria; 24 presented with SRNS-FSGS and 52 with FSGS-UC. We detected FSGS-related disease-causing variants in 27/76 patients (35.5%). There were no differences between genetic and non-genetic causes in age, proteinuria, glomerular filtration rate, serum albumin, body mass index, hypertension, diabetes or family history. Hematuria was more prevalent among patients with genetic causes. We found 19 pathogenic variants in COL4A3–5 genes in 16 (29.3%) patients. NPHS2 mutations were identified in 6 (16.2%) patients. The remaining cases had variants affecting INF2, OCRL, ACTN4 genes or APOL1 high-risk alleles. FSGS-related genetic variants were more common in SRNS-FSGS than in FSGS-UC (41.7% vs 32.7%). Four SRNS-FSGS patients presented with NPHS2 disease-causing variants. COL4A variants were the most prevalent finding in FSGS-UC patients, with 12 patients carrying disease-causing variants in these genes. Conclusions FSGS-related variants were detected in a substantial number of patients with SRNS-FSGS or FSGS-UC, regardless of age of onset of disease or the patient's family history. In our experience, genetic testing should be performed in routine clinical practice for the diagnosis of this group of patients. [ABSTRACT FROM AUTHOR]

Measurements of the luminosity function of active galactic nuclei (AGN) at high redshift (z ≳ 6) are expected to suffer from field-to-field variance, including cosmic and Poisson variances. Future surveys, such as those from the Euclid telescope and JWST, will also be affected by field variance. We use the Uchuu simulation, a state-of-the-art cosmological N -body simulation with 2.1 trillion particles in a volume of 25.7 Gpc3, combined with a semi-analytic galaxy and AGN formation model, to generate the Uchuu–ν2GC catalogue, publicly available, that allows us to investigate the field-to-field variance of the luminosity function of AGN. With this Uchuu–ν2GC model, we quantify the cosmic variance as a function of survey area, AGN luminosity, and redshift. In general, cosmic variance decreases with increasing survey area and decreasing redshift. We find that at z ∼ 6 − 7, the cosmic variance depends weakly on AGN luminosity. This is because the typical mass of dark matter haloes in which AGN reside does not significantly depend on luminosity. Due to the rarity of AGN, Poisson variance dominates the total field-to-field variance, especially for bright AGN. We also examine the effect of parameters related to galaxy formation physics on the field variance. We discuss uncertainties present in the estimation of the faint-end of the AGN luminosity function from recent observations, and extend this to make predictions for the expected number of AGN and their variance for upcoming observations with Euclid , JWST, and the Legacy Survey of Space and Time (LSST). [ABSTRACT FROM AUTHOR]

The shear measurement from the Dark Energy Camera Legacy Survey (DECaLS) provides an excellent opportunity for galaxy–galaxy lensing study with the Dark Energy Spectroscopic Instrument (DESI) galaxies, given the large (∼9000 deg2) sky overlap. We explore this potential by combining the DESI 1 per cent survey and DECaLS Data Release 8 (DR8). With ∼106 deg2 sky overlap, we achieve significant detection of galaxy–galaxy lensing for Bright Galaxy Survey (BGS) and luminous red galaxy (LRG) as lenses. Scaled to the full BGS sample, we expect the statistical errors to improve from |$18(12)\,{\rm per \ cent}$| to a promising level of |$2(1.3)\,{\rm per \ cent}$| at |$\theta \gt 8\,\mathrm{ arcmin} \, (\lt 8\,\mathrm{ arcmin})$|⁠. This brings stronger requirements for future systematics control. To fully realize such potential, we need to control the residual multiplicative shear bias | m | < 0.006 and the bias in the mean redshift |Δ z | < 0.008, requiring the introduced bias in the measurement is <0.31σ. We also expect significant detection of galaxy–galaxy lensing with DESI LRG/emission line galaxy (ELG) full samples as lenses, and cosmic magnification of ELG through cross-correlation with low-redshift DECaLS shear. If such systematical error control can be achieved, we find the advantages of DECaLS, comparing with the Kilo Degree Survey (KiDS) and the Hyper Suprime-Cam (HSC), are at low redshift, large scale, and in measuring the shear ratio (to σ R ∼ 0.04) and cosmic magnification. [ABSTRACT FROM AUTHOR]

Background: Despite the broad adoption of Soleris® technology in the food industry as semiquantitative method, it is almost completely unexplored in the pharmaceutical industry as a quantitative method for quantification of Burkholderia cepacia complex (Bcc). Objective: The efficacy of an automated growth-based system for a quantitative determination of the Bcc in an antacid oral suspension was studied. The main purpose of this validation study was to prove that the alternative method's entire performance is not inferior to the conventional method for a quantitative determination of Bcc. Method: The antacid oral suspension's preservatives were neutralized, leading to the Burkholderia complex's recovery by means of the alternative method and the reference method. A calibration curve was generated for each strain by plotting DTs relative to the corresponding log CFU values. An equivalence of results was done through the construction of calibration curves that allowed the establishment of numerically equivalent results between the enumeration data from the reference method and the alternative method. Results: Thus following the guidelines of USP, essential validation parameters were shown, such as equivalence of results (CC >0.95), linearity (R² >0.9025), accuracy (% recovery >70%), operating range, precision and ruggedness (DS <5 and CV <35%), specificity (inclusivity and exclusivity), limit of detection (LOD), and limit of quantification (LOQ). Conclusions: It was shown that all the test results obtained from the alternative method were in statistical agreement with the standard method. Thus this new technology was found to meet all the validation criteria needed to be considered as an alternative method for the quantification of the Burkholderia complex in the antacid oral suspension tested. Highlights: As outlined in USP chapter <1223> and demonstrated in this research the implementation of alternative methods can offer benefits in execution and automation while improving accuracy, sensitivity, and precision and can reduce the microbiological process time compared to the traditional ones. [ABSTRACT FROM AUTHOR]

