bluuebunny/crossref_metadata_2025 huggingface dataset:
The joint memory effect: challenging the selfish stigma in Huntington’s disease?
Authors: Dalléry Romain , Fraisse Nicolas , Cléret de Langavant Laurent , Youssov Katia , Morgado Graça , Massart Renaud , Schubert Robin , Reilmann Ralf , Jacquemot Charlotte , Bapst Blanche , Busse Monica , Craufurd David , Rosser Anne , Lunven Marine , Bachoud-Lévi Anne-Catherine
Published: December 2024

The prevalent belief that individuals with Huntington’s disease exhibit selfish behaviour, disregarding the thoughts, feelings and actions of others, has been challenged by patient organizations and clinical experts. To further investigate this issue and study whether participants with Huntington’s disease can pay attention to others, a joint memory task was carried out in patients with Huntington’s disease with and without a partner. This study involved 69 participants at an early stage of Huntington’s disease and 56 healthy controls from the UK, France and Germany, who participated in the international Repair-HD multicentre study (NCT03119246). Participants completed a semantic categorization task across three categories: animals, fruits and vegetables and manufactured objects. They performed the task either alone (Alone condition) or with the examiner acting as a partner (Pair condition). In the Pair condition, the participant was assigned one category, their partner was assigned another and one category was left unassigned. Afterwards, participants engaged in a surprise free recall task to remember as many words as possible. Words not assigned to anyone were considered socially irrelevant in contrast to the ones assigned to the participant and to the partner. Both groups demonstrated the expected self-prioritization effect, recalling their assigned words better than their partner’s or unassigned words in both conditions. Additionally, a joint memory effect was observed, with better recall for the partner’s assigned words than the unassigned words in the Pair condition (controls: difference = 0.45, P < 0.001; participants with Huntington’s disease: difference = 0.34, P < 0.001). Socially relevant words were thus better recalled than irrelevant words. The number of recalled words correlated with cognitive performance (all P-values < 0.05) and MRI analysis revealed a negative correlation between the joint memory effect and right orbitofrontal grey matter density in participants with Huntington’s disease. These findings challenge the notion that individuals with Huntington’s disease display selfish behaviours because of disinterest in others. They show the ability to process information about their partners, implying that their social difficulties may arise from factors other than social cognition deficits. This opens the door for more ecological assessments of social cognition in patients with Huntington’s disease.
Verbal working memory and syntactic comprehension segregate into the dorsal and ventral streams, respectively
Authors: Matchin William , Mollasaraei Zeinab K , Bonilha Leonardo , Rorden Christopher , Hickok Gregory , den Ouden Dirk , Fridriksson Julius
Published: December 2024

Syntactic processing and verbal working memory are both essential components to sentence comprehension. Nonetheless, the separability of these systems in the brain remains unclear. To address this issue, we performed causal-inference analyses based on lesion and connectome network mapping using MRI and behavioural testing in two groups of individuals with chronic post-stroke aphasia. We employed a rhyme judgement task with heavy working memory load without articulatory confounds, controlling for the overall ability to match auditory words to pictures and to perform a metalinguistic rhyme judgement, isolating the effect of working memory load (103 individuals). We assessed non-canonical sentence comprehension, isolating syntactic processing by incorporating residual rhyme judgement performance as a covariate for working memory load (78 individuals). Voxel-based lesion analyses and structural connectome-based lesion symptom mapping controlling for total lesion volume were performed, with permutation testing to correct for multiple comparisons (4000 permutations). We observed that effects of working memory load localized to dorsal stream damage: posterior temporal-parietal lesions and frontal-parietal white matter disconnections. These effects were differentiated from syntactic comprehension deficits, which were primarily associated with ventral stream damage: lesions to temporal lobe and temporal-parietal white matter disconnections, particularly when incorporating the residual measure of working memory load as a covariate. Our results support the conclusion that working memory and syntactic processing are associated with distinct brain networks, largely loading onto dorsal and ventral streams, respectively.
Type I collagen extracellular matrix facilitates nerve regeneration via the construction of a favourable microenvironment
Authors: Lu Panjian , Chen Zhiying , Wu Mingjun , Feng Shuyue , Chen Sailing , Cheng Xiyang , Zhao Yahong , Liu Xingyu , Gong Leilei , Bian Lijing , Yi Sheng , Wang Hongkui
Published: December 2024

Background

The extracellular matrix (ECM) provides essential physical support and biochemical cues for diverse biological activities, including tissue remodelling and regeneration, and thus is commonly applied in the construction of artificial peripheral nerve grafts. Nevertheless, the specific functions of essential peripheral nerve ECM components have not been fully determined. Our research aimed to differentially represent the neural activities of main components of ECM on peripheral nerve regeneration.

