bluuebunny/crossref_metadata_2025_split huggingface dataset:
QOT: Quantized Optimal Transport for sample-level distance matrix in single-cell omics
Authors: Wang Zexuan , Zhan Qipeng , Yang Shu , Mu Shizhuo , Chen Jiong , Garai Sumita , Orzechowski Patryk , Wagenaar Joost , Shen Li 
Published: January 2025

Abstract
Single-cell technologies have enabled the high-dimensional characterization of cell populations at an unprecedented scale. The innate complexity and increasing volume of data pose significant computational and analytical challenges, especially in comparative studies delineating cellular architectures across various biological conditions (i.e. generation of sample-level distance matrices). Optimal Transport is a mathematical tool that captures the intrinsic structure of data geometrically and has been applied to many bioinformatics tasks. In this paper, we propose QOT (Quantized Optimal Transport), a new method enabling efficient computation of sample-level distance matrix from large-scale single-cell omics data through a quantization step. We apply our algorithm to real-world single-cell genomics and pathomics datasets, aiming to extrapolate cell-level insights to inform sample-level categorizations. Our empirical study shows that QOT outperforms existing two OT-based algorithms in accuracy and robustness when obtaining a distance matrix from high throughput single-cell measures at the sample level. Moreover, the sample level distance matrix could be used in the downstream analysis (i.e. uncover the trajectory of disease progression), highlighting its usage in biomedical informatics and data science.
Identifying cancer prognosis genes through causal learning
Authors: Wu Siwei , Yin Chaoyi , Wang Yuezhu , Sun Huiyan 
Published: January 2025

Abstract
Accurate identification of causal genes for cancer prognosis is critical for estimating disease progression and guiding treatment interventions. In this study, we propose CPCG (Cancer Prognosis’s Causal Gene), a two-stage framework identifying gene sets causally associated with patient prognosis across diverse cancer types using transcriptomic data. Initially, an ensemble approach models gene expression’s impact on survival with parametric and semiparametric hazard models. Subsequently, an iterative conditional independence test combined with graph pruning is utilized to infer the causal skeleton, thereby pinpointing prognosis-related genes. Experiments on transcriptomic data from 18 cancer types sourced from The Cancer Genome Atlas Project demonstrate CPCG’s effectiveness in predicting prognosis under four evaluation metrics. Validations on 24 additional datasets covering 12 cancer types from the Gene Expression Omnibus and the Chinese Glioma Genome Atlas Project further demonstrate CPCG’s robustness and generalizability. CPCG identifies a concise but reliable set of genes, obviating the need for gene combination enumeration for survival time estimation. These genes are also proved closely linked to crucial biological processes in cancer. Moreover, CPCG constructs a stable causal skeleton and exhibits insensitivity to the order of data shuffling. Overall, CPCG is a powerful tool for extracting cancer prognostic biomarkers, offering interpretability, generalizability, and robustness. CPCG holds promise for facilitating targeted interventions in clinical treatment strategies.
Recent advances of precision immunotherapy in sepsis
Authors: Arapis Antonios , Panagiotopoulos Dimitrios , Giamarellos-Bourboulis Evangelos J 
Published: January 2025

Abstract
Precision immunotherapy signifies the administration of the required type of immune intervention tailored to the state of immune activation at the appropriate time window. The classification of patients into the different states of immune activation is usually done by either a protein blood biomarker or a molecular blood endotype that is diagnostic of the precise immune state. Evidence coming from trials of the last decade suggests that immune interventions should be split into strategies aiming to attenuate the exaggerated immune responses, restore sepsis-induced immunoparalysis (SII) and restore the vascular tone. Suggested strategies to attenuate the immune responses are anakinra, nangibotide and tocilizumab. Biomarkers that guide their use are ferritin, soluble triggering receptor expressed on myeloid cells-1 and C-reactive protein. Suggested strategies to restore SII are nivolumab, recombinant human interferon-gamma, CYT107, granulocyte macrophage colony stimulating factor and IgM-enriched immunoglobulin prepapations. Biomarkers that guide their use are the expression of the human leukocyte antigen DR on blood monocytes, the absolute lymphocyte count and blood levels of immunoglobulin M. One recently suggested strategy to restore vascular tone is adrecizumab, the use of which is guided by blood levels of bio-adrenomedulin. The use of these precision treatment strategies is still hampered by the need for large-scale randomized controlled trials.
Contributions of short- and long-range white matter tracts in dynamic compensation with aging
Authors: Chakraborty Priyanka , Saha Suman , Deco Gustavo , Banerjee Arpan , Roy Dipanjan 
Published: January 2025

