bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Physalis system: discovery of ORC-like radio shells around a massive pair of interacting early-type galaxies with offset X-ray emission
Authors: Koribalski Bärbel S , Khabibullin Ildar , Dolag Klaus , Churazov Eugene , Norris Ray P , Carretti Ettore , Hopkins Andrew M , Vernstrom Tessa , Shabala Stanislav S , Gupta Nikhel 
Published: July 2024

ABSTRACT
We present the discovery of large radio shells around a massive pair of interacting galaxies and extended diffuse X-ray emission within the shells. The radio data were obtained with the Australian Square Kilometre Array Pathfinder (ASKAP) in two frequency bands centred at 944 MHz and 1.4 GHz, respectively, while the X-ray data are from the XMM–Newton observatory. The host galaxy pair, which consists of the early-type galaxies ESO 184-G042 and LEDA 418116, is part of a loose group at a distance of only 75 Mpc (redshift $z = 0.017$). The observed outer radio shells (diameter ${\sim}$145 kpc) and ridge-like central emission of the system, ASKAP J1914−5433 (Physalis), are likely associated with merger shocks during the formation of the central galaxy (ESO 184-G042) and resemble the new class of odd radio circles (ORCs). This is supported by the brightest X-ray emission found offset from the centre of the Physalis system, instead centred at the less massive galaxy, LEDA 418116. The host galaxy pair is embedded in an irregular envelope of diffuse light, highlighting ongoing interactions. We complement our combined radio and X-ray study with high-resolution simulations of the circumgalactic medium (CGM) around galaxy mergers from the Magneticum project to analyse the evolutionary state of the Physalis system. We argue that ORCs/radio shells could be produced by a combination of energy release from the central active galactic nucleus and subsequent lightening up in radio emission by merger shocks travelling through the CGM of these systems.
Theorizing Musical Improvisation for Social Analysis
Authors: Martin Ryan 
Published: July 2024

Abstract
The connections between musical improvisation and society are a topic of frequent scholarly interest. These investigations take a range of analytical approaches, often adapted to the specifics of the improvised musicking being examined. This paper synthesizes existing concepts and theories to produce a framework for improvisation that is applicable to the social analysis of a wide range of improvisatory musical practices. The three foundational tenets of this framework are: (1) improvisation is one musical property among many that occurs to varying degrees and in different ways that fluctuate across space, time, and relevant actors; (2) the interactions between musical improvisation and the other properties of a given musical event are crucial for understanding its social implications; and (3) understanding these properties and their interactions requires examining the specific actions taken by improvisers in context. After outlining these tenets, the paper explores the role of various social, material, and individual factors in shaping improvisation and why examining these is crucial to social analysis. Finally, the paper demonstrates this model with a brief analysis of musical improvisation’s political impacts during the cacerolazos of the 2001–2002 Argentine Financial Crisis. The result of this paper is a theorization of improvisatory musicking especially suited to social analysis.
Glioma oncogenesis in the Constitutional mismatch repair deficiency (CMMRD) syndrome
Authors: Guerrini-Rousseau Lea , Merlevede Jane , Denizeau Philippe , Andreiuolo Felipe , Varlet Pascale , Puget Stéphanie , Beccaria Kevin , Blauwblomme Thomas , Cabaret Odile , Hamzaoui Nadim , Bourdeaut Franck , Faure-Conter Cécile , Muleris Martine , Colas Chrystelle , Adam de Beaumais Tiphaine , Castel David , Rouleau Etienne , Brugières Laurence , Grill Jacques , Debily Marie-Anne 
Published: July 2024

Abstract

Background
Constitutional mismatch repair deficiency (CMMRD) is a cancer predisposition due to biallelic mutations in one of the mismatch repair (MMR) genes associated with early onset of cancers, especially high-grade gliomas. Our aim was to decipher the molecular specificities of these gliomas.

Methods
Clinical, histopathological, and whole exome sequencing data were analyzed in 12 children with genetically proven CMMRD and a high-grade glioma.

