bluuebunny/crossref_metadata_2025 huggingface dataset:
Designing a blockchain technology platform for enhancing the pre-exposure prophylaxis care continuum
Authors: Khurshid Anjum , Harrell Daniel Toshio , Li Dennis , Hallmark Camden , Hanson Ladd , Viswanathan Nishi , Carr Michelle , Brown Armand , McNeese Marlene , Fujimoto Kayo
Published: December 2024

Objectives

Pre-exposure prophylaxis (PrEP) is a key biomedical intervention for ending the HIV epidemic in the United States, but its uptake is impeded by systemic barriers, including fragmented workflows and ineffective data coordination. This study aims to design PrEPLinker, a blockchain-based, client-centered platform to enhance care to address these challenges by improving care coordination and enabling clients to securely manage their identity and PrEP-related data.

Materials and Methods

Using Houston, Texas, as a use case, we conducted a needs assessment with PrEP collaborators to evaluate existing workflows and identify barriers in the PrEP care continuum. Based on these findings, we designed PrEPinker, a blockchain-based identity framework and digital wallet using self-sovereign identity and verifiable credentials (VCs). These features enable clients to securirely control their identity data and facilitate efficient, privacy-serving data sharing across PrEP service points, such as community testing sites, clinics, and pharmacies.

Results

The needs assessment identified significant gaps in data exchange for PrEP referrals and follow-up appointments. In response, PrEPLinker was designed to incorporate decentralized identifiers—unique, secure digital identifiers that are not linked to any centralized authority—and VCs for ensuring seamless transfer of digital medical records. Preliminary usability testing with 15 participants showed that over 70% rated the interactive design positively, finding it easy to use, learn, and navigate without technical support. Additionally, more than 80% expressed confidence in using the blockchain based platform to manage sensitive health information securely.

Discussion and Conclusion

Blockchain technology offers a promising, client-centered solution for addressing systemic barriers in PrEP care by improving data cordination, security, and client control over personal health information. The design of PrEPLinker demorates the potential to streamline PrEP referrals, follow-up processes, and data managent. These advancements in data coordination and secruity could improve PrEP uptake and adherence, supporting efforts to reduce HIV transmission in Houston and beyond.
Ionic control of small GTPase HRas using calmodulin
Authors: Sabek Yassine , Zhang Ziyun , Nishibe Nobuyuki , Maruta Shinsaku
Published: December 2024

HRas is a small GTPase that plays physiologically important roles in various intracellular signal transduction processes, such as cell growth and proliferation. The structure and action mechanisms of HRas have been well characterized, leading to its widespread use as a molecular switch in bionanomachines. Calmodulin (CaM), a calcium ion-binding protein, acts as an ion-binding molecular switch and activates the target enzymes. We previously demonstrated that the fusion protein of HRas (M13-HRas) with the CaM target peptide M13 at the N-terminus of HRas exhibits reversible regulation of GTPase activity and the interaction between M13-HRas and the downstream signalling factor Raf by calcium ions with CaM. In this study, we prepared two new HRas fusion proteins with the M13 peptide at the C-terminus (HRas-M13) and both termini (M13-HRas-M13) of HRas and analysed the calcium-dependent regulation of HRas function. M13-HRas-M13 more efficiently controlled GTPase, interaction with Raf and the HRas regulator GEF by calcium ions with CaM.
Supplementation of essential amino acids suppresses age-associated sleep loss and sleep fragmentation but not loss of rhythm strength under yeast-restricted malnutrition in Drosophila
Authors: Chikamatsu Sachie , Sakakibara Yasufumi , Takei Kimi , Nishijima Risa , Iijima Koichi M , Sekiya Michiko
Published: December 2024

