bluuebunny/crossref_metadata_2025_split huggingface dataset:
How Do MRI Findings Influence Rectal Cancer Management?
Authors: Ramakrishnan Ayloor Seshadri , Pradeep Jeyakumar 
Published: January 2025

AbstractTreatment of rectal cancer is currently guided by the need to reduce local recurrence, improve survival, reduce treatment-related toxicity, and improve the patient's quality of life (QoL). Magnetic resonance imaging (MRI) scan is now the imaging modality of choice for rectal cancer. However, the role of MRI in rectal cancer has transformed beyond describing the local stage of cancer to becoming a tool to predict the prognosis of a patient by its ability to detect features associated with a high risk of recurrence and poor survival. This greatly helps the multidisciplinary team (MDT) responsible for treating patients with rectal cancer to stratify them based on the potential for recurrence and decide on the need for and type of preoperative treatment to be offered. MRI also has the ability to assess the response to such treatments, based on which the MDT can tailor the subsequent treatment. This has the potential to spare the patient from unnecessary treatment, thus improving the QoL. MRI provides a roadmap to the surgeon while planning the surgery. In this review, we give a brief overview of the current management strategies for rectal cancer and highlight the role of MRI in the decision-making process.
Think About Possibility
Authors: Allen Peter 
Published: January 2025

Abstract
In politics, people regularly end up doing the thing they thought was impossible, suddenly and unexpectedly. Such actions reveal something about the fundamentally uncertain state of politics and the underlying possibility this presents. But individuals often don’t do those things even if they can; something is framed as inevitable, and it doesn’t occur. Why? This chapter shows how the stories that are told about the world are powerful. They guide actions and they shape lives. Stories are arguments that the world is, can be, and will be, a certain way. Stories matter—they show what is possible and what is inevitable. But if one can look through a story, think past it, and see around it, it is possible see that a story is, ultimately, just that: a story. With sufficient will, a different one can be told instead.
Thinking About Politics in the Polycrisis
Authors: Allen Peter 
Published: January 2025

Abstract
This chapter brings the five ideas outlined in the book to bear on the very real political problems presented by the polycrisis. Considering the interaction of the environmental, geopolitical, and economic crises that characterize the current political moment, the chapter demonstrates how the five fundamental ideas discussed in the book can be used to think about the different aspects of these problems. What can they illuminate? The chapter argues that, despite the apparent novelty and complexity of the issues facing democratic societies, they can be understood by focusing on the fundamental ideas of power, knowledge, representation, interests, and possibility. Taken together, the lesson to be drawn from this is that the scope of what politics is and what it can achieve might be more than is commonly thought.
Rethinking ‘farmer–herder’ conflicts in the Ivorian internal frontier
Authors: Allouche Jeremy , Yao Yao Cyprien , Soumahoro Amédée Kando 
Published: January 2025

Abstract
There is a heightened concern among the media, United Nations (UN) agencies, and security experts about the rising number of localized conflicts in West Africa. While many of these conflicts are labelled as farmer–herder conflicts, they are, in fact, more complex and multidimensional. This article demonstrates as much for the Ivorian case by building on the concept of the internal frontier in West African rural institutions. Population mobility has been central to state policies and practices towards the internal frontier in order to optimize conditions for economic growth and capital accumulation. Drawing on the case of Bouna, Côte d’Ivoire in 2016, this article argues that the conflict is driven by a reconfiguration of local social orders, whereby the state’s internal frontier logic faces a crisis due to the ideological contradictions between capital accumulation and autochthony.
Deciphering cell states and the cellular ecosystem to improve risk stratification in acute myeloid leukemia
Authors: Zhang Zheyang , Tang Ronghan , Zhu Ming , Zhu Zhijuan , Zhu Jiali , Li Hua , Tong Mengsha , Li Nainong , Huang Jialiang 
Published: January 2025

