bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prioritizing chemicals of emerging concern in the Great Lakes Basin using covariance of chemical concentrations and diverse biological responses from a variety of species
Authors: Vitense Kelsey , Loken Luke C , Maloney Erin M , Blackwell Brett R , Collette Timothy W , Corsi Steven R , Custer Christine M , Davenport Erik D , Kohno Satomi , Hummel Stephanie L 
Published: January 2025

Abstract
The Great Lakes Restoration Initiative aims to protect and restore the nation’s largest freshwater resource, in part, by furthering our understanding of the effects of contaminants of emerging concern (CECs) and chemical mixtures on aquatic and terrestrial organisms. To address this goal, an interagency team conducted field studies at sites along the Maumee River in Ohio, USA, in 2016–2017, monitoring CEC levels along with diverse in vitro and in vivo biological effects in ecologically relevant species (fathead minnows, tree swallows, and golden clams). The objective of the present work was to prioritize the CECs in these studies for further monitoring and assessment by determining if there are patterns in chemical–bioeffect relations across data sets, species, and response types that indicate relatively high or low hazard to aquatic life from CEC exposure. Of the 748 monitored chemicals, 425 were detected and were analyzed for covariance with bioeffects. All 748 chemicals were placed into 10 bins based on their frequencies of monitoring, detection, and covariance with bioeffects across studies and species. We describe how chemicals can be prioritized across bins to aid monitoring and assessment efforts. Our approach using effects-based monitoring data is especially useful for prioritizing chemicals with little or no traditional toxicity testing data. Similar evidence-based prioritizations will allow agencies to more efficiently allocate limited resources to improve the ability to protect aquatic and terrestrial organisms from adverse impacts due to contaminant exposure.
Fish early-life stage toxicity and environmental relevance: what does high-dose toxicity testing tell us?
Authors: Meador James P , Escher Beate I 
Published: January 2025

Abstract
The early-life stage (ELS) toxicity syndrome for fish is well described and has been reported in hundreds of toxicity studies. It is generally characterized by a reduced heart rate, yolk sac and pericardial edemas, and various morphological abnormalities, the most common being spinal curvature. For many of those studies, it appears that the ELS toxicity syndrome is the result of nonspecific (baseline) toxicity that occurs at aqueous and whole-body concentrations that are just below lethal concentrations. Baseline toxicity is essentially a nonspecific response that results from chemicals accumulating in and disturbing the function of biological membranes that leads to lethality and sublethal effects at relatively high doses. The commonality of this acute ELS toxicity syndrome among highly diverse organic and inorganic chemicals is remarkable. It is important to identify baseline toxicity because it is considered minimal toxicity that acts in all tissues and cells, and it has the potential to impair all cellular functions. This means if an effect is observed around baseline-toxic concentrations, it is likely that other cellular functions are also affected (i.e., the effect is not specific). The fish ELS toxicity syndrome can also be the result of specific effects involving receptor interactions; therefore, we emphasize the importance of distinguishing between specific and nonspecific toxicity responses to provide the most relevant data for environmental risk assessment.
Older adults with acute coronary syndrome: the impact of frailty and nutritional status on in-hospital complications
Authors: Jiménez-Salva María , Carmona-Segovia Ada , Molina-Ramos Ana Isabel , García-Rodríguez Luis , Puyol-Ruiz Fernando , Doncel-Abad Victoria , Romero-Cuevas Miguel , Serrano Antonia , Muñoz-García Antonio , Flores-López María , Ortega-Gómez Almudena , Gutiérrez-Bedmar Mario , Rodríguez-Capitán Jorge , Jiménez-Navarro Manuel , Pavón-Morón Francisco Javier 
Published: January 2025

Abstract

Aims
The optimal management of older patients with acute coronary syndrome (ACS) remains unclear. The most effective evaluation methods for frailty and malnutrition are yet to be delineated, despite being proposed as predictors of adverse outcomes. Consequently, this study aims to assess the significance of these factors in predicting in-hospital complications within this population.