Background We performed a nationwide population-based retrospective study to describe the epidemiology of bacterial co-infections in coronavirus disease 2019 (COVID-19)-hospitalized patients in Spain in 2020. We also analyzed the risk factors for co-infection, the etiology and the impact in the outcome. Methods Data were obtained from records in the Minimum Basic Data Set (MBDS) of the National Surveillance System for Hospital Data in Spain, provided by the Ministry of Health and annually published with 2 years lag. COVID-19 circulated in two waves in 2020: from its introduction to 31st June and from 1st July to 31st December. The risk of developing a healthcare-associated bacterial co-infection and the risk for in-hospital and intensive care unit (ICU) mortality in co-infected patients was assessed using an adjusted logistic regression model. Results The incidence of bacterial co-infection in COVID-19 hospitalized patients was 2.3%. The main risk factors associated with bacterial co-infection were organ failure, obesity and male sex. Co-infection was associated with worse outcomes including higher in-hospital, in-ICU mortality and higher length of stay. Gram-negative bacteria caused most infections. Causative agents were similar between waves, although higher co-infections with Pseudomonas spp. were detected in the first wave and with Haemophilus influenzae and Streptococcus pneumoniae in the second. Conclusions Co-infections are not as common as those found in other viral respiratory infections; therefore, antibiotics should be used carefully. Screening for actual co-infection to prescribe antibiotic therapy when required should be performed. [ABSTRACT FROM AUTHOR]

Echinometra lucunter , the rock-boring sea urchin, is a widely distributed echinoid and a model for ecological studies of reproduction, responses to climate change, and speciation. We present a near chromosome-level genome assembly of E. lucunter , including 21 scaffolds larger than 10 Mb predicted to represent each of the chromosomes of the species. The 760.4 Mb assembly includes a scaffold N50 of 30.0 Mb and BUSCO (benchmarking universal single-copy orthologue) single copy and a duplicated score of 95.8% and 1.4%, respectively. Ab-initio gene model prediction and annotation with transcriptomic data constructed 33,989 gene models composing 50.4% of the assembly, including 37,036 transcripts. Repetitive elements make up approximately 39.6% of the assembly, and unresolved gap sequences are estimated to be 0.65%. Whole genome alignment with Echinometra sp. EZ revealed high synteny and conservation between the two species, further bolstering Echinometra as an emerging genus for comparative genomics studies. This genome assembly represents a high-quality genomic resource for future evolutionary and developmental studies of this species and more broadly of echinoderms. [ABSTRACT FROM AUTHOR]

We performed an observational cohort study to assess associations between genetic factors of dengue fever (DF) severity in children in the Dominican Republic. A total of 488 participants had serologically confirmed DF. We replicated the association between the IFIH1 gene (rs1990760) and severe DF (n = 80/488, p = 0.006) and identified novel associations needing further investigation. [ABSTRACT FROM AUTHOR]

Background Neglected tropical diseases (NTDs) disproportionately affect populations living in resource-limited settings. In the Amazon basin, substantial numbers of NTDs are zoonotic, transmitted by vertebrate (dogs, bats, snakes) and invertebrate species (sand flies and triatomine insects). However, no dedicated consortia exist to find commonalities in the risk factors for or mitigations against bite-associated NTDs such as rabies, snake envenoming, Chagas disease and leishmaniasis in the region. The rapid expansion of COVID-19 has further reduced resources for NTDs, exacerbated health inequality and reiterated the need to raise awareness of NTDs related to bites. Methods The nine countries that make up the Amazon basin have been considered (Bolivia, Brazil, Colombia, Ecuador, French Guiana, Guyana, Peru, Surinam and Venezuela) in the formation of a new network. Results The Amazonian Tropical Bites Research Initiative (ATBRI) has been created, with the aim of creating transdisciplinary solutions to the problem of animal bites leading to disease in Amazonian communities. The ATBRI seeks to unify the currently disjointed approach to the control of bite-related neglected zoonoses across Latin America. Conclusions The coordination of different sectors and inclusion of all stakeholders will advance this field and generate evidence for policy-making, promoting governance and linkage across a One Health arena. [ABSTRACT FROM AUTHOR]

We present the public data release of the Uchuu-UM galaxy catalogues by applying the UniverseMachine algorithm to assign galaxies to the dark matter haloes in the Uchuu N -body cosmological simulation. It includes a variety of baryonic properties for all galaxies down to ∼5 × 108 M⊙ with haloes in a mass range of 1010 < M halo/M⊙ < 5 × 1015 up to redshift z = 10. Uchuu-UM includes more than 104 cluster-size haloes in a volume of 8(h −1Gpc)3, reproducing observed stellar mass functions across the redshift range of z = 0−7, galaxy quenched fractions, and clustering statistics at low redshifts. Compared to the previous largest UM catalogue, the Uchuu-UM catalogue includes significantly more massive galaxies hosted by large-mass dark matter haloes. Overall, the number density profile of galaxies in dark matter haloes follows the dark matter profile, with the profile becoming steeper around the splashback radius and flattening at larger radii. The number density profile of galaxies tends to be steeper for larger stellar masses and depends on the colour of galaxies, with red galaxies having steeper slopes at all radii than blue galaxies. The quenched fraction exhibits a strong dependence on the stellar mass and increases towards the inner regions of clusters. The publicly available Uchuu-UM galaxy catalogue presented here can serve to model ongoing and upcoming large galaxy surveys. [ABSTRACT FROM AUTHOR]

