New quasar proximity zone size measurements at z∼6z\sim 6 using the enlarged XQR-30 sample

Proximity zones of high-redshift quasars are unique probes of their central supermassive black holes as well as the intergalactic medium in the last stages of reionization. We present 22 new measurements of proximity zones of quasars with redshifts between 5.8 and 6.6, using the enlarged XQR-30 sample of high-resolution, high-SNR quasar spectra. The quasars in our sample have UV magnitudes of $M_{1450}\sim -27$ and black hole masses of $10^9$\unicode{x2013}$10^{10}$ M$_\odot$. Our inferred proximity zone sizes are 2\unicode{x2013}7 physical Mpc, with a typical uncertainty of less than 0.5 physical Mpc, which, for the first time, also includes uncertainty in the quasar continuum. We find that the correlation between proximity zone sizes and the quasar redshift, luminosity, or black hole mass, indicates a large diversity of quasar lifetimes. Two of our proximity zone sizes are exceptionally small. The spectrum of one of these quasars, with $z=6.02$, displays, unusually for this redshift, damping wing absorption without any detectable metal lines, which could potentially originate from the IGM. The other quasar has a high-ionization absorber $\sim$0.5 pMpc from the edge of the proximity zone. This work increases the number of proximity zone measurements available in the last stages of cosmic reionization to 87. This data will lead to better constraints on quasar lifetimes and obscuration fractions at high redshift, which in turn will help probe the seed mass and formation redshift of supermassive black holes.Comment: 16 pages, 9 figures, Accepted in MNRA

Measuring the photo-ionization rate, neutral fraction and mean free path of HI ionizing photons at 4.9≤z≤6.04.9 \leq z \leq 6.0 from a large sample of XShooter and ESI spectra

We measure the mean free path ($\lambda_{\rm mfp,HI}$), photo-ionization rate ($\langle \Gamma_{\rm HI} \rangle$) and neutral fraction ($\langle f_{\rm HI} \rangle$) of hydrogen in 12 redshift bins at $4.85<z<6.05$ from a large sample of moderate resolution XShooter and ESI QSO absorption spectra. The fluctuations in ionizing radiation field are modeled by post-processing simulations from the Sherwood suite using our new code ''EXtended reionization based on the Code for Ionization and Temperature Evolution'' (EX-CITE). EX-CITE uses efficient Octree summation for computing intergalactic medium attenuation and can generate large number of high resolution $\Gamma_{\rm HI}$ fluctuation models. Our simulation with EX-CITE shows remarkable agreement with simulations performed with the radiative transfer code Aton and can recover the simulated parameters within $1\sigma$ uncertainty. We measure the three parameters by forward-modeling the Ly$\alpha$ forest and comparing the effective optical depth ($\tau_{\rm eff, HI}$) distribution in simulations and observations. The final uncertainties in our measured parameters account for the uncertainties due to thermal parameters, modeling parameters, observational systematics and cosmic variance. Our best fit parameters show significant evolution with redshift such that $\lambda_{\rm mfp,HI}$ and $\langle f_{\rm HI} \rangle$ decreases and increases by a factor $\sim 6$ and $\sim 10^{4}$, respectively from $z \sim 5$ to $z \sim 6$. By comparing our $\lambda_{\rm mfp,HI}$, $\langle \Gamma_{\rm HI} \rangle$ and $\langle f_{\rm HI} \rangle$ evolution with that in state-of-the-art Aton radiative transfer simulations and the Thesan and CoDa-III simulations, we find that our best fit parameter evolution is consistent with a model in which reionization completes by $z \sim 5.2$.Comment: 30 pages (+14 pages appendices), 14 figures (+18 figures appendices); submitted to MNRAS; Main results are summarized in Fig. 10, Fig. 11 and Table

Applied immuno-epidemiological research: an approach for integrating existing knowledge into the statistical analysis of multiple immune markers.

BACKGROUND: Immunologists often measure several correlated immunological markers, such as concentrations of different cytokines produced by different immune cells and/or measured under different conditions, to draw insights from complex immunological mechanisms. Although there have been recent methodological efforts to improve the statistical analysis of immunological data, a framework is still needed for the simultaneous analysis of multiple, often correlated, immune markers. This framework would allow the immunologists' hypotheses about the underlying biological mechanisms to be integrated. RESULTS: We present an analytical approach for statistical analysis of correlated immune markers, such as those commonly collected in modern immuno-epidemiological studies. We demonstrate i) how to deal with interdependencies among multiple measurements of the same immune marker, ii) how to analyse association patterns among different markers, iii) how to aggregate different measures and/or markers to immunological summary scores, iv) how to model the inter-relationships among these scores, and v) how to use these scores in epidemiological association analyses. We illustrate the application of our approach to multiple cytokine measurements from 818 children enrolled in a large immuno-epidemiological study (SCAALA Salvador), which aimed to quantify the major immunological mechanisms underlying atopic diseases or asthma. We demonstrate how to aggregate systematically the information captured in multiple cytokine measurements to immunological summary scores aimed at reflecting the presumed underlying immunological mechanisms (Th1/Th2 balance and immune regulatory network). We show how these aggregated immune scores can be used as predictors in regression models with outcomes of immunological studies (e.g. specific IgE) and compare the results to those obtained by a traditional multivariate regression approach. CONCLUSION: The proposed analytical approach may be especially useful to quantify complex immune responses in immuno-epidemiological studies, where investigators examine the relationship among epidemiological patterns, immune response, and disease outcomes

