bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomics of historical museum collections clarifies species diversity in Cuban hutias (Capromys)
Authors: Henriksen Rasmus Amund , Woods Roseina , Barnes Ian , Kennerley Rosalind J , Borroto-Páez Rafael , Brace Selina , Turvey Samuel T 
Published: October 2024

Abstract
Specimen-based taxonomic research is essential for understanding diversity and setting management frameworks for threatened mammal faunas, and ancient DNA techniques are increasingly used to extract information from taxonomically relevant historical specimens. The largest survivors of the depleted Caribbean mammal fauna are hutias in the genus Capromys, which is usually interpreted as containing a single species, C. pilorides. Previous studies have demonstrated genetic differentiation of Capromys populations across Cuba, but infrageneric species diversity and nomenclature remain unclear. We conducted ancient DNA analysis of historical Capromys samples using cytochrome b and complete mitogenome data sets, and including the 19th-century holotypes of 2 species now considered synonyms, C. fournieri and C. geayi. Our analyses identify distinct western and central/eastern Capromys clades that diverged 1.75 Mya based upon mitogenome data. These clades are separated by the Havana–Matanzas Channel, which represented a barrier to dispersal throughout the Neogene–Quaternary. Divergence date comparisons with other hutia species provide support for interpreting divergence between Capromys populations as species-level differentiation. Although we were unable to yield amplifiable DNA from the C. fournieri holotype, our analyses confidently assign the C. geayi holotype to the western Capromys clade. We therefore recognize 2 extant Capromys species: C. geayi (western Cuba) and C. pilorides (central/eastern Cuba and Cayman Islands).
Transcriptomic markers of biological aging in breast cancer survivors: a longitudinal study
Authors: Carroll Judith E , Crespi Catherine M , Cole Steve , Ganz Patricia A , Petersen Laura , Bower Julienne E 
Published: October 2024

Abstract

Background
The purpose of this study was to examine the impact of breast cancer therapy on biological aging as measured by expression of genes for cellular senescence (p16INK4a, SenMayo), DNA damage response, and proinflammatory senescence-associated secretory phenotype.

Methods
This longitudinal, observational study evaluated women diagnosed with breast cancer (stage 0-III) prior to radiation therapy (RT) and/or chemotherapy (CT) and at repeated visits out to 2 years. Peripheral blood mononuclear cell gene expression was assessed using RNA sequencing on quality-verified RNA. Longitudinal data were analyzed using mixed linear models and a zero-inflated 2-part model.

Results
Women (mean age = 55.5 years) receiving CT with or without RT (n = 73) had higher odds (odds ratio = 2.97, 95% confidence interval = 1.52 to 5.8) of having detectable p16INK4a following treatment compared with RT (n = 76) or surgery alone (n = 37). The proportion of women expressing 16INK4a over the follow-up period increased in all treatment groups (P &lt; .001), with no interaction by treatment. All groups also increased over time in DNA damage response (P &lt; .001), SenMayo (P &lt; .001), and senescence-associated secretory phenotype (P &lt; .001). Groups differed in the pattern of increase over time with statistically significant quadratic time by group differences for CT with or without RT compared with RT alone for DNA damage response (P = .05), SenMayo (P = .006), and the senescence-associated secretory phenotype (P = .02).

Conclusions
Results revealed activation of genes associated with biological aging in women with breast cancer from diagnosis through early survivorship, including DNA damage response, cell senescence, and the inflammatory secretome. Increases were evident across cancer treatments, although women receiving CT showed sustained increases, whereas RT exhibited slowing at later time points. Overall, findings suggest that women treated for breast cancer are aging within their immune cells.
Symbolic Communication and Cross-Domain Deterrence
Authors: Gurantz Ron 
Published: October 2024