In this work, we investigate the structural properties, distribution and abundance of ΛCDM dark matter subhaloes using the Phi-4096 and Uchuu suite of N-body cosmological simulations. Thanks to the combination of their large volume, high mass resolution and superb statistics, we are able to quantify – for the first time consistently over more than seven decades in ratio of subhalo-to-host-halo mass – dependencies of subhalo properties on mass, maximum circular velocity, V max, host halo mass, and distance to host halo centre. We also dissect the evolution of these dependencies over cosmic time. We provide accurate fits for the subhalo mass and velocity functions, both exhibiting decreasing power-law slopes and with no significant dependence on redshift. We also find subhalo abundance to depend weakly on host halo mass. Subhalo structural properties are codified via a concentration parameter, c V, that does not depend on any pre-defined density profile and relies only on V max. We derive the c V− V max relation and find an important dependence on distance of the subhalo to the host halo centre. Interestingly, we also find subhaloes of the same mass to be significantly more concentrated when they reside inside more massive hosts. Finally, we investigate the redshift evolution of c V, and provide accurate fits. Our results offer an unprecedented detailed characterization of the subhalo population, consistent over a wide range of subhalo and host halo masses, as well as cosmic times. Thus, we expect our work to be particularly useful for any future research involving dark matter halo substructure. [ABSTRACT FROM AUTHOR]

Fly larvae cause myiasis. The most common of these are Cordylobia anthropophaga and Dermatobia hominis. Clinically, myiasis manifests as an erythematous papule that may become ulcerated and form furuncular lesions. In patients who have been in endemic areas, these larvae are to be suspected. Below, we present a 75-year-old male with a clinical picture of a palpable mass in the areola associated with the outflow of serohematic fluid through a central orifice. A breast intraductal lesion was suspected, so a breast ultrasound and biopsy were performed, which showed a structure compatible with myiasis. The diagnostic challenge was the high number of different diagnoses and the little knowledge of health professionals about tropical diseases. [ABSTRACT FROM AUTHOR]

Loss-of-function mutations in the X-linked endosomal Na+/H+ exchanger 6 (NHE6) cause Christianson syndrome in males. Christianson syndrome involves endosome dysfunction leading to early cerebellar degeneration, as well as later-onset cortical and subcortical neurodegeneration, potentially including tau deposition as reported in post-mortem studies. In addition, there is reported evidence of modulation of amyloid-β levels in experimental models wherein NHE6 expression was targeted. We have recently shown that loss of NHE6 causes defects in endosome maturation and trafficking underlying lysosome deficiency in primary mouse neurons in vitro. For in vivo studies, rat models may have an advantage over mouse models for the study of neurodegeneration, as rat brain can demonstrate robust deposition of endogenously-expressed amyloid-β and tau in certain pathological states. Mouse models generally do not show the accumulation of insoluble, endogenously-expressed (non-transgenic) tau or amyloid-β. Therefore, to study neurodegeneration in Christianson syndrome and the possibility of amyloid-β and tau pathology, we generated an NHE6-null rat model of Christianson syndrome using CRISPR-Cas9 genome-editing. Here, we present the sequence of pathogenic events in neurodegenerating NHE6-null male rat brains across the lifespan. NHE6-null rats demonstrated an early and rapid loss of Purkinje cells in the cerebellum, as well as a more protracted neurodegenerative course in the cerebrum. In both the cerebellum and cerebrum, lysosome deficiency is an early pathogenic event, preceding autophagic dysfunction. Microglial and astrocyte activation also occur early. In the hippocampus and cortex, lysosome defects precede loss of pyramidal cells. Importantly, we subsequently observed biochemical and in situ evidence of both amyloid-β and tau aggregation in the aged NHE6-null hippocampus and cortex (but not in the cerebellum). Tau deposition is widely distributed, including cortical and subcortical distributions. Interestingly, we observed tau deposition in both neurons and glia, as has been reported in Christianson syndrome post-mortem studies previously. In summary, this experimental model is among very few examples of a genetically modified animal that exhibits neurodegeneration with deposition of endogenously-expressed amyloid-β and tau. This NHE6-null rat will serve as a new robust model for Christianson syndrome. Furthermore, these studies provide evidence for linkages between endolysosome dysfunction and neurodegeneration involving protein aggregations, including amyloid-β and tau. Therefore these studies may provide insight into mechanisms of more common neurodegenerative disorders, including Alzheimer's disease and related dementias. [ABSTRACT FROM AUTHOR]

Synaptic dysfunction is an early mechanism in Alzheimer's disease that involves progressively larger areas of the brain over time. However, how it starts and propagates is unknown. Here we show that amyloid-β released by microglia in association with large extracellular vesicles (Aβ-EVs) alters dendritic spine morphology in vitro, at the site of neuron interaction, and impairs synaptic plasticity both in vitro and in vivo in the entorhinal cortex-dentate gyrus circuitry. One hour after Aβ-EV injection into the mouse entorhinal cortex, long-term potentiation was impaired in the entorhinal cortex but not in the dentate gyrus, its main target region, while 24 h later it was also impaired in the dentate gyrus, revealing a spreading of long-term potentiation deficit between the two regions. Similar results were obtained upon injection of extracellular vesicles carrying Aβ naturally secreted by CHO7PA2 cells, while neither Aβ42 alone nor inflammatory extracellular vesicles devoid of Aβ were able to propagate long-term potentiation impairment. Using optical tweezers combined to time-lapse imaging to study Aβ-EV-neuron interaction, we show that Aβ-EVs move anterogradely at the axon surface and that their motion can be blocked through annexin-V coating. Importantly, when Aβ-EV motility was inhibited, no propagation of long-term potentiation deficit occurred along the entorhinal-hippocampal circuit, implicating large extracellular vesicle motion at the neuron surface in the spreading of long-term potentiation impairment. Our data indicate the involvement of large microglial extracellular vesicles in the rise and propagation of early synaptic dysfunction in Alzheimer's disease and suggest a new mechanism controlling the diffusion of large extracellular vesicles and their pathogenic signals in the brain parenchyma, paving the way for novel therapeutic strategies to delay the disease. [ABSTRACT FROM AUTHOR]

