bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cell-to-cell heterogeneity drives host–virus coexistence in a bloom-forming alga
Authors: Joffe Nir , Kuhlisch Constanze , Schleyer Guy , Ahlers Nadia S , Shemi Adva , Vardi Assaf 
Published: March 2024

Abstract
Algal blooms drive global biogeochemical cycles of key nutrients and serve as hotspots for biological interactions in the ocean. The massive blooms of the cosmopolitan coccolithophore Emiliania huxleyi are often infected by the lytic E. huxleyi virus, which is a major mortality agent triggering bloom demise. This multi-annual “boom and bust” pattern of E. huxleyi blooms suggests that coexistence is essential for these host–virus dynamics. To investigate host–virus coexistence, we developed a new model system from an E. huxleyi culture that recovered from viral infection. The recovered population coexists with the virus, as host cells continue to divide in parallel to viral production. By applying single-molecule fluorescence in situ hybridization (smFISH) to quantify the fraction of infected cells, and assessing infection-specific lipid biomarkers, we identified a small subpopulation of cells that were infected and produced new virions, whereas most of the host population could resist infection. To further assess population heterogeneity, we generated clonal strain collections using single-cell sorting and subsequently phenotyped their susceptibility to E. huxleyi virus infection. This unraveled substantial cell-to-cell heterogeneity across a continuum of susceptibility to resistance, highlighting that infection outcome may vary depending on the individual cell. These results add a new dimension to our understanding of the complexity of host–virus interactions that are commonly assessed in bulk and described by binary definitions of resistance or susceptibility. We propose that phenotypic heterogeneity drives the host–virus coexistence and demonstrate how the coexistence with a lytic virus provides an ecological advantage for the host by killing competing strains.
Advancing a major US airline’s practice in flight-level checked baggage prediction
Authors: Chen Shijie , Park Chiwoo , Guo Qianwen , Sun Yanshuo 
Published: March 2024

Abstract
In this paper, we aim to address a relevant estimation problem that aviation professionals encounter in their daily operations. Specifically, aircraft load planners require information on the expected number of checked bags for a flight several hours prior to its scheduled departure to properly palletize and load the aircraft. However, the checked baggage prediction problem has not been sufficiently studied in the literature, particularly at the flight level. Existing prediction approaches have not properly accounted for the different impacts of overestimating and underestimating checked baggage volumes on airline operations. Therefore, we propose a custom loss function, in the form of a piecewise quadratic function, which aligns with airline operations practice and utilizes machine learning algorithms to optimize checked baggage predictions incorporating the new loss function. We consider multiple linear regression, LightGBM, and XGBoost, as supervised learning algorithms. We apply our proposed methods to baggage data from a major airline and additional data from various US government agencies. We compare the performance of the three customized supervised learning algorithms. We find that the two gradient boosting methods (i.e., LightGBM and XGBoost) yield higher accuracy than the multiple linear regression; XGBoost outperforms LightGBM while LightGBM requires much less training time than XGBoost. We also investigate the performance of XGBoost on samples from different categories and provide insights for selecting an appropriate prediction algorithm to improve baggage prediction practices. Our modeling framework can be adapted to address other prediction challenges in aviation, such as predicting the number of standby passengers or no-shows.
Why do users override alerts? Utilizing large language model to summarize comments and optimize clinical decision support
Authors: Liu Siru , McCoy Allison B , Wright Aileen P , Nelson Scott D , Huang Sean S , Ahmad Hasan B , Carro Sabrina E , Franklin Jacob , Brogan James , Wright Adam 
Published: March 2024

Abstract

Objectives
To evaluate the capability of using generative artificial intelligence (AI) in summarizing alert comments and to determine if the AI-generated summary could be used to improve clinical decision support (CDS) alerts.

Materials and Methods
We extracted user comments to alerts generated from September 1, 2022 to September 1, 2023 at Vanderbilt University Medical Center. For a subset of 8 alerts, comment summaries were generated independently by 2 physicians and then separately by GPT-4. We surveyed 5 CDS experts to rate the human-generated and AI-generated summaries on a scale from 1 (strongly disagree) to 5 (strongly agree) for the 4 metrics: clarity, completeness, accuracy, and usefulness.

