Modeling of Exoplanet Atmospheres

Spectrally characterizing exoplanet atmospheres will be one of the fastest moving astronomical disciplines in the years to come. Especially the upcoming James Webb Space Telescope (JWST) will provide spectral measurements from the near- to mid-infrared of unprecedented precision. With other next generation instruments on the horizon, it is crucial to possess the tools necessary for interpretating observations. To this end I wrote the petitCODE, which solves for the self-consistent atmospheric structures of exoplanets, assuming chemical and radiative-convective equilibrium. The code includes scattering, and models clouds. The code outputs the planet’s observable emission and transmission spectra. In addition, I constructed a spectral retrieval code, which derives the full posterior probability distribution of atmospheric parameters from observations. I used petitCODE to systematically study the atmospheres of hot jupiters and found, e.g., that their structures depend strongly on the type of their host stars. Moreover, I found that C/O ratios around unity can lead to atmospheric inversions. Next, I produced synthetic observations of prime exoplanet targets for JWST, and studied how well we will be able to distinguish various atmospheric scenarios. Finally, I verified the implementation of my retrieval code using mock JWST observations

A Region at the C-Terminus of the <i>Escherichia coli</i> Global Transcription Factor FNR Negatively Mediates Its Degradation by the ClpXP Protease

The anaerobic global regulator FNR from <i>Escherichia coli</i> is a [4Fe-4S]²⁺ cluster-containing dimer that is inactivated by O₂ through disruption of the Fe–S cluster and conversion to the monomeric apoprotein. It was shown that apo-FNR is subject to ClpXP proteolysis, and two recognition sites, amino acids 5–11 and amino acids 249 and 250, are responsible for targeting FNR to the protease. However, how the exposure of these sites is mediated such that only apo-FNR is recognized by the ClpXP protease and is degraded in a regulated manner so that a sufficient and similar FNR level is maintained in both anaerobic and aerobic conditions is unknown. To investigate this, we performed three-alanine scanning on amino acids 2–19 and 236–250 that are in the proximity of the two ClpXP recognition sites, and their functions remain unknown. We found that three-alanine substitution of residues 239–241 (LAQ239–241A₃) and 242–244 (LAG242–244A₃) caused reduced FNR protein levels, transcription activities, and growth rates under anaerobic conditions. In vivo degradation assays demonstrated that these mutants were degraded significantly faster than the wild type (WT), and either deletion of <i>clpXP</i> or blocking the ClpXP recognition site of amino acids 249 and 250 stabilizes these proteins. Circular dichroism analysis revealed that introduction of LAQ239–241A₃ caused conformational changes with a significant loss of secondary structures in both WT and an O₂ stable FNR dimer, FNR D154A. We propose that the region of amino acids 239–244 plays a negative role in the proteolysis of FNR by promoting a structural fold that limits the exposure of the proximal ClpXP site to the protease

sj-pdf-1-smm-10.1177_09622802221129042 - Supplemental material for Standardization of continuous and categorical covariates in sparse penalized regressions

Supplemental material, sj-pdf-1-smm-10.1177_09622802221129042 for Standardization of continuous and categorical covariates in sparse penalized regressions by Xiang Li, Yong Ma and Qing Pan in Statistical Methods in Medical Research</p

Statistical Procedures for Assessing the Need for an Affirmative Action Plan: A Reanalysis of <i>Shea v. Kerry</i>

In the 1980s, reports from Congress and the Government Accountability Office (GAO) presented statistical evidence showing that employees in the Foreign Service were overwhelmingly White male, especially in the higher positions. To remedy this historical discrimination, the State Department instituted an affirmative action plan during 1990–1992 that allowed females and race-ethnic minorities to apply directly for mid-level positions. A White male employee claimed that he had been disadvantaged by the plan. The appellate court unanimously held that the manifest statistical imbalance supported the Department’s instituting the plan. One judge identified two statistical issues in the analysis of the data that neither party brought up. This article provides an empirical guideline for sample size and a one-sided Hotelling’s T2 test to answer these problems. First, an approximate rule is developed for the minimum number of expected minority appointments needed for a meaningful statistical analysis of under-representation. To avoid the multiple comparison issue when several protected groups are involved, a modification of Hotelling’s T2 test is developed for testing the null hypothesis of fair representation against a one-sided alternative of under-representation in at least one minority group. The test yields p-values less than 1 in 10,000 indicating that minorities were substantially under-represented. Excluding secretarial and clerical jobs led to even larger disparities. Supplemental materials for this article are available online.</p

MOESM1 of Woody forages effect the intestinal bacteria diversity of golden pompano Trachinotus ovatus

Additional file 1. Additional table

Synthesis and Dehydration Activity of Novel Lewis Acidic Ordered Mesoporous Silicate: Zr-KIT‑6