Background A large number of studies have assessed risk factors for infection with soil-transmitted helminths (STH), but few have investigated the interactions between the different parasites or compared these between host species across hosts. Here, we assessed the associations between Ascaris, Trichuris , hookworm, strongyle and Toxocara infections in the Philippines in human and animal hosts. Methods Faecal samples were collected from humans and animals (dogs, cats and pigs) in 252 households from four villages in southern Philippines and intestinal helminth infections were assessed by microscopy. Associations between worm species were assessed using multiple logistic regression. Results Ascaris infections showed a similar prevalence in humans (13.9%) and pigs (13.7%). Hookworm was the most prevalent infection in dogs (48%); the most prevalent infection in pigs was strongyles (42%). The prevalences of hookworm and Toxocara in cats were similar (41%). Statistically significant associations were observed between Ascaris and Trichuris and between Ascaris and hookworm infections in humans, and also between Ascaris and Trichuris infections in pigs. Dual and triple infections were observed, which were more common in dogs, cats and pigs than in humans. Conclusions Associations are likely to exist between STH species in humans and animals, possibly due to shared exposures and transmission routes. Individual factors and behaviours will play a key role in the occurrence of co-infections, which will have effects on disease severity. Moreover, the implications of co-infection for the emergence of zoonoses need to be explored further. [ABSTRACT FROM AUTHOR]

The coming generation of galaxy surveys will provide measurements of galaxy clustering with unprecedented accuracy and data size, which will allow us to test cosmological models at much higher precision than achievable previously. This means that we must have more accurate theoretical predictions to compare with future observational data. As a first step towards more accurate modelling of the redshift space distortions (RSD) of small-scale galaxy clustering in modified gravity (MG) cosmologies, we investigate the validity of the so-called Skew-T (ST) probability distribution function (PDF) of halo pairwise peculiar velocities in these models. We show that, combined with the streaming model of RSD, the ST PDF substantially improves the small-scale predictions by incorporating skewness and kurtosis, for both Λ cold dark matter (ΛCDM) and two leading MG models: f (R) gravity and the DGP braneworld model. The ST model reproduces the velocity PDF and redshift-space halo clustering measured from MG N -body simulations very well down to |$\sim 5 \, h^{-1}\, \mathrm{Mpc}$|⁠. In particular, we investigate the enhancements of halo pairwise velocity moments with respect to ΛCDM for a larger range of MG variants than previous works, and present simple explanations to the behaviours observed. By performing a simple Fisher analysis, we find a significant increase in constraining power to detect modifications of General Relativity by introducing small-scale information in the RSD analyses. [ABSTRACT FROM AUTHOR]

The refugee crisis of 2015 became a major issue of both national and pan-European debate. Behavioral reactions among natives in the form of support for radical-right parties or leaving neighborhoods following influxes of non-Westerners are well documented, but a detailed account of how asylum seekers contribute to these dynamics remains elusive. In this paper, I study how asylum centers and refugees choosing their own residences prompt each of these two behavioral outcomes using register data for the whole of Sweden (2013–2018). The analyses show a divergence depending on the particular type of refugee exposure experienced and the specific behavior under analysis. Only increased radical-right support is observed following the establishment of a new asylum center, whereas greater native out-mobility is found following refugees self-selecting into native-based areas. [ABSTRACT FROM AUTHOR]

Background Despite decades of interventions, 240 million people have schistosomiasis. Infections cannot be directly observed, and egg-based Kato-Katz thick smears lack sensitivity, affected treatment efficacy and reinfection rate estimates. The point-of-care circulating cathodic antigen (referred to from here as POC-CCA+) test is advocated as an improvement on the Kato-Katz method, but improved estimates are limited by ambiguities in the interpretation of trace results. Method We collected repeated Kato-Katz egg counts from 210 school-aged children and scored POC-CCA tests according to the manufacturer's guidelines (referred to from here as POC-CCA+) and the externally developed G score. We used hidden Markov models parameterized with Kato-Katz; Kato-Katz and POC-CCA+; and Kato-Katz and G-Scores, inferring latent clearance and reinfection probabilities at four timepoints over six-months through a more formal statistical reconciliation of these diagnostics than previously conducted. Our approach required minimal but robust assumptions regarding trace interpretations. Results Antigen-based models estimated higher infection prevalence across all timepoints compared with the Kato-Katz model, corresponding to lower clearance and higher reinfection estimates. Specifically, pre-treatment prevalence estimates were 85% (Kato-Katz; 95% CI: 79%–92%), 99% (POC-CCA+; 97%–100%) and 98% (G-Score; 95%–100%). Post-treatment, 93% (Kato-Katz; 88%–96%), 72% (POC-CCA+; 64%–79%) and 65% (G-Score; 57%–73%) of those infected were estimated to clear infection. Of those who cleared infection, 35% (Kato-Katz; 27%–42%), 51% (POC-CCA+; 41%–62%) and 44% (G-Score; 33%–55%) were estimated to have been reinfected by 9-weeks. Conclusions Treatment impact was shorter-lived than Kato-Katz–based estimates alone suggested, with lower clearance and rapid reinfection. At 3 weeks after treatment, longer-term clearance dynamics are captured. At 9 weeks after treatment, reinfection was captured, but failed clearance could not be distinguished from rapid reinfection. Therefore, frequent sampling is required to understand these important epidemiological dynamics. [ABSTRACT FROM AUTHOR]

