bluuebunny/crossref_metadata_2025 huggingface dataset:
Securing Territory
Authors: Altamirano Rayo Giorleny
Published: January 2025

Indigenous peoples demand that their respective states comply with international treaties and national constitutions that institutionalize their communal property rights to land and natural resources by titling Indigenous lands. However, Indigenous land titling varies dramatically, across and within countries as well as through time. In particular, the rate and timing, as well as the geographical concentration of Indigenous land titling is highly uneven. Securing Territory shows that Indigenous land titling depends on state interests. Based on in-depth fieldwork in three countries, the book demonstrates that state elites have been more willing to implement costly Indigenous rights to land and natural resources when the central government can use them to secure territory and govern people in remote otherwise stateless areas. Communal property rights of Indigenous people and other ethnic groups were more consistently implemented in Nicaragua and Honduras than in Brazil, despite differences in demands from national or transnational social movements, resistance from capitalist interests, and the state’s administrative capacity between countries. The importance of state interests is also true for Indigenous land titling patterns in Kenya and Indonesia. By emphasizing the importance of state interests and national security concerns, the book’s findings inform debates about how formal institutions work in developing countries, as well as international efforts to support the human rights of historically marginalized communities and communal natural resource management policies.
Introduction
Authors: Altamirano Rayo Giorleny
Published: January 2025

This chapter frames the book by showing the spatial and temporal variations of Indigenous land titling in Latin America, articulating the research questions that arose from analyzing the titling patterns between and within countries, and pointing out the limitations of prevailing explanations. The chapter then provides a brief summary of the main argument that emphasizes the importance of state interest in controlling territory and reinforcing territorial power in remote localities to explain communal land titling patterns. In addition, the chapter points out the broader appeal of the study to both academics and practitioners. Finally, the chapter presents the research design rationale for using Nicaragua, Honduras, and Brazil as case studies, a summary of the evidence compiled during fifteen months of fieldwork, and a roadmap of the book.
Communal Property Rights of Indigenous Peoples and Ethnic Groups
Authors: Altamirano Rayo Giorleny
Published: January 2025

This chapter describes the variation in the specific set of property rights that the state formally grants to Indigenous and ethnic groups in Nicaragua, Honduras, and Brazil. In addition, the chapter traces the origin of specific communal property rights in each country. The chapter also describes how each country differs in their categorization of ethnic communities and, in turn, how that variation maps to these communities’ formal rights to property and natural resource management.
Honduras
Authors: Altamirano Rayo Giorleny
Published: January 2025

This chapter describes the temporal and spatial patterns of communal land titling to Indigenous and Afro-descendent peoples in Honduras. The chapter shows how political elites issued communal land titles selectively. While ethnic communities received titles to small plots of land after long administrative processes in the west, the central government titled vast expanses of communal lands quickly in the east. State elites acted strategically in the east to reinforce state power and retake territorial control through Indigenous land titling. Based on primary evidence collected during fieldwork, the chapter shows that the state uses a differentiated titling strategy to meet its security needs.
Economic and Monetary Union
Authors: Schoeller Magnus G , Weismann Paul
Published: January 2025

Over the past fifteen years, the Economic and Monetary Union (EMU) has been repeatedly exposed to pressure emanating from crises, notably the euro crisis and the COVID-19 pandemic. This contribution traces the development of EMU as a result of this pressure and assesses it from both a legal and a political science perspective. Flawed from the outset by an institutional and policy asymmetry, EMU’s crisis-induced reforms brought about remarkable changes at different levels. These changes concern economic and fiscal policy rules, the emergence of common fiscal capacities—notably the European Stability Mechanism (ESM) and the Recovery and Resilience Facility (RRF)—and the evolving role of the European Central Bank (ECB). However, without major Treaty revision, these changes rest on questionable legal bases and their political-economic scope is only incremental. Overall, the reforms thus failed to remedy the incomplete design of EMU.
Financial Regulation and Supervision
Authors: Bauerschmidt Jonathan , Quaglia Lucia
Published: January 2025

The European Union (EU) responded to the Great Financial Crisis in several ways. First, it established a European System of Financial Supervision, which comprises the European Systemic Risk Board and three sectoral European Supervisory Authorities (ESAs). Second, it created the banking union, with a view to breaking the vicious circle of dependence between banks and sovereigns. In the banking union, the competence for banking supervision and resolution were partly transferred to the supranational level. Third, it proposed the creation of the capital markets union, to unlock new sources of funding, be less reliant on banks, reduce financial market fragmentation, and increase cross-border capital flows. On the whole, the EU replaced many soft laws with hard laws and made greater use of regulations rather than directives. At the same time, the ESAs and the European Central Bank issued a considerable amount of soft law. While undertaking these post-crisis reforms, the EU had to deal with two main challenges: to reconcile the competing interests and different priorities of Member States, and to combine the depoliticization of certain financial issues with a sufficient level of accountability.
State Aid Control
Authors: López Juan Jorge Piernas , Cini Michelle
Published: January 2025

