bluuebunny/crossref_metadata_2025_split huggingface dataset:
Merging white dwarf binaries produce Type Ia supernovae in elliptical galaxies
Authors: Tucker Michael A 
Published: December 2024

ABSTRACT
I find that Type Ia supernovae (SNe Ia) with bimodal nebular emission profiles occur almost exclusively in massive (${\rm M_\star } \gtrsim 10^{11}~{\rm M_\odot }$) galaxies with low star formation rates (SFR $\lesssim 0.5~{\rm M_\odot }$ yr−1). The bimodal profiles are likely produced by two white dwarfs (WDs) that exploded during a merger or collision, supported by a correlation between the peak-to-peak velocity separation ($v_{\rm sep}$) and the SN Ia peak luminosity ($M_V$) which arises naturally from more massive WD binaries synthesizing more $^{56}$Ni during the explosion. The distributions of SNe Ia with and without bimodal nebular lines differ in host mass, SFR, and specific SFR with Kolmogorov–Smirnov test probabilities of $3.1{{\ \rm per\ cent}}$, $0.03{{\ \rm per\ cent}}$, and $0.02{{\ \rm per\ cent}}$, respectively. Viewing angle effects can fully explain the SNe Ia in quiescent hosts without bimodal emission profiles and the dearth of merger/collision driven SNe Ia in star-forming hosts requires at least two distinct progenitor channels for normal SNe Ia. $30\!-\!40{{\ \rm per\ cent}}$ of all SNe Ia originate from mergers or collisions depending on how cleanly host environment distinguishes progenitor scenarios. Existing models for WD mergers and collisions broadly reproduce the $v_{\rm sep}$–$M_V$ correlation and future analyses may be able to infer the masses/mass-ratios of merging WDs in external galaxies.
The knowledge and skills required for the onco-rheumatologist: Study of four-year consultation records of a high-volume cancer centre
Authors: Takeda Koichi , Shiga Taro 
Published: December 2024

ABSTRACT

Objectives
Onco-rheumatology, the intersection of oncology and rheumatology, is an emerging field requiring further definition. This study aimed to identify the knowledge and skills essential for rheumatologists in clinical oncology.

Methods
We retrospectively reviewed consultations with the onco-rheumatology department of a high-volume tertiary cancer centre in Japan from January 2020 to December 2023.

Results
We analysed 417 consultations. The most common consultation (229, 55%) was related to immune checkpoint inhibitor-induced immune-related adverse events (irAEs). Of the 238 irAEs in 185 patients, 15% were rheumatic and 85% were nonrheumatic (e.g. hepatobiliary toxicities, colitis). Approximately 25% of nonendocrine irAEs were refractory/relapsing, requiring second-line therapy (e.g. mycophenolate mofetil, biologics, immunoglobulin). In addition to irAE consultations, 137 (33%) consultations were about possible rheumatic diseases. The final diagnosis often related to cancer treatment, such as granulocyte colony-stimulating factor-related aortitis (15 patients, 11%), olaparib-related erythema nodosum (10 patients, 7.3%), and surgical menopause-related arthralgia (10 patients, 7.3%). Five patients (3.6%) were diagnosed with autoinflammatory bone disease mimicking bone tumours.

Conclusions
Onco-rheumatologists are expected to play a central role in the management of a wide range of irAEs, not limited to rheumatic irAEs. They must also manage rheumatologic manifestations during cancer treatment and rheumatic diseases that mimic tumours.
Tylomys nudicaudus (Rodentia: Cricetidae)
Authors: Monroy-Gamboa Alina Gabriela , Álvarez-Castañeda Sergio Ticul , Trujano-Álvarez Ana Lilia 
Published: December 2024

Abstract
Tylomys nudicaudus Peters, 1866, is a large cricetid commonly called Peter’s Climbing Rat. It can be distinguished from other members of Tylomys by its reddish-brown to light brown dorsal pelage, which becomes more intense on the flanks, whitish or pale reddish-yellow ventral pelage, and large, dark, naked ears. The tail length is almost as long as head–body length, naked, and shiny with large scales forming wide rings along the dark, proximal two-thirds; the distal portion of the tail is white. It is a nocturnal and crepuscular arboreal species that inhabits deciduous and evergreen tropical forests in México, Belize, Guatemala, Honduras, El Salvador, and Nicaragua. Globally, it is listed as “Least Concern” by the International Union for Conservation of Nature.
TSS-Captur: a user-friendly pipeline for characterizing unclassified RNA transcripts
Authors: Witte Paz Mathias , Vogel Thomas , Nieselt Kay 
Published: December 2024