Abstract
Acute myeloid leukemia (AML) demonstrates significant cellular heterogeneity in both leukemic and immune cells, providing valuable insights into clinical outcomes. Here, we constructed an AML single-cell transcriptome atlas and proposed sciNMF workflow to systematically dissect underlying cellular heterogeneity. Notably, sciNMF identified 26 leukemic and immune cell states that linked to clinical variables, mutations, and prognosis. By examining the co-existence patterns among these cell states, we highlighted a unique AML cellular ecosystem (ACE) that signifies aberrant tumor milieu and poor survival, which is confirmed by public RNA-seq cohorts. We further developed the ACE signature (ACEsig), comprising 12 genes, which accurately predicts AML prognosis, and outperforms existing signatures. When applied to cytogenetically normal AML or intensively treated patients, the ACEsig continues to demonstrate strong performance. Our results demonstrate that large-scale systematic characterization of cellular heterogeneity has the potential to enhance our understanding of AML heterogeneity and contribute to more precise risk stratification strategy.
tagtango: an application to compare single-cell annotations
Authors: Bramon Mora Bernat , Lindsay Helen , Thiébaut Antonin , Stuart Kenneth D , Gottardo Raphael 
Published: January 2025

Abstract

Summary
In this article, we present tagtango, an innovative R package and web application designed for robust and intuitive comparison of single-cell clusters and annotations. It offers an interactive platform that simplifies the exploration of differences and similarities among different clustering and annotation methods. Leveraging single-cell data analysis and different visualizations, it allows researchers to dissect the underlying biological differences across groups. tagtango is a user-friendly application that is portable and works seamlessly across multiple operating systems.

Availability and implementation
tagtango is freely available at https://github.com/bernibra/tagtango as an R package as well as an online web service at https://tagtango.unil.ch.
Quantitative susceptibility mapping is more sensitive and specific than phase imaging in detecting chronic active multiple sclerosis lesion rims: pathological validation
Authors: Gillen Kelly M , Nguyen Thanh D , Dimov Alexey , Kovanlikaya Ilhami , Luu Ha Manh , Demmon Emily , Markowitz Daniel M , Bagnato Francesca , Pitt David , Gauthier Susan A , Wang Yi 
Published: January 2025

Abstract
Quantitative susceptibility mapping and phase imaging are used to identify multiple sclerosis lesions with paramagnetic rims that slowly expand over time and are associated with earlier progression to disability, decreased brain volume and increased frequency of clinical relapse. However, the presence of iron-laden microglia/macrophages at the lesion rim and demyelination within the lesion both contribute to phase and quantitative susceptibility mapping images. Therefore, simultaneous pathological validation is needed to assess accuracies in identifying iron-positive lesions. MRI was performed on 15 multiple sclerosis brain slabs; 32 lesions of interest were processed for myelin, iron and microglial markers. Three experienced readers classified lesions as rim positive or negative on quantitative susceptibility mapping and phase; these classifications were compared with Perls’ stain as the gold standard. All 10 of the quantitative susceptibility mapping-positive lesions had iron-positive rims on histology. Of the 16 phase-positive lesions, only 10 had iron-positive rims on histology. Using Perls’ stain as the ground truth, the positive predictive value was 100% for quantitative susceptibility mapping and 63% for phase; the negative predictive value was 95% for quantitative susceptibility mapping and 94% for phase. Post-mortem imaging results demonstrate that quantitative susceptibility mapping is a more reliable indicator of an iron-positive rim compared with phase imaging.
Parathyroid gland volume and treatment resistance in patients with secondary hyperparathyroidism: a 4-year retrospective cohort study
Authors: Kato Kazuhiko , Nakashima Akio , Morishita Masamitsu , Ohkido Ichiro , Yokoo Takashi 
Published: January 2025

ABSTRACT

Background
The role of parathyroid gland (PTG) ultrasonography in the management of secondary hyperparathyroidism after the introduction of calcimimetics remains unclear. Recent investigations have prompted renewed interest in the use of PTG ultrasonography for assessing treatment resistance to calcimimetics and determining the optimal timing for surgical intervention. This study aimed to explore the hypothesis that the PTG volume correlates with the calcimimetic dose.

Methods
We retrospectively observed outpatients undergoing haemodialysis at baseline and a 4-year follow-up. PTG volume was measured using ultrasonography between January and December 2017 and January and December 2021. We examined the association between baseline PTG volume and calcimimetic doses after 4 years.