Results
Five CDS experts participated in the survey. A total of 16 human-generated summaries and 8 AI-generated summaries were assessed. Among the top 8 rated summaries, five were generated by GPT-4. AI-generated summaries demonstrated high levels of clarity, accuracy, and usefulness, similar to the human-generated summaries. Moreover, AI-generated summaries exhibited significantly higher completeness and usefulness compared to the human-generated summaries (AI: 3.4 ± 1.2, human: 2.7 ± 1.2, P = .001).

Conclusion
End-user comments provide clinicians’ immediate feedback to CDS alerts and can serve as a direct and valuable data resource for improving CDS delivery. Traditionally, these comments may not be considered in the CDS review process due to their unstructured nature, large volume, and the presence of redundant or irrelevant content. Our study demonstrates that GPT-4 is capable of distilling these comments into summaries characterized by high clarity, accuracy, and completeness. AI-generated summaries are equivalent and potentially better than human-generated summaries. These AI-generated summaries could provide CDS experts with a novel means of reviewing user comments to rapidly optimize CDS alerts both online and offline.
Ensuring useful adoption of generative artificial intelligence in healthcare
Authors: Jindal Jenelle A , Lungren Matthew P , Shah Nigam H 
Published: March 2024

Abstract

Objectives
This article aims to examine how generative artificial intelligence (AI) can be adopted with the most value in health systems, in response to the Executive Order on AI.

Materials and Methods
We reviewed how technology has historically been deployed in healthcare, and evaluated recent examples of deployments of both traditional AI and generative AI (GenAI) with a lens on value.

Results
Traditional AI and GenAI are different technologies in terms of their capability and modes of current deployment, which have implications on value in health systems.

Discussion
Traditional AI when applied with a framework top-down can realize value in healthcare. GenAI in the short term when applied top-down has unclear value, but encouraging more bottom-up adoption has the potential to provide more benefit to health systems and patients.

Conclusion
GenAI in healthcare can provide the most value for patients when health systems adapt culturally to grow with this new technology and its adoption patterns.
Reparations in environmental cases: should the International Criminal Court consider the Inter-American Court of Human Rights’ jurisprudence?
Authors: Perez-Leon-Acevedo Juan-Pablo 
Published: March 2024

Abstract
In a context where supranational courts order reparations in environmental cases, this article examines whether the International Criminal Court (ICC) should pay attention to the Inter-American Court of Human Rights (IACtHR) reparations jurisprudence in environmental cases. The ICC has yet to engage with environmental cases and order ensuing reparations. However, the ICC Statute contains an environmental war crime, ‘ecocide’ may be incorporated into it, and some ICC cases/ICC complaints involved environmental damages. This article examines constraints of a potential extrapolation of IACtHR’s reparation jurisprudence to the ICC’s reparations system in environmental cases: differences between IACtHR’s and ICC’s mandates, particularly their reparations systems; and potential backlash from states/other actors vis-à-vis ‘green’ reparations jurisprudence. This article also provides justifications for ICC/IACtHR cross-fertilization: international human rights law is embedded in ICC’s reparations law and practice, and need for a coherent international law of reparations in environmental cases across supranational courts. Through adapted cross-fertilization, the ICC’s reparations system should consider IACtHR’s reparations practice concerning environmental cases.
Effects of a neuropsychosocial teleassistance intervention on social cognition and health-related quality of life of pediatric patients with neuromuscular diseases
Authors: García Irune , Martínez Oscar , Amayra Imanol , Salgueiro Monika , Rodríguez Alicia Aurora , López-Paz Juan Francisco 
Published: March 2024

Abstract

Objective
This study aimed to determine the effects of a neuropsychosocial teleassistance group-based intervention on improving social cognitive functioning and health-related quality of life (HRQoL) in pediatric neuromuscular diseases (NMD).