Abstract
RNA-seq and its 5′-enrichment methods for prokaryotes have enabled the precise identification of transcription start sites (TSSs), improving gene expression analysis. Computational methods are applied to these data to identify TSSs and classify them based on proximal annotated genes. While some TSSs cannot be classified at all (orphan TSSs), other TSSs are found on the reverse strand of known genes (antisense TSSs) but are not associated with the direct transcription of any known gene. Here, we introduce TSS-Captur, a novel pipeline, which uses computational approaches to characterize genomic regions starting from experimentally confirmed but unclassified TSSs. By analyzing TSS data, TSS-Captur characterizes unclassified signals, complementing prokaryotic genome annotation tools. TSS-Captur categorizes extracted transcripts as either messenger RNA for genes with coding potential or non-coding RNA (ncRNA) for non-translated genes. Additionally, it predicts the transcription termination site for each putative transcript. For ncRNA genes, the secondary structure is computed. Moreover, all putative promoter regions are analyzed to identify enriched motifs. An interactive report allows seamless data exploration. We validated TSS-Captur with a Campylobacter jejuni dataset and characterized unlabeled ncRNAs in Streptomyces coelicolor. TSS-Captur is available both as a web-application and as a command-line tool.
ReAlign-N: an integrated realignment approach for multiple nucleic acid sequence alignment, combining global and local realignments
Authors: Zhai Yixiao , Zhou Tong , Wei Yanming , Zou Quan , Wang Yansu 
Published: December 2024

Abstract
Ensuring accurate multiple sequence alignment (MSA) is essential for comprehensive biological sequence analysis. However, the complexity of evolutionary relationships often results in variations that generic alignment tools may not adequately address. Realignment is crucial to remedy this issue. Currently, there is a lack of realignment methods tailored for nucleic acid sequences, particularly for lengthy sequences. Thus, there’s an urgent need for the development of realignment methods better suited to address these challenges. This study presents ReAlign-N, a realignment method explicitly designed for multiple nucleic acid sequence alignment. ReAlign-N integrates both global and local realignment strategies for improved accuracy. In the global realignment phase, ReAlign-N incorporates K-Band and innovative memory-saving technology into the dynamic programming approach, ensuring high efficiency and minimal memory requirements for large-scale realignment tasks. The local realignment stage employs full matching and entropy scoring methods to identify low-quality regions and conducts realignment through MAFFT. Experimental results demonstrate that ReAlign-N consistently outperforms initial alignments on simulated and real datasets. Furthermore, compared to ReformAlign, the only existing multiple nucleic acid sequence realignment tool, ReAlign-N, exhibits shorter running times and occupies less memory space. The source code and test data for ReAlign-N are available on GitHub (https://github.com/malabz/ReAlign-N).
IDclust: Iterative clustering for unsupervised identification of cell types with single cell transcriptomics and epigenomics
Authors: Prompsy Pacôme , Saichi Mélissa , Raimundo Félix , Vallot Céline 
Published: December 2024