Results
PDL1 expression was present in immunohistochemistry in 50% of the samples. In 9 patients, the glioma harbored an ultra-hypermutated phenotype (104–635 coding single nucleotide variants (SNV) per Mb, median 204). Driver mutations in POLE and POLD1 exonuclease domains were described for 8 and 1 patients respectively and were always present in the mutation burst with the highest variant allele frequency (VAF). The mutational signatures were dominated by MMR-related ones and similar in the different mutation bursts of a same patient without subsequent enrichment of the mutation signatures with POL-driven ones. Median number of coding SNV with VAF above one of the driving polymerase mutation per Mb was 57 (17–191). Our findings suggest that somatic polymerase alterations does not entirely explain the ultra-hypermutant phenotype. SETD2, TP53, NF1, EPHB2, PRKDC, and DICER1 genes were frequently mutated with higher VAF than the deleterious somatic polymerase mutation.

Conclusions
CMMRD-associated gliomas have a specific oncogenesis that does not involve usual pathways and mutations seen in sporadic pediatric or adult glioblastomas. Frequent alterations in other pathways such as MAPK may suggest the use of other targeted therapies along with PD1 inhibitors.
Comprehensive multimodal deep learning survival prediction enabled by a transformer architecture: A multicenter study in glioblastoma
Authors: Gomaa Ahmed , Huang Yixing , Hagag Amr , Schmitter Charlotte , Höfler Daniel , Weissmann Thomas , Breininger Katharina , Schmidt Manuel , Stritzelberger Jenny , Delev Daniel , Coras Roland , Dörfler Arnd , Schnell Oliver , Frey Benjamin , Gaipl Udo S , Semrau Sabine , Bert Christoph , Hau Peter , Fietkau Rainer , Putz Florian 
Published: July 2024

Abstract

Background
This research aims to improve glioblastoma survival prediction by integrating MR images, clinical, and molecular-pathologic data in a transformer-based deep learning model, addressing data heterogeneity and performance generalizability.

Methods
We propose and evaluate a transformer-based nonlinear and nonproportional survival prediction model. The model employs self-supervised learning techniques to effectively encode the high-dimensional MRI input for integration with nonimaging data using cross-attention. To demonstrate model generalizability, the model is assessed with the time-dependent concordance index (Cdt) in 2 training setups using 3 independent public test sets: UPenn-GBM, UCSF-PDGM, and Rio Hortega University Hospital (RHUH)-GBM, each comprising 378, 366, and 36 cases, respectively.

Results
The proposed transformer model achieved a promising performance for imaging as well as nonimaging data, effectively integrating both modalities for enhanced performance (UCSF-PDGM test-set, imaging Cdt 0.578, multimodal Cdt 0.672) while outperforming state-of-the-art late-fusion 3D-CNN-based models. Consistent performance was observed across the 3 independent multicenter test sets with Cdt values of 0.707 (UPenn-GBM, internal test set), 0.672 (UCSF-PDGM, first external test set), and 0.618 (RHUH-GBM, second external test set). The model achieved significant discrimination between patients with favorable and unfavorable survival for all 3 datasets (log-rank P 1.9 × 10−8, 9.7 × 10−3, and 1.2 × 10−2). Comparable results were obtained in the second setup using UCSF-PDGM for training/internal testing and UPenn-GBM and RHUH-GBM for external testing (Cdt 0.670, 0.638, and 0.621).

Conclusions
The proposed transformer-based survival prediction model integrates complementary information from diverse input modalities, contributing to improved glioblastoma survival prediction compared to state-of-the-art methods. Consistent performance was observed across institutions supporting model generalizability.
Sun-related knowledge and practices in Irish construction and agricultural workers
Authors: Hogan V , Hogan M , Kirwan O , Langan Walsh C , McLaughlin C , Moynihan Á , Connolly A , Walsh J , Coggins M 
Published: July 2024

Abstract

Background
Agricultural and construction workers spend much of their work time outdoors and have higher risks of developing skin cancer when compared to indoor workers. However, there is limited research on ultraviolet radiation (UVR) exposure knowledge, sun safety practices and constraints within these occupational groups in Ireland.

Aims
This study aimed to examine self-reported time spent outdoors in a sample of Irish agricultural and construction workers; to describe and compare UVR exposure knowledge, safety practices and perceived constraints in both occupational groups, and to assess the association of demographic, personal and occupational factors with sun-related knowledge, practices and perceived constraints.