Before 2008, the state aid regime had grown in experience and confidence. Since 2008, it has witnessed multiple crises. Of relevance here are the Great Financial Crisis, the COVID-19 crisis, and the most recent iteration of the Ukraine crisis. This chapter, resting on a qualitative analysis of official documents, analyses the EU response to crises as it relates to state aid control, and more specifically the extent to which new rule-making and rule change have played a part in that response. Of note, empirically, is the innovative use by the European Commission of soft law (temporary frameworks) and the application of a little-used provision of the Treaty on the Functioning of the European Union (TFEU)—Article 107(3)(b). The chapter argues that the legacy of the EU response to recent crises in this field is mixed. The use of rarely applied provisions and the swift adoption of temporary frameworks has allowed for a coordinated response, avoiding subsidy races while providing legal certainty. The flexibility of the Commission’s responses risks undermining the social, territorial, and economic cohesion of the internal market, while also provoking allegations of discrimination before the EU courts. The chapter concludes that the crisis responses made in this area have led to an increased demand for the federalization of financial instruments— for centralized EU aid instead of merely coordinated national aid—of which the Recovery and Resilience Facility, the largest element of the EU’s post-pandemic temporary recovery instrument, NextGeneration EU, is the best example.
Membership of EU Treaties
Authors: Steinbach Armin
Published: January 2025

This chapter explores how founding or incumbent EU members design and determine membership to the EU Treaties and what the implications of the rules of membership are for the substantive commitment level of EU Treaties. For the EU, the rational membership design can be discussed with reference to EU Treaties as integrating elements of closed Treaties and semi-open Treaties. For semi-open Treaty sections (like the euro membership), the rational Treaty designer anticipates growing heterogeneity of preferences between participating states, and thus designs rules in a way that minimizes negative repercussions. Contrary to what distributive rationalist approaches suggest, at least regarding the voting structure of the EU, large incumbent EU members have not translated their comparative low opportunity costs into relative advantages to smaller acceding states. Regarding EU enlargement, this happens when benefits for incumbent and acceding members are significant, where the general rationales for EU cooperation apply.
Flexibility
Authors: Steinbach Armin
Published: January 2025

This chapter discusses the economics behind Treaty flexibility. As inherently incomplete contracts, the EU Treaties have not anticipated all future state-contingencies. An economic approach asks why EU states retain flexibility through treaty design. Depending on the need for flexibility, adaptive or transformative clauses can be integrated into the treaties. They allow for efficient non-application of the rules (adaptivity) or to react to more fundamental uncertainty about the future state of the world (transformative). The wide use of soft law in EU legislation leads to the question of identifying the conditions under which governments prefer soft law over formal hard law, and vice versa. The EU Treaties are characterized as both incomplete and overcomplete, with characterizations implying different economic rationales and problems.
The European Council and Council of Ministers
Authors: Steinbach Armin
Published: January 2025

This chapter and the ones that follow examine perspectives native to law and economics while considering the European institutions as actors under EU law. In separate chapters devoted to the European Council, the Parliament, the ECJ, the ECB, and the Commission, the institutional structures and payoff logics that incentivize and constrain behaviour are discussed. Principal–agent theory sheds important light on why Union actors may act in violation of Treaty mandates, thus creating misalignment with the preferences of Member States or citizens as principals. The decision-making mode (unanimity versus qualified majority voting) in the Council can be analysed as a cost minimization exercise, where the direct costs of decision-making relate to the costs of reaching a majority consensus while indirect or agency costs reflect the probability of a Member State being overruled and having to accept an outcome that runs counter to its preferences. This finding interacts with fiscal federalism that relies on preference heterogeneity as a core criterion for assessing whether the provision of public goods should take place in a centralized or decentralized manner.
Evaluating bias in electronic health record data: using agent-based models to examine whether geographic disparities in community-acquired Methicillin-resistant Staphylococcus aureus are due to differential healthcare-seeking behaviors
Authors: Morgan Bustamante Brittany L , Gomez-Vazquez Jose Pablo , Crespo Carlos Gonzalez , May Larissa , Fejerman Laura , Martínez-López Beatriz
Published: January 2025