Abstract
Optimal brain function is shaped by a combination of global information integration, facilitated by long-range connections, and local processing, which relies on short-range connections and underlying biological factors. With aging, anatomical connectivity undergoes significant deterioration, which affects the brain’s overall function. Despite the structural loss, previous research has shown that normative patterns of functions remain intact across the lifespan, defined as the compensatory mechanism of the aging brain. However, the crucial components in guiding the compensatory preservation of the dynamical complexity and the underlying mechanisms remain uncovered. Moreover, it remains largely unknown how the brain readjusts its biological parameters to maintain optimal brain dynamics with age; in this work, we provide a parsimonious mechanism using a whole-brain generative model to uncover the role of sub-communities comprised of short-range and long-range connectivity in driving the dynamic compensation process in the aging brain.
We utilize two neuroimaging datasets to demonstrate how short- and long-range white matter tracts affect compensatory mechanisms. We unveil their modulation of intrinsic global scaling parameters, such as global coupling strength and conduction delay, via a personalized large-scale brain model. Our key finding suggests that short-range tracts predominantly amplify global coupling strength with age, potentially representing an epiphenomenon of the compensatory mechanism. This mechanistically explains the significance of short-range connections in compensating for the major loss of long-range connections during aging. This insight could help identify alternative avenues to address aging-related diseases where long-range connections are significantly deteriorated.
Equations for estimating resting energy expenditure in patients on peritoneal dialysis
Authors: Xu Xiao , Abi Nanzha , Yang Zhikai , Ma Tiantian , Zhang Nan , Zheng Yingdong , Dong Jie 
Published: January 2025

ABSTRACT

Background
In peritoneal dialysis (PD) patients, determining energy expenditure is essential for recommending energy intake in nutrition management.

Objective
We aimed to develop and validate a resting energy expenditure (REE) equation for patients with PD and compare it to previously available REE equations in dialysis patients.

Design
This cross-sectional study enrolled 200 patients with PD from two hospitals in Beijing, China. Stepwise linear regression analysis was used to derive a new REE equation (eREE-PD) based on actual REE (aREE) measured using indirect calorimetry (IC) in the development dataset. The eREE-PD value was then validated with aREE in the validation dataset and compared with values from existing equations obtained in general populations and those developed for chronic kidney disease and dialysis patients, in terms of bias, precision, and accuracy.

Results
The bias, precision, and accuracy of the eREE-PD equation were significantly better than those of the Harris–Benedict, WHO, and Schofield equations (P &lt; .005) and comparable to the Mifflin equation (P = .541 for bias, .988 for precision, and .359 for accuracy), with IC as the reference method. Either bias, precision or accuracy of the eREE-PD were significantly better than eREE-V, eREE-Bscr, and eREE-CFFM equations significantly (P &lt; .005) and similar to eREE-CKD, eREE-Bcrp, and eREE-Cweighht equations (P &gt; .05 for bias, precision, and accuracy). The bias, precision, and accuracy of the eREE-PD equation were consistent across subgroups categorized by hs-CRP levels.

Conclusion
The eREE-PD equation, based on age, sex, and weight data, may serve as a reliable and practical tool for estimating REE in patients with PD, aiding in individualized nutritional management. However, external validation in other populations is required to confirm its generalizability beyond the studied cohort.
Real-world continuous smartwatch-based user authentication
Authors: Al-Naffakh N , Clarke N , Li F , Haskell-Dowland P 
Published: January 2025