Methods
Agricultural workers (n = 154) and construction workers (n = 467) completed a questionnaire, which measured solar UVR exposure knowledge, safety practices, and perceived constraints to sun personal protective equipment and sunscreen use in addition to demographic, personal, and workplace characteristics. Mann–Whitney and Kruskal–Wallis tests were used to examine differences in knowledge, practices and perceived constraints by these characteristics.

Results
Both groups spend a significant proportion of their working week outdoors (25 hours per week on average). Although participation in sun safety training was high for both groups, UVR exposure knowledge and sunscreen use were low, and annual rates of reported sunburn were high. Knowledge, practices and perceived constraints also differed significantly according to demographic, personal, occupational and workplace characteristics.

Conclusions
In addition to training by employers and advisory groups, interventions are required to address perceived barriers that impede the uptake and usage of control measures that can lower risk.
Positive correlation between Ammospiza caudacuta (Saltmarsh Sparrow) capture and productivity supports use of a novel rapid assessment monitoring protocol
Authors: Sanchez Arthur , Roeder Mackenzie R , Olsen Brian J , Elizondo Elisa C , Ruskin Katharine J , Hotopp Alice M , Elphick Chris S , Apgar Sam E , Field Christopher R , Cohen Jonathan B , Kocek Alison R , Kovach Adrienne I , Longenecker Rebecca A , Shriver W Gregory 
Published: July 2024

Abstract
Salt marshes in the northeastern United States provide critical breeding habitat for tidal marsh specialist birds like the Ammospiza caudacuta (Saltmarsh Sparrow). The Ammospiza caudacuta population declined by 9% annually from 1998 to 2012, necessitating immediate conservation actions for this vulnerable species. However, estimating species vital rates across a large geographic region is logistically challenging and cost prohibitive. Therefore, we developed and tested a rapid assessment monitoring protocol focused on reproductive metrics to enhance future conservation planning. We used 3 years (2018, 2019, and 2021) of intensive demographic data from 12 sites to estimate daily nest survival, nest period success, fledglings produced per female, and successful broods per female. We implemented the rapid assessment protocol co-located at intensive sites in the same years to estimate the number of captured females and juveniles. We used Pearson’s correlation analyses to determine the association of intensive metrics with rapid metrics. We found that the sum of Ammospiza caudacuta female and juvenile captures was positively correlated with daily nest survival (r = 0.61, P = 0.01), nest period success (r = 0.70, P = 0.002), fledglings produced per female (r = 0.82, P &lt; 0.001), and successful broods per female (r = 0.82, P &lt; 0.001). Our results demonstrate that fixed-effort mist-netting from our rapid assessment protocol is an informative and time-efficient sampling method that can aid in making informed management decisions related to Ammospiza caudacuta conservation.
Viromes of Antarctic fish resemble the diversity found at lower latitudes
Authors: Grimwood Rebecca M , Waller Stephanie J , Wierenga Janelle R , Lim Lauren , Dubrulle Jérémy , Holmes Edward C , Geoghegan Jemma L 
Published: July 2024

Abstract
Antarctica harbours some of the most isolated and extreme environments on Earth, concealing a largely unexplored and unique component of the global animal virosphere. To understand the diversity and evolutionary histories of viruses in these polar species, we determined the viromes of gill metatranscriptomes from 11 Antarctic fish species with 248 samples collected from the Ross Sea region spanning the Perciformes, Gadiformes, and Scorpaeniformes orders. The continent’s shift southward and cooling temperatures &gt;20 million years ago led to a reduction in biodiversity and subsequent radiation of some marine fauna, such as the notothenioid fishes. Despite decreased host species richness in polar regions, we revealed a surprisingly complex virome diversity in Ross Sea fish, with the types and numbers of viruses per host species and individuals sampled comparable to that of fish in warmer marine environments with higher host community diversity. We also observed a higher number of closely related viruses likely representing instances of recent and historic host-switching events among the Perciformes (all notothenioids) than in the Gadiformes, suggesting that rapid speciation events within this order generated closely related host species with few genetic barriers to cross-species transmission. Additionally, we identified novel genomic variation in an arenavirus with a split nucleoprotein sequence containing a stable helical structure, indicating potential adaptation of viral proteins to extreme temperatures. These findings enhance our understanding of virus evolution and virus-host interactions in response to environmental shifts, especially in less diverse ecosystems that are more vulnerable to the impacts of anthropogenic and climate changes.
Origins, diversity, and adaptive evolution of DWV in the honey bees of the Azores: the impact of the invasive mite Varroa destructor
Authors: Lopes Ana R , Low Matthew , Martín-Hernández Raquel , Pinto M Alice , De Miranda Joachim R 
Published: July 2024