Electronic health records (EHR) are increasingly used in public health research. However, biases may exist when using EHR due to whether someone is captured in the data. Assessing the impact of bias in generating disparities identified with EHR data is difficult because information about healthcare-seeking behaviors is not included in the record. We developed an agent-based model (ABM) to simulate the healthcare-seeking behavior for community-acquired Methicillin-resistant Staphylococcus aureus (CA-MRSA) infection in a subregion of California. The ABM assumed no difference in prevalence across the study area. We modeled the healthcare-seeking process to see if geographic differences in prevalence would emerge from the ABM when only looking at those who sought treatment, matching empirical data. The ABM reproduced prevalence in observed data for nine of the 21 geographies. Simulated differences in prevalence across geographies did not reach the magnitude in observed data, and spatial patterns had low to moderate agreement. Our results suggest that geographic disparities in the CA-MRSA prevalence previously identified in California EHR data may be due to determinants beyond bias and healthcare-seeking behaviors. Future studies could adapt this model for other health outcomes by adjusting the healthcare-seeking behavior parameters and modifying the disease progression process.
Gaussian processes for time series with lead–lag effects with applications to biology data
Authors: Mu Wancen , Chen Jiawen , Davis Eric S , Reed Kathleen , Phanstiel Douglas , Love Michael I , Li Didong
Published: January 2025

Investigating the relationship, particularly the lead–lag effect, between time series is a common question across various disciplines, especially when uncovering biological processes. However, analyzing time series presents several challenges. Firstly, due to technical reasons, the time points at which observations are made are not at uniform intervals. Secondly, some lead–lag effects are transient, necessitating time-lag estimation based on a limited number of time points. Thirdly, external factors also impact these time series, requiring a similarity metric to assess the lead–lag relationship. To counter these issues, we introduce a model grounded in the Gaussian process, affording the flexibility to estimate lead–lag effects for irregular time series. In addition, our method outputs dissimilarity scores, thereby broadening its applications to include tasks such as ranking or clustering multiple pairwise time series when considering their strength of lead–lag effects with external factors. Crucially, we offer a series of theoretical proofs to substantiate the validity of our proposed kernels and the identifiability of kernel parameters. Our model demonstrates advances in various simulations and real-world applications, particularly in the study of dynamic chromatin interactions, compared to other leading methods.
Linear nodules on the face: a case of facial lymphocutaneous sporotrichosis
Authors: Li Xingyu , Ma Dong-Lai
Published: January 2025

We report a case of facial lymphocutaneous sporotrichosis, which is a relatively uncommon infection and may lead to misdiagnosis if not properly recognized.
In-cell design of solid biocatalyst via crystalline inclusion protein A and ferritin fusion
Authors: Tian Jiaxin , Nakasuji Yuto , Maity Basudev , Date Koki , Ueno Takafumi
Published: January 2025

Crystalline inclusion protein A is a protein crystal that spontaneously forms in living cells. To construct a hybrid solid material, we engineered crystalline inclusion protein A by fusion with functionalized ferritin at the C-terminal. When ferritin was mutated with His residues, the resulting solid material exhibited peroxidase mimetic oxidation of 3,3ʹ,5,5ʹ-tetramethylbenzidine in the presence of hydrogen peroxide. This study provides a simple method to develop functional solid materials.
Predictors of Cryptococcus gattii Clinical Presentation and Outcome: An International Study
Authors: Galanis Eleni , MacDougall Laura , Rose Caren , Chen Sharon C A , Oltean Hanna N , Cieslak Paul R , DeBess Emilio , Chong Mei , Sorrell Tania C , Baddley John W , Hoang Linda M N , Lockhart Shawn R , Pappas Peter G , Phillips Peter
Published: January 2025

Background

Infection by Cryptococcus gattii can lead to pulmonary or central nervous system (CNS) disease, or both. Whether the sites of infection and disease severity are associated with C. gattii species and lineages or with certain underlying medical conditions, or both is unclear. We conducted a retrospective cohort study to identify factors associated with site of infection and mortality among C. gattii cases.

Methods

We extracted data on 258 C. gattii cases from Australia, Canada, and the United States reported from 1999 to 2011. We conducted unadjusted and multivariable logistic regression analyses to evaluate factors associated with site of infection and C. gattii mortality among hospitalized cases (N = 218).

Results

Hospitalized C. gattii cases with CNS and other extrapulmonary disease were younger, more likely to reside in Australia, and be infected with variety gattii I (VGI) lineage but less likely to have comorbidities and die as compared to cases with pulmonary disease. The odds of having CNS and/or other extrapulmonary disease were 9 times higher in cases with VGI infection (adjusted odds ratio [aOR] = 9.21, 95% confidence interval [CI] = 3.28–25.89). Age ≥70 years (aOR = 6.69, 95% CI = 2.44–18.30), chronic lung disease (aOR = 2.62, 95% CI = 1.05–6.51) and an immunocompromised status (aOR = 2.08, 95% CI = 1.05–6.51) were associated with higher odds of C. gattii mortality.

