Chromosome 7 and 19 Trisomy in Cultured Human Neural Progenitor Cells

BACKGROUND:Stem cell expansion and differentiation is the foundation of emerging cell therapy technologies. The potential applications of human neural progenitor cells (hNPCs) are wide ranging, but a normal cytogenetic profile is important to avoid the risk of tumor formation in clinical trials. FDA approved clinical trials are being planned and conducted for hNPC transplantation into the brain or spinal cord for various neurodegenerative disorders. Although human embryonic stem cells (hESCs) are known to show recurrent chromosomal abnormalities involving 12 and 17, no studies have revealed chromosomal abnormalities in cultured hNPCs. Therefore, we investigated frequently occurring chromosomal abnormalities in 21 independent fetal-derived hNPC lines and the possible mechanisms triggering such aberrations. METHODS AND FINDINGS:While most hNPC lines were karyotypically normal, G-band karyotyping and fluorescent in situ hybridization (FISH) analyses revealed the emergence of trisomy 7 (hNPC(+7)) and trisomy 19 (hNPC(+19)), in 24% and 5% of the lines, respectively. Once detected, subsequent passaging revealed emerging dominance of trisomy hNPCs. DNA microarray and immunoblotting analyses demonstrate epidermal growth factor receptor (EGFR) overexpression in hNPC(+7) and hNPC(+19) cells. We observed greater levels of telomerase (hTERT), increased proliferation (Ki67), survival (TUNEL), and neurogenesis (beta(III)-tubulin) in hNPC(+7) and hNPC(+19), using respective immunocytochemical markers. However, the trisomy lines underwent replicative senescence after 50-60 population doublings and never showed neoplastic changes. Although hNPC(+7) and hNPC(+19) survived better after xenotransplantation into the rat striatum, they did not form malignant tumors. Finally, EGF deprivation triggered a selection of trisomy 7 cells in a diploid hNPC line. CONCLUSIONS:We report that hNPCs are susceptible to accumulation of chromosome 7 and 19 trisomy in long-term cell culture. These results suggest that micro-environmental cues are powerful factors in the selection of specific hNPC aneuploidies, with trisomy of chromosome 7 being the most common. Given that a number of stem cell based clinical trials are being conducted or planned in USA and a recent report in PLoS Medicine showing the dangers of grafting an inordinate number of cells, these data substantiate the need for careful cytogenetic evaluation of hNPCs (fetal or hESC-derived) before their use in clinical or basic science applications

Preliminary Target Selection for the DESI Milky Way Survey (MWS)

The DESI Milky Way Survey (MWS) will observe $\ge$8 million stars between $16 < r < 19$ mag, supplemented by observations of brighter targets under poor observing conditions. The survey will permit an accurate determination of stellar kinematics and population gradients; characterize diffuse substructure in the thick disk and stellar halo; enable the discovery of extremely metal-poor stars and other rare stellar types; and improve constraints on the Galaxy's 3D dark matter distribution from halo star kinematics. MWS will also enable a detailed characterization of the stellar populations within 100 pc of the Sun, including a complete census of white dwarfs. The target catalog from the preliminary selection described here is public

Detecting and Characterizing Mg ii Absorption in DESI Survey Validation Quasar Spectra

We present findings of the detection of Magnesium II (Mg ii, λ = 2796, 2803 Å) absorbers from the early data release of the Dark Energy Spectroscopic Instrument (DESI). DESI is projected to obtain spectroscopy of approximately 3 million quasars (QSOs), of which over 99% are anticipated to be at redshifts greater than z > 0.3, such that DESI would be able to observe an associated or intervening Mg ii absorber illuminated by the background QSO. We have developed an autonomous supplementary spectral pipeline that detects these systems through an initial line-fitting process and then confirms the line properties using a Markov Chain Monte Carlo sampler. Based upon a visual inspection of the resulting systems, we estimate that this sample has a purity greater than 99%. We have also investigated the completeness of our sample in regard to both the signal-to-noise properties of the input spectra and the rest-frame equivalent width (W 0) of the absorber systems. From a parent catalog containing 83,207 quasars, we detect a total of 23,921 Mg ii absorption systems following a series of quality cuts. Extrapolating from this occurrence rate of 28.8% implies a catalog at the completion of the five-year DESI survey that will contain over eight hundred thousand Mg ii absorbers. The cataloging of these systems will enable significant further research because they carry information regarding circumgalactic medium environments, the distribution of intervening galaxies, and the growth of metallicity across the redshift range 0.3 ≤ z < 2.5

A striking relationship between dust extinction and radio detection in DESI QSOs: evidence for a dusty blow-out phase in red QSOs

We present the first eight months of data from our secondary target programme within the ongoing Dark Energy Spectroscopic Instrument (DESI) survey. Our programme uses a mid-infrared and optical colour selection to preferentially target dust-reddened quasi-stellar objects (QSOs) that would have otherwise been missed by the nominal DESI QSO selection. So far, we have obtained optical spectra for 3038 candidates, of which ∼70 per cent of the high-quality objects (those with robust redshifts) are visually confirmed to be Type 1 QSOs, consistent with the expected fraction from the main DESI QSO survey. By fitting a dust-reddened blue QSO composite to the QSO spectra, we find they are well-fitted by a normal QSO with up to AV ∼4 mag of line-of-sight dust extinction. Utilizing radio data from the LOFAR Two-metre Sky Survey (LoTSS) DR2, we identify a striking positive relationship between the amount of line-of-sight dust extinction towards a QSO and the radio detection fraction, that is not driven by radio-loud systems, redshift and/or luminosity effects. This demonstrates an intrinsic connection between dust reddening and the production of radio emission in QSOs, whereby the radio emission is most likely due to low-powered jets or winds/outflows causing shocks in a dusty environment. On the basis of this evidence, we suggest that red QSOs may represent a transitional 'blow-out' phase in the evolution of QSOs, where winds and outflows evacuate the dust and gas to reveal an unobscured blue QSO

The Target-selection Pipeline for the Dark Energy Spectroscopic Instrument

In 2021 May, the Dark Energy Spectroscopic Instrument (DESI) began a 5 yr survey of approximately 50 million total extragalactic and Galactic targets. The primary DESI dark-time targets are emission line galaxies, luminous red galaxies, and quasars. In bright time, DESI will focus on two surveys known as the Bright Galaxy Survey and the Milky Way Survey. DESI also observes a selection of “secondary” targets for bespoke science goals. This paper gives an overview of the publicly available pipeline (desitarget) used to process targets for DESI observations. Highlights include details of the different DESI survey targeting phases, the targeting ID (TARGETID) used to define unique targets, the bitmasks used to indicate a particular type of target, the data model and structure of DESI targeting files, and examples of how to access and use the desitarget code base. This paper will also describe “supporting” DESI target classes, such as standard stars, sky locations, and random catalogs that mimic the angular selection function of DESI targets. The DESI target-selection pipeline is complex and sizable; this paper attempts to summarize the most salient information required to understand and work with DESI targeting data

Target Selection and Validation of DESI Quasars

The Dark Energy Spectroscopic Instrument (DESI) survey will measure large-scale structures using quasars as direct tracers of dark matter in the redshift range 0.9 2.1. We present several methods to select candidate quasars for DESI, using input photometric imaging in three optical bands (g, r, z) from the DESI Legacy Imaging Surveys and two infrared bands (W1, W2) from the Wide-field Infrared Survey Explorer. These methods were extensively tested during the Survey Validation of DESI. In this paper, we report on the results obtained with the different methods and present the selection we optimized for the DESI main survey. The final quasar target selection is based on a random forest algorithm and selects quasars in the magnitude range of 16.5 2.1), exceeding the project requirements by 20%. The redshift distribution of the selected quasars is in excellent agreement with quasar luminosity function predictions

Overview of the DESI Milky Way Survey

We describe the Milky Way Survey (MWS) that will be undertaken with the Dark Energy Spectroscopic Instrument (DESI) on the Mayall 4 m telescope at the Kitt Peak National Observatory. Over the next 5 yr DESI MWS will observe approximately seven million stars at Galactic latitudes ∣b∣ > 20°, with an inclusive target selection scheme focused on the thick disk and stellar halo. MWS will also include several high-completeness samples of rare stellar types, including white dwarfs, low-mass stars within 100 pc of the Sun, and horizontal branch stars. We summarize the potential of DESI to advance understanding of the Galactic structure and stellar evolution. We introduce the final definitions of the main MWS target classes and estimate the number of stars in each class that will be observed. We describe our pipelines for deriving radial velocities, atmospheric parameters, and chemical abundances. We use ≃500,000 spectra of unique stellar targets from the DESI Survey Validation program (SV) to demonstrate that our pipelines can measure radial velocities to ≃1 km s−1 and [Fe/H] accurate to ≃0.2 dex for typical stars in our main sample. We find the stellar parameter distributions from ≈100 deg2 of SV observations with ≳90% completeness on our main sample are in good agreement with expectations from mock catalogs and previous surveys

Early inhaled budesonide for the prevention of bronchopulmonary dysplasia

BACKGROUND Systemic glucocorticoids reduce the incidence of bronchopulmonary dysplasia among extremely preterm infants, but they may compromise brain development. The effects of inhaled glucocorticoids on outcomes in these infants are unclear. METHODS We randomly assigned 863 infants (gestational age, 23 weeks 0 days to 27 weeks 6 days) to early (within 24 hours after birth) inhaled budesonide or placebo until they no longer required oxygen and positive-pressure support or until they reached a postmenstrual age of 32 weeks 0 days. The primary outcome was death or bronchopulmonary dysplasia, confirmed by means of standardized oxygen-saturation monitoring, at a postmenstrual age of 36 weeks. RESULTS A total of 175 of 437 infants assigned to budesonide for whom adequate data were available (40.0%), as compared with 194 of 419 infants assigned to placebo for whom adequate data were available (46.3%), died or had bronchopulmonary dysplasia (relative risk, stratified according to gestational age, 0.86; 95% confidence interval [CI], 0.75 to 1.00; P = 0.05). The incidence of bronchopulmonary dysplasia was 27.8% in the budesonide group versus 38.0% in the placebo group (relative risk, stratified according to gestational age, 0.74; 95% CI, 0.60 to 0.91; P = 0.004); death occurred in 16.9% and 13.6% of the patients, respectively (relative risk, stratified according to gestational age, 1.24; 95% CI, 0.91 to 1.69; P = 0.17). The proportion of infants who required surgical closure of a patent ductus arteriosus was lower in the budesonide group than in the placebo group (relative risk, stratified according to gestational age, 0.55; 95% CI, 0.36 to 0.83; P = 0.004), as was the proportion of infants who required reintubation (relative risk, stratified according to gestational age, 0.58; 95% CI, 0.35 to 0.96; P = 0.03). Rates of other neonatal illnesses and adverse events were similar in the two groups. CONCLUSIONS Among extremely preterm infants, the incidence of bronchopulmonary dysplasia was lower among those who received early inhaled budesonide than among those who received placebo, but the advantage may have been gained at the expense of increased mortality

†Kenyaichthyidae fam. nov and †Kenyaichthys gen. nov - First Record of a Fossil Aplocheiloid Killifish (Teleostei, Cyprinodontiformes)

The extant Cyprinodontiformes (killifishes) with their two suborders Cyprinodontoidei and Aplocheiloidei represent a diverse and well-studied group of fishes. However, their fossil record is comparatively sparse and has so far yielded members of the Cyprinodontoidei only. Here we report on cyprinodontiform fossils from the upper Miocene Lukeino Formation in the Tugen Hills of the Central Rift Valley of Kenya, which represent the first fossil record of an aplocheiloid killifish. A total of 169 specimens - mostly extraordinarily well preserved and a sample of ten extant cyprinodontiform species were studied on the basis of morphometrics, meristics and osteology. A phylogenetic analysis using PAUP was also conducted for the fossils. Both the osteological data and the phylogenetic analysis provide strong evidence for the assignment of the fossils to the Aplocheiloidei, and justify the definition of the new family dagger Kenyaichthyidae, the new genus dagger Kenyaichthys and the new species dagger K. kipkechi sp. nov. The phylogenetic analysis unexpectedly places dagger Kenyaichthys gen. nov. in a sister relationship to the Rivulidae (a purely Neotropical group),a probable explanation might be lack of available synapomorphies for the Rivulidae, Nothobranchiidae and Aplocheilidae. The specimens of dagger K. kipkechi sp. nov. show several polymorphic characters and large overlap in meristic traits, which justifies their interpretation as a species flock in statu nascendi. Patterns of variation in neural and haemal spine dimensions in the caudal vertebrae of dagger Kenyaichthys gen. nov. and the extant species studied indicate that some previously suggested synapomorphies of the Cyprinodontoidei and Aplocheiloidei need to be revised