bluuebunny/crossref_metadata_2025_split huggingface dataset:
Detecting directional epistasis and dominance from cross-line analyses in alpine populations of Arabidopsis thaliana
Authors: Le Rouzic Arnaud , Roumet Marie , Widmer Alex , Clo Josselin 
Published: May 2024

Abstract
The contribution of non-additive genetic effects to the genetic architecture of fitness and to the evolutionary potential of populations has been a topic of theoretical and empirical interest for a long time. Yet, the empirical study of these effects in natural populations remains scarce, perhaps because measuring dominance and epistasis relies heavily on experimental line crosses. In this study, we explored the contribution of dominance and epistasis in natural alpine populations of Arabidopsis thaliana for 2 fitness traits, the dry biomass and the estimated number of siliques, measured in a greenhouse. We found that, on average, crosses between inbred lines of A. thaliana led to mid-parent heterosis for dry biomass but outbreeding depression for an estimated number of siliques. While heterosis for dry biomass was due to dominance, we found that outbreeding depression for an estimated number of siliques could be attributed to the breakdown of beneficial epistatic interactions. We simulated and discussed the implication of these results for the adaptive potential of the studied populations, as well as the use of line-cross analyses to detect non-additive genetic effects.
Drift drives the evolution of chromosome number II: The impact of range size on genome evolution in Carnivora
Authors: Jonika Michelle M , Wilhoit Kayla T , Chin Maximos , Arekere Abhimanyu , Blackmon Heath 
Published: May 2024

Abstract
Chromosome number is a fundamental genomic trait that is often the first recorded characteristic of a genome. Across large clades, a common pattern emerges: many or even most lineages exhibit relative stasis, while a handful of lineages or species exhibit striking variation. Despite recent developments in comparative methods, most of this heterogeneity is still poorly understood. It is essential to understand why some lineages have rapid rates of chromosome number evolution, as it can impact a variety of other traits. Previous research suggests that biased female meiotic drive may shape rates of karyotype evolution in some mammals. However, Carnivora exhibits variation that this female meiotic drive model cannot explain. We hypothesize that variation in effective population size may underlie rate variation in Carnivora. To test this hypothesis, we estimated rates of fusions and fissions while accounting for range size, which we use as a proxy for effective population size. We reason fusions and fissions are deleterious or underdominant and that only in lineages with small range sizes will these changes be able to fix due to genetic drift. In this study, we find that the rates of fusions and fissions are elevated in taxa with small range sizes relative to those with large range sizes. Based on these findings, we conclude that 1) naturally occurring structural mutations that change chromosome number are underdominant or mildly deleterious, and 2) when population sizes are small, structural rearrangements may play an important role in speciation and reduction in gene flow among populations.
Incidence and risk factors of PICC-related thrombosis in breast cancer: a meta-analysis
Authors: Meng Fanlun , Fan Shujun , Guo Lingmin , Jia Zhongfeng , Chang Hongjun , Liu Feng 
Published: May 2024

Abstract

Background
The incidence and risk factors of peripherally inserted central catheter-related thrombosis in patients with breast cancer have not been fully elucidated.

Method
Meta-analysis was performed by searching all studies on the incidence of peripherally inserted central catheter-associated thrombosis and risk factors for its formation in breast cancer patients from the establishment of the database to May 2023, including PubMed, Embase, Web of Science, China Knowledge Network, China Biomedical Literature Service System (SinoMed) and Wanfang databases. Then the incidence of peripherally inserted central catheter-related thrombosis and risk factors for its formation were analyzed in breast cancer patients.

Results
A total of 15 articles were included, involving 8635 patients. The total incidence of peripherally inserted central catheter-related thrombosis in breast cancer patients was 7.0% (95% confidence interval: 4.0–13.0%) and 12.9% (95% confidence interval: 7.0–22.5%) after correction. Thirty-two risk factors were included, and eight risk factors could be combined. Among these risk factors, there were statistically significant differences (P &lt; 0.05) in body mass index ≥ 25 (odds ratio = 6.319, 95% confidence interval: 2.733–14.613; P &lt; 0.001), D-dimer &gt;500 ng/ml (odds ratio = 1.436, 95% confidence interval: 1.113–1.854; P = 0.005), increased fibrinogen (odds ratio = 4.733, 95% confidence interval: 1.562–14.346; P = 0.006), elevated platelet count (odds ratio = 4.134, 95% confidence interval: 2.694–6.346; P &lt; 0.001) and catheter malposition (odds ratio = 8.475, 95% confidence interval: 2.761–26.011; P &lt; 0.001).