Conclusions

Among hospitalized cases, C. gattii species and lineage are associated with site of infection but not with the risk of death, whereas older age and comorbidities increase the risk of death.
Machine learning for automated identification of anatomical landmarks in ultrasound periodontal imaging
Authors: Qi Baiyan , Sasi Lekshmi , Khan Suhel , Luo Jordan , Chen Casey , Rahmani Keivan , Jahed Zeinab , Jokerst Jesse V
Published: January 2025

Objectives

To identify landmarks in ultrasound periodontal images and automate the image-based measurements of gingival recession (iGR), gingival height (iGH), and alveolar bone level (iABL) using machine learning.

Methods

We imaged 184 teeth from 29 human subjects. The dataset included 1580 frames for training and validating the U-Net convolutional neural network machine learning model, and 250 frames from new teeth that were not used in training for testing the generalization performance. The predicted landmarks, including the tooth, gingiva, bone, gingival margin (GM), cementoenamel junction (CEJ), and alveolar bone crest (ABC), were compared to manual annotations. We further demonstrated automated measurements of the clinical metrics iGR, iGH, and iABL.

Results

Over 98% of predicted GM, CEJ, and ABC distances are within 200 µm of the manual annotation. Bland-Altman analysis revealed biases (bias of machine learning vs ground truth) of −0.1 µm, −37.6 µm, and −40.9 µm, with 95% limits of agreement of [−281.3, 281.0] µm, [−203.1, 127.9] µm, and [−297.6, 215.8] µm for iGR, iGH, and iABL, respectively, when compared to manual annotations. On the test dataset, the biases were 167.5 µm, 40.1 µm, and 78.7 µm with 95% CIs of [−1175 to 1510] µm, [−910.3 to 990.4] µm, and [−1954 to 1796] µm for iGR, iGH, and iABL, respectively.

Conclusions

The proposed machine learning model demonstrates robust prediction performance, with the potential to enhance the efficiency of clinical periodontal diagnosis by automating landmark identification and clinical metrics measurements.
Comprehensive 4D-flow cardiac magnetic resonance evaluation of the descending thoracic aorta in aortic regurgitation
Authors: Urmeneta Ulloa J , Álvarez Vázquez A , Martínez de Vega V , Martínez de Vega L , Andreu-Vázquez C , Thuissard-Vasallo I J , Recio Rodríguez M , Cabrera J A
Published: January 2025

Aims

To assess the reproducibility of 4D-Flow cardiac magnetic resonance (CMR) parameters in the descending thoracic aorta—DTAo—(regurgitant fraction [RF], end-diastolic reverse flow [EDRF], and holodiastolic flow reversal [HDR]), and the relationship with RF in the sinotubular junction (STJ), and the left ventricular end-diastolic volume index (LVEDVI) in patients with chronic aortic regurgitation (AR).

Methods and results

A descriptive study of these variables was conducted. A receiver operating characteristic curve was used to determine the optimal cut-off point. Thirty patients had severe AR (RF ≥ 30%, STJ) and 60 mild-to-moderate (RF < 30%). The mean age was 59 ± 17 years. Left ventricular ejection fraction (LVEF) was 56% (53–61%) and LVEDVI was 94 (76–128) mL/m2. Flow in the DTAo at the left inferior pulmonary vein (LIPV) was easily identifiable and measurements were highly reproducible. The intraclass correlation coefficient was 0.969 (95% CI: 0.954–0.980) for RF and 0.929 (95% CI: 0.893–0.952) for EDRF. Flow parameters measured at the LIPV were all significantly greater in the severe AR group: RF (21% vs. 6%, P < 0.001), EDRF (20 vs. 4 mL/s; P < 0.001), and HDR (20% vs. 8%; P < 0.001). Three parameters—presence of HDR, RF ≥ 17%, and EDRF ≥ 7 mL/s at the LIPV—were associated with RF ≥ 30% in the STJ and elevated LVEDVI.