Sleep quality and quantity decrease with age, and sleep disturbance increases the risk of many age-associated diseases. There is a significant relationship between nutritional status and sleep outcomes, with malnutrition inducing poor sleep quality in older adults. However, it remains elusive whether, and if so how, nutritional supplementation prevents age-associated sleep problems. Here, we utilized Drosophila to investigate the effects of a malnutrition diet with restricted yeast, a primary protein source, and supplementation of 10 essential amino acids (EAAs) on sleep profiles during ageing. Compared with the standard diet containing 2.7% yeast, the malnutrition diet containing 0.27% yeast significantly decreased target of rapamycin (TOR) signalling and shortened the lifespan of male Canton-S flies. By contrast, age-associated sleep loss, sleep fragmentation and loss of rhythm strength were similarly observed under both diets. Supplementation of the malnutrition diet with EAAs in restricted yeast significantly ameliorated age-associated sleep loss and sleep fragmentation without altering loss of rhythm strength. It also rescued decreased TOR signalling activity but not the shortened lifespan, suggesting that the effects of EAAs on sleep integrity are independent of TOR activity and lifespan regulation. These results may help to develop dietary interventions that improve age-related sleep problems in humans.
First, ‘things’ first: prioritizing environmental goods tariff reductions at the WTO
Authors: Hinman Maureen , Stewart Sarah V
Published: December 2024

Negotiations to liberalize trade in environmental goods are a key indicator for the World Trade Organization’s (WTO) capacity to pursue climate and environmental objectives. Experience with Environmental Goods Agreement negotiations within the WTO demonstrates the necessity to establish obligations and/or procedures that link environment and trade law as the WTO pursues a sustainability agenda.
Bayesian SAR Model with Stochastic Volatility and Multiple Time-Varying Weights
Authors: Costola Michele , Iacopini Matteo , Wichers Casper
Published: December 2024

A novel spatial autoregressive model with time-varying structural variance for panels of time series data is introduced. It incorporates multilayer networks and accounts for dynamic relationships, thus enabling the analysis of shock propagation through time-varying spillover effects. The proposed method outperforms alternative spatial model benchmarks in an empirical application investigating the impact of cooperative and conflictual geopolitical relationships on G7 stock markets. The results indicate that cooperative interactions have a greater influence on stock markets than conflictual ones, highlighting the collaborative nature of the G7. They also reveal heterogeneous network exposures and distinct patterns of direct and indirect spillover effects.
Pregnancy is associated with a simultaneous but independent increase in circulating CD177pos and immature low-density granulocytes
Authors: Dahlstrand Rudin Agnes , Torell Agnes , Popovic Jordan , Stockfelt Marit , Jacobsson Bo , Rudin Anna , Christenson Karin , Lundell Anna-Carin , Bylund Johan
Published: December 2024

The neutrophil marker CD177 (NB1, HNA-2a) is expressed by 0-100% of circulating neutrophils in any given donor, dividing neutrophils into two distinct subpopulations (CD177pos and CD177neg). High proportions of CD177pos blood neutrophils have been linked to both systemic infections and a range of inflammatory pathologies, but whether this is a cause or a consequence of disease is not known. Many conditions displaying elevated CD177pos neutrophil proportions are also accompanied by the presence of circulating low-density granulocytes (LDGs). Accordingly, it is tempting to speculate that these two events are connected, i.e., that proportions of CD177pos neutrophils increase as a result of an enlarged pool of circulating LDGs. A temporary increase in CD177pos neutrophils, in combination with the presence of LDGs has been reported during pregnancy. The present study aimed to investigate whether elevated proportions of CD177pos neutrophils in peripheral blood from pregnant women can be attributed to the presence of LDGs. We found that LDGs were indeed present in pregnancy and included both immature, and activated mature neutrophils. The proportion of CD177pos LDGs increased over time during pregnancy and correlated with a simultaneous increase in immature cells. However, a majority of immature neutrophils were CD177neg, meaning that increased release of immature cells cannot explain the increased proportions of the CD177pos subtype. Therefore, although LDGs and CD177pos neutrophils are expanded simultaneously during pregnancy these events occur independent from each other.
Drivers of nine-banded armadillo occupancy and expansion near the edge of their northern range
Authors: Larreur Max R , Remmers Justin J , Audia Ellen M , Suriyamongkol Thanchira , Buckman Katherine M , Pershyn Nadine A , Pease Brent S , Bastille-Rousseau Guillaume , Nielsen Clayton K
Published: December 2024