Abstract
Deformed wing virus (DWV) is a honey bee virus, whose emergence from relative obscurity is driven by the recent host-switch, adaptation, and global dispersal of the ectoparasitic mite Varroa destructor (a highly efficient vector of DWV) to reproduction on honey bees (Apis mellifera). Our study examines how varroa affects the continuing evolution of DWV, using the Azores archipelago, where varroa is present on only three out of the eight Islands, as a natural experimental system for comparing different evolutionary conditions and trajectories. We combined qPCR of 494 honey bee colonies sampled across the archipelago with amplicon deep sequencing to reveal how the DWV genetic landscape is altered by varroa. Two of the varroa-free Islands were also free of DWV, while a further two Islands were intriguingly dominated by the rare DWV-C major variant. The other four Islands, including the three varroa-infested Islands, were dominated by the common DWV-A and DWV-B variants. The varroa-infested Islands had, as expected, an elevated DWV prevalence relative to the uninfested Islands, but not elevated DWV loads, due the relatively high prevalence and loads of DWV-C on the varroa-free Islands. This establishes the Azores as a stable refuge for DWV-C and provides the most convincing evidence to date that at least some major strains of DWV may be capable of not just surviving, but actually thriving in honey bees in the absence of varroa-mediated transmission. We did not detect any change in DWV genetic diversity associated with island varroa status but did find a positive association of DWV diversity with virus load, irrespective of island varroa status.
CMV retinitis in non-HIV immunocompromised individuals on tofacitinib for rheumatoid arthritis
Authors: Smith Meghan J. , Lim Jennifer I. , Chau Felix Y. , Lobo-Chan Ann-Marie 
Published: July 2024

Purpose:
To describe two patients with long-standing rheumatoid arthritis (RA) who developed cytomegalovirus (CMV) retinitis (CMVR) while taking tofacitinib.

Methods:
Retrospective case series.

Results:
A 79-year-old woman with RA, treated with oral tofacitinib 11mg once daily, presented with blurred vision and pain in the right eye. Visual acuity (VA) was hand motion, anterior segment showed iritis and the intraocular pressure (IOP) was 35mmHg. Ophthalmoscopy revealed retinal hemorrhages and overlying vitreous hemorrhage. HIV serology was negative, serum CMV IgG was positive and aqueous polymerase chain reaction (PCR) was positive for CMV (802,000 IU/mL). An 82-year-old woman with a history of RA, treated with tofacitinib 11mg once daily, was referred for a white retinal lesion in the left eye. VA was 20/50, anterior segment was quiet and IOP was 23mmHg. Ophthalmoscopy revealed a yellow retinal lesion with ill-defined margins in the macula. She subsequently developed a new area of peripheral retinal whitening in the right eye. HIV serology was negative, serum CMV IgG was positive and aqueous PCR was positive for CMV (5,200,000 IU/mL).

Conclusion:
Diagnosis of CMVR in non-HIV individuals requires awareness of the risk of infectious retinitis in patients taking JAK inhibitors for the treatment of autoimmune disease.
Efficacy of intravenous acetaminophen on postoperative shivering: A meta-analysis of randomized controlled trials
Authors: Liu Jikai , Cao Qian , Zeng Jinfang , Liang Xiao 
Published: July 2024

Purpose:
Postoperative shivering (POS) is a common and vital complication after anesthesia, which may result in serious consequences and uncomfortable experiences. Acetaminophen has been used to treat fever and mild to moderate pain. However, there is not enough evidence to prove its advantage for POS. This meta-analysis aimed to explore the prophylactic use of acetaminophen as a valid agent for POS.

