bluuebunny/crossref_metadata_2025_split huggingface dataset:
Zooming in on the circumgalactic medium with GIBLE: Resolving small-scale gas structure in cosmological simulations
Authors: Ramesh Rahul , Nelson Dylan 
Published: January 2024

ABSTRACT
We introduce Project GIBLE (Gas Is Better resoLved around galaxiEs), a suite of cosmological zoom-in simulations where gas in the circumgalactic medium (CGM) is preferentially simulated at ultra-high numerical resolution. Our initial sample consists of eight galaxies, all selected as Milky Way-like galaxies at z = 0 from the TNG50 simulation. Using the same galaxy formation model as IllustrisTNG, and the moving-mesh code arepo, we re-simulate each of these eight galaxies maintaining a resolution equivalent to TNG50-2 (mgas ∼ 8 × 105 M⊙). However, we use our super-Lagrangian refinement scheme to more finely resolve gas in the CGM around these galaxies. Our highest resolution runs achieve 512 times better mass resolution (∼103 M⊙). This corresponds to a median spatial resolution of ∼75 pc at 0.15 R200, c, which coarsens with increasing distance to ∼700 pc at the virial radius. We make predictions for the covering fractions of several observational tracers of multiphase CGM gas: H i, Mg ii, C iv, and O vii. We then study the impact of improved resolution on small scale structure. While the abundance of the smallest cold, dense gas clouds continues to increase with improving resolution, the number of massive clouds is well converged. We conclude by quantifying small scale structure with the velocity structure function and the autocorrelation function of the density field, assessing their resolution dependence. The GIBLE cosmological hydrodynamical simulations enable us to improve resolution in a computationally efficient manner, thereby achieving numerical convergence of a subset of key CGM gas properties and observables.
Antioxidant sericin averts the disruption of oocyte–follicular cell communication triggered by oxidative stress
Authors: Khatun Hafiza , Yamanaka Ken-ichi , Sugimura Satoshi 
Published: January 2024

Abstract
Antioxidants are free radical scavengers that increase oocyte quality and improve female fertility by suppressing oxidative stress. However, the related mechanisms remain unclear. The present study was designed to examine whether a reduction of oxidative stress from using the antioxidant sericin led to expanded cumulus cell (CC)–oocyte communication and oocyte developmental acquisition in a bovine model. We found that cumulus–oocyte complexes (COCs) matured in the presence of sericin showed a significantly increased oocyte meiotic maturation rate (P &lt; 0.01) and accelerated subsequent blastocyst formation, as more blastocysts were found at the hatched stage (P &lt; 0.05) compared to that in the control group. In contrast to the control group, sericin suppressed H2O2 levels in COCs, resulting in a markedly enhanced CC–oocyte gap junction communication index and number of transzonal projections, which were preserved until 18 h of oocyte maturation. These findings indicate that sericin reduces disruption of oocyte–follicular cell communication induced by oxidative stress. Sericin consistently increased intra-oocyte glutathione (GSH) levels and reduced oocyte H2O2 levels (P &lt; 0.05), both of which were ablated when GSH synthesis was inhibited by buthionine sulfoximide (an inhibitor of GSH synthesis). Furthermore, the inhibition of GSH synthesis counteracted the positive effects of sericin on subsequent embryo developmental competence (P &lt; 0.01). Intra-oocyte GSH levels were positively associated with blastocyst development and quality. These outcomes demonstrate new perspectives for the improvement of oocyte quality in assisted reproductive technology and may contribute to developing treatment strategies for infertility and cancer.
Multimodal imaging with magnetization transfer and diffusion tensor imaging reveals evidence of myelin damage in children and youth treated for a brain tumor
Authors: Skocic Jovanka , Richard Logan , Ferkul Ashley , Cox Elizabeth , Tseng Julie , Laughlin Suzanne , Bouffet Eric , Mabbott Donald James 
Published: January 2024

Abstract

Background
The microstructural damage underlying compromise of white matter following treatment for pediatric brain tumors is unclear. We use multimodal imaging employing advanced diffusion tensor imaging (DTI) and magnetization transfer imaging (MTI) MRI methods to examine chronic microstructural damage to white matter in children and adolescents treated for pediatric brain tumor. Notably, MTI may be more sensitive to macromolecular content, including myelin, than DTI.

Methods
Fifty patients treated for brain tumors (18 treated with surgery ± chemotherapy and 32 treated with surgery followed by cranial–spinal radiation; time from diagnosis to scan ~6 years) and 45 matched healthy children completed both MTI and DTI scans. Voxelwise and region-of-interest approaches were employed to compare white matter microstructure metrics (magnetization transfer ratio (MTR); DTI— fractional anisotropy [FA], radial diffusivity [RD], axial diffusivity [AD], mean diffusivity [MD]) between patients and healthy controls.

Results
MTR was decreased across multiple white matter tracts in patients when compared to healthy children, P &lt; .001. These differences were observed for both patients treated with radiation and those treated with only surgery, P &lt; .001. We also found that children and adolescents treated for brain tumors exhibit decreased FA and increased RD/AD/MD compared to their healthy counterparts in several white matter regions, Ps &lt; .02. Finally, we observed that MTR and DTI metrics were related to multiple white matter tracts in patients, Ps &lt; .01, but not healthy control children.

Conclusions
Our findings provide evidence that the white matter damage observed in patients years after treatment of pediatric posterior fossa tumors, likely reflects myelin disruption.
Life-Course Associations Between Smoking and Depressive Symptoms. A 30-Year Finnish Follow-up Study
Authors: Kiviruusu Olli , Berg Noora , Piirtola Maarit , Viertiö Satu , Suvisaari Jaana , Korhonen Tellervo , Marttunen Mauri 
Published: January 2024

Abstract

Introduction
Relatively little is known about whether the association between smoking and depressive symptoms changes with age and how the trajectories of smoking and depressive symptoms are intertwined during the life course. In this population-based study, these associations were examined from young adulthood to middle age.

Methods
Participants of a Finnish cohort study (N = 1955) were assessed at the ages of 22, 32, 42, and 52 using questionnaires covering daily smoking (yes/no) and the short 13-item Beck Depression Inventory. Longitudinal latent class and longitudinal latent profile analyses were used to identify life course trajectories of smoking and depressive symptoms.

Results
The proportions of daily smokers decreased, while levels of depressive symptoms increased among both females and males from age 22 to 52 years. Smoking was associated with higher levels of depressive symptoms from age 22 to 42 years, while not at 52. Associations among males prevailed when adjusting for education, marital status, and alcohol use. Four life course classes of daily smoking (nonsmokers, decreasing prevalence of smoking, persistent smokers, and increasing prevalence of smoking) and four trajectories of depressive symptoms (low, increasing/moderate, decreasing/moderate, and high) were identified. In males, persistent daily smokers (relative risk ratio (RRR) = 4.5, 95% confidence interval (CI): 2.2 to 9.2) and those in the class with increasing smoking prevalence (RRR = 3.2, 95% CI: 1.1 to 9.1) had an increased risk of belonging to the high depressive symptoms profile. In females these associations were nonsignificant.

Conclusions
Compared to females, the relationship between smoking and depressive symptoms seems more robust among males during adulthood. Specifically, males smoking persistently from young adulthood to middle age have an increased risk of high depressive symptoms trajectory.

Implications
This population-based cohort with 30 years of follow-up showed that the life course trajectories of daily smoking and depressive symptoms are associated. Persistent daily smokers and those starting late had an increased risk of belonging to the profile with constantly high levels of depressive symptoms during the life course. However, these associations were statistically significant only in males. Actions should be strengthened, especially in males, to prevent smoking initiation, to help smoking cessation, and to identify and treat depression in smokers with significant depressive symptoms.
Rural-Urban Disparities in Colorectal Cancer Screening, Diagnosis, Treatment, and Survivorship Care: A Systematic Review and Meta-Analysis
Authors: Sepassi Aryana , Li Meng , A. Zell Jason , Chan Alexandre , Saunders Ila M , Mukamel Dana B 
Published: January 2024

Abstract

Background
Rural residents have a higher prevalence of colorectal cancer (CRC) mortality compared to urban individuals. Policies have been aimed at improving access to CRC screening to reduce these outcomes. However, little attention has been paid to other determinants of CRC-related outcomes, such as stage at diagnosis, treatment, or survivorship care. The main objective of this analysis was to evaluate literature describing differences in CRC screening, stage at diagnosis, treatment, and survivorship care between rural and urban individuals.

Materials and Methods
We conducted a systematic review of electronic databases using a combination of MeSH and free-text search terms related to CRC screening, stage at diagnosis, treatment, survivorship care, and rurality. We identified 921 studies, of which 39 were included. We assessed methodological quality using the ROBINS-E tool and summarized findings descriptively. A meta-analysis was performed of studies evaluating CRC screening using a random-effects model.

Results
Seventeen studies reported disparities between urban and rural populations in CRC screening, 12 on treatment disparities, and 8 on staging disparities. We found that rural individuals were significantly less likely to report any type of screening at any time period (pooled odds ratio = 0.81, 95% CI, 0.76-0.86). Results were inconclusive for disparities in staging at diagnosis and treatment. One study reported a lower likelihood of use of CRC survivorship care for rural individuals compared to urban individuals.

Conclusion
There remains an urgent need to evaluate and address CRC disparities in rural areas. Investigators should focus future work on assessing the quality of staging at diagnosis, treatment, and survivorship care in rural areas.
Survey of public attitudes toward astronomy in Japan
Authors: Takanashi Naohiro , Hiramatsu Masaaki , Kawagoe Shio , Kusakabe Nobuhiko , Sawada Koki , Tamazawa Harufumi 
Published: January 2024

Abstract
We report on the results of a survey we conducted on the Japanese public’s attitudes toward astronomy. This survey was conducted via an online questionnaire, with 2000 responses received. Based on these data, we present what kind of interest the general public in Japan has in astronomy. We also conducted a questionnaire survey of those involved in communicating astronomy to the public, in order to examine how they differ from the general public. The results suggest that while there are clear differences between these groups in terms of their engagement in astronomy, there is also continuity between them when looking at their attributes in more detail. The data presented in this paper could help us to promote the communication of astronomy to the public.
Histone deacetylase OsHDA716 represses rice chilling tolerance by deacetylating OsbZIP46 to reduce its transactivation function and protein stability
Authors: Sun Ying , Xie Zizhao , Jin Liang , Qin Tian , Zhan Chenghang , Huang Junli 
Published: January 2024

Abstract
Low temperature is a major environmental factor limiting plant growth and crop production. Epigenetic regulation of gene expression is important for plant adaptation to environmental changes, whereas the epigenetic mechanism of cold signaling in rice (Oryza sativa) remains largely elusive. Here, we report that the histone deacetylase (HDAC) OsHDA716 represses rice cold tolerance by interacting with and deacetylating the transcription factor OsbZIP46. The loss-of-function mutants of OsHDA716 exhibit enhanced chilling tolerance, compared with the wild-type plants, while OsHDA716 overexpression plants show chilling hypersensitivity. On the contrary, OsbZIP46 confers chilling tolerance in rice through transcriptionally activating OsDREB1A and COLD1 to regulate cold-induced calcium influx and cytoplasmic calcium elevation. Mechanistic investigation showed that OsHDA716-mediated OsbZIP46 deacetylation in the DNA-binding domain reduces the DNA-binding ability and transcriptional activity as well as decreasing OsbZIP46 protein stability. Genetic evidence indicated that OsbZIP46 deacetylation mediated by OsHDA716 reduces rice chilling tolerance. Collectively, these findings reveal that the functional interplay between the chromatin regulator and transcription factor fine-tunes the cold response in plant and uncover a mechanism by which HDACs repress gene transcription through deacetylating nonhistone proteins and regulating their biochemical functions.
Domestication and the evolution of crops: variable syndromes, complex genetic architectures, and ecological entanglements
Authors: Alam Ornob , Purugganan Michael D 
Published: January 2024

Abstract
Domestication can be considered a specialized mutualism in which a domesticator exerts control over the reproduction or propagation (fitness) of a domesticated species to gain resources or services. The evolution of crops by human-associated selection provides a powerful set of models to study recent evolutionary adaptations and their genetic bases. Moreover, the domestication and dispersal of crops such as rice, maize, and wheat during the Holocene transformed human social and political organization by serving as the key mechanism by which human societies fed themselves. Here we review major themes and identify emerging questions in three fundamental areas of crop domestication research: domestication phenotypes and syndromes, genetic architecture underlying crop evolution, and the ecology of domestication. Current insights on the domestication syndrome in crops largely come from research on cereal crops such as rice and maize, and recent work indicates distinct domestication phenotypes can arise from different domestication histories. While early studies on the genetics of domestication often identified single large-effect loci underlying major domestication traits, emerging evidence supports polygenic bases for many canonical traits such as shattering and plant architecture. Adaptation in human-constructed environments also influenced ecological traits in domesticates such as resource acquisition rates and interactions with other organisms such as root mycorrhizal fungi and pollinators. Understanding the ecological context of domestication will be key to developing resource-efficient crops and implementing more sustainable land management and cultivation practices.
Transcription factor WRKY75 maintains auxin homeostasis to promote tomato defense against Pseudomonas syringae
Authors: Yang Minmin , Wang Yixuan , Chen Chong , Xin Xin , Dai Shanshan , Meng Chen , Ma Nana 
Published: January 2024

Abstract
The hemibiotrophic bacterial pathogen Pseudomonas syringae infects a range of plant species and causes enormous economic losses. Auxin and WRKY transcription factors play crucial roles in plant responses to P. syringae, but their functional relationship in plant immunity remains unclear. Here, we characterized tomato (Solanum lycopersicum) SlWRKY75, which promotes defenses against P. syringae pv. tomato (Pst) DC3000 by regulating plant auxin homeostasis. Overexpressing SlWRKY75 resulted in low free indole-3-acetic acid (IAA) levels, leading to attenuated auxin signaling, decreased expansin transcript levels, upregulated expression of PATHOGENESIS-RELATED GENES (PRs) and NONEXPRESSOR OF PATHOGENESIS-RELATED GENE 1 (NPR1), and enhanced tomato defenses against Pst DC3000. RNA interference-mediated repression of SlWRKY75 increased tomato susceptibility to Pst DC3000. Yeast one-hybrid, electrophoretic mobility shift assays, and luciferase activity assays suggested that SlWRKY75 directly activates the expression of GRETCHEN HAGEN 3.3 (SlGH3.3), which encodes an IAA-amido synthetase. SlGH3.3 enhanced tomato defense against Pst DC3000 by converting free IAA to the aspartic acid (Asp)-conjugated form IAA-Asp. In addition, SlWRKY75 interacted with a tomato valine-glutamine (VQ) motif-containing protein 16 (SlVQ16) in vivo and in vitro. SlVQ16 enhanced SlWRKY75-mediated transcriptional activation of SlGH3.3 and promoted tomato defense responses to Pst DC3000. Our findings illuminate a mechanism in which the SlVQ16–SlWRKY75 complex participates in tomato pathogen defense by positively regulating SlGH3.3-mediated auxin homeostasis.
From environmental responses to adaptation: the roles of plant lncRNAs
Authors: Traubenik Soledad , Charon Céline , Blein Thomas 
Published: January 2024

Abstract
As sessile organisms, plants are continuously exposed to heterogeneous and changing environments and constantly need to adapt their growth strategies. They have evolved complex mechanisms to recognize various stress factors, activate appropriate signaling pathways, and respond accordingly by reprogramming the expression of multiple genes at the transcriptional, post-transcriptional, and even epigenome levels to tolerate stressful conditions such as drought, high temperature, nutrient deficiency, and pathogenic interactions. Apart from protein-coding genes, long non-coding RNAs (lncRNAs) have emerged as key players in plant adaptation to environmental stresses. They are transcripts larger than 200 nucleotides without protein-coding potential. Still, they appear to regulate a wide range of processes, including epigenetic modifications and chromatin reorganization, as well as transcriptional and post-transcriptional modulation of gene expression, allowing plant adaptation to various environmental stresses. LncRNAs can positively or negatively modulate stress responses, affecting processes such as hormone signaling, temperature tolerance, and nutrient deficiency adaptation. Moreover, they also seem to play a role in stress memory, wherein prior exposure to mild stress enhances plant ability to adapt to subsequent stressful conditions. In this review, we summarize the contribution of lncRNAs in plant adaptation to biotic and abiotic stresses, as well as stress memory. The complex evolutionary conservation of lncRNAs is also discussed and provides insights into future research directions in this field.
A framework to forestall systemic police misconduct: Applying DOJ’S pattern or practice findings to municipal police
Authors: Ostrowe Jason W 
Published: January 2024

Abstract
The 1994 crime bill authorized the DOJ to investigate and initiate reform against law enforcement agencies for patterns or practices of systemic misconduct and unconstitutional policing. Among the 78 investigations conducted under this authority, 35 involve municipal police agencies with DOJ issued “findings letters” detailing policy, procedural, and operational deficiencies within the subject agency. These DOJ-issued documents were analyzed for consistent thematic insufficiencies across investigations, and tested for association with police organizational and environmental variables. From this analysis, a four-step framework was developed to offer police leadership the knowledge, tools, timing, and insight to forestall patterns or practices of systemic misconduct and unconstitutional policing within their agency.
Emotional coping by chance: Experiences of emotional coping strategies among on-scene commanders in the Norwegian police services
Authors: Filstad Cathrine , Rød Anne 
Published: January 2024

Abstract
The purpose of our research is to identify the emotional coping strategies used by on-scene commanders, both to safeguard their own well-being and that of their policing colleagues. However, understanding the conditions and application of sustainable coping strategies has proven to be more complex than the literature considers. Using explorative qualitative methods, the data collection includes two studies with on-scene commanders across Norway covering minor and major incidents. We found that when on-scene commanders are left to develop their own coping strategies, they rely on random practices that can have negative long-term consequences on officers’ emotional well-being. We identified four conditions as crucial for the development of healthy emotional coping strategies: mandatory defuse and debrief practices, level of experience, social support, and leadership. The main conclusion emerging from our research is the necessary institutionalization of formal and appropriate defuse and debrief practices, including the use of colleague support and psychologists.
Explainable artificial intelligence model for mortality risk prediction in the intensive care unit: a derivation and validation study
Authors: Hu Chang , Gao Chao , Li Tianlong , Liu Chang , Peng Zhiyong 
Published: January 2024

Abstract

Background
The lack of transparency is a prevalent issue among the current machine-learning (ML) algorithms utilized for predicting mortality risk. Herein, we aimed to improve transparency by utilizing the latest ML explicable technology, SHapley Additive exPlanation (SHAP), to develop a predictive model for critically ill patients.

Methods
We extracted data from the Medical Information Mart for Intensive Care IV database, encompassing all intensive care unit admissions. We employed nine different methods to develop the models. The most accurate model, with the highest area under the receiver operating characteristic curve, was selected as the optimal model. Additionally, we used SHAP to explain the workings of the ML model.

Results
The study included 21 395 critically ill patients, with a median age of 68 years (interquartile range, 56–79 years), and most patients were male (56.9%). The cohort was randomly split into a training set (N = 16 046) and a validation set (N = 5349). Among the nine models developed, the Random Forest model had the highest accuracy (87.62%) and the best area under the receiver operating characteristic curve value (0.89). The SHAP summary analysis showed that Glasgow Coma Scale, urine output, and blood urea nitrogen were the top three risk factors for outcome prediction. Furthermore, SHAP dependency analysis and SHAP force analysis were used to interpret the Random Forest model at the factor level and individual level, respectively.

Conclusion
A transparent ML model for predicting outcomes in critically ill patients using SHAP methodology is feasible and effective. SHAP values significantly improve the explainability of ML models.