Abstract
New military technologies in space and cyberspace have led to an interest in cross-domain deterrence, the threat of one type of attack to deter an attack of a different type. However, fundamental questions remain unanswered. Previous studies do not explain why threats often default to in-domain or “in-kind” retaliations or why cross-domain threats often lack credibility. In this article, I argue that “in-kind” retaliation is essentially a symbolic act. In its resemblance or relationship to the original attack, it communicates its purpose as a retaliation for that attack. I also argue that cross-domain threats can sometimes be imbued with the same symbolic meaning and be redefined as an “in-kind” response, and I explore mechanisms through which this can be done.
A dissipative extension to ideal hydrodynamics
Authors: Hatton Marcus John , Hawke Ian 
Published: October 2024

ABSTRACT
We present a formulation of special relativistic dissipative hydrodynamics (SRDHD) derived from the well-established Müller–Israel–Stewart (MIS) formalism using an expansion in deviations from ideal behaviour. By re-summing the non-ideal terms, our approach extends the Euler equations of motion for an ideal fluid through a series of additional source terms that capture the effects of bulk viscosity, shear viscosity, and heat flux. For efficiency these additional terms are built from purely spatial derivatives of the primitive fluid variables. The series expansion is parametrized by the dissipation strength and time-scale coefficients, and is therefore rapidly convergent near the ideal limit. We show, using numerical simulations, that our model reproduces the dissipative fluid behaviour of other formulations. As our formulation is designed to avoid the numerical stiffness issues that arise in the traditional MIS formalism for fast relaxation time-scales, it is roughly an order of magnitude faster than standard methods near the ideal limit.
scATAcat: cell-type annotation for scATAC-seq data
Authors: Altay Aybuge , Vingron Martin 
Published: October 2024

Abstract
Cells whose accessibility landscape has been profiled with scATAC-seq cannot readily be annotated to a particular cell type. In fact, annotating cell-types in scATAC-seq data is a challenging task since, unlike in scRNA-seq data, we lack knowledge of ‘marker regions’ which could be used for cell-type annotation. Current annotation methods typically translate accessibility to expression space and rely on gene expression patterns. We propose a novel approach, scATAcat, that leverages characterized bulk ATAC-seq data as prototypes to annotate scATAC-seq data. To mitigate the inherent sparsity of single-cell data, we aggregate cells that belong to the same cluster and create pseudobulk. To demonstrate the feasibility of our approach we collected a number of datasets with respective annotations to quantify the results and evaluate performance for scATAcat. scATAcat is available as a python package at https://github.com/aybugealtay/scATAcat.
TrajectoryGeometry suggests cell fate decisions can involve branches rather than bifurcations
Authors: Laddach Anna , Pachnis Vassilis , Shapiro Michael 
Published: October 2024

Abstract
Differentiation of multipotential progenitor cells is a key process in the development of any multi-cellular organism and often continues throughout its life. It is often assumed that a bi-potential progenitor develops along a (relatively) straight trajectory until it reaches a decision point where the trajectory bifurcates. At this point one of two directions is chosen, each direction representing the unfolding of a new transcriptional programme. However, we have lacked quantitative means for testing this model. Accordingly, we have developed the R package TrajectoryGeometry. Applying this to published data we find several examples where, rather than bifurcate, developmental pathways branch. That is, the bipotential progenitor develops along a relatively straight trajectory leading to one of its potential fates. A second relatively straight trajectory branches off from this towards the other potential fate. In this sense only cells that branch off to follow the second trajectory make a ‘decision’. Our methods give precise descriptions of the genes and cellular pathways involved in these trajectories. We speculate that branching may be the more common behaviour and may have advantages from a control-theoretic viewpoint.
Burden of Illness Associated With Respiratory Syncytial Virus, Influenza, and Coronavirus Disease 2019 in Infants and Young Children in Ontario, Canada, 2018–2023: A Population-Based Canadian Immunization Research Network Study
Authors: Jorgensen Sarah C J , Hernandez Alejandro , Buchan Sarah A , Fitzpatrick Tiffany , Guttmann Astrid , Morris Shaun K , Kwong Jeffrey C 
Published: October 2024

Abstract

Background
As severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transitions to endemicity and respiratory syncytial virus (RSV) and influenza reestablish their seasonal circulation patterns, understanding their comparative burden on infants and children can guide health system responses and funding priorities.