Results
Of the 121 patients {median age 64 years [interquartile range (IQR) 54–72]}, 71 had PTG nodules on ultrasonography and the median total PTG volume was 34 mm3 (IQR 0–178). In the short dialysis vintage group, baseline parathyroid hormone levels tended to correlate with baseline calcimimetic doses; however, this trend was not observed in the extended dialysis vintage group. Baseline PTG volume correlated with the cinacalcet-equivalent calcimimetic dose (correlation coefficient 0.46; P &lt; .001) after 4 years. The calcimimetic dose in the group with an estimated PTG volume &gt;500 mm3 was ≈80 mg/day higher than that in the non-PTG nodule group after 4 years. In multivariate linear regression analysis, PTG volume &gt;500 mm3 was associated with a high calcimimetic dose at 4 years in all analysis models.

Conclusions
Assessing PTG volume using ultrasonography may help predict high calcimimetic doses.
HoloFood Data Portal: holo-omic datasets for analysing host–microbiota interactions in animal production
Authors: Rogers Alexander B , Kale Varsha , Baldi Germana , Alberdi Antton , Gilbert M Thomas P , Gupta Dipayan , Limborg Morten T , Li Sen , Payne Thomas , Petersen Bent , Rasmussen Jacob A , Richardson Lorna , Finn Robert D 
Published: January 2025

Abstract
The HoloFood project used a hologenomic approach to understand the impact of host–microbiota interactions on salmon and chicken production by analysing multiomic data, phenotypic characteristics, and associated metadata in response to novel feeds. The project’s raw data, derived analyses, and metadata are deposited in public, open archives (BioSamples, European Nucleotide Archive, MetaboLights, and MGnify), so making use of these diverse data types may require access to multiple resources. This is especially complex where analysis pipelines produce derived outputs such as functional profiles or genome catalogues. The HoloFood Data Portal is a web resource that simplifies access to the project datasets. For example, users can conveniently access multiomic datasets derived from the same individual or retrieve host phenotypic data with a linked gut microbiome sample. Project-specific metagenome-assembled genome and viral catalogues are also provided, linking to broader datasets in MGnify. The portal stores only data necessary to provide these relationships, with possible linking to the underlying repositories. The portal showcases a model approach for how future multiomics datasets can be made available.
Database URL: https://www.holofooddata.org
Migration of toxic elements from recycled paper food contact materials to food simulants: compatibility and influence of sample preparation methods
Authors: Kourkopoulos Athanasios , Sijm Dick Theodorus Hubertus Maria , Vrolijk Misha 
Published: January 2025

Abstract
The presence of toxic elements in paper and board food contact materials (FCMs) has been previously shown by various studies employing different sample preparation methods. This study elucidates the influence of migration methods on the migration of toxic elements from recycled paper FCMs to food simulants and compares these methods with exhaustive extraction approaches. Migration samples were prepared with four food simulants as specified in Commission Regulation (EU) 10/2011: 3% acetic acid (volume fraction), 10% and 50% ethanol (volume fraction), and Tenax. The extraction process underestimated the number and quantity of elements. Migration methodologies revealed distinct element transfer patterns influenced by the physicochemical properties of the food simulants. Toxic elements, including aluminum, cobalt, nickel, arsenic, lead, cadmium, barium, and uranium, were detected in quantities exceeding safety reference values. These findings underscore the need for harmonized migration testing and regulatory specific migration limits (SMLs).
Improvement of plant growth and fruit quality by introducing a phosphoribosylpyrophosphate synthetase mutation into Methylorubrum populi
Authors: Zhang Cong , Yao Lu , Zhang Ming-Ming , Tian Dan-Dan , Wu Jing , Hu Yu-Zheng , Bao Kai , Ma Zeng-Xin , Tan Ling-Ling , Yang Song 
Published: January 2025

Abstract

Aims
The aim of this study was to evaluate the impact of the introduction of a phosphoribosylpyrophosphate synthetase (PRS) mutation into a plant growth-promoting strain of Methylorubrum on the enhancement of phyllosphere colonization, with the ultimate goal of improving plant growth and quality.