Since the 1850s, nine-banded armadillos (Dasypus novemcinctus) have expanded their range northward and eastward and have behaviorally plastic diurnal activity patterns. However, landscape features influencing their distribution and activity are generally unknown in recently colonized areas. We used occupancy modeling and activity analysis to investigate spatiotemporal patterns of armadillos at multiple spatial scales in newly colonized areas near the leading edge of their northerly range in southern Illinois, USA. We placed 848 camera traps (in clusters of 3 cameras) across 17,146 trap nights throughout a 16,058 km2 study area from January to April 2022 to 2023. We documented 242 detections of armadillos yielding a naïve occupancy (i.e., the proportion of camera clusters with a detection) of 0.23. Predicted occupancy was 0.00 to 0.92 across our study extent. At the 200 m scale, armadillo occupancy increased with greater forest connectivity and proximity to major roads but decreased in areas with greater agricultural connectivity. At the 500 and 1,000 m scales, occupancy increased as forest cover and proximity to major roads increased. At the 1,000 m scale, however, occupancy decreased as agricultural connectivity increased. Additionally, armadillo activity was predominantly nocturnal. Roadways may be influencing armadillo spatiotemporal behavior by providing dispersal corridors into heavily forested areas and acting as thermal refugia as armadillos expand into northern environments. Naïve occupancy of armadillos a decade ago was <0.01 and has experienced a >30-fold increase, potentially bolstered by climate change and anthropogenic land use practices. Expansion of armadillos may continue as land use practices continue to create seminatural refugia and dispersal corridors in forested areas along roadways.
Climate warming intensifies plant–soil causal relationships in a coastal wetland
Authors: Sun Baoyu , Ping Jiaye , Jiang Ming , Xia Jianyang , Xia Fanyu , Han Guangxuan , Yan Liming
Published: December 2024

The intricate interplay among plant productivity and soil factors is a pivotal driver for sustaining the carbon sequestration capacity of coastal wetlands. Yet, it remains uncertain whether climate warming will reshape the cause-and-effect interactions between coastal plant productivity and soil factors. In this study, we combined a manipulative warming experiment with a convergent cross-mapping technique to quantify the causal relationships, which can be either unidirectional or bidirectional, between plants (gross primary productivity, GPP) and soil environment (e.g. soil temperature, moisture and salinity). Our findings revealed that warming amplified the interaction between GPP and soil salinity in the coastal wetland ecosystem. While soil temperature primarily drove this causal relationship in control plots, a more complex interaction emerged in warming plots: soil salinity not only directly influenced GPP but also indirectly affected it by altering soil temperature and moisture. Overall, warming increased the number of causal pathways linking GPP with soil environmental factors, such as the effect of soil salinity on GPP and the impacts of GPP on soil moisture. These findings provide experimental evidence of intensified plant–soil causality in coastal wetlands under climate warming.
Features of internal absorbed dose microdistribution in biological tissue irradiated by 31SiO2 microparticles compared with dose microdistribution from exposure to 56MnO2 particles
Authors: Stepanenko Valeriy , Kaprin Andrey , Ivanov Sergey , Shegay Peter , Bogacheva Viktoria , Shinkarev Sergey , Sato Hitoshi , Kawano Noriyuki , Ohtaki Megu , Fujimoto Nariaki , Endo Satoru , Sakaguchi Aya , Ostroumova Evgenia , Zhumadilov Kassym , Kushugulova Almagul , Hoshi Masaharu
Published: December 2024

Radiobiological studies are ongoing to understand the consequences of internal exposure to neutron-activated radioactive microparticles, which were sprayed over experimental rats and mice. Special attention in these experiments is given to internal irradiation with radioactive microparticles with short-lived neutron-activated radionuclides 31Si (T1/2 = 2.62 h) and 56Mn (T1/2 = 2.58 h), which are among the main dose-forming factors from residual radioactivity activated in soils by neutrons in the first hours after atmospheric nuclear explosions. The presented work is devoted to microdosimetry peculiarities of 31SiO2 and 56MnO2 microparticles. The radiation from 31Si consists of intensive short-range beta particles and gamma rays with very low intensity. It differs from the radiation of 56Mn, which includes intensive beta particles, low energy Auger electrons and very intensive gamma rays. Differences in the energies and intensities of short-range beta particles and penetrating gamma rays emitted by 31SiO2 and 56MnO2 microparticles can lead to differences in the spatial microdistribution of absorbed dose around the corresponding radioactive microparticles embedded in biological tissue. It was found in the presented work that the absorbed doses of beta radiation emitted by 56MnO2 and 31SiO2 microparticles has significant but different spatial gradients with distances in biological tissue that correspond to the typical thickness of epithelial cells of lungs’ alveoli and bronchioles. The results obtained are necessary for a better understanding of radiobiological effects of internal exposure by radioactive microparticles with 56Mn and 31Si observed in framework of performed and ongoing radiobiological studies with experimental animals—rats and mice.
Quantifying the Impact of Sustained Acceleration on Critical Care Transport Medical Equipment
Authors: Babcock Lyle , Brawley Hayley , Freeman David , Hegedus Joseph , Beer Jeremy , Nowadly Craig
Published: December 2024