Methods and results
In this single-centre, intrahospital case–control study, 217 older patients (aged &gt;70 years) with ACS were categorized into two groups based on the occurrence of net adverse clinical events (NACE) during hospitalization: the NACE (n = 59) and non-NACE (n = 158) groups. Demographic and clinical variables, including assessments of frailty using the FRAIL scale (FS), dependency using the Barthel index, and nutritional status using both the prognostic nutritional index (PNI) and geriatric nutritional risk index, were collected. Regression models and receiver operating characteristics curves were constructed to predict NACE. Patients in the NACE group exhibited higher frailty (P &lt; 0.001), increased dependency (P &lt; 0.001), and poorer nutritional status (P &lt; 0.05) compared with those in the non-NACE group. The FS [odds ratios (OR) 95% confidence interval (CI) = 2.03 (1.39–2.95), P &lt; 0.001] and PNI [OR (95% CI) = 0.64 (0.41–0.99), P &lt; 0.05] scores emerged as independent predictors of NACE in a multivariable model including age, sex, and traditional cardiovascular risk factors. This model demonstrated a high discriminatory power [area under the curve (95% CI) = 0.834 (0.768–0.899), P &lt; 0.001] for NACE.

Conclusion
Frailty and nutritional status could significantly contribute to the stratification and identification of older adults with ACS who are at risk of developing in-hospital complications.
Detection, assessment, and control strategies for managing Vibrio parahaemolyticus risk in seafood
Authors: Liu Jing , Xiong Rongrong , Wu Qian , Xu Tianming , Caridad Olivera Castro Osaris , Zhu Yongheng , Pan Yingjie , Malakar Pradeep K , Zhao Yong , Zhang Zhaohuan 
Published: January 2025

Abstract
Vibrio parahaemolyticus, a prevalent foodborne pathogen, is widely distributed in aquatic environments and seafoods, posing a significant hazard to seafood safety and consumer health. The integration of detection, assessment, and control methodologies for V. parahaemolyticus constitutes a robust framework, facilitating the systematic monitoring, assessment, and mitigation of associated risks in seafood. This review provides a comprehensive overview of current advancements and applications in cultivation and detection techniques specific to V. parahaemolyticus, with an emphasis on predictive modeling and risk assessment, tracing their historical evolution. Additionally, effective preventive and control measures targeting V. parahaemolyticus, including physical, chemical, and biological interventions, are discussed. Further improvements in detection methods, the refinement of risk assessment tools, and the optimization of sterilization techniques are recommended. These efforts aim to establish more efficient and accurate protocols for monitoring, predicting, and controlling V. parahaemolyticus, ensuring the safety and quality of seafood.
Guidance framework to apply best practices in ecological data analysis: lessons learned from building Galaxy-Ecology
Authors: Royaux Coline , Mihoub Jean-Baptiste , Jossé Marie , Pelletier Dominique , Norvez Olivier , Reecht Yves , Fouilloux Anne , Rasche Helena , Hiltemann Saskia , Batut Bérénice , Marc Eléaume , Seguineau Pauline , Massé Guillaume , Amossé Alan , Bissery Claire , Lorrilliere Romain , Martin Alexis , Bas Yves , Virgoulay Thimothée , Chambon Valentin , Arnaud Elie , Michon Elisa , Urfer Clara , Trigodet Eloïse , Delannoy Marie , Loïs Gregoire , Julliard Romain , Grüning Björn , Le Bras Yvan ,   The Galaxy-E community
Published: January 2025

Abstract
Numerous conceptual frameworks exist for best practices in research data and analysis (e.g., Open Science and FAIR principles). In practice, there is a need for further progress to improve transparency, reproducibility, and confidence in ecology. Here, we propose a practical and operational framework for researchers and experts in ecology to achieve best practices for building analytical procedures from individual research projects to production-level analytical pipelines. We introduce the concept of atomization to identify analytical steps that support generalization by allowing us to go beyond single analyses. The term atomization is employed to convey the idea of single analytical steps as “atoms” composing an analytical procedure. When generalized, “atoms” can be used in more than a single case analysis. These guidelines were established during the development of the Galaxy-Ecology initiative, a web platform dedicated to data analysis in ecology. Galaxy-Ecology allows us to demonstrate a way to reach higher levels of reproducibility in ecological sciences by increasing the accessibility and reusability of analytical workflows once atomized and generalized.
Capacity and crisis: examining the state-level policy response to COVID-19 in Tamil Nadu, India
Authors: Sriram Veena , Vaidyanathan Girija , Adithyan G S , Thakur Shambo Basu , Kaur Simran , GL Hari Narayanan , Haque Sabah , Muraleedharan V R 
Published: January 2025