Methods
Thirty-five pediatric patients with NMD were assigned to the neuropsychosocial intervention program (n = 20) or waiting list control condition (n = 15). The intervention group received an integrative approach that combines training in social cognition with cognitive behavioral therapy. All participants completed a neuropsychological and clinical assessment at baseline and follow-up, which included tests of social cognition, both for emotion recognition and theory of mind, and HRQoL. Repeated-measures multivariate analysis of covariance was used to determine the effects of the teleassistance program.

Results
Group × Time interactions revealed significant improvements in the intervention group as compared with the control group for different social cognition’s indicators (AR NEPSY-II: p = .003, η2p = .24; TM NEPSY: p &lt; .001, η2p = .35; Verbal task: p &lt; .001, η2p = .35; Happé’s Strange Stories: p = .049, η2p = .11) and HRQoL (Psychosocial health: p = .012, η2p = .18; Emotional functioning: p = .037, η2p = 0.13; Social functioning: p = .006, η2p = .21; Total: p = .013, η2p = .17), showing medium to large effects.

Conclusions
Patients receiving the neuropsychosocial intervention showed improvements in their social cognition performance and psychosocial HRQoL, providing evidence about the positive effects of the program in pediatric patients with NMD. This should be considered in further research and interventions in this field.
The transcription factor RhMYB17 regulates the homeotic transformation of floral organs in rose (Rosa hybrida) under cold stress
Authors: Yang Tuo , Wang Yi , Li Yuqi , Liang Shangyi , Yang Yunyao , Huang Ziwei , Li Yonghong , Gao Junping , Ma Nan , Zhou Xiaofeng 
Published: March 2024

Abstract
Low temperatures affect flower development in rose (Rosa hybrida), increasing petaloid stamen number and reducing normal stamen number. We identified the low-temperature-responsive R2R3-MYB transcription factor RhMYB17, which is homologous to Arabidopsis MYB17 by similarity of protein sequences. RhMYB17 was up-regulated at low temperatures, and RhMYB17 transcripts accumulated in floral buds. Transient silencing of RhMYB17 by virus-induced gene silencing decreased petaloid stamen number and increased normal stamen number. According to the ABCDE model of floral organ identity, class A genes APETALA 1 (AP1) and AP2 contribute to sepal and petal formation. Transcription factor binding analysis identified RhMYB17 binding sites in the promoters of rose APETALA 2 (RhAP2) and APETALA 2-LIKE (RhAP2L). Yeast one-hybrid assays, dual-luciferase reporter assays, and electrophoretic mobility shift assays confirmed that RhMYB17 directly binds to the promoters of RhAP2 and RhAP2L, thereby activating their expression. RNA sequencing further demonstrated that RhMYB17 plays a pivotal role in regulating the expression of class A genes, and indirectly influences the expression of the class C gene. This study reveals a novel mechanism for the homeotic transformation of floral organs in response to low temperatures.
A pathogenesis-related protein, PRP1, negatively regulates root nodule symbiosis in Lotus japonicus
Authors: Li Hao , Ou Yajuan , Huang Kui , Zhang Zhongming , Cao Yangrong , Zhu Hui 
Published: March 2024

Abstract
The legume-rhizobium symbiosis represents a unique model within the realm of plant-microbe interactions. Unlike typical cases of pathogenic invasion, the infection of rhizobia and their residence within symbiotic cells do not elicit a noticeable immune response in plants. Nevertheless, there is still much to uncover regarding the mechanisms through which plant immunity influences rhizobial symbiosis. In this study, we identify an important player in this intricate interplay: Lotus japonicus PRP1, which serves as a positive regulator of plant immunity but also exhibits the capacity to decrease rhizobial colonization and nitrogen fixation within nodules. The PRP1 gene encodes an uncharacterized protein and is named Pathogenesis-Related Protein1, owing to its orthologue in Arabidopsis thaliana, a pathogenesis-related family protein (At1g78780). The PRP1 gene displays high expression levels in nodules compared to other tissues. We observed an increase in rhizobium infection in the L. japonicus prp1 mutants, whereas PRP1-overexpressing plants exhibited a reduction in rhizobium infection compared to control plants. Intriguingly, L. japonicus prp1 mutants produced nodules with a pinker colour compared to wild-type controls, accompanied by elevated levels of leghaemoglobin and an increased proportion of infected cells within the prp1 nodules. The transcription factor Nodule Inception (NIN) can directly bind to the PRP1 promoter, activating PRP1 gene expression. Furthermore, we found that PRP1 is a positive mediator of innate immunity in plants. In summary, our study provides clear evidence of the intricate relationship between plant immunity and symbiosis. PRP1, acting as a positive regulator of plant immunity, simultaneously exerts suppressive effects on rhizobial infection and colonization within nodules.
Biocontrol strategies against Botrytis cinerea in viticulture: evaluating the efficacy and mode of action of selected winemaking yeast strains
Authors: Tsioka Artemis , Psilioti Dourmousi Konstantina , Poulaki Eirini G , Papoutsis Georgios , Tjamos Sotirios E , Gkizi Danai 
Published: March 2024

Abstract
Botrytis cinerea poses a recurring threat to viticulture, causing significant yield losses each year. The study explored the biocontrol capabilities of commercially used winemaking yeasts as a strategy to manage B. cinerea in grape berries. The winemaking yeast strains—Saccharomyces cerevisiae ES181, Saccharomyces pastorianus KBG6, S. cerevisiae BCS103, Lachancea thermotolerans Omega, and Torulaspora delbrueckii TD291-reduced B. cinerea growth and conidiation in vitro. Furthermore, they demonstrated a decreased disease severity and number of conidia in grape berries. Among these strains, S. cerevisiae BCS103 was the most effective, inducing the expression of the defense-related gene PR4 in berries. Its diffusible compounds and volatile organic compounds also reduced the expression of BcLTF2, a positive regulator of B. cinerea conidiogenesis. The examined winemaking yeast strains, especially S. cerevisiae BCS103, demonstrated effective inhibition of B. cinerea in vitro and in grape berries, influencing key defense genes and reducing BcLTF2 expression, offering potential solutions for disease management in viticulture. The study underscores the promise of commercially available winemaking yeast strains as eco-friendly tools against B. cinerea in viticulture. Leveraging their safety and existing use in winemaking offers a potential avenue for sustainable disease management.
Does a tragic event affect different aspects of attitudes toward immigration?
Authors: Heizler Odelia , Israeli Osnat 
Published: March 2024

Abstract
Dramatic events can evoke feelings of compassion, fear, or threat, and can affect public opinion regarding controversial issues. Such an event was the drowning of 3-year-old Alan Kurdi, a Syrian boy whose body washed up on a Turkish shore, and was photographed, producing an iconic image that was seen worldwide. The image evoked empathy and compassion that neuroscience and psychological research associate with a motivation to help. This article examines the impact of this event on four different aspects of attitudes toward immigration. The timing of the European Social Survey in Portugal allowed us to use this tragic event as a natural experiment. Our results suggest that Kurdi’s drowning had a significant effect on only two sentiments, but no such impact was detected on other attitudes. The results show that the event did not change the respondents’ opinion regarding the possible negative consequences of immigration on the host country’s economy, crime level, or culture, nor did it change their perception of the skills required by immigrants. On the other hand, the empathy induced by the tragic event increased their willingness to have a less restrictive immigration policy and their openness to having close social relationships with immigrants, although these changes were short-lived.
How galaxy properties vary with filament proximity in the Simba simulations
Authors: Bulichi Teodora-Elena , Davé Romeel , Kraljic Katarina 
Published: March 2024

ABSTRACT
We explore the dependence of global galaxy properties in the Simba simulation as a function of distance from filaments identified using DisPerSE. We exclude haloes with mass Mh &gt; 1013 M⊙ to mitigate the impact of group and cluster environments. Galaxies near filaments are more massive and have more satellites, which we control for by examining deviations from best-fitting scaling relations. At z = 0, star formation (SF) is significantly suppressed within $\lesssim 100$ kpc of filaments, more strongly for satellites, indicating substantial pre-processing in filaments. By z = 2, the trend is weak and if anything indicates an increase in SF activity close to filaments. The suppression at $z\lesssim 1$ is accompanied by lowered H i fractions, and increased metallicities, quenched fractions, and dispersion-dominated systems. H2 fractions are not strongly suppressed when controlling for stellar mass, suggesting that SF efficiency drives the drop in SF. By comparing amongst different Simba feedback variant runs, we show that the majority of SF suppression owes to filamentary shock-heating, but there is a non-trivial additional effect from AGN feedback. When looking around massive (Mh &gt; 1013 M⊙) haloes, those galaxies near filaments behave somewhat differently, indicating that filaments provide an additional environmental effect relative to haloes. Finally, we compare Simba results to EAGLE and IllustrisTNG at z = 0, showing that all models predict SF suppression within $\lesssim 100$  kpc of filaments, none the less, detailed differences may be observationally testable.
Disease-modifying antirheumatic drug selection in Japanese patients with rheumatoid arthritis treated with biologics or JAK inhibitors without methotrexate: A retrospective hospital-based administrative claims database study
Authors: Miyakawa Naohisa , Tsuritani Katsuki , Teixeira Bruno Casaes , Fujio Keishi 
Published: March 2024

ABSTRACT

Objectives
We evaluated the medication selection and clinical characteristics of rheumatoid arthritis patients who started treatment with/without methotrexate (MTX) (using biologic disease-modifying antirheumatic drugs or Janus kinase inhibitors instead) in Japan.

Methods
Using a Japanese hospital-based administrative claims database, rheumatoid arthritis patients who received treatment [abatacept (ABA), interleukin-6 receptor inhibitor, tumor necrosis factor inhibitor, or Janus kinase inhibitor] between 1 January 2015 and 31 December 2019 were enrolled.

Results
Overall, 19,301 patients were included (10,530 receiving MTX; 8771 not receiving MTX within 60 days of the first treatment). Mean ages at diagnosis were 60.7 and 65.9 years in the MTX and non-MTX groups, respectively (P &lt; .0001). The non-MTX group had higher proportions of patients with Charlson Comorbidity Index ≥1 (P &lt; .0001) and higher comorbidity rates. ABA was the most frequently used drug among patients with infectious/parasitic, circulatory, and respiratory diseases at baseline. Interleukin-6 receptor inhibitor had the highest use rate among patients with neoplasms; blood, gastrointestinal, and genitourinary diseases; and abnormal clinical/laboratory findings. ABA had the highest persistence probability from 6 months onward.

Conclusions
MTX is used less frequently among older Japanese rheumatoid arthritis patients or those with comorbidities. In such patients, ABA is the most frequently used drug, followed by interleukin-6 receptor inhibitor, when MTX is not used at treatment start.
DNA fragility at topologically associated domain boundaries is promoted by alternative DNA secondary structure and topoisomerase II activity
Authors: Raimer Young Heather M , Hou Pei-Chi , Bartosik Anna R , Atkin Naomi D , Wang Lixin , Wang Zhenjia , Ratan Aakrosh , Zang Chongzhi , Wang Yuh-Hwa 
Published: March 2024

Abstract
CCCTC-binding factor (CTCF) binding sites are hotspots of genome instability. Although many factors have been associated with CTCF binding site fragility, no study has integrated all fragility-related factors to understand the mechanism(s) of how they work together. Using an unbiased, genome-wide approach, we found that DNA double-strand breaks (DSBs) are enriched at strong, but not weak, CTCF binding sites in five human cell types. Energetically favorable alternative DNA secondary structures underlie strong CTCF binding sites. These structures coincided with the location of topoisomerase II (TOP2) cleavage complex, suggesting that DNA secondary structure acts as a recognition sequence for TOP2 binding and cleavage at CTCF binding sites. Furthermore, CTCF knockdown significantly increased DSBs at strong CTCF binding sites and at CTCF sites that are located at topologically associated domain (TAD) boundaries. TAD boundary-associated CTCF sites that lost CTCF upon knockdown displayed increased DSBs when compared to the gained sites, and those lost sites are overrepresented with G-quadruplexes, suggesting that the structures act as boundary insulators in the absence of CTCF, and contribute to increased DSBs. These results model how alternative DNA secondary structures facilitate recruitment of TOP2 to CTCF binding sites, providing mechanistic insight into DNA fragility at CTCF binding sites.