Methods
This was a population-based cohort study of children aged &lt;5 years in Ontario, Canada, from September 2018 to August 2023 using linked health administrative databases.

Results
Seasonal cohorts comprised 731 838 to 763 660 children. RSV- and influenza-related hospital admission rates immediately decreased in March 2020. In 2021–2022, RSV-related admissions rebounded but remained 8%–11% lower than prepandemic seasons, whereas 2022–2023 RSV-related admissions increased 105%–113% versus prepandemic seasons and peak admissions occurred in November versus December. Influenza did not rebound until 2022–2023, when admissions were 28%–37% higher than prepandemic seasons. Coronavirus disease 2019 (COVID-19)–related admissions remained low until 2021–2022 and were lower than RSV-related admissions across all age groups during prepandemic and pandemic seasons. By contrast, 2021–2022 COVID-19-related admissions exceeded prepandemic influenza-related admissions by 30%–40% but decreased by 45% in 2022–2023 and were lower than prepandemic influenza-related admissions, except among infants aged &lt;12 months who remained at highest risk. There was no distinct seasonal pattern for COVID-19–related admissions during the study.

Conclusions
RSV remains a major cause of childhood hospitalization. Although COVID-19 appears to be receding, its disease burden as it transitions to endemicity remains to be established. The unprecedented peaks in RSV-related hospital admissions during 2022–2023, together with the return of influenza and ongoing SARS-CoV-2 transmission, underscore the need to strengthen systems for real-time surveillance and to proactively prepare for critical healthcare scenarios.
Microphase iron particle growth promoted by solar wind implantation in lunar soils
Authors: Lu Xuejin , Chen Jian , Cao Haijun , Fu Xiaohui , Zeng Xiaojia , Qiao Le , Liu Chengbao , Zhang Guang , Zhang Peng , Ling Zongcheng 
Published: October 2024

Abstract
Lunar soils record the history and spectral changes resulting from the space-weathering process. The solar wind and micrometeoroids are the main space-weathering agents leading to darkening (decreasing albedo) and reddening (increasing reflectance with longer wavelength) of visible and near-infrared spectra. Nevertheless, their relative contributions are not well constrained and understood. In this study, we examine the near-infrared spectral variation as a function of lunar latitude and chemical composition using remote spectroscopic analysis of mare basalts and swirl regions. The results indicate that the reflectance of lunar mature soils darkens and the spectral slope flattens (reddening effect saturation) in areas of enhanced solar wind flux. We propose a previously unrecognized stage of space weathering (the post-mature stage), in which solar wind implantation may contribute to the growth and coarsening of metallic iron particles into larger microphase iron. This space-weathering mechanism is dominated by the solar wind and has important implications for understanding the alteration processes of airless bodies across our solar system.
T2 MRI visible perivascular spaces in Parkinson’s disease: clinical significance and association with polysomnography measured sleep
Authors: Meinhold Lena , Gennari Antonio G , Baumann-Vogel Heide , Werth Esther , Schreiner Simon J , Ineichen Christian , Baumann Christian R , O’Gorman Tuura Ruth 
Published: October 2024

