Handling Overlapping Asymmetric Data Sets—A Twice Penalized P-Spline Approach

\ua9 2024 by the authors.Aims: Overlapping asymmetric data sets are where a large cohort of observations have a small amount of information recorded, and within this group there exists a smaller cohort which have extensive further information available. Missing imputation is unwise if cohort size differs substantially; therefore, we aim to develop a way of modelling the smaller cohort whilst considering the larger. Methods: Through considering traditionally once penalized P-Spline approximations, we create a second penalty term through observing discrepancies in the marginal value of covariates that exist in both cohorts. Our now twice penalized P-Spline is designed to firstly prevent over/under-fitting of the smaller cohort and secondly to consider the larger cohort. Results: Through a series of data simulations, penalty parameter tunings, and model adaptations, our twice penalized model offers up to a 58% and 46% improvement in model fit upon a continuous and binary response, respectively, against existing B-Spline and once penalized P-Spline methods. Applying our model to an individual’s risk of developing steatohepatitis, we report an over 65% improvement over existing methods. Conclusions: We propose a twice penalized P-Spline method which can vastly improve the model fit of overlapping asymmetric data sets upon a common predictive endpoint, without the need for missing data imputation

Comments on alternative calculations of the broadening of spectral lines of neutral sodium by H-atom collisions

With the exception of the sodium D-lines recent calculations of line broadening cross-sections for several multiplets of sodium by Leininger et al (2000) are in substantial disagreement with cross-sections interpolated from the tables of Anstee and O'Mara (1995) and Barklem and O'Mara (1997). The discrepancy is as large as a factor of three for the 3p-4d multiplet. The two theories are tested by using the results of each to synthesize lines in the solar spectrum. It is found that generally the data from the theory of Anstee, Barklem and O'Mara produce the best match to the observed solar spectrum. It is found, using a simple model for reflection of the optical electron by the potential barrier between the two atoms, that the reflection coefficient is too large for avoided crossings with the upper states of subordinate lines to contribute to line broadening, supporting the neglect of avoided ionic crossings by Anstee, Barklem and O'Mara for these lines. The large discrepancies between the two sets of calculations is a result of an approximate treatment of avoided ionic crossings for these lines by Leininger et al (2000).Comment: 18 pages, 5 ps figures included, to appear in J Phys B: At. Mol. Opt. Phy

First-Digit Law in Nonextensive Statistics

Nonextensive statistics, characterized by a nonextensive parameter $q$, is a promising and practically useful generalization of the Boltzmann statistics to describe power-law behaviors from physical and social observations. We here explore the unevenness of the first digit distribution of nonextensive statistics analytically and numerically. We find that the first-digit distribution follows Benford's law and fluctuates slightly in a periodical manner with respect to the logarithm of the temperature. The fluctuation decreases when $q$ increases, and the result converges to Benford's law exactly as $q$ approaches 2. The relevant regularities between nonextensive statistics and Benford's law are also presented and discussed.Comment: 11 pages, 3 figures, published in Phys. Rev.

Optimal General Matchings

Given a graph $G=(V,E)$ and for each vertex $v \in V$ a subset $B(v)$ of the set $\{0,1,\ldots, d_G(v)\}$, where $d_G(v)$ denotes the degree of vertex $v$ in the graph $G$, a $B$-factor of $G$ is any set $F \subseteq E$ such that $d_F(v) \in B(v)$ for each vertex $v$, where $d_F(v)$ denotes the number of edges of $F$ incident to $v$. The general factor problem asks the existence of a $B$-factor in a given graph. A set $B(v)$ is said to have a {\em gap of length} $p$ if there exists a natural number $k \in B(v)$ such that $k+1, \ldots, k+p \notin B(v)$ and $k+p+1 \in B(v)$. Without any restrictions the general factor problem is NP-complete. However, if no set $B(v)$ contains a gap of length greater than $1$, then the problem can be solved in polynomial time and Cornuejols \cite{Cor} presented an algorithm for finding a $B$-factor, if it exists. In this paper we consider a weighted version of the general factor problem, in which each edge has a nonnegative weight and we are interested in finding a $B$-factor of maximum (or minimum) weight. In particular, this version comprises the minimum/maximum cardinality variant of the general factor problem, where we want to find a $B$-factor having a minimum/maximum number of edges. We present an algorithm for the maximum/minimum weight $B$-factor for the case when no set $B(v)$ contains a gap of length greater than $1$. This also yields the first polynomial time algorithm for the maximum/minimum cardinality $B$-factor for this case