Abstract
User authentication is often regarded as the “gatekeeper” of cyber security. It has, however, long suffered from significant usability issues that have resulted in research focussing upon frictionless and transparent biometric approaches. Activity-based user authentication—a technique that authenticates a user by what they are physically doing at a specific point in time has attracted significant attention, particularly due to the increasing popularity of smartwatches. This research aims to overcome limitations in prior work by exploring the viability of the approach in real-world conditions. The study presents two principal experiments, one focused upon a constrained environment to provide a control and a second reflecting real-life. With over 1000 h of sampled data across 60 participants, the study sought to explore sensor, feature composition, and classifier design to explore the practical viability of the approach. Whilst the control experiment achieved best case Equal Error Rate of 0.29%, an improvement upon the prior art using optimisation, the best-case real-world results were not too far behind at 0.7%. This demonstrates that whilst the feature generated in the real-life experiment are subject to increased levels of noise, the performance is viable within the context of a transparent and continuous user authentication approach.
Dysplasia and Colorectal Cancer Surveillance in Ulcerative Colitis Patients in Latin America: Real-World Data
Authors: Parra-Izquierdo Viviana , Otero-Regino William , Juliao-Baños Fabian , Frías-Ordoñez Juan Sebastián , Ibañez-Pinilla Edgar , Gil-Parada Fabio Leonel , Marulanda-Fernández Hernando , Otero-Parra Lina , Otero-Ramos Elder , Puentes-Manosalva Fabian Eduardo , Guzmán Rojas Gerardo Andrés , Ernest-Suárez Kenneth , Villa-Ovalles Keyla , Paredes-Mendez Juan Eloy , Jara-Alba María Luisa , Andrade-Zamora David , Ardila-Báez Manuel Alonso , Flórez-Sarmiento Cristian , Veitia Guillermo , Sánchez Abel , Arango-Molano Lazaro Antonio , Fluxa Fernando , Freitas Queiroz Natália Sousa , Serrano Mariastella 
Published: January 2025

Abstract

Background
The prevalence of colorectal cancer (CRC) in patients with ulcerative colitis (UC) is higher than in the general population, in Latin America there is a progressive increase of UC, and information about CRC screening in inflammatory bowel disease (IBD) is scarce. The aim of this study was to analyze the findings of endoscopic surveillance of CRC in patients with IBD according to available technology.

Methods
Multicenter, cross-sectional, analytical study conducted in Latin American countries, in patients with UC, predominantly with more than 8 years of diagnosis and different degrees of disease activity. Surveillance colonoscopies were performed according to available technology. Risk factors for dysplasia detection were analyzed.

Results
One hundred and forty-four patients, 55.5% women, mean age 47.3 (range 17.1 to 90; SD 15.64) years and mean duration of disease 12.71 (range 0.64 to 57.13; SD 8.08) years. Forty-nine lesions were identified, 18 corresponded to dysplasia. The detection rate of dysplasia per lesion and per procedure was 36.7% and 12.5%, respectively. By logistic regression analysis, the duration of disease (OR 1.12;95%CI:1.047 to 1.215, P = .002) and the presence of post-inflammatory polyps (OR 3.4;95%CI:1.11 to 10.36, P = .031) were risk factors for higher detection of dysplasia. Digital chromoendoscopy was associated with greater detection of dysplasia (OR 4.99, 95%CI: 1.092 to 22.864, P = .038).

Conclusions
In our region, the duration of disease and the presence of post-inflammatory polyps were the factors with the highest association for dysplasia detection, and digital chromoendoscopy with directed biopsies was the technique of choice. The implementation of a specific surveillance program in colonoscopy in IBD is an effective strategy to achieve high detection rates.
Cardiometabolic Multimorbidity and Dementia Onset among Middle-aged and Older Adults: Differences by Race/Ethnicity
Authors: Chen Siting , Quiñones Ana R , Nagel Corey L , Bishop Nicholas , Allore Heather G , Newsom Jason T , Kaye Jeffrey , Botoseneanu Anda 
Published: January 2025

Abstract

Background
Racial/ethnic minoritized groups in the U.S. have higher prevalence of cardiometabolic multimorbidity and experience higher risk of dementia. This study evaluates the relationship between cardiometabolic multimorbidity and dementia onset according to racial/ethnic group in a nationally representative cohort of U.S. middle-aged and older adults.