Abstract
Poor sleep quality might contribute to the risk and progression of neurodegenerative disorders via deficient cerebral waste clearance functions during sleep. In this retrospective cross-sectional study, we explore the link between enlarged perivascular spaces (PVS), a putative marker of sleep-dependent glymphatic clearance, with sleep quality and motor symptoms in patients with Parkinson’s disease (PD). T2-weighted magnetic resonance imaging (MRI) images of 20 patients and 17 healthy control participants were estimated visually for PVS in the basal ganglia (BG) and centrum semiovale (CSO). The patient group additionally underwent a single-night polysomnography. Readouts included polysomnographic sleep features and slow-wave activity (SWA), a quantitative EEG marker of sleep depth. Associations between PVS counts, PD symptoms (MDS-UPDRS scores), and sleep parameters were evaluated using correlation and regression analyses. Intra- and inter-rater reproducibility was assessed with weighted Cohen`s kappa coefficient. BG and CSO PVS counts in both patients and controls did not differ significantly between groups. In patients, PVS in both brain regions was negatively associated with SWA (1–2 Hz; BG: r(15) = −.58, padj = .015 and CSO: r(15) = −.6, padj = .015). Basal ganglia PVS counts were positively associated with motor symptoms of daily living (IRR = 1.05, CI [1.01, 1.09], p = .007, padj = .026) and antidepressant use (IRR = 1.37, CI [1.05, 1.80], p = .021, padj = .043) after controlling for age. Centrum Semiovale PVS counts in patients were positively associated with a diagnosis of REM sleep behavior disorder (IRR = 1.39, CI [1.06, 1.84], p = .018, padj = .11). These results add to evidence that sleep deterioration may play a role in impairing glymphatic clearance via altered perivascular function, potentially contributing to disease severity in PD patients.
Selective depletion of kisspeptin neurons in the hypothalamic arcuate nucleus in early juvenile life reduces pubertal LH secretion and delays puberty onset in mice
Authors: Coutinho Eulalia A. , Esparza Lourdes A. , Steffen Paige H. , Liaw Reanna , Bolleddu Shreyana , Kauffman Alexander S. 
Published: October 2024

AbstractPuberty is the critical developmental transition to reproductive capability driven by the activation of gonadotropin‐releasing hormone (GnRH) neurons. The complex neural mechanisms underlying pubertal activation of GnRH secretion still remain unknown, yet likely include kisspeptin neurons. However, kisspeptin neurons reside in several hypothalamic areas and the specific kisspeptin population timing pubertal onset remains undetermined. To investigate this, we strategically capitalized on the differential ontological expression of the Kiss1 gene in different hypothalamic nuclei to selectively ablate just arcuate kisspeptin neurons (aka KNDy neurons) during the early juvenile period, well before puberty, while sparing RP3V kisspeptin neurons. Both male and female transgenic mice with a majority of their KNDy neurons ablated (KNDyABL) by diphtheria toxin treatment in juvenile life demonstrated significantly delayed puberty onset and lower peripubertal LH secretion than controls. In adulthood, KNDyABL mice demonstrated normal in vivo LH pulse frequency with lower basal and peak LH levels, suggesting that only a small subset of KNDy neurons is sufficient for normal GnRH pulse timing but more KNDy cells are needed to secrete normal LH concentrations. Unlike prior KNDy ablation studies in rats, there was no alteration in the occurrence or magnitude of estradiol‐induced LH surges in KNDyABL female mice, indicating that a complete KNDy neuronal population is not essential for normal LH surge generation. This study teases apart the contributions of different kisspeptin neural populations to the control of puberty onset, demonstrating that a majority of KNDy neurons in the arcuate nucleus are necessary for the proper timing of puberty in both sexes.
Targeting KRAS in gynecological malignancies
Authors: Peng Yuanyuan , Yang Qing 
Published: October 2024

AbstractCervical, endometrial, and ovarian cancers stand prominently as the leading gynecological malignancies of the female reproductive system. The conventional therapeutic modalities for gynecological malignancies have predominantly encompassed surgery, chemotherapy, and radiotherapy. However, efficacy of these approaches remains limited in cases of relapse or drug resistance. KRAS is one of the most frequently mutated oncogenes in human cancers. The KRAS gene encodes a small guanosine triphosphatase protein that acts as a molecular switch for crucial intracellular signaling pathways. KRAS mutations are deeply involved in the occurrence and development of gynecological malignancies. The present review aims to expound upon the role of oncogenic KRAS as a biomarker, elucidating various therapeutic approaches under investigation targeting the KRAS pathway in gynecological tumors.
Masking Effects Caused by Contralateral Distractors in Participants With Versus Without Listening Difficulties
Authors: Kawase Tetsuaki , Obuchi Chie , Suzuki Jun , Katori Yukio , Sakamoto Shuichi 
Published: October 2024

Objectives:
To examine the effects of distractor sounds presented to the contralateral ear on speech intelligibility in patients with listening difficulties without apparent peripheral pathology and in control participants.