Abstract
The increasing diversity of single-cell datasets require systematic cell type characterization. Clustering is a critical step in single-cell analysis, heavily influencing downstream analyses. However, current unsupervised clustering algorithms rely on biologically irrelevant parameters that require manual optimization and fail to capture hierarchical relationships between clusters. We developed IDclust, a framework that identifies clusters with significant biological features at multiple resolutions using biologically meaningful thresholds like fold change, adjusted P-value and fraction of expressing cells. By iteratively processing and clustering subsets of the dataset, IDclust guarantees that all clusters found have significantly different features and stops only when no more interpretable cluster is found. It also creates a hierarchy of clusters, enabling visualization of the hierarchical relationships between different clusters. Analyzing multiple single-cell transcriptomic reference datasets, IDclust achieves superior clustering accuracy compared to state of the art algorithms. We showcase its utility by identifying previously unannotated clusters and identifying branching patterns in scATAC datasets. Using it’s unsupervised nature and ability to analyze different -omics, we compare the resolution of different histone marks in multi-omic paired-tag dataset. Overall, IDclust automates single-cell exploration, facilitates cell type annotation and provides a biologically interpretable basis for clustering.
Radiographic and visual response to the type II RAF inhibitor tovorafenib in children with relapsed/refractory optic pathway glioma in the FIREFLY-1 trial
Authors: Nysom Karsten , Kilburn Lindsay B , Leary Sarah E S , Landi Daniel B , de Vos-Kerkhof Evelien , Perreault Sébastien , Witt Olaf , Ziegler David S , Hernáiz Driever Pablo , Franson Andrea T , Baxter Patricia A , Whipple Nicholas S , Kline Cassie , Segal Devorah , Jabado Nada , Bailey Simon , McCowage Geoffrey , Hansford Jordan R , Khuong-Quang Dong-Anh , Gottardo Nicholas G , Hassall Timothy , Han Jung Woo , Yalon Oren Michal , Chi Susan N , Qiu Jiaheng , Da Costa Daniel , Govinda Raju Sandya , Manley Peter , Hargrave Darren 
Published: December 2024

Abstract

Background
Due to their anatomical locations, optic pathway gliomas (OPGs) can rarely be cured by resection. Given the importance of preserving visual function, we analyzed radiological and visual acuity (VA) outcomes for the type II RAF inhibitor tovorafenib in the OPG subgroup of the phase 2 FIREFLY-1 trial.

Methods
FIREFLY-1 investigated the efficacy (arm 1, n = 77), safety, and tolerability (arms 1/2) of tovorafenib (420 mg/m2 once weekly; 600 mg maximum) in patients with BRAF-altered relapsed/refractory pediatric low-grade glioma (pLGG). In this post hoc analysis, anti-tumor activity and VA were analyzed in arm 1 patients with OPG. Anti-tumor activity was independently assessed per Response Assessment in Neuro-Oncology high-grade glioma (RANO-HGG), Response Assessment in Pediatric Neuro-Oncology-LGG (RAPNO), and RANO-LGG criteria. The data cutoff was June 5, 2023.

Results
Forty-two of 77 patients had OPGs; 35 of 42 had ≥2 VA assessments. The overall response rate in the OPG subgroup according to RANO-HGG, RAPNO, and RANO-LGG criteria were 64%, 50%, and 55%, with clinical benefit rates of 95%, 88%, and 90%, respectively. VA per patient was preserved for 80% of patients; 31% demonstrated improved VA; VA per eye was preserved in 87%, with 27% improving. The safety profile in the arm 1 OPG subgroup was similar to the overall FIREFLY-1 safety analysis set.

Conclusions
Tovorafenib demonstrated anti-tumor activity in relapsed/refractory BRAF-altered OPG across radiological assessment criteria and was generally well tolerated. Importantly, vision remained stable or improved in most patients.
Exploring spirituality in everyday neuro-oncology practice – nurses’ and physicians’ spiritual care toolbox
Authors: Völz Daniela , Grabenweger Reinhard , Best Megan C , Hau Peter , Jones Kate F , Linker Ralf , Paal Piret , Bumes Elisabeth 
Published: December 2024

Abstract

Background
Patients with primary malignant brain tumors suffer from symptoms of both neoplastic and neurological disease, resulting in a limited prognosis and high symptomatic burden, including aphasia and mental deterioration. Thus, special spiritual care needs arise for these patients, which may be challenging. We explore spiritual tools that neurological and neurosurgical healthcare workers use when confronted with spiritual distress of their patients.

Methods
A vignette-based, cross-sectional, multicenter online survey was conducted to collect qualitative data. In total, 143 nurses and physicians working on 41 neurological and neurosurgical units in Bavarian hospitals participated and their self-reported behavior was analyzed using reflexive thematic analysis.

Results
A total of 5 themes regarding the spiritual tools implemented by nurses and physicians in neuro-oncology were generated: (1) from physical to spiritual care, (2) feeling togetherness between the words, (3) listening to each other: one word at a time, (4) away from the dooming “why”—escaping the thought spirals, and (5) taking life back into one’s own hands. These themes represent a spectrum including nonverbal tools like building a physical connection, allowing for emotional connection, and active listening. The verbal approach focuses on conversation strategies to relieve patients of guilt, facilitate spiritual discussions at the end-of-life, and communicate the diagnosis, prognosis, and treatment to strengthen self-efficacy.

