bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ethics of artificial intelligence in embryo assessment: mapping the terrain
Authors: Koplin Julian J , Johnston Molly , Webb Amy N S , Whittaker Andrea , Mills Catherine 
Published: December 2024

Abstract
Artificial intelligence (AI) has the potential to standardize and automate important aspects of fertility treatment, improving clinical outcomes. One promising application of AI in the fertility clinic is the use of machine learning (ML) tools to assess embryos for transfer. The successful clinical implementation of these tools in ways that do not erode consumer trust requires an awareness of the ethical issues that these technologies raise, and the development of strategies to manage any ethical concerns. However, to date, there has been little published literature on the ethics of using ML in embryo assessment. This mini-review contributes to this nascent area of discussion by surveying the key ethical concerns raised by ML technologies in healthcare and medicine more generally, and identifying which are germane to the use of ML in the assessment of embryos. We report concerns about the ‘dehumanization’ of human reproduction, algorithmic bias, responsibility, transparency and explainability, deskilling, and justice.
Preoperative interatrial block is associated with postoperative atrial fibrillation after cardiac surgery
Authors: Leiler Spela , Bauer Andre , Hitzl Wolfgang , Bernik Rok , Guenzler Valentin , Angerer Matthias , Fischlein Theodor , Kalisnik Jurij Matija 
Published: December 2024

Abstract

OBJECTIVES
Atrial fibrillation is common complication after heart surgery potentially leading to chronic atrial fibrillation, heart failure, and mortality. The aim of this study was to explore the relationship between preoperative interatrial block and the occurrence of postoperative atrial fibrillation.

METHODS
Perioperative 12-channel ECGs of patients in sinus rhythm, scheduled for heart surgery including bypass and/or valve surgery were analysed. Patients with pre-existing atrial fibrillation, amiodarone therapy, atrioventricular block II or III, or pacemaker were excluded from the study. Clinical parameters in patients with vs without atrial fibrillation were compared. To evaluate the association between interatrial block and postoperative atrial fibrillation univariable and multivariable regression analysis was performed.

RESULTS
Out of 2374 patients, 1350 were amenable to analysis. Postoperative atrial fibrillation was documented in 505 (37.4%). In multivariable regression analysis prediction models with and without interatrial block were established. Step-wise regression analysis identified interatrial block (2.64[2.02; 3.46], p &lt; 0.001), age (1.11[1.03; 1.20], p = 0.007), EuroScore II (1.05[1.03; 1.07], p &lt; 0.001), pulmonary hypertension (1.91[1.24; 2.97], p = 0.006), history of cardiogenic shock (2.05[1.11; 3.87], p = 0.032), statins (1.66[1.21; 2.27], p = 0.002), COPD (2.11[1.25; 3.65], p = 0.009), and cardiopulmonary bypass time (1.78[1.04; 3.05], p = 0.047) as independent predictors for postoperative atrial fibrillation.

CONCLUSIONS
Preoperative interatrial block was associated with higher incidence of postoperative atrial fibrillation. Inclusion of ECG-derived preoperative conduction disturbances can enhance risk stratification of postoperative atrial fibrillation after heart surgery.
Bilirubin reductase shows host-specific associations in animal large intestines
Authors: Dufault-Thompson Keith , Levy Sophia , Hall Brantley , Jiang Xiaofang 
Published: December 2024

Abstract
Animal gastrointestinal tracts contain diverse metabolites, including various host-derived compounds that gut-associated microbes interact with. Here, we explore the diversity and evolution of bilirubin reductase, a bacterial enzyme that metabolizes the host-derived tetrapyrrole bilirubin, performing a key role in the animal heme degradation pathway. Through an analysis of the bilirubin reductase phylogeny and predicted structures, we found that the enzyme family can be divided into three distinct clades with different structural features. Using these clade definitions, we analyzed metagenomic sequencing data from multiple animal species, finding that bilirubin reductase is significantly enriched in the large intestines of animals and that the clades exhibit differences in distribution among animals. Combined with phylogenetic signal analysis, we find that the bilirubin reductase clades exhibit significant associations with specific animals and animal physiological traits like gastrointestinal anatomy and diet. These patterns demonstrate that bilirubin reductase is specifically adapted to the anoxic lower gut environment of animals and that its evolutionary history is complex, involving adaptation to a diverse collection of animals harboring bilirubin-reducing microbes. The findings suggest that bilirubin reductase evolution has been shaped by the host environment, providing a new perspective on heme metabolism in animals and highlighting the importance of the microbiome in animal physiology and evolution.
Side effects associated with itraconazole therapy
Authors: Osborn Matthew R , Zuniga-Moya Julio C , Mazi Patrick B , Rauseo Adriana M , Spec Andrej 
Published: December 2024

Abstract

Background
Itraconazole is the treatment of choice for many fungal infections, including histoplasmosis. While the tolerability of itraconazole has been described in short-term trial settings, there are few studies on side effects during long-term therapy. Fluconazole, which is usually thought to be less toxic, is associated with 52% toxicity in long-term treatment.

Objectives
To determine the frequency, types, and timing of side effects from itraconazole therapy, the resulting changes to treatment plans, and associations between patient characteristics and itraconazole serum levels with side effect status.

Methods
We conducted a single-centre, retrospective study of adult patients with histoplasmosis receiving itraconazole therapy for at least 28 days from 2002 to 2021. Reported side effects were characterized, and propensity score matching was used to compare itraconazole serum levels between patients with and without side effects.

Results
Sixty-three out of 227 (27.8%) patients experienced at least one side effect, the most common of which were hepatotoxicity (7.0%), nausea/vomiting (6.6%), and diarrhoea (6.2%). 12 (19.0%) patients with side effects underwent an itraconazole dose reduction and 29 (46.0%) had itraconazole discontinued. The median time to side effect was 45 days. Median itraconazole serum levels were significantly higher among patients with side effects than in a propensity score-matched population without side effects (2.9 versus 1.8 mcg/mL, P = 0.009).

Conclusions
Side effects were experienced by approximately one-quarter of patients with histoplasmosis receiving long-term itraconazole therapy. About two-thirds of these patients had a therapeutic intervention. Itraconazole resulted in a lower frequency of side effects than fluconazole, as measured in other studies.
Integrated electronic health record tools to access real-world data in oncology research
Authors: Casagni Michelle , Llewellyn Nicole , Kokolus Maeve , Chan Miranda , Dingwell Robert , Chow Selina , Campbell Nancy , Elrahi Cassandra , Piantadosi Steven , Quina Andre 
Published: December 2024

Abstract

Objectives
The Integrating Clinical Trials and Real-World Endpoints (ICAREdata) project aimed to demonstrate that electronic health record (EHR) data, expressed in a standard structured format, can be extracted and transmitted to contribute to clinical research. Using the minimal Common Oncology Data Elements (mCODE), we collected standardized oncology outcome data from EHRs across 10 clinical sites and 15 trials. This report details and assesses the ICAREdata technical implementation and offers recommendations to benefit future projects with similar goals.

Materials and Methods
In the ICAREdata project, we implemented tools to collect structured clinical outcome data within EHRs, then extract and transmit the mCODE-formatted data to a secure cloud storage platform. Using the socio-technical model of health information technology, we systematically assessed the technical implementations in this multi-institutional project.

Results
We evaluated the ICAREdata method across the 8 inter-related dimensions of the socio-technical model. For each dimension, we identified challenges and developed recommendations that implementers of future initiatives can leverage.

Discussion
The ICAREdata project successfully demonstrated the feasibility of using data standards for structured data capture and transmission in clinical trials. The lessons learned from this project can accelerate the success of similar initiatives using standards-based real-world data (RWD) capture and transmission for research.

Conclusion
The ICAREdata project represents a step towards a future where researchers can access high-quality, standardized RWD leading to advances in research and improved care delivery.
Arthropod mtDNA paraphyly: a case study of introgressive origin
Authors: Noguerales Víctor , Emerson Brent C 
Published: December 2024

Abstract
Mitochondrial paraphyly between arthropod species is not uncommon and has been speculated to largely be the result of incomplete lineage sorting (ILS) of ancestral variation within the common ancestor of both species, with hybridization playing only a minor role. However, in the absence of comparable nuclear genetic data, the relative roles of ILS and hybridization in explaining mitochondrial DNA (mtDNA) paraphyly remain unclear. Hybridization itself is a multifaceted gateway to mtDNA paraphyly, which may lead to paraphyly across both the nuclear and mitochondrial genomes, or paraphyly that is largely restricted to the mitochondrial genome. These different outcomes will depend upon the frequency of hybridization, its demographic context, and the extent to which mtDNA is subject to direct selection, indirect selection, or neutral processes. Here, we describe extensive mtDNA paraphyly between two species of iron-clad beetle (Zopheridae) and evaluate competing explanations for its origin. We first test between hypotheses of ILS and hybridization, revealing strong nuclear genetic differentiation between species, but with the complete replacement of Tarphius simplex mtDNA through the introgression of at least 5 mtDNA haplotypes from T. canariensis. We then contrast explanations of direct selection, indirect selection, or genetic drift for observed patterns of mtDNA introgression. Our results highlight how introgression can lead to complex patterns of mtDNA paraphyly across arthropod species, while simultaneously revealing the challenges for understanding the selective or neutral drivers that underpin such patterns.
Biological agency: a concept without a research program
Authors: DiFrisco James , Gawne Richard 
Published: December 2024

Abstract
This paper evaluates recent work purporting to show that the “agency” of organisms is an important phenomenon for evolutionary biology to study. Biological agency is understood as the capacity for goal-directed, self-determining activity—a capacity that is present in all organisms irrespective of their complexity and whether or not they have a nervous system. Proponents of the “agency perspective” on biological systems have claimed that agency is not explainable by physiological or developmental mechanisms, or by adaptation via natural selection. We show that this idea is theoretically unsound and unsupported by current biology. There is no empirical evidence that the agency perspective has the potential to advance experimental research in the life sciences. Instead, the phenomena that the agency perspective purports to make sense of are better explained using the well-established idea that complex multiscale feedback mechanisms evolve through natural selection.
Comparative analysis of surgical outcomes between the hinotori™ surgical robot system and da Vinci® Xi for simple hysterectomy with sentinel lymph node biopsy in low-risk endometrial cancer
Authors: Togami Shinichi , Furuzono Nozomi , Fukuda Mika , Mizuno Mika , Yanazume Shintaro , Kobayashi Hiroaki 
Published: December 2024

Abstract

Objectives
This study aimed to compare the surgical outcomes of simple hysterectomy with sentinel lymph node biopsy for low-risk endometrial cancer performed using the hinotori™ Surgical Robot System and the da Vinci® Xi system.

Materials and Methods
We retrospectively analyzed the data of 234 patients who underwent simple hysterectomy with sentinel lymph node biopsy at Kagoshima University Hospital between January 2017 and June 2024. Amongst them, 20 patients underwent surgery using the hinotori™ Surgical Robot System and 214 using the da Vinci® Xi. Surgical factors, including operative time, cockpit/console time, blood loss and sentinel lymph node detection, were evaluated. Statistical analyses included chi-square and Wilcoxon tests, with significance set at P &lt; 0.05.

Results
The median operative and cockpit/console times were comparable between the two systems. However, the time from roll-in to the start of cockpit/console surgery was significantly longer for the hinotori™ Surgical Robot System than for the da Vinci® Xi (P = 0.0039). No significant differences were observed for blood loss, length of hospital stay, or complication rates. The sentinel lymph node detection rates and number of sentinel lymph nodes resected were similar between the two systems, with metastatic sentinel lymph node rates of 6% in both groups.

Conclusion
Simple hysterectomy with sentinel lymph node biopsy performed using the hinotori™ Surgical Robot System demonstrated outcomes comparable with those using the da Vinci® Xi system, with no significant differences in key surgical factors. These results suggest that the hinotori™ Surgical Robot System is a viable alternative for minimally invasive surgery in low-risk endometrial cancer. Further studies with larger sample sizes are required to validate these findings.
HPV genotype-specific prevalence and infection risks: A 10-year population-based study from the United States
Authors: Wheeler Cosette M , Adcock Rachael , Hunt William C , Robertson Michael , Torrez-Martinez Norah E , McDonald Ruth , Merchasin Emily , Jenison Steven , Saslow Debbie , Joste Nancy E , Castle Philip E , Kim Jane J , Cuzick Jack ,   New Mexico HPV Pap Registry Steering Committee Members
Published: December 2024

Abstract

Background
Various studies have reported on the impact of human papillomavirus (HPV) vaccines. Here we present the largest population-based investigation of genotype-specific distributions over the decade following implementation of the 4-valent HPV vaccine (HPV6/11/16/18) in the United States.

Methods
Liquid-based cervical cytology samples from individuals aged 15-30 years undergoing cervical screening throughout New Mexico were tested by broad-spectrum HPV genotyping. Weighted relative differences in HPV type-specific prevalence (RDP) and 95% confidence intervals (95%CI) were calculated comparing individuals screened in 2007-2009 (n = 95,915) to those screened in 2013-2016 (n = 103,371). Weighted logistic regression was used to estimate relative risk of type-specific HPV infections. Tests of significance were 2-sided.

Results
Genotype-specific prevalence reduced significantly for HPV16 (RDP=-52.6%, 95%CI -56.9 to -48.3), HPV18 (RDP=-62.1%, 95%CI -68.5 to -55.8), HPV31 (RDP=-34.2%, 95%CI -42.1 to -26.3) and HPV33 (RDP=-31.8%, 95%CI -48.4 to -15.1). The RDP increased for other carcinogenic HPV types by 19.5% (95%CI +14.3 to + 24.6) when excluding HPV16/18. Large reductions in HPV6/11 RDP were observed but overall, non-carcinogenic, non-vaccine types increased. Comparing females born in 1996 to those born in 1989, risk of infection with HPV6/11/16/18 decreased by 80.0% among individuals aged 21-25 years. High-grade squamous intraepithelial lesions or worse (HSIL+) decreased by 49.4% when extending the evaluation from 2007 to 2018.

Conclusion(s)
HSIL+ incidence is decreasing with large reductions in the prevalence of 4-valent HPV vaccine types and non-vaccine types HPV31 and 33, reflecting vaccine cross-protection. Increases in non-vaccine HPVs may attenuate anticipated reductions in HPV-related abnormalities including cancers however the benefits of HPV vaccination remain substantial.
Empirical relations in thermal Comptonization
Authors: Bagi Richárd , Alamaa Filip , Ryde Felix 
Published: December 2024

ABSTRACT
In many astrophysical systems, photons interact with matter through thermal Comptonization. In these cases, under certain simplifying assumptions, the evolution of the photon spectrum is described by an energy diffusion equation such as the Kompaneets equation, having dependencies on the seed photon temperature, $\theta _i$, the electron temperature, $\theta _e$, and the Compton y-parameter. The resulting steady-state spectrum is characterized by the average photon energy and the Compton temperature, which both lack analytical dependencies on the initial parameters. Here, we present empirical relations of these two quantities as functions of $\theta _i$, $\theta _e$, and y, obtained by evaluating the steady-state solution of the Kompaneets equation accounting for energy diffusion and electron recoil. The relations have average fractional errors ${\sim} 1~{{\ \rm per\ cent}}$ across a wide range of the initial parameters, which make them useful in numerical applications.
Theoretical Rotational and Vibrational Investigation of Oxygen-Functionalized Interstellar PAHs
Authors: Mishra Shivani , Vats Akant , Srivastav Satyam , Pathak Amit , Sarre Peter J , Onaka Takashi , Sakon Itsuki 
Published: December 2024

ABSTRACT
Oxygen-functionalized polycyclic aromatic hydrocarbons (OPAHs) with OH, CHO, and CO side groups can form in the interstellar medium (ISM) mainly through the UV irradiation of PAHs in water ice. Inspired by the detection of nitrogen-containing PAHs in the ISM, this study uses highly accurate computational techniques to investigate the rotational and vibrational spectra of oxygen-functionalized pyrene derivatives (Py-OH, Py-CHO, Py-HO, and Py-O$_{2}$) for comparison with experiments that could aid in their future detection. All four OPAHs exhibit strong dipole moments and rotational lines, observable in denser ISM regions near 12 GHz, 10.2 GHz, 12.6 GHz, and 9.6 GHz, respectively. The strongest IR absorption features are identified at 1179.9 cm$^{-1}$ (8.47 $\mu$m) and 1385.0 cm$^{-1}$ (7.22 $\mu$m) for Py-OH, 1733.4 cm$^{-1}$ (5.77 $\mu$m) for Py-CHO, 1747.7 cm$^{-1}$ (5.72 $\mu$m) for Py-HO, and 1613.0 cm$^{-1}$ (6.20 $\mu$m) for Py-O$_{2}$. The IR features of Py-OH and Py-O$_{2}$ exhibit peaks in the CO stretching region around 6.0 $\mu$m, while those of Py-CHO and Py-HO are blue-shifted due to anharmonicity from the additional CH bond. This suggests PAHs with CO group and no additional peripheral CH bond better explain the observed 6.0 $\mu$m PAH emission. However, to explain the observed PAH emission bands with the OPAHs, a fully emission-cascade treatment is required in the anharmonic IR spectra. The accurate spectral data presented here are crucial for experimental classification and potential interstellar observations.
Detecting eclipsing double white dwarfs with electromagnetic and gravitational waves
Authors: Jin Hong-Ming , Ma Bo , Shao Yong , Wang Yan 
Published: December 2024

ABSTRACT
Galactic double white dwarfs (DWDs) are predominant sources of gravitational waves in the millihertz frequencies accessible to space-borne gravitational wave (GW) detectors. With advances in multimessenger astronomy, an increasing number of DWD systems will be discovered through both electromagnetic (EM) and GW observations. In this paper, we simulated two populations of DWDs originating from different star formation histories (hereafter referred to as Model 1 and Model 2) using the binary population synthesis method. We predicted the number of DWDs in our Galaxy detectable by TianQin and Laser Interferometer Space Antenna (LISA) individually, as well as through their joint observation. In addition, we performed an analysis to evaluate the accuracy of the parameter estimation using the Fisher information matrix. Furthermore, we predicted the number of detached eclipsing DWDs detectable by Gaia and the Vera C. Rubin Observatory (VRO). Our study found that over the nominal mission durations, TianQin, LISA, and their joint observation can detect at least 5000 and potentially several tens of thousands of DWDs with signal-to-noise ratios greater than 7. Gaia and VRO are expected to detect at least several dozen and up to several hundred eclipsing DWDs with orbital periods less than 30 h. We also found that several dozen eclipsing DWDs can be detected jointly through EM and GW observations.
Evaluating cosmological biases using photometric redshifts for Type Ia Supernova cosmology with the Dark Energy Survey Supernova Program
Authors: Chen R C , Scolnic D , Vincenzi M , Rykoff E S , Myles J , Kessler R , Popovic B , Sako M , Smith M , Armstrong P , Brout D , Davis T M , Galbany L , Lee J , Lidman C , Möller A , Sánchez B O , Sullivan M , Qu H , Wiseman P , Abbott T M C , Aguena M , Allam S , Alves O , Andrade-Oliveira F , Annis J , Bacon D , Brooks D , Carnero Rosell A , Carretero J , Choi A , Conselice C , da Costa L N , Pereira M E S , Diehl H T , Doel P , Everett S , Ferrero I , Flaugher B , Frieman J , García-Bellido J , Gatti M , Gaztanaga E , Giannini G , Gruen D , Gruendl R A , Gutierrez G , Herner K , Hinton S R , Hollowood D L , Honscheid K , Huterer D , James D J , Kuehn K , Lewis G F , Lima M , Marshall J L , Mena-Fernández J , Menanteau F , Miquel R , Ogando R L C , Palmese A , Pieres A , Plazas Malagón A A , Roodman A , Samuroff S , Sanchez E , Sanchez Cid D , Sevilla-Noarbe I , Suchyta E , Swanson M E C , Tarle G , To C , Tucker D L , Vikram V , Weaverdyck N , Weller J ,   DES Collaboration
Published: December 2024

ABSTRACT
Cosmological analyses with Type Ia Supernovae (SNe Ia) have traditionally been reliant on spectroscopy for both classifying the type of supernova and obtaining reliable redshifts to measure the distance–redshift relation. While obtaining a host-galaxy spectroscopic redshift for most SNe is feasible for small-area transient surveys, it will be too resource intensive for upcoming large-area surveys such as the Vera Rubin Observatory Legacy Survey of Space and Time, which will observe on the order of millions of SNe. Here, we use data from the Dark Energy Survey (DES) to address this problem with photometric redshifts (photo-z) inferred directly from the SN light curve in combination with Gaussian and full $p(z)$ priors from host-galaxy photo-z estimates. Using the DES 5-yr photometrically classified SN sample, we consider several photo-z algorithms as host-galaxy photo-z priors, including the Self-Organizing Map redshifts (SOMPZ), Bayesian Photometric Redshifts (BPZ), and Directional-Neighbourhood Fitting (DNF) redshift estimates employed in the DES 3 × 2 point analyses. With detailed catalogue-level simulations of the DES 5-yr sample, we find that the simulated w can be recovered within $\pm 0.02$ when using SN+SOMPZ or DNF prior photo-z, smaller than the average statistical uncertainty for these samples of 0.03. With data, we obtain biases in w consistent with simulations within ${\sim} 1\sigma$ for three of the five photo-z variants. We further evaluate how photo-z systematics interplay with photometric classification and find classification introduces a subdominant systematic component. This work lays the foundation for next-generation fully photometric SNe Ia cosmological analyses.