Background The value of myeloperoxidase (MPO) and proteinase 3 (PR3) antibody titres in the assessment of renal disease activity and flare prediction in patients with anti-neutrophil cytoplasmic antibody–associated vasculitis (AAV) is not well known. Methods We performed a retrospective study including 113 AVV patients with renal biopsy–proven pauci-immune necrotizing glomerulonephritis from seven Spanish hospitals. The main inclusion criteria were assessment of MPO antibodies using multiplex flow immunoassay and PR3 antibody measurements using immunoassay chemiluminescence with an identical range of values for all participating centres. Results Serum MPO antibodies 3 ± 1.2 months before relapse were higher in patients who relapsed [19.2 ± 12.2 versus 3.2 ± 5.1 antibody index (AI); P < 0.001]. The discrimination value of MPO antibodies 3 months before renal relapse had an area under the receiver operating characteristics curve (AUC) of 0.82 [95% confidence interval (CI) 0.73–0.92; P < 0.001]. ΔMPO antibodies (change in antibodies titration 6 months before relapse) were higher in patients who relapsed (8.3 ± 12 versus 0.9 ± 3.1 AI; P = 0.001). The discrimination value of ΔMPO had an AUC of 0.76 (95% CI 0.63–0.88; P < 0.001). The positive predictive value of renal relapse in PR3 patients is 100% and the negative predictive value of renal relapse in patients with PR3-positive titres is 57.1%. Serum PR3 antibodies were higher in patients who relapsed 2.8 ± 1.4 months before relapse (58.6 ± 24.6 versus 2.0 ± 0.6 AI; P < 0.001). Conclusions MPO level monitoring using multiplex flow immunoassay and PR3 measurements using immunoassay chemiluminescence are useful and sensitive tools for the prediction of renal relapse in the follow-up of AAV patients with renal disease and relevant surrogate markers of renal disease activity. [ABSTRACT FROM AUTHOR]

Idiopathic Parkinson's disease is characterized by a progressive loss of dopaminergic neurons, but the exact disease aetiology remains largely unknown. To date, Parkinson's disease research has mainly focused on nigral dopaminergic neurons, although recent studies suggest disease-related changes also in non-neuronal cells and in midbrain regions beyond the substantia nigra. While there is some evidence for glial involvement in Parkinson's disease, the molecular mechanisms remain poorly understood. The aim of this study was to characterize the contribution of all cell types of the midbrain to Parkinson's disease pathology by single-nuclei RNA sequencing and to assess the cell type-specific risk for Parkinson's disease using the latest genome-wide association study. We profiled >41 000 single-nuclei transcriptomes of post-mortem midbrain from six idiopathic Parkinson's disease patients and five age-/sex-matched controls. To validate our findings in a spatial context, we utilized immunolabelling of the same tissues. Moreover, we analysed Parkinson's disease-associated risk enrichment in genes with cell type-specific expression patterns. We discovered a neuronal cell cluster characterized by CADPS2 overexpression and low TH levels, which was exclusively present in idiopathic Parkinson's disease midbrains. Validation analyses in laser-microdissected neurons suggest that this cluster represents dysfunctional dopaminergic neurons. With regard to glial cells, we observed an increase in nigral microglia in Parkinson's disease patients. Moreover, nigral idiopathic Parkinson's disease microglia were more amoeboid, indicating an activated state. We also discovered a reduction in idiopathic Parkinson's disease oligodendrocyte numbers with the remaining cells being characterized by a stress-induced upregulation of S100B. Parkinson's disease risk variants were associated with glia- and neuron-specific gene expression patterns in idiopathic Parkinson's disease cases. Furthermore, astrocytes and microglia presented idiopathic Parkinson's disease-specific cell proliferation and dysregulation of genes related to unfolded protein response and cytokine signalling. While reactive patient astrocytes showed CD44 overexpression, idiopathic Parkinson's disease microglia revealed a pro-inflammatory trajectory characterized by elevated levels of IL1B, GPNMB and HSP90AA1. Taken together, we generated the first single-nuclei RNA sequencing dataset from the idiopathic Parkinson's disease midbrain, which highlights a disease-specific neuronal cell cluster as well as 'pan-glial' activation as a central mechanism in the pathology of the movement disorder. This finding warrants further research into inflammatory signalling and immunomodulatory treatments in Parkinson's disease. [ABSTRACT FROM AUTHOR]

Spectroscopy from the final internal data release of the Gaia –ESO Survey (GES) has been combined with Gaia EDR3 to assign membership probabilities to targets observed towards 63 Galactic open clusters and 7 globular clusters. The membership probabilities are based chiefly on maximum likelihood modelling of the 3D kinematics of the targets, separating them into cluster and field populations. From 43 211 observed targets, 13 985 are identified as highly probable cluster members (P > 0.9), with an average membership probability of 0.993. The addition of GES radial velocities successfully drives down the fraction of false positives and we achieve better levels of discrimination in most clusters over the use of astrometric data alone, especially those at larger distances. Since the membership selection is almost purely kinematic, the union of this catalogue with GES and Gaia is ideal for investigating the photometric and chemical properties of clusters as a function of stellar mass, age, and Galactic position. [ABSTRACT FROM AUTHOR]