Methods and results
A strain of Methylorubrum populi (named HS04) was isolated from the groundnut leaves and found to process the plant-promoting traits, including the ability to produce indole acetic acid, siderophore, 1-aminocyclopropane-1-carboxylate deaminase, and to fix nitrogen. The application via foliar spray significantly increased the fresh weight of cucumber seedlings cultivated in a standard growth chamber, with 43.0% higher than the control group. Genomic analysis revealed that the presence of an array of genes involved in plant growth promotion, including accD, aldB, and ltaE, as well as potential nitrogen-fixation-related genes, including nifA, bchlLNB, and bchXYZ, in the HS04 strain. The introduction of the PRS mutation (an aspartic acid to an asparagine residue, D38N) in the HS04 strain (named HS04PTR) enhanced the utilization capacity of low concentrations of methanol and multi-carbon sources (C2–C5 carbon sources). The HS04PTR strain indicated a notable enhancement in the phyllosphere colonization, with the subsequent application further promoting the growth of cucumber seedlings. An agricultural solar greenhouse experiment was thus performed to assess the efficiency of the HS04PTR strain, sprayed at low abundance, in improving the growth and quality of cucumber plants, including vitamin C, reducing sugars, and total sugars.

Conclusions
Our findings provide insights into the potential of Methylorubrum/Methylobacterium strains with the PRS mutations as an efficient inoculant for advantageous agricultural applications.
A novel multi-task algorithm for operational optimization of coal mine integrated energy system under multiple uncertainties
Authors: Fei Xiaotian , Ma Jun , Zhang Jianhua , Zhang Yong , Gong Dunwei 
Published: January 2025

Abstract
The operational optimization of the coal mine integrated energy system (CMIES) is crucial for reducing costs and carbon emissions. However, the system’s multi-objective nature, stringent constraints, and the uncertainty of renewable and mine-derived energy make solving its optimization challenging. Thus, this paper first presents a data-driven uncertainty transformation method to address the uncertainty of renewable energy and mining derived energy output; then, a multi-task multi-objective evolutionary algorithm based on adaptive auxiliary tasks (MMOEA-AS) is proposed, which includes a main task and three auxiliary tasks. Meanwhile, an adaptive update strategy for auxiliary tasks and a matching degree-guided knowledge transfer mechanism are proposed to improve the performance of the algorithm. Finally, taking the energy scheduling problem of a coal mine in Shanxi, China as an example, MMOEA-AS is compared with five advanced evolutionary algorithms. The results show that MMOEA-AS can effectively solve the operation optimization of the CMIES, and obtain the optimal scheduling results.
R. Joseph Kimḥi's translation of Baḥya Ibn Paquda's Duties of the Hearts: A revised reading of MS Leipzig UBL B.H. 39, and its implications
Authors: Avirbach Barak 
Published: January 2025

Abstract
Baḥya ibn Paquda's Al-Hidāya ‘ilā Farā‘iḍ Al-Qulūb was translated from Arabic into medieval Hebrew by R. Judah Ibn Tibbon and R. Joseph Kimḥi. While Ibn Tibbon's translation has many surviving witnesses, only a fragment of Kimḥi's remains in four sources: one manuscript (MS Leipzig UBL B.H. 39) and three printed editions. A study of MS Leipzig reveals the inaccuracies in all editions of Kimḥi's translation, which were treated as an appendix to Ibn Tibbon's translation. These inaccuracies include abbreviations, word replacements, changes in verb tenses, pronouns, verbal stems, omissions, and additions. The impact of these discrepancies on the text's meaning and the study of medieval Hebrew and Kimḥi's translation method are significant. This article analyzes the codicological and philological aspects of MS Leipzig, presents a new reading of the manuscript, and discusses the central linguistic significance of the new reading compared to the printed editions and their implications for the text's meaning and linguistic nature.
‘The Last Day’ in John: Future or Realized?
Authors: Méndez Hugo 
Published: January 2025