Methods
Data from the Health & Retirement Study (1998-2018, N=7,960, mean baseline age 59.4 years) and discrete-time survival models were used to estimate differences in the risk of dementia onset, defined by Langa-Weir classification. Models included race/ethnicity (non-Hispanic White, non-Hispanic Black, Hispanic), chronic disease/multimorbidity categories (no disease, one disease, cardiovascular multimorbidity, metabolic multimorbidity, cardiometabolic multimorbidity, other multimorbidity), age, sex, education, wealth, body-mass index, and proxy status.

Results
Over a mean follow-up of 14.6 years, 7.7% of the participants (n=614) developed dementia. In the fully adjusted model, participants with cardiometabolic multimorbidity had the highest risk of dementia onset (HR:3.27, 95%CI: 2.06,5.21), followed by metabolic (HR:1.83, 95%CI: 1.14,2.94) and cardiovascular (HR:1.81, 95%CI: 1.24,2.64) multimorbidity, relative to participants with no disease. The risk of dementia was significantly greater among Black (HR: 6.40, 95% CI: 3.84,10.67) and Hispanic participants (HR: 4.90, 95% CI: 2.85,8.43) with cardiometabolic multimorbidity, compared to White adults with no disease.

Conclusions
Individuals from racial/ethnic minoritized groups have a higher risk of dementia. The risk of dementia onset was significantly greater for Black and Hispanic participants experiencing cardiometabolic multimorbidity, highlighting the value of intervening on cardiometabolic conditions among middle-age and older adults, in particular those from racial/ethnic minoritized backgrounds to reduce the risk of developing dementia.
Life-Space Restriction Following Disruptive Life Events: Evidence From the COVID-19 Pandemic
Authors: Lin Sapphire H , Chew Mary Su-Lynn , Lim Gek Hsiang , Ng Yee Sien 
Published: January 2025

Abstract

Objectives
Restriction of life-space mobility is associated with adverse health outcomes including depression, morbidity, mortality, and poorer quality of life. In this study, we aimed to determine the impact of coronavirus disease 2019 (COVID-19) and associated employment loss on the life space of older adults in Singapore.

Methods
An in-person survey was administered to a cohort of older Singaporeans above 50 years old (N = 1,118). Data collected included self-report measures of life space, sensory function, well-being, cognitive function, depression, frailty, and objective measures of muscle mass and body mass index. Tests of association and linear regression were performed to test the hypotheses while accounting for the effects of health and sociodemographic covariates.

Results
The life space of older adults has significantly diminished after the pandemic. This loss remained significant despite controlling for covariates and was more pronounced among those who had lost employment during the pandemic. In addition, losing employment during the pandemic was associated with having smaller life spaces.

Discussion
Life-space assessments are a potential important noninvasive marker for not only health and longevity but also the ability to sustain employment. Public health crises like the COVID-19 pandemic and employment loss negatively affect the life spaces of older adults. It is needful to emphasize the maintenance of life space when faced with disruptive life events and provide multidisciplinary collaborative solutions to restore the quality of life among vulnerable older adults.
Developing the ambition for action in the Ocean Decade to 2030
Authors: Bassan Niccolo’ , Flamand Aude , Clausen Alison 
Published: January 2025

Abstract
The ocean is vital for regulating climate, supporting biodiversity, and sustaining human livelihoods. However, as climate change accelerates ocean acidification, deoxygenation, warming, and biodiversity loss, the ocean’s ability to provide solutions is at risk. Addressing critical gaps in ocean science is essential, and the United Nations Decade of Ocean Science for Sustainable Development 2021–2030 (the “Ocean Decade”) seeks to bridge these gaps. Its transformative framework is built around 10 key challenges representing urgent needs for ocean knowledge. The Vision 2030 process, initiated in the Decade’s third year, refines these challenges, setting quantifiable success measures by 2030. Informed by contributions from around 150 experts and 10 White Papers, the Vision 2030 process highlights priorities such as actively considering Indigenous knowledge, co-designing innovative solutions, and enhancing investment in ocean science. This article introduces the insights of the Vision 2030 process, emphasizing the need for inclusive, coordinated action across the science–policy–society interface. It underscores the urgency of prioritizing ocean health and securing sustainable financing for ocean initiatives, particularly as Sustainable Development Goal (SDG) 14 remains the least funded SDG. Through advancing knowledge, fostering innovation, and promoting inclusivity, the Ocean Decade aims to protect ocean ecosystems and ensure a sustainable future for future generations.
Regularity of the Solution to a Real Monge–Ampère Equation on the Boundary of a Simplex
Authors: Andreasson Rolf , Hultgren Jakob , Jonsson Mattias , Mazzon Enrica , McCleerey Nicholas 
Published: January 2025