We characterize the selection cuts and clustering properties of a magnitude-limited sample of bright galaxies that is part of the Bright Galaxy Survey (BGS) of the Dark Energy Spectroscopic Instrument (DESI) using the ninth data release of the Legacy Imaging Surveys (DR9). We describe changes in the DR9 selection compared to the DR8 one and we also compare the DR9 selection in three distinct regions: BASS/MzLS in the north Galactic Cap (NGC), DECaLS in the NGC, and DECaLS in the south Galactic Cap (SGC). We investigate the systematics associated with the selection and assess its completeness by matching the BGS targets with the Galaxy and Mass Assembly (GAMA) survey. We measure the angular clustering for the overall bright sample (r mag ≤ 19.5) and as function of apparent magnitude and colour. This enables to determine the clustering strength r 0 and slope γ by fitting a power-law model that can be used to generate accurate mock catalogues for this tracer. We use a counts-in-cells technique to explore higher order statistics and cross-correlations with external spectroscopic data sets in order to check the evolution of the clustering with redshift and the redshift distribution of the BGS targets using clustering redshifts. While this work validates the properties of the BGS bright targets, the final target selection pipeline and clustering properties of the entire DESI BGS will be fully characterized and validated with the spectroscopic data of Survey Validation. [ABSTRACT FROM AUTHOR]

Summary: Background: Onychoscopy is a technique that uses a dermatoscope for the evaluation of specific features of different skin conditions that are not visible to the naked eye. There are few studies establishing parameters for the diagnosis of onychomycosis based on onychoscopy. Determining the sensitivity and specificity of a potentially new diagnostic test for onychomycosis requires an evaluation study of this new diagnostic test, as there are limited studies reporting onychoscopy results. Aim: To determine the sensitivity, specificity, positive predictive value and negative predictive value of onychoscopy findings in a Colombian population with onychomycosis. Methods: We assessed outpatients with a diagnosis of toenail onychomycosis confirmed by potassium hydroxide preparation or fungal culture. Onychoscopy was performed using a dermatoscope, and digital images collected using a smartphone. Results: The onychoscopy findings were: longitudinal striae, distal spiked pattern, distal irregular termination, linear edge and ruins aspect, while some patients were confirmed as having traumatic onycholysis. A statistically significant association was found between the clinical symptoms of onychomycosis and both the clinical feature of dyschromia and the onychoscopy feature of longitudinal striae. Conclusion: We suggest that this technique is an alternative method that should be used in patients with onychopathies because it has the potential to differentiate onychomycosis from traumatic onycholysis and another nail involvement. [ABSTRACT FROM AUTHOR]

Background Carbapenem-resistant Klebsiella pneumoniae (CRKP) is an emerging public health problem. This study explores the specifics of CRKP epidemiology in Colombia based on whole genome sequencing (WGS) of the National Reference Laboratory at Instituto Nacional de Salud (INS)'s 2013–2017 sample collection. Methods A total of 425 CRKP isolates from 21 departments were analyzed by HiSeq-X10®Illumina high-throughput sequencing. Bioinformatic analysis was performed, primarily using the pipelines developed collaboratively by the National Institute for Health Research Global Health Research Unit (GHRU) on Genomic Surveillance of Antimicrobial Resistance (AMR), and AGROSAVIA. Results Of the 425 CRKP isolates, 91.5% were carbapenemase-producing strains. The data support a recent expansion and the endemicity of CRKP in Colombia with the circulation of 7 high-risk clones, the most frequent being CG258 (48.39% of isolates). We identified genes encoding carbapenemases bla KPC-3, bla KPC-2, bla NDM-1, bla NDM-9, bla VIM-2, bla VIM-4, and bla VIM-24, and various mobile genetic elements (MGE). The virulence of CRKP isolates was low, but colibactin (clb3) was present in 25.2% of isolates, and a hypervirulent CRKP clone (CG380) was reported for the first time in Colombia. ST258, ST512, and ST4851 were characterized by low levels of diversity in the core genome (ANI > 99.9%). Conclusions The study outlines complex CRKP epidemiology in Colombia. CG258 expanded clonally and carries specific carbapenemases in specific MGEs, while the other high-risk clones (CG147, CG307, and CG152) present a more diverse complement of carbapenemases. The specifics of the Colombian situation stress the importance of WGS-based surveillance to monitor evolutionary trends of sequence types (STs), MGE, and resistance and virulence genes. [ABSTRACT FROM AUTHOR]

Background Many Spanish hospitals converted scheduled in-person visits to telephone visits during the COVID-19 lockdown. There is scarce information about the performance of those visits. Aim To compare telephone visits during the COVID-19 lockdown period with previous in-person visits. Design Retrospective descriptive study. Methods Telephone visits from 15 March to 31 May 2020 were compared with in-person visits during the same period in 2019. Main measures The proportions of both groups were compared in term of failure to contact patient, requested diagnostic tests/referrals, discharges, admissions and emergency visits within 30–60 days. A sample of patients, and all participating physicians completed surveys. Z -score test was used (statistical significance P <0.05). Results A total of 5602 telephone visits were conducted. In comparison to in-person visits, telephone visits showed higher rates of visit compliance (95.9% vs. 85.2%, P <0.001) and discharges (22.12% vs. 11.82%; P <0.001), and lower number of ancillary tests and referrals. During the 30- and 60-day periods following the telephone visit, a reduction of 52% and 47% in the combined number of emergency department visits and hospital admissions was observed compared to in-person visits (P <0.01). Of the 120 patients surveyed, 95% were satisfied/very satisfied with the telephone visits. Of the 26 physicians, 84.6% considered telephone visits were useful to prioritize patients. Conclusions During health emergencies, previously scheduled outpatient in-person visits can be converted to telephone visits, reducing absenteeism, increasing the rate of discharges and reducing ancillary tests and referrals without increasing the rate of hospital admissions or emergency department visits. [ABSTRACT FROM AUTHOR]