Abstract
The Gospel of John applies many terms associated with future eschatology to describe realized-eschatological realities (‘judgment’, ‘death’, ‘condemnation’, ‘eternal life’, the ‘hour’, and ‘coming’). This paper defends the view that the Gospel’s six references to the ‘last day’ fit the same pattern (6:39–40, 44, 54; 11:24; 12:48). John’s Jesus takes up the language of a ‘last day’ from the sphere of future-eschatological expectations, but by his peculiar uses of the phrase, he guides the reader into a figurative, Spirit-realized interpretation of that language. In John, the ‘last day’ is not a specific, single day in the remote future. Rather, it is a cipher for the time materializing with Jesus’ coming into the word and fully realized at his departure and the coming of the Spirit, through which humans experience a spiritual resurrection and receive eternal life. The paper develops this thesis with special attention to such verses as 6:38–39; 7:37–39; and 11:24–26.
Posttraumatic Stress Disorder and Weight Loss in Male and Female Active-duty Service Members: A Weight Management Study
Authors: Morse Jessica L , Fishbein Joel N , Wooldridge Jennalee S , Herbert Matthew S , Afari Niloofar 
Published: January 2025

ABSTRACT

Background
Overweight and obesity are critical public health concerns with relevance to U.S. military personnel, as active duty service members must meet physical fitness and body composition standards. Biological sex and posttraumatic stress disorder (PTSD) diagnosis may affect service members’ weight management efforts, but it is unclear what contribution each of these factors independently or in combination have on weight loss.

Method
Addressing this gap in knowledge, the current study used multilevel models to examine the effects of sex and self-reported PTSD diagnosis on change in weight of active duty Navy service members (n = 178, 61% female, 24% PTSD) over the course of and after a behavioral weight management intervention.

Results
On average, participants’ weights decreased significantly during the intervention (P &lt; .001), and there was a significant sex-by-PTSD interaction effect such that male participants without a self-reported PTSD diagnosis and female participants with a self-reported PTSD diagnosis lost significantly more weight during the intervention than their counterparts (P = .015). The main effects of sex and self-reported PTSD diagnosis on weight change during the intervention were nonsignificant (P’s ≥ .24). While weight remained stable on average during the follow-up period (P = .28), female sex marginally predicted weight loss during the follow-up period (P = .07), whereas self-reported PTSD diagnosis and the sex-by-PTSD interaction were not significant (P’s ≥ .16).

Conclusions
These results highlight the importance of considering both sex and PTSD diagnosis as factors that together may influence the efficacy of behavioral weight management programs for active duty service members.

Clinical Trial Registration
NCT01757847
Azimuthal metallicity variations, spiral structure, and the failure of radial actions based on assuming axisymmetry
Authors: Debattista Victor P , Khachaturyants Tigran , Amarante João A S , Carr Christopher , Beraldo e Silva Leandro , Laporte Chervin F P 
Published: January 2025

ABSTRACT
We study azimuthal variations in the mean stellar metallicity, $\langle {\rm{[Fe/H]}}\rangle $, in a self-consistent, isolated simulation in which all stars form out of gas. We find $\langle {\rm{[Fe/H]}}\rangle$ variations comparable to those observed in the Milky Way and which are coincident with the spiral density waves. The azimuthal variations are present in young and old stars and therefore are not a result of recently formed stars. Similar variations are present in the mean age and $\rm \alpha$-abundance. We measure the pattern speeds of the $\langle {\rm{[Fe/H]}}\rangle$-variations and find that they match those of the spirals, indicating that spirals are the cause of the metallicity patterns. Because younger stellar populations are not just more $\rm [Fe/H]$-rich and $\rm \alpha$-poor but also dynamically cooler, we expect them to more strongly support spirals, which is indeed the case in the simulation. However, if we measure the radial action, $J_{R}$, using the Stäckel axisymmetric approximation, we find that the spiral ridges are traced by regions of high $J_{R}$, contrary to expectations. Assuming that the passage of stars through the spirals leads to unphysical variations in the measured $J_{R}$, we obtain an improved estimate of $J_{R}$ by averaging over a $1\rm{\:{Gyr}}$ time interval. This time-averaged $J_{R}$ is a much better tracer of the spiral structure, with minima at the spiral ridges. We conclude that the errors incurred by the axisymmetric approximation introduce correlated deviations large enough to render the instantaneous radial actions inadequate for tracing spirals.