HELIOS-K 2.0 Opacity Calculator and Open-source Opacity Database for Exoplanetary Atmospheres

Computing and using opacities is a key part of modeling and interpreting data of exoplanetary atmospheres. Since the underlying spectroscopic line lists are constantly expanding and currently include up to ∼1010–1011 transition lines, the opacity calculator codes need to become more powerful. Here we present major upgrades to the HELIOS-K GPU-accelerated opacity calculator and describe the necessary steps to process large line lists within a reasonable amount of time. Besides performance improvements, we include more capabilities and present a toolbox for handling different atomic and molecular data sets, from downloading and preprocessing the data to performing the opacity calculations in a user-friendly way. HELIOS-K supports line lists from ExoMol, HITRAN, HITEMP, NIST, Kurucz, and VALD3. By matching the resolution of 0.1 cm−1 and cutting length of 25 cm−1 used by the ExoCross code for timing performance (251 s excluding data read-in time), HELIOS-K can process the ExoMol BT2 water line list in 12.5 s. Using a resolution of 0.01 cm−1, it takes 45 s, equivalent to about 107 lines s−1. As a wavenumber resolution of 0.01 cm−1 suffices for most exoplanetary atmosphere spectroscopic calculations, we adopt this resolution in calculating opacity functions for several hundred atomic and molecular species and make them freely available on the open-access DACE database. For the opacity calculations of the database, we use a cutting length of 100 cm−1 for molecules and no cutting length for atoms. Our opacities are available for downloading from https://dace.unige.ch/opacityDatabase and may be visualized using https://dace.unige.ch/opacity

Neurocognitive function in HIV infected patients on antiretroviral therapy

OBJECTIVE To describe factors associated with neurocognitive (NC) function in HIV-positive patients on stable combination antiretroviral therapy. DESIGN We undertook a cross-sectional analysis assessing NC data obtained at baseline in patients entering the Protease-Inhibitor-Monotherapy-Versus-Ongoing-Triple therapy (PIVOT) trial. MAIN OUTCOME MEASURE NC testing comprised of 5 domains. Raw results were z-transformed using standard and demographically adjusted normative datasets (ND). Global z-scores (NPZ-5) were derived from averaging the 5 domains and percentage of subjects with test scores >1 standard deviation (SD) below population means in at least two domains (abnormal Frascati score) calculated. Patient characteristics associated with NC results were assessed using multivariable linear regression. RESULTS Of the 587 patients in PIVOT, 557 had full NC results and were included. 77% were male, 68% Caucasian and 28% of Black ethnicity. Mean (SD) baseline and nadir CD4+ lymphocyte counts were 553(217) and 177(117) cells/µL, respectively, and HIV RNA was <50 copies/mL in all. Median (IQR) NPZ-5 score was -0.5 (-1.2/-0) overall, and -0.3 (-0.7/0.1) and -1.4 (-2/-0.8) in subjects of Caucasian and Black ethnicity, respectively. Abnormal Frascati scores using the standard-ND were observed in 51%, 38%, and 81%, respectively, of subjects overall, Caucasian and Black ethnicity (p<0.001), but in 62% and 69% of Caucasian and Black subjects using demographically adjusted-ND (p = 0.20). In the multivariate analysis, only Black ethnicity was associated with poorer NPZ-5 scores (P<0.001). CONCLUSIONS In this large group of HIV-infected subjects with viral load suppression, ethnicity but not HIV-disease factors is closely associated with NC results. The prevalence of abnormal results is highly dependent on control datasets utilised. TRIAL REGISTRY ClinicalTrials.gov, NCT01230580

The RadFxSat-2 Mission to Measure SEU Rates in FinFET Microelectronics

The RadFxSat-2 mission was launched January 17, 2021 with Virgin Orbit\u27s LauncherOne under the NASA ELaNa-20 initiative. RadFxSat-2 carries a radiation effects payload designed to investigate single event upsets (SEUs) in sub-65 nm commercial memories, including a FinFET-based memory. Sub-65 nm technologies have demonstrated enhanced sensitivity to low-energy protons, but current models have not considered low-energy protons as a source of SEUs. Missions utilizing the latest commercial technologies could experience a higher error rate than predicted. RadFxSat-2 was designed to assess SEU rates for FinFET SRAMs operated in low-Earth orbit (LEO), a proton-heavy environment. Details of the mission and data collected over the previous two years are presented. Results from RadFxSat-2 suggest that FinFET-based microelectronic technologies are suitable for high-performance, high-density storage in LEO