Conclusion
The incidence rate of peripherally inserted central catheter-related thrombosis in breast cancer patients was 7.0% (95% confidence interval: 4.0–13.0%). Body mass index ≥ 25, D-dimer &gt;500 ng/ml, elevated fibrinogen, elevated platelet count and catheter malposition were risk factors for peripherally inserted central catheter-related thrombosis in breast cancer patients.
IRG1/ACOD1 promotes neutrophil reverse migration and alleviates local inflammation
Authors: Ji Jingjing , Zhong Hanhui , Li Yuehua , Billiar Timothy R , Wilson Mark A , Scott Melanie J , Fan Jie 
Published: May 2024

Abstract
Polymorphonuclear neutrophil (PMN) infiltration at inflammatory site plays a critical role in inflammation. PMN reverse migration (rM) describes the phenomenon that PMNs migrate away from inflammatory site back into the vasculature, and its role within inflammatory scenarios remains to be fully determined. This study aimed to investigate the mechanism underlying PMN rM and its role in inflammation. First, we demonstrated PMN rM in a mouse model of lipopolysaccharide-induced acute lung inflammation. By single-cell RNA sequencing, we demonstrated that reverse migrated (rM-ed) PMNs in blood expressed a high level of immune-responsive gene 1 (Irg1), the encoding gene of cis-aconitate decarboxylase (ACOD1). Using a mouse air pouch model, which enabled us to directly track rM-ed PMNs in vivo, we detected higher expression of ACOD1 in the rM-ed PMNs in circulation. Furthermore, mice with Irg1 knockout exhibited decreased PMN rM and higher levels of inflammatory cytokine in inflammatory site. Mechanistically, we found that itaconate, the product of ACOD1 catalyzation, decreased PMN ICAM-1 expression at the inflammation site. Furthermore, inflammatory site showed a high level of shed Cd11a, the ligand of ICAM-1. Neutralization of either ICAM-1 or Cd11a led to increased PMN rM. These findings suggest that the binding of ICAM-1 and shed Cd11a serves as a retaining force to hold PMNs in the site of inflammation, and ACOD1-decreased PMN surface expression of ICAM-1 weakens the retaining force, promoting PMNs to leave the inflammatory site. These results indicate a regulatory role of IRG1 in PMN rM and subsequent contributions to inflammation resolution.
Recent and projected incidence trends and risk of anal cancer among people with HIV in North America
Authors: Deshmukh Ashish A , Lin Yueh-Yun , Damgacioglu Haluk , Shiels Meredith , Coburn Sally B , Lang Raynell , Althoff Keri N , Moore Richard , Silverberg Michael J , Nyitray Alan G , Chhatwal Jagpreet , Sonawane Kalyani , Sigel Keith 
Published: May 2024

Abstract

Background
Anal cancer risk is elevated among people with HIV. Recent anal cancer incidence patterns among people with HIV in the United States and Canada remain unclear. It is unknown how the incidence patterns may evolve.

Methods
Using data from the North American AIDS Cohort Collaboration on Research and Design, we investigated absolute anal cancer incidence and incidence trends nationally in the United States and Canada and in different US regions. We further estimated relative risk compared with people without HIV, relative risk among various subgroups, and projected future anal cancer burden among American people with HIV.

Results
Between 2001 and 2016 in the United States, age-standardized anal cancer incidence declined 2.2% per year (95% confidence interval = ‒4.4% to ‒0.1%), particularly in the Western region (‒3.8% per year, 95% confidence interval = ‒6.5% to ‒0.9%). In Canada, incidence remained stable. Considerable geographic variation in risk was observed by US regions (eg, more than 4-fold risk in the Midwest and Southeast compared with the Northeast among men who have sex with men who have HIV). Anal cancer risk increased with a decrease in nadir CD4 cell count and was elevated among those individuals with opportunistic illnesses. Anal cancer burden among American people with HIV is expected to decrease through 2035, but more than 70% of cases will continue to occur in men who have sex with men who have HIV and in people with AIDS.

Conclusion
Geographic variation in anal cancer risk and trends may reflect underlying differences in screening practices and HIV epidemic. Men who have sex with men who have HIV and people with prior AIDS diagnoses will continue to bear the highest anal cancer burden, highlighting the importance of precision prevention.
A Bayesian latent variable model for the optimal identification of disease incidence rates given information constraints
Authors: Kubinec Robert , Carvalho Luiz Max , Barceló Joan , Cheng Cindy , Messerschmidt Luca , Cottrell Matthew Sean 
Published: May 2024

Abstract
We present an original approach for measuring infections as a latent variable and making use of serological and expert surveys to provide ground truth identification during the early pandemic period. Compared to existing approaches, our model relies more on empirical information than strong structural forms, permitting inference with relatively few assumptions of cumulative infections. We also incorporate a range of political, economic, and social covariates to richly parameterize the relationship between epidemic spread and human behaviour. To show the utility of the model, we provide robust estimates of total infections that account for biases in COVID-19 cases and tests counts in the U.S. from March to July of 2020, a period of time when accurate data about the nature of the SARS-CoV-2 virus was of limited availability. In addition, we can show how sociopolitical factors like the Black Lives Matter protests and support for President Donald Trump are associated with the spread of the virus via changes in fear of the virus and cell phone mobility. A reproducible version of this article is available as an Rmarkdown file at https://github.com/CoronaNetDataScience/covid_model.
A bi-endpoint expectation-maximisation algorithm for re-estimating sample size for the time-to-event endpoint under the blind condition
Authors: Xie Longshen , Lu Hui 
Published: May 2024

Abstract
The expectation-maximisation (EM) algorithm can be used to adjust the sample size for the time-to-event endpoint without unblinding. Nevertheless, censoring or unreliable initial estimates may render inconsistent estimates by the EM algorithm. To address these limitations, we propose a bi-endpoint EM algorithm that incorporates the time-to-event endpoint and another endpoint, which can encompass various endpoint types and is not limited to efficacy indicators, during the EM iterations. Additionally, we suggest 2 approaches for choosing initial estimates. The application conditions are as follows: (i) at least one endpoint’s initial estimate is reliable and (ii) the influence of this endpoint on the posterior distribution of the latent variable exceeds that of another endpoint.
Genetics of phenological development and implications for seed yield in lentil
Authors: Lake Lachlan , Hayes Julie E , Ortega Martinez Raul , Weller Jim L , Javid Muhammad , Butler Jacob B , James Laura E , Gimenez Raul , Dreccer M Fernanda , French Robert , Sadras Victor O 
Published: May 2024

Abstract
Understanding phenology, its genetics and agronomic consequences, is critical for crop adaptation. Here we aim to (i) characterize lentil response to photoperiod with a focus on five loci: the lentil ELF3 orthologue Sn, two loci linked to clusters of lentil FT orthologues, and two loci without candidates in chromosomes 2 and 5 (Experiment 1: 36 lines, short and long days in a phytotron), and (ii) establish the phenology–yield relationship (Experiment 2: 25 lines, 11 field environments). A vintage perspective, where we quantify time trends in phenotype over three decades of breeding, links both experiments. Yield increased linearly from older to newer varieties at 29 kg ha–1 year–1 or 1.5% year–1, correlated negatively with flowering time in both winter- and summer-rainfall regimes, and decoupled from biomass in favourable environments. Time to flowering shortened from older to newer varieties at –0.56% year–1 in the field, and –0.42% year–1 (short days) and –0.99% year–1 (long days) in the phytotron. Early-flowering lines of diverse origin carried multiple early alleles for the five loci, indicating that at least some of these loci affect phenology additively. Current germplasm primarily features the early-flowering haplotype for an FTb cluster region, hence the potential to increase phenological diversity with yield implications.
Impact of a Mentorship Program to Prepare Medical Students for the Military Residency Match
Authors: Boedeker David , Hunkler Kiley , Strohm Samantha , Zamani Michael , Chatfield Lindsay , MacKinnon Rene , Shvartsman Katerina 
Published: May 2024

ABSTRACT

Introduction
Mentorship programs have well-documented benefits to both mentees and mentors. Military medical students face unique challenges in medical school given their service-specific requirements and separate military match process. We therefore aimed to determine whether military medical students’ participation in a mentorship program impacts their confidence in applying to obstetrics and gynecology (OB/GYN) residency.

Materials and Methods
First, a needs assessment survey regarding the use of a mentorship program was sent to medical students, residents, fellows, and attendings. A structured mentorship program was then developed for military medical students applying to OB/GYN residency based on the survey results. Mentors were randomly paired with mentees and asked to appraise curriculum vitaes, review personal statements, and perform mock interviews. Following completion of these activities, participants were sent a post-intervention questionnaire. This project was exempt by our institution’s Institutional Review Board.

Results
Our program had 56 participants, with 29 individuals completing our post-intervention survey (response rate 51.8%). After participating in the program, 92.3% of mentors stated they plan to continue a relationship with their mentee. All the mentee respondents stated they would participate in this program again. Before participating in the program, 16.7% of mentees felt “prepared” or “extremely prepared” for the match, compared to 87.6% post-intervention. Most mentee respondents (75%) reported that this program made them a more competitive applicant. Following the mentorship program, 66.7% of participants successfully matched into OB/GYN residency.

Conclusions
This reproducible, well-received intervention can be implemented to facilitate mentoring connections regardless of geographic location. As the OB/GYN specialty develops its own application process, civilian medical schools should consider adopting similar programs to aid their students in navigating the match process.
Presence of Epstein–Barr virus in cerebrospinal fluid is associated with increased mortality in HIV-negative cryptococcal meningitis
Authors: Lu Yi , Li Shubo , Su Zhihui , Luo Chongliang , Gu Meifeng , Yuan Dasen , Qin Bang-e , Dai Kai , Xia Han , Chen Yong , Peng Fuhua , Jiang Ying 
Published: May 2024

Abstract
Cryptococcus neoformans is the most common cause of fungal meningitis and is associated with a high mortality. The clinical significance of concurrent Epstein–Barr virus (EBV) in the cerebrospinal fluid (CSF) of human immunodeficiency virus (HIV)-negative patients with cryptococcal meningitis (CM) remains unclear.
A retrospective cohort study was performed by analyzing CSF samples from 79 HIV-negative Chinese Han patients with confirmed CM. We identified CSF viral DNA in these patients by metagenomic next-generation sequencing (mNGS) and compared 10-week survival rates among those with and without EBV DNA in CSF.
Of the 79 CSF samples tested, 44.3% (35/79) had detectable viral DNA in CSF, while 55.7% (44/79) were virus-negative. The most frequent viral pathogen was EBV, which was detected in 22.8% (18/79) patients. The median number of CSF-EBV DNA reads was 4 reads with a range from 1 to 149 reads. The 10-week mortality rates were 22.2% (4/18) in those with positive CSF-EBV and 2.3% (1/44) in those with negative CSF-virus (hazard ratio 8.20, 95% confidence interval [CI] 1.52-81.80; P = 0.014), which remained significant after a multivariate adjustment for the known risk factors of mortality (adjusted hazard ratio 8.15, 95% CI 1.14-92.87; P = 0.037).
mNGS can identify viruses that coexist in CSF of HIV-negative patients with CM. EBV DNA is most commonly found together with C. neoformans in CSF and its presence is associated with increased mortality in HIV-negative CM patients.
Detailed mapping of the Galactic disc structure in the solar neighbourhood through LAMOST K dwarfs
Authors: Tang Xi-Can , Tian Hao , Li Jing , Chen Bing-qiu , Chen Yi-Rong , Liu Chao , Qiu Dan 
Published: May 2024

ABSTRACT
The Galactic disc is one of the main components of the Milky Way, which contributes most of the luminosity. Its structure is essential for understanding the formation and evolution of the Milky Way. Using 174 443 K-type dwarf stars observed by both Large Sky Area Multi-Object Fiber Spectroscopic Telescope and Gaia Data Release 3, we study the disc density profile in the local volume within 1200 pc. In the azimuthal dimension, we find strong asymmetric signal of the thin disc. The surface density and the scale height of the southern disc significantly change versus the azimuthal angle at the same Galactocentric distance R. Meanwhile, in the vertical dimension, the scale height of the northern disc has quite different trend than that of the southern one. The scale height of the southern disc shows a decreasing trend with ϕ ∼ −2.5°, and change to an increasing one with ϕ ∼ 5.0°. Meanwhile, the scale height of the northern disc has a consistently smaller increase. Finally, we divide the entire sample into three subsamples based on metallicity and all three subsamples show significant non-axisymmetric and north–south asymmetric signals in the Galactic disc. Furthermore, we find that the scale height of the metal-poor ([Fe/H] &lt; −0.4 dex) subsample in the northern disc is greater than that of the metal-rich ([Fe/H] &gt; −0.1 dex) subsample. However, in the southern disc, the scale height exhibits varying relationships across different metallicity slices.
Orbital period change of SW Sex star TT Tri
Authors: Fang Xiaohui , Wang Qishan , Qian Shengbang 
Published: May 2024

ABSTRACT
SW Sex-type stars are the dominate population of cataclysmic variables (CVs) just above the period gap and are vital for understanding of CV evolution. We have monitored TT Tri for nearly 15 yr, and more observations yield a more reliable estimation for its orbital period variation. In this work, we present a detailed analysis about its orbital period variation. TT Tri experiences a rapid period decay with a decay rate of $-5.67\times 10^{-11}\, \mathrm{s/s}$ plus a period oscillation at about 9.6 yr. The oscillation could be caused by the magnetic activities of the low-mass star or/and a circumbinary body, while the rapid period decrease cannot be accounted for by the magnetic braking or even including an intensive disc wind. We find that mass overflow though the L3 point can take the angular momentum away effectively and that this mass overflow could account for the rapid period decay observed in TT Tri. We propose that this kind of angular momentum loss may play a crucial role in CV evolution, and further research is in progress.
The case for hot-mode accretion in Abell 2029
Authors: Prasad Deovrat , Voit G Mark , O’Shea Brian W 
Published: May 2024

ABSTRACT
Radiative cooling and active galactic nucleus heating are thought to form a feedback loop that regulates the evolution of low-redshift cool-core galaxy clusters. Numerical simulations suggest that the formation of multiphase gas in the cluster core imposes a floor on the ratio of cooling time (tcool) to free-fall time (tff) at min(tcool/tff) ≈ 10. Observations of galaxy clusters show evidence for such a floor, and usually the cluster cores with min(tcool/tff) ≲ 30 contain abundant multiphase gas. However, there are important outliers. One of them is Abell 2029 (A2029), a massive galaxy cluster (M200 ≳ 1015 M⊙) with min(tcool/tff) ∼ 20, but little apparent multiphase gas. In this paper, we present high-resolution 3D hydrodynamic adaptive mesh refinement simulations of a cluster similar to A2029 and study how it evolves over a period of 1–2 Gyr. Those simulations suggest that A2029 self-regulates without producing multiphase gas because the mass of its central black hole (${\sim} 5 \times 10^{10} \, \mathrm{ M}_\odot$) is great enough for Bondi accretion of hot ambient gas to produce enough feedback energy to compensate for radiative cooling.
Asymmetric drift in MaNGA: mass and radially dependent stratification rates in galaxy discs
Authors: Bershady Matthew A , Westfall Kyle B , Shetty Shravan , Law David R , Cappellari Michele , Drory Niv , Bundy Kevin , Yan Renbin 
Published: May 2024

ABSTRACT
We measure the age–velocity relationship from the lag between ionized gas and stellar tangential speeds in ∼500 nearby disc galaxies from MaNGA in Sloan Digital Sky Survey IV (SDSS-IV). Selected galaxies are kinematically axisymmetric. Velocity lags are asymmetric drift, seen in the Milky Way’s (MW) solar neighbourhood and other Local Group galaxies; their amplitude correlates with stellar population age. The trend is qualitatively consistent in rate ($\dot{\sigma }$) with a simple power-law model where σ ∝ tb that explains the dynamical phase-space stratification in the solar neighbourhood. The model is generalized based on disc dynamical times to other radii and other galaxies. We find in-plane radial stratification parameters σ0,r (dispersion of the youngest populations) in the range of 10–40 km s−1 and 0.2 &lt; br &lt; 0.5 for MaNGA galaxies. Overall, brincreases with galaxy mass, decreases with radius for galaxies above 10.4 dex (M⊙) in stellar mass, but is ∼constant with radius at lower mass. The measurement scatter indicates the stratification model is too simple to capture the complexity seen in the data, unsurprising given the many possible astrophysical processes that may lead to stellar population dynamical stratification. None the less, the data show dynamical stratification is broadly present in the galaxy population, with systematic trends in mass and density. The amplitude of the asymmetric drift signal is larger for the MaNGA sample than the MW, and better represented in the mean by what is observed in the discs of M31 and M33. Either typical discs have higher surface-density or, more likely, are dynamically hotter (hence thicker) than the MW.