We introduce the Uchuu suite of large high-resolution cosmological N -body simulations. The largest simulation, named Uchuu, consists of 2.1 trillion (12 8003) dark matter particles in a box of side-length 2.0 |$\, h^{-1} \, \rm Gpc$|⁠ , with particle mass of 3.27 × 108 |$\, h^{-1}\, \rm M_{\odot }$|⁠. The highest resolution simulation, Shin-Uchuu, consists of 262 billion (64003) particles in a box of side-length 140 |$\, h^{-1} \, \rm Mpc$|⁠ , with particle mass of 8.97 × 105 |$\, h^{-1}\, \rm M_{\odot }$|⁠. Combining these simulations, we can follow the evolution of dark matter haloes and subhaloes spanning those hosting dwarf galaxies to massive galaxy clusters across an unprecedented volume. In this first paper, we present basic statistics, dark matter power spectra, and the halo and subhalo mass functions, which demonstrate the wide dynamic range and superb statistics of the Uchuu suite. From an analysis of the evolution of the power spectra, we conclude that our simulations remain accurate from the baryon acoustic oscillation scale down to the very small. We also provide parameters of a mass–concentration model, which describes the evolution of halo concentration and reproduces our simulation data to within 5 per cent for haloes with masses spanning nearly eight orders of magnitude at redshift 0 ≤ z ≤ 14. There is an upturn in the mass–concentration relation for the population of all haloes and of relaxed haloes at z ≳ 0.5, whereas no upturn is detected at z < 0.5. We make publicly available various N -body products as part of Uchuu Data Release 1 on the Skies & Universes site. 1 Future releases will include gravitational lensing maps and mock galaxy, X-ray cluster, and active galactic nucleus catalogues. [ABSTRACT FROM AUTHOR]

Sponges in the subfamily Phyllospongiinae are important components of coral reefs. However, significant taxonomic inconsistencies exist in this group due to the lack of useful morphological characters for species delineation. This study assesses the systematics of some common phyllospongiinids in the genera Carteriospongia , Phyllospongia and Strepsichordaia from tropical Australia and the Red Sea, by using a multigene approach that utilizes the Internal Transcribed Spacer 2, the complete ribosomal 18S rRNA and three 28s rRNA gene regions (D1‒D2, D3‒D5 and D6‒D8), which produced a phylogenetic framework in which complementary morphological taxonomic assessments were performed. Type specimens were included, where available, and six species clades were recovered, including the well-established Phyllospongia papyracea and Strepsichordaia lendenfeldi. Carteriospongia foliascens , the type species for the genus Carteriospongia, is transferred to the genus Phyllospongia , resulting in Carteriospongia becoming a synonym of Phyllospongia. Consequently, Carteriospongia flabellifera is removed from Carteriospongia and is reinstated to its original designation of Polyfibrospongia flabellifera. Two new species, Phyllospongia bergquistae sp. nov. and Polyfibrospongia kulit sp. nov. , are described. With phyllospongiinid sponges increasingly used as models for assessing the effects of climate change and anthropogenic stressors, this study provides a reliable systematics framework for the accurate identification of common phyllospongiinids across the Indo-Pacific. [ABSTRACT FROM AUTHOR]

Vector control is widely considered an important tool for lymphatic filariasis (LF) elimination but is not usually included in program budgets and has often been secondary to other policy questions in modelling studies. Evidence from the field demonstrates that vector control can have a large impact on program outcomes and even halt transmission entirely, but implementation is expensive. Models of LF have the potential to inform where and when resources should be focused, but often simplify vector dynamics and focus on capturing human prevalence trends, making them comparatively ill-designed for direct analysis of vector control measures. We review the recent modelling literature and present additional results using a well-established model, highlighting areas of agreement between model predictions and field evidence, and discussing the possible determinants of existing disagreements. We conclude that there are likely to be long-term benefits of vector control, both on accelerating programs and preventing resurgence. [ABSTRACT FROM AUTHOR]

Background Tremendous progress towards elimination of trachoma as a public health problem has been made. However, there are areas where the clinical indicator of disease, trachomatous inflammation—follicular (TF), remains prevalent. We quantify the progress that has been made, and forecast how TF prevalence will evolve with current interventions. We also determine the probability that a district is a transmission-hotspot based on its TF prevalence (ie, reproduction number greater than one). Methods Data on trachoma prevalence come from the GET2020 global repository organized by the World Health Organization and the International Trachoma Initiative. Forecasts of TF prevalence and the percent of districts with local control is achieved by regressing the coefficients of a fitted exponential distribution for the year-by-year distribution of TF prevalence. The probability of a district being a transmission-hotspot is extrapolated from the residuals of the regression. Results Forecasts suggest that with current interventions, 96.5% of surveyed districts will have TF prevalence among children aged 1–9 years <5% by 2030 (95% CI: 86.6%–100.0%). Districts with TF prevalence < 20% appear unlikely to be transmission-hotspots. However, a district having TF prevalence of over 28% in 2016–2019 corresponds to at least 50% probability of being a transmission-hotspot. Conclusions Sustainable control of trachoma appears achievable. However there are transmission-hotspots that are not responding to annual mass drug administration of azithromycin and require enhanced treatment in order to reach local control. [ABSTRACT FROM AUTHOR]

Upcoming surveys will use a variety of galaxy selections to map the large-scale structure of the Universe. It is important to make accurate predictions for the properties and clustering of such galaxies, including the errors on these statistics. Here, we describe a novel technique which uses the semi-analytical model of galaxy formation galform , embedded in the high-resolution N -body Planck-Millennium simulation, to populate a thousand halo catalogues generated using the Parallel-PM N -body glam code. Our hybrid scheme allows us to make clustering predictions on scales that cannot be modelled in the original N -body simulation. We focus on luminous red galaxies (LRGs) selected in the redshift range z = 0.6 − 1 from the galform output using similar colour-magnitude cuts in the r, z , and W 1 bands to those that will be applied in the Dark Energy Spectroscopic Instrument (DESI) survey, and call this illustrative sample 'DESI-like' LRGs. We find that the LRG-halo connection is non-trivial, leading to the prediction of a non-standard halo occupation distribution; in particular, the occupation of central galaxies does not reach unity for the most massive haloes, and drops with increasing mass. The glam catalogues reproduce the abundance and clustering of the LRGs predicted by galform. We use the glam mocks to compute the covariance matrices for the two-point correlation function and power spectrum of the LRGs and their background dark matter density field, revealing important differences. We also make predictions for the linear-growth rate and the baryon acoustic oscillations distances at z = 0.6, 0.74, and 0.93. All 'DESI-like' LRG catalogues are made publicly available. [ABSTRACT FROM AUTHOR]

We search for the baryon acoustic oscillations in the projected cross-correlation function binned into transverse comoving radius between the SDSS-IV DR16 eBOSS quasars and a dense photometric sample of galaxies selected from the DESI Legacy Imaging Surveys. We estimate the density of the photometric sample of galaxies in this redshift range to be about 2900 deg−2, which is deeper than the official DESI emission line galaxy selection, and the density of the spectroscopic sample is about 20 deg−2. In order to mitigate the systematics related to the use of different imaging surveys close to the detection limit, we use a neural network approach that accounts for complex dependences between the imaging attributes and the observed galaxy density. We find that we are limited by the depth of the imaging surveys that affects the density and purity of the photometric sample and its overlap in redshift with the quasar sample, which thus affects the performance of the method. When cross-correlating the photometric galaxies with quasars in the range 0.6 ≤ z ≤ 1.2, the cross-correlation function can provide better constraints on the comoving angular distance D M (6 per cent precision) compared to the constraint on the spherically averaged distance D V (9 per cent precision) obtained from the autocorrelation. Although not yet competitive, this technique will benefit from the arrival of deeper photometric data from upcoming surveys that will enable it to go beyond the current limitations we have identified in this work. [ABSTRACT FROM AUTHOR]

Improving feed efficiency in cattle is a long-standing aim of the beef industry. However, discrepancies in the ranking of bulls based on the diets used and calculation methods employed for defining feed efficiency have been observed. Hence, the objective of this research was to assess the extent to which different factors influence feed efficiency in Brahman steers. Individual DMI and ADG were measured, and residual feed intake (RFI) calculated using linear regression of DMI on ADG and midtest metabolic body weight. Eight-nine steers were initially fed a low-protein diet (LP, 8.8% CP) for 70 days, followed by a high-protein (HP, 13.5% CP) diet for another 70 days. The genetic variation among steers and the proportion of Bos indicus genes were determined using the GGP Indicus 50K assay (Neogen Corporation, Ipswich, Australia). Rumen bacteriome variation was determined with 16S rRNA gene sequencing of rumen fluid collected before and after feeding. Daily diet refusals were visually scored for the proportion of pellets versus hay and expressed as a diet selection index (1 to 3). Organic matter digestibility (OMD) was determined using total feces collection in metabolism crates. Plasma urea nitrogen (PUN) was measured in blood samples collected at four time points. The dietanimal fractionation of nitrogen isotopes (Δ15Ntail hair) was quantified in tail hair using isotope-ratio mass spectroscopy to indicate differences in nitrogen metabolism. Finally, carcass characteristics were determined at slaughter. Including carcass fat depth improved (P = 0.01) DMI prediction (R² increased from 78.4 to 80.4%) in the LP diet but had a smaller effect (P = 0.39) in the HP diet (R² increased from 75.0 to 75.2%). In the LP diet, the variation in carcass fat-correct RFI (RFIc) could be explained by DMI (14.5% of the variation), rumen bacteriome (5.89%), diet selection index (3.08%), PUN (1.88%), genetic distance (0.76%) and OMD (0.50%), accounting for a total of 26.6% of the RFIc variation. In the HP diet, the regression model explained 35.3% of the RFIc variation, with DMI explaining 25.9%, diet selection index 7.19%, rumen bacteriome 1.02%, genetic distance 0.73% and Δ15Ntail hair 0.50%. In conclusion, this study highlights the importance of measuring diet selection to accurately determine RFI in cattle. The results also suggest that variations in the rumen bacteriome and nitrogen metabolism parameters play a role in individual variations of feed efficiency. However, most of the variation in feed efficiency remained unexplained. [ABSTRACT FROM AUTHOR]

Motivation Clustering enables TNF receptors to stimulate intracellular signaling. The differential soluble ligand-induced clustering behavior of TNF receptor 1 (TNFR1) and TNFR2 was modeled. A structured, rule-based model implemented ligand-independent pre-ligand binding assembly domain (PLAD)-mediated homotypic low affinity interactions of unliganded and liganded TNF receptors. Results Soluble TNF initiates TNFR1 signaling but not TNFR2 signaling despite receptor binding unless it is secondarily oligomerized. We consider high affinity binding of TNF to signaling-incompetent pre-assembled dimeric TNFR1 and TNFR2 molecules and secondary clustering of liganded dimers to signaling competent ligand–receptor clusters. Published receptor numbers, affinities and measured different activities of clustered receptors validated model simulations for a large range of receptor and ligand concentrations. Different PLAD–PLAD affinities and different activities of receptor clusters explain the observed differences in the TNF receptor stimulating activities of soluble TNF. Availability and implementation All scripts and data are in manuscript and supplement at Bioinformatics online. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]