A zirconium-incorporated <i>Ia</i>3<i>d</i> cubic three-dimensional (3-D) mesoporous silicate, KIT-6, with different zirconium loadings, was synthesized via a one-step direct hydrothermal synthesis procedure employing Pluronic P123 triblock copolymer as the structure-directing agent under acidic conditions. Various characterization techniques, such as two-dimensional (2-D) small-angle X-ray scattering (SAXS), nitrogen sorption, temperature-programmed desorption of ammonia (NH₃-TPD), and ultraviolet–visible-light (UV-Vis) spectra, showed that zirconium was incorporated as Zr⁴⁺ ions in the KIT-6 framework, which retained the structural integrity with a highly ordered pore structure. The Zr-KIT-6 materials exhibit very high surface areas (810–980 m²/g) and large pore volumes (1.07–1.65 cm³/g) that decrease with an increase in zirconium content. In contrast, the pore size distribution remains relatively unaffected by zirconium loading with an average pore diameter of ∼9.3 nm. The Zr-KIT-6 materials possess Lewis acidity that increases with zirconium loading. In the 180–300 °C range, the Zr-KIT-6 materials are shown to be highly active for the test reaction of isopropanol (IPA) dehydration to propylene (selectivity >98%). The activation energy for IPA dehydration, estimated from intrinsic rate constants normalized with respect to the Lewis acid sites, was ∼49 ± 1 kJ/mol and found to be lower than most other Brønsted or Lewis acidic heterogeneous catalysts reported in the literature for IPA dehydration. Furthermore, these catalysts showed nearly stable activity with very little deactivation during extended runs at 260 and 300 °C

Additional file 1 of Molecular characterization of the FCoV-like canine coronavirus HLJ-071 in China

Additional file 1: Table S1. Primers used for identifying and completely sequencing the strain

Additional file 2 of Molecular characterization of the FCoV-like canine coronavirus HLJ-071 in China

Additional file 2: Table S2. RNA copies (log10(CoV genome copies per 103 GAPDH copies)) of template in the samples of dead puppy, tested by specific real time RT-PC

Time-resolved mid-infrared dual-comb spectroscopy

Dual-comb spectroscopy can provide broad spectral bandwidth and high spectral resolution in a short acquisition time, enabling time-resolved measurements. Specifically, spectroscopy in the mid-infrared wavelength range is of particular interest, since most of the molecules have their strongest rotational-vibrational transitions in this "fingerprint" region. Here we report time-resolved mid-infrared dual-comb spectroscopy for the first time, covering ~300 nm bandwidth around 3.3 {\mu}m with 6 GHz spectral resolution and 20 {\mu}s temporal resolution. As a demonstration, we study a CH4/He gas mixture in an electric discharge, while the discharge is modulated between dark and glow regimes. We simultaneously monitor the production of C2H6 and the vibrational excitation of CH4 molecules, observing the dynamics of both processes. This approach to broadband, high-resolution, and time-resolved mid-infrared spectroscopy provides a new tool for monitoring the kinetics of fast chemical reactions, with potential applications in various fields such as physical chemistry and plasma/combustion analysis

Canonical and non-canonical HERVs on human non-coding region and their relationships with cancer.

(A) the relationship between 357 canonical HERV element on human non-coding region and cancers. The CIRCOS plot shows the number of SNVs in each canonical HERV element within human non-coding region and how they are associated with multiple cancer types. The proportion of Gamma-retrovirus/Epsilon-retrovirus-related canonical HERV elements which includes HERV-H/LTR7, HERV-9/LTR12, HERV-IP10F/LTR10F and HUERSP/MER52/LTR25 is close 60%. They are associated with multiple cancer types including skin cancer, esophageal cancer, and breast cancer. The proportion of Alpha-retrovirus/ Beta-retrovirus-related canonical HERV elements which includes HML-8/HERVK11I/MER11A is close 42%. They are associated with multiple cancer types including skin cancer. The proportion of Spumavirus-related canonical HERV elements which includes HERV-L/MLT2 is close 93.7%. They are associated with multiple cancer types including skin cancer. (B) the relationship between 431 non-canonical HERV element on human non-coding region and cancers. The CIRCOS plot shows the number of SNVs in each non-canonical HERV element within non-coding region and how they are associated with multiple cancer types. The proportion of Gamma-retrovirus/Epsilon-retrovirus-related non-canonical HERV elements which includes HERVH/LTR7, HERV9/LTR12 and HERV-IP10F/LTR10F is close 63% and their association with multiple cancer types including skin cancer, esophageal cancer, and breast cancer. The proportion of Alpha-retrovirus/ Beta-retrovirus-related canonical HERV elements which includes HML-3/HERVK9I/MER9 is close to 37%. The proportion of Spumavirus-related canonical HERV elements which includes HERV-L/MLT2 is close to 62.7%. They are found in multiple cancer types including skin cancer. Please note that all HERVs nomenclatures are presented by supergroups and see their relative/similar element in S2 Table and that three HERVs minor supergroups (MER52, THE, and HARLEQUIN) which present in the Fig 3 are listed in S2 Table.</p