TOI-1685 b Is a Hot Rocky Super-Earth: Updates to the Stellar and Planet Parameters of a Popular JWST Cycle 2 Target

We present an updated characterization of the TOI-1685 planetary system, which consists of a P b = 0.69 day ultra-short-period super-Earth planet orbiting a nearby (d = 37.6 pc) M2.5V star (TIC 28900646, 2MASS J04342248+4302148). This planet was previously featured in two contemporaneous discovery papers, but the best-fit planet mass, radius, and bulk density values were discrepant, allowing it to be interpreted either as a hot, bare rock or a 50% H2O/50% MgSiO3 water world. TOI-1685 b will be observed in three independent JWST Cycle 2 programs, two of which assume the planet is a water world, while the third assumes that it is a hot rocky planet. Here we include a refined stellar classification with a focus on addressing the host star’s metallicity, an updated planet radius measurement that includes two sectors of TESS data and multicolor photometry from a variety of ground-based facilities, and a more accurate dynamical mass measurement from a combined CARMENES, InfraRed Doppler, and MAROON-X radial velocity data set. We find that the star is very metal-rich ([Fe/H] ≃ +0.3) and that the planet is systematically smaller, lower mass, and higher density than initially reported, with new best-fit parameters of R pl = 1.468 −0.051+0.050 R ⊕ and M pl = 3.03−0.32+0.33 M ⊕. These results fall in between the previously derived values and suggest that TOI-1685 b is a hot rocky planet with an Earth-like density (ρ pl = 5.3 ± 0.8 g cm−3, or 0.96 ρ ⊕), high equilibrium temperature (T eq = 1062 ± 27 K), and negligible volatiles, rather than a water world

Cannabis use as a potential mediator between childhood adversity and first-episode psychosis: results from the EU-GEI case-control study

Background Childhood adversity and cannabis use are considered independent risk factors for psychosis, but whether different patterns of cannabis use may be acting as mediator between adversity and psychotic disorders has not yet been explored. The aim of this study is to examine whether cannabis use mediates the relationship between childhood adversity and psychosis. Methods Data were utilised on 881 first-episode psychosis patients and 1231 controls from the European network of national schizophrenia networks studying Gene–Environment Interactions (EU-GEI) study. Detailed history of cannabis use was collected with the Cannabis Experience Questionnaire. The Childhood Experience of Care and Abuse Questionnaire was used to assess exposure to household discord, sexual, physical or emotional abuse and bullying in two periods: early (0–11 years), and late (12–17 years). A path decomposition method was used to analyse whether the association between childhood adversity and psychosis was mediated by (1) lifetime cannabis use, (2) cannabis potency and (3) frequency of use. Results The association between household discord and psychosis was partially mediated by lifetime use of cannabis (indirect effect coef. 0.078, s.e. 0.022, 17%), its potency (indirect effect coef. 0.059, s.e. 0.018, 14%) and by frequency (indirect effect coef. 0.117, s.e. 0.038, 29%). Similar findings were obtained when analyses were restricted to early exposure to household discord. Conclusions Harmful patterns of cannabis use mediated the association between specific childhood adversities, like household discord, with later psychosis. Children exposed to particularly challenging environments in their household could benefit from psychosocial interventions aimed at preventing cannabis misuse

Virological failure and development of new resistance mutations according to CD4 count at combination antiretroviral therapy initiation