Abstract
The capacity of government agencies to develop effective policy responses to external shocks is an important area of focus for health policy processes, as illustrated by the coronavirus (COVID-19) pandemic. However, few empirical studies exploring the subnational capacity of governments and the influence of institutional, organizational and political factors in shaping the policy response to complex emergencies have been conducted. The purpose of this study is to examine the governance capacity to develop and implement a policy response to a major health emergency—COVID-19—in Tamil Nadu, India, and to understand the factors shaping governance capacity during the first and second waves (2020–21). Tamil Nadu offers a useful case for exploring governance capacity due to its long-standing public health institutions and previous experiences with disaster and outbreak response. We utilized three sources of data: (1) a review of key policy documents (n = 164); (2) a review of English-language media articles in the Indian press (n = 336); and (3) in-depth interviews with senior decision makers, technical experts and other stakeholders (n = 10). We present four key findings from this analysis. Firstly, Tamil Nadu’s institutional framework enabled state-level governance capacity during an emergency of massive complexity, allowing for flexibility and nimbleness to adapt to evolving dynamics of centralization and decentralization over the course of the pandemic. Secondly, the ability to integrate public health expertise was circumscribed at important phases. Thirdly, while coordination with external experts was utilized extensively, engagement with civil society groups was perceived as limited. Fourthly, the electoral cycle was perceived by some to have constrained governance capacity at a critical point in the pandemic. By analysing the dynamics of state-level capacity in Tamil Nadu during a complex emergency, this study provides important learnings for other contexts globally regarding the drivers shaping capacity to develop and implement policy responses to crises.
Risk assessment of perishable products supply chains amidst COVID-19 through multi-criteria visualization
Authors: Khan Jehangir , Ishizaka Alessio , Kheybari Siamak 
Published: January 2025

Abstract
Accepted by: M. Zied BABAI
In recent years, global disruptions, such as the COVID-19 pandemic, have significantly exposed vulnerabilities in supply chains, particularly in the handling of perishable goods. Addressing these vulnerabilities, this study focuses on assessing risks in perishable supply chains by employing a novel decision-making approach that integrates the outranking method with a visualization technique. This study makes a methodological contribution to scholarly work by integrating VIseKriterijumska Optimizacija I Kompromisno Resenje, which provides the best compromise ranking, with Graphical Analysis for Interactive Assistance, which enhances clarity through detailed visual representation. The integration is further reinforced by a sensitivity analysis, ensuring robust and reliable findings. From a practical perspective, this study evaluates the supply chain performance of nine perishable items based on eight critical risks. The outcomes provide insights into the risk intensity of supply chains disruptions for each perishable product, facilitating the development of effective management policies. These findings offer valuable managerial insights, equipping researchers and practitioners with essential tool to formulate effective strategies and enhance decision-making processes during undesirable circumstances.
Cobalt Chloride–Mimicked Hepatocyte Cell Hypoxia Induces TREX1, Leading to Hepatitis B Virus Restriction
Authors: Suspène Rodolphe , Caval Vincent , Khalfi Pierre , Pitré Emmanuelle , Marchio Agnès , Pineau Pascal , Vartanian Jean-Pierre 
Published: January 2025

Abstract

Background
Restriction factors are host cell proteins that limit virus replication and form part of the intrinsic immune response, acting as a first line of defense. Hepatitis B virus (HBV) does not escape this rule and TREX1, a host restriction enzyme, plays a key role in inhibiting HBV replication.

Methods
TREX1-expressing constructs were generated and modified by site-directed mutagenesis. The location and activity of these constructs were analyzed by immunofluorescence and fluorescence-activated cell sorting. HepaD38 cells were transfected or transduced with TREX1 constructs with or without cobalt chloride–mimicked hypoxia and HBV replication was quantified by quantitative polymerase chain reaction.