Brief report: Autism and herpes simplex encephalitis

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/44606/1/10803_2005_Article_BF01046406.pd

DATA.awi.de: A one-stop-shop framework for discovery

DATA.awi.de is a component of our data flow framework designed to enable a semi-automated flow of sensor observations to archives (acronym O2A). The dramatic increase in the number and type of platforms and respective sensors operated by Alfred Wegener Institute along with complex project-driven requirements in terms of satellite communication, sensor monitoring, quality control and validation, processing pipelines, visualization, and archival under FAIR principles, led us to build a generic and cost-effective data flow framework. Most important, all components and services which make up this framework are extensible and exchangeble, were built using open access technologies (e.g. elastic search) and vocabularies (SeaVox NERC 2.0 vocabulary) and are compliant with various interoperability standards recommended by the international community. In this poster we illustrate the DATA.awi.de component which is a one-stop-shop framework for enabling discovery and dissemination of heterogeneous scientific information. Because the metadata and data generated and captured by the other O2A components are machine-readable and interoperable, we were able to build harvesting and indexing solutions which enable scientists and other stakeholders to discover content ranging from platforms/sensors, tracklines, field reports, near real-time data to quality-controlled data, map products and peer-reviewed publications. Scientific Disciplin/Research Area: Findability, Interoperability, Integration, Re-use. Relevance/Link to RDA: In the context of our harvesting approach, we are interacting with the RDA "Brokering Framework" Working Group and "Brokering" Interest Group

Measuring the photo-ionization rate, neutral fraction and mean free path of HI ionizing photons at 4.9≤z≤6.0 from a large sample of XShooter and ESI spectra

We measure the mean free path (⁠λmfp,HI⁠), photo-ionization rate (⁠⟨ΓHI⟩⁠) and neutral fraction (⁠⟨fHI⟩⁠) of hydrogen in 12 redshift bins at 4.85 < z < 6.05 from a large sample of moderate resolution XShooter and ESI QSO absorption spectra. The fluctuations in ionizing radiation field are modeled by post-processing simulations from the Sherwood suite using our new code ‘EXtended reionization based on the Code for Ionization and Temperature Evolution’ (EX-CITE). EX-CITE uses efficient Octree summation for computing intergalactic medium attenuation and can generate large number of high resolution ΓHI fluctuation models. Our simulation with EX-CITE shows remarkable agreement with simulations performed with the radiative transfer code Aton and can recover the simulated parameters within 1σ uncertainty. We measure the three parameters by forward-modeling the Lyα forest and comparing the effective optical depth (⁠τeff,HI⁠) distribution in simulations and observations. The final uncertainties in our measured parameters account for the uncertainties due to thermal parameters, modeling parameters, observational systematics and cosmic variance. Our best fit parameters show significant evolution with redshift such that λmfp,HI and ⟨fHI⟩ decreases and increases by a factor ∼6 and ∼104, respectively from z ∼ 5 to z ∼ 6. By comparing our λmfp,HI⁠, ⟨ΓHI⟩ and ⟨fHI⟩ evolution with that in state-of-the-art Aton radiative transfer simulations and the Thesan and CoDa-III simulations, we find that our best fit parameter evolution is consistent with a model in which reionization completes by z ∼ 5.2. Our best fit model that matches the τeff,HI distribution also reproduces the dark gap length distribution and transmission spike height distribution suggesting robustness and accuracy of our measured parameters

A SPectroscopic Survey of Biased Halos in the Reionization Era (ASPIRE): JWST Reveals a Filamentary Structure around a z = 6.61 Quasar