Objectives: No randomized controlled trials have yet reported an individual patient benefit of initiating combination antiretroviral therapy (cART) at CD4 counts > 350 cells/μL. It is hypothesized that earlier initiation of cART in asymptomatic and otherwise healthy individuals may lead to poorer adherence and subsequently higher rates of resistance development. Methods: In a large cohort of HIV-positive individuals, we investigated the emergence of new resistance mutations upon virological treatment failure according to the CD4 count at the initiation of cART. Results: Of 7918 included individuals, 6514 (82.3%), 996 (12.6%) and 408 (5.2%) started cART with a CD4 count ≤ 350, 351-499 and ≥ 500 cells/μL, respectively. Virological rebound occurred while on cART in 488 (7.5%), 46 (4.6%) and 30 (7.4%) with a baseline CD4 count ≤ 350, 351-499 and ≥ 500 cells/μL, respectively. Only four (13.0%) individuals with a baseline CD4 count > 350 cells/μL in receipt of a resistance test at viral load rebound were found to have developed new resistance mutations. This compared to 107 (41.2%) of those with virological failure who had initiated cART with a CD4 count < 350 cells/μL. Conclusions: We found no evidence of increased rates of resistance development when cART was initiated at CD4 counts above 350 cells/μL. HIV Medicin

The Gene Ontology knowledgebase in 2023

The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins and noncoding RNAs). GO annotations cover genes from organisms across the tree of life as well as viruses, though most gene function knowledge currently derives from experiments carried out in a relatively small number of model organisms. Here, we provide an updated overview of the GO knowledgebase, as well as the efforts of the broad, international consortium of scientists that develops, maintains, and updates the GO knowledgebase. The GO knowledgebase consists of three components: (1) the GO-a computational knowledge structure describing the functional characteristics of genes; (2) GO annotations-evidence-supported statements asserting that a specific gene product has a particular functional characteristic; and (3) GO Causal Activity Models (GO-CAMs)-mechanistic models of molecular "pathways" (GO biological processes) created by linking multiple GO annotations using defined relations. Each of these components is continually expanded, revised, and updated in response to newly published discoveries and receives extensive QA checks, reviews, and user feedback. For each of these components, we provide a description of the current contents, recent developments to keep the knowledgebase up to date with new discoveries, and guidance on how users can best make use of the data that we provide. We conclude with future directions for the project

Genetic mechanisms of critical illness in COVID-19.

Host-mediated lung inflammation is present1, and drives mortality2, in the critical illness caused by coronavirus disease 2019 (COVID-19). Host genetic variants associated with critical illness may identify mechanistic targets for therapeutic development3. Here we report the results of the GenOMICC (Genetics Of Mortality In Critical Care) genome-wide association study in 2,244 critically ill patients with COVID-19 from 208 UK intensive care units. We have identified and replicated the following new genome-wide significant associations: on chromosome 12q24.13 (rs10735079, P = 1.65 × 10-8) in a gene cluster that encodes antiviral restriction enzyme activators (OAS1, OAS2 and OAS3); on chromosome 19p13.2 (rs74956615, P = 2.3 × 10-8) near the gene that encodes tyrosine kinase 2 (TYK2); on chromosome 19p13.3 (rs2109069, P = 3.98 ×  10-12) within the gene that encodes dipeptidyl peptidase 9 (DPP9); and on chromosome 21q22.1 (rs2236757, P = 4.99 × 10-8) in the interferon receptor gene IFNAR2. We identified potential targets for repurposing of licensed medications: using Mendelian randomization, we found evidence that low expression of IFNAR2, or high expression of TYK2, are associated with life-threatening disease; and transcriptome-wide association in lung tissue revealed that high expression of the monocyte-macrophage chemotactic receptor CCR2 is associated with severe COVID-19. Our results identify robust genetic signals relating to key host antiviral defence mechanisms and mediators of inflammatory organ damage in COVID-19. Both mechanisms may be amenable to targeted treatment with existing drugs. However, large-scale randomized clinical trials will be essential before any change to clinical practice

Measurement of the inclusive isolated-photon cross section in pp collisions at √s = 13 TeV using 36 fb−1 of ATLAS data

The differential cross section for isolated-photon production in pp collisions is measured at a centre-of-mass energy of 13 TeV with the ATLAS detector at the LHC using an integrated luminosity of 36.1 fb. The differential cross section is presented as a function of the photon transverse energy in different regions of photon pseudorapidity. The differential cross section as a function of the absolute value of the photon pseudorapidity is also presented in different regions of photon transverse energy. Next-to-leading-order QCD calculations from Jetphox and Sherpa as well as next-to-next-to-leading-order QCD calculations from Nnlojet are compared with the measurement, using several parameterisations of the proton parton distribution functions. The predictions provide a good description of the data within the experimental and theoretical uncertainties. [Figure not available: see fulltext.