Conclusion

4D-flow CMR can reproducibly assess flow in the DTAo in patients with chronic AR. An RF ≥ 17%, EDRF ≥ 7 mL/s, and/or the presence of HDR in the DTAo (LIPV) were associated with an RF ≥ 30% in STJ and elevated LVEDVI.
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

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

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

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 >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 < 0.001), increased dependency (P < 0.001), and poorer nutritional status (P < 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 < 0.001] and PNI [OR (95% CI) = 0.64 (0.41–0.99), P < 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 < 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

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

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

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

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

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

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

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

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

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.
Real-world study of medication-related osteonecrosis of the jaw from 2010 to 2023 based on Food and Drug Administration Adverse Event Reporting System
Authors: Zhong Yuhao , Dai Wei , Yin Lin , Wu Guomin , Wang Xiaoying
Published: January 2025

Medication-related osteonecrosis of the jaw (MRONJ) is a rare and severe adverse drug reaction (ADR) commonly seen in people taking drugs prescribed for metastatic cancer and osteoporosis. Prior studies only analyzed this ADR utilizing the public database Food and Drug Administration Adverse Event Reporting System (FAERS) by different stages (2010-2014, 2015-2021); a more comprehensive study is needed to analyze the MRONJ cases and the associated drugs from a longer time span. We conducted a retrospective pharmacovigilance analysis for all reported MRONJ cases between 2010 and 2023 in FAERS, using preferred terms and the primary suspect drug as searching conditions. Thus, this study aimed to analyze the MRONJ cases and the associated drugs more comprehensively. The reporting odds ratios (RORs) and 95% CIs were calculated for each queried drug. To distinguish the signal levels, we calculated the expected information component (EIC) and its 95% CI, using the Bayesian confidence propagation neural network (BCPNN) methods. We identified 22 846 MRONJ cases. A total of 15 drug classes including 30 suspect drugs showed different positive signal levels; among these drugs, 8, 5, and 17 had strong, medium, and weak intensity signals (+++, ++, and +), respectively. Drug classes involved bisphosphonate, RANKL inhibitor, radiotherapy drug, monoclonal antibody for cancer, corticosteroid, tyrosine kinase inhibitor, mammalian target of rapamycin inhibitor, aromatase inhibitor, cyclin-dependent kinase 4/6 inhibitor, immunomodulator, microtubule inhibitor, selective estrogen receptor modulator, sclerostin monoclonal antibody, estrogen receptor antagonist, and cytotoxic drug. Bisphosphonate, RANKL inhibitor, and radiotherapy drug exhibited higher risk than other classes with higher ROR or EIC 95% CI lower limit. Females had higher MRONJ incidence than males, and the mean age was 67.33 ± 11.71 yr. Compared with previous research, this study identified more drug classes and more novel medications with positive MRONJ signals that warrant further attention.
Circumstances of clinical fracture events with advancing age in older men
Authors: Ensrud Kristine E , Patel Sheena , Langsetmo Lisa , Cawthon Peggy M , Fink Howard A , Schousboe John T , Bauer Douglas C , Cauley Jane A , Orwoll Eric S ,   for the Osteoporotic Fractures in Men (MrOS) Study
Published: January 2025

To characterize fracture circumstances by age at time of fracture among community-dwelling older men, we analyzed incident clinical fractures in the Osteoporotic Fractures in Men study. Participants were contacted every 4 mo to identify fractures confirmed by radiographic reports. Fractures were classified as fall- or non-fall-related and further categorized by degree of trauma: minimal (fall from ≤ standing height), moderate (fall on stairs, steps or curb), or severe (fall from > standing height) for fall-related fractures; and minimal (eg, coughing), moderate (eg, collisions with objects during normal activity without falling), or severe (eg, motor vehicle accident) for non-fall-related fractures. Of 2351 clinical fractures in 1424 men during an average follow-up of 9.9 yr, 12.7% occurred at age <75 yr, 15.7% at age 75-79 yr, 26.1% at age 80-84 yr, and 45.5% at age ≥85 yr. A total of 1891 fractures (80.4% of all fractures) were the result of a fall. The proportion of fall-related fractures steadily rose with increasing age at time of fracture, ranging from 65.8% in men <75 yr rising to 84.7% in men ≥85 yr (p < .001). Most fall-related fractures (76.4%) were due to minimal trauma; the proportion of all fractures due to a fall with minimal trauma steadily rose with increasing age (p < .001). In contrast, approximately half of non-fall-related fractures (53.5%) were due to severe trauma. The proportion of all fractures due to severe trauma (whether fall-related or not) declined with advancing age (p < .001). In conclusion, the most frequently occurring fracture circumstance in older men was a fall from ≤standing height. This circumstance was increasingly common with advancing age occurring in 7 of every 10 fractures in men ≥85 yr, while a fracture (fall-related or not) due to severe trauma was less common with advancing age. Findings have implications for development of fracture prevention strategies in older men.