Methods

Schwann cells from sciatic nerves and neurons from dorsal root ganglia were isolated and cultured in vitro. The cells were seeded onto noncoated dishes, Matrigel-coated dishes, and dishes coated with the four major ECM components fibronectin, laminin, collagen I, and collagen IV. The effects of these ECM components on Schwann cell proliferation were determined via methylthiazolyldiphenyl-tetrazolium bromide (MTT), Cell Counting Kit-8, and 5-ethynyl-2'-deoxyuridine (EdU) assays, whereas their effects on cell migration were determined via wound healing and live-cell imaging. Neurite growth in neurons cultured on different ECM components was observed. Furthermore, the two types of collagen were incorporated into chitosan artificial nerves and used to repair sciatic nerve defects in rats. Immunofluorescence analysis and a behavioural assessment, including gait, electrophysiology, and target muscle analysis, were conducted.

Results

ECM components, especially collagen I, stimulated the DNA synthesis and movement of Schwann cells. Direct measurement of the neurite lengths of neurons cultured on ECM components further revealed the beneficial effects of ECM components on neurite outgrowth. Injection of collagen I into chitosan and poly(lactic-co-glycolic acid) artificial nerves demonstrated that collagen I facilitated axon regeneration and functional recovery after nerve defect repair by stimulating the migration of Schwann cells and the formation of new blood vessels. In contrast, collagen IV recruited excess fibroblasts and inflammatory macrophages and thus had disadvantageous effects on nerve regeneration.

Conclusions

These findings reveal the modulatory effects of specific ECM components on cell populations of peripheral nerves, reveal the contributing roles of collagen I in microenvironment construction and axon regeneration, and highlight the use of collagen I for the healing of injured peripheral nerves.
A study of changes in hematologic parameters in patients with migraine
Authors: Wu Jiaonan , Fu Lulan , Deng Ziru , Li Hanli , Zhong Linyan , Gao Rupan , Gui Wei
Published: December 2024

Introduction

To evaluate the characteristics of hematological parameters and peripheral inflammatory markers (PIMs) in migraine, including chronic migraine (CM) and episodic migraine (EM), and to explore their underlying mechanisms.

Method

A total of 88 subjects were enrolled, 58 with migraine (28 with CM and 30 with EM) and 30 healthy controls. All subjects were matched for age, gender, and body mass index, and peripheral blood was collected. Hematological parameters and PIMs were compared between migraineurs and healthy controls. The patients underwent hematological laboratory testing and calculated the PIMs. PIMs included neutrophil/lymphocyte ratio, lymphocyte/monocyte ratio (LMR), neutrophil/monocyte ratio, platelet/lymphocyte ratio, and platelet/monocyte ratio (PMR) ratio.

Result

Monocyte counts in migraine patients were significantly lower compared with healthy controls, while LMR and PMR were significantly higher. Statistically significant differences were observed in monocyte counts, LMR, and PMR among the three groups of CM, EM, and HC patients. Post hoc Bonferroni t-test showed that monocyte counts were significantly lower in the EM group compared with the HC group, while LMR and PMR were significantly higher. Comparison between the EM and CM groups showed that LMR was significantly higher in the EM group. Differences in monocyte counts, LMR, and PMR between the CM and HC groups were not statistically significant. Receiver operating characteristic curve analysis indicated that the area under the curve (AUC) for the diagnosing migraine using the combination of Mon, LMR, and PMR was 0.707, and the AUC for the diagnosis of EM was 0.758. The AUC value of PMR for diagnosing CM was 0.669, while the AUC for the combination of LMR and platelet/lymphocyte ratio in distinguishing CM and EM was 0.705.

Conclusion

Our findings indicate that migraine and its subtypes exhibit abnormalities in monocyte counts and PIMs, which possess diagnostic predictive value for differentiating migraine and its subtypes. This suggests that systemic inflammation may play a role in the pathogenesis of migraine.
Case report of early signs of aortic stenosis decompensation detected via ambient sensor-derived digital biomarkers
Authors: Arenja Nisha , Schütz Narayan , Buluschek Philipp , Nef Tobias , Saner Hugo
Published: December 2024

Background

Aortic stenosis is a progressive condition with a grim prognosis, underscoring the importance of timely intervention to prevent decompensation. Home monitoring systems, particularly those utilizing ambient sensors, offer promise in detecting early signs of deterioration.