Conclusions
Verbal, nonverbal, and holistic approaches to spiritual care in neuro-oncology were identified and can be used to develop a spiritual care toolbox for nurses and physicians in neuro-oncology, given the unique needs of patients with primary malignant brain tumors.
Cigarette Smoking Trajectories of US Young Adults by Sex
Authors: Harton Moriah R , Parker Maria A 
Published: December 2024

Abstract

Introduction
While cigarette smoking is the leading cause of preventable morbidity and mortality in the United States, nearly one-fifth of young adults continue to smoke cigarettes; however, the prevalence remains higher in males than females.

Methods
The restricted panel data from the Monitoring the Future study was used, which follows a nationally representative sample of 12th-grade students (modal age 18) from 1976 to 2019 (n = 24 293). A group-based trajectory model was fit to the data for each sex (male/female), where groups were determined by cigarette smoking (yes/no) from the base year through the six biennial follow-up questionnaires. The analysis was then repeated overall and by decade.

Results
Four trajectory groups of cigarette smoking emerged for both sexes (male/female). Group 1 (60.8/62.0%) included participants with nonuse of cigarettes. Group 2 (13.1/14.2%) captured individuals with a moderate probability of use of cigarettes at baseline that decreased over time. Group 3 (7.1/5.5%) was the opposite of group 2, where participants had a low/moderate probability of cigarette smoking at baseline that increased over time. Group 4 (19.0/18.3%) captured individuals with high/moderate to high use of cigarettes throughout the study period. Overall and by decade analyses produced similar results.

Conclusions
Almost one-quarter of the sample had increasing or high cigarette smoking, which suggests prioritizing interventions on recent high school graduates, regardless of sex, who begin with low cigarette smoking and increase over time and those with consistently high cigarette smoking. Future research will examine how different cigarette smoking trajectories relate to substance use and mental health outcomes.

Implications
This study provides a novel viewpoint on cigarette trajectory analysis for the young adult population, stratified by sex. This stratification showed that regardless of sex, the same four distinct trajectory groups were present. This result was somewhat unanticipated as there are known discrepancies in both cigarette smoking initiation and cessation between the sexes.
Risk Factors for Disseminated Tuberculosis and Associated Survival in Adults Without Human Immunodeficiency Virus
Authors: Huang Wei , Fei Zhentao , Yan Bo , Liu Xuhui , Liu Ping , Xia Lu , Liu Huarui , Xi Xiuhong , Ye Dan , Shen Yinzhong 
Published: December 2024

Abstract

Background
The global resurgence of disseminated tuberculosis (TB) after the coronavirus disease 2019 pandemic highlights the necessity of understanding host risk factors, especially in adults without human immunodeficiency virus.

Methods
We reviewed TB cases admitted to Shanghai Public Health Clinical Center from 2017 to 2022. We analyzed baseline characteristics and outcomes. To identify risk factors for disseminated TB, as well as its subsite distribution and mortality, we employed logistic regression and Cox proportional hazards models.

Results
Among 1062 patients, including 283 with disseminated TB, 558 with pulmonary TB (PTB), and 221 with extrapulmonary TB, those with disseminated TB had the highest mortality rate. The following factors were associated with disseminated TB: age ≥45 years, body mass index (BMI) &lt;18.5 kg/m², immunosuppressive therapy, and end-stage renal disease (ESRD). A BMI &lt;18.5 kg/m² was found to correlate with all subsites of disseminated TB, while aged ≥45 years specifically increased incidence of bone and joint TB. Female patients showed a higher risk for lymphatic, peritoneal, and intestinal TB. Additionally, immunosuppressive therapy and ESRD were linked to various TB subsites. During a 12-month follow-up period, 19.8% of patients with disseminated TB died. Factors contributing to reduced survival included BMI &lt;18.5 kg/m², immunosuppressive therapy, ESRD, pulmonary cavities, and meningeal involvement.