Results
TREX1 was identified as a restriction factor that suppresses HBV replication. Furthermore, TREX1 expression was enhanced under cobalt chloride-induced hypoxia, leading to a 2-fold reduction in HBV replication. Analysis of 36 HBV-infected patients with hepatocellular carcinoma revealed that TREX1 expression was inversely correlated to the HBV viral load and HBV covalently closed episomal circular DNA (cccDNA).

Conclusions
Current treatments fail to eliminate HBV genomic reservoirs, which persist as cccDNA. It would be therapeutically relevant to study whether HBV nucleocapsid recycling containing TREX1 enzyme could be released into the nucleus and degrade the viral and nuclear DNA of infected cells.
Distinguishing Multisystem Inflammatory Syndrome in Children From Typhus Using Artificial Intelligence: MIS-C Versus Endemic Typhus (AI-MET)
Authors: Chun Angela , Bautista-Castillo Abraham , Osuna Isabella , Nasto Kristiana , Munoz Flor M , Schutze Gordon E , Devaraj Sridevi , Muscal Eyal , de Guzman Marietta M , Sexson Tejtel Kristen , Vogel Tiphanie P , Kakadiaris Ioannis A 
Published: January 2025

Abstract

Background
The pandemic emergent disease multisystem inflammatory syndrome in children (MIS-C) following coronavirus disease-19 infection can mimic endemic typhus. We aimed to use artificial intelligence (AI) to develop a clinical decision support system that accurately distinguishes MIS-C versus endemic typhus (MET).

Methods
Demographic, clinical, and laboratory features rapidly available following presentation were extracted for 133 patients with MIS-C and 87 patients hospitalized due to typhus. An attention module assigned importance to inputs used to create the 2-phase AI-MET. Phase 1 uses 17 features to arrive at a classification manually (MET-17). If the confidence level is not surpassed, 13 additional features are added to calculate MET-30 using a recurrent neural network.

Results
While 24 of 30 features differed statistically, the values overlapped sufficiently that the features were clinically irrelevant distinguishers as individual parameters. However, AI-MET successfully classified typhus and MIS-C with 100% accuracy. A validation cohort of 111 additional patients with MIS-C was classified with 99% accuracy.

Conclusions
Artificial intelligence can successfully distinguish MIS-C from typhus using rapidly available features. This decision support system will be a valuable tool for front-line providers facing the difficulty of diagnosing a febrile child in endemic areas.
Intestinal Foxl1+ cell-derived CXCL12 maintains epithelial homeostasis by modulating cellular metabolism
Authors: Yagita-Sakamaki Mayu , Ito Takayoshi , Sakaguchi Taiki , Shimma Shuichi , Li Bo , Okuzaki Daisuke , Motooka Daisuke , Nakamura Shota , Hase Koji , Fukusaki Eiichiro , Kikuchi Akira , Nagasawa Takashi , Kumanogoh Atsushi , Takeda Kiyoshi , Kayama Hisako 
Published: January 2025

Abstract
Several mesenchymal cell populations are known to regulate intestinal stem cell (ISC) self-renewal and differentiation. However, the influences of signaling mediators derived from mesenchymal cells other than ISC niche factors on epithelial homeostasis remain poorly understood. Here, we show that host and microbial metabolites, such as taurine and gamma-aminobutyric acid (GABA), act on PDGFRαhigh Foxl1high sub-epithelial mesenchymal cells to regulate their transcription. In addition, we found that CXC chemokine ligand 12 (CXCL12) produced from Foxl1high sub-epithelial mesenchymal cells induces epithelial cell cycle arrest through modulation of the mevalonate–cholesterol synthesis pathway, which suppresses tumor progression in ApcMin/+ mice. We identified that Foxl1high sub-epithelial cells highly express CXCL12 among colonic mesenchymal cells. Foxl1-cre; Cxcl12f/f mice showed an increased number of Ki67+ colonic epithelial cells. CXCL12-induced Ca2+ mobilization facilitated phosphorylation of AMPK in intestinal epithelial cells, which inhibits the maturation of sterol regulatory element-binding proteins (SREBPs) that are responsible for mevalonate pathway activation. Furthermore, Cxcl12 deficiency in Foxl1-expressing cells promoted tumor development in the small and large intestines of ApcMin/+ mice. Collectively, these results demonstrate that CXCL12 secreted from Foxl1high mesenchymal cells manipulates intestinal epithelial cell metabolism, which links to the prevention of tumor progression in ApcMin/+ mice.
Magnetotactic bacteria affiliated with diverse Pseudomonadota families biomineralize intracellular Ca-carbonate
Authors: Mangin Camille C , Benzerara Karim , Bergot Marine , Menguy Nicolas , Alonso Béatrice , Fouteau Stéphanie , Méheust Raphaël , Chevrier Daniel M , Godon Christian , Turrini Elsa , Mehta Neha , Duverger Arnaud , Travert Cynthia , Busigny Vincent , Duprat Elodie , Bolzoni Romain , Cruaud Corinne , Viollier Eric , Jézéquel Didier , Vallenet David , Lefèvre Christopher T , Monteil Caroline L 
Published: January 2025