Case summary

We present the case of an 89-year-old woman who was asymptomatic but monitored using such a system prior to experiencing acute decompensation. Key clinical indicators, including increased night-time heart rate, respiration rate, toss and turns in bed, and nocturia, were observed several months before hospitalization. Additionally, reduced physical activity and increased toilet visits were noted.

Discussion

These findings highlight the potential of ambient sensor systems in identifying pre-clinical stages of cardiac decompensation, especially in severe aortic stenosis cases. Integrating ambient sensor systems into routine clinical practice holds promise for enhancing proactive management strategies and reducing adverse outcomes associated with cardiovascular disease progression.
Contributions of hemolytic proteins in virulent Aeromonas hydrophila to motile Aeromonas septicemia disease of channel catfish (Ictalurus punctatus)
Authors: Zhang Dunhua , Feng Jun , Wang Yi , Shoemaker Craig A , Wise Allison A , Beck Benjamin H
Published: December 2024

Hemolytic proteins are a major group of virulence factors in pathogenic Aeromonas hydrophila. Six genes encoding presumable hemolytic proteins were revealed from the genome of virulent A. hydrophila (vAh) that caused severe disease in channel catfish. The aim of this study was to assess the contribution of these hemolytic proteins to the virulence of this bacterium. Genes coding for following six proteins were investigated: aerolysin (Arl), 21-kDa hemolysin (Hly1), thermostable hemolysin (Hly2), phospholipase/lecithinase-related hemolysin (Hly3), membrane-associated hemolysin III (Hly4), and cytolysin-associated hemolysin (Hly5). Individual genes were deleted from the bacterium using CRISPR-Cas9 mediated methods. Assessment showed that deletion of Arl gene (Δarl) completely abolished hemolytic activity of this mutant while Δhly1–Δhly5 mutants had the same activity as the wild vAh. Extracellular proteins (ECPs) of the Δarl mutant caused significantly (p < 0.01) less cell death in vitro with viability increased by approximately 20%, compared to the wild vAh. ECPs of mutants Δhly1–Δhly5 remained the same cell toxicity as the wild vAh. A second deletion of hly5 from the Δarl mutant further lowered the cell toxicity of the ECP of the mutant (Δarl + Δhly5). Assays in vivo showed that both Δarl and Δhly5 mutants caused less fish mortality with reduction of 57% and 16%, respectively, compared to the wild vAh; the Δarl + Δhly5 mutant caused the least mortality with approximately 87% of reduction; and other mutants had the same virulence as the wild vAh. Analyses of SDS-PAGE (sodium dodecyl sulfate-polyacrylamide gel electrophoresis) and Western blotting evidently indicate that both Arl and Hly5 proteins formed hexamer-like stable structures post secretion from the bacterium. Arl and Hly5 apparently had synergistic action in cytotoxicity and causing disease and were the major virulence factors among the six hemolytic proteins analyzed in this study.
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

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

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 < 0.001), age (1.11[1.03; 1.20], p = 0.007), EuroScore II (1.05[1.03; 1.07], p < 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

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

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

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

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

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

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 < 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

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

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

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

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

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.
Multiwavelength monitoring and reverberation mapping of NGC 2617 at deepest minimum with a sharp upward turn during 2021–2024
Authors: Oknyansky V L , Brotherton M S , Tsygankov S S , Dodin A V , Tatarnikov A M , Du P , Burlak M A , Ikonnikova N P , Metlov V G , Belinski A A , Shatsky N I , Wang J -M , Bao D -W , Fang F , Zhai S , Fu Y -X , Bai H -R , Zastrocky T E , Chelouche D , Figaredo C Sobrino , Kaspi S , Gaskell C M
Published: December 2024

We present the results of a new X-ray to near-IR photometric and spectroscopic monitoring of the changing look active galactic nucleus NGC 2617 carried out from March 2022 to March 2024. We found significant variability at all wavelengths and in the intensities and profiles of the broad Balmer lines. Reverberation mapping was carried out for three observing seasons during 2021–2024. We obtained time delays of $\sim$4 d for the response of the H ${\beta }$ line to optical continuum variations. The X-ray variations correlate well with the UV and optical, with a few days lag for longer wavelengths. The K band lagged the B band by $\sim$ 15 d during the last three seasons, which is significantly shorter than the delays reported previously by the 2016 and 2017–2019 campaigns. Near-IR variability arises from two different emission regions: the outer part of the accretion disc and a more distant dust component. The $HK$-band variability is governed primarily by dust. The H ${\beta }$/H ${\alpha }$ ratio variations (for broad components only) correlate with the X-ray and UV fluxes. The spectral type changed from type 1.8 to type 1.9 during 2023 October–2024 January and then a more rapid change to type 1.5 occurred in 2024 February. We interpret these changes as a combination of two factors: changes in the accretion rate as a dominant cause but also the sublimation or recovery of dust along the line of sight.
Near-infrared spectroscopy of the LMC recurrent nova LMCN 1968-12a
Authors: Evans A , Banerjee D P K , Geballe T R , Polin A , Hsiao E Y , Page K L , Woodward C E , Starrfield S
Published: December 2024

