Diagnosis of Taenia solium infections based on “mail order” RNA-sequencing of single tapeworm egg isolates from stool samples

Combined community health programs aiming at health education, preventive anti-parasitic chemotherapy, and vaccination of pigs have proven their potential to regionally reduce and even eliminate Taenia solium infections that are associated with a high risk of neurological disease through ingestion of T. solium eggs. Yet it remains challenging to target T. solium endemic regions precisely or to make exact diagnoses in individual patients. One major reason is that the widely available stool microscopy may identify Taenia ssp. eggs in stool samples as such, but fails to distinguish between invasive (T. solium) and less invasive Taenia (T. saginata, T. asiatica, and T. hydatigena) species. The identification of Taenia ssp. eggs in routine stool samples often prompts a time-consuming and frequently unsuccessful epidemiologic workup in remote villages far away from a diagnostic laboratory. Here we present "mail order" single egg RNA-sequencing, a new method allowing the identification of the exact Taenia ssp. based on a few eggs found in routine diagnostic stool samples. We provide first T. solium transcriptome data, which show extremely high mitochondrial DNA (mtDNA) transcript counts that can be used for subspecies classification. "Mail order" RNA-sequencing can be administered by health personnel equipped with basic laboratory tools such as a microscope, a Bunsen burner, and access to an international post office for shipment of samples to a next generation sequencing facility. Our suggested workflow combines traditional stool microscopy, RNA-extraction from single Taenia eggs with mitochondrial RNA-sequencing, followed by bioinformatic processing with a basic laptop computer. The workflow could help to better target preventive healthcare measures and improve diagnostic specificity in individual patients based on incidental findings of Taenia ssp. eggs in diagnostic laboratories with limited resources

Association, effects and validation of polymorphisms within the NCAPG - LCORL locus located on BTA6 with feed intake, gain, meat and carcass traits in beef cattle

<p>Abstract</p> <p>Background</p> <p>In a previously reported genome-wide association study based on a high-density bovine SNP genotyping array, 8 SNP were nominally associated (<it>P </it>≤ 0.003) with average daily gain (ADG) and 3 of these were also associated (<it>P </it>≤ 0.002) with average daily feed intake (ADFI) in a population of crossbred beef cattle. The SNP were clustered in a 570 kb region around 38 Mb on the draft sequence of bovine chromosome 6 (BTA6), an interval containing several positional and functional candidate genes including the bovine <it>LAP3, NCAPG</it>, and <it>LCORL </it>genes. The goal of the present study was to develop and examine additional markers in this region to optimize the ability to distinguish favorable alleles, with potential to identify functional variation.</p> <p>Results</p> <p>Animals from the original study were genotyped for 47 SNP within or near the gene boundaries of the three candidate genes. Sixteen markers in the <it>NCAPG-LCORL </it>locus displayed significant association with both ADFI and ADG even after stringent correction for multiple testing (P ≤ 005). These markers were evaluated for their effects on meat and carcass traits. The alleles associated with higher ADFI and ADG were also associated with higher hot carcass weight (HCW) and ribeye area (REA), and lower adjusted fat thickness (AFT). A reduced set of markers was genotyped on a separate, crossbred population including genetic contributions from 14 beef cattle breeds. Two of the markers located within the <it>LCORL </it>gene locus remained significant for ADG (P ≤ 0.04).</p> <p>Conclusions</p> <p>Several markers within the <it>NCAPG-LCORL </it>locus were significantly associated with feed intake and body weight gain phenotypes. These markers were also associated with HCW, REA and AFT suggesting that they are involved with lean growth and reduced fat deposition. Additionally, the two markers significant for ADG in the validation population of animals may be more robust for the prediction of ADG and possibly the correlated trait ADFI, across multiple breeds and populations of cattle.</p

Phenotypic redshifts with self-organizing maps: A novel method to characterize redshift distributions of source galaxies for weak lensing