The Carina Project. V. The impact of NLTE effects on the iron content

We have performed accurate iron abundance measurements for 44 red giants (RGs) in the Carina dwarf spheroidal (dSph) galaxy. We used archival, high-resolution spectra (R~38,000) collected with UVES at ESO/VLT either in slit mode (5) or in fiber mode (39, FLAMES/GIRAFFE-UVES). The sample is more than a factor of four larger than any previous spectroscopic investigation of stars in dSphs based on high-resolution (R>38,000) spectra. We did not impose the ionization equilibrium between neutral and singly-ionized iron lines. The effective temperatures and the surface gravities were estimated by fitting stellar isochrones in the V, B-V color-magnitude diagram. To measure the iron abundance of individual lines we applied the LTE spectrum synthesis fitting method using MARCS model atmospheres of appropriate metallicity. We found evidence of NLTE effects between neutral and singly-ionized iron abundances. Assuming that the FeII abundances are minimally affected by NLTE effects, we corrected the FeI stellar abundances using a linear fit between FeI and FeII stellar abundance determinations. We found that the Carina metallicity distribution based on the corrected FeI abundances (44 RGs) has a weighted mean metallicity of [Fe/H]=-1.80 and a weighted standard deviation of sigma=0.24 dex. The Carina metallicity distribution based on the FeII abundances (27 RGs) gives similar estimates ([Fe/H]=-1.72, sigma=0.24 dex). The current weighted mean metallicities are slightly more metal poor when compared with similar estimates available in the literature. Furthermore, if we restrict our analysis to stars with the most accurate iron abundances, ~20 FeI and at least three FeII measurements (15 stars), we found that the range in iron abundances covered by Carina RGs (~1 dex) agrees quite well with similar estimates based on high-resolution spectra.Comment: Accepted for publication in PASP, 16 pages, 7 figures, 3 tables, 1 MR table Note: the electronic version of Table1 is included, but commented, in the tex fil

Stellar Iron Abundances: non-LTE Effects

We report new statistical equilibrium calculations for Fe I and Fe II in the atmosphere of Late-Type stars. We used atomic models for Fe I and Fe II having respectively 256 and 190 levels, as well as 2117 and 3443 radiative transitions. Photoionization cross-sections are from the Iron Project. These atomic models were used to investigate non-LTE effects in iron abundances of Late-Type stars with different atmospheric parameters. We found that most Fe I lines in metal-poor stars are formed in conditions far from LTE. We derived metallicity corrections of about 0.3 dex with respect to LTE values, for the case of stars with [Fe/H] ~ -3.0. Fe II is found not to be affected by significant non-LTE effects. The main non-LTE effect invoked in the case of Fe I is overionization by ultraviolet radiation, thus classical ionization equilibrium is far to be satisfied. An important consequence is that surface gravities derived by LTE analysis are in error and should be corrected before final abundances corrections. This apparently solves the observed discrepancy between spectroscopic surface gravities derived by LTE analyses and those derived from Hipparcos parallaxes. A table of non-LTE [Fe/H] and log g values for a sample of metal-poor late-type stars is given.Comment: 22 pages, 9 figures, 1 table, ApJ style, accepte

Pharmacogene expression during progression of metabolic dysfunction-associated steatotic liver disease: Studies on mRNA and protein levels and their relevance to drug treatment

\ua9 2024. Metabolic dysfunction-associated steatotic liver disease (MASLD) is common worldwide. Genes and proteins contributing to drug disposition may show altered expression as MASLD progresses. To assess this further, we undertook transcriptomic and proteomic analysis of 137 pharmacogenes in liver biopsies from a large MASLD cohort. We performed sequencing on RNA from 216 liver biopsies (206 MASLD and 10 controls). Untargeted mass spectrometry proteomics was performed on a 103 biopsy subgroup. Selected RNA sequencing signals were replicated with an additional 187 biopsies. Comparison of advanced MASLD (fibrosis score 3/4) with milder disease (fibrosis score 0–2) by RNA sequencing showed significant alterations in expression of certain phase I, phase II and ABC transporters. For cytochromes P450, CYP2C19 showed the most significant decreased expression (30 % of that in mild disease) but significant decreased expression of other CYPs (including CYP2C8 and CYP2E1) also occurred. CYP2C19 also showed a significant decrease comparing the inflammatory form of MASLD (MASH) with non-MASH biopsies. Findings for CYP2C19 were confirmed in the replication cohort. Proteomics on the original discovery cohort confirmed decreased levels of several CYPs as MASLD advanced but this decrease was greatest for CYP2C19 where levels fell to 40 % control. This decrease may result in decreased CYP2C19 activity that could be problematic for prescription of drugs activated or metabolized by CYP2C19 as MASLD advances. More limited decreases for other P450s suggest fewer issues with non-CYP2C19 drug substrates. Negative correlations at RNA level between CYP2C19 and several cytokine genes provided initial insights into the mechanism underlying decreased expression