We have obtained near-infrared (0.80–2.45 $\, \mu$m) spectra of the recurrent nova LMCN 1968-12a on two occasions during its 2024 August eruption. This is the first near-infrared spectroscopy of an extragalactic nova. The initial spectrum, on day 8.48, caught the nova in the coronal phase, with the [Si x] 1.43 $\, \mu$m line being extremely strong. This line had a luminosity of $\sim 95$ $\rm L_\odot$, and is clearly a very powerful coolant. Its presence, together with the absence of [Si ix] 1.56$\, \mu$m, implies a coronal temperature $\gtrsim 3\times 10^6$ K, possibly amongst the highest recorded coronal temperature in a nova eruption. With the exception of the [Si x] line, the near-infrared spectra are remarkable for being devoid of metal lines. We suggest that this is due, in part, to the exceptionally high temperature of the coronal gas, causing ions, whose emission lines would normally appear in the near-infrared spectrum, to be collisionally ionized to higher stages.
Estimating photometric redshifts for galaxies from the DESI Legacy Imaging Surveys with Bayesian neural networks trained by DESI EDR
Authors: Zhou Xingchen , Li Nan , Zou Hu , Gong Yan , Deng Furen , Chen Xuelei , Yu Qian , He Zizhao , Ding Boyi
Published: December 2024

We present a catalogue of photometric redshifts for galaxies from Dark Energy Spectroscopic Instrument (DESI) Legacy Imaging Surveys, which includes $\sim 0.18$ billion sources covering 14 000 $\deg ^2$. The photometric redshifts, along with their uncertainties, are estimated through galaxy images in three optical bands (g, r, and z) from DESI and two near-infrared bands ($W1$ and $W2$) from Wide-field Infrared Survey Explorer (WISE) using a Bayesian neural network (BNN). The training of BNN is performed by above images and their corresponding spectroscopic redshifts given in DESI Early Data Release (EDR). Our results show that categorizing galaxies into individual groups based on their inherent characteristics and estimating their photo-zs within their group separately can effectively improve the performance. Specifically, the galaxies are categorized into four distinct groups based on DESI’s target selection criteria: bright galaxy sample (BGS), luminous red galaxies (LRG), emission-line galaxies (ELG), and a group comprising the remaining sources, referred to as NON. As measured by outliers of $|\Delta z| \gt 0.15 (1 + z_{\rm true})$, accuracy $\sigma _{\rm NMAD}$, and mean uncertainty $\overline{E}$ for BNN, we achieve low outlier percentage, high accuracy, and low uncertainty: 0.14  per cent, 0.018, and 0.0212 for BGS and 0.45  per cent, 0.026, and 0.0293 for LRG respectively, surpassing results without categorization. However, the photo-zs for ELG cannot be reliably estimated, showing result of $\gt 15~\,\mathrm{ per\,cent}$, $\sim 0.1$, and $\sim 0.1$ irrespective of training strategy. On the other hand, NON sources can reach 1.9  per cent, 0.039, and 0.0445 when a magnitude cut of $z\lt 21.3$ is applied. Our findings demonstrate that estimating photo-zs directly from galaxy images is significantly potential, and to achieve high-quality photo-z measurement for ongoing and future large-scale imaging survey, it is sensible to implement categorization of sources based on their characteristics.
TDP1 splice-site mutation causes HAP1 cell hypersensitivity to topoisomerase I inhibition
Authors: Goh Chen Gang , Bader Aldo S , Tran Tuan-Anh , Belotserkovskaya Rimma , D’Alessandro Giuseppina , Jackson Stephen P
Published: December 2024