Abstract
Intracellular calcium carbonate formation has long been associated with a single genus of giant Gammaproteobacteria, Achromatium. However, this biomineralization has recently received increasing attention after being observed in photosynthetic Cyanobacteriota and in two families of magnetotactic bacteria affiliated with the Alphaproteobacteria. In the latter group, bacteria form not only intracellular amorphous calcium carbonates into large inclusions that are refringent under the light microscope, but also intracellular ferrimagnetic crystals into organelles called magnetosomes. Here new observations suggest that magnetotactic bacteria previously identified in the sediments and water column of Lake Pavin (France) were only a small fraction of the diversity of bacteria producing intracellular amorphous calcium carbonates. To explore this diversity further, we conducted a comprehensive investigation of magnetotactic populations with refractive granules using a combination of environmental microbiology, genomic and mineralogy approaches on cells sorted by micromanipulation. Several species belonging to divergent genera of two Pseudomonadota classes were identified and characterized. Scanning transmission electron microscopy coupled with energy-dispersive X-ray spectrometry support that all these species indeed form intracellular amorphous calcium carbonates. Cryo soft X-ray tomography experiments conducted on ice-vitrified cells, enabled 3D investigation of inclusions volume, which was found to occupy 44–68% of the cell volume. Metabolic network modeling highlighted different metabolic abilities of Alpha- and Gammaproteobacteria, including methylotrophy and CO2 fixation via the reverse Krebs cycle or the Calvin-Benson-Bassham cycle. Overall, this study strengthens a convergent evolution scenario for intracellular carbonatogenesis in Bacteria, and further supports that it is promoted by the fixation of CO2 in anoxic environments.
Diving, Grabbing and Teleporting: Methods for Medical 3D Image Manipulation in VR
Authors: Orsmaa Lotta , Kangas Jari , Rasouli Nastaran , Jaskari Joel , Sahlsten Jaakko , Mehtonen Helena , Järnstedt Jorma , Kaski Kimmo , Raisamo Roope 
Published: January 2025

Abstract
In Virtual Reality (VR), locomotion methods allow users to adjust their location in the virtual environment. These methods are sometimes used in 3D-VR medical image manipulation, which has gained interest in VR in the medical field due to the immersive environment and increased number of possible interaction techniques. However, the medical 3D-VR image manipulation context differs from typical VR locomotion, as the focus is not on the navigation of the VR space, but rather on the point of view of the user to the 3D image. For this study, we recruited 24 participants to find and observe easy targets from simplified medical images. We compared whether the three VR locomotion methods, Diving, Grabbing and Teleporting, were suitable for medical 3D image manipulation tasks. Diving was found to be significantly more successful than Teleporting while being an equally fast method. Locomotion method preferences varied. Therefore, a VR system is suggested to provide various manipulation methods for the user. However, the methods need development before they can be used with radiologists for actual medical image analysis tasks. We fill a research gap from the VR medical image manipulation context, where even though VR locomotion methods, such as Teleporting have been sometimes used, there has been a lack of interaction technique studies of these methods. Therefore, we provide necessary data on locomotion methods for the designers and developers of 3D-VR medical image applications. This is an initial study to validate different techniques for medical image analysis tasks in VR.