Introduction

Military and commercial stakeholders are investing to explore the use of hypersonic aircraft and orbital spacecraft to transport cargo, medical supplies, passengers, and casualties. These vehicle platforms require periods of sustained acceleration, but to date, these dynamic forces have not been comprehensively considered in the environment of critical care patient movement because injured patients and advanced aeromedical evacuation (AE) equipment are rarely subjected to these conditions. While military AE equipment does undergo crash hazard acceleration testing, equipment functionality during or after sustained acceleration remains to be evaluated. This study was performed to fill that knowledge gap.

Materials and Methods

AE equipment currently used by the U.S. Air Force and Critical Care Air Transport Teams (ZOLL EMV+ 731 ventilator and ZOLL Propaq MD cardiac monitor) was subjected to low (2.5 g), moderate (4.5 g), and variable acceleration (1.5–4.5 g) for 3-minute periods at the KBR Brooks Centrifuge. AE equipment was tested for functionality in 3 different orientations (gX, gY, and gZ). Predetermined variations were made in equipment input settings to ensure each equipment item would function across mission-relevant conditions (differing ventilator tidal volumes, differing cardiac monitor arterial pressure inputs, etc.). AE was evaluated for accuracy compared to controlled inputs, alarm conditions, and equipment failure.

Results

The EMV+ 731 ventilator and Propaq MD cardiac monitor had no equipment failures during testing. The ventilator had clinically negligible variations in tidal volume, peak pressure, and fraction of inspired oxygen during acceleration. At the highest tidal volume tested (480 mL), the ventilator had elevated peak pressure results. However, we believe this was due to limitations in test-lung resistance and was not related to a ventilator fault. Mild effects of sensor orientation were recorded in the Propaq MD blood pressure results; for example, gX and gY differed by 5.9 ± 1.21 mmHg at 75 mmHg input (P < .01) and 6.45 ± 1.229 mmHg with 150 mmHg input (P < .001).

Conclusions

The EMV+ 731 ventilator and Propaq MD cardiac monitor had reliable clinical performance despite sustained acceleration. This knowledge will facilitate immediate follow-on experimentation with advanced models of combat injury during simulated medical evacuation in sustained acceleration environments.
Hydrostatic mass bias for galaxy groups and clusters in the FLAMINGO simulations
Authors: Braspenning Joey , Schaye Joop , Schaller Matthieu , Kugel Roi , Kay Scott T
Published: December 2024

The masses of galaxy clusters are commonly measured from X-ray observations under the assumption of hydrostatic equilibrium (HSE). This technique is known to underestimate the true mass systematically. The fiducial FLAMINGO (Full-hydro Large-scale structure simulations with All-sky Mapping for the Interpretation of Next Generation Observations) cosmological hydrodynamical simulation predicts the median hydrostatic mass bias to increase from $b_\text{HSE} \equiv (M_\text{HSE,500c}-M_\text{500c})/M_\text{500c} \approx -0.1$ to −0.2 when the true mass increases from group to cluster mass scales. However, the bias is nearly independent of the hydrostatic mass. The scatter at fixed true mass is minimum for $M_\text{500c}\sim 10^{14}~\text{M}_\odot$, where $\sigma (b_\text{HSE})\approx 0.1$, but increases rapidly towards lower and higher masses. At a fixed true mass, the hydrostatic masses increase (decrease) with redshift on group (cluster) scales, and the scatter increases. The bias is insensitive to the choice of analytic functions assumed to represent the density and temperature profiles, but it is sensitive to the goodness of fit, with poorer fits corresponding to a stronger median bias and a larger scatter. The bias is also sensitive to the strength of stellar and active galactic nucleus feedback. Models predicting lower gas fractions yield more (less) biased masses for groups (clusters). The scatter in the bias at fixed true mass is due to differences in the pressure gradients rather than in the temperature at $R_\text{500c}$. The total kinetic energies within $r_\text{500c}$ in low- and high-mass clusters are sub- and supervirial, respectively, though all become subvirial when external pressure is accounted for. Analyses of the terms in the virial and Euler equations suggest that non-thermal motions, including rotation, account for most of the hydrostatic mass bias. However, we find that the mass bias estimated from X-ray luminosity weighted profiles strongly overestimates the deviations from HSE.
Merging white dwarf binaries produce Type Ia supernovae in elliptical galaxies
Authors: Tucker Michael A
Published: December 2024