Abstract
Motivated by conjectures in Mirror Symmetry, we continue the study of the real Monge–Ampère operator on the boundary of a simplex. This can be formulated in terms of optimal transport, and we consider, more generally, the problem of optimal transport between symmetric probability measures on the boundary of a simplex and of the dual simplex. For suitably regular measures, we obtain regularity properties of the transport map, and of its convex potential. To do so, we exploit boundary regularity results for optimal transport maps by Caffarelli, together with the symmetries of the simplex.
Range expansion of the tropical predatory crab Eurytium limosum (Say, 1818) (Decapoda: Brachyura: Panopeidae) into temperate salt marshes along the eastern coast of the United States
Authors: Silliman Parker D R , Zhang Y Stacy , Morton Joseph P 
Published: January 2025

Abstract
We document the range expansion of Eurytium limosum (Say, 1818), a panopeid, mud crab commonly found in Florida mangroves and in southeastern US salt marshes, from its historically known northern range limit in southern South Carolina to newly observed range in central North Carolina (NC) salt marshes. Through field surveys conducted in 2024, we recorded E. limosum populations in two salt marshes on Bogue Banks-Atlantic Beach, NC. Field surveys conducted in two salt marshes showed that this predatory crab is very abundant in both marshes, and its densities vary by marsh zone, with the highest abundance occurring in the low marsh. Compilation and analysis of published and unpublished data on mud-crab density in these same marshes reveal that E. limosum was not present in these marshes in the mid-1990’s but were at low densities in 2016, 88% lower than they were in 2024. Combined, these findings indicate a significant northward expansion (at least ~400 km) of E. limosum likely influenced by rising sea temperatures in NC. Given their current abundances and past studies that show this mesopedatory crab preys on two key salt marsh consumers, fiddler crabs and plant-grazing snails, and that it is an aggressive competitor, E. limosum will likely alter top-down forcing of marsh structure and function and/or competitive interactions with other infaunal marsh predators. We document what is likely the beginning of the tropicalization of the predator assemblage of temperate salt marshes, underscoring the importance of monitoring the distribution of marine species in response to climate change, and suggests potential impacts on local ecosystems and biodiversity that warrant future investigations.
Evaluation of a fluorophore for marking navel orangeworm (Lepidoptera: Pyralidae)
Authors: Liu Tzu-Chin (Jean) , Burks Charles S , Wilson Houston 
Published: January 2025

Abstract
Navel orangeworm, Amyelois transitella (Walker), is a key pest in California’s almonds, pistachios, and walnuts. This insect’s strong dispersal capacity can potentially undermine the efficacy of localized management efforts. The timing and extent of A. transitella movement between orchards remain unclear, and more studies are needed to better characterize its landscape ecology. Mark-release-recapture studies offer a potential solution but require a reliable insect marker that is durable, easily identifiable and has minimal impacts on A. transitella longevity and flight ability. To address this, we evaluated 4 colors (red, blue, green, and yellow) of a fluorophore marker (SmartWater) for adult A. transitella. We conducted laboratory assays to assess moth flight ability and mortality, as well as marker persistence over time using both quantitative (plate reader) and qualitative (visual observation) fluorophore detection methods. Results demonstrated that none of the 4 colors negatively affected A. transitella flight ability or mortality. Green and yellow markers were persistent and readily identified by both detection methods, unlike blue and red markers. Although marker degradation was observed over time with the quantitative method, a high percentage of moths (70.3%) retained green and yellow markers after 14 days. In contrast, these markers did not show significant degradation using the qualitative method, with over 94.2% of moths showing fluorescence 14 days postmarking. These findings highlight the strong potential of green and yellow markers for field studies with A. transitella. We discuss their use in future mark-release-recapture studies and compare the 2 fluorophore detection methods.