Conclusions
Age, low BMI, immunosuppressive therapy, and ESRD are significant risk factors for disseminated TB and also significantly impact patient survival rates. These findings are of great importance for the development of clinical management and preventive measures.
The Employment Value Proposition
Authors: Shepherd William J. 
Published: December 2024

Abstract
This chapter describes the business case for employee value propositions (EVPs) that will aid in an organization’s employment branding efforts. The “4 Ps” marketing model and segmentation analysis is applied to create compelling “why us” messaging. Examples and a template are provided. Defining a target demographic is essential for filling the pipeline of critical talent segments. The authors outline a four-step process of evaluating an EVP with research: (1) define the focus; (2) identify the target market; (3) gather data; and (4) analyze the data.
Introduction
Authors: McIver Lopes Dominic , Matherne Samantha , Matthen Mohan , Nanay Bence 
Published: December 2024

Abstract
People do not appreciate unfamiliar art as deeply as those who have known it all their lives; empirical studies confirm that few features in any art category have universal appeal. From the eighteenth century onward, relatively few European philosophers built this diversity into the foundations of their aesthetic theories, and their critics argue that this deficiency stems from colonialist and other discriminatory ideologies. Recent analytic philosophers of art inherit some of this indifference to diversity, though some have fashioned tools that could assist in understanding the phenomenon. This introduction surveys highlights of this history.
Land Concentration in Early Modern European Development and Its Intellectual Legacy
Authors: Berry Albert 
Published: December 2024

Abstract
A prominent belief or narrative around British agriculture has been the existence of economies of scale, such that the enclosures of past centuries raised overall productivity and facilitated agriculture’s contribution to the Industrial Revolution. Those enclosures both increased the area operated by the main landholders and reduced the amount operated as commons; both trends were seen as raising overall productivity. The availability of more empirical evidence and its analysis over the last few decades have thrown both contentions into doubt and have suggested that small units can be as productive, or even more so, than larger ones and that open fields (commons) are not necessarily less productive. The traditional British narrative has, however, been widely disseminated around the world, and it is still widely believed, even as evidence of the greater efficiency of small farms in some settings has grown.
Twentieth-Century Land Reforms in the East Asian Tigers, India, the Middle East, and the Philippines
Authors: Berry Albert 
Published: December 2024

Abstract
The land reform experiences carried out in Asia and the Middle East have ranged from the most successful anywhere (in Korea, Taiwan, and Japan), to only marginally or modestly helpful (in the Philippines and Egypt), to tragic, when an opening in Iran under President Mossadegh was blocked by oil-dependent Britain and the US. In India, the reform experiences of individual states ranged from impressive (in Kerala and East Bengal) to absent, reflecting, among other things, the differing political power of lower income groups. The very special conditions of the three great success stories, which left a legacy of fast and egalitarian growth leading, over time, to democratic rule, underlines how seldom those conditions are likely to be met and helps to explain the low success rate of reforms. At the other extreme, the special conditions of Iran in the 1950s exemplify the recipe for lasting socio-political disaster when a potential reform is blocked.
The Last Battleground for Rural Land Issues
Authors: Berry Albert 
Published: December 2024

Abstract
Contemporary Sub-Saharan Africa (SSA) is the lowest-income and most agriculture-dependent region in the world. Population growth remains fast, and the average farm size is very small, with over sixty percent having no more than one hectare. Most countries have less hierarchical social and economic systems than found elsewhere, with every family’s right to some land being generally recognized and few families being totally landless. This community-oriented system has, however, been evolving toward a more individual rights-based one. The current context in most of the region involves low average incomes, often accompanied by the damaging effects of climate change, by ethnic and other violence (Ethiopia, Sudan, Congo, and others) and by autocratic governments. Small farming typically provides the most promising short- and medium-term employment opportunities. The standard inverse relationship (IR) between farm size and land productivity appears to be generally present but less systematic and less marked than elsewhere. Major successes in terms of raising small farm productivity have been registered in Rwanda and Ethiopia over select periods. Various political factors, including a lack of understanding in government of the potential of small-scale farming, along with pressure from larger farmers to bias policy in their favor, and from foreign business interests to sell and subsidize their products, give rise to the threat that much of the region may follow Latin America’s path to high concentrations of land and of income. Improved policy and better support from outside are needed to stop or slow this trend.