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

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

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

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

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

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

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

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

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

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) <18.5 kg/m², immunosuppressive therapy, and end-stage renal disease (ESRD). A BMI <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 <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

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

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

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

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

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.
We Need a Larger Data Toolbox
Authors: Bhargava Rahul
Published: December 2024

Community-level organizations are increasingly using data to further their goals but struggle to connect to people via standard tools such as tables, charts, and graphs. At the same time a growing number of public decisions are made based on data; key global challenges are best understood using data, and data production is increasing in all parts of our lives. I’ve been working on this disconnect for over fifteen years, applying my experiences as a computer engineer and educator to design learning activities and collaborations across newspapers, museums, libraries, civil society organizations, and government. My experiences have shown me how radical pedagogies and arts practices from those pro-social institutions inspire alternative approaches to working with and representing data, ones that can help avoid replicating the burdened history of data as a tool for control.
Center Impact
Authors: Bhargava Rahul
Published: December 2024

When working with data in community settings you can align your efforts with social goals by learning from other local institutions. The origins of data production date back to the invention of language and communication, but more recently norms have emerged from statistics and science. A case study of gender rights activists in Mexico demonstrates an alternative, how an arts-based approach to producing and sharing data via public spectacle can create impacts across society. This is more in line with the goals of museums, newspapers, libraries, civil society organizations, and civic governance. A brief history and evocative example from each of those sectors lays the foundation for more appropriate and effective ways to use data in the community settings they work in. We can learn from the methods and goals of how the pro-social sector works to promote the common good with data in communities.
Focus on Participation
Authors: Bhargava Rahul
Published: December 2024

Opportunities for creative participation, offered at any part of the process of working with data, empower and engage community members who might otherwise feel left out of data-centered processes. Standard approaches only connect to those who already feel comfortable with math, statistics, or computation. The theories and approaches of data for good, critical data literacy, data justice, and data feminism all inform alternative approaches to engaging more groups of people around data. Two case studies about participatory community murals introduce the idea of creating data murals as an example of a process that focuses on participation at every step of working with data in a community setting. Combined with a survey of work putting participatory data on screens and walls, we can see how growing a toolbox for participatory data storytelling can engage larger sets of people in empowering ways, putting the justice-focused critiques of datafication into action.
Build Mirrors, not Windows
Authors: Bhargava Rahul
Published: December 2024

Data windows are used to observe some other group and make decisions that impact them from afar; data mirrors reflect information about a community back to itself for informing action. Eugenicists in the 1920s used data as a window, leading to examples like racist data collection that inform the sizes of women’s clothing still today. Surveying modern educational data literacy programs showcases the tension between using data as a window and using data as a mirror. The growing practice of creating data sculptures, physical representations of data in 3D, offers strong opportunities for building data mirrors for and with communities. Government officials, artists, academic researchers, and others are exploring how data sculptures offer understandable forms of data to broad audiences. They operate as data mirrors, opening opportunities to engage diverse populations around data about their own communities for their own needs.
Open many Doors
Authors: Bhargava Rahul
Published: December 2024

Data stories that use sound, taste, and smell open doors for new types of learners to engage with data stories, pushing beyond the visual-focused approaches that dominate data work. Taxonomies that describe different ways of knowing show how critical it is to engage community members in a variety of ways around data. Diving deeper into our senses of hearing, smelling, and tasting adds more radical approaches to the expanded toolbox needed for data representation in community settings. A case study about a physical data display showing environmental contaminant data offers early evidence for how creative multi-sensory representations can change how people engage with data. Sonification, edibilization, and smellification are emerging and growing as playful and evocative forms of representing data. Journalists, museums, nonprofits, and others are well positioned to build multi-sensory data experiences using culturally relevant forms to engage communities that are otherwise left out of formal visual-focused data processes.