Methods:
Two researchers independently searched PubMed, the Cochrane Library, and Embase for controlled clinical trials. The meta-analysis of randomized controlled trials (RCTs) was performed by Review Manager.

Results:
Nine trials with 856 patients were included in our meta-analysis. Acetaminophen significantly reduced POS compared with placebo (pooled risk ratio [RR]: 0.43, 95% confidence interval [CI]: 0.35–0.52). What is more, not only 15 mg/kg but also 1000 mg intravenous acetaminophen could reduce the incidence of shivering compared with placebo.

Conclusion:
Our present meta-analysis demonstrates that the intravenous prophylactic infusion of acetaminophen may prevent POS, and the results may provide new evidence to expand the clinical value of acetaminophen in addition to its routine usage.
Ichthyosis uteri complicated by endometrial adenocarcinoma with transitional cell differentiation: A case report
Authors: Ding Liya , Liu Wangwang , Li Hui , Huang Dingpin , Chen Yang , An Huimin 
Published: July 2024

Rationale:
Ichthyosis uteri is a rare pathological condition characterized by the replacement of the endometrial lining by stratified squamous epithelium. Yet its occurrence with endometrial adenocarcinoma is very rare.

Patient concerns:
A 68-year-old woman has been experiencing sporadic, minor vaginal hemorrhages for a few months. The gynecological evaluation revealed a uterine enlargement and imaging demonstrated an irregular mass within the uterus.

Diagnosis:
Endometrial adenocarcinoma with transitional cell differentiation; ichthyosis uteri with dysplasia.

Interventions:
Radical hysterectomy with pelvic lymphadenectomy was performed followed by postoperative radiotherapy.

Outcomes:
Postoperative follow-up at 8 months showed a favorable outcome without signs of recurrence and metastasis.

Lessons:
Adequate pathological sampling is crucial to identifying the accompanying lesions of ichthyosis uteri. Finding molecular alterations in various pathological morphologies is important to understand the evolution of disease.
Unexpected rare uterine carcinosarcoma with neuroendocrine differentiation: Reflections on clinical diagnosis and treatment of a case report
Authors: Shi Qichong , Wang Longmei , Yao Juan 
Published: July 2024

Rationale:
Uterine carcinosarcoma (UCS) is a rare and highly invasive malignant tumor.It exhibits an ectopic growth pattern of the uterus,and its histological features are biphasic differentiation of malignant epithelial components (cancer) and malignant mesenchymal components (sarcoma). The pathological pattern of high-component neuroendocrine differentiation is extremely rare. Due to the inherent heterogeneity of tumors, it increases the difficulty of accurate identification and diagnosis. The author introduces a rare case of primary endometrial carcinosarcoma (heterologous) with small cell neuroendocrine carcinoma (SCNEC) components. There is limited literature on this rare pathological differentiation pattern and a lack of guidelines for the best treatment methods, which prompts reflection on the diagnosis, optimal treatment strategies, and how preoperative diagnosis can affect patient prognosis for endometrial carcinosarcoma with neuroendocrine differentiation.

Patient concerns:
The patient is an elderly woman who presents with abnormal vaginal bleeding after menopause. Transvaginal ultrasound examination shows that the uterus is slightly enlarged, and there is a lack of homogeneous echogenicity in the uterine cavity. Subsequently, a hysteroscopic curettage was performed, and a space-occupying lesion was observed on the anterior wall of the uterine cavity.

Diagnoses:
Preoperative endometrial biopsy revealed SCNEC of the endometrium. The patient underwent radical hysterectomy, and the postoperative pathological results showed that UCS (heterologous) was accompanied by SCNEC components (about 80%).

Intervention:
The patient received radical hysterectomy, followed by adjuvant chemotherapy.

Outcome:
After 7 months of follow-up, no tumor recurrence or metastasis was found at the time of writing this article.

Lessons:
The histological type of UCS (heterologous) with cell neuroendocrine carcinoma components is rare and highly invasive, with a high misdiagnosis rate in preoperative biopsy. There are currently no effective treatment guidelines for this type of case. The unusual appearance of SCNEC components in this case poses a challenge for both pathologists and surgeon. The rare differentiation pattern of this case exposes the complexity of its management and the necessity of prospective trials to determine the optimal treatment plan.