Wide-field imaging surveys such as the Dark Energy Survey (DES) rely on coarse measurements of spectral energy distributions in a few filters to estimate the redshift distribution of source galaxies. In this regime, sample variance, shot noise, and selection effects limit the attainable accuracy of redshift calibration and thus of cosmological constraints. We present a new method to combine wide-field, few-filter measurements with catalogs from deep fields with additional filters and sufficiently low photometric noise to break degeneracies in photometric redshifts. The multi-band deep field is used as an intermediary between wide-field observations and accurate redshifts, greatly reducing sample variance, shot noise, and selection effects. Our implementation of the method uses self-organizing maps to group galaxies into phenotypes based on their observed fluxes, and is tested using a mock DES catalog created from N-body simulations. It yields a typical uncertainty on the mean redshift in each of five tomographic bins for an idealized simulation of the DES Year 3 weak-lensing tomographic analysis of $\sigma_{\Delta z} = 0.007$, which is a 60% improvement compared to the Year 1 analysis. Although the implementation of the method is tailored to DES, its formalism can be applied to other large photometric surveys with a similar observing strategy.Comment: 24 pages, 11 figures; matches version accepted to MNRA

Dystonia Linked to EIF4A2 Haploinsufficiency: A Disorder of Protein Translation Dysfunction

Background: Protein synthesis is a tightly controlled process, involving a host of translation-initiation factors and microRNA-associated repressors. Variants in the translational regulator EIF2AK2 were first linked to neurodevelopmental-delay phenotypes, followed by their implication in dystonia. Recently, de novo variants in EIF4A2, encoding eukaryotic translation initiation factor 4A isoform 2 (eIF4A2), have been described in pediatric cases with developmental delay and intellectual disability. Objective: We sought to characterize the role of EIF4A2 variants in dystonic conditions. Methods: We undertook an unbiased search for likely deleterious variants in mutation-constrained genes among 1100 families studied with dystonia. Independent cohorts were screened for EIF4A2 variants. Western blotting and immunocytochemical studies were performed in patient-derived fibroblasts. Results: We report the discovery of a novel heterozygous EIF4A2 frameshift deletion (c.896_897del) in seven patients from two unrelated families. The disease was characterized by adolescence- to adulthood-onset dystonia with tremor. In patient-derived fibroblasts, eIF4A2 production amounted to only 50% of the normal quantity. Reduction of eIF4A2 was associated with abnormally increased levels of IMP1, a target of Ccr4-Not, the complex that interacts with eIF4A2 to mediate microRNA-dependent translational repression. By complementing the analyses with fibroblasts bearing EIF4A2 biallelic mutations, we established a correlation between IMP1 expression alterations and eIF4A2 functional dosage. Moreover, eIF4A2 and Ccr4-Not displayed significantly diminished colocalization in dystonia patient cells. Review of international databases identified EIF4A2 deletion variants (c.470_472del, c.1144_1145del) in another two dystonia-affected pedigrees. Conclusions: Our findings demonstrate that EIF4A2 haploinsufficiency underlies a previously unrecognized dominant dystonia-tremor syndrome. The data imply that translational deregulation is more broadly linked to both early neurodevelopmental phenotypes and later-onset dystonic conditions. © 2023 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society

The Astropy Problem

The Astropy Project (http://astropy.org) is, in its own words, "a community effort to develop a single core package for Astronomy in Python and foster interoperability between Python astronomy packages." For five years this project has been managed, written, and operated as a grassroots, self-organized, almost entirely volunteer effort while the software is used by the majority of the astronomical community. Despite this, the project has always been and remains to this day effectively unfunded. Further, contributors receive little or no formal recognition for creating and supporting what is now critical software. This paper explores the problem in detail, outlines possible solutions to correct this, and presents a few suggestions on how to address the sustainability of general purpose astronomical software

Discovery of the lensed quasar system DES J0408-5354

We report the discovery and spectroscopic confirmation of the quad-like lensed quasar system DES J0408-5354 found in the Dark Energy Survey (DES) Year 1 (Y1) data. This system was discovered during a search for DES Y1 strong lensing systems using a method that identified candidates as red galaxies with multiple blue neighbors. DES J0408-5354 consists of a central red galaxy surrounded by three bright (i<20) blue objects and a fourth red object. Subsequent spectroscopic observations using the Gemini South telescope confirmed that the three blue objects are indeed the lensed images of a quasar with redshift z = 2.375, and that the central red object is an early-type lensing galaxy with redshift z = 0.597. DES J0408-5354 is the first quad lensed quasar system to be found in DES and begins to demonstrate the potential of DES to discover and dramatically increase the sample size of these very rare objects