Design:
This study examined and analyzed 15 control participants (age range, 22 to 30 years) without any complaints of listening difficulties and 15 patients (age range, 15 to 33 years) diagnosed as having listening difficulties without apparent peripheral pathology in the outpatient clinic of the Department of Otolaryngology-Head and Neck Surgery, Tohoku University Hospital. Speech intelligibility for 50 Japanese monosyllables presented to the right ear was examined under the following three different conditions: “without contralateral sound,” “with continuous white noise in the contralateral ear,” and “with music stimuli in the contralateral ear.”

Results:
The results indicated the following: (1) speech intelligibility was significantly worse in the patient group with contralateral music stimuli and noise stimuli; (2) speech intelligibility was significantly worse with contralateral music stimuli than with contralateral noise stimuli in the patient group; (3) there was no significant difference in speech intelligibility among three contralateral masking conditions (without contra-stimuli, with contra-noise, and with contra-music) in the control group, although average and median values of speech intelligibility tended to be worse with contralateral music stimuli than without contralateral stimuli.

Conclusions:
Significantly larger masking effects due to a contralateral distractor sound observed in patients with listening difficulties without apparent peripheral pathology may suggest the possible involvement of masking mechanisms other than the energetic masking mechanism occurring in the periphery in these patients. In addition, it was also shown that the masking effect is more pronounced with real environmental sounds, that is, music with lyrics, than with continuous steady noise, which is often used as a masker for speech-in-noise testing in clinical trials. In other words, it should be noted that a speech-in-noise test using such steady noise may underestimate the degree of listening problems of patients with listening difficulties in their daily lives, and a speech-in-noise test using a masker such as music and/or speech sounds could make listening problems more obvious in patients with listening difficulties.
The Effect of Night-time versus Full-time Bracing on the Sagittal Profile in Adolescent Idiopathic Scoliosis
Authors: Heegaard Martin , Ragborg Lærke , McIntosh Amy L. , Johnson Megan E. , Gehrchen Martin , Sucato Daniel J , Dahl Benny , Ohrt-Nissen Søren 
Published: October 2024

Study Design.
Retrospective multicenter cohort study

Objective.
To investigate the impact of night-time bracing (NTB) and full-time bracing (FTB) on the sagittal profile in adolescent idiopathic scoliosis (AIS) patients.

Summary of background data.
Recent studies have shown that FTB in AIS patients may induce hypokyphosis. Whether this effect differs between NTB and FTB is unknown.

Methods.
We included skeletally immature AIS patients with main curves ranging from 20-45° treated with either NTB or FTB. The two cohorts were propensity-score matched on Risser stage, age, major curve size, and kyphosis at brace initiation. Coronal and sagittal radiographic parameters were gathered at the initiation and completion of brace treatment.

Results.
Two-hundred fifty-seven patients were eligible for inclusion. The matched cohorts included 62 patients in each group. During bracing, the thoracic kyphosis increased from 31±11° to 35±13° in the NTB group compared to a decrease from 30±12° to 28±13° in the FTB group (P=0.011). Eight percent were hypokyphotic (<20°) after bracing in the NTB group compared to 24% in the FTB group (P=0.015). Pelvic incidence, sacral slope, and pelvic tilt were not significantly different between the groups. In the coronal plane, curve progression >50° was seen in 50% in the NTB group and 31% in FTB (P=0.028).

Conclusion.
We saw a small increase in thoracic kyphosis in the NTB group vs. a small decrease in the FTB group. Eight percent in the NTB group vs 24% in the FTB group showed substantial hypokyphosis after bracing. The impact of minor changes in thoracic kyphosis remains uncertain; however, a threefold difference in the occurrence of hypokyphosis is notable and merits further attention.