HAP1 is a near-haploid human cell line commonly used for mutagenesis and genome editing studies due to its hemizygous nature. We noticed an unusual hypersensitivity of HAP1 to camptothecin, an antineoplastic drug that stabilizes topoisomerase I cleavage complexes (TOP1ccs). We have attributed this hypersensitivity to a deficiency of TDP1, a key phosphodiesterase involved in resolving abortive TOP1ccs. Through whole-exome sequencing and subsequent restoration of TDP1 protein via CRISPR-Cas9 endogenous genome editing, we demonstrate that TDP1 deficiency and camptothecin hypersensitivity in HAP1 cells are a result of a splice-site mutation (TDP1 c.660–1G > A) that causes exon skipping and TDP1 loss of function. The lack of TDP1 in HAP1 cells should be considered when studying topoisomerase-associated DNA lesions and when generalizing mechanisms of DNA damage repair using HAP1 cells. Finally, we also report the generation of HAP1 STAR clones with restored TDP1 expression and function, which may be useful in further studies to probe cellular phenotypes relating to TOP1cc repair.
Long G4-rich enhancers target promoters via a G4 DNA-based mechanism
Authors: DeMeis Jeffrey D , Roberts Justin T , Delcher Haley A , Godang Noel L , Coley Alexander B , Brown Cana L , Shaw Michael H , Naaz Sayema , Dahal Ayush , Alqudah Shahem Y , Nguyen Kevin N , Nguyen Anita D , Paudel Sunita S , Shell John E , Patil Suhas S , Dang Hong , O’Neal Wanda K , Knowles Michael R , Houserova Dominika , Gillespie Mark N , Borchert Glen M
Published: December 2024

Several studies have now described instances where G-rich sequences in promoters and enhancers regulate gene expression through forming G-quadruplex (G4) structures. Relatedly, our group recently identified 301 long genomic stretches significantly enriched for minimal G4 motifs (LG4s) in humans and found the majority of these overlap annotated enhancers, and furthermore, that the promoters regulated by these LG4 enhancers are similarly enriched with G4-capable sequences. While the generally accepted model for enhancer:promoter specificity maintains that interactions are dictated by enhancer- and promoter-bound transcriptional activator proteins, the current study tested an alternative hypothesis: that LG4 enhancers interact with cognate promoters via a direct G4:G4 DNA-based mechanism. This work establishes the nuclear proximity of LG4 enhancer:promoter pairs, biochemically demonstrates the ability of individual LG4 single-stranded DNAs (ssDNAs) to directly interact target promoter ssDNAs, and confirms that these interactions, as well as the ability of LG4 enhancers to activate target promoters in culture, are mediated by G4 DNA.
Force-induced melting and S-DNA pathways for DNA overstretching exhibit distinct kinetics
Authors: Sundar Rajan Vinoth , Levin Sune , McCauley Micah J , Williams Mark C , Rouzina Ioulia , Wilhelmsson L Marcus , Westerlund Fredrik
Published: December 2024

It is widely appreciated that double stranded DNA (dsDNA) is subjected to strong and dynamic mechanical forces in cells. Under increasing tension B-DNA, the most stable double-stranded (ds) form of DNA, undergoes cooperative elongation into a mixture of S-DNA and single stranded DNA (ssDNA). Despite significant effort, the structure, energetics, kinetics and the biological role of S-DNA remains obscure. We here stretch 60 base pair (bp) dsDNA oligonucleotides with a variable number of tricyclic cytosine, tC, modifications using optical tweezers. We observe multiple fast cooperative and reversible two-state transitions between B-DNA and S-DNA. Notably, tC modifications increase the transition force, while reducing the transition extension and free energy due to progressively increasing fraying of the dsDNA ends. We quantify the average number of bps undergoing the B-to-S transition, as well as the free energies and rates. This allows us to reconstruct the B-to-S free energy profiles in absence of force. We conclude that S-DNA is an entirely force-induced state, and that the B-to-S transition is much faster than internal dsDNA melting. We hypothesize that S-DNA may have a role as a transient intermediate in, for example, molecular motor-induced local dsDNA strand separation.
GIN-TONIC: non-hierarchical full-text indexing for graph genomes
Authors: Öztürk Ünsal , Mattavelli Marco , Ribeca Paolo
Published: December 2024

This paper presents a new data structure, GIN-TONIC (Graph INdexing Through Optimal Near Interval Compaction), designed to index arbitrary string-labelled directed graphs representing, for instance, pangenomes or transcriptomes. GIN-TONIC provides several capabilities not offered by other graph-indexing methods based on the FM-Index. It is non-hierarchical, handling a graph as a monolithic object; it indexes at nucleotide resolution all possible walks in the graph without the need to explicitly store them; it supports exact substring queries in polynomial time and space for all possible walk roots in the graph, even if there are exponentially many walks corresponding to such roots. Specific ad-hoc optimizations, such as precomputed caches, allow GIN-TONIC to achieve excellent performance for input graphs of various topologies and sizes. Robust scalability capabilities and a querying performance close to that of a linear FM-Index are demonstrated for two real-world applications on the scale of human pangenomes and transcriptomes. Source code and associated benchmarks are available on GitHub.