Density split statistics: Joint model of counts and lensing in cells

© 2018 American Physical Society. We present density split statistics, a framework that studies lensing and counts-in-cells as a function of foreground galaxy density, thereby providing a large-scale measurement of both 2-point and 3-point statistics. Our method extends our earlier work on trough lensing and is summarized as follows: given a foreground (low redshift) population of galaxies, we divide the sky into subareas of equal size but distinct galaxy density. We then measure lensing around uniformly spaced points separately in each of these subareas, as well as counts-in-cells statistics (CiC). The lensing signals trace the matter density contrast around regions of fixed galaxy density. Through the CiC measurements this can be related to the density profile around regions of fixed matter density. Together, these measurements constitute a powerful probe of cosmology, the skewness of the density field and the connection of galaxies and matter. In this paper we show how to model both the density split lensing signal and CiC from basic ingredients: a non-linear power spectrum, clustering hierarchy coefficients from perturbation theory and a parametric model for galaxy bias and shot-noise. Using N-body simulations, we demonstrate that this model is sufficiently accurate for a cosmological analysis on year 1 data from the Dark Energy Survey

Dark energy survey year 1 results: detection of intracluster light at redshift ∼ 0.25

International audienceUsing data collected by the Dark Energy Survey (DES), we report the detection of intracluster light (ICL) with ∼300 galaxy clusters in the redshift range of 0.2–0.3. We design methods to mask detected galaxies and stars in the images and stack the cluster light profiles, while accounting for several systematic effects (sky subtraction, instrumental point-spread function, cluster selection effects, and residual light in the ICL raw detection from background and cluster galaxies). The methods allow us to acquire high signal-to-noise measurements of the ICL and central galaxies (CGs), which we separate with radial cuts. The ICL appears as faint and diffuse light extending to at least 1 Mpc from the cluster center, reaching a surface brightness level of 30 mag arcsec−2. The ICL and the cluster CG contribute 44% ± 17% of the total cluster stellar luminosity within 1 Mpc. The ICL color is overall consistent with that of the cluster red sequence galaxies, but displays the trend of becoming bluer with increasing radius. The ICL demonstrates an interesting self-similarity feature—for clusters in different richness ranges, their ICL radial profiles are similar after scaling with cluster R 200m , and the ICL brightness appears to be a good tracer of the cluster radial mass distribution. These analyses are based on the DES redMaPPer cluster sample identified in the first year of observations

Dark Energy Survey Year 1 results: validation of weak lensing cluster member contamination estimates from P(z) decomposition

Weak lensing source galaxy catalogues used in estimating the masses of galaxy clusters can be heavily contaminated by cluster members, prohibiting accurate mass calibration. In this study, we test the performance of an estimator for the extent of cluster member contamination based on decomposing the photometric redshift P(z) of source galaxies into contaminating and background components. We perform a full scale mock analysis on a simulated sky survey approximately mirroring the observational properties of the Dark Energy Survey Year One observations (DES Y1), and find excellent agreement between the true number profile of contaminating cluster member galaxies in the simulation and the estimated one. We further apply the method to estimate the cluster member contamination for the DES Y1 redMaPPer cluster mass calibration analysis, and compare the results to an alternative approach based on the angular correlation of weak lensing source galaxies. We find indications that the correlation based estimates are biased by the selection of the weak lensing sources in the cluster vicinity, which does not strongly impact the P(z) decomposition method. Collectively, these benchmarks demonstrate the strength of the P(z) decomposition method in alleviating membership contamination and enabling highly accurate cluster weak lensing studies without broad exclusion of source galaxies, thereby improving the total constraining power of cluster mass calibration via weak lensing