© 2023. The Author(s). Published by the American Astronomical Society. This is an open access article distributed under the Creative Commons Attribution License, to view a copy of the license, see: https://creativecommons.org/licenses/by/4.0/We present the first results from the JWST program A SPectroscopic survey of biased halos In the Reionization Era (ASPIRE). This program represents an imaging and spectroscopic survey of 25 reionization-era quasars and their environments by utilizing the unprecedented capabilities of NIRCam Wide Field Slitless Spectroscopy (WFSS) mode. ASPIRE will deliver the largest ( ∼280arcmin2 ) galaxy redshift survey at 3–4 μm among JWST Cycle 1 programs and provide extensive legacy values for studying the formation of the earliest supermassive black holes, the assembly of galaxies, early metal enrichment, and cosmic reionization. In this first ASPIRE paper, we report the discovery of a filamentary structure traced by the luminous quasar J0305–3150 and 10 [O iii] emitters at z = 6.6. This structure has a 3D galaxy overdensity of δ gal = 12.6 over 637 cMpc3, one of the most overdense structures known in the early universe, and could eventually evolve into a massive galaxy cluster. Together with existing VLT/MUSE and ALMA observations of this field, our JWST observations reveal that J0305–3150 traces a complex environment where both UV-bright and dusty galaxies are present and indicate that the early evolution of galaxies around the quasar is not simultaneous. In addition, we discovered 31 [O iii] emitters in this field at other redshifts, 5.3 < z < 6.7, with half of them situated at z ∼ 5.4 and 6.2. This indicates that star-forming galaxies, such as [O iii] emitters, are generally clustered at high redshifts. These discoveries demonstrate the unparalleled redshift survey capabilities of NIRCam WFSS and the potential of the full ASPIRE survey data set.Peer reviewe

A SPectroscopic Survey of Biased Halos in the Reionization Era (ASPIRE): A First Look at the Rest-frame Optical Spectra of z > 6.5 Quasars Using JWST

© 2023. The Author(s). Published by the American Astronomical Society. This is an open access article distributed under the Creative Commons Attribution License, to view a copy of the license, see: https://creativecommons.org/licenses/by/4.0/Studies of rest-frame optical emission in quasars at z > 6 have historically been limited by the wavelengths accessible by ground-based telescopes. The James Webb Space Telescope (JWST) now offers the opportunity to probe this emission deep into the reionization epoch. We report the observations of eight quasars at z > 6.5 using the JWST/NIRCam Wide Field Slitless Spectroscopy as a part of the “A SPectroscopic survey of biased halos In the Reionization Era (ASPIRE)” program. Our JWST spectra cover the quasars’ emission between rest frame ∼4100 and 5100 Å. The profiles of these quasars’ broad Hβ emission lines span a full width at half maximum from 3000 to 6000 km s−1. The Hβ-based virial black hole (BH) masses, ranging from 0.6 to 2.1 billion solar masses, are generally consistent with their Mg ii-based BH masses. The new measurements based on the more reliable Hβ tracer thus confirm the existence of a billion solar-mass BHs in the reionization epoch. In the observed [O iii] λ λ 4960,5008 doublets of these luminous quasars, broad components are more common than narrow core components (≤ 1200 km s−1), and only one quasar shows stronger narrow components than broad. Two quasars exhibit significantly broad and blueshifted [O iii] emission, thought to trace galactic-scale outflows, with median velocities of −610 and −1430 km s−1 relative to the [C ii] 158 μm line. All eight quasars show strong optical Fe ii emission and follow the eigenvector 1 relations defined by low-redshift quasars. The entire ASPIRE program will eventually cover 25 quasars and provide a statistical sample for the studies of the BHs and quasar spectral properties.Peer reviewe

The Action Mechanism of the Myc Inhibitor Termed Omomyc May Give Clues on How to Target Myc for Cancer Therapy

Recent evidence points to Myc – a multifaceted bHLHZip transcription factor deregulated in the majority of human cancers – as a priority target for therapy. How to target Myc is less clear, given its involvement in a variety of key functions in healthy cells. Here we report on the action mechanism of the Myc interfering molecule termed Omomyc, which demonstrated astounding therapeutic efficacy in transgenic mouse cancer models in vivo. Omomyc action is different from the one that can be obtained by gene knockout or RNA interference, approaches designed to block all functions of a gene product. This molecule – instead – appears to cause an edge-specific perturbation that destroys some protein interactions of the Myc node and keeps others intact, with the result of reshaping the Myc transcriptome. Omomyc selectively targets Myc protein interactions: it binds c- and N-Myc, Max and Miz-1, but does not bind Mad or select HLH proteins. Specifically, it prevents Myc binding to promoter E-boxes and transactivation of target genes while retaining Miz-1 dependent binding to promoters and transrepression. This is accompanied by broad epigenetic changes such as decreased acetylation and increased methylation at H3 lysine 9. In the presence of Omomyc, the Myc interactome is channeled to repression and its activity appears to switch from a pro-oncogenic to a tumor suppressive one. Given the extraordinary therapeutic impact of Omomyc in animal models, these data suggest that successfully targeting Myc for cancer therapy might require a similar twofold action, in order to prevent Myc/Max binding to E-boxes and, at the same time, keep repressing genes that would be